From 93e8b71f60ab64e742c95814a510408c8c59e8fd Mon Sep 17 00:00:00 2001 From: Alexander Grigorievskiy Date: Thu, 8 Oct 2015 15:30:34 +0300 Subject: [PATCH] UPD: Added testing, and bug fixing. --- GPy/examples/state_space.py | 33 +- GPy/models/__init__.py | 2 +- GPy/models/state_space_cython.c | 8640 +++++++++-------- GPy/models/state_space_cython.pyx | 31 +- GPy/models/state_space_main.py | 284 +- ...tate_space_new.py => state_space_model.py} | 29 +- GPy/models/state_space_setup.py | 8 + GPy/testing/gpy_kernels_state_space_tests.py | 330 + GPy/testing/state_space_main_tests.py | 975 ++ 9 files changed, 6084 insertions(+), 4248 deletions(-) rename GPy/models/{state_space_new.py => state_space_model.py} (94%) create mode 100644 GPy/models/state_space_setup.py create mode 100644 GPy/testing/gpy_kernels_state_space_tests.py create mode 100644 GPy/testing/state_space_main_tests.py diff --git a/GPy/examples/state_space.py b/GPy/examples/state_space.py index a9d770e6..fdb7fdd5 100644 --- a/GPy/examples/state_space.py +++ b/GPy/examples/state_space.py @@ -2,36 +2,11 @@ import GPy import numpy as np import matplotlib.pyplot as plt -import GPy.models.state_space_new as SS_new +import GPy.models.state_space_model as SS_model X = np.linspace(0, 10, 2000)[:, None] Y = np.sin(X) + np.random.randn(*X.shape)*0.1 -# Need to run these lines when X and Y are imported -> -#X.shape = (X.shape[0],1) -#Y.shape = (Y.shape[0],1) -# Need to run these lines when X and Y are imported <- - -## Generation of minimal example data -> -#X = np.random.rand(3) -#sort_index = np.argsort(X) -#X = X[sort_index]; X.shape = (X.shape[0],1) -#Y = np.sin(10*X) + np.random.randn(*X.shape)*0.1 -## Generation of minimal example data <- - -#plt.figure() -#plt.plot( X, Y) -#plt.show() - -kernel = GPy.kern.Matern32(X.shape[1]) -m = GPy.models.StateSpace(X,Y, kernel) - -print m -# -m.optimize(optimizer='bfgs',messages=True) -# -print m - kernel1 = GPy.kern.Matern32(X.shape[1]) m1 = GPy.models.GPRegression(X,Y, kernel1) @@ -40,9 +15,9 @@ m1.optimize(optimizer='bfgs',messages=True) print m1 -kernel2 = GPy.kern.Matern32(X.shape[1]) -m2 = SS_new.StateSpace(X,Y, kernel2) - +kernel2 = GPy.kern.sde_Matern32(X.shape[1]) +#m2 = SS_model.StateSpace(X,Y, kernel2) +m2 = GPy.models.StateSpace(X,Y, kernel2) print m2 m2.optimize(optimizer='bfgs',messages=True) diff --git a/GPy/models/__init__.py b/GPy/models/__init__.py index 849865b3..c31d68dd 100644 --- a/GPy/models/__init__.py +++ b/GPy/models/__init__.py @@ -23,4 +23,4 @@ from .one_vs_all_classification import OneVsAllClassification from .one_vs_all_sparse_classification import OneVsAllSparseClassification from .dpgplvm import DPBayesianGPLVM -from state_space import StateSpace +from .state_space_model import StateSpace diff --git a/GPy/models/state_space_cython.c b/GPy/models/state_space_cython.c index eb54c00c..45a66358 100644 --- a/GPy/models/state_space_cython.c +++ b/GPy/models/state_space_cython.c @@ -250,13 +250,14 @@ class __Pyx_FakeReference { #define _USE_MATH_DEFINES #endif #include -#define __PYX_HAVE__state_space_cython -#define __PYX_HAVE_API__state_space_cython +#define __PYX_HAVE__GPy__models__state_space_cython +#define __PYX_HAVE_API__GPy__models__state_space_cython #include "string.h" #include "stdio.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" +#include "numpy/npy_math.h" #ifdef _OPENMP #include #endif /* _OPENMP */ @@ -460,7 +461,7 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { - "state_space_cython.pyx", + "GPy/models/state_space_cython.pyx", "__init__.pxd", "type.pxd", }; @@ -500,7 +501,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -509,7 +510,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -518,7 +519,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -527,7 +528,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -536,7 +537,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -545,7 +546,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -554,7 +555,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -563,7 +564,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -572,7 +573,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -581,7 +582,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -590,7 +591,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -599,7 +600,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -608,7 +609,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -617,7 +618,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -626,7 +627,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -635,7 +636,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -644,7 +645,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -653,7 +654,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -662,7 +663,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -671,7 +672,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -680,7 +681,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -689,23 +690,23 @@ typedef npy_double __pyx_t_5numpy_double_t; */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; -/* "state_space_cython.pyx":13 +/* "GPy/models/state_space_cython.pyx":17 * DTYPE_int = np.int64 * * ctypedef np.float64_t DTYPE_t # <<<<<<<<<<<<<< * ctypedef np.int64_t DTYPE_int_t * */ -typedef __pyx_t_5numpy_float64_t __pyx_t_18state_space_cython_DTYPE_t; +typedef __pyx_t_5numpy_float64_t __pyx_t_3GPy_6models_18state_space_cython_DTYPE_t; -/* "state_space_cython.pyx":14 +/* "GPy/models/state_space_cython.pyx":18 * * ctypedef np.float64_t DTYPE_t * ctypedef np.int64_t DTYPE_int_t # <<<<<<<<<<<<<< * * # Template class for dynamic callables */ -typedef __pyx_t_5numpy_int64_t __pyx_t_18state_space_cython_DTYPE_int_t; +typedef __pyx_t_5numpy_int64_t __pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t; #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; @@ -728,15 +729,15 @@ typedef __pyx_t_5numpy_int64_t __pyx_t_18state_space_cython_DTYPE_int_t; /*--- Type declarations ---*/ -struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython; -struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython; -struct __pyx_obj_18state_space_cython_R_handling_Cython; -struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython; -struct __pyx_obj_18state_space_cython_Q_handling_Cython; -struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython; -struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; +struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -745,7 +746,7 @@ struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -754,7 +755,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -763,7 +764,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -771,94 +772,94 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; * cdef inline object PyArray_MultiIterNew1(a): */ typedef npy_cdouble __pyx_t_5numpy_complex_t; -struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset; -struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset; -struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset; -struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset; +struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset; +struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset; +struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_reset; +struct __pyx_opt_args_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_reset; -/* "state_space_cython.pyx":36 +/* "GPy/models/state_space_cython.pyx":40 * raise NotImplemented("(cython) dQk is not implemented!") * * cpdef reset(self, bint compute_derivatives = False): # <<<<<<<<<<<<<< * raise NotImplemented("(cython) reset is not implemented!") * */ -struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset { +struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset { int __pyx_n; int compute_derivatives; }; -/* "state_space_cython.pyx":59 +/* "GPy/models/state_space_cython.pyx":63 * raise NotImplemented("(cython) dQk is not implemented!") * * cpdef reset(self,compute_derivatives = False): # <<<<<<<<<<<<<< * raise NotImplemented("(cython) reset is not implemented!") * */ -struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset { +struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset { int __pyx_n; PyObject *compute_derivatives; }; -/* "state_space_cython.pyx":361 +/* "GPy/models/state_space_cython.pyx":365 * * * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< * """ * For reusing this object e.g. in smoother computation. It makes sence */ -struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset { +struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_reset { int __pyx_n; int compute_derivatives; }; -/* "state_space_cython.pyx":440 +/* "GPy/models/state_space_cython.pyx":444 * return np.dot(A, m) # default dynamic model * * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< * """ * For reusing this object e.g. in smoother computation. It makes sence */ -struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset { +struct __pyx_opt_args_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_reset { int __pyx_n; int compute_derivatives; }; -/* "state_space_cython.pyx":17 +/* "GPy/models/state_space_cython.pyx":21 * * # Template class for dynamic callables * cdef class Dynamic_Callables_Cython: # <<<<<<<<<<<<<< * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): * raise NotImplemented("(cython) f_a is not implemented!") */ -struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython { +struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython { PyObject_HEAD - struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtab; + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtab; }; -/* "state_space_cython.pyx":40 +/* "GPy/models/state_space_cython.pyx":44 * * # Template class for measurement callables * cdef class Measurement_Callables_Cython: # <<<<<<<<<<<<<< * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): * raise NotImplemented("(cython) f_a is not implemented!") */ -struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython { +struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython { PyObject_HEAD - struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *__pyx_vtab; + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_vtab; }; -/* "state_space_cython.pyx":62 +/* "GPy/models/state_space_cython.pyx":66 * raise NotImplemented("(cython) reset is not implemented!") * * cdef class R_handling_Cython(Measurement_Callables_Cython): # <<<<<<<<<<<<<< * """ * The calss handles noise matrix R. */ -struct __pyx_obj_18state_space_cython_R_handling_Cython { - struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython __pyx_base; +struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython { + struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython __pyx_base; PyArrayObject *R; PyArrayObject *index; int R_time_var_index; @@ -868,30 +869,30 @@ struct __pyx_obj_18state_space_cython_R_handling_Cython { }; -/* "state_space_cython.pyx":161 +/* "GPy/models/state_space_cython.pyx":165 * * * cdef class Std_Measurement_Callables_Cython(R_handling_Cython): # <<<<<<<<<<<<<< * * cdef: */ -struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython { - struct __pyx_obj_18state_space_cython_R_handling_Cython __pyx_base; +struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython { + struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython __pyx_base; PyArrayObject *H; int H_time_var_index; PyArrayObject *dH; }; -/* "state_space_cython.pyx":208 +/* "GPy/models/state_space_cython.pyx":212 * * * cdef class Q_handling_Cython(Dynamic_Callables_Cython): # <<<<<<<<<<<<<< * * cdef: */ -struct __pyx_obj_18state_space_cython_Q_handling_Cython { - struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython __pyx_base; +struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython { + struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython __pyx_base; PyArrayObject *Q; PyArrayObject *index; int Q_time_var_index; @@ -901,30 +902,30 @@ struct __pyx_obj_18state_space_cython_Q_handling_Cython { }; -/* "state_space_cython.pyx":314 +/* "GPy/models/state_space_cython.pyx":318 * return square_root * * cdef class Std_Dynamic_Callables_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< * cdef: * np.ndarray A */ -struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython { - struct __pyx_obj_18state_space_cython_Q_handling_Cython __pyx_base; +struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython { + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython __pyx_base; PyArrayObject *A; int A_time_var_index; PyArrayObject *dA; }; -/* "state_space_cython.pyx":369 +/* "GPy/models/state_space_cython.pyx":373 * return self * * cdef class AQcompute_batch_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< * """ * Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter */ -struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython { - struct __pyx_obj_18state_space_cython_Q_handling_Cython __pyx_base; +struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython { + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython __pyx_base; PyArrayObject *As; PyArrayObject *Qs; PyArrayObject *dAs; @@ -936,7 +937,7 @@ struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython { -/* "state_space_cython.pyx":17 +/* "GPy/models/state_space_cython.pyx":21 * * # Template class for dynamic callables * cdef class Dynamic_Callables_Cython: # <<<<<<<<<<<<<< @@ -944,19 +945,19 @@ struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython { * raise NotImplemented("(cython) f_a is not implemented!") */ -struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython { - PyObject *(*f_a)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); - PyObject *(*Ak)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); - PyObject *(*Qk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*Q_srk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*dAk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*dQk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*reset)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython { + PyObject *(*f_a)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Ak)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Qk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*Q_srk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dAk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dQk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*reset)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); }; -static struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; -/* "state_space_cython.pyx":40 +/* "GPy/models/state_space_cython.pyx":44 * * # Template class for measurement callables * cdef class Measurement_Callables_Cython: # <<<<<<<<<<<<<< @@ -964,19 +965,19 @@ static struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *__ * raise NotImplemented("(cython) f_a is not implemented!") */ -struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython { - PyObject *(*f_h)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); - PyObject *(*Hk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); - PyObject *(*Rk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*R_isrk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*dHk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*dRk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); - PyObject *(*reset)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython { + PyObject *(*f_h)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Hk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Rk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*R_isrk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dHk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dRk)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*reset)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); }; -static struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *__pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; -/* "state_space_cython.pyx":62 +/* "GPy/models/state_space_cython.pyx":66 * raise NotImplemented("(cython) reset is not implemented!") * * cdef class R_handling_Cython(Measurement_Callables_Cython): # <<<<<<<<<<<<<< @@ -984,13 +985,13 @@ static struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython * The calss handles noise matrix R. */ -struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython { - struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython __pyx_base; +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_R_handling_Cython { + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython __pyx_base; }; -static struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython *__pyx_vtabptr_18state_space_cython_R_handling_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_R_handling_Cython; -/* "state_space_cython.pyx":161 +/* "GPy/models/state_space_cython.pyx":165 * * * cdef class Std_Measurement_Callables_Cython(R_handling_Cython): # <<<<<<<<<<<<<< @@ -998,13 +999,13 @@ static struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython *__pyx_vta * cdef: */ -struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cython { - struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython __pyx_base; +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython { + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_R_handling_Cython __pyx_base; }; -static struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; -/* "state_space_cython.pyx":208 +/* "GPy/models/state_space_cython.pyx":212 * * * cdef class Q_handling_Cython(Dynamic_Callables_Cython): # <<<<<<<<<<<<<< @@ -1012,13 +1013,13 @@ static struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cy * cdef: */ -struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython { - struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython __pyx_base; +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Q_handling_Cython { + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython __pyx_base; }; -static struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython *__pyx_vtabptr_18state_space_cython_Q_handling_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython; -/* "state_space_cython.pyx":314 +/* "GPy/models/state_space_cython.pyx":318 * return square_root * * cdef class Std_Dynamic_Callables_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< @@ -1026,13 +1027,13 @@ static struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython *__pyx_vta * np.ndarray A */ -struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython { - struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_base; +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython { + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Q_handling_Cython __pyx_base; }; -static struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; -/* "state_space_cython.pyx":369 +/* "GPy/models/state_space_cython.pyx":373 * return self * * cdef class AQcompute_batch_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< @@ -1040,10 +1041,10 @@ static struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython * Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter */ -struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython { - struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_base; +struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_AQcompute_batch_Cython { + struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Q_handling_Cython __pyx_base; }; -static struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython *__pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_vtabptr_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; /* --- Runtime support code (head) --- */ #ifndef CYTHON_REFNANNY @@ -1411,40 +1412,40 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_Hk, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_R_isrk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dHk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dRk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_Rk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_dRk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_dHk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Qk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_dQk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_reset(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset *__pyx_optional_args); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Qk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dAk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dQk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Q_srk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dAk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dQk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_Hk, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Hk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Rk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_R_isrk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_dHk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_dRk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_Rk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_dRk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_R_isrk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_dHk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_Qk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_reset(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Qk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ /* Module declarations from 'cpython.buffer' */ @@ -1475,76 +1476,76 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha /* Module declarations from 'cython' */ -/* Module declarations from 'state_space_cython' */ -static PyTypeObject *__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_Measurement_Callables_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_R_handling_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_Std_Measurement_Callables_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_Q_handling_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_Std_Dynamic_Callables_Cython = 0; -static PyTypeObject *__pyx_ptype_18state_space_cython_AQcompute_batch_Cython = 0; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_18state_space_cython_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_int_t = { "DTYPE_int_t", NULL, sizeof(__pyx_t_18state_space_cython_DTYPE_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_18state_space_cython_DTYPE_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_18state_space_cython_DTYPE_int_t), 0 }; -#define __Pyx_MODULE_NAME "state_space_cython" -int __pyx_module_is_main_state_space_cython = 0; +/* Module declarations from 'GPy.models.state_space_cython' */ +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_R_handling_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_Q_handling_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_3GPy_6models_18state_space_cython_AQcompute_batch_Cython = 0; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3GPy_6models_18state_space_cython_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t = { "DTYPE_int_t", NULL, sizeof(__pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t), 0 }; +#define __Pyx_MODULE_NAME "GPy.models.state_space_cython" +int __pyx_module_is_main_GPy__models__state_space_cython = 0; -/* Implementation of 'state_space_cython' */ +/* Implementation of 'GPy.models.state_space_cython' */ static PyObject *__pyx_builtin_NotImplemented; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_super; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_4Qk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_6Q_srk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_8dAk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_h(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_Hk); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2Hk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_4Rk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_6R_isrk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_8dHk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_10dRk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, PyObject *__pyx_v_compute_derivatives); /* proto */ -static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_p_unique_R_number, PyArrayObject *__pyx_v_dR); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_2Rk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_4dRk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_6R_isrk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static int __pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython___init__(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_H, int __pyx_v_H_time_var_index, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_unique_R_number, PyArrayObject *__pyx_v_dH, PyArrayObject *__pyx_v_dR); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_6dHk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_p_unique_Q_number, PyArrayObject *__pyx_v_dQ); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_2Qk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_4dQk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_A, int __pyx_v_A_time_var_index, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_unique_Q_number, PyArrayObject *__pyx_v_dA, PyArrayObject *__pyx_v_dQ); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_6dAk(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ -static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, PyArrayObject *__pyx_v_As, PyArrayObject *__pyx_v_Qs, PyArrayObject *__pyx_v_reconstruct_indices, PyArrayObject *__pyx_v_dAs, PyArrayObject *__pyx_v_dQs); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_6Ak(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_8Qk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_10dAk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_12dQk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_14Q_srk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ -static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, PyArrayObject *__pyx_v_measurement, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ -static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_state_dim, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, CYTHON_UNUSED PyObject *__pyx_v_X, PyObject *__pyx_v_Y, PyArrayObject *__pyx_v_m_init, PyArrayObject *__pyx_v_P_init, CYTHON_UNUSED PyObject *__pyx_v_p_kalman_filter_type, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, int __pyx_v_grad_params_no, PyArrayObject *__pyx_v_dm_init, PyArrayObject *__pyx_v_dP_init); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_2Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_4Qk(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_6Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_8dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_10dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_12reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_Hk); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_2Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_4Rk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_6R_isrk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_8dHk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_10dRk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_12reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, PyObject *__pyx_v_compute_derivatives); /* proto */ +static int __pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_p_unique_R_number, PyArrayObject *__pyx_v_dR); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython_2Rk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython_4dRk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython_6R_isrk(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_H, int __pyx_v_H_time_var_index, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_unique_R_number, PyArrayObject *__pyx_v_dH, PyArrayObject *__pyx_v_dR); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_6dHk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_p_unique_Q_number, PyArrayObject *__pyx_v_dQ); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython_2Qk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython_4dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython_6Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_A, int __pyx_v_A_time_var_index, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_unique_Q_number, PyArrayObject *__pyx_v_dA, PyArrayObject *__pyx_v_dQ); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_6dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static int __pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, PyArrayObject *__pyx_v_As, PyArrayObject *__pyx_v_Qs, PyArrayObject *__pyx_v_reconstruct_indices, PyArrayObject *__pyx_v_dAs, PyArrayObject *__pyx_v_dQs); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_2f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_4reset(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_6Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_8Qk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_10dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_12dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_14Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython__kalman_prediction_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_2_kalman_update_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, PyArrayObject *__pyx_v_measurement, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_state_dim, struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, CYTHON_UNUSED PyObject *__pyx_v_X, PyObject *__pyx_v_Y, PyArrayObject *__pyx_v_m_init, PyArrayObject *__pyx_v_P_init, CYTHON_UNUSED PyObject *__pyx_v_p_kalman_filter_type, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, int __pyx_v_grad_params_no, PyArrayObject *__pyx_v_dm_init, PyArrayObject *__pyx_v_dP_init); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ -static PyObject *__pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_R_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_Std_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_R_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static char __pyx_k_A[] = "A"; static char __pyx_k_B[] = "B"; static char __pyx_k_H[] = "H"; @@ -1593,6 +1594,7 @@ static char __pyx_k_dv[] = "dv"; static char __pyx_k_np[] = "np"; static char __pyx_k_pi[] = "pi"; static char __pyx_k_sp[] = "sp"; +static char __pyx_k_all[] = "all"; static char __pyx_k_any[] = "any"; static char __pyx_k_dAk[] = "dAk"; static char __pyx_k_dAs[] = "dAs"; @@ -1703,7 +1705,6 @@ static char __pyx_k_p_unique_Q_number[] = "p_unique_Q_number"; static char __pyx_k_p_unique_R_number[] = "p_unique_R_number"; static char __pyx_k_dP_pred_all_params[] = "dP_pred_all_params"; static char __pyx_k_dm_pred_all_params[] = "dm_pred_all_params"; -static char __pyx_k_state_space_cython[] = "state_space_cython"; static char __pyx_k_total_size_of_data[] = "total_size_of_data"; static char __pyx_k_calc_log_likelihood[] = "calc_log_likelihood"; static char __pyx_k_compute_derivatives[] = "compute_derivatives"; @@ -1725,6 +1726,7 @@ static char __pyx_k_cython_Ak_is_not_implemented[] = "(cython) Ak is not impleme static char __pyx_k_cython_Hk_is_not_implemented[] = "(cython) Hk is not implemented!"; static char __pyx_k_cython_Qk_is_not_implemented[] = "(cython) Qk is not implemented!"; static char __pyx_k_cython_Rk_is_not_implemented[] = "(cython) Rk is not implemented!"; +static char __pyx_k_GPy_models_state_space_cython[] = "GPy.models.state_space_cython"; static char __pyx_k_cython_dAk_is_not_implemented[] = "(cython) dAk is not implemented!"; static char __pyx_k_cython_dQk_is_not_implemented[] = "(cython) dQk is not implemented!"; static char __pyx_k_cython_f_a_is_not_implemented[] = "(cython) f_a is not implemented!"; @@ -1736,10 +1738,11 @@ static char __pyx_k_cython_Q_srk_is_not_implemented[] = "(cython) Q_srk is not i static char __pyx_k_cython_reset_is_not_implemented[] = "(cython) reset is not implemented!"; static char __pyx_k_kalman_prediction_step_SVD_Cyth[] = "_kalman_prediction_step_SVD_Cython"; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; -static char __pyx_k_users_agrigori_SpiderOak_sp_hiv[] = "/users/agrigori/SpiderOak/sp_hive/Programming/python/my_utils/state_space/state_space_cython.pyx"; +static char __pyx_k_users_agrigori_SpiderOak_sp_hiv[] = "/users/agrigori/SpiderOak/sp_hive/Programming/python/GPy/build/lib.linux-x86_64-2.7/GPy/models/state_space_cython.pyx"; static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_Kalman_Filter_Update_SVD_S_is_ne[] = "Kalman Filter Update SVD: S is negative step %i"; static char __pyx_k_Measurement_dimension_larger_the[] = "Measurement dimension larger then 1 is currently not supported"; +static char __pyx_k_Nan_measurements_are_currently_n[] = "Nan measurements are currently not supported if\n they are intermixed with not NaN measurements"; static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; @@ -1751,6 +1754,7 @@ static PyObject *__pyx_n_s_DTYPE; static PyObject *__pyx_n_s_DTYPE_int; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_GPy_models_state_space_cython; static PyObject *__pyx_n_s_H; static PyObject *__pyx_n_s_H_time_var_index; static PyObject *__pyx_n_s_Hk; @@ -1758,6 +1762,7 @@ static PyObject *__pyx_n_s_K; static PyObject *__pyx_kp_s_Kalman_Filter_Update_SVD_S_is_ne; static PyObject *__pyx_n_s_M; static PyObject *__pyx_kp_s_Measurement_dimension_larger_the; +static PyObject *__pyx_kp_s_Nan_measurements_are_currently_n; static PyObject *__pyx_kp_s_Nan_values_in_likelihood_update; static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_s_NotImplemented; @@ -1794,6 +1799,7 @@ static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_Vh; static PyObject *__pyx_n_s_X; static PyObject *__pyx_n_s_Y; +static PyObject *__pyx_n_s_all; static PyObject *__pyx_n_s_any; static PyObject *__pyx_n_s_axis; static PyObject *__pyx_n_s_calc_grad_log_likelihood; @@ -1903,7 +1909,6 @@ static PyObject *__pyx_n_s_shape; static PyObject *__pyx_n_s_sp; static PyObject *__pyx_n_s_sqrt; static PyObject *__pyx_n_s_state_dim; -static PyObject *__pyx_n_s_state_space_cython; static PyObject *__pyx_n_s_steps_no; static PyObject *__pyx_n_s_sum; static PyObject *__pyx_n_s_super; @@ -2035,24 +2040,25 @@ static PyObject *__pyx_slice__100; static PyObject *__pyx_slice__101; static PyObject *__pyx_slice__102; static PyObject *__pyx_slice__103; -static PyObject *__pyx_slice__104; static PyObject *__pyx_slice__105; static PyObject *__pyx_slice__106; static PyObject *__pyx_slice__107; -static PyObject *__pyx_tuple__108; +static PyObject *__pyx_slice__108; +static PyObject *__pyx_tuple__104; static PyObject *__pyx_tuple__109; static PyObject *__pyx_tuple__110; static PyObject *__pyx_tuple__111; static PyObject *__pyx_tuple__112; static PyObject *__pyx_tuple__113; static PyObject *__pyx_tuple__114; -static PyObject *__pyx_tuple__116; -static PyObject *__pyx_tuple__118; -static PyObject *__pyx_codeobj__115; -static PyObject *__pyx_codeobj__117; -static PyObject *__pyx_codeobj__119; +static PyObject *__pyx_tuple__115; +static PyObject *__pyx_tuple__117; +static PyObject *__pyx_tuple__119; +static PyObject *__pyx_codeobj__116; +static PyObject *__pyx_codeobj__118; +static PyObject *__pyx_codeobj__120; -/* "state_space_cython.pyx":18 +/* "GPy/models/state_space_cython.pyx":22 * # Template class for dynamic callables * cdef class Dynamic_Callables_Cython: * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): # <<<<<<<<<<<<<< @@ -2060,8 +2066,8 @@ static PyObject *__pyx_codeobj__119; * */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -2089,23 +2095,23 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_1f_a)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -2120,7 +2126,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -2134,7 +2140,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_A)); __Pyx_GIVEREF(((PyObject *)__pyx_v_A)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -2146,20 +2152,20 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":19 + /* "GPy/models/state_space_cython.pyx":23 * cdef class Dynamic_Callables_Cython: * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): * raise NotImplemented("(cython) f_a is not implemented!") # <<<<<<<<<<<<<< * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":18 + /* "GPy/models/state_space_cython.pyx":22 * # Template class for dynamic callables * cdef class Dynamic_Callables_Cython: * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): # <<<<<<<<<<<<<< @@ -2180,7 +2186,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_A.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -2193,8 +2199,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYT } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_1f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m = 0; PyArrayObject *__pyx_v_A = 0; @@ -2225,16 +2231,16 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(P case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_A)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -2243,21 +2249,21 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(P values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m = ((PyArrayObject *)values[1]); __pyx_v_A = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); /* function exit code */ goto __pyx_L0; @@ -2268,7 +2274,7 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a(P return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -2290,16 +2296,16 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(st __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(__pyx_v_self, __pyx_v_k, __pyx_v_m, __pyx_v_A, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a(__pyx_v_self, __pyx_v_k, __pyx_v_m, __pyx_v_A, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -2313,7 +2319,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(st __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_A.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -2325,7 +2331,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(st return __pyx_r; } -/* "state_space_cython.pyx":21 +/* "GPy/models/state_space_cython.pyx":25 * raise NotImplemented("(cython) f_a is not implemented!") * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -2333,8 +2339,8 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(st * */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P; __Pyx_Buffer __pyx_pybuffer_P; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -2362,23 +2368,23 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH __pyx_pybuffernd_P.rcbuffer = &__pyx_pybuffer_P; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_v_P, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_v_P, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P.diminfo[0].strides = __pyx_pybuffernd_P.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P.diminfo[0].shape = __pyx_pybuffernd_P.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P.diminfo[1].strides = __pyx_pybuffernd_P.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P.diminfo[1].shape = __pyx_pybuffernd_P.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_3Ak)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -2393,7 +2399,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -2407,7 +2413,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_P)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -2419,20 +2425,20 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":22 + /* "GPy/models/state_space_cython.pyx":26 * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix * raise NotImplemented("(cython) Ak is not implemented!") # <<<<<<<<<<<<<< * * cpdef Qk(self, int k): */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":21 + /* "GPy/models/state_space_cython.pyx":25 * raise NotImplemented("(cython) f_a is not implemented!") * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -2453,7 +2459,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -2466,8 +2472,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTH } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_3Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m = 0; PyArrayObject *__pyx_v_P = 0; @@ -2498,16 +2504,16 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(Py case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_P)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Ak") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Ak") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -2516,21 +2522,21 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(Py values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m = ((PyArrayObject *)values[1]); __pyx_v_P = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P), __pyx_ptype_5numpy_ndarray, 1, "P", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_P); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P), __pyx_ptype_5numpy_ndarray, 1, "P", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_2Ak(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_P); /* function exit code */ goto __pyx_L0; @@ -2541,7 +2547,7 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak(Py return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_2Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P; __Pyx_Buffer __pyx_pybuffer_P; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -2563,16 +2569,16 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(st __pyx_pybuffernd_P.rcbuffer = &__pyx_pybuffer_P; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_v_P, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_v_P, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P.diminfo[0].strides = __pyx_pybuffernd_P.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P.diminfo[0].shape = __pyx_pybuffernd_P.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P.diminfo[1].strides = __pyx_pybuffernd_P.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P.diminfo[1].shape = __pyx_pybuffernd_P.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(__pyx_v_self, __pyx_v_k, __pyx_v_m, __pyx_v_P, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Ak(__pyx_v_self, __pyx_v_k, __pyx_v_m, __pyx_v_P, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -2586,7 +2592,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(st __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -2598,7 +2604,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(st return __pyx_r; } -/* "state_space_cython.pyx":24 +/* "GPy/models/state_space_cython.pyx":28 * raise NotImplemented("(cython) Ak is not implemented!") * * cpdef Qk(self, int k): # <<<<<<<<<<<<<< @@ -2606,8 +2612,8 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(st * */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -2624,11 +2630,11 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTH if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Qk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Qk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); 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__pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -2665,20 +2671,20 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTH __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":25 + /* "GPy/models/state_space_cython.pyx":29 * * cpdef Qk(self, int k): * raise NotImplemented("(cython) Qk is not implemented!") # <<<<<<<<<<<<<< * * cpdef Q_srk(self, int k): */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":24 + /* "GPy/models/state_space_cython.pyx":28 * raise NotImplemented("(cython) Ak is not implemented!") * * cpdef Qk(self, int k): # <<<<<<<<<<<<<< @@ -2694,7 +2700,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTH __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Qk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.Qk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -2703,8 +2709,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTH } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_5Qk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -2713,22 +2719,22 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_5Qk(Py __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("Qk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":27 + /* "GPy/models/state_space_cython.pyx":31 * raise NotImplemented("(cython) Qk is not implemented!") * * cpdef Q_srk(self, int k): # <<<<<<<<<<<<<< @@ -2850,7 +2856,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(C __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -2859,8 +2865,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(C } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -2869,22 +2875,22 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("Q_srk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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__Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -2893,7 +2899,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_6Q_srk int __pyx_clineno = 0; __Pyx_RefNannySetupContext("Q_srk", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -2902,7 +2908,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_6Q_srk /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); 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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":30 + /* "GPy/models/state_space_cython.pyx":34 * raise NotImplemented("(cython) Q_srk is not implemented!") * * cpdef dAk(self, int k): # <<<<<<<<<<<<<< @@ -3006,7 +3012,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk(CYT __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.dAk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.dAk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3015,8 +3021,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk(CYT } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_9dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_9dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_9dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_9dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -3025,22 +3031,22 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_9dAk(P __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("dAk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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/*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dQk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3092,11 +3098,11 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk(CYT if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dQk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dQk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); 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/*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_11dQk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_11dQk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_11dQk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -3181,22 +3187,22 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_11dQk( __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("dQk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.dQk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.dQk", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), ((int)__pyx_v_k)); + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_10dQk(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), ((int)__pyx_v_k)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_10dQk(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3205,7 +3211,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk( int __pyx_clineno = 0; __Pyx_RefNannySetupContext("dQk", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dQk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -3214,7 +3220,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk( /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.dQk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.dQk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3222,7 +3228,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk( return __pyx_r; } -/* "state_space_cython.pyx":36 +/* "GPy/models/state_space_cython.pyx":40 * raise NotImplemented("(cython) dQk is not implemented!") * * cpdef reset(self, bint compute_derivatives = False): # <<<<<<<<<<<<<< @@ -3230,8 +3236,8 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk( * */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args) { int __pyx_v_compute_derivatives = ((int)0); PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -3254,11 +3260,11 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(C if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -3295,20 +3301,20 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(C __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":37 + /* "GPy/models/state_space_cython.pyx":41 * * cpdef reset(self, bint compute_derivatives = False): * raise NotImplemented("(cython) reset is not implemented!") # <<<<<<<<<<<<<< * * # Template class for measurement callables */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":36 + /* "GPy/models/state_space_cython.pyx":40 * raise NotImplemented("(cython) dQk is not implemented!") * * cpdef reset(self, bint compute_derivatives = False): # <<<<<<<<<<<<<< @@ -3324,7 +3330,7 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(C __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3333,8 +3339,8 @@ static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(C } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_compute_derivatives; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -3362,7 +3368,7 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13rese } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -3372,31 +3378,31 @@ static PyObject *__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13rese } } if (values[0]) { - __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_compute_derivatives = ((int)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12reset(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_12reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_12reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; - struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; + struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -3404,7 +3410,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12rese __Pyx_XDECREF(__pyx_r); __pyx_t_2.__pyx_n = 1; __pyx_t_2.compute_derivatives = __pyx_v_compute_derivatives; - __pyx_t_1 = __pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython->reset(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython->reset(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -3413,7 +3419,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12rese /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3421,7 +3427,7 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12rese return __pyx_r; } -/* "state_space_cython.pyx":41 +/* "GPy/models/state_space_cython.pyx":45 * # Template class for measurement callables * cdef class Measurement_Callables_Cython: * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): # <<<<<<<<<<<<<< @@ -3429,8 +3435,8 @@ static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12rese * */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_Hk, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_Hk, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_Hk; __Pyx_Buffer __pyx_pybuffer_Hk; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -3458,23 +3464,23 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h __pyx_pybuffernd_Hk.rcbuffer = &__pyx_pybuffer_Hk; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer, (PyObject*)__pyx_v_Hk, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer, (PyObject*)__pyx_v_Hk, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; 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goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f_h)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_1f_h)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -3489,7 +3495,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -3503,7 +3509,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_Hk)); __Pyx_GIVEREF(((PyObject *)__pyx_v_Hk)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -3515,20 +3521,20 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":42 + /* "GPy/models/state_space_cython.pyx":46 * cdef class Measurement_Callables_Cython: * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): * raise NotImplemented("(cython) f_a is not implemented!") # <<<<<<<<<<<<<< * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":41 + /* "GPy/models/state_space_cython.pyx":45 * # Template class for measurement callables * cdef class Measurement_Callables_Cython: * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): # <<<<<<<<<<<<<< @@ -3549,7 +3555,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -3562,8 +3568,8 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_1f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m_pred = 0; PyArrayObject *__pyx_v_Hk = 0; @@ -3594,16 +3600,16 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_Hk)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_h") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_h") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -3612,21 +3618,21 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m_pred = ((PyArrayObject *)values[1]); __pyx_v_Hk = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Hk), __pyx_ptype_5numpy_ndarray, 1, "Hk", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_h(((struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_Hk); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Hk), __pyx_ptype_5numpy_ndarray, 1, "Hk", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_Hk); /* function exit code */ goto __pyx_L0; @@ -3637,7 +3643,7 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_h(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_Hk) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_Hk) { __Pyx_LocalBuf_ND __pyx_pybuffernd_Hk; __Pyx_Buffer __pyx_pybuffer_Hk; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -3659,16 +3665,16 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_ __pyx_pybuffernd_Hk.rcbuffer = &__pyx_pybuffer_Hk; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer, (PyObject*)__pyx_v_Hk, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer, (PyObject*)__pyx_v_Hk, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_Hk.diminfo[0].strides = __pyx_pybuffernd_Hk.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Hk.diminfo[0].shape = __pyx_pybuffernd_Hk.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Hk.diminfo[1].strides = __pyx_pybuffernd_Hk.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Hk.diminfo[1].shape = __pyx_pybuffernd_Hk.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h(__pyx_v_self, __pyx_v_k, __pyx_v_m_pred, __pyx_v_Hk, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h(__pyx_v_self, __pyx_v_k, __pyx_v_m_pred, __pyx_v_Hk, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -3682,7 +3688,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_Hk.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -3694,7 +3700,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_ return __pyx_r; } -/* "state_space_cython.pyx":44 +/* "GPy/models/state_space_cython.pyx":48 * raise NotImplemented("(cython) f_a is not implemented!") * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -3702,8 +3708,8 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_ * */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Hk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -3731,23 +3737,23 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Hk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Hk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3Hk)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_3Hk)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -3762,7 +3768,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -3776,7 +3782,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_P_pred)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P_pred)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -3788,20 +3794,20 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":45 + /* "GPy/models/state_space_cython.pyx":49 * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix * raise NotImplemented("(cython) Hk is not implemented!") # <<<<<<<<<<<<<< * * cpdef Rk(self, int k): */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplemented, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":44 + /* "GPy/models/state_space_cython.pyx":48 * raise NotImplemented("(cython) f_a is not implemented!") * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -3822,7 +3828,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -3835,8 +3841,8 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk( } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_3Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m_pred = 0; PyArrayObject *__pyx_v_P_pred = 0; @@ -3867,16 +3873,16 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3H case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_P_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Hk") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Hk") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -3885,21 +3891,21 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3H values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m_pred = ((PyArrayObject *)values[1]); __pyx_v_P_pred = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2Hk(((struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_2Hk(((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); /* function exit code */ goto __pyx_L0; @@ -3910,7 +3916,7 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3H return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2Hk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_2Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -3932,16 +3938,16 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2H __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk(__pyx_v_self, __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Hk(__pyx_v_self, __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -3955,7 +3961,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2H __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -3967,7 +3973,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2H return __pyx_r; } -/* "state_space_cython.pyx":47 +/* "GPy/models/state_space_cython.pyx":51 * raise NotImplemented("(cython) Hk is not implemented!") * * cpdef Rk(self, int k): # <<<<<<<<<<<<<< @@ -3975,8 +3981,8 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2H * */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_5Rk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_5Rk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Rk(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3993,11 +3999,11 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk( if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Rk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Rk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_5Rk)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_5Rk)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -4011,17 +4017,17 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk( } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; 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/*proto*/ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_5Rk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_5Rk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_5Rk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -4082,22 +4088,22 @@ static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_5R __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("Rk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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__pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":59 + /* "GPy/models/state_space_cython.pyx":63 * raise NotImplemented("(cython) dQk is not implemented!") * * cpdef reset(self,compute_derivatives = False): # <<<<<<<<<<<<<< @@ -4688,7 +4694,7 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_res __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4697,8 +4703,8 @@ static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_res } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_13reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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+ __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_12reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, PyObject *__pyx_v_compute_derivatives) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_12reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, PyObject *__pyx_v_compute_derivatives) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; - struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset __pyx_t_2; + struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset __pyx_t_2; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4765,7 +4771,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12 __Pyx_XDECREF(__pyx_r); __pyx_t_2.__pyx_n = 1; __pyx_t_2.compute_derivatives = __pyx_v_compute_derivatives; - __pyx_t_1 = __pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython->reset(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython->reset(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -4774,7 +4780,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12 /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Measurement_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Measurement_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4782,7 +4788,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12 return __pyx_r; } -/* "state_space_cython.pyx":74 +/* "GPy/models/state_space_cython.pyx":78 * dict R_square_root * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, # <<<<<<<<<<<<<< @@ -4791,12 +4797,12 @@ static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12 */ /* Python wrapper */ -static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_17R_handling_Cython___init__[] = "\n Input: \n ---------------\n R - array with noise on various steps. The result of preprocessing\n the noise input.\n \n index - for each step of Kalman filter contains the corresponding index\n in the array.\n \n R_time_var_index - another index in the array R. Computed earlier and passed here.\n \n unique_R_number - number of unique noise matrices below which square roots\n are cached and above which they are computed each time.\n \n dR: 3D array[:, :, param_num]\n derivative of R. Derivative is supported only when R do not change over time\n \n Output:\n --------------\n Object which has two necessary functions:\n f_R(k)\n inv_R_square_root(k)\n "; +static int __pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_17R_handling_Cython___init__[] = "\n Input: \n ---------------\n R - array with noise on various steps. The result of preprocessing\n the noise input.\n \n index - for each step of Kalman filter contains the corresponding index\n in the array.\n \n R_time_var_index - another index in the array R. Computed earlier and passed here.\n \n unique_R_number - number of unique noise matrices below which square roots\n are cached and above which they are computed each time.\n \n dR: 3D array[:, :, param_num]\n derivative of R. Derivative is supported only when R do not change over time\n \n Output:\n --------------\n Object which has two necessary functions:\n f_R(k)\n inv_R_square_root(k)\n "; #if CYTHON_COMPILING_IN_CPYTHON -struct wrapperbase __pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__; +struct wrapperbase __pyx_wrapperbase_3GPy_6models_18state_space_cython_17R_handling_Cython___init__; #endif -static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_R = 0; PyArrayObject *__pyx_v_index = 0; int __pyx_v_R_time_var_index; @@ -4812,7 +4818,7 @@ static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_R,&__pyx_n_s_index,&__pyx_n_s_R_time_var_index,&__pyx_n_s_p_unique_R_number,&__pyx_n_s_dR,0}; PyObject* values[5] = {0,0,0,0,0}; - /* "state_space_cython.pyx":75 + /* "GPy/models/state_space_cython.pyx":79 * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, * int R_time_var_index, int p_unique_R_number, np.ndarray[DTYPE_t, ndim=3] dR = None): # <<<<<<<<<<<<<< @@ -4840,17 +4846,17 @@ static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_R_time_var_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_unique_R_number)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (kw_args > 0) { @@ -4859,7 +4865,7 @@ static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -4874,24 +4880,24 @@ static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject } __pyx_v_R = ((PyArrayObject *)values[0]); __pyx_v_index = ((PyArrayObject *)values[1]); - __pyx_v_R_time_var_index = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_R_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_p_unique_R_number = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_p_unique_R_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_R_time_var_index = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_R_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_p_unique_R_number = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_p_unique_R_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_dR = ((PyArrayObject *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.R_handling_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.R_handling_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_R), __pyx_ptype_5numpy_ndarray, 1, "R", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dR), __pyx_ptype_5numpy_ndarray, 1, "dR", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_17R_handling_Cython___init__(((struct __pyx_obj_18state_space_cython_R_handling_Cython *)__pyx_v_self), __pyx_v_R, __pyx_v_index, __pyx_v_R_time_var_index, __pyx_v_p_unique_R_number, __pyx_v_dR); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_R), __pyx_ptype_5numpy_ndarray, 1, "R", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dR), __pyx_ptype_5numpy_ndarray, 1, "dR", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython___init__(((struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *)__pyx_v_self), __pyx_v_R, __pyx_v_index, __pyx_v_R_time_var_index, __pyx_v_p_unique_R_number, __pyx_v_dR); - /* "state_space_cython.pyx":74 + /* "GPy/models/state_space_cython.pyx":78 * dict R_square_root * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, # <<<<<<<<<<<<<< @@ -4908,7 +4914,7 @@ static int __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__(PyObject return __pyx_r; } -static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_p_unique_R_number, PyArrayObject *__pyx_v_dR) { +static int __pyx_pf_3GPy_6models_18state_space_cython_17R_handling_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_p_unique_R_number, PyArrayObject *__pyx_v_dR) { int __pyx_v_unique_len; __Pyx_LocalBuf_ND __pyx_pybuffernd_R; __Pyx_Buffer __pyx_pybuffer_R; @@ -4942,21 +4948,21 @@ static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __p __pyx_pybuffernd_dR.rcbuffer = &__pyx_pybuffer_dR; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_v_R, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_v_R, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_R.diminfo[0].strides = __pyx_pybuffernd_R.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_R.diminfo[0].shape = __pyx_pybuffernd_R.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_R.diminfo[1].strides = __pyx_pybuffernd_R.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_R.diminfo[1].shape = __pyx_pybuffernd_R.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_R.diminfo[2].strides = __pyx_pybuffernd_R.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_R.diminfo[2].shape = __pyx_pybuffernd_R.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_index.rcbuffer->pybuffer, (PyObject*)__pyx_v_index, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_index.rcbuffer->pybuffer, (PyObject*)__pyx_v_index, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_index.diminfo[1].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_index.diminfo[1].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dR.rcbuffer->pybuffer, (PyObject*)__pyx_v_dR, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dR.rcbuffer->pybuffer, (PyObject*)__pyx_v_dR, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_dR.diminfo[0].strides = __pyx_pybuffernd_dR.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_dR.diminfo[0].shape = __pyx_pybuffernd_dR.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_dR.diminfo[1].strides = __pyx_pybuffernd_dR.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_dR.diminfo[1].shape = __pyx_pybuffernd_dR.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_dR.diminfo[2].strides = __pyx_pybuffernd_dR.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_dR.diminfo[2].shape = __pyx_pybuffernd_dR.rcbuffer->pybuffer.shape[2]; - /* "state_space_cython.pyx":100 + /* "GPy/models/state_space_cython.pyx":104 * """ * * self.R = R # <<<<<<<<<<<<<< @@ -4969,7 +4975,7 @@ static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __p __Pyx_DECREF(((PyObject *)__pyx_v_self->R)); __pyx_v_self->R = ((PyArrayObject *)__pyx_v_R); - /* "state_space_cython.pyx":101 + /* "GPy/models/state_space_cython.pyx":105 * * self.R = R * self.index = index # <<<<<<<<<<<<<< @@ -4982,7 +4988,7 @@ static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __p __Pyx_DECREF(((PyObject *)__pyx_v_self->index)); 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goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_ind); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_slice__18); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_slice__18); @@ -5659,16 +5665,16 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->R), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->R), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_8 = ((PyArrayObject *)__pyx_t_2); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_R = ((PyArrayObject *)Py_None); 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if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_inv_square_root, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_inv_square_root, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_11); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_13); __Pyx_RaiseBufferFallbackError(); } else { @@ -5742,7 +5748,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct } } __pyx_pybuffernd_inv_square_root.diminfo[0].strides = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_inv_square_root.diminfo[0].shape = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.shape[0]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_14 = Py_TYPE(__pyx_t_6)->tp_iternext; @@ -5854,7 +5860,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __Pyx_GOTREF(__pyx_t_1); index = 2; __pyx_t_2 = __pyx_t_14(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_6), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_6), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = NULL; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; goto __pyx_L6_unpacking_done; @@ -5862,20 +5868,20 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __Pyx_DECREF(__pyx_t_6); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_16 = 0; __pyx_v_S = ((PyArrayObject *)__pyx_t_1); @@ -5912,10 +5918,10 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer); - __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_v_Vh, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_v_Vh, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_13); 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__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer); - __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_inv_square_root, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_inv_square_root, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_13); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_11); __Pyx_RaiseBufferFallbackError(); } else { @@ -6047,7 +6053,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct } } __pyx_pybuffernd_inv_square_root.diminfo[0].strides = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_inv_square_root.diminfo[0].shape = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_inv_square_root.diminfo[1].strides = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_inv_square_root.diminfo[1].shape = __pyx_pybuffernd_inv_square_root.rcbuffer->pybuffer.shape[1]; - if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_10 = 0; __pyx_v_inv_square_root = ((PyArrayObject *)__pyx_t_2); @@ -6056,49 +6062,49 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct } /*else*/ { - /* "state_space_cython.pyx":151 + /* "GPy/models/state_space_cython.pyx":155 * inv_square_root = self.R_square_root[ind] * else: * U,S,Vh = sp.linalg.svd( R,full_matrices=False, compute_uv=True, # <<<<<<<<<<<<<< * overwrite_a=False,check_finite=True) * */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_sp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_sp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_linalg); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_linalg); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_svd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_svd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(((PyObject *)__pyx_v_R)); PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_R)); __Pyx_GIVEREF(((PyObject *)__pyx_v_R)); - __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_full_matrices, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_compute_uv, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_full_matrices, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_compute_uv, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":152 + /* "GPy/models/state_space_cython.pyx":156 * else: * U,S,Vh = sp.linalg.svd( R,full_matrices=False, compute_uv=True, * overwrite_a=False,check_finite=True) # <<<<<<<<<<<<<< * * inv_square_root = U * 1.0/np.sqrt(S) */ - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_overwrite_a, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_check_finite, Py_True) < 0) {__pyx_filename = __pyx_f[0]; 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goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -6113,7 +6119,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -6129,17 +6135,17 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_2); #else - __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); #endif __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { Py_ssize_t index = -1; - __pyx_t_1 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_14 = Py_TYPE(__pyx_t_1)->tp_iternext; @@ -6149,7 +6155,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __Pyx_GOTREF(__pyx_t_3); index = 2; __pyx_t_2 = __pyx_t_14(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_1), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_1), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = NULL; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L9_unpacking_done; @@ -6157,20 +6163,20 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_14 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L9_unpacking_done:; } - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_15 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_U.rcbuffer->pybuffer); - __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_15, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_15, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_v_U, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_v_U, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_11); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_13); __Pyx_RaiseBufferFallbackError(); } else { @@ -6178,7 +6184,7 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct } } __pyx_pybuffernd_U.diminfo[0].strides = __pyx_pybuffernd_U.rcbuffer->pybuffer.strides[0]; 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__pyx_pybuffernd_S.diminfo[0].shape = __pyx_pybuffernd_S.rcbuffer->pybuffer.shape[0]; - if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_16 = 0; __pyx_v_S = ((PyArrayObject *)__pyx_t_3); @@ -6207,10 +6213,10 @@ static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer); - __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); 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+ __Pyx_AddTraceback("GPy.models.state_space_cython.R_handling_Cython.R_isrk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -6420,7 +6426,7 @@ static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_6R_isrk(struc return __pyx_r; } -/* "state_space_cython.pyx":168 +/* "GPy/models/state_space_cython.pyx":172 * np.ndarray dH * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] H, int H_time_var_index, # <<<<<<<<<<<<<< @@ -6429,8 +6435,8 @@ static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_6R_isrk(struc */ /* Python wrapper */ -static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_H = 0; int __pyx_v_H_time_var_index; PyArrayObject *__pyx_v_R = 0; @@ -6449,7 +6455,7 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_H,&__pyx_n_s_H_time_var_index,&__pyx_n_s_R,&__pyx_n_s_index,&__pyx_n_s_R_time_var_index,&__pyx_n_s_unique_R_number,&__pyx_n_s_dH,&__pyx_n_s_dR,0}; PyObject* values[8] = {0,0,0,0,0,0,0,0}; - /* "state_space_cython.pyx":170 + /* "GPy/models/state_space_cython.pyx":174 * def __init__(self, np.ndarray[DTYPE_t, ndim=3] H, int H_time_var_index, * np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, int R_time_var_index, * int unique_R_number, np.ndarray[DTYPE_t, ndim=3] dH = None, # <<<<<<<<<<<<<< @@ -6458,7 +6464,7 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i */ values[6] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":171 + /* "GPy/models/state_space_cython.pyx":175 * np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, int R_time_var_index, * int unique_R_number, np.ndarray[DTYPE_t, ndim=3] dH = None, * np.ndarray[DTYPE_t, ndim=3] dR=None): # <<<<<<<<<<<<<< @@ -6489,27 +6495,27 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_H_time_var_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_R)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_R_time_var_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_unique_R_number)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (kw_args > 0) { @@ -6523,7 +6529,7 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -6540,30 +6546,30 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i } } __pyx_v_H = ((PyArrayObject *)values[0]); - __pyx_v_H_time_var_index = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_H_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_H_time_var_index = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_H_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_R = ((PyArrayObject *)values[2]); __pyx_v_index = ((PyArrayObject *)values[3]); - __pyx_v_R_time_var_index = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_R_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_unique_R_number = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_unique_R_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_R_time_var_index = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_R_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_unique_R_number = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_unique_R_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_dH = ((PyArrayObject *)values[6]); __pyx_v_dR = ((PyArrayObject *)values[7]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_H), __pyx_ptype_5numpy_ndarray, 1, "H", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_R), __pyx_ptype_5numpy_ndarray, 1, "R", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 169; 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__pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dH), __pyx_ptype_5numpy_ndarray, 1, "dH", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dR), __pyx_ptype_5numpy_ndarray, 1, "dR", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython___init__(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_H, __pyx_v_H_time_var_index, __pyx_v_R, __pyx_v_index, __pyx_v_R_time_var_index, __pyx_v_unique_R_number, __pyx_v_dH, __pyx_v_dR); - /* "state_space_cython.pyx":168 + /* "GPy/models/state_space_cython.pyx":172 * np.ndarray dH * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] H, int H_time_var_index, # <<<<<<<<<<<<<< @@ -6580,7 +6586,7 @@ static int __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__i return __pyx_r; } -static int __pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython___init__(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_H, int __pyx_v_H_time_var_index, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_unique_R_number, PyArrayObject *__pyx_v_dH, PyArrayObject *__pyx_v_dR) { +static int __pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_H, int __pyx_v_H_time_var_index, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_unique_R_number, PyArrayObject *__pyx_v_dH, PyArrayObject *__pyx_v_dR) { __Pyx_LocalBuf_ND __pyx_pybuffernd_H; 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@@ -6870,7 +6876,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_H)); __Pyx_GIVEREF(((PyObject *)__pyx_v_H)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -6882,7 +6888,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":187 + /* "GPy/models/state_space_cython.pyx":191 * """ * * return np.dot(H, m) # <<<<<<<<<<<<<< @@ -6890,9 +6896,9 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = NULL; @@ -6907,7 +6913,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_2) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL; @@ -6918,7 +6924,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_INCREF(((PyObject *)__pyx_v_m)); PyTuple_SET_ITEM(__pyx_t_7, 1+__pyx_t_6, ((PyObject *)__pyx_v_m)); __Pyx_GIVEREF(((PyObject *)__pyx_v_m)); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -6926,7 +6932,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __pyx_t_1 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":179 + /* "GPy/models/state_space_cython.pyx":183 * self.dH = dH * * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] H): # <<<<<<<<<<<<<< @@ -6947,7 +6953,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_H.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -6960,9 +6966,9 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h[] = "\n function (k, x_{k}, H_{k}). Measurement function.\n k (iteration number), starts at 0\n x_{k} state \n H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}.\n "; -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h[] = "\n function (k, x_{k}, H_{k}). Measurement function.\n k (iteration number), starts at 0\n x_{k} state \n H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m = 0; PyArrayObject *__pyx_v_H = 0; @@ -6993,16 +6999,16 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_H)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_h") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_h") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -7011,21 +7017,21 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m = ((PyArrayObject *)values[1]); __pyx_v_H = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_h", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_H), __pyx_ptype_5numpy_ndarray, 1, "H", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(((struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_H); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_H), __pyx_ptype_5numpy_ndarray, 1, "H", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_H); /* function exit code */ goto __pyx_L0; @@ -7036,7 +7042,7 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H) { __Pyx_LocalBuf_ND __pyx_pybuffernd_H; __Pyx_Buffer __pyx_pybuffer_H; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -7058,16 +7064,16 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho __pyx_pybuffernd_H.rcbuffer = &__pyx_pybuffer_H; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_H.rcbuffer->pybuffer, (PyObject*)__pyx_v_H, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_H.rcbuffer->pybuffer, (PyObject*)__pyx_v_H, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_H.diminfo[0].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_H.diminfo[0].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_H.diminfo[1].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_H.diminfo[1].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_f_h(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_H), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_f_h(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_H), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -7081,7 +7087,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_H.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.f_h", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -7093,7 +7099,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho return __pyx_r; } -/* "state_space_cython.pyx":189 +/* "GPy/models/state_space_cython.pyx":193 * return np.dot(H, m) * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -7101,8 +7107,8 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho * function (k, m, P) return Jacobian of measurement function, it is */ -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -7131,23 +7137,23 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Hk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Hk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -7162,7 +7168,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -7176,7 +7182,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_P_pred)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P_pred)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -7188,7 +7194,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":198 + /* "GPy/models/state_space_cython.pyx":202 * """ * * return self.H[:,:, self.index[self.H_time_var_index, k]] # <<<<<<<<<<<<<< @@ -7196,11 +7202,11 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython * cpdef dHk(self,int k): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->H_time_var_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->H_time_var_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); @@ -7208,14 +7214,14 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_GIVEREF(__pyx_t_2); __pyx_t_1 = 0; __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->__pyx_base.index), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->__pyx_base.index), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyInt_From_int(((int)__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(((int)__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_slice__20); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_slice__20); @@ -7226,14 +7232,14 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->H), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->H), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":189 + /* "GPy/models/state_space_cython.pyx":193 * return np.dot(H, m) * * cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -7254,7 +7260,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -7267,9 +7273,9 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk[] = "\n function (k, m, P) return Jacobian of measurement function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n "; -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk[] = "\n function (k, m, P) return Jacobian of measurement function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m_pred = 0; PyArrayObject *__pyx_v_P_pred = 0; @@ -7300,16 +7306,16 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_P_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Hk") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Hk") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -7318,21 +7324,21 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m_pred = ((PyArrayObject *)values[1]); __pyx_v_P_pred = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Hk", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(((struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); /* function exit code */ goto __pyx_L0; @@ -7343,7 +7349,7 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -7365,16 +7371,16 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; 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__pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -7388,7 +7394,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.Hk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -7400,7 +7406,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho return __pyx_r; } -/* "state_space_cython.pyx":200 +/* "GPy/models/state_space_cython.pyx":204 * return self.H[:,:, self.index[self.H_time_var_index, k]] * * cpdef dHk(self,int k): # <<<<<<<<<<<<<< @@ -7408,8 +7414,8 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho * raise ValueError("dH derivative is None") */ -static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dHk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; 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if (__pyx_t_8) { - /* "state_space_cython.pyx":202 + /* "GPy/models/state_space_cython.pyx":206 * cpdef dHk(self,int k): * if self.dH is None: * raise ValueError("dH derivative is None") # <<<<<<<<<<<<<< * * return self.dH # the same dirivative on each iteration */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "state_space_cython.pyx":204 + /* "GPy/models/state_space_cython.pyx":208 * raise ValueError("dH derivative is None") * * return self.dH # the same dirivative on each iteration # <<<<<<<<<<<<<< @@ -7506,7 +7512,7 @@ static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython __pyx_r = ((PyObject *)__pyx_v_self->dH); 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/*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -7541,22 +7547,22 @@ static PyObject *__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cytho __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("dHk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.dHk", __pyx_clineno, __pyx_lineno, __pyx_filename); 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__Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -7565,7 +7571,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho int __pyx_clineno = 0; __Pyx_RefNannySetupContext("dHk", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_dHk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_dHk(__pyx_v_self, __pyx_v_k, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -7574,7 +7580,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Std_Measurement_Callables_Cython.dHk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Measurement_Callables_Cython.dHk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -7582,7 +7588,7 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho return __pyx_r; } -/* "state_space_cython.pyx":218 +/* "GPy/models/state_space_cython.pyx":222 * bint svd_each_time * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] Q, np.ndarray[DTYPE_t, ndim=2] index, # <<<<<<<<<<<<<< @@ -7591,12 +7597,12 @@ static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cytho */ /* Python wrapper */ -static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_17Q_handling_Cython___init__[] = "\n Input: \n ---------------\n Q - array with noise on various steps. The result of preprocessing\n the noise input.\n \n index - for each step of Kalman filter contains the corresponding index\n in the array.\n \n Q_time_var_index - another index in the array R. Computed earlier and passed here.\n \n unique_Q_number - number of unique noise matrices below which square roots\n are cached and above which they are computed each time.\n \n dQ: 3D array[:, :, param_num]\n derivative of Q. Derivative is supported only when Q do not change over time\n \n Output:\n --------------\n Object which has three necessary functions:\n Qk(k)\n dQk(k)\n Q_srkt(k)\n "; +static int __pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__[] = "\n Input: \n ---------------\n Q - array with noise on various steps. The result of preprocessing\n the noise input.\n \n index - for each step of Kalman filter contains the corresponding index\n in the array.\n \n Q_time_var_index - another index in the array R. Computed earlier and passed here.\n \n unique_Q_number - number of unique noise matrices below which square roots\n are cached and above which they are computed each time.\n \n dQ: 3D array[:, :, param_num]\n derivative of Q. Derivative is supported only when Q do not change over time\n \n Output:\n --------------\n Object which has three necessary functions:\n Qk(k)\n dQk(k)\n Q_srkt(k)\n "; #if CYTHON_COMPILING_IN_CPYTHON -struct wrapperbase __pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__; +struct wrapperbase __pyx_wrapperbase_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__; #endif -static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_Q = 0; PyArrayObject *__pyx_v_index = 0; int __pyx_v_Q_time_var_index; @@ -7612,7 +7618,7 @@ static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_Q,&__pyx_n_s_index,&__pyx_n_s_Q_time_var_index,&__pyx_n_s_p_unique_Q_number,&__pyx_n_s_dQ,0}; PyObject* values[5] = {0,0,0,0,0}; - /* "state_space_cython.pyx":219 + /* "GPy/models/state_space_cython.pyx":223 * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] Q, np.ndarray[DTYPE_t, ndim=2] index, * int Q_time_var_index, int p_unique_Q_number, np.ndarray[DTYPE_t, ndim=3] dQ = None): # <<<<<<<<<<<<<< @@ -7640,17 +7646,17 @@ static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_Q_time_var_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_unique_Q_number)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (kw_args > 0) { @@ -7659,7 +7665,7 @@ static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -7674,24 +7680,24 @@ static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject } __pyx_v_Q = ((PyArrayObject *)values[0]); __pyx_v_index = ((PyArrayObject *)values[1]); - __pyx_v_Q_time_var_index = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_Q_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_p_unique_Q_number = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_p_unique_Q_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_Q_time_var_index = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_Q_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_p_unique_Q_number = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_p_unique_Q_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_dQ = ((PyArrayObject *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Q_handling_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Q_handling_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Q), __pyx_ptype_5numpy_ndarray, 1, "Q", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQ), __pyx_ptype_5numpy_ndarray, 1, "dQ", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(((struct __pyx_obj_18state_space_cython_Q_handling_Cython *)__pyx_v_self), __pyx_v_Q, __pyx_v_index, __pyx_v_Q_time_var_index, __pyx_v_p_unique_Q_number, __pyx_v_dQ); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Q), __pyx_ptype_5numpy_ndarray, 1, "Q", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQ), __pyx_ptype_5numpy_ndarray, 1, "dQ", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__(((struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)__pyx_v_self), __pyx_v_Q, __pyx_v_index, __pyx_v_Q_time_var_index, __pyx_v_p_unique_Q_number, __pyx_v_dQ); - /* "state_space_cython.pyx":218 + /* "GPy/models/state_space_cython.pyx":222 * bint svd_each_time * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] Q, np.ndarray[DTYPE_t, ndim=2] index, # <<<<<<<<<<<<<< @@ -7708,7 +7714,7 @@ static int __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__(PyObject return __pyx_r; } -static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_p_unique_Q_number, PyArrayObject *__pyx_v_dQ) { +static int __pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_p_unique_Q_number, PyArrayObject *__pyx_v_dQ) { int __pyx_v_unique_len; __Pyx_LocalBuf_ND __pyx_pybuffernd_Q; __Pyx_Buffer __pyx_pybuffer_Q; @@ -7742,21 +7748,21 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p __pyx_pybuffernd_dQ.rcbuffer = &__pyx_pybuffer_dQ; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q.rcbuffer->pybuffer, (PyObject*)__pyx_v_Q, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q.rcbuffer->pybuffer, (PyObject*)__pyx_v_Q, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_Q.diminfo[0].strides = __pyx_pybuffernd_Q.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Q.diminfo[0].shape = __pyx_pybuffernd_Q.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Q.diminfo[1].strides = __pyx_pybuffernd_Q.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Q.diminfo[1].shape = __pyx_pybuffernd_Q.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_Q.diminfo[2].strides = __pyx_pybuffernd_Q.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_Q.diminfo[2].shape = __pyx_pybuffernd_Q.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_index.rcbuffer->pybuffer, (PyObject*)__pyx_v_index, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_index.rcbuffer->pybuffer, (PyObject*)__pyx_v_index, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_index.diminfo[1].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_index.diminfo[1].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dQ.rcbuffer->pybuffer, (PyObject*)__pyx_v_dQ, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dQ.rcbuffer->pybuffer, (PyObject*)__pyx_v_dQ, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_dQ.diminfo[0].strides = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_dQ.diminfo[0].shape = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_dQ.diminfo[1].strides = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_dQ.diminfo[1].shape = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_dQ.diminfo[2].strides = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_dQ.diminfo[2].shape = __pyx_pybuffernd_dQ.rcbuffer->pybuffer.shape[2]; - /* "state_space_cython.pyx":245 + /* "GPy/models/state_space_cython.pyx":249 * """ * * self.Q = Q # <<<<<<<<<<<<<< @@ -7769,7 +7775,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p __Pyx_DECREF(((PyObject *)__pyx_v_self->Q)); __pyx_v_self->Q = ((PyArrayObject *)__pyx_v_Q); - /* "state_space_cython.pyx":246 + /* "GPy/models/state_space_cython.pyx":250 * * self.Q = Q * self.index = index # <<<<<<<<<<<<<< @@ -7782,7 +7788,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p __Pyx_DECREF(((PyObject *)__pyx_v_self->index)); __pyx_v_self->index = ((PyArrayObject *)__pyx_v_index); - /* "state_space_cython.pyx":247 + /* "GPy/models/state_space_cython.pyx":251 * self.Q = Q * self.index = index * self.Q_time_var_index = Q_time_var_index # <<<<<<<<<<<<<< @@ -7791,7 +7797,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p */ __pyx_v_self->Q_time_var_index = __pyx_v_Q_time_var_index; - /* "state_space_cython.pyx":248 + /* "GPy/models/state_space_cython.pyx":252 * self.index = index * self.Q_time_var_index = Q_time_var_index * self.dQ = dQ # <<<<<<<<<<<<<< @@ -7804,16 +7810,16 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p __Pyx_DECREF(((PyObject *)__pyx_v_self->dQ)); __pyx_v_self->dQ = ((PyArrayObject *)__pyx_v_dQ); - /* "state_space_cython.pyx":250 + /* "GPy/models/state_space_cython.pyx":254 * self.dQ = dQ * * cdef int unique_len = len(np.unique(index)) # <<<<<<<<<<<<<< * * if (unique_len > p_unique_Q_number): */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_unique); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_unique); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = NULL; @@ -7827,25 +7833,25 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p } } if (!__pyx_t_2) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_3, ((PyObject *)__pyx_v_index)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_3, ((PyObject *)__pyx_v_index)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); } else { - __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL; __Pyx_INCREF(((PyObject *)__pyx_v_index)); PyTuple_SET_ITEM(__pyx_t_4, 0+1, ((PyObject *)__pyx_v_index)); __Pyx_GIVEREF(((PyObject *)__pyx_v_index)); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_5 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_unique_len = __pyx_t_5; - /* "state_space_cython.pyx":252 + /* "GPy/models/state_space_cython.pyx":256 * cdef int unique_len = len(np.unique(index)) * * if (unique_len > p_unique_Q_number): # <<<<<<<<<<<<<< @@ -7855,7 +7861,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p __pyx_t_6 = ((__pyx_v_unique_len > __pyx_v_p_unique_Q_number) != 0); if (__pyx_t_6) { - /* "state_space_cython.pyx":253 + /* "GPy/models/state_space_cython.pyx":257 * * if (unique_len > p_unique_Q_number): * self.svd_each_time = True # <<<<<<<<<<<<<< @@ -7867,7 +7873,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p } /*else*/ { - /* "state_space_cython.pyx":255 + /* "GPy/models/state_space_cython.pyx":259 * self.svd_each_time = True * else: * self.svd_each_time = False # <<<<<<<<<<<<<< @@ -7878,14 +7884,14 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p } __pyx_L3:; - /* "state_space_cython.pyx":257 + /* "GPy/models/state_space_cython.pyx":261 * self.svd_each_time = False * * self.Q_square_root = {} # <<<<<<<<<<<<<< * * */ - __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; 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__pyx_r = -1; goto __pyx_L2; __pyx_L0:; @@ -7927,7 +7933,7 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p return __pyx_r; } -/* "state_space_cython.pyx":260 +/* "GPy/models/state_space_cython.pyx":264 * * * cpdef Qk(self, int k): # <<<<<<<<<<<<<< @@ -7935,8 +7941,8 @@ static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __p * function (k). 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+ __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_square_root, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_square_root.rcbuffer->pybuffer, (PyObject*)__pyx_v_square_root, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_11); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_13); __Pyx_RaiseBufferFallbackError(); } else { @@ -8540,7 +8546,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ } } __pyx_pybuffernd_square_root.diminfo[0].strides = __pyx_pybuffernd_square_root.rcbuffer->pybuffer.strides[0]; 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if (__pyx_t_9) { - /* "state_space_cython.pyx":296 + /* "GPy/models/state_space_cython.pyx":300 * if self.svd_each_time: * * U,S,Vh = sp.linalg.svd( Q,full_matrices=False, compute_uv=True, # <<<<<<<<<<<<<< * overwrite_a=False,check_finite=True) * */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_sp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_sp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_linalg); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_linalg); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_svd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_svd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_v_Q)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_Q)); __Pyx_GIVEREF(((PyObject *)__pyx_v_Q)); - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -8616,7 +8622,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -8632,17 +8638,17 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ __Pyx_INCREF(__pyx_t_1); __Pyx_INCREF(__pyx_t_2); #else - __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); #endif __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } else { Py_ssize_t index = -1; - __pyx_t_3 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_14 = Py_TYPE(__pyx_t_3)->tp_iternext; @@ -8652,7 +8658,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ __Pyx_GOTREF(__pyx_t_1); index = 2; __pyx_t_2 = __pyx_t_14(__pyx_t_3); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_3), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_3), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = NULL; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L6_unpacking_done; @@ -8660,20 +8666,20 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_14 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L6_unpacking_done:; } - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_15 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_U.rcbuffer->pybuffer); - __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_15, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_15, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_v_U, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_v_U, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_13); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_11); __Pyx_RaiseBufferFallbackError(); } else { @@ -8681,7 +8687,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ } } __pyx_pybuffernd_U.diminfo[0].strides = __pyx_pybuffernd_U.rcbuffer->pybuffer.strides[0]; 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+ __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_t_16, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_v_S, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_v_S, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_11); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_13); __Pyx_RaiseBufferFallbackError(); } else { @@ -8701,7 +8707,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ } } __pyx_pybuffernd_S.diminfo[0].strides = __pyx_pybuffernd_S.rcbuffer->pybuffer.strides[0]; 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+ __pyx_t_7 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_t_16, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack); if (unlikely(__pyx_t_7 < 0)) { PyErr_Fetch(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_v_S, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S.rcbuffer->pybuffer, (PyObject*)__pyx_v_S, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_13); Py_XDECREF(__pyx_t_12); Py_XDECREF(__pyx_t_11); __Pyx_RaiseBufferFallbackError(); } else { @@ -8993,7 +8999,7 @@ static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct _ } } __pyx_pybuffernd_S.diminfo[0].strides = __pyx_pybuffernd_S.rcbuffer->pybuffer.strides[0]; 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__pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Q_handling_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Q_handling_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(((struct __pyx_obj_18state_space_cython_Q_handling_Cython *)__pyx_v_self), ((int)__pyx_v_k)); + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython_6Q_srk(((struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)__pyx_v_self), ((int)__pyx_v_k)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_17Q_handling_Cython_6Q_srk(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k) { PyObject *__pyx_r = NULL; 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+ __Pyx_AddTraceback("GPy.models.state_space_cython.Q_handling_Cython.Q_srk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -9212,7 +9218,7 @@ static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(struct return __pyx_r; } -/* "state_space_cython.pyx":320 +/* "GPy/models/state_space_cython.pyx":324 * np.ndarray dA * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] A, int A_time_var_index, # <<<<<<<<<<<<<< @@ -9221,8 +9227,8 @@ static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(struct */ /* Python wrapper */ -static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_A = 0; int __pyx_v_A_time_var_index; PyArrayObject *__pyx_v_Q = 0; @@ -9241,7 +9247,7 @@ static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init_ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_A,&__pyx_n_s_A_time_var_index,&__pyx_n_s_Q,&__pyx_n_s_index,&__pyx_n_s_Q_time_var_index,&__pyx_n_s_unique_Q_number,&__pyx_n_s_dA,&__pyx_n_s_dQ,0}; PyObject* values[8] = {0,0,0,0,0,0,0,0}; - /* "state_space_cython.pyx":324 + /* "GPy/models/state_space_cython.pyx":328 * np.ndarray[DTYPE_t, ndim=2] index, * int Q_time_var_index, int unique_Q_number, * np.ndarray[DTYPE_t, ndim=3] dA = None, # <<<<<<<<<<<<<< @@ -9250,7 +9256,7 @@ static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init_ */ values[6] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":325 + /* "GPy/models/state_space_cython.pyx":329 * int Q_time_var_index, int unique_Q_number, * np.ndarray[DTYPE_t, ndim=3] dA = None, * np.ndarray[DTYPE_t, ndim=3] dQ=None): # <<<<<<<<<<<<<< @@ -9281,27 +9287,27 @@ static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init_ case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_A_time_var_index)) != 0)) kw_args--; 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_Q_time_var_index)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_unique_Q_number)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (kw_args > 0) { @@ -9315,7 +9321,7 @@ static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init_ } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -9332,30 +9338,30 @@ static int __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init_ } } __pyx_v_A = ((PyArrayObject *)values[0]); - __pyx_v_A_time_var_index = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_A_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_A_time_var_index = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_A_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_Q = ((PyArrayObject *)values[2]); __pyx_v_index = ((PyArrayObject *)values[3]); - __pyx_v_Q_time_var_index = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_Q_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_unique_Q_number = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_unique_Q_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_Q_time_var_index = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_Q_time_var_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_unique_Q_number = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_unique_Q_number == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_dA = ((PyArrayObject *)values[6]); __pyx_v_dQ = ((PyArrayObject *)values[7]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 6, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Q), __pyx_ptype_5numpy_ndarray, 1, "Q", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dA), __pyx_ptype_5numpy_ndarray, 1, "dA", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQ), __pyx_ptype_5numpy_ndarray, 1, "dQ", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__(((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_A, __pyx_v_A_time_var_index, __pyx_v_Q, __pyx_v_index, __pyx_v_Q_time_var_index, __pyx_v_unique_Q_number, __pyx_v_dA, __pyx_v_dQ); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Q), __pyx_ptype_5numpy_ndarray, 1, "Q", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dA), __pyx_ptype_5numpy_ndarray, 1, "dA", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQ), __pyx_ptype_5numpy_ndarray, 1, "dQ", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython___init__(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_A, __pyx_v_A_time_var_index, __pyx_v_Q, __pyx_v_index, __pyx_v_Q_time_var_index, __pyx_v_unique_Q_number, __pyx_v_dA, __pyx_v_dQ); 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__pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_Q_time_var_index); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_unique_Q_number); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_unique_Q_number); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = NULL; __pyx_t_6 = 0; @@ -9479,7 +9485,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(5+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(5+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -9499,13 +9505,13 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ __Pyx_GIVEREF(((PyObject *)__pyx_v_dQ)); __pyx_t_3 = 0; __pyx_t_4 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":329 + /* "GPy/models/state_space_cython.pyx":333 * super(Std_Dynamic_Callables_Cython,self).__init__(Q, index, Q_time_var_index, unique_Q_number,dQ) * * self.A = A # <<<<<<<<<<<<<< @@ -9518,7 +9524,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ __Pyx_DECREF(((PyObject *)__pyx_v_self->A)); __pyx_v_self->A = ((PyArrayObject *)__pyx_v_A); - /* "state_space_cython.pyx":330 + /* "GPy/models/state_space_cython.pyx":334 * * self.A = A * self.A_time_var_index = A_time_var_index # <<<<<<<<<<<<<< @@ -9527,7 +9533,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ */ __pyx_v_self->A_time_var_index = __pyx_v_A_time_var_index; - /* "state_space_cython.pyx":331 + /* "GPy/models/state_space_cython.pyx":335 * self.A = A * self.A_time_var_index = A_time_var_index * self.dA = dA # <<<<<<<<<<<<<< @@ -9540,7 +9546,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ __Pyx_DECREF(((PyObject *)__pyx_v_self->dA)); __pyx_v_self->dA = ((PyArrayObject *)__pyx_v_dA); - /* "state_space_cython.pyx":320 + /* "GPy/models/state_space_cython.pyx":324 * np.ndarray dA * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] A, int A_time_var_index, # <<<<<<<<<<<<<< @@ -9566,7 +9572,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dQ.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_index.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; goto __pyx_L2; __pyx_L0:; @@ -9580,7 +9586,7 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ return __pyx_r; } -/* "state_space_cython.pyx":333 +/* "GPy/models/state_space_cython.pyx":337 * self.dA = dA * * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): # <<<<<<<<<<<<<< @@ -9588,8 +9594,8 @@ static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__ * f_a: function (k, x_{k-1}, A_{k}). Dynamic function. */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -9617,23 +9623,23 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; 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__pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -9648,7 +9654,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -9662,7 +9668,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_A)); __Pyx_GIVEREF(((PyObject *)__pyx_v_A)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9674,7 +9680,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":341 + /* "GPy/models/state_space_cython.pyx":345 * """ * * return np.dot(A,m) # <<<<<<<<<<<<<< @@ -9682,9 +9688,9 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = NULL; @@ -9699,7 +9705,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_2) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL; @@ -9710,7 +9716,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __Pyx_INCREF(((PyObject *)__pyx_v_m)); PyTuple_SET_ITEM(__pyx_t_7, 1+__pyx_t_6, ((PyObject *)__pyx_v_m)); __Pyx_GIVEREF(((PyObject *)__pyx_v_m)); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9718,7 +9724,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __pyx_t_1 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":333 + /* "GPy/models/state_space_cython.pyx":337 * self.dA = dA * * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): # <<<<<<<<<<<<<< @@ -9739,7 +9745,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_A.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -9752,9 +9758,9 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a[] = "\n f_a: function (k, x_{k-1}, A_{k}). Dynamic function. \n k (iteration number), starts at 0\n x_{k-1} State from the previous step\n A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}.\n "; -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a[] = "\n f_a: function (k, x_{k-1}, A_{k}). Dynamic function. \n k (iteration number), starts at 0\n x_{k-1} State from the previous step\n A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m = 0; PyArrayObject *__pyx_v_A = 0; @@ -9785,16 +9791,16 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_A)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -9803,21 +9809,21 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m = ((PyArrayObject *)values[1]); __pyx_v_A = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); /* function exit code */ goto __pyx_L0; @@ -9828,7 +9834,7 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -9850,16 +9856,16 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_A), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_A), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -9873,7 +9879,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_A.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -9885,7 +9891,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f return __pyx_r; } -/* "state_space_cython.pyx":343 +/* "GPy/models/state_space_cython.pyx":347 * return np.dot(A,m) * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -9893,8 +9899,8 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f * function (k, m, P) return Jacobian of measurement function, it is */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -9923,23 +9929,23 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -9954,7 +9960,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -9968,7 +9974,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_P_pred)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P_pred)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9980,7 +9986,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":352 + /* "GPy/models/state_space_cython.pyx":356 * """ * * return self.A[:,:, self.index[self.A_time_var_index, k]] # <<<<<<<<<<<<<< @@ -9988,11 +9994,11 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( * cpdef dAk(self, int k): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->A_time_var_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->A_time_var_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); @@ -10000,14 +10006,14 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( __Pyx_GIVEREF(__pyx_t_2); __pyx_t_1 = 0; __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->__pyx_base.index), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->__pyx_base.index), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyInt_From_int(((int)__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(((int)__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_slice__28); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_slice__28); @@ -10018,14 +10024,14 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->A), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_2 = PyObject_GetItem(((PyObject *)__pyx_v_self->A), __pyx_t_4); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":343 + /* "GPy/models/state_space_cython.pyx":347 * return np.dot(A,m) * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix # <<<<<<<<<<<<<< @@ -10046,7 +10052,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; goto __pyx_L2; __pyx_L0:; @@ -10059,9 +10065,9 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak( } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak[] = "\n function (k, m, P) return Jacobian of measurement function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n "; -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak[] = "\n function (k, m, P) return Jacobian of measurement function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m_pred = 0; PyArrayObject *__pyx_v_P_pred = 0; @@ -10092,16 +10098,16 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5A case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_P_pred)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Ak") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "Ak") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -10110,21 +10116,21 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5A values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m_pred = ((PyArrayObject *)values[1]); __pyx_v_P_pred = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("Ak", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_pred), __pyx_ptype_5numpy_ndarray, 1, "m_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_pred), __pyx_ptype_5numpy_ndarray, 1, "P_pred", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m_pred, __pyx_v_P_pred); /* function exit code */ goto __pyx_L0; @@ -10135,7 +10141,7 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5A return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P_pred; __Pyx_Buffer __pyx_pybuffer_P_pred; __Pyx_LocalBuf_ND __pyx_pybuffernd_m_pred; @@ -10157,16 +10163,16 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4A __pyx_pybuffernd_P_pred.rcbuffer = &__pyx_pybuffer_P_pred; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_v_P_pred, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -10180,7 +10186,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4A __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.Ak", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -10192,7 +10198,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4A return __pyx_r; } -/* "state_space_cython.pyx":354 +/* "GPy/models/state_space_cython.pyx":358 * return self.A[:,:, self.index[self.A_time_var_index, k]] * * cpdef dAk(self, int k): # <<<<<<<<<<<<<< @@ -10200,8 +10206,8 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4A * raise ValueError("dA derivative is None") */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -10220,11 +10226,11 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dAk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dAk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -10238,17 +10244,17 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; 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if (__pyx_t_8) { - /* "state_space_cython.pyx":356 + /* "GPy/models/state_space_cython.pyx":360 * cpdef dAk(self, int k): * if self.dA is None: * raise ValueError("dA derivative is None") # <<<<<<<<<<<<<< * * return self.dA # the same dirivative on each iteration */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "state_space_cython.pyx":358 + /* "GPy/models/state_space_cython.pyx":362 * raise ValueError("dA derivative is None") * * return self.dA # the same dirivative on each iteration # <<<<<<<<<<<<<< @@ -10298,7 +10304,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk __pyx_r = ((PyObject *)__pyx_v_self->dA); goto __pyx_L0; - /* "state_space_cython.pyx":354 + /* "GPy/models/state_space_cython.pyx":358 * return self.A[:,:, self.index[self.A_time_var_index, k]] * * cpdef dAk(self, int k): # <<<<<<<<<<<<<< @@ -10314,7 +10320,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.dAk", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.dAk", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -10323,8 +10329,8 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k); /*proto*/ +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk(PyObject *__pyx_v_self, PyObject *__pyx_arg_k) { int __pyx_v_k; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -10333,22 +10339,22 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7d __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("dAk (wrapper)", 0); assert(__pyx_arg_k); { - __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(__pyx_arg_k); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.dAk", __pyx_clineno, __pyx_lineno, __pyx_filename); 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__pyx_t_1 = 0; } - /* "state_space_cython.pyx":367 + /* "GPy/models/state_space_cython.pyx":371 * time steps. * """ * return self # <<<<<<<<<<<<<< @@ -10459,7 +10465,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_res __pyx_r = ((PyObject *)__pyx_v_self); goto __pyx_L0; - /* "state_space_cython.pyx":361 + /* "GPy/models/state_space_cython.pyx":365 * * * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< @@ -10475,7 +10481,7 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_res __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -10484,9 +10490,9 @@ static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_res } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset[] = "\n For reusing this object e.g. in smoother computation. It makes sence\n because necessary matrices have been already computed for all\n time steps.\n "; -static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset[] = "\n For reusing this object e.g. in smoother computation. It makes sence\n because necessary matrices have been already computed for all\n time steps.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_compute_derivatives; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -10514,7 +10520,7 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9r } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -10524,31 +10530,31 @@ static PyObject *__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9r } } if (values[0]) { - __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_compute_derivatives = ((int)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; - struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; + struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -10556,7 +10562,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8r __Pyx_XDECREF(__pyx_r); __pyx_t_2.__pyx_n = 1; __pyx_t_2.compute_derivatives = __pyx_v_compute_derivatives; - __pyx_t_1 = __pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython->__pyx_base.__pyx_base.reset(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython->__pyx_base.__pyx_base.reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -10565,7 +10571,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8r /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.Std_Dynamic_Callables_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -10573,7 +10579,7 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8r return __pyx_r; } -/* "state_space_cython.pyx":395 +/* "GPy/models/state_space_cython.pyx":399 * int last_k * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] As, np.ndarray[DTYPE_t, ndim=3] Qs, # <<<<<<<<<<<<<< @@ -10582,12 +10588,12 @@ static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8r */ /* Python wrapper */ -static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_22AQcompute_batch_Cython___init__[] = "\n Constructor. 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All necessary parameters are passed here and stored \n in the opject. \n \n Input:\n -------------------\n F, L, Qc, P_inf : matrices\n Parameters of corresponding continuous state model\n dt: array\n All time steps\n compute_derivatives: bool\n Whether to calculate derivatives\n \n dP_inf, dF, dQc: 3D array\n Derivatives if they are required\n \n Output:\n -------------------\n \n "; #if CYTHON_COMPILING_IN_CPYTHON -struct wrapperbase __pyx_wrapperbase_18state_space_cython_22AQcompute_batch_Cython___init__; +struct wrapperbase __pyx_wrapperbase_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython___init__; #endif -static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyArrayObject *__pyx_v_As = 0; PyArrayObject *__pyx_v_Qs = 0; PyArrayObject *__pyx_v_reconstruct_indices = 0; @@ -10603,7 +10609,7 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_As,&__pyx_n_s_Qs,&__pyx_n_s_reconstruct_indices,&__pyx_n_s_dAs,&__pyx_n_s_dQs,0}; PyObject* values[5] = {0,0,0,0,0}; - /* "state_space_cython.pyx":397 + /* "GPy/models/state_space_cython.pyx":401 * def __init__(self, np.ndarray[DTYPE_t, ndim=3] As, np.ndarray[DTYPE_t, ndim=3] Qs, * np.ndarray[DTYPE_int_t, ndim=1] reconstruct_indices, * np.ndarray[DTYPE_t, ndim=4] dAs=None, # <<<<<<<<<<<<<< @@ -10612,7 +10618,7 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb */ values[3] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":398 + /* "GPy/models/state_space_cython.pyx":402 * np.ndarray[DTYPE_int_t, ndim=1] reconstruct_indices, * np.ndarray[DTYPE_t, ndim=4] dAs=None, * np.ndarray[DTYPE_t, ndim=4] dQs=None): # <<<<<<<<<<<<<< @@ -10640,12 +10646,12 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_Qs)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_reconstruct_indices)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (kw_args > 0) { @@ -10659,7 +10665,7 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -10680,20 +10686,20 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_As), __pyx_ptype_5numpy_ndarray, 1, "As", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Qs), __pyx_ptype_5numpy_ndarray, 1, "Qs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_reconstruct_indices), __pyx_ptype_5numpy_ndarray, 1, "reconstruct_indices", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dAs), __pyx_ptype_5numpy_ndarray, 1, "dAs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQs), __pyx_ptype_5numpy_ndarray, 1, "dQs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(((struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_As, __pyx_v_Qs, __pyx_v_reconstruct_indices, __pyx_v_dAs, __pyx_v_dQs); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_As), __pyx_ptype_5numpy_ndarray, 1, "As", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Qs), __pyx_ptype_5numpy_ndarray, 1, "Qs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_reconstruct_indices), __pyx_ptype_5numpy_ndarray, 1, "reconstruct_indices", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dAs), __pyx_ptype_5numpy_ndarray, 1, "dAs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dQs), __pyx_ptype_5numpy_ndarray, 1, "dQs", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython___init__(((struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_As, __pyx_v_Qs, __pyx_v_reconstruct_indices, __pyx_v_dAs, __pyx_v_dQs); - /* "state_space_cython.pyx":395 + /* "GPy/models/state_space_cython.pyx":399 * int last_k * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] As, np.ndarray[DTYPE_t, ndim=3] Qs, # <<<<<<<<<<<<<< @@ -10710,7 +10716,7 @@ static int __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__(PyOb return __pyx_r; } -static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, PyArrayObject *__pyx_v_As, PyArrayObject *__pyx_v_Qs, PyArrayObject *__pyx_v_reconstruct_indices, PyArrayObject *__pyx_v_dAs, PyArrayObject *__pyx_v_dQs) { +static int __pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython___init__(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, PyArrayObject *__pyx_v_As, PyArrayObject *__pyx_v_Qs, PyArrayObject *__pyx_v_reconstruct_indices, PyArrayObject *__pyx_v_dAs, PyArrayObject *__pyx_v_dQs) { __Pyx_LocalBuf_ND __pyx_pybuffernd_As; __Pyx_Buffer __pyx_pybuffer_As; __Pyx_LocalBuf_ND __pyx_pybuffernd_Qs; @@ -10753,31 +10759,31 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __pyx_pybuffernd_dQs.rcbuffer = &__pyx_pybuffer_dQs; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_As.rcbuffer->pybuffer, (PyObject*)__pyx_v_As, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_As.rcbuffer->pybuffer, (PyObject*)__pyx_v_As, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_As.diminfo[0].strides = __pyx_pybuffernd_As.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_As.diminfo[0].shape = __pyx_pybuffernd_As.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_As.diminfo[1].strides = __pyx_pybuffernd_As.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_As.diminfo[1].shape = __pyx_pybuffernd_As.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_As.diminfo[2].strides = __pyx_pybuffernd_As.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_As.diminfo[2].shape = __pyx_pybuffernd_As.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Qs.rcbuffer->pybuffer, (PyObject*)__pyx_v_Qs, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Qs.rcbuffer->pybuffer, (PyObject*)__pyx_v_Qs, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_Qs.diminfo[0].strides = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Qs.diminfo[0].shape = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Qs.diminfo[1].strides = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Qs.diminfo[1].shape = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_Qs.diminfo[2].strides = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_Qs.diminfo[2].shape = __pyx_pybuffernd_Qs.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_reconstruct_indices.rcbuffer->pybuffer, (PyObject*)__pyx_v_reconstruct_indices, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_int_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_reconstruct_indices.rcbuffer->pybuffer, (PyObject*)__pyx_v_reconstruct_indices, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_int_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_reconstruct_indices.diminfo[0].strides = __pyx_pybuffernd_reconstruct_indices.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_reconstruct_indices.diminfo[0].shape = __pyx_pybuffernd_reconstruct_indices.rcbuffer->pybuffer.shape[0]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dAs.rcbuffer->pybuffer, (PyObject*)__pyx_v_dAs, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 4, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dAs.rcbuffer->pybuffer, (PyObject*)__pyx_v_dAs, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 4, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_dAs.diminfo[0].strides = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_dAs.diminfo[0].shape = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_dAs.diminfo[1].strides = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_dAs.diminfo[1].shape = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_dAs.diminfo[2].strides = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_dAs.diminfo[2].shape = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.shape[2]; __pyx_pybuffernd_dAs.diminfo[3].strides = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.strides[3]; __pyx_pybuffernd_dAs.diminfo[3].shape = __pyx_pybuffernd_dAs.rcbuffer->pybuffer.shape[3]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dQs.rcbuffer->pybuffer, (PyObject*)__pyx_v_dQs, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 4, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dQs.rcbuffer->pybuffer, (PyObject*)__pyx_v_dQs, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 4, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_dQs.diminfo[0].strides = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_dQs.diminfo[0].shape = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_dQs.diminfo[1].strides = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_dQs.diminfo[1].shape = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_dQs.diminfo[2].strides = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_dQs.diminfo[2].shape = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.shape[2]; __pyx_pybuffernd_dQs.diminfo[3].strides = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.strides[3]; __pyx_pybuffernd_dQs.diminfo[3].shape = __pyx_pybuffernd_dQs.rcbuffer->pybuffer.shape[3]; - /* "state_space_cython.pyx":420 + /* "GPy/models/state_space_cython.pyx":424 * """ * * self.As = As # <<<<<<<<<<<<<< @@ -10790,7 +10796,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_DECREF(((PyObject *)__pyx_v_self->As)); __pyx_v_self->As = ((PyArrayObject *)__pyx_v_As); - /* "state_space_cython.pyx":421 + /* "GPy/models/state_space_cython.pyx":425 * * self.As = As * self.Qs = Qs # <<<<<<<<<<<<<< @@ -10803,7 +10809,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_DECREF(((PyObject *)__pyx_v_self->Qs)); __pyx_v_self->Qs = ((PyArrayObject *)__pyx_v_Qs); - /* "state_space_cython.pyx":422 + /* "GPy/models/state_space_cython.pyx":426 * self.As = As * self.Qs = Qs * self.dAs = dAs # <<<<<<<<<<<<<< @@ -10816,7 +10822,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_DECREF(((PyObject *)__pyx_v_self->dAs)); __pyx_v_self->dAs = ((PyArrayObject *)__pyx_v_dAs); - /* "state_space_cython.pyx":423 + /* "GPy/models/state_space_cython.pyx":427 * self.Qs = Qs * self.dAs = dAs * self.dQs = dQs # <<<<<<<<<<<<<< @@ -10829,7 +10835,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_DECREF(((PyObject *)__pyx_v_self->dQs)); __pyx_v_self->dQs = ((PyArrayObject *)__pyx_v_dQs); - /* "state_space_cython.pyx":424 + /* "GPy/models/state_space_cython.pyx":428 * self.dAs = dAs * self.dQs = dQs * self.reconstruct_indices = reconstruct_indices # <<<<<<<<<<<<<< @@ -10842,23 +10848,23 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_DECREF(((PyObject *)__pyx_v_self->reconstruct_indices)); __pyx_v_self->reconstruct_indices = ((PyArrayObject *)__pyx_v_reconstruct_indices); - /* "state_space_cython.pyx":425 + /* "GPy/models/state_space_cython.pyx":429 * self.dQs = dQs * self.reconstruct_indices = reconstruct_indices * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ # <<<<<<<<<<<<<< * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->As), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->As), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->Qs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->Qs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "state_space_cython.pyx":426 + /* "GPy/models/state_space_cython.pyx":430 * self.reconstruct_indices = reconstruct_indices * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ # <<<<<<<<<<<<<< @@ -10867,7 +10873,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc */ __pyx_t_4 = (((PyObject *)__pyx_v_self->dAs) != Py_None); if ((__pyx_t_4 != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->dAs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->dAs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __pyx_t_1; __pyx_t_1 = 0; @@ -10876,19 +10882,19 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __pyx_t_2 = __pyx_int_0; } - /* "state_space_cython.pyx":425 + /* "GPy/models/state_space_cython.pyx":429 * self.dQs = dQs * self.reconstruct_indices = reconstruct_indices * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ # <<<<<<<<<<<<<< * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ */ - __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "state_space_cython.pyx":427 + /* "GPy/models/state_space_cython.pyx":431 * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ # <<<<<<<<<<<<<< @@ -10897,7 +10903,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc */ __pyx_t_4 = (((PyObject *)__pyx_v_self->dQs) != Py_None); if ((__pyx_t_4 != 0)) { - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->dQs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->dQs), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = __pyx_t_3; __pyx_t_3 = 0; @@ -10906,19 +10912,19 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __pyx_t_2 = __pyx_int_0; } - /* "state_space_cython.pyx":426 + /* "GPy/models/state_space_cython.pyx":430 * self.reconstruct_indices = reconstruct_indices * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ # <<<<<<<<<<<<<< * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ * (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) */ - __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "state_space_cython.pyx":428 + /* "GPy/models/state_space_cython.pyx":432 * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ * (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) # <<<<<<<<<<<<<< @@ -10927,7 +10933,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc */ __pyx_t_4 = (((PyObject *)__pyx_v_self->reconstruct_indices) != Py_None); if ((__pyx_t_4 != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->reconstruct_indices), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self->reconstruct_indices), __pyx_n_s_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __pyx_t_1; __pyx_t_1 = 0; @@ -10936,36 +10942,36 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __pyx_t_2 = __pyx_int_0; } - /* "state_space_cython.pyx":427 + /* "GPy/models/state_space_cython.pyx":431 * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ # <<<<<<<<<<<<<< * (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) * */ - __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "state_space_cython.pyx":425 + /* "GPy/models/state_space_cython.pyx":429 * self.dQs = dQs * self.reconstruct_indices = reconstruct_indices * self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ # <<<<<<<<<<<<<< * (self.dAs.nbytes if (self.dAs is not None) else 0) +\ * (self.dQs.nbytes if (self.dQs is not None) else 0) +\ */ - if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_total_size_of_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_total_size_of_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":430 + /* "GPy/models/state_space_cython.pyx":434 * (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) * * self.Q_svd_dict = {} # <<<<<<<<<<<<<< * self.last_k = 0 * # !!!Print statistics! Which object is created */ - __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __Pyx_GOTREF(__pyx_v_self->Q_svd_dict); @@ -10973,7 +10979,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __pyx_v_self->Q_svd_dict = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":431 + /* "GPy/models/state_space_cython.pyx":435 * * self.Q_svd_dict = {} * self.last_k = 0 # <<<<<<<<<<<<<< @@ -10982,7 +10988,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc */ __pyx_v_self->last_k = 0; - /* "state_space_cython.pyx":395 + /* "GPy/models/state_space_cython.pyx":399 * int last_k * * def __init__(self, np.ndarray[DTYPE_t, ndim=3] As, np.ndarray[DTYPE_t, ndim=3] Qs, # <<<<<<<<<<<<<< @@ -11005,7 +11011,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dQs.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_reconstruct_indices.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; goto __pyx_L2; __pyx_L0:; @@ -11019,7 +11025,7 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc return __pyx_r; } -/* "state_space_cython.pyx":434 +/* "GPy/models/state_space_cython.pyx":438 * # !!!Print statistics! Which object is created * # !!!Print statistics! Print sizes of matrices * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): # <<<<<<<<<<<<<< @@ -11027,8 +11033,8 @@ static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struc * Dynamic model */ -static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -11056,23 +11062,23 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_f_a); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_3f_a)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -11087,7 +11093,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -11101,7 +11107,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_A)); __Pyx_GIVEREF(((PyObject *)__pyx_v_A)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -11113,7 +11119,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":438 + /* "GPy/models/state_space_cython.pyx":442 * Dynamic model * """ * return np.dot(A, m) # default dynamic model # <<<<<<<<<<<<<< @@ -11121,9 +11127,9 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO * cpdef reset(self, bint compute_derivatives=False): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dot); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = NULL; @@ -11138,7 +11144,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_2) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL; @@ -11149,7 +11155,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __Pyx_INCREF(((PyObject *)__pyx_v_m)); PyTuple_SET_ITEM(__pyx_t_7, 1+__pyx_t_6, ((PyObject *)__pyx_v_m)); __Pyx_GIVEREF(((PyObject *)__pyx_v_m)); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -11157,7 +11163,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHO __pyx_t_1 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":434 + /* "GPy/models/state_space_cython.pyx":438 * # !!!Print statistics! Which object is created * # !!!Print statistics! 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-static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_2f_a[] = "\n Dynamic model\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_k; PyArrayObject *__pyx_v_m = 0; PyArrayObject *__pyx_v_A = 0; @@ -11224,16 +11230,16 @@ static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyO case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_A)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "f_a") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -11242,21 +11248,21 @@ static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyO values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); } - __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_m = ((PyArrayObject *)values[1]); __pyx_v_A = ((PyArrayObject *)values[2]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("f_a", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(((struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m), __pyx_ptype_5numpy_ndarray, 1, "m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_2f_a(((struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_k, __pyx_v_m, __pyx_v_A); /* function exit code */ goto __pyx_L0; @@ -11267,7 +11273,7 @@ static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a(PyO return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_2f_a(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A) { __Pyx_LocalBuf_ND __pyx_pybuffernd_A; __Pyx_Buffer __pyx_pybuffer_A; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -11289,16 +11295,16 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(str __pyx_pybuffernd_A.rcbuffer = &__pyx_pybuffer_A; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_A), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_f_a(__pyx_v_self, __pyx_v_k, ((PyArrayObject *)__pyx_v_m), ((PyArrayObject *)__pyx_v_A), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -11312,7 +11318,7 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(str __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_A.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_m.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.f_a", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -11324,7 +11330,7 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(str return __pyx_r; } -/* "state_space_cython.pyx":440 +/* "GPy/models/state_space_cython.pyx":444 * return np.dot(A, m) # default dynamic model * * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< @@ -11332,8 +11338,8 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(str * For reusing this object e.g. in smoother computation. 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__Pyx_RefNannyDeclarations @@ -11356,11 +11362,11 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(str if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_5reset)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_v_compute_derivatives); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_v_compute_derivatives); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -11374,17 +11380,17 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(str } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; 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__pyx_t_1 = 0; } - /* "state_space_cython.pyx":446 + /* "GPy/models/state_space_cython.pyx":450 * time steps. * """ * return self # <<<<<<<<<<<<<< @@ -11409,7 +11415,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(str __pyx_r = ((PyObject *)__pyx_v_self); goto __pyx_L0; - /* "state_space_cython.pyx":440 + /* "GPy/models/state_space_cython.pyx":444 * return np.dot(A, m) # default dynamic model * * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< @@ -11425,7 +11431,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(str __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -11434,9 +11440,9 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(str } /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_4reset[] = "\n For reusing this object e.g. in smoother computation. 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It makes sence\n because necessary matrices have been already computed for all\n time steps.\n "; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_5reset(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_compute_derivatives; int __pyx_lineno = 0; const char *__pyx_filename = NULL; @@ -11464,7 +11470,7 @@ static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset(P } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reset") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -11474,31 +11480,31 @@ static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset(P } } if (values[0]) { - __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_compute_derivatives = __Pyx_PyObject_IsTrue(values[0]); if (unlikely((__pyx_v_compute_derivatives == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_compute_derivatives = ((int)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("reset", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(((struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_4reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)__pyx_v_self), __pyx_v_compute_derivatives); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_4reset(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_compute_derivatives) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; - struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; + struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_2; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -11506,7 +11512,7 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(s __Pyx_XDECREF(__pyx_r); __pyx_t_2.__pyx_n = 1; __pyx_t_2.compute_derivatives = __pyx_v_compute_derivatives; - __pyx_t_1 = __pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython->__pyx_base.__pyx_base.reset(((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_vtabptr_3GPy_6models_18state_space_cython_AQcompute_batch_Cython->__pyx_base.__pyx_base.reset(((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_self), 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -11515,7 +11521,7 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(s /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython.AQcompute_batch_Cython.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -11523,7 +11529,7 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(s return __pyx_r; } -/* "state_space_cython.pyx":448 +/* "GPy/models/state_space_cython.pyx":452 * return self * * cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # <<<<<<<<<<<<<< @@ -11531,8 +11537,8 @@ static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(s * return self.As[:,:, self.reconstruct_indices[k]] */ -static PyObject *__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_7Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_7Ak(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch) { __Pyx_LocalBuf_ND __pyx_pybuffernd_P; __Pyx_Buffer __pyx_pybuffer_P; __Pyx_LocalBuf_ND __pyx_pybuffernd_m; @@ -11561,23 +11567,23 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_pybuffernd_P.rcbuffer = &__pyx_pybuffer_P; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m.diminfo[0].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m.diminfo[0].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m.diminfo[1].strides = __pyx_pybuffernd_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m.diminfo[1].shape = __pyx_pybuffernd_m.rcbuffer->pybuffer.shape[1]; 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/* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_Ak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_7Ak)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_7Ak)) { __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_k); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL; @@ -11592,7 +11598,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_5) { PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; @@ -11606,7 +11612,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct PyTuple_SET_ITEM(__pyx_t_7, 2+__pyx_t_6, ((PyObject *)__pyx_v_P)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -11618,7 +11624,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "state_space_cython.pyx":449 + /* "GPy/models/state_space_cython.pyx":453 * * cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): * self.last_k = k # <<<<<<<<<<<<<< @@ -11627,7 +11633,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct */ __pyx_v_self->last_k = __pyx_v_k; - /* "state_space_cython.pyx":450 + /* "GPy/models/state_space_cython.pyx":454 * cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): * self.last_k = k * return self.As[:,:, self.reconstruct_indices[k]] # <<<<<<<<<<<<<< @@ -11635,13 +11641,13 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct * cpdef Qk(self,int k): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->reconstruct_indices), __pyx_v_k, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->reconstruct_indices), __pyx_v_k, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_1); - __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_1); 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__pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_slice__31); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_slice__31); @@ -11652,14 +11658,14 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_self->As), __pyx_t_2); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_self->As), __pyx_t_2); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":448 + /* "GPy/models/state_space_cython.pyx":452 * return self * * cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # <<<<<<<<<<<<<< @@ -11680,7 +11686,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P.rcbuffer->pybuffer); 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if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -12646,7 +12652,7 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Q_srk(str if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -12662,17 +12668,17 @@ static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Q_srk(str __Pyx_INCREF(__pyx_t_4); 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Returns noise matrix of dynamic model on iteration k.\n k (iteration number). starts at 0\n \n p_f_Qsr: function (k). Returns square root of noise matrix of the \n dynamic model on iteration k. k (iteration number). starts at 0\n \n calc_grad_log_likelihood: boolean\n Whether to calculate gradient of the marginal likelihood \n of the state-space model. If true then the next parameter must \n provide the extra parameters for gradient calculation.\n \n p_dm: 3D array (state_dim, time_series_no, parameters_no)\n Mean derivatives from the previous step. For \"multiple time series mode\" \n it is 3D array, second dimension"" of which correspond to different\n time series.\n \n p_dP: 3D array (state_dim, state_dim, parameters_no)\n Mean derivatives from the previous step\n \n grad_calc_params_1: List or None\n List with derivatives. The first component is 'f_dA' - function(k)\n which returns the derivative of A. The second element is 'f_dQ'\n - function(k). Function which returns the derivative of Q.\n \n Output:\n ----------------------------\n m_pred, P_pred, dm_pred, dP_pred: metrices, 3D objects\n Results of the prediction steps. \n \n "; -static PyMethodDef __pyx_mdef_18state_space_cython_1_kalman_prediction_step_SVD_Cython = {"_kalman_prediction_step_SVD_Cython", (PyCFunction)__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cython, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython__kalman_prediction_step_SVD_Cython}; -static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_1_kalman_prediction_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython__kalman_prediction_step_SVD_Cython[] = "\n Desctrete prediction function \n \n Input:\n k:int\n Iteration No. Starts at 0. Total number of iterations equal to the \n number of measurements.\n \n p_m: matrix of size (state_dim, time_series_no)\n Mean value from the previous step. For \"multiple time series mode\" \n it is matrix, second dimension of which correspond to different\n time series.\n \n p_P: tuple (Prev_cov, S, V)\n Covariance matrix from the previous step and its SVD decomposition.\n Prev_cov = V * S * V.T The tuple is (Prev_cov, S, V) \n \n p_a: function (k, x_{k-1}, A_{k}). Dynamic function. \n k (iteration number), starts at 0\n x_{k-1} State from the previous step\n A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}.\n \n p_f_A: function (k, m, P) return Jacobian of dynamic function, it is\n passed into p_a.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n \n p_f_Q: function (k). Returns noise matrix of dynamic model on iteration k.\n k (iteration number). starts at 0\n \n p_f_Qsr: function (k). Returns square root of noise matrix of the \n dynamic model on iteration k. k (iteration number). starts at 0\n \n calc_grad_log_likelihood: boolean\n Whether to calculate gradient of the marginal likelihood \n of the state-space model. If true then the next parameter must \n provide the extra parameters for gradient calculation.\n \n p_dm: 3D array (state_dim, time_series_no, parameters_no)\n Mean derivatives from the previous step. For \"multiple time series mode\" \n it is 3D array, second dimension"" of which correspond to different\n time series.\n \n p_dP: 3D array (state_dim, state_dim, parameters_no)\n Mean derivatives from the previous step\n \n grad_calc_params_1: List or None\n List with derivatives. The first component is 'f_dA' - function(k)\n which returns the derivative of A. The second element is 'f_dQ'\n - function(k). Function which returns the derivative of Q.\n \n Output:\n ----------------------------\n m_pred, P_pred, dm_pred, dP_pred: metrices, 3D objects\n Results of the prediction steps. \n \n "; +static PyMethodDef __pyx_mdef_3GPy_6models_18state_space_cython_1_kalman_prediction_step_SVD_Cython = {"_kalman_prediction_step_SVD_Cython", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_1_kalman_prediction_step_SVD_Cython, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython__kalman_prediction_step_SVD_Cython}; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_1_kalman_prediction_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { long __pyx_v_k; PyArrayObject *__pyx_v_p_m = 0; PyObject *__pyx_v_p_P = 0; - struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables = 0; + struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables = 0; int __pyx_v_calc_grad_log_likelihood; PyArrayObject *__pyx_v_p_dm = 0; PyArrayObject *__pyx_v_p_dP = 0; @@ -12973,7 +12979,7 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_k,&__pyx_n_s_p_m,&__pyx_n_s_p_P,&__pyx_n_s_p_dynamic_callables,&__pyx_n_s_calc_grad_log_likelihood,&__pyx_n_s_p_dm,&__pyx_n_s_p_dP,0}; PyObject* values[7] = {0,0,0,0,0,0,0}; - /* "state_space_cython.pyx":509 + /* "GPy/models/state_space_cython.pyx":513 * Dynamic_Callables_Cython p_dynamic_callables, * bint calc_grad_log_likelihood=False, * np.ndarray[DTYPE_t, ndim=3] p_dm = None, # <<<<<<<<<<<<<< @@ -12982,7 +12988,7 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth */ values[5] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":510 + /* "GPy/models/state_space_cython.pyx":514 * bint calc_grad_log_likelihood=False, * np.ndarray[DTYPE_t, ndim=3] p_dm = None, * np.ndarray[DTYPE_t, ndim=3] p_dP = None): # <<<<<<<<<<<<<< @@ -13012,17 +13018,17 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_P)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_dynamic_callables)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (kw_args > 0) { @@ -13041,7 +13047,7 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_kalman_prediction_step_SVD_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_kalman_prediction_step_SVD_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -13056,15 +13062,15 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth default: goto __pyx_L5_argtuple_error; } } - __pyx_v_k = __Pyx_PyInt_As_long(values[0]); if (unlikely((__pyx_v_k == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_long(values[0]); if (unlikely((__pyx_v_k == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_p_m = ((PyArrayObject *)values[1]); __pyx_v_p_P = ((PyObject*)values[2]); - __pyx_v_p_dynamic_callables = ((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)values[3]); + __pyx_v_p_dynamic_callables = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)values[3]); if (values[4]) { - __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[4]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[4]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { - /* "state_space_cython.pyx":508 + /* "GPy/models/state_space_cython.pyx":512 * def _kalman_prediction_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m , tuple p_P, * Dynamic_Callables_Cython p_dynamic_callables, * bint calc_grad_log_likelihood=False, # <<<<<<<<<<<<<< @@ -13078,20 +13084,20 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_prediction_step_SVD_Cython", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython._kalman_prediction_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython._kalman_prediction_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_m), __pyx_ptype_5numpy_ndarray, 1, "p_m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_P), (&PyTuple_Type), 1, "p_P", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dynamic_callables), __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython, 1, "p_dynamic_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dm), __pyx_ptype_5numpy_ndarray, 1, "p_dm", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dP), __pyx_ptype_5numpy_ndarray, 1, "p_dP", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cython(__pyx_self, __pyx_v_k, __pyx_v_p_m, __pyx_v_p_P, __pyx_v_p_dynamic_callables, __pyx_v_calc_grad_log_likelihood, __pyx_v_p_dm, __pyx_v_p_dP); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_m), __pyx_ptype_5numpy_ndarray, 1, "p_m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_P), (&PyTuple_Type), 1, "p_P", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dynamic_callables), __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython, 1, "p_dynamic_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dm), __pyx_ptype_5numpy_ndarray, 1, "p_dm", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dP), __pyx_ptype_5numpy_ndarray, 1, "p_dP", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython__kalman_prediction_step_SVD_Cython(__pyx_self, __pyx_v_k, __pyx_v_p_m, __pyx_v_p_P, __pyx_v_p_dynamic_callables, __pyx_v_calc_grad_log_likelihood, __pyx_v_p_dm, __pyx_v_p_dP); - /* "state_space_cython.pyx":506 + /* "GPy/models/state_space_cython.pyx":510 * * @cython.boundscheck(False) * def _kalman_prediction_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m , tuple p_P, # <<<<<<<<<<<<<< @@ -13108,7 +13114,7 @@ static PyObject *__pyx_pw_18state_space_cython_1_kalman_prediction_step_SVD_Cyth return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython__kalman_prediction_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP) { PyArrayObject *__pyx_v_Prev_cov = 0; PyArrayObject *__pyx_v_S_old = 0; PyArrayObject *__pyx_v_V_old = 0; @@ -13314,21 +13320,21 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_pybuffernd_p_dP.rcbuffer = &__pyx_pybuffer_p_dP; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_m.diminfo[0].strides = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_m.diminfo[0].shape = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_m.diminfo[1].strides = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_m.diminfo[1].shape = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dm.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dm, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dm.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dm, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_dm.diminfo[0].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_dm.diminfo[0].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_dm.diminfo[1].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_dm.diminfo[1].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_p_dm.diminfo[2].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_p_dm.diminfo[2].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dP.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dP, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dP.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dP, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_dP.diminfo[0].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_dP.diminfo[0].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_dP.diminfo[1].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_dP.diminfo[1].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_p_dP.diminfo[2].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_p_dP.diminfo[2].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[2]; - /* "state_space_cython.pyx":571 + /* "GPy/models/state_space_cython.pyx":575 * * # covariance from the previous step# p_prev_cov = v * S * V.T * cdef np.ndarray[DTYPE_t, ndim=2] Prev_cov = p_P[0] # <<<<<<<<<<<<<< @@ -13337,23 +13343,23 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 0)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 0), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 0)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 0), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 0); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_Prev_cov = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_Prev_cov.diminfo[0].strides = __pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Prev_cov.diminfo[0].shape = __pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Prev_cov.diminfo[1].strides = __pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Prev_cov.diminfo[1].shape = __pyx_pybuffernd_Prev_cov.rcbuffer->pybuffer.shape[1]; } } __pyx_v_Prev_cov = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":572 + /* "GPy/models/state_space_cython.pyx":576 * # covariance from the previous step# p_prev_cov = v * S * V.T * cdef np.ndarray[DTYPE_t, ndim=2] Prev_cov = p_P[0] * cdef np.ndarray[DTYPE_t, ndim=1] S_old = p_P[1] # <<<<<<<<<<<<<< @@ -13362,23 +13368,23 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 1)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 1), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 1)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 1), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 1); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_old.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_old.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { __pyx_v_S_old = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_S_old.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_S_old.diminfo[0].strides = __pyx_pybuffernd_S_old.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_S_old.diminfo[0].shape = __pyx_pybuffernd_S_old.rcbuffer->pybuffer.shape[0]; } } __pyx_v_S_old = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":573 + /* "GPy/models/state_space_cython.pyx":577 * cdef np.ndarray[DTYPE_t, ndim=2] Prev_cov = p_P[0] * cdef np.ndarray[DTYPE_t, ndim=1] S_old = p_P[1] * cdef np.ndarray[DTYPE_t, ndim=2] V_old = p_P[2] # <<<<<<<<<<<<<< @@ -13387,38 +13393,38 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 2)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 2), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 2)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 2), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 2); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_old.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_old.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_V_old = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_V_old.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_V_old.diminfo[0].strides = __pyx_pybuffernd_V_old.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_V_old.diminfo[0].shape = __pyx_pybuffernd_V_old.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_V_old.diminfo[1].strides = __pyx_pybuffernd_V_old.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_V_old.diminfo[1].shape = __pyx_pybuffernd_V_old.rcbuffer->pybuffer.shape[1]; } } __pyx_v_V_old = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":577 + /* "GPy/models/state_space_cython.pyx":581 * * # index correspond to values from previous iteration. * cdef np.ndarray[DTYPE_t, ndim=2] A = p_dynamic_callables.Ak(k,p_m,Prev_cov) # state transition matrix (or Jacobian) # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=2] Q = p_dynamic_callables.Qk(k) # state noise matrx. This is necessary for the square root calculation (next step) * cdef np.ndarray[DTYPE_t, ndim=2] Q_sr = p_dynamic_callables.Q_srk(k) */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Ak(__pyx_v_p_dynamic_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_p_m), ((PyArrayObject *)__pyx_v_Prev_cov), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Ak(__pyx_v_p_dynamic_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_p_m), ((PyArrayObject *)__pyx_v_Prev_cov), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_t_2, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_t_2, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_A = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_A.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_A.diminfo[1].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_A.diminfo[1].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[1]; } } @@ -13426,22 +13432,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_A = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":578 + /* "GPy/models/state_space_cython.pyx":582 * # index correspond to values from previous iteration. * cdef np.ndarray[DTYPE_t, ndim=2] A = p_dynamic_callables.Ak(k,p_m,Prev_cov) # state transition matrix (or Jacobian) * cdef np.ndarray[DTYPE_t, ndim=2] Q = p_dynamic_callables.Qk(k) # state noise matrx. This is necessary for the square root calculation (next step) # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=2] Q_sr = p_dynamic_callables.Q_srk(k) * # Prediction step -> */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Qk(__pyx_v_p_dynamic_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Qk(__pyx_v_p_dynamic_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q.rcbuffer->pybuffer, (PyObject*)__pyx_t_3, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q.rcbuffer->pybuffer, (PyObject*)__pyx_t_3, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_Q = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_Q.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_Q.diminfo[0].strides = __pyx_pybuffernd_Q.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Q.diminfo[0].shape = __pyx_pybuffernd_Q.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Q.diminfo[1].strides = __pyx_pybuffernd_Q.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Q.diminfo[1].shape = __pyx_pybuffernd_Q.rcbuffer->pybuffer.shape[1]; } } @@ -13449,22 +13455,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_Q = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":579 + /* "GPy/models/state_space_cython.pyx":583 * cdef np.ndarray[DTYPE_t, ndim=2] A = p_dynamic_callables.Ak(k,p_m,Prev_cov) # state transition matrix (or Jacobian) * cdef np.ndarray[DTYPE_t, ndim=2] Q = p_dynamic_callables.Qk(k) # state noise matrx. This is necessary for the square root calculation (next step) * cdef np.ndarray[DTYPE_t, ndim=2] Q_sr = p_dynamic_callables.Q_srk(k) # <<<<<<<<<<<<<< * # Prediction step -> * cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_dynamic_callables.f_a(k, p_m, A) # predicted mean */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Q_srk(__pyx_v_p_dynamic_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->Q_srk(__pyx_v_p_dynamic_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 583; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 583; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q_sr.rcbuffer->pybuffer, (PyObject*)__pyx_t_4, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Q_sr.rcbuffer->pybuffer, (PyObject*)__pyx_t_4, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_Q_sr = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_Q_sr.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 583; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_Q_sr.diminfo[0].strides = __pyx_pybuffernd_Q_sr.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_Q_sr.diminfo[0].shape = __pyx_pybuffernd_Q_sr.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_Q_sr.diminfo[1].strides = __pyx_pybuffernd_Q_sr.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_Q_sr.diminfo[1].shape = __pyx_pybuffernd_Q_sr.rcbuffer->pybuffer.shape[1]; } } @@ -13472,22 +13478,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_Q_sr = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":581 + /* "GPy/models/state_space_cython.pyx":585 * cdef np.ndarray[DTYPE_t, ndim=2] Q_sr = p_dynamic_callables.Q_srk(k) * # Prediction step -> * cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_dynamic_callables.f_a(k, p_m, A) # predicted mean # <<<<<<<<<<<<<< * * # coavariance prediction have changed: */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->f_a(__pyx_v_p_dynamic_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_p_m), ((PyArrayObject *)__pyx_v_A), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)__pyx_v_p_dynamic_callables->__pyx_vtab)->f_a(__pyx_v_p_dynamic_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_p_m), ((PyArrayObject *)__pyx_v_A), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; 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goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_sqrt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_8 = NULL; @@ -13523,23 +13529,23 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho } } if (!__pyx_t_8) { - __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_9, ((PyObject *)__pyx_v_S_old)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_9, ((PyObject *)__pyx_v_S_old)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); } else { - __pyx_t_10 = PyTuple_New(1+1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; 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if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Q_sr), __pyx_n_s_T); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_9); __Pyx_GIVEREF(__pyx_t_9); @@ -13597,28 +13603,28 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho } } if (!__pyx_t_8) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_GOTREF(__pyx_t_1); } else { - __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = NULL; PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_13 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_svd_1_matr.rcbuffer->pybuffer, (PyObject*)__pyx_t_13, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_svd_1_matr.rcbuffer->pybuffer, (PyObject*)__pyx_t_13, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_svd_1_matr = ((PyArrayObject *)Py_None); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(((PyObject *)__pyx_v_svd_1_matr)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_svd_1_matr)); __Pyx_GIVEREF(((PyObject *)__pyx_v_svd_1_matr)); - __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); 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if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_7, __pyx_t_9); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -13676,22 +13682,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_res = __pyx_t_6; __pyx_t_6 = 0; - /* "state_space_cython.pyx":588 + /* "GPy/models/state_space_cython.pyx":592 * overwrite_a=False,check_finite=True) * # (U,S,Vh) * cdef np.ndarray[DTYPE_t, ndim=2] U = res[0] # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=1] S = res[1] * cdef np.ndarray[DTYPE_t, ndim=2] Vh = res[2] */ - __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_res, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_res, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_14, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_14, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_U = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_U.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_U.diminfo[0].strides = __pyx_pybuffernd_U.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_U.diminfo[0].shape = __pyx_pybuffernd_U.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_U.diminfo[1].strides = __pyx_pybuffernd_U.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_U.diminfo[1].shape = __pyx_pybuffernd_U.rcbuffer->pybuffer.shape[1]; } } @@ -13699,22 +13705,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_U = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "state_space_cython.pyx":589 + /* "GPy/models/state_space_cython.pyx":593 * # (U,S,Vh) * cdef np.ndarray[DTYPE_t, ndim=2] U = res[0] * cdef np.ndarray[DTYPE_t, ndim=1] S = res[1] # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=2] Vh = res[2] * # predicted variance computed by the regular method. 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For testing * #P_pred_tst = A.dot(Prev_cov).dot(A.T) + Q * cdef np.ndarray[DTYPE_t, ndim=2] V_new = Vh.T # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=1] S_new = S**2 * */ - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_17 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_new.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_new.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_V_new = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_V_new.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_V_new.diminfo[0].strides = __pyx_pybuffernd_V_new.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_V_new.diminfo[0].shape = __pyx_pybuffernd_V_new.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_V_new.diminfo[1].strides = __pyx_pybuffernd_V_new.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_V_new.diminfo[1].shape = __pyx_pybuffernd_V_new.rcbuffer->pybuffer.shape[1]; } } @@ -13768,22 +13774,22 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_V_new = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "state_space_cython.pyx":594 + /* "GPy/models/state_space_cython.pyx":598 * #P_pred_tst = A.dot(Prev_cov).dot(A.T) + Q * cdef np.ndarray[DTYPE_t, ndim=2] V_new = Vh.T * cdef np.ndarray[DTYPE_t, ndim=1] S_new = S**2 # <<<<<<<<<<<<<< * * cdef np.ndarray[DTYPE_t, ndim=2] P_pred = np.dot(V_new * S_new, V_new.T) # prediction covariance */ - __pyx_t_6 = PyNumber_Power(((PyObject *)__pyx_v_S), __pyx_int_2, Py_None); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyNumber_Power(((PyObject *)__pyx_v_S), __pyx_int_2, Py_None); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_18 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_new.rcbuffer->pybuffer, (PyObject*)__pyx_t_18, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_new.rcbuffer->pybuffer, (PyObject*)__pyx_t_18, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { __pyx_v_S_new = ((PyArrayObject *)Py_None); 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if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_dot); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_dot); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = PyNumber_Multiply(((PyObject *)__pyx_v_V_new), ((PyObject *)__pyx_v_S_new)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyNumber_Multiply(((PyObject *)__pyx_v_V_new), ((PyObject *)__pyx_v_S_new)); 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__pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_12); if (__pyx_t_8) { PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = NULL; @@ -13830,17 +13836,17 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __Pyx_GIVEREF(__pyx_t_1); __pyx_t_9 = 0; __pyx_t_1 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_12, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_12, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_19 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_t_19, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)__pyx_t_19, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_P_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; 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__pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_21 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dA_all_params.rcbuffer->pybuffer); - __pyx_t_22 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dA_all_params.rcbuffer->pybuffer, (PyObject*)__pyx_t_21, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack); + __pyx_t_22 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dA_all_params.rcbuffer->pybuffer, (PyObject*)__pyx_t_21, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack); if (unlikely(__pyx_t_22 < 0)) { PyErr_Fetch(&__pyx_t_23, &__pyx_t_24, &__pyx_t_25); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dA_all_params.rcbuffer->pybuffer, (PyObject*)__pyx_v_dA_all_params, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dA_all_params.rcbuffer->pybuffer, (PyObject*)__pyx_v_dA_all_params, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_23); 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goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_j); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_slice__49); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_slice__49); @@ -14268,28 +14274,28 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; - if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_dm_pred), __pyx_t_1, __pyx_t_6) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_dm_pred), __pyx_t_1, __pyx_t_6) < 0)) {__pyx_filename = __pyx_f[0]; 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Py_XDECREF(__pyx_t_24); Py_XDECREF(__pyx_t_23); __Pyx_RaiseBufferFallbackError(); } else { @@ -14646,7 +14652,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho } } __pyx_pybuffernd_dP_pred.diminfo[0].strides = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_dP_pred.diminfo[0].shape = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_dP_pred.diminfo[1].strides = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_dP_pred.diminfo[1].shape = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_dP_pred.diminfo[2].strides = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_dP_pred.diminfo[2].shape = __pyx_pybuffernd_dP_pred.rcbuffer->pybuffer.shape[2]; - if (unlikely(__pyx_t_22 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_22 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_28 = 0; __Pyx_INCREF(Py_None); @@ -14654,16 +14660,16 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho } __pyx_L3:; - /* "state_space_cython.pyx":639 + /* "GPy/models/state_space_cython.pyx":643 * dP_pred = None * * ret = (P_pred, S_new, Vh.T) # <<<<<<<<<<<<<< * return m_pred, ret, dm_pred, dP_pred * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(((PyObject *)__pyx_v_P_pred)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_P_pred)); @@ -14677,7 +14683,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_v_ret = ((PyObject*)__pyx_t_7); __pyx_t_7 = 0; - /* "state_space_cython.pyx":640 + /* "GPy/models/state_space_cython.pyx":644 * * ret = (P_pred, S_new, Vh.T) * return m_pred, ret, dm_pred, dP_pred # <<<<<<<<<<<<<< @@ -14685,7 +14691,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(((PyObject *)__pyx_v_m_pred)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_m_pred)); @@ -14703,7 +14709,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __pyx_t_7 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":506 + /* "GPy/models/state_space_cython.pyx":510 * * @cython.boundscheck(False) * def _kalman_prediction_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m , tuple p_P, # <<<<<<<<<<<<<< @@ -14749,7 +14755,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_p_m.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_svd_1_matr.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} - __Pyx_AddTraceback("state_space_cython._kalman_prediction_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython._kalman_prediction_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; goto __pyx_L2; __pyx_L0:; @@ -14804,7 +14810,7 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho return __pyx_r; } -/* "state_space_cython.pyx":645 +/* "GPy/models/state_space_cython.pyx":649 * * @cython.boundscheck(False) * def _kalman_update_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m, tuple p_P, # <<<<<<<<<<<<<< @@ -14813,14 +14819,14 @@ static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cytho */ /* Python wrapper */ -static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_18state_space_cython_2_kalman_update_step_SVD_Cython[] = "\n Input:\n \n k: int\n Iteration No. Starts at 0. Total number of iterations equal to the \n number of measurements.\n \n m_P: matrix of size (state_dim, time_series_no)\n Mean value from the previous step. For \"multiple time series mode\" \n it is matrix, second dimension of which correspond to different\n time series.\n \n p_P: tuple (P_pred, S, V)\n Covariance matrix from the prediction step and its SVD decomposition.\n P_pred = V * S * V.T The tuple is (P_pred, S, V)\n \n p_h: function (k, x_{k}, H_{k}). Measurement function.\n k (iteration number), starts at 0\n x_{k} state \n H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}.\n \n p_f_H: function (k, m, P) return Jacobian of dynamic function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n \n p_f_R: function (k). Returns noise matrix of measurement equation \n on iteration k.\n k (iteration number). starts at 0\n \n p_f_iRsr: function (k). Returns the square root of the noise matrix of \n measurement equation on iteration k. \n k (iteration number). starts at 0\n \n measurement: (measurement_dim, time_series_no) matrix\n One measurement used on the current update step. For \n \"multiple time series mode\" it is matrix, second dimension of \n which correspond to different time series.\n \n calc_log_likelihood: boolean\n Whether to calculate marginal likelihood of the state-space model.\n \n calc_grad_log_likelihood: boolean\n Whether to calculate gradient of the marginal likelihood \n of the state-space model. If true then the next parameter must \n provide the extra parameters for gradient cal""culation.\n \n p_dm: 3D array (state_dim, time_series_no, parameters_no)\n Mean derivatives from the prediction step. For \"multiple time series mode\" \n it is 3D array, second dimension of which correspond to different\n time series.\n \n p_dP: array\n Covariance derivatives from the prediction step.\n \n grad_calc_params_2: List or None\n List with derivatives. The first component is 'f_dH' - function(k)\n which returns the derivative of H. The second element is 'f_dR'\n - function(k). Function which returns the derivative of R.\n \n Output:\n ----------------------------\n m_upd, P_upd, dm_upd, dP_upd: metrices, 3D objects\n Results of the prediction steps.\n \n log_likelihood_update: double or 1D array\n Update to the log_likelihood from this step \n \n d_log_likelihood_update: (grad_params_no, time_series_no) matrix\n Update to the gradient of log_likelihood, \"multiple time series mode\"\n adds extra columns to the gradient.\n \n "; -static PyMethodDef __pyx_mdef_18state_space_cython_3_kalman_update_step_SVD_Cython = {"_kalman_update_step_SVD_Cython", (PyCFunction)__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_2_kalman_update_step_SVD_Cython}; -static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_3_kalman_update_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_3GPy_6models_18state_space_cython_2_kalman_update_step_SVD_Cython[] = "\n Input:\n \n k: int\n Iteration No. Starts at 0. Total number of iterations equal to the \n number of measurements.\n \n m_P: matrix of size (state_dim, time_series_no)\n Mean value from the previous step. For \"multiple time series mode\" \n it is matrix, second dimension of which correspond to different\n time series.\n \n p_P: tuple (P_pred, S, V)\n Covariance matrix from the prediction step and its SVD decomposition.\n P_pred = V * S * V.T The tuple is (P_pred, S, V)\n \n p_h: function (k, x_{k}, H_{k}). Measurement function.\n k (iteration number), starts at 0\n x_{k} state \n H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}.\n \n p_f_H: function (k, m, P) return Jacobian of dynamic function, it is\n passed into p_h.\n k (iteration number), starts at 0\n m: point where Jacobian is evaluated\n P: parameter for Jacobian, usually covariance matrix.\n \n p_f_R: function (k). Returns noise matrix of measurement equation \n on iteration k.\n k (iteration number). starts at 0\n \n p_f_iRsr: function (k). Returns the square root of the noise matrix of \n measurement equation on iteration k. \n k (iteration number). starts at 0\n \n measurement: (measurement_dim, time_series_no) matrix\n One measurement used on the current update step. For \n \"multiple time series mode\" it is matrix, second dimension of \n which correspond to different time series.\n \n calc_log_likelihood: boolean\n Whether to calculate marginal likelihood of the state-space model.\n \n calc_grad_log_likelihood: boolean\n Whether to calculate gradient of the marginal likelihood \n of the state-space model. If true then the next parameter must \n provide the extra parameters for gradient cal""culation.\n \n p_dm: 3D array (state_dim, time_series_no, parameters_no)\n Mean derivatives from the prediction step. For \"multiple time series mode\" \n it is 3D array, second dimension of which correspond to different\n time series.\n \n p_dP: array\n Covariance derivatives from the prediction step.\n \n grad_calc_params_2: List or None\n List with derivatives. The first component is 'f_dH' - function(k)\n which returns the derivative of H. The second element is 'f_dR'\n - function(k). Function which returns the derivative of R.\n \n Output:\n ----------------------------\n m_upd, P_upd, dm_upd, dP_upd: metrices, 3D objects\n Results of the prediction steps.\n \n log_likelihood_update: double or 1D array\n Update to the log_likelihood from this step \n \n d_log_likelihood_update: (grad_params_no, time_series_no) matrix\n Update to the gradient of log_likelihood, \"multiple time series mode\"\n adds extra columns to the gradient.\n \n "; +static PyMethodDef __pyx_mdef_3GPy_6models_18state_space_cython_3_kalman_update_step_SVD_Cython = {"_kalman_update_step_SVD_Cython", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_3_kalman_update_step_SVD_Cython, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_2_kalman_update_step_SVD_Cython}; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_3_kalman_update_step_SVD_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { long __pyx_v_k; PyArrayObject *__pyx_v_p_m = 0; PyObject *__pyx_v_p_P = 0; - struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables = 0; + struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables = 0; PyArrayObject *__pyx_v_measurement = 0; int __pyx_v_calc_log_likelihood; int __pyx_v_calc_grad_log_likelihood; @@ -14836,7 +14842,7 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_k,&__pyx_n_s_p_m,&__pyx_n_s_p_P,&__pyx_n_s_p_measurement_callables,&__pyx_n_s_measurement,&__pyx_n_s_calc_log_likelihood,&__pyx_n_s_calc_grad_log_likelihood,&__pyx_n_s_p_dm,&__pyx_n_s_p_dP,0}; PyObject* values[9] = {0,0,0,0,0,0,0,0,0}; - /* "state_space_cython.pyx":650 + /* "GPy/models/state_space_cython.pyx":654 * bint calc_log_likelihood= False, * bint calc_grad_log_likelihood=False, * np.ndarray[DTYPE_t, ndim=3] p_dm = None, # <<<<<<<<<<<<<< @@ -14845,7 +14851,7 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P */ values[7] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":651 + /* "GPy/models/state_space_cython.pyx":655 * bint calc_grad_log_likelihood=False, * np.ndarray[DTYPE_t, ndim=3] p_dm = None, * np.ndarray[DTYPE_t, ndim=3] p_dP = None): # <<<<<<<<<<<<<< @@ -14877,22 +14883,22 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_m)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_P)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_measurement_callables)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_measurement)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (kw_args > 0) { @@ -14916,7 +14922,7 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_kalman_update_step_SVD_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_kalman_update_step_SVD_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -14933,16 +14939,16 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P default: goto __pyx_L5_argtuple_error; } } - __pyx_v_k = __Pyx_PyInt_As_long(values[0]); if (unlikely((__pyx_v_k == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_As_long(values[0]); if (unlikely((__pyx_v_k == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_p_m = ((PyArrayObject *)values[1]); __pyx_v_p_P = ((PyObject*)values[2]); - __pyx_v_p_measurement_callables = ((struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *)values[3]); + __pyx_v_p_measurement_callables = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)values[3]); __pyx_v_measurement = ((PyArrayObject *)values[4]); if (values[5]) { - __pyx_v_calc_log_likelihood = __Pyx_PyObject_IsTrue(values[5]); if (unlikely((__pyx_v_calc_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_calc_log_likelihood = __Pyx_PyObject_IsTrue(values[5]); if (unlikely((__pyx_v_calc_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { - /* "state_space_cython.pyx":648 + /* "GPy/models/state_space_cython.pyx":652 * Measurement_Callables_Cython p_measurement_callables, * np.ndarray[DTYPE_t, ndim=2] measurement, * bint calc_log_likelihood= False, # <<<<<<<<<<<<<< @@ -14952,10 +14958,10 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P __pyx_v_calc_log_likelihood = ((int)0); } if (values[6]) { - __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[6]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[6]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { - /* "state_space_cython.pyx":649 + /* "GPy/models/state_space_cython.pyx":653 * np.ndarray[DTYPE_t, ndim=2] measurement, * bint calc_log_likelihood= False, * bint calc_grad_log_likelihood=False, # <<<<<<<<<<<<<< @@ -14969,21 +14975,21 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_kalman_update_step_SVD_Cython", 0, 5, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython._kalman_update_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython._kalman_update_step_SVD_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_m), __pyx_ptype_5numpy_ndarray, 1, "p_m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_P), (&PyTuple_Type), 1, "p_P", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_measurement_callables), __pyx_ptype_18state_space_cython_Measurement_Callables_Cython, 1, "p_measurement_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_measurement), __pyx_ptype_5numpy_ndarray, 1, "measurement", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dm), __pyx_ptype_5numpy_ndarray, 1, "p_dm", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dP), __pyx_ptype_5numpy_ndarray, 1, "p_dP", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(__pyx_self, __pyx_v_k, __pyx_v_p_m, __pyx_v_p_P, __pyx_v_p_measurement_callables, __pyx_v_measurement, __pyx_v_calc_log_likelihood, __pyx_v_calc_grad_log_likelihood, __pyx_v_p_dm, __pyx_v_p_dP); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_m), __pyx_ptype_5numpy_ndarray, 1, "p_m", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_P), (&PyTuple_Type), 1, "p_P", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_measurement_callables), __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython, 1, "p_measurement_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_measurement), __pyx_ptype_5numpy_ndarray, 1, "measurement", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dm), __pyx_ptype_5numpy_ndarray, 1, "p_dm", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dP), __pyx_ptype_5numpy_ndarray, 1, "p_dP", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_2_kalman_update_step_SVD_Cython(__pyx_self, __pyx_v_k, __pyx_v_p_m, __pyx_v_p_P, __pyx_v_p_measurement_callables, __pyx_v_measurement, __pyx_v_calc_log_likelihood, __pyx_v_calc_grad_log_likelihood, __pyx_v_p_dm, __pyx_v_p_dP); - /* "state_space_cython.pyx":645 + /* "GPy/models/state_space_cython.pyx":649 * * @cython.boundscheck(False) * def _kalman_update_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m, tuple p_P, # <<<<<<<<<<<<<< @@ -15000,7 +15006,7 @@ static PyObject *__pyx_pw_18state_space_cython_3_kalman_update_step_SVD_Cython(P return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, PyArrayObject *__pyx_v_measurement, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_2_kalman_update_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, PyArrayObject *__pyx_v_measurement, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP) { PyArrayObject *__pyx_v_m_pred = 0; PyArrayObject *__pyx_v_P_pred = 0; PyArrayObject *__pyx_v_S_pred = 0; @@ -15329,26 +15335,26 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C __pyx_pybuffernd_p_dP.rcbuffer = &__pyx_pybuffer_p_dP; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_m, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_m.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_m, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_m.diminfo[0].strides = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_m.diminfo[0].shape = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_m.diminfo[1].strides = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_m.diminfo[1].shape = __pyx_pybuffernd_p_m.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_measurement.rcbuffer->pybuffer, (PyObject*)__pyx_v_measurement, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_measurement.rcbuffer->pybuffer, (PyObject*)__pyx_v_measurement, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_measurement.diminfo[0].strides = __pyx_pybuffernd_measurement.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_measurement.diminfo[0].shape = __pyx_pybuffernd_measurement.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_measurement.diminfo[1].strides = __pyx_pybuffernd_measurement.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_measurement.diminfo[1].shape = __pyx_pybuffernd_measurement.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dm.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dm, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dm.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dm, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_dm.diminfo[0].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_dm.diminfo[0].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_dm.diminfo[1].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_dm.diminfo[1].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_p_dm.diminfo[2].strides = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_p_dm.diminfo[2].shape = __pyx_pybuffernd_p_dm.rcbuffer->pybuffer.shape[2]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dP.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dP, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_p_dP.rcbuffer->pybuffer, (PyObject*)__pyx_v_p_dP, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_p_dP.diminfo[0].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_p_dP.diminfo[0].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_p_dP.diminfo[1].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_p_dP.diminfo[1].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_p_dP.diminfo[2].strides = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_p_dP.diminfo[2].shape = __pyx_pybuffernd_p_dP.rcbuffer->pybuffer.shape[2]; - /* "state_space_cython.pyx":727 + /* "GPy/models/state_space_cython.pyx":731 * """ * * cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_m # from prediction step # <<<<<<<<<<<<<< @@ -15357,16 +15363,16 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C */ { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_v_p_m), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_v_p_m), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_m_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_m_pred.diminfo[0].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_pred.diminfo[0].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_pred.diminfo[1].strides = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_pred.diminfo[1].shape = __pyx_pybuffernd_m_pred.rcbuffer->pybuffer.shape[1]; } } __Pyx_INCREF(((PyObject *)__pyx_v_p_m)); __pyx_v_m_pred = ((PyArrayObject *)__pyx_v_p_m); - /* "state_space_cython.pyx":729 + /* "GPy/models/state_space_cython.pyx":733 * cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_m # from prediction step * #P_pred,S_pred,V_pred = p_P # from prediction step * cdef np.ndarray[DTYPE_t, ndim=2] P_pred = p_P[0] # <<<<<<<<<<<<<< @@ -15375,23 +15381,23 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 0)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 0), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 0)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 0), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 0); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_P_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_P_pred.diminfo[0].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_P_pred.diminfo[0].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_P_pred.diminfo[1].strides = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_P_pred.diminfo[1].shape = __pyx_pybuffernd_P_pred.rcbuffer->pybuffer.shape[1]; } } __pyx_v_P_pred = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":730 + /* "GPy/models/state_space_cython.pyx":734 * #P_pred,S_pred,V_pred = p_P # from prediction step * cdef np.ndarray[DTYPE_t, ndim=2] P_pred = p_P[0] * cdef np.ndarray[DTYPE_t, ndim=1] S_pred = p_P[1] # <<<<<<<<<<<<<< @@ -15400,23 +15406,23 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 1)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 1), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 1)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 1), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 1); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { __pyx_v_S_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_S_pred.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_S_pred.diminfo[0].strides = __pyx_pybuffernd_S_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_S_pred.diminfo[0].shape = __pyx_pybuffernd_S_pred.rcbuffer->pybuffer.shape[0]; } } __pyx_v_S_pred = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":731 + /* "GPy/models/state_space_cython.pyx":735 * cdef np.ndarray[DTYPE_t, ndim=2] P_pred = p_P[0] * cdef np.ndarray[DTYPE_t, ndim=1] S_pred = p_P[1] * cdef np.ndarray[DTYPE_t, ndim=2] V_pred = p_P[2] # <<<<<<<<<<<<<< @@ -15425,38 +15431,38 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C */ if (unlikely(__pyx_v_p_P == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 2)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 2), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((PyTuple_GET_ITEM(__pyx_v_p_P, 2)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_p_P, 2), __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 2); __Pyx_INCREF(__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_V_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_V_pred.diminfo[0].strides = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_V_pred.diminfo[0].shape = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_V_pred.diminfo[1].strides = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_V_pred.diminfo[1].shape = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.shape[1]; } } __pyx_v_V_pred = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":733 + /* "GPy/models/state_space_cython.pyx":737 * cdef np.ndarray[DTYPE_t, ndim=2] V_pred = p_P[2] * * cdef np.ndarray[DTYPE_t, ndim=2] H = p_measurement_callables.Hk(k, m_pred, P_pred) # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=2] R = p_measurement_callables.Rk(k) * cdef np.ndarray[DTYPE_t, ndim=2] R_isr =p_measurement_callables.R_isrk(k) # square root of the inverse of R matrix */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->Hk(__pyx_v_p_measurement_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->Hk(__pyx_v_p_measurement_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_P_pred), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_H.rcbuffer->pybuffer, (PyObject*)__pyx_t_2, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_H.rcbuffer->pybuffer, (PyObject*)__pyx_t_2, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_H = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_H.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_H.diminfo[0].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_H.diminfo[0].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_H.diminfo[1].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_H.diminfo[1].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[1]; } } @@ -15464,22 +15470,22 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C __pyx_v_H = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":734 + /* "GPy/models/state_space_cython.pyx":738 * * cdef np.ndarray[DTYPE_t, ndim=2] H = p_measurement_callables.Hk(k, m_pred, P_pred) * cdef np.ndarray[DTYPE_t, ndim=2] R = p_measurement_callables.Rk(k) # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=2] R_isr =p_measurement_callables.R_isrk(k) # square root of the inverse of R matrix * */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->Rk(__pyx_v_p_measurement_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->Rk(__pyx_v_p_measurement_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_t_3, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R.rcbuffer->pybuffer, (PyObject*)__pyx_t_3, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_R = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_R.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_R.diminfo[0].strides = __pyx_pybuffernd_R.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_R.diminfo[0].shape = __pyx_pybuffernd_R.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_R.diminfo[1].strides = __pyx_pybuffernd_R.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_R.diminfo[1].shape = __pyx_pybuffernd_R.rcbuffer->pybuffer.shape[1]; } } @@ -15487,22 +15493,22 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C __pyx_v_R = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":735 + /* "GPy/models/state_space_cython.pyx":739 * cdef np.ndarray[DTYPE_t, ndim=2] H = p_measurement_callables.Hk(k, m_pred, P_pred) * cdef np.ndarray[DTYPE_t, ndim=2] R = p_measurement_callables.Rk(k) * cdef np.ndarray[DTYPE_t, ndim=2] R_isr =p_measurement_callables.R_isrk(k) # square root of the inverse of R matrix # <<<<<<<<<<<<<< * * cdef int time_series_no = p_m.shape[1] # number of time serieses */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->R_isrk(__pyx_v_p_measurement_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->R_isrk(__pyx_v_p_measurement_callables, __pyx_v_k, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R_isr.rcbuffer->pybuffer, (PyObject*)__pyx_t_4, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_R_isr.rcbuffer->pybuffer, (PyObject*)__pyx_t_4, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_R_isr = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_R_isr.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_R_isr.diminfo[0].strides = __pyx_pybuffernd_R_isr.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_R_isr.diminfo[0].shape = __pyx_pybuffernd_R_isr.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_R_isr.diminfo[1].strides = __pyx_pybuffernd_R_isr.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_R_isr.diminfo[1].shape = __pyx_pybuffernd_R_isr.rcbuffer->pybuffer.shape[1]; } } @@ -15510,7 +15516,7 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C __pyx_v_R_isr = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":737 + /* "GPy/models/state_space_cython.pyx":741 * cdef np.ndarray[DTYPE_t, ndim=2] R_isr =p_measurement_callables.R_isrk(k) # square root of the inverse of R matrix * * cdef int time_series_no = p_m.shape[1] # number of time serieses # <<<<<<<<<<<<<< @@ -15519,25 +15525,25 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C */ __pyx_v_time_series_no = (__pyx_v_p_m->dimensions[1]); - /* "state_space_cython.pyx":742 + /* "GPy/models/state_space_cython.pyx":746 * # Update step (only if there is data) * #if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. * cdef np.ndarray[DTYPE_t, ndim=2] v = measurement-p_measurement_callables.f_h(k, m_pred, H) # <<<<<<<<<<<<<< * * cdef np.ndarray[DTYPE_t, ndim=2] svd_2_matr = np.vstack( ( np.dot( R_isr.T, np.dot(H, V_pred)) , np.diag( 1.0/np.sqrt(S_pred) ) ) ) */ - __pyx_t_1 = ((struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->f_h(__pyx_v_p_measurement_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_H), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)__pyx_v_p_measurement_callables->__pyx_vtab)->f_h(__pyx_v_p_measurement_callables, __pyx_v_k, ((PyArrayObject *)__pyx_v_m_pred), ((PyArrayObject *)__pyx_v_H), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyNumber_Subtract(((PyObject *)__pyx_v_measurement), __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Subtract(((PyObject *)__pyx_v_measurement), __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = ((PyArrayObject *)__pyx_t_5); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_v.rcbuffer->pybuffer, (PyObject*)__pyx_t_6, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_v.rcbuffer->pybuffer, (PyObject*)__pyx_t_6, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_v = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_v.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_v.diminfo[0].strides = __pyx_pybuffernd_v.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_v.diminfo[0].shape = __pyx_pybuffernd_v.rcbuffer->pybuffer.shape[0]; 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__pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_vstack); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_vstack); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_dot); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_dot); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_R_isr), __pyx_n_s_T); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_R_isr), __pyx_n_s_T); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); 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__pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_7, __pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -15785,22 +15791,22 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C __pyx_v_res = __pyx_t_10; __pyx_t_10 = 0; - /* "state_space_cython.pyx":750 + /* "GPy/models/state_space_cython.pyx":754 * * #(U,S,Vh) * cdef np.ndarray[DTYPE_t, ndim=2] U = res[0] # <<<<<<<<<<<<<< * cdef np.ndarray[DTYPE_t, ndim=1] S_svd = res[1] * cdef np.ndarray[DTYPE_t, ndim=2] Vh = res[2] */ - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_res, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_res, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_10); - if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_16 = ((PyArrayObject *)__pyx_t_10); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_16, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_U.rcbuffer->pybuffer, (PyObject*)__pyx_t_16, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_U = ((PyArrayObject *)Py_None); 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if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_res, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_10); - if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_17 = ((PyArrayObject *)__pyx_t_10); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_svd.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_S_svd.rcbuffer->pybuffer, (PyObject*)__pyx_t_17, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { __pyx_v_S_svd = ((PyArrayObject *)Py_None); 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if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_res, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_10); - if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_18 = ((PyArrayObject *)__pyx_t_10); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_18, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_Vh.rcbuffer->pybuffer, (PyObject*)__pyx_t_18, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { __pyx_v_Vh = ((PyArrayObject *)Py_None); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_dot); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_dot); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_Vh), __pyx_n_s_T); 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if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_10) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_10, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_36 = ((PyArrayObject *)__pyx_t_10); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dm_pred.rcbuffer->pybuffer); - __pyx_t_37 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dm_pred.rcbuffer->pybuffer, (PyObject*)__pyx_t_36, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_37 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dm_pred.rcbuffer->pybuffer, (PyObject*)__pyx_t_36, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); 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goto __pyx_L1_error;} + if (!(likely(((__pyx_t_12) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_12, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_36 = ((PyArrayObject *)__pyx_t_12); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_tmp3.rcbuffer->pybuffer); - __pyx_t_37 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_tmp3.rcbuffer->pybuffer, (PyObject*)__pyx_t_36, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); + __pyx_t_37 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_tmp3.rcbuffer->pybuffer, (PyObject*)__pyx_t_36, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack); if (unlikely(__pyx_t_37 < 0)) { PyErr_Fetch(&__pyx_t_26, &__pyx_t_27, &__pyx_t_28); - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_tmp3.rcbuffer->pybuffer, (PyObject*)__pyx_v_tmp3, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_tmp3.rcbuffer->pybuffer, (PyObject*)__pyx_v_tmp3, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { Py_XDECREF(__pyx_t_26); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_32 = 0; __Pyx_INCREF(Py_None); __pyx_v_dm_upd = ((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":861 + /* "GPy/models/state_space_cython.pyx":865 * else: * dm_upd = None * dP_upd = None # <<<<<<<<<<<<<< @@ -18291,10 +18297,10 @@ static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(C { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dP_upd.rcbuffer->pybuffer); - __pyx_t_25 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dP_upd.rcbuffer->pybuffer, (PyObject*)__pyx_t_33, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack); + __pyx_t_25 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_dP_upd.rcbuffer->pybuffer, (PyObject*)__pyx_t_33, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack); if (unlikely(__pyx_t_25 < 0)) { PyErr_Fetch(&__pyx_t_26, &__pyx_t_27, &__pyx_t_28); 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/*proto*/ +static PyMethodDef __pyx_mdef_3GPy_6models_18state_space_cython_5_cont_discr_kalman_filter_raw_Cython = {"_cont_discr_kalman_filter_raw_Cython", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_5_cont_discr_kalman_filter_raw_Cython, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_3GPy_6models_18state_space_cython_5_cont_discr_kalman_filter_raw_Cython(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_state_dim; - struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables = 0; - struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables = 0; + struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables = 0; + struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables = 0; CYTHON_UNUSED PyObject *__pyx_v_X = 0; PyObject *__pyx_v_Y = 0; PyArrayObject *__pyx_v_m_init = 0; @@ -18617,7 +18623,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_state_dim,&__pyx_n_s_p_dynamic_callables,&__pyx_n_s_p_measurement_callables,&__pyx_n_s_X,&__pyx_n_s_Y,&__pyx_n_s_m_init,&__pyx_n_s_P_init,&__pyx_n_s_p_kalman_filter_type,&__pyx_n_s_calc_log_likelihood,&__pyx_n_s_calc_grad_log_likelihood,&__pyx_n_s_grad_params_no,&__pyx_n_s_dm_init,&__pyx_n_s_dP_init,0}; PyObject* values[13] = {0,0,0,0,0,0,0,0,0,0,0,0,0}; - /* "state_space_cython.pyx":873 + /* "GPy/models/state_space_cython.pyx":877 * def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython p_dynamic_callables, * Measurement_Callables_Cython p_measurement_callables, X, Y, * np.ndarray[DTYPE_t, ndim=2] m_init=None, np.ndarray[DTYPE_t, ndim=2] P_init=None, # <<<<<<<<<<<<<< @@ -18628,7 +18634,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy values[6] = (PyObject *)((PyArrayObject *)Py_None); values[7] = ((PyObject *)__pyx_n_s_regular); - /* "state_space_cython.pyx":878 + /* "GPy/models/state_space_cython.pyx":882 * bint calc_grad_log_likelihood=False, * int grad_params_no=0, * np.ndarray[DTYPE_t, ndim=3] dm_init=None, # <<<<<<<<<<<<<< @@ -18637,7 +18643,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy */ values[11] = (PyObject *)((PyArrayObject *)Py_None); - /* "state_space_cython.pyx":879 + /* "GPy/models/state_space_cython.pyx":883 * int grad_params_no=0, * np.ndarray[DTYPE_t, ndim=3] dm_init=None, * np.ndarray[DTYPE_t, ndim=3] dP_init=None): # <<<<<<<<<<<<<< @@ -18673,22 +18679,22 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_dynamic_callables)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_p_measurement_callables)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_X)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_Y)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (kw_args > 0) { @@ -18732,7 +18738,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_cont_discr_kalman_filter_raw_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_cont_discr_kalman_filter_raw_Cython") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -18753,19 +18759,19 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy default: goto __pyx_L5_argtuple_error; } } - __pyx_v_state_dim = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_state_dim == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_p_dynamic_callables = ((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)values[1]); - __pyx_v_p_measurement_callables = ((struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *)values[2]); + __pyx_v_state_dim = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_state_dim == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_p_dynamic_callables = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)values[1]); + __pyx_v_p_measurement_callables = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)values[2]); __pyx_v_X = values[3]; __pyx_v_Y = values[4]; __pyx_v_m_init = ((PyArrayObject *)values[5]); __pyx_v_P_init = ((PyArrayObject *)values[6]); __pyx_v_p_kalman_filter_type = values[7]; if (values[8]) { - __pyx_v_calc_log_likelihood = __Pyx_PyObject_IsTrue(values[8]); if (unlikely((__pyx_v_calc_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_calc_log_likelihood = __Pyx_PyObject_IsTrue(values[8]); if (unlikely((__pyx_v_calc_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { - /* "state_space_cython.pyx":875 + /* "GPy/models/state_space_cython.pyx":879 * np.ndarray[DTYPE_t, ndim=2] m_init=None, np.ndarray[DTYPE_t, ndim=2] P_init=None, * p_kalman_filter_type='regular', * bint calc_log_likelihood=False, # <<<<<<<<<<<<<< @@ -18775,10 +18781,10 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy __pyx_v_calc_log_likelihood = ((int)0); } if (values[9]) { - __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[9]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_calc_grad_log_likelihood = __Pyx_PyObject_IsTrue(values[9]); if (unlikely((__pyx_v_calc_grad_log_likelihood == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { - /* "state_space_cython.pyx":876 + /* "GPy/models/state_space_cython.pyx":880 * p_kalman_filter_type='regular', * bint calc_log_likelihood=False, * bint calc_grad_log_likelihood=False, # <<<<<<<<<<<<<< @@ -18788,7 +18794,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy __pyx_v_calc_grad_log_likelihood = ((int)0); } if (values[10]) { - __pyx_v_grad_params_no = __Pyx_PyInt_As_int(values[10]); if (unlikely((__pyx_v_grad_params_no == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_grad_params_no = __Pyx_PyInt_As_int(values[10]); if (unlikely((__pyx_v_grad_params_no == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_grad_params_no = ((int)0); } @@ -18797,21 +18803,21 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_cont_discr_kalman_filter_raw_Cython", 0, 5, 13, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("state_space_cython._cont_discr_kalman_filter_raw_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("GPy.models.state_space_cython._cont_discr_kalman_filter_raw_Cython", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dynamic_callables), __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython, 1, "p_dynamic_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_measurement_callables), __pyx_ptype_18state_space_cython_Measurement_Callables_Cython, 1, "p_measurement_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_init), __pyx_ptype_5numpy_ndarray, 1, "m_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_init), __pyx_ptype_5numpy_ndarray, 1, "P_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dm_init), __pyx_ptype_5numpy_ndarray, 1, "dm_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dP_init), __pyx_ptype_5numpy_ndarray, 1, "dP_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(__pyx_self, __pyx_v_state_dim, __pyx_v_p_dynamic_callables, __pyx_v_p_measurement_callables, __pyx_v_X, __pyx_v_Y, __pyx_v_m_init, __pyx_v_P_init, __pyx_v_p_kalman_filter_type, __pyx_v_calc_log_likelihood, __pyx_v_calc_grad_log_likelihood, __pyx_v_grad_params_no, __pyx_v_dm_init, __pyx_v_dP_init); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_dynamic_callables), __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython, 1, "p_dynamic_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_p_measurement_callables), __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython, 1, "p_measurement_callables", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_init), __pyx_ptype_5numpy_ndarray, 1, "m_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_P_init), __pyx_ptype_5numpy_ndarray, 1, "P_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dm_init), __pyx_ptype_5numpy_ndarray, 1, "dm_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_dP_init), __pyx_ptype_5numpy_ndarray, 1, "dP_init", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_3GPy_6models_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(__pyx_self, __pyx_v_state_dim, __pyx_v_p_dynamic_callables, __pyx_v_p_measurement_callables, __pyx_v_X, __pyx_v_Y, __pyx_v_m_init, __pyx_v_P_init, __pyx_v_p_kalman_filter_type, __pyx_v_calc_log_likelihood, __pyx_v_calc_grad_log_likelihood, __pyx_v_grad_params_no, __pyx_v_dm_init, __pyx_v_dP_init); - /* "state_space_cython.pyx":871 + /* "GPy/models/state_space_cython.pyx":875 * * @cython.boundscheck(False) * def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython p_dynamic_callables, # <<<<<<<<<<<<<< @@ -18828,7 +18834,7 @@ static PyObject *__pyx_pw_18state_space_cython_5_cont_discr_kalman_filter_raw_Cy return __pyx_r; } -static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_state_dim, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, CYTHON_UNUSED PyObject *__pyx_v_X, PyObject *__pyx_v_Y, PyArrayObject *__pyx_v_m_init, PyArrayObject *__pyx_v_P_init, CYTHON_UNUSED PyObject *__pyx_v_p_kalman_filter_type, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, int __pyx_v_grad_params_no, PyArrayObject *__pyx_v_dm_init, PyArrayObject *__pyx_v_dP_init) { +static PyObject *__pyx_pf_3GPy_6models_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_state_dim, struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, CYTHON_UNUSED PyObject *__pyx_v_X, PyObject *__pyx_v_Y, PyArrayObject *__pyx_v_m_init, PyArrayObject *__pyx_v_P_init, CYTHON_UNUSED PyObject *__pyx_v_p_kalman_filter_type, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, int __pyx_v_grad_params_no, PyArrayObject *__pyx_v_dm_init, PyArrayObject *__pyx_v_dP_init) { int __pyx_v_steps_no; int __pyx_v_time_series_no; PyArrayObject *__pyx_v_M = 0; @@ -18920,13 +18926,14 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy Py_ssize_t __pyx_t_23; PyArrayObject *__pyx_t_24 = NULL; PyArrayObject *__pyx_t_25 = NULL; - PyObject *__pyx_t_26 = NULL; + int __pyx_t_26; PyObject *__pyx_t_27 = NULL; - PyArrayObject *__pyx_t_28 = NULL; + PyObject *__pyx_t_28 = NULL; PyArrayObject *__pyx_t_29 = NULL; PyArrayObject *__pyx_t_30 = NULL; - int __pyx_t_31; - struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_32; + PyArrayObject *__pyx_t_31 = NULL; + int __pyx_t_32; + struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset __pyx_t_33; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -19018,76 +19025,76 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __pyx_pybuffernd_dP_init.rcbuffer = &__pyx_pybuffer_dP_init; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_init.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_init, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_init.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_init, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_m_init.diminfo[0].strides = __pyx_pybuffernd_m_init.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_init.diminfo[0].shape = __pyx_pybuffernd_m_init.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_init.diminfo[1].strides = __pyx_pybuffernd_m_init.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_init.diminfo[1].shape = __pyx_pybuffernd_m_init.rcbuffer->pybuffer.shape[1]; 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__pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_P.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_3GPy_6models_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) { __pyx_v_P = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_P.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; 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__pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_sp); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_linalg); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_linalg); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_svd); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_svd); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(((PyObject *)__pyx_v_P_init)); PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_P_init)); __Pyx_GIVEREF(((PyObject *)__pyx_v_P_init)); - __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_full_matrices, Py_False) < 0) {__pyx_filename = __pyx_f[0]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_check_finite, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_overwrite_a, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_check_finite, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "state_space_cython.pyx":897 + /* "GPy/models/state_space_cython.pyx":901 * cdef np.ndarray[DTYPE_t, ndim=2] Vh * * U,S,Vh = sp.linalg.svd( P_init,full_matrices=False, compute_uv=True, # <<<<<<<<<<<<<< * overwrite_a=False,check_finite=True) * S[ (S==0) ] = 1e-17 # allows to run algorithm for singular initial variance */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -19309,7 +19316,7 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -19325,17 +19332,17 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __Pyx_INCREF(__pyx_t_5); __Pyx_INCREF(__pyx_t_4); #else - __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); #endif __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } else { Py_ssize_t index = -1; - __pyx_t_1 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_14 = Py_TYPE(__pyx_t_1)->tp_iternext; @@ -19345,7 +19352,7 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __Pyx_GOTREF(__pyx_t_5); index = 2; __pyx_t_4 = __pyx_t_14(__pyx_t_1); if (unlikely(!__pyx_t_4)) goto __pyx_L3_unpacking_failed; __Pyx_GOTREF(__pyx_t_4); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_1), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_1), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = NULL; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L4_unpacking_done; @@ -19353,20 +19360,20 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_14 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L4_unpacking_done:; } - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_time_series_no); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_time_series_no); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_int_1); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_int_1); @@ -19474,29 +19481,29 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; 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goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_8, __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_8, __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_1 = PyTuple_New(5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_v_M)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_M)); @@ -20341,14 +20748,14 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __Pyx_INCREF(((PyObject *)__pyx_v_grad_log_likelihood)); PyTuple_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_v_grad_log_likelihood)); __Pyx_GIVEREF(((PyObject *)__pyx_v_grad_log_likelihood)); - PyTuple_SET_ITEM(__pyx_t_1, 4, __pyx_t_26); - __Pyx_GIVEREF(__pyx_t_26); - __pyx_t_26 = 0; + PyTuple_SET_ITEM(__pyx_t_1, 4, __pyx_t_5); + __Pyx_GIVEREF(__pyx_t_5); + __pyx_t_5 = 0; __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "state_space_cython.pyx":871 + /* "GPy/models/state_space_cython.pyx":875 * * @cython.boundscheck(False) * def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython p_dynamic_callables, # <<<<<<<<<<<<<< @@ -20364,8 +20771,8 @@ static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cy __Pyx_XDECREF(__pyx_t_5); 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} -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -20491,7 +20898,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -20504,7 +20911,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -20513,7 +20920,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__110, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -20653,7 +21060,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -20662,7 +21069,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -20672,7 +21079,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -20681,7 +21088,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); 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__pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -20710,7 +21117,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -20723,7 +21130,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -20732,7 +21139,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -20743,7 +21150,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -20752,7 +21159,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -20761,7 +21168,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -20770,7 +21177,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -20779,7 +21186,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -20791,7 +21198,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -20800,7 +21207,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -20818,7 +21225,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -20834,7 +21241,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< @@ -20849,7 +21256,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -20859,7 +21266,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -20869,7 +21276,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -20889,7 +21296,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -20907,21 +21314,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L19_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__110, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__111, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -20930,7 +21337,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ switch (__pyx_v_t) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -20941,7 +21348,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -20952,7 +21359,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -20963,7 +21370,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -20974,7 +21381,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -20985,7 +21392,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -20996,7 +21403,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -21007,7 +21414,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -21018,7 +21425,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -21029,7 +21436,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -21040,7 +21447,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -21051,7 +21458,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -21062,7 +21469,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -21073,7 +21480,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -21084,7 +21491,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -21095,7 +21502,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -21106,7 +21513,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -21118,7 +21525,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -21144,7 +21551,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -21153,7 +21560,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -21165,7 +21572,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -21174,7 +21581,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = ((char *)malloc(255)); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -21183,7 +21590,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -21192,7 +21599,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -21202,7 +21609,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_7; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -21212,7 +21619,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -21244,7 +21651,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -21268,7 +21675,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -21278,7 +21685,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< @@ -21290,7 +21697,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s } __pyx_L3:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -21300,7 +21707,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":295 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":295 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< @@ -21312,7 +21719,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s } __pyx_L4:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -21324,7 +21731,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -21341,7 +21748,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":772 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":772 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -21355,7 +21762,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -21374,7 +21781,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -21391,7 +21798,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":775 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":775 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -21405,7 +21812,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -21424,7 +21831,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -21441,7 +21848,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< @@ -21455,7 +21862,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -21474,7 +21881,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -21491,7 +21898,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":781 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":781 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< @@ -21505,7 +21912,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -21524,7 +21931,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; 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- /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -21574,7 +21981,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -21606,7 +22013,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_util_dtypestring", 0); 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- /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -21719,21 +22126,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (__pyx_t_6) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__111, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__112, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -21753,7 +22160,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -21771,21 +22178,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_L7_bool_binop_done:; if (__pyx_t_6) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__112, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__113, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -21801,7 +22208,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -21810,7 +22217,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 120; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -21819,7 +22226,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -21830,7 +22237,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -21840,7 +22247,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -21850,7 +22257,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -21862,7 +22269,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":825 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":825 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -21872,21 +22279,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_6) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__113, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__114, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -21904,7 +22311,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -21922,7 +22329,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -21940,7 +22347,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -21958,7 +22365,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -21976,7 +22383,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -21994,7 +22401,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -22012,7 +22419,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -22030,7 +22437,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -22048,7 +22455,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -22066,7 +22473,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -22084,7 +22491,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -22102,7 +22509,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -22120,7 +22527,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -22140,7 +22547,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":843 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":843 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -22160,7 +22567,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -22180,7 +22587,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -22199,7 +22606,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":847 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":847 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -22222,7 +22629,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":848 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":848 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -22234,7 +22641,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":852 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":852 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -22246,7 +22653,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -22256,7 +22663,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -22266,7 +22673,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -22291,7 +22698,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -22306,7 +22713,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -22317,7 +22724,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -22329,7 +22736,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -22338,7 +22745,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":975 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":975 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -22349,7 +22756,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -22358,7 +22765,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -22367,7 +22774,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -22379,7 +22786,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 +/* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -22393,7 +22800,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -22403,7 +22810,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":981 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":981 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -22417,7 +22824,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py } /*else*/ { - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":983 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":983 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -22428,7 +22835,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -22442,10 +22849,10 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __Pyx_RefNannyFinishContext(); return __pyx_r; } -static struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { - struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *p; +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *p; PyObject *o; if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { o = (*t->tp_alloc)(t, 0); @@ -22453,12 +22860,12 @@ static PyObject *__pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(PyTy o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); } if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *)o); - p->__pyx_vtab = __pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *)o); + p->__pyx_vtab = __pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; return o; } -static void __pyx_tp_dealloc_18state_space_cython_Dynamic_Callables_Cython(PyObject *o) { +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython(PyObject *o) { #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -22467,23 +22874,23 @@ static void __pyx_tp_dealloc_18state_space_cython_Dynamic_Callables_Cython(PyObj (*Py_TYPE(o)->tp_free)(o); } -static PyMethodDef __pyx_methods_18state_space_cython_Dynamic_Callables_Cython[] = { - {"f_a", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_1f_a, METH_VARARGS|METH_KEYWORDS, 0}, - {"Ak", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_3Ak, METH_VARARGS|METH_KEYWORDS, 0}, - {"Qk", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_5Qk, METH_O, 0}, - {"Q_srk", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk, METH_O, 0}, - {"dAk", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_9dAk, METH_O, 0}, - {"dQk", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_11dQk, METH_O, 0}, - {"reset", (PyCFunction)__pyx_pw_18state_space_cython_24Dynamic_Callables_Cython_13reset, METH_VARARGS|METH_KEYWORDS, 0}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython[] = { + {"f_a", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_1f_a, METH_VARARGS|METH_KEYWORDS, 0}, + {"Ak", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_3Ak, METH_VARARGS|METH_KEYWORDS, 0}, + {"Qk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_5Qk, METH_O, 0}, + {"Q_srk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_7Q_srk, METH_O, 0}, + {"dAk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_9dAk, METH_O, 0}, + {"dQk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_11dQk, METH_O, 0}, + {"reset", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_13reset, METH_VARARGS|METH_KEYWORDS, 0}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_Dynamic_Callables_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.Dynamic_Callables_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.Dynamic_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_Dynamic_Callables_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -22510,7 +22917,7 @@ static PyTypeObject __pyx_type_18state_space_cython_Dynamic_Callables_Cython = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_Dynamic_Callables_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -22520,7 +22927,7 @@ static PyTypeObject __pyx_type_18state_space_cython_Dynamic_Callables_Cython = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -22534,10 +22941,10 @@ static PyTypeObject __pyx_type_18state_space_cython_Dynamic_Callables_Cython = { 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython __pyx_vtable_18state_space_cython_Measurement_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_Measurement_Callables_Cython(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { - struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *p; +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Measurement_Callables_Cython(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *p; PyObject *o; if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { o = (*t->tp_alloc)(t, 0); @@ -22545,12 +22952,12 @@ static PyObject *__pyx_tp_new_18state_space_cython_Measurement_Callables_Cython( o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); } if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *)o); - p->__pyx_vtab = __pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *)o); + p->__pyx_vtab = __pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; return o; } -static void __pyx_tp_dealloc_18state_space_cython_Measurement_Callables_Cython(PyObject *o) { +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Measurement_Callables_Cython(PyObject *o) { #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -22559,23 +22966,23 @@ static void __pyx_tp_dealloc_18state_space_cython_Measurement_Callables_Cython(P (*Py_TYPE(o)->tp_free)(o); } -static PyMethodDef __pyx_methods_18state_space_cython_Measurement_Callables_Cython[] = { - {"f_h", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_1f_h, METH_VARARGS|METH_KEYWORDS, 0}, - {"Hk", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_3Hk, METH_VARARGS|METH_KEYWORDS, 0}, - {"Rk", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_5Rk, METH_O, 0}, - {"R_isrk", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_7R_isrk, METH_O, 0}, - {"dHk", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_9dHk, METH_O, 0}, - {"dRk", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_11dRk, METH_O, 0}, - {"reset", (PyCFunction)__pyx_pw_18state_space_cython_28Measurement_Callables_Cython_13reset, METH_VARARGS|METH_KEYWORDS, 0}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_Measurement_Callables_Cython[] = { + {"f_h", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_1f_h, METH_VARARGS|METH_KEYWORDS, 0}, + {"Hk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_3Hk, METH_VARARGS|METH_KEYWORDS, 0}, + {"Rk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_5Rk, METH_O, 0}, + {"R_isrk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_7R_isrk, METH_O, 0}, + {"dHk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_9dHk, METH_O, 0}, + {"dRk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_11dRk, METH_O, 0}, + {"reset", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_13reset, METH_VARARGS|METH_KEYWORDS, 0}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_Measurement_Callables_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.Measurement_Callables_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.Measurement_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_Measurement_Callables_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Measurement_Callables_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -22602,7 +23009,7 @@ static PyTypeObject __pyx_type_18state_space_cython_Measurement_Callables_Cython 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_Measurement_Callables_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_Measurement_Callables_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -22612,7 +23019,7 @@ static PyTypeObject __pyx_type_18state_space_cython_Measurement_Callables_Cython 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_Measurement_Callables_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_Measurement_Callables_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -22626,14 +23033,14 @@ static PyTypeObject __pyx_type_18state_space_cython_Measurement_Callables_Cython 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython __pyx_vtable_18state_space_cython_R_handling_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_R_handling_Cython __pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_R_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_18state_space_cython_R_handling_Cython *p; - PyObject *o = __pyx_tp_new_18state_space_cython_Measurement_Callables_Cython(t, a, k); +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_R_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *p; + PyObject *o = __pyx_tp_new_3GPy_6models_18state_space_cython_Measurement_Callables_Cython(t, a, k); if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_R_handling_Cython *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython*)__pyx_vtabptr_18state_space_cython_R_handling_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython*)__pyx_vtabptr_3GPy_6models_18state_space_cython_R_handling_Cython; p->R = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->index = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->dR = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); @@ -22641,8 +23048,8 @@ static PyObject *__pyx_tp_new_18state_space_cython_R_handling_Cython(PyTypeObjec return o; } -static void __pyx_tp_dealloc_18state_space_cython_R_handling_Cython(PyObject *o) { - struct __pyx_obj_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_18state_space_cython_R_handling_Cython *)o; +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_R_handling_Cython(PyObject *o) { + struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *)o; #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -22657,13 +23064,13 @@ static void __pyx_tp_dealloc_18state_space_cython_R_handling_Cython(PyObject *o) if (PyType_IS_GC(Py_TYPE(o)->tp_base)) #endif PyObject_GC_Track(o); - __pyx_tp_dealloc_18state_space_cython_Measurement_Callables_Cython(o); + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Measurement_Callables_Cython(o); } -static int __pyx_tp_traverse_18state_space_cython_R_handling_Cython(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_3GPy_6models_18state_space_cython_R_handling_Cython(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_18state_space_cython_R_handling_Cython *)o; - e = ((likely(__pyx_ptype_18state_space_cython_Measurement_Callables_Cython)) ? ((__pyx_ptype_18state_space_cython_Measurement_Callables_Cython->tp_traverse) ? __pyx_ptype_18state_space_cython_Measurement_Callables_Cython->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_18state_space_cython_R_handling_Cython)); if (e) return e; + struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *)o; + e = ((likely(__pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython)) ? ((__pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython->tp_traverse) ? __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_3GPy_6models_18state_space_cython_R_handling_Cython)); if (e) return e; if (p->R) { e = (*v)(((PyObject*)p->R), a); if (e) return e; } @@ -22679,10 +23086,10 @@ static int __pyx_tp_traverse_18state_space_cython_R_handling_Cython(PyObject *o, return 0; } -static int __pyx_tp_clear_18state_space_cython_R_handling_Cython(PyObject *o) { +static int __pyx_tp_clear_3GPy_6models_18state_space_cython_R_handling_Cython(PyObject *o) { PyObject* tmp; - struct __pyx_obj_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_18state_space_cython_R_handling_Cython *)o; - if (likely(__pyx_ptype_18state_space_cython_Measurement_Callables_Cython)) { if (__pyx_ptype_18state_space_cython_Measurement_Callables_Cython->tp_clear) __pyx_ptype_18state_space_cython_Measurement_Callables_Cython->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_18state_space_cython_R_handling_Cython); + struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython *)o; + if (likely(__pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython)) { if (__pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython->tp_clear) __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_3GPy_6models_18state_space_cython_R_handling_Cython); tmp = ((PyObject*)p->R); p->R = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -22698,19 +23105,19 @@ static int __pyx_tp_clear_18state_space_cython_R_handling_Cython(PyObject *o) { return 0; } -static PyMethodDef __pyx_methods_18state_space_cython_R_handling_Cython[] = { - {"Rk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_3Rk, METH_O, 0}, - {"dRk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_5dRk, METH_O, 0}, - {"R_isrk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_7R_isrk, METH_O, __pyx_doc_18state_space_cython_17R_handling_Cython_6R_isrk}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_R_handling_Cython[] = { + {"Rk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_3Rk, METH_O, 0}, + {"dRk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_5dRk, METH_O, 0}, + {"R_isrk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_7R_isrk, METH_O, __pyx_doc_3GPy_6models_18state_space_cython_17R_handling_Cython_6R_isrk}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_R_handling_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.R_handling_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_R_handling_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.R_handling_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_R_handling_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_R_handling_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_R_handling_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -22731,13 +23138,13 @@ static PyTypeObject __pyx_type_18state_space_cython_R_handling_Cython = { 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ "\n The calss handles noise matrix R.\n ", /*tp_doc*/ - __pyx_tp_traverse_18state_space_cython_R_handling_Cython, /*tp_traverse*/ - __pyx_tp_clear_18state_space_cython_R_handling_Cython, /*tp_clear*/ + __pyx_tp_traverse_3GPy_6models_18state_space_cython_R_handling_Cython, /*tp_traverse*/ + __pyx_tp_clear_3GPy_6models_18state_space_cython_R_handling_Cython, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_R_handling_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_R_handling_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -22745,9 +23152,9 @@ static PyTypeObject __pyx_type_18state_space_cython_R_handling_Cython = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__, /*tp_init*/ + __pyx_pw_3GPy_6models_18state_space_cython_17R_handling_Cython_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_R_handling_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_R_handling_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -22761,21 +23168,21 @@ static PyTypeObject __pyx_type_18state_space_cython_R_handling_Cython = { 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cython __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython __pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_Std_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p; - PyObject *o = __pyx_tp_new_18state_space_cython_R_handling_Cython(t, a, k); +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *p; + PyObject *o = __pyx_tp_new_3GPy_6models_18state_space_cython_R_handling_Cython(t, a, k); if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o); - p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython*)__pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)o); + p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Measurement_Callables_Cython*)__pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; p->H = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->dH = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); return o; } -static void __pyx_tp_dealloc_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o) { - struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o; +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)o; #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -22785,13 +23192,13 @@ static void __pyx_tp_dealloc_18state_space_cython_Std_Measurement_Callables_Cyth Py_CLEAR(p->H); Py_CLEAR(p->dH); PyObject_GC_Track(o); - __pyx_tp_dealloc_18state_space_cython_R_handling_Cython(o); + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_R_handling_Cython(o); } -static int __pyx_tp_traverse_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o; - e = __pyx_tp_traverse_18state_space_cython_R_handling_Cython(o, v, a); if (e) return e; + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)o; + e = __pyx_tp_traverse_3GPy_6models_18state_space_cython_R_handling_Cython(o, v, a); if (e) return e; if (p->H) { e = (*v)(((PyObject*)p->H), a); if (e) return e; } @@ -22801,10 +23208,10 @@ static int __pyx_tp_traverse_18state_space_cython_Std_Measurement_Callables_Cyth return 0; } -static int __pyx_tp_clear_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o) { +static int __pyx_tp_clear_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o) { PyObject* tmp; - struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o; - __pyx_tp_clear_18state_space_cython_R_handling_Cython(o); + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython *)o; + __pyx_tp_clear_3GPy_6models_18state_space_cython_R_handling_Cython(o); tmp = ((PyObject*)p->H); p->H = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -22814,19 +23221,19 @@ static int __pyx_tp_clear_18state_space_cython_Std_Measurement_Callables_Cython( return 0; } -static PyMethodDef __pyx_methods_18state_space_cython_Std_Measurement_Callables_Cython[] = { - {"f_h", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h}, - {"Hk", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk}, - {"dHk", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk, METH_O, 0}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython[] = { + {"f_h", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h}, + {"Hk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk}, + {"dHk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk, METH_O, 0}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.Std_Measurement_Callables_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.Std_Measurement_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -22847,13 +23254,13 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Measurement_Callables_Cy 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_traverse*/ - __pyx_tp_clear_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_clear*/ + __pyx_tp_traverse_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_traverse*/ + __pyx_tp_clear_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -22861,9 +23268,9 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Measurement_Callables_Cy 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__, /*tp_init*/ + __pyx_pw_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -22877,14 +23284,14 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Measurement_Callables_Cy 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_vtable_18state_space_cython_Q_handling_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Q_handling_Cython __pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_18state_space_cython_Q_handling_Cython *p; - PyObject *o = __pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(t, a, k); +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *p; + PyObject *o = __pyx_tp_new_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython(t, a, k); if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_Q_handling_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython; p->Q = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->index = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->dQ = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); @@ -22892,8 +23299,8 @@ static PyObject *__pyx_tp_new_18state_space_cython_Q_handling_Cython(PyTypeObjec return o; } -static void __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(PyObject *o) { - struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Q_handling_Cython(PyObject *o) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)o; #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -22908,13 +23315,13 @@ static void __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(PyObject *o) if (PyType_IS_GC(Py_TYPE(o)->tp_base)) #endif PyObject_GC_Track(o); - __pyx_tp_dealloc_18state_space_cython_Dynamic_Callables_Cython(o); + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython(o); } -static int __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_3GPy_6models_18state_space_cython_Q_handling_Cython(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; - e = ((likely(__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython)) ? ((__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_traverse) ? __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_18state_space_cython_Q_handling_Cython)); if (e) return e; + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)o; + e = ((likely(__pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython)) ? ((__pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython->tp_traverse) ? __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_3GPy_6models_18state_space_cython_Q_handling_Cython)); if (e) return e; if (p->Q) { e = (*v)(((PyObject*)p->Q), a); if (e) return e; } @@ -22930,10 +23337,10 @@ static int __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(PyObject *o, return 0; } -static int __pyx_tp_clear_18state_space_cython_Q_handling_Cython(PyObject *o) { +static int __pyx_tp_clear_3GPy_6models_18state_space_cython_Q_handling_Cython(PyObject *o) { PyObject* tmp; - struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; - if (likely(__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython)) { if (__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_clear) __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_18state_space_cython_Q_handling_Cython); + struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython *)o; + if (likely(__pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython)) { if (__pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython->tp_clear) __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_3GPy_6models_18state_space_cython_Q_handling_Cython); tmp = ((PyObject*)p->Q); p->Q = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -22949,19 +23356,19 @@ static int __pyx_tp_clear_18state_space_cython_Q_handling_Cython(PyObject *o) { return 0; } -static PyMethodDef __pyx_methods_18state_space_cython_Q_handling_Cython[] = { - {"Qk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_3Qk, METH_O, __pyx_doc_18state_space_cython_17Q_handling_Cython_2Qk}, - {"dQk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_5dQk, METH_O, 0}, - {"Q_srk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_7Q_srk, METH_O, __pyx_doc_18state_space_cython_17Q_handling_Cython_6Q_srk}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_Q_handling_Cython[] = { + {"Qk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_3Qk, METH_O, __pyx_doc_3GPy_6models_18state_space_cython_17Q_handling_Cython_2Qk}, + {"dQk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_5dQk, METH_O, 0}, + {"Q_srk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_7Q_srk, METH_O, __pyx_doc_3GPy_6models_18state_space_cython_17Q_handling_Cython_6Q_srk}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_Q_handling_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.Q_handling_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_Q_handling_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.Q_handling_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_Q_handling_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Q_handling_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -22982,13 +23389,13 @@ static PyTypeObject __pyx_type_18state_space_cython_Q_handling_Cython = { 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_18state_space_cython_Q_handling_Cython, /*tp_traverse*/ - __pyx_tp_clear_18state_space_cython_Q_handling_Cython, /*tp_clear*/ + __pyx_tp_traverse_3GPy_6models_18state_space_cython_Q_handling_Cython, /*tp_traverse*/ + __pyx_tp_clear_3GPy_6models_18state_space_cython_Q_handling_Cython, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_Q_handling_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_Q_handling_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -22996,9 +23403,9 @@ static PyTypeObject __pyx_type_18state_space_cython_Q_handling_Cython = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__, /*tp_init*/ + __pyx_pw_3GPy_6models_18state_space_cython_17Q_handling_Cython_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_Q_handling_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_Q_handling_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23012,21 +23419,21 @@ static PyTypeObject __pyx_type_18state_space_cython_Q_handling_Cython = { 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p; - PyObject *o = __pyx_tp_new_18state_space_cython_Q_handling_Cython(t, a, k); +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *p; + PyObject *o = __pyx_tp_new_3GPy_6models_18state_space_cython_Q_handling_Cython(t, a, k); if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o); - p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)o); + p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; p->A = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->dA = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); return o; } -static void __pyx_tp_dealloc_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { - struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)o; #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -23036,13 +23443,13 @@ static void __pyx_tp_dealloc_18state_space_cython_Std_Dynamic_Callables_Cython(P Py_CLEAR(p->A); Py_CLEAR(p->dA); PyObject_GC_Track(o); - __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(o); + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Q_handling_Cython(o); } -static int __pyx_tp_traverse_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; - e = __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)o; + e = __pyx_tp_traverse_3GPy_6models_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; if (p->A) { e = (*v)(((PyObject*)p->A), a); if (e) return e; } @@ -23052,10 +23459,10 @@ static int __pyx_tp_traverse_18state_space_cython_Std_Dynamic_Callables_Cython(P return 0; } -static int __pyx_tp_clear_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { +static int __pyx_tp_clear_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { PyObject* tmp; - struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; - __pyx_tp_clear_18state_space_cython_Q_handling_Cython(o); + struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython *)o; + __pyx_tp_clear_3GPy_6models_18state_space_cython_Q_handling_Cython(o); tmp = ((PyObject*)p->A); p->A = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -23065,20 +23472,20 @@ static int __pyx_tp_clear_18state_space_cython_Std_Dynamic_Callables_Cython(PyOb return 0; } -static PyMethodDef __pyx_methods_18state_space_cython_Std_Dynamic_Callables_Cython[] = { - {"f_a", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a}, - {"Ak", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak}, - {"dAk", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk, METH_O, 0}, - {"reset", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython[] = { + {"f_a", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a}, + {"Ak", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak}, + {"dAk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk, METH_O, 0}, + {"reset", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.Std_Dynamic_Callables_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.Std_Dynamic_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23099,13 +23506,13 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_traverse*/ - __pyx_tp_clear_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_clear*/ + __pyx_tp_traverse_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_traverse*/ + __pyx_tp_clear_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23113,9 +23520,9 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__, /*tp_init*/ + __pyx_pw_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23129,14 +23536,14 @@ static PyTypeObject __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython 0, /*tp_finalize*/ #endif }; -static struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython __pyx_vtable_18state_space_cython_AQcompute_batch_Cython; +static struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_AQcompute_batch_Cython __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; -static PyObject *__pyx_tp_new_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p; - PyObject *o = __pyx_tp_new_18state_space_cython_Q_handling_Cython(t, a, k); +static PyObject *__pyx_tp_new_3GPy_6models_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *p; + PyObject *o = __pyx_tp_new_3GPy_6models_18state_space_cython_Q_handling_Cython(t, a, k); if (unlikely(!o)) return 0; - p = ((struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o); - p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython; + p = ((struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)o); + p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; p->As = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->Qs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); p->dAs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); @@ -23146,8 +23553,8 @@ static PyObject *__pyx_tp_new_18state_space_cython_AQcompute_batch_Cython(PyType return o; } -static void __pyx_tp_dealloc_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { - struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; +static void __pyx_tp_dealloc_3GPy_6models_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { + struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)o; #if PY_VERSION_HEX >= 0x030400a1 if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; @@ -23161,13 +23568,13 @@ static void __pyx_tp_dealloc_18state_space_cython_AQcompute_batch_Cython(PyObjec Py_CLEAR(p->reconstruct_indices); Py_CLEAR(p->Q_svd_dict); PyObject_GC_Track(o); - __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(o); + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_Q_handling_Cython(o); } -static int __pyx_tp_traverse_18state_space_cython_AQcompute_batch_Cython(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_3GPy_6models_18state_space_cython_AQcompute_batch_Cython(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; - e = __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; + struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)o; + e = __pyx_tp_traverse_3GPy_6models_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; if (p->As) { e = (*v)(((PyObject*)p->As), a); if (e) return e; } @@ -23189,10 +23596,10 @@ static int __pyx_tp_traverse_18state_space_cython_AQcompute_batch_Cython(PyObjec return 0; } -static int __pyx_tp_clear_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { +static int __pyx_tp_clear_3GPy_6models_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { PyObject* tmp; - struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; - __pyx_tp_clear_18state_space_cython_Q_handling_Cython(o); + struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython *)o; + __pyx_tp_clear_3GPy_6models_18state_space_cython_Q_handling_Cython(o); tmp = ((PyObject*)p->As); p->As = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -23214,23 +23621,23 @@ static int __pyx_tp_clear_18state_space_cython_AQcompute_batch_Cython(PyObject * return 0; } -static PyMethodDef __pyx_methods_18state_space_cython_AQcompute_batch_Cython[] = { - {"f_a", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_2f_a}, - {"reset", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_4reset}, - {"Ak", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_7Ak, METH_VARARGS|METH_KEYWORDS, 0}, - {"Qk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_9Qk, METH_O, 0}, - {"dAk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_11dAk, METH_O, 0}, - {"dQk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_13dQk, METH_O, 0}, - {"Q_srk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_15Q_srk, METH_O, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_14Q_srk}, +static PyMethodDef __pyx_methods_3GPy_6models_18state_space_cython_AQcompute_batch_Cython[] = { + {"f_a", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_2f_a}, + {"reset", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_5reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_4reset}, + {"Ak", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_7Ak, METH_VARARGS|METH_KEYWORDS, 0}, + {"Qk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_9Qk, METH_O, 0}, + {"dAk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_11dAk, METH_O, 0}, + {"dQk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_13dQk, METH_O, 0}, + {"Q_srk", (PyCFunction)__pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_15Q_srk, METH_O, __pyx_doc_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_14Q_srk}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_type_18state_space_cython_AQcompute_batch_Cython = { +static PyTypeObject __pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython = { PyVarObject_HEAD_INIT(0, 0) - "state_space_cython.AQcompute_batch_Cython", /*tp_name*/ - sizeof(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython), /*tp_basicsize*/ + "GPy.models.state_space_cython.AQcompute_batch_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_3GPy_6models_18state_space_cython_AQcompute_batch_Cython), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_18state_space_cython_AQcompute_batch_Cython, /*tp_dealloc*/ + __pyx_tp_dealloc_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23251,13 +23658,13 @@ static PyTypeObject __pyx_type_18state_space_cython_AQcompute_batch_Cython = { 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ "\n Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter\n from the matrices F, L, Qc, P_ing, dF, dQc, dP_inf of the continuos state\n equation. dt - time steps. \n \n It has the same interface as AQcompute_once.\n \n It computes matrices for all time steps. This object is used when\n there are not so many (controlled by internal variable) \n different time steps and storing all the matrices do not take too much memory.\n \n Since all the matrices are computed all together, this object can be used\n in smoother without repeating the computations. \n ", /*tp_doc*/ - __pyx_tp_traverse_18state_space_cython_AQcompute_batch_Cython, /*tp_traverse*/ - __pyx_tp_clear_18state_space_cython_AQcompute_batch_Cython, /*tp_clear*/ + __pyx_tp_traverse_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, /*tp_traverse*/ + __pyx_tp_clear_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_18state_space_cython_AQcompute_batch_Cython, /*tp_methods*/ + __pyx_methods_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23265,9 +23672,9 @@ static PyTypeObject __pyx_type_18state_space_cython_AQcompute_batch_Cython = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_18state_space_cython_22AQcompute_batch_Cython_1__init__, /*tp_init*/ + __pyx_pw_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_18state_space_cython_AQcompute_batch_Cython, /*tp_new*/ + __pyx_tp_new_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23313,6 +23720,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_DTYPE_int, __pyx_k_DTYPE_int, sizeof(__pyx_k_DTYPE_int), 0, 0, 1, 1}, {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, + {&__pyx_n_s_GPy_models_state_space_cython, __pyx_k_GPy_models_state_space_cython, sizeof(__pyx_k_GPy_models_state_space_cython), 0, 0, 1, 1}, {&__pyx_n_s_H, __pyx_k_H, sizeof(__pyx_k_H), 0, 0, 1, 1}, {&__pyx_n_s_H_time_var_index, __pyx_k_H_time_var_index, sizeof(__pyx_k_H_time_var_index), 0, 0, 1, 1}, {&__pyx_n_s_Hk, __pyx_k_Hk, sizeof(__pyx_k_Hk), 0, 0, 1, 1}, @@ -23320,6 +23728,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Kalman_Filter_Update_SVD_S_is_ne, __pyx_k_Kalman_Filter_Update_SVD_S_is_ne, sizeof(__pyx_k_Kalman_Filter_Update_SVD_S_is_ne), 0, 0, 1, 0}, {&__pyx_n_s_M, __pyx_k_M, sizeof(__pyx_k_M), 0, 0, 1, 1}, {&__pyx_kp_s_Measurement_dimension_larger_the, __pyx_k_Measurement_dimension_larger_the, sizeof(__pyx_k_Measurement_dimension_larger_the), 0, 0, 1, 0}, + {&__pyx_kp_s_Nan_measurements_are_currently_n, __pyx_k_Nan_measurements_are_currently_n, sizeof(__pyx_k_Nan_measurements_are_currently_n), 0, 0, 1, 0}, {&__pyx_kp_s_Nan_values_in_likelihood_update, __pyx_k_Nan_values_in_likelihood_update, sizeof(__pyx_k_Nan_values_in_likelihood_update), 0, 0, 1, 0}, {&__pyx_kp_u_Non_native_byte_order_not_suppor, __pyx_k_Non_native_byte_order_not_suppor, sizeof(__pyx_k_Non_native_byte_order_not_suppor), 0, 1, 0, 0}, {&__pyx_n_s_NotImplemented, __pyx_k_NotImplemented, sizeof(__pyx_k_NotImplemented), 0, 0, 1, 1}, @@ -23356,6 +23765,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_Vh, __pyx_k_Vh, sizeof(__pyx_k_Vh), 0, 0, 1, 1}, {&__pyx_n_s_X, __pyx_k_X, sizeof(__pyx_k_X), 0, 0, 1, 1}, {&__pyx_n_s_Y, __pyx_k_Y, sizeof(__pyx_k_Y), 0, 0, 1, 1}, + {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1}, {&__pyx_n_s_any, __pyx_k_any, sizeof(__pyx_k_any), 0, 0, 1, 1}, {&__pyx_n_s_axis, __pyx_k_axis, sizeof(__pyx_k_axis), 0, 0, 1, 1}, {&__pyx_n_s_calc_grad_log_likelihood, __pyx_k_calc_grad_log_likelihood, sizeof(__pyx_k_calc_grad_log_likelihood), 0, 0, 1, 1}, @@ -23465,7 +23875,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_sp, __pyx_k_sp, sizeof(__pyx_k_sp), 0, 0, 1, 1}, {&__pyx_n_s_sqrt, __pyx_k_sqrt, sizeof(__pyx_k_sqrt), 0, 0, 1, 1}, {&__pyx_n_s_state_dim, __pyx_k_state_dim, sizeof(__pyx_k_state_dim), 0, 0, 1, 1}, - {&__pyx_n_s_state_space_cython, __pyx_k_state_space_cython, sizeof(__pyx_k_state_space_cython), 0, 0, 1, 1}, {&__pyx_n_s_steps_no, __pyx_k_steps_no, sizeof(__pyx_k_steps_no), 0, 0, 1, 1}, {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1}, {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1}, @@ -23490,10 +23899,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {0, 0, 0, 0, 0, 0, 0} }; 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if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_s_cython_f_a_is_not_implemented); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "state_space_cython.pyx":22 + /* "GPy/models/state_space_cython.pyx":26 * * cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix * raise NotImplemented("(cython) Ak is not implemented!") # <<<<<<<<<<<<<< * * cpdef Qk(self, int k): */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_cython_Ak_is_not_implemented); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_cython_Ak_is_not_implemented); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_tuple__119)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__119); + __Pyx_GIVEREF(__pyx_tuple__119); + __pyx_codeobj__120 = (PyObject*)__Pyx_PyCode_New(13, 0, 35, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__119, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_users_agrigori_SpiderOak_sp_hiv, __pyx_n_s_cont_discr_kalman_filter_raw_Cy, 875, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -24441,14 +24861,14 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif - if (__pyx_module_is_main_state_space_cython) { + if (__pyx_module_is_main_GPy__models__state_space_cython) { if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } #if PY_MAJOR_VERSION >= 3 { PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!PyDict_GetItemString(modules, "state_space_cython")) { - if (unlikely(PyDict_SetItemString(modules, "state_space_cython", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "GPy.models.state_space_cython")) { + if (unlikely(PyDict_SetItemString(modules, "GPy.models.state_space_cython", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif @@ -24460,122 +24880,122 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - __pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython = &__pyx_vtable_18state_space_cython_Dynamic_Callables_Cython; 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- __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.dAk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk; - __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.dQk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk; - __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset; - if (PyType_Ready(&__pyx_type_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_Dynamic_Callables_Cython.tp_print = 0; 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- __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.Hk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk; - __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.Rk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk; - __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.R_isrk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_R_isrk; - __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.dHk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dHk; - __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.dRk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dRk; - __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_reset; - if (PyType_Ready(&__pyx_type_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_Measurement_Callables_Cython.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "Measurement_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_Measurement_Callables_Cython = &__pyx_type_18state_space_cython_Measurement_Callables_Cython; - __pyx_vtabptr_18state_space_cython_R_handling_Cython = &__pyx_vtable_18state_space_cython_R_handling_Cython; - __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython; - __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.Rk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_Rk; - __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.R_isrk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk; - __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.dRk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_dRk; - __pyx_type_18state_space_cython_R_handling_Cython.tp_base = __pyx_ptype_18state_space_cython_Measurement_Callables_Cython; - if (PyType_Ready(&__pyx_type_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_R_handling_Cython.tp_print = 0; + __pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.f_a = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_f_a; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.Ak = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Ak; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.Qk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Qk; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.Q_srk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_Q_srk; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.dAk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dAk; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.dQk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_dQk; + __pyx_vtable_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Dynamic_Callables_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython = &__pyx_type_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.f_h = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_f_h; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.Hk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Hk; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.Rk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_Rk; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.R_isrk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_R_isrk; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.dHk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_dHk; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.dRk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_dRk; + __pyx_vtable_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args))__pyx_f_3GPy_6models_18state_space_cython_28Measurement_Callables_Cython_reset; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Measurement_Callables_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython = &__pyx_type_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_R_handling_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython.__pyx_base = *__pyx_vtabptr_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython.__pyx_base.Rk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_Rk; + __pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython.__pyx_base.R_isrk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_R_isrk; + __pyx_vtable_3GPy_6models_18state_space_cython_R_handling_Cython.__pyx_base.dRk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17R_handling_Cython_dRk; + __pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython.tp_base = __pyx_ptype_3GPy_6models_18state_space_cython_Measurement_Callables_Cython; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython.tp_print = 0; #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_18state_space_cython_R_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__.doc = __pyx_doc_18state_space_cython_17R_handling_Cython___init__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__; + __pyx_wrapperbase_3GPy_6models_18state_space_cython_17R_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_3GPy_6models_18state_space_cython_17R_handling_Cython___init__.doc = __pyx_doc_3GPy_6models_18state_space_cython_17R_handling_Cython___init__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_3GPy_6models_18state_space_cython_17R_handling_Cython___init__; } } #endif - if (__Pyx_SetVtable(__pyx_type_18state_space_cython_R_handling_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "R_handling_Cython", (PyObject *)&__pyx_type_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_R_handling_Cython = &__pyx_type_18state_space_cython_R_handling_Cython; - __pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython; - __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_R_handling_Cython; - __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.f_h = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_f_h; - __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.Hk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk; - __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.dHk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_dHk; - __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_base = __pyx_ptype_18state_space_cython_R_handling_Cython; - if (PyType_Ready(&__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "Std_Measurement_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython; - __pyx_vtabptr_18state_space_cython_Q_handling_Cython = &__pyx_vtable_18state_space_cython_Q_handling_Cython; - __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython; - __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.Qk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_Qk; - __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.Q_srk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk; - __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.dQk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_dQk; - __pyx_type_18state_space_cython_Q_handling_Cython.tp_base = __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython; - if (PyType_Ready(&__pyx_type_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_Q_handling_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "R_handling_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_R_handling_Cython = &__pyx_type_3GPy_6models_18state_space_cython_R_handling_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base = *__pyx_vtabptr_3GPy_6models_18state_space_cython_R_handling_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.f_h = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_f_h; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.Hk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_Hk; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.dHk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_32Std_Measurement_Callables_Cython_dHk; + __pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.tp_base = __pyx_ptype_3GPy_6models_18state_space_cython_R_handling_Cython; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Std_Measurement_Callables_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_type_3GPy_6models_18state_space_cython_Std_Measurement_Callables_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython.__pyx_base = *__pyx_vtabptr_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython.__pyx_base.Qk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_Qk; + __pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython.__pyx_base.Q_srk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_Q_srk; + __pyx_vtable_3GPy_6models_18state_space_cython_Q_handling_Cython.__pyx_base.dQk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_17Q_handling_Cython_dQk; + __pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython.tp_base = __pyx_ptype_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython.tp_print = 0; #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_18state_space_cython_Q_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__.doc = __pyx_doc_18state_space_cython_17Q_handling_Cython___init__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__; + __pyx_wrapperbase_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__.doc = __pyx_doc_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_3GPy_6models_18state_space_cython_17Q_handling_Cython___init__; } } #endif - if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Q_handling_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "Q_handling_Cython", (PyObject *)&__pyx_type_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_Q_handling_Cython = &__pyx_type_18state_space_cython_Q_handling_Cython; - __pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython = &__pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython; - __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Q_handling_Cython; - __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.f_a = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a; - __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.Ak = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak; - __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.dAk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk; - __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_reset; - __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython.tp_base = __pyx_ptype_18state_space_cython_Q_handling_Cython; - if (PyType_Ready(&__pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "Std_Dynamic_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_Std_Dynamic_Callables_Cython = &__pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython; - __pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython = &__pyx_vtable_18state_space_cython_AQcompute_batch_Cython; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Q_handling_Cython; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.f_a = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Ak = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Qk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Qk; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Q_srk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Q_srk; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.dAk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dAk; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.dQk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dQk; - __pyx_vtable_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset; - __pyx_type_18state_space_cython_AQcompute_batch_Cython.tp_base = __pyx_ptype_18state_space_cython_Q_handling_Cython; - if (PyType_Ready(&__pyx_type_18state_space_cython_AQcompute_batch_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_18state_space_cython_AQcompute_batch_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Q_handling_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_Q_handling_Cython = &__pyx_type_3GPy_6models_18state_space_cython_Q_handling_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base = *__pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.f_a = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.Ak = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.dAk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk; + __pyx_vtable_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.__pyx_base.__pyx_base.reset = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_3GPy_6models_18state_space_cython_28Std_Dynamic_Callables_Cython_reset; + __pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.tp_base = __pyx_ptype_3GPy_6models_18state_space_cython_Q_handling_Cython; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Std_Dynamic_Callables_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython = &__pyx_type_3GPy_6models_18state_space_cython_Std_Dynamic_Callables_Cython; + __pyx_vtabptr_3GPy_6models_18state_space_cython_AQcompute_batch_Cython = &__pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base = *__pyx_vtabptr_3GPy_6models_18state_space_cython_Q_handling_Cython; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.f_a = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_f_a; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Ak = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Ak; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Qk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Qk; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.Q_srk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_Q_srk; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.dAk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_dAk; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.dQk = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_dQk; + __pyx_vtable_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.__pyx_base.__pyx_base.reset = (PyObject *(*)(struct __pyx_obj_3GPy_6models_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_3GPy_6models_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_3GPy_6models_18state_space_cython_22AQcompute_batch_Cython_reset; + __pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.tp_base = __pyx_ptype_3GPy_6models_18state_space_cython_Q_handling_Cython; + if (PyType_Ready(&__pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.tp_print = 0; #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_18state_space_cython_AQcompute_batch_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_18state_space_cython_22AQcompute_batch_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; 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__pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_18state_space_cython_AQcompute_batch_Cython = &__pyx_type_18state_space_cython_AQcompute_batch_Cython; + if (__Pyx_SetVtable(__pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython.tp_dict, __pyx_vtabptr_3GPy_6models_18state_space_cython_AQcompute_batch_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "AQcompute_batch_Cython", (PyObject *)&__pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_3GPy_6models_18state_space_cython_AQcompute_batch_Cython = &__pyx_type_3GPy_6models_18state_space_cython_AQcompute_batch_Cython; /*--- Type import code ---*/ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", #if CYTHON_COMPILING_IN_PYPY @@ -24593,7 +25013,7 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) /*--- Function import code ---*/ /*--- Execution code ---*/ - /* "state_space_cython.pyx":5 + /* "GPy/models/state_space_cython.pyx":5 * Contains some cython code for state space modelling. * """ * import numpy as np # <<<<<<<<<<<<<< @@ -24605,7 +25025,7 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_int64); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_int64); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE_int, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE_int, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":506 + /* "GPy/models/state_space_cython.pyx":510 * * @cython.boundscheck(False) * def _kalman_prediction_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m , tuple p_P, # <<<<<<<<<<<<<< * Dynamic_Callables_Cython p_dynamic_callables, * bint calc_grad_log_likelihood=False, */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_18state_space_cython_1_kalman_prediction_step_SVD_Cython, NULL, __pyx_n_s_state_space_cython); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3GPy_6models_18state_space_cython_1_kalman_prediction_step_SVD_Cython, NULL, __pyx_n_s_GPy_models_state_space_cython); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_kalman_prediction_step_SVD_Cyth, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3GPy_6models_18state_space_cython_5_cont_discr_kalman_filter_raw_Cython, NULL, __pyx_n_s_GPy_models_state_space_cython); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_cont_discr_kalman_filter_raw_Cy, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_cont_discr_kalman_filter_raw_Cy, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "state_space_cython.pyx":1 + /* "GPy/models/state_space_cython.pyx":1 * # -*- coding: utf-8 -*- # <<<<<<<<<<<<<< * """ * Contains some cython code for state space modelling. @@ -24693,7 +25113,7 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 + /* "../../../../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -24709,11 +25129,11 @@ PyMODINIT_FUNC PyInit_state_space_cython(void) __Pyx_XDECREF(__pyx_t_2); if (__pyx_m) { if (__pyx_d) { - __Pyx_AddTraceback("init state_space_cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init GPy.models.state_space_cython", __pyx_clineno, __pyx_lineno, __pyx_filename); } Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_ImportError, "init state_space_cython"); + PyErr_SetString(PyExc_ImportError, "init GPy.models.state_space_cython"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); diff --git a/GPy/models/state_space_cython.pyx b/GPy/models/state_space_cython.pyx index 877f7e7c..ae09d1cd 100644 --- a/GPy/models/state_space_cython.pyx +++ b/GPy/models/state_space_cython.pyx @@ -7,6 +7,10 @@ cimport numpy as np import scipy as sp cimport cython +#from libc.math cimport isnan # for nan checking in kalman filter cycle +cdef extern from "numpy/npy_math.h": + bint npy_isnan(double x) + DTYPE = np.float64 DTYPE_int = np.int64 @@ -913,6 +917,8 @@ def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython cdef np.ndarray[DTYPE_t, ndim=3] dm_pred, dP_pred cdef np.ndarray[DTYPE_t, ndim=2] log_likelihood_update, d_log_likelihood_update cdef int k + + #print "Hi I am cython" for k in range(0,steps_no): # In this loop index for new estimations is (k+1), old - (k) # This happened because initial values are stored at 0-th index. @@ -925,16 +931,27 @@ def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython calc_grad_log_likelihood, dm_upd, dP_upd) k_measurment = Y[k,:,:] - + if (np.any(np.isnan(k_measurment)) == False): # if np.any(np.isnan(k_measurment)): # raise ValueError("Nan measurements are currently not supported") - m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - _kalman_update_step_SVD_Cython(k, m_pred , P_pred, p_measurement_callables, - k_measurment, calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred) - + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + _kalman_update_step_SVD_Cython(k, m_pred , P_pred, p_measurement_callables, + k_measurment, calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred) + else: + if not np.all(np.isnan(k_measurment)): + raise ValueError("""Nan measurements are currently not supported if + they are intermixed with not NaN measurements""") + else: + m_upd = m_pred; P_upd = P_pred; dm_upd = dm_pred; dP_upd = dP_pred + if calc_log_likelihood: + log_likelihood_update = np.zeros((1,time_series_no)) + if calc_grad_log_likelihood: + d_log_likelihood_update = np.zeros((grad_params_no,time_series_no)) + + if calc_log_likelihood: log_likelihood += log_likelihood_update diff --git a/GPy/models/state_space_main.py b/GPy/models/state_space_main.py index f8320f63..461922d6 100644 --- a/GPy/models/state_space_main.py +++ b/GPy/models/state_space_main.py @@ -12,21 +12,37 @@ import numpy as np import scipy as sp import scipy.linalg as linalg + +#import pdb; pdb.set_trace() + +try: + import state_space_setup + setup_available = True +except ImportError as e: + setup_available = False + + print_verbose = False try: import state_space_cython cython_code_available = True - print("state_space: cython is available") + if print_verbose: + print("state_space: cython is available") except ImportError as e: cython_code_available = False - #cython_code_available = False -if cython_code_available: - print("state_space: cython is used") -else: - print("state_space: cython is NOT used") +# Use cython by default +use_cython = False +if setup_available: + use_cython = state_space_setup.use_cython + +if print_verbose: + if use_cython: + print("state_space: cython is used") + else: + print("state_space: cython is NOT used") class Dynamic_Callables_Python(object): @@ -88,7 +104,7 @@ class Dynamic_Callables_Python(object): raise NotImplemented("reset is not implemented!") -if cython_code_available: +if use_cython: Dynamic_Callables_Class = state_space_cython.Dynamic_Callables_Cython else: Dynamic_Callables_Class = Dynamic_Callables_Python @@ -157,7 +173,7 @@ class Measurement_Callables_Python(object): raise NotImplemented("reset is not implemented!") -if cython_code_available: +if use_cython: Measurement_Callables_Class = state_space_cython.Measurement_Callables_Cython else: Measurement_Callables_Class = Measurement_Callables_Python @@ -241,7 +257,7 @@ class R_handling_Python(Measurement_Callables_Class): return inv_square_root -if cython_code_available: +if use_cython: R_handling_Class = state_space_cython.R_handling_Cython else: R_handling_Class = R_handling_Python @@ -281,7 +297,7 @@ class Std_Measurement_Callables_Python(R_handling_Class): return self.dH # the same dirivative on each iteration -if cython_code_available: +if use_cython: Std_Measurement_Callables_Class = state_space_cython.Std_Measurement_Callables_Cython else: Std_Measurement_Callables_Class = Std_Measurement_Callables_Python @@ -374,7 +390,7 @@ class Q_handling_Python(Dynamic_Callables_Class): return square_root -if cython_code_available: +if use_cython: Q_handling_Class = state_space_cython.Q_handling_Cython else: Q_handling_Class = Q_handling_Python @@ -382,7 +398,7 @@ else: class Std_Dynamic_Callables_Python(Q_handling_Class): def __init__(self, A, A_time_var_index, Q, index, Q_time_var_index, unique_Q_number, dA = None, dQ=None): - super(Std_Measurement_Callables_Python,self).__init__(Q, index, Q_time_var_index, unique_Q_number,dQ) + super(Std_Dynamic_Callables_Python,self).__init__(Q, index, Q_time_var_index, unique_Q_number,dQ) self.A = A self.A_time_var_index = A_time_var_index @@ -414,8 +430,15 @@ class Std_Dynamic_Callables_Python(Q_handling_Class): raise ValueError("dA derivative is None") return self.dA # the same dirivative on each iteration - -if cython_code_available: + + def reset(self,compute_derivatives = False): + """ + Return the state of this object to the beginning of iteration (to k eq. 0) + """ + + return self + +if use_cython: Std_Dynamic_Callables_Class = state_space_cython.Std_Dynamic_Callables_Cython else: Std_Dynamic_Callables_Class = Std_Dynamic_Callables_Python @@ -460,7 +483,7 @@ class DescreteStateSpaceMeta(type): After thos method the class object is created """ - if cython_code_available: + if use_cython: if '_kalman_prediction_step_SVD' in attributes: attributes['_kalman_prediction_step_SVD'] = AddMethodToClass(state_space_cython._kalman_prediction_step_SVD_Cython) @@ -542,7 +565,8 @@ class DescreteStateSpace(object): @classmethod def kalman_filter(cls,p_A, p_Q, p_H, p_R, Y, index = None, m_init=None, - P_init=None, calc_log_likelihood=False, + P_init=None, p_kalman_filter_type='regular', + calc_log_likelihood=False, calc_grad_log_likelihood=False, grad_params_no=None, grad_calc_params=None): """ @@ -670,7 +694,9 @@ class DescreteStateSpace(object): use in smoother for convenience. They are: 'p_a', 'p_f_A', 'p_f_Q' The dictionary contains the same fields. """ - + + #import pdb; pdb.set_trace() + # Parameters checking -> # index p_A = np.atleast_1d(p_A) @@ -735,6 +761,9 @@ class DescreteStateSpace(object): P_init = np.eye(state_dim) elif not isinstance(P_init, collections.Iterable): #scalar P_init = P_init*np.eye(state_dim) + + if p_kalman_filter_type not in ('regular', 'svd'): + raise ValueError("Kalman filer type neither 'regular nor 'svd'.") # Functions to pass to the kalman_filter algorithm: # Parameters: @@ -745,7 +774,6 @@ class DescreteStateSpace(object): c_p_Q = p_A.copy() # create a copy because this object is passed to the smoother c_index = index.copy() # create a copy because this object is passed to the smoother - grad_calc_params_pass_further = None if calc_grad_log_likelihood: if model_matrices_chage_with_time: raise ValueError("When computing likelihood gradient A and Q can not change over time.") @@ -757,25 +785,32 @@ class DescreteStateSpace(object): dm_init = grad_calc_params.get('dm_init') if dm_init is None: + # multiple time series mode. Keep grad_params always as a last dimension dm_init = np.zeros((state_dim, time_series_no, grad_params_no)) dP_init = grad_calc_params.get('dP_init') if dP_init is None: dP_init = np.zeros((state_dim,state_dim,grad_params_no)) + else: + dA = None + dQ = None + dH = None + dR = None + dm_init = None + dP_init = None - grad_calc_params_pass_further = {} - grad_calc_params_pass_further['dm_init'] = dm_init - grad_calc_params_pass_further['dP_init'] = dP_init - dynamic_callables = Std_Dynamic_Callables_Class(c_p_A, A_time_var_index, c_p_Q, c_index, Q_time_var_index, 20, dA, dQ) measurement_callables = Std_Measurement_Callables_Class(p_H, H_time_var_index, p_R, index, R_time_var_index, 20, dH, dR) - (M, P,log_likelihood, grad_log_likelihood) = cls._kalman_algorithm_raw(state_dim, dynamic_callables, + (M, P,log_likelihood, grad_log_likelihood, dynamic_callables) = \ + cls._kalman_algorithm_raw(state_dim, dynamic_callables, measurement_callables, Y, m_init, - P_init, calc_log_likelihood=calc_log_likelihood, + P_init, p_kalman_filter_type = p_kalman_filter_type, + calc_log_likelihood=calc_log_likelihood, calc_grad_log_likelihood=calc_grad_log_likelihood, - grad_calc_params=grad_calc_params_pass_further) - + grad_params_no=grad_params_no, + dm_init=dm_init, dP_init=dP_init) + # restore shapes so that input parameters are unchenged if old_index_shape is not None: index.shape = old_index_shape @@ -968,8 +1003,10 @@ class DescreteStateSpace(object): @classmethod def _kalman_algorithm_raw(cls,state_dim, p_dynamic_callables, p_measurement_callables, Y, m_init, - P_init, calc_log_likelihood=False, - calc_grad_log_likelihood=False, grad_calc_params=None): + P_init, p_kalman_filter_type='regular', + calc_log_likelihood=False, + calc_grad_log_likelihood=False, grad_params_no=None, + dm_init=None, dP_init=None): """ General nonlinear filtering algorithm for inference in the state-space model: @@ -1040,6 +1077,9 @@ class DescreteStateSpace(object): "multiple time series mode" does not affect it, since it does not affect anything related to state variaces. + p_kalman_filter_type: string + + calc_log_likelihood: boolean Whether to calculate marginal likelihood of the state-space model. @@ -1081,19 +1121,21 @@ class DescreteStateSpace(object): steps_no = Y.shape[0] # number of steps in the Kalman Filter time_series_no = Y.shape[2] # multiple time series mode - if calc_grad_log_likelihood: - dm_init = grad_calc_params['dm_init']; dP_init = grad_calc_params['dP_init'] - else: - dm_init = None; dP_init = None - # Allocate space for results # Mean estimations. Initial values will be included M = np.empty(((steps_no+1),state_dim,time_series_no)) M[0,:,:] = m_init # Initialize mean values # Variance estimations. Initial values will be included P = np.empty(((steps_no+1),state_dim,state_dim)) + P_init = 0.5*( P_init + P_init.T) # symmetrize initial covariance. In some ustable cases this is uiseful P[0,:,:] = P_init # Initialize initial covariance matrix + if p_kalman_filter_type == 'svd': + (U,S,Vh) = sp.linalg.svd( P_init,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + S[ (S==0) ] = 1e-17 # allows to run algorithm for singular initial variance + P_upd = (P_init, S,U) + log_likelihood = 0 if calc_log_likelihood else None grad_log_likelihood = 0 if calc_grad_log_likelihood else None @@ -1107,21 +1149,63 @@ class DescreteStateSpace(object): prev_mean = M[k,:,:] # mean from the previous step - m_pred, P_pred, dm_pred, dP_pred = \ - cls._kalman_prediction_step(k, prev_mean ,P[k,:,:], p_dynamic_callables, - calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_upd, p_dP = dP_upd) + if p_kalman_filter_type == 'svd': + m_pred, P_pred, dm_pred, dP_pred = \ + cls._kalman_prediction_step_SVD(k, prev_mean ,P_upd, p_dynamic_callables, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_upd, p_dP = dP_upd) + else: + m_pred, P_pred, dm_pred, dP_pred = \ + cls._kalman_prediction_step(k, prev_mean ,P[k,:,:], p_dynamic_callables, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_upd, p_dP = dP_upd ) k_measurment = Y[k,:,:] - if np.any(np.isnan(k_measurment)): - raise ValueError("Nan measurements are currently not supported") + if (np.any(np.isnan(k_measurment)) == False): + if p_kalman_filter_type == 'svd': + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + cls._kalman_update_step_SVD(k, m_pred , P_pred, p_measurement_callables, + k_measurment, calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred ) + + + # m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + # cls._kalman_update_step(k, m_pred , P_pred[0], f_h, f_H, p_R.f_R, k_measurment, + # calc_log_likelihood=calc_log_likelihood, + # calc_grad_log_likelihood=calc_grad_log_likelihood, + # p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = (dH, dR)) + # + # (U,S,Vh) = sp.linalg.svd( P_upd,full_matrices=False, compute_uv=True, + # overwrite_a=False,check_finite=True) + # P_upd = (P_upd, S,U) + else: + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, + calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred ) + + else: +# if k_measurment.shape != (1,1): +# raise ValueError("Nan measurements are currently not supported for \ +# multidimensional output and multiple time series.") +# else: +# m_upd = m_pred; P_upd = P_pred; dm_upd = dm_pred; dP_upd = dP_pred +# log_likelihood_update = 0.0; +# d_log_likelihood_update = 0.0; + + if not np.all(np.isnan(k_measurment)): + raise ValueError("""Nan measurements are currently not supported if + they are intermixed with not NaN measurements""") + else: + m_upd = m_pred; P_upd = P_pred; dm_upd = dm_pred; dP_upd = dP_pred + if calc_log_likelihood: + log_likelihood_update = np.zeros((time_series_no,)) + if calc_grad_log_likelihood: + d_log_likelihood_update = np.zeros((grad_params_no,time_series_no)) - m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, - calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred) if calc_log_likelihood: log_likelihood += log_likelihood_update @@ -1131,7 +1215,10 @@ class DescreteStateSpace(object): M[k+1,:,:] = m_upd # separate mean value for each time series - P[k+1,:,:] = P_upd + if p_kalman_filter_type == 'svd': + P[k+1,:,:] = P_upd[0] + else: + P[k+1,:,:] = P_upd # !!!Print statistics! Print sizes of matrices # !!!Print statistics! Print iteration time base on another boolean variable @@ -1372,6 +1459,7 @@ class DescreteStateSpace(object): adds extra columns to the gradient. """ + #import pdb; pdb.set_trace() m_pred = p_m # from prediction step P_pred = p_P # from prediction step @@ -1596,19 +1684,27 @@ class DescreteStateSpace(object): S = H.dot(P_pred).dot(H.T) + R if measurement.shape[0]==1: # measurements are one dimensional if (S < 0): - raise ValueError("Kalman Filter Update SVD: S is negative step %i" % k ) - #import pdb; pdb.set_trace() + raise ValueError("Kalman Filter Update: S is negative step %i" % k ) + #import pdb; pdb.set_trace() K = P_pred.dot(H.T) / S if calc_log_likelihood: log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + - v*v / S) + v*v / S) + #log_likelihood_update = log_likelihood_update[0,0] # to make int if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. raise ValueError("Nan values in likelihood update!") LL = None; islower = None else: - raise ValueError("""Measurement dimension larger then 1 is currently not supported""") - + LL,islower = linalg.cho_factor(S) + K = linalg.cho_solve((LL,islower), H.dot(P_pred.T)).T + + if calc_log_likelihood: + log_likelihood_update = -0.5 * ( v.shape[0]*np.log(2*np.pi) + + 2*np.sum( np.log(np.diag(LL)) ) +\ + np.sum((linalg.cho_solve((LL,islower),v)) * v, axis = 0) ) # diagonal of v.T*S^{-1}*v + + # Old method of computing updated covariance (for testing) -> #P_upd_tst = K.dot(S).dot(K.T) #P_upd_tst = 0.5*(P_upd_tst + P_upd_tst.T) @@ -1816,7 +1912,7 @@ class DescreteStateSpace(object): p_m ,filter_covars[k,:,:], m_pred, P_pred, p_m_prev_step ,P[k+1,:,:], p_dynamic_callables) - M[k,:] = np.squeeze(m_upd) + M[k,:] = m_upd#np.squeeze(m_upd) P[k,:,:] = P_upd #G[k,:,:] = G_upd.T # store transposed G. # Return values @@ -2545,13 +2641,10 @@ class ContDescrStateSpace(DescreteStateSpace): raise ValueError("Only one dimensional X data is supported.") Y.shape, old_Y_shape = cls._reshape_input_data(Y.shape) # represent as column + state_dim = F.shape[0] measurement_dim = Y.shape[1] - - if len(Y.shape) == 2: - time_series_no = 1 # regular case - elif len(Y.shape) == 3: - time_series_no = Y.shape[2] # multiple time series mode + time_series_no = Y.shape[2] # multiple time series mode if ((len(p_H.shape) == 3) and (len(p_H.shape[2]) != 1)) or\ ((len(p_R.shape) == 3) and (len(p_R.shape[2]) != 1)): @@ -2592,8 +2685,6 @@ class ContDescrStateSpace(DescreteStateSpace): if P_init is None: P_init = P_inf.copy() - - if p_kalman_filter_type not in ('regular', 'svd'): raise ValueError("Kalman filer type neither 'regular nor 'svd'.") @@ -2608,8 +2699,8 @@ class ContDescrStateSpace(DescreteStateSpace): if calc_grad_log_likelihood: - dF = cls._check_grad_state_matrices( grad_calc_params.get('dF'), state_dim, grad_params_no, which = 'dA') - dQc = cls._check_grad_state_matrices( grad_calc_params.get('dQc'), state_dim, grad_params_no, which = 'dQ') + dF = cls._check_grad_state_matrices(grad_calc_params.get('dF'), state_dim, grad_params_no, which = 'dA') + dQc = cls._check_grad_state_matrices(grad_calc_params.get('dQc'), state_dim, grad_params_no, which = 'dQ') dP_inf = cls._check_grad_state_matrices(grad_calc_params.get('dP_inf'), state_dim, grad_params_no, which = 'dA') dH = cls._check_grad_measurement_matrices(grad_calc_params.get('dH'), state_dim, grad_params_no, measurement_dim, which = 'dH') @@ -2670,10 +2761,11 @@ class ContDescrStateSpace(DescreteStateSpace): @classmethod def _cont_discr_kalman_filter_raw(cls,state_dim, p_dynamic_callables, p_measurement_callables, X, Y, - m_init=None, P_init=None, + m_init, P_init, p_kalman_filter_type='regular', calc_log_likelihood=False, - calc_grad_log_likelihood=False, grad_params_no=None, dm_init=None, dP_init=None): + calc_grad_log_likelihood=False, grad_params_no=None, + dm_init=None, dP_init=None): """ General filtering algorithm for inference in the continuos-discrete state-space model: @@ -2772,7 +2864,7 @@ class ContDescrStateSpace(DescreteStateSpace): P_init = 0.5*( P_init + P_init.T) # symmetrize initial covariance. In some ustable cases this is uiseful P[0,:,:] = P_init # Initialize initial covariance matrix - #import pdb; pdb.set_trace() + #import pdb;pdb.set_trace() if p_kalman_filter_type == 'svd': (U,S,Vh) = sp.linalg.svd( P_init,full_matrices=False, compute_uv=True, overwrite_a=False,check_finite=True) @@ -2798,43 +2890,51 @@ class ContDescrStateSpace(DescreteStateSpace): m_pred, P_pred, dm_pred, dP_pred = \ cls._kalman_prediction_step_SVD(k, prev_mean ,P_upd, p_dynamic_callables, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_upd, p_dP = dP_upd ) + p_dm = dm_upd, p_dP = dP_upd) else: m_pred, P_pred, dm_pred, dP_pred = \ - cls._kalman_prediction_step(k, M[k,:] ,P[k,:,:], p_dynamic_callables, + cls._kalman_prediction_step(k, prev_mean ,P[k,:,:], p_dynamic_callables, calc_grad_log_likelihood=calc_grad_log_likelihood, p_dm = dm_upd, p_dP = dP_upd ) #import pdb; pdb.set_trace() k_measurment = Y[k,:,:] - if np.any(np.isnan(k_measurment)): - raise ValueError("Nan measurements are currently not supported") + if (np.any(np.isnan(k_measurment)) == False): - if p_kalman_filter_type == 'svd': - m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step_SVD(k, m_pred , P_pred, p_measurement_callables, - k_measurment, calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred ) - - -# m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ -# cls._kalman_update_step(k, m_pred , P_pred[0], f_h, f_H, p_R.f_R, k_measurment, -# calc_log_likelihood=calc_log_likelihood, -# calc_grad_log_likelihood=calc_grad_log_likelihood, -# p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = (dH, dR)) -# -# (U,S,Vh) = sp.linalg.svd( P_upd,full_matrices=False, compute_uv=True, -# overwrite_a=False,check_finite=True) -# P_upd = (P_upd, S,U) + if p_kalman_filter_type == 'svd': + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + cls._kalman_update_step_SVD(k, m_pred , P_pred, p_measurement_callables, + k_measurment, calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred ) + + + # m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + # cls._kalman_update_step(k, m_pred , P_pred[0], f_h, f_H, p_R.f_R, k_measurment, + # calc_log_likelihood=calc_log_likelihood, + # calc_grad_log_likelihood=calc_grad_log_likelihood, + # p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = (dH, dR)) + # + # (U,S,Vh) = sp.linalg.svd( P_upd,full_matrices=False, compute_uv=True, + # overwrite_a=False,check_finite=True) + # P_upd = (P_upd, S,U) + else: + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, + calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred ) else: - m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, - calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred ) - + if k_measurment.shape != (1,1): + raise ValueError("Nan measurements are currently not supported for \ + multidimensional output and multiple tiem series.") + else: + m_upd = m_pred; P_upd = P_pred; dm_upd = dm_pred; dP_upd = dP_pred + log_likelihood_update = 0.0; + d_log_likelihood_update = 0.0; + + if calc_log_likelihood: log_likelihood += log_likelihood_update @@ -2882,7 +2982,7 @@ class ContDescrStateSpace(DescreteStateSpace): A, Q, dA, dQ fro discrete model from the continuos model. X, F, L, Qc: matrices - If AQcomp thiese matrices are used to create this object from scratch. + If AQcomp is None, these matrices are used to create this object from scratch. Output: ------------- @@ -2973,7 +3073,7 @@ class ContDescrStateSpace(DescreteStateSpace): number_unique_indices = len(unique_indices) #import pdb; pdb.set_trace() - if cython_code_available: + if use_cython: class AQcompute_batch(state_space_cython.AQcompute_batch_Cython): def __init__(self, F,L,Qc,dt,compute_derivatives=False, grad_params_no=None, P_inf=None, dP_inf=None, dF = None, dQc=None): As, Qs, reconstruct_indices, dAs, dQs = ContDescrStateSpace.lti_sde_to_descrete(F, diff --git a/GPy/models/state_space_new.py b/GPy/models/state_space_model.py similarity index 94% rename from GPy/models/state_space_new.py rename to GPy/models/state_space_model.py index 324f8522..2a8ca1fd 100644 --- a/GPy/models/state_space_new.py +++ b/GPy/models/state_space_model.py @@ -29,9 +29,10 @@ import GPy from .. import likelihoods from . import state_space_main as ssm +from . import state_space_setup as ss_setup class StateSpace(Model): - def __init__(self, X, Y, kernel=None, noise_var=1.0, kalman_filter_type = 'regular', name='StateSpace'): + def __init__(self, X, Y, kernel=None, noise_var=1.0, kalman_filter_type = 'regular', use_cython = False, name='StateSpace'): super(StateSpace, self).__init__(name=name) self.num_data, input_dim = X.shape assert input_dim==1, "State space methods for time only" @@ -43,9 +44,15 @@ class StateSpace(Model): assert self.output_dim == 1, "State space methods for single outputs only" self.kalman_filter_type = kalman_filter_type - self.kalman_filter_type = 'svd' # temp test + #self.kalman_filter_type = 'svd' # temp test + ss_setup.use_cython = use_cython + #import pdb; pdb.set_trace() + global ssm + #from . import state_space_main as ssm + if (ssm.cython_code_available) and (ssm.use_cython != ss_setup.use_cython): + reload(ssm) # Make sure the observations are ordered in time sort_index = np.argsort(X[:,0]) self.X = X[sort_index] @@ -73,7 +80,7 @@ class StateSpace(Model): Parameters have now changed """ np.set_printoptions(16) - print(self.param_array) + #print(self.param_array) #import pdb; pdb.set_trace() # Get the model matrices from the kernel @@ -111,6 +118,10 @@ class StateSpace(Model): grad_calc_params['dP_init'] = dP0 kalman_filter_type = self.kalman_filter_type + +# if ss_use_cython: +# reload(ssm) +# from . import state_space_main as ssm (filter_means, filter_covs, log_likelihood, grad_log_likelihood,SmootherMatrObject) = ssm.ContDescrStateSpace.cont_discr_kalman_filter(F,L,Qc,H, @@ -123,10 +134,12 @@ class StateSpace(Model): #import pdb; pdb.set_trace() if np.any( np.isfinite(log_likelihood) == False): - import pdb; pdb.set_trace() + #import pdb; pdb.set_trace() + print("State-Space: NaN valkues in the log_likelihood") if np.any( np.isfinite(grad_log_likelihood) == False): - import pdb; pdb.set_trace() + #import pdb; pdb.set_trace() + print("State-Space: NaN valkues in the grad_log_likelihood") #print(grad_log_likelihood) grad_log_likelihood_sum = np.sum(grad_log_likelihood,axis=1) @@ -191,16 +204,14 @@ class StateSpace(Model): (F,L,Qc,H,P_inf, P0, dF,dQc,dP_inf,dP0) = self.kern.sde() state_dim = F.shape[0] - #import pdb; pdb.set_trace() #Y = self.Y[:, 0,0] # Run the Kalman filter #import pdb; pdb.set_trace() - kalman_filter_type = self.kalman_filter_type - (M, P, log_likelihood, + (M, P, log_likelihood, grad_log_likelihood,SmootherMatrObject) = ssm.ContDescrStateSpace.cont_discr_kalman_filter( - F,L,Qc,H,float(self.Gaussian_noise.variance),P_inf,self.X,Y,m_init=None, + F,L,Qc,H,float(self.Gaussian_noise.variance),P_inf,X,Y,m_init=None, P_init=P0, p_kalman_filter_type = kalman_filter_type, calc_log_likelihood=False, calc_grad_log_likelihood=False) diff --git a/GPy/models/state_space_setup.py b/GPy/models/state_space_setup.py new file mode 100644 index 00000000..d9b66a65 --- /dev/null +++ b/GPy/models/state_space_setup.py @@ -0,0 +1,8 @@ +# -*- coding: utf-8 -*- +""" +This module is intended for the setup of state_space_main module. +The need of this module appeared because of the way state_space_main module +connected with cython code. +""" + +use_cython = False \ No newline at end of file diff --git a/GPy/testing/gpy_kernels_state_space_tests.py b/GPy/testing/gpy_kernels_state_space_tests.py new file mode 100644 index 00000000..27cb90fe --- /dev/null +++ b/GPy/testing/gpy_kernels_state_space_tests.py @@ -0,0 +1,330 @@ +# -*- coding: utf-8 -*- +""" +Testing state space related functions. +""" +import unittest +import numpy as np +import GPy +import GPy.models.state_space_model as SS_model +from state_space_main_tests import generate_x_points, generate_sine_data, \ + generate_linear_data, generate_brownian_data, generate_linear_plus_sin + + +class StateSpaceKernelsTests(np.testing.TestCase): + def setUp(self): + pass + + def run_for_model(self, X, Y, ss_kernel, kalman_filter_type = 'regular', + use_cython=False, check_gradients=True, + optimize = True, predict_X=None, + compare_with_GP=True, gp_kernel=None, + mean_compare_decimal=10, var_compare_decimal=7): + + m1 = SS_model.StateSpace(X,Y, ss_kernel, + kalman_filter_type=kalman_filter_type, + use_cython=use_cython) + + if check_gradients: + self.assertTrue(m1.checkgrad()) + + #import pdb; pdb.set_trace() + + if optimize: + m1.optimize(optimizer='bfgs') + + if compare_with_GP and (predict_X is None): + predict_X = X + + if (predict_X is not None): + x_pred_reg_1 = m1.predict(predict_X) + x_quant_reg_1 = m1.predict_quantiles(predict_X) + + if compare_with_GP: + m2 = GPy.models.GPRegression(X,Y, gp_kernel) + m2.optimize(optimizer='bfgs') + #print(m2) + + x_pred_reg_2 = m2.predict(predict_X) + x_quant_reg_2 = m2.predict_quantiles(predict_X) + + # Test values + #print np.max(np.abs(x_pred_reg_1[0]-x_pred_reg_2[0])) + np.testing.assert_almost_equal(np.max(np.abs(x_pred_reg_1[0]- \ + x_pred_reg_2[0])), 0, decimal=mean_compare_decimal) + + # Test variances + #print np.max(np.abs(x_pred_reg_1[1]-x_pred_reg_2[1])) + + np.testing.assert_almost_equal(np.max(np.abs(x_pred_reg_1[1]- \ + x_pred_reg_2[1])), 0, decimal=var_compare_decimal) + + def test_Matern32_kernel(self,): + np.random.seed(234) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Matern32(1,active_dims=[0,]) + gp_kernel = GPy.kern.Matern32(1,active_dims=[0,]) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + compare_with_GP=True, + gp_kernel=gp_kernel, + mean_compare_decimal=10, var_compare_decimal=7) + + def test_Matern52_kernel(self,): + np.random.seed(234) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Matern52(1,active_dims=[0,]) + gp_kernel = GPy.kern.Matern52(1,active_dims=[0,]) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + optimize = True, predict_X=X, + compare_with_GP=True, gp_kernel=gp_kernel, + mean_compare_decimal=8, var_compare_decimal=7) + + def test_RBF_kernel(self,): + np.random.seed(234) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_RBF(1,active_dims=[0,]) + gp_kernel = GPy.kern.RBF(1,active_dims=[0,]) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=1, var_compare_decimal=1) + + def test_periodic_kernel(self,): + np.random.seed(322) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel.lengthscales.constrain_bounded(0.25, 1000) + ss_kernel.wavelengths.constrain_bounded(0.15, 100) + + gp_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel.lengthscales.constrain_bounded(0.25, 1000) + gp_kernel.wavelengths.constrain_bounded(0.15, 100) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=4, var_compare_decimal=4) + + def test_quasi_periodic_kernel(self,): + np.random.seed(329) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Matern32(1)*GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + gp_kernel = GPy.kern.Matern32(1)*GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=1, var_compare_decimal=2) + + def test_linear_kernel(self,): + + np.random.seed(234) # seed the random number generator + (X,Y) = generate_linear_data(x_points=None, tangent=2.0, add_term=20.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + GPy.kern.sde_Bias(1, active_dims=[0,]) + gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + + self.run_for_model(X, Y, ss_kernel, check_gradients= False, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=5, var_compare_decimal=5) + + def test_brownian_kernel(self,): + np.random.seed(234) # seed the random number generator + (X,Y) = generate_brownian_data(x_points=None, kernel_var=2.0, noise_var = 0.1, + plot = False, points_num=50, x_interval = (0, 20), random=True) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Brownian() + gp_kernel = GPy.kern.Brownian() + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=10, var_compare_decimal=7) + + def test_exponential_kernel(self,): + np.random.seed(234) # seed the random number generator + (X,Y) = generate_linear_data(x_points=None, tangent=1.0, add_term=20.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + ss_kernel = GPy.kern.sde_Exponential(1, active_dims=[0,]) + gp_kernel = GPy.kern.Exponential(1, active_dims=[0,]) + + self.run_for_model(X, Y, ss_kernel, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=5, var_compare_decimal=6) + + def test_kernel_addition(self,): + np.random.seed(329) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + def get_new_kernels(): + ss_kernel = GPy.kern.sde_Matern32(1) + GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + gp_kernel = GPy.kern.Matern32(1) + GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + return ss_kernel, gp_kernel + + # Cython is available only with svd. + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', + use_cython=True, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=0, var_compare_decimal=-1) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'regular', + use_cython=False, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=4, var_compare_decimal=3) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', + use_cython=False, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=0, var_compare_decimal=-1) + + + + def test_kernel_multiplication(self,): + np.random.seed(329) # seed the random number generator + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=50, x_interval = (0, 20), random=True) + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + + def get_new_kernels(): + ss_kernel = GPy.kern.sde_Matern32(1)*GPy.kern.sde_Matern52(1) + gp_kernel = GPy.kern.Matern32(1)*GPy.kern.sde_Matern52(1) + + return ss_kernel, gp_kernel + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', + use_cython=True, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=-1, var_compare_decimal=0) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'regular', + use_cython=False, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=-1, var_compare_decimal=0) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X, Y, ss_kernel, kalman_filter_type = 'svd', + use_cython=False, check_gradients=True, + predict_X=X, + gp_kernel=gp_kernel, + mean_compare_decimal=-1, var_compare_decimal=0) + + def test_forecast(self,): + """ + Test time series forecaasting. + """ + + # Generate data -> + np.random.seed(339) # seed the random number generator + #import pdb; pdb.set_trace() + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=5.0, noise_var=2.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + (X1,Y1) = generate_linear_data(x_points=X, tangent=1.0, add_term=20.0, noise_var=0.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + Y = Y + Y1 + + X_train = X[X <= 20] + Y_train = Y[X <= 20] + X_test = X[X > 20] + Y_test = Y[X > 20] + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + X_train.shape = (X_train.shape[0],1); Y_train.shape = (Y_train.shape[0],1) + X_test.shape = (X_test.shape[0],1); Y_test.shape = (Y_test.shape[0],1) + # Generate data <- + + #import pdb; pdb.set_trace() + + def get_new_kernels(): + periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel + gp_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ + GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel + + ss_kernel.std_periodic.lengthscales.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.wavelengths.constrain_bounded(0.15, 100) + + return ss_kernel, gp_kernel + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'regular', + use_cython=False, check_gradients=True, + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=0, var_compare_decimal=0) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', + use_cython=False, check_gradients=False, + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=0, var_compare_decimal=-1) + + ss_kernel, gp_kernel = get_new_kernels() + self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', + use_cython=True, check_gradients=False, + predict_X=X_test, + gp_kernel=gp_kernel, + mean_compare_decimal=0, var_compare_decimal=-1) + +if __name__ == "__main__": + print("Running state-space inference tests...") + unittest.main() \ No newline at end of file diff --git a/GPy/testing/state_space_main_tests.py b/GPy/testing/state_space_main_tests.py new file mode 100644 index 00000000..1eb1f9a5 --- /dev/null +++ b/GPy/testing/state_space_main_tests.py @@ -0,0 +1,975 @@ +# -*- coding: utf-8 -*- +""" +Test module for state_space_main.py +""" + +import unittest +import numpy as np +import matplotlib.pyplot as plt +from scipy.stats import norm + +import GPy.models.state_space_setup as ss_setup +import GPy.models.state_space_main as ssm + +def generate_x_points(points_num=100, x_interval = (0, 20), random=True): + """ + Function generates (sorted) points on the x axis. + + Input: + --------------------------- + points_num: int + How many points to generate + x_interval: tuple (a,b) + On which interval to generate points + random: bool + Regular points or random + + Output: + --------------------------- + x_points: np.array + Generated points + """ + + x_interval = np.asarray( x_interval ) + + if random: + x_points = np.random.rand(points_num) * ( x_interval[1] - x_interval[0] ) + x_interval[0] + x_points = np.sort( x_points ) + else: + x_points = np.linspace(x_interval[0], x_interval[1], num=points_num ) + + return x_points + +def generate_sine_data(x_points=None, sin_period=2.0, sin_ampl=10.0, noise_var=2.0, + plot = False, points_num=100, x_interval = (0, 20), random=True): + """ + Function generates sinusoidal data. + + Input: + -------------------------------- + + x_points: np.array + Previously generated X points + sin_period: float + Sine period + sin_ampl: float + Sine amplitude + noise_var: float + Gaussian noise variance added to the sine function + plot: bool + Whether to plot generated data + + (if x_points is None, the the following parameters are used to generate + those. They are the same as in 'generate_x_points' function) + + points_num: int + + x_interval: tuple (a,b) + + random: bool + """ + + sin_function = lambda xx: sin_ampl * np.sin( 2*np.pi/sin_period * xx ) + + if x_points is None: + x_points = generate_x_points(points_num, x_interval, random) + + y_points = sin_function( x_points ) + np.random.randn( len(x_points) ) * np.sqrt(noise_var) + + if plot: + pass + + return x_points, y_points + +def generate_linear_data(x_points=None, tangent=2.0, add_term=1.0, noise_var=2.0, + plot = False, points_num=100, x_interval = (0, 20), random=True): + """ + Function generates linear data. + + Input: + -------------------------------- + + x_points: np.array + Previously generated X points + tangent: float + Factor with which independent variable is multiplied in linear equation. + add_term: float + Additive term in linear equation. + noise_var: float + Gaussian noise variance added to the sine function + plot: bool + Whether to plot generated data + + (if x_points is None, the the following parameters are used to generate + those. They are the same as in 'generate_x_points' function) + + points_num: int + + x_interval: tuple (a,b) + + random: bool + """ + + linear_function = lambda xx: tangent*xx + add_term + + if x_points is None: + x_points = generate_x_points(points_num, x_interval, random) + + y_points = linear_function( x_points ) + np.random.randn( len(x_points) ) * np.sqrt(noise_var) + + if plot: + pass + + return x_points, y_points + +def generate_brownian_data(x_points=None, kernel_var = 2.0, noise_var = 2.0, + plot = False, points_num=100, x_interval = (0, 20), random=True): + """ + Generate brownian data - data from Brownian motion. + First point is always 0, and \Beta(0) = 0 - standard conditions for Brownian motion. + + Input: + -------------------------------- + + x_points: np.array + Previously generated X points + variance: float + Gaussian noise variance added to the sine function + plot: bool + Whether to plot generated data + + (if x_points is None, the the following parameters are used to generate + those. They are the same as in 'generate_x_points' function) + + points_num: int + + x_interval: tuple (a,b) + + random: bool + + """ + if x_points is None: + x_points = generate_x_points(points_num, x_interval, random) + if x_points[0] != 0: + x_points[0] = 0 + + y_points = np.zeros( (points_num,) ) + for i in range(1, points_num): + noise = np.random.randn() * np.sqrt(kernel_var * (x_points[i] - x_points[i-1])) + y_points[i] = y_points[i-1] + noise + + y_points += np.random.randn( len(x_points) ) * np.sqrt(noise_var) + + return x_points, y_points + +def generate_linear_plus_sin(x_points=None, tangent=2.0, add_term=1.0, noise_var=2.0, + sin_period=2.0, sin_ampl=10.0, plot = False, + points_num=100, x_interval = (0, 20), random=True): + """ + Generate the sum of linear trend and the sine function. + + For parameters see the 'generate_linear' and 'generate_sine'. + + Comment: Gaussian noise variance is added only once (for linear function). + """ + + x_points, y_linear_points = generate_linear_data(x_points, tangent, add_term, noise_var, + False, points_num, x_interval, random) + + x_points, y_sine_points = generate_sine_data(x_points, sin_period, sin_ampl, 0.0, + False, points_num, x_interval, random) + + y_points = y_linear_points + y_sine_points + + if plot: + pass + + return x_points, y_points + +def generate_random_y_data(samples, dim, ts_no): + """ + Generate data: + + Input: + ------------------ + + samples - how many samples + dim - dimensionality of the data + ts_no - number of time series + + Output: + -------------------------- + Y: np.array((samples, dim, ts_no)) + """ + + Y = np.empty((samples, dim, ts_no)); + + for i in range(0,samples): + for j in range(0,ts_no): + sample = np.random.randn(dim) + Y[i,:,j] = sample + + if (Y.shape[2] == 1): # ts_no = 1 + Y.shape=(Y.shape[0], Y.shape[1]) + return Y + + +class StateSpaceKernelsTests(np.testing.TestCase): + def setUp(self): + pass + + def run_descr_model(self, measurements, A,Q,H,R, true_states=None, + mean_compare_decimal=8, + m_init=None, P_init=None, dA=None,dQ=None, + dH=None,dR=None, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True): + + #import pdb; pdb.set_trace() + + state_dim = 1 if not isinstance(A,np.ndarray) else A.shape[0] + ts_no = 1 if (len(measurements.shape) < 3) else measurements.shape[2] + grad_params_no = None if dA is None else dA.shape[2] + + + ss_setup.use_cython = use_cython + global ssm + if (ssm.cython_code_available) and (ssm.use_cython != use_cython): + reload(ssm) + + grad_calc_params = None + if calc_grad_log_likelihood: + grad_calc_params = {} + grad_calc_params['dA'] = dA + grad_calc_params['dQ'] = dQ + grad_calc_params['dH'] = dH + grad_calc_params['dR'] = dR + + (f_mean, f_var, loglikelhood, g_loglikelhood, \ + dynamic_callables_smoother) = ssm.DescreteStateSpace.kalman_filter(A, Q, H, R, measurements, index=None, + m_init=m_init, P_init=P_init, p_kalman_filter_type = kalman_filter_type, + calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + grad_params_no=grad_params_no, + grad_calc_params=grad_calc_params) + + f_mean_squeezed = np.squeeze(f_mean[1:,:]) # exclude initial value + f_var_squeezed = np.squeeze(f_var[1:,:]) # exclude initial value + + if true_states is not None: + #print np.max(np.abs(f_mean_squeezed-true_states)) + np.testing.assert_almost_equal(np.max(np.abs(f_mean_squeezed- \ + true_states)), 0, decimal=mean_compare_decimal) + + np.testing.assert_equal(f_mean.shape, (measurements.shape[0]+1,state_dim,ts_no) ) + np.testing.assert_equal(f_var.shape, (measurements.shape[0]+1,state_dim,state_dim) ) + + (M_smooth, P_smooth) = ssm.DescreteStateSpace.rts_smoother(state_dim, dynamic_callables_smoother, f_mean, + f_var) + + return f_mean, f_var + + def run_continuous_model(self, F, L, Qc, p_H, p_R, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=None, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=0, grad_calc_params=None): + + #import pdb; pdb.set_trace() + + state_dim = 1 if not isinstance(F,np.ndarray) else F.shape[0] + ts_no = 1 if (len(Y_data.shape) < 3) else Y_data.shape[2] + + ss_setup.use_cython = use_cython + global ssm + if (ssm.cython_code_available) and (ssm.use_cython != use_cython): + reload(ssm) + + (f_mean, f_var, loglikelhood, g_loglikelhood, \ + dynamic_callables_smoother) = ssm.ContDescrStateSpace.cont_discr_kalman_filter(F, L, Qc, p_H, p_R, + P_inf, X_data, Y_data, index = None, + m_init=None, P_init=None, + p_kalman_filter_type='regular', + calc_log_likelihood=False, + calc_grad_log_likelihood=False, + grad_params_no=0, grad_calc_params=grad_calc_params) + + f_mean_squeezed = np.squeeze(f_mean[1:,:]) # exclude initial value + f_var_squeezed = np.squeeze(f_var[1:,:]) # exclude initial value + + np.testing.assert_equal(f_mean.shape, (Y_data.shape[0]+1,state_dim,ts_no)) + np.testing.assert_equal(f_var.shape, (Y_data.shape[0]+1,state_dim,state_dim)) + + (M_smooth, P_smooth) = ssm.ContDescrStateSpace.cont_discr_rts_smoother(state_dim, f_mean, \ + f_var,dynamic_callables_smoother) + + return f_mean, f_var + + def test_discrete_ss_first(self,plot=False): + """ + Tests discrete State-Space model with different data dimensions. + """ + np.random.seed(235) # seed the random number generator + + A = 1.0 # For cython code to run properly need float input + H = 1.0 + Q = 1.0 + R = 1.0 + + steps_num = 100 + + # generate data -> + true_states = np.zeros((steps_num,)) + init_state = 0 + measurements = np.zeros((steps_num,)) + + for s in range(0, steps_num): + if s== 0: + true_states[0] = init_state + np.sqrt(Q)*np.random.randn() + else: + true_states[s] = true_states[s-1] + np.sqrt(R)*np.random.randn() + measurements[s] = true_states[s] + np.sqrt(R)*np.random.randn() + # generate data <- + + # descrete kalman filter -> + m_init = 0; P_init = 1 + d_num = 1000 + state_discr = np.linspace(-10,10,d_num) + + state_trans_matrix = np.empty((d_num,d_num)) + for i in range(d_num): + state_trans_matrix[:,i] = norm.pdf(state_discr, loc=A*state_discr[i], scale=np.sqrt(Q)) + + m_prev = norm.pdf(state_discr, loc = m_init, scale = np.sqrt(P_init)); #m_prev / np.sum(m_prev) + m = np.zeros((d_num, steps_num)) + i_mean = np.zeros((steps_num,)) + + for s in range(0, steps_num): + # Prediction step: + if (s==0): + m[:,s] = np.dot(state_trans_matrix, m_prev) + else: + m[:,s] = np.dot(state_trans_matrix, m[:,s-1]) + # Update step: + #meas_ind = np.argmin(np.abs(state_discr - measurements[s]) + y_vec = np.zeros( (d_num,)) + for i in range(d_num): + y_vec[i] = norm.pdf(measurements[s], loc=H*state_discr[i], scale=np.sqrt(R)) + norm_const = np.dot( y_vec, m[:,s] ) + m[:,s] = y_vec * m[:,s] / norm_const + + i_mean[s] = state_discr[ np.argmax(m[:,s]) ] + # descrete kalman filter <- + + (f_mean, f_var) = self.run_descr_model(measurements, A,Q,H,R, true_states=i_mean, + mean_compare_decimal=1, + m_init=m_init, P_init=P_init,use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=False) + + (f_mean, f_var) = self.run_descr_model(measurements, A,Q,H,R, true_states=i_mean, + mean_compare_decimal=1, + m_init=m_init, P_init=P_init,use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=False) + + (f_mean, f_var) = self.run_descr_model(measurements, A,Q,H,R, true_states=i_mean, + mean_compare_decimal=1, + m_init=m_init, P_init=P_init,use_cython=True, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=False) + + if plot: + # plotting -> + plt.figure() + plt.plot( true_states, 'g.-',label='true states') + #plt.plot( measurements, 'b.-', label='measurements') + plt.plot( f_mean, 'r.-',label='Kalman filter estimates') + plt.plot( i_mean, 'k.-', label='Discretization') + + plt.plot( f_mean + 2*np.sqrt(f_var), 'r.--') + plt.plot( f_mean - 2*np.sqrt(f_var), 'r.--') + plt.legend() + plt.show() + # plotting <- + return None + + def test_discrete_ss_1D(self,plot=False): + """ + This function tests Kalman filter and smoothing when the state + dimensionality is one dimensional. + """ + + np.random.seed(234) # seed the random number generator + + # 1D ss model + state_dim = 1; + param_num = 2 # sigma_Q, sigma_R - parameters + measurement_dim = 1 # dimensionality od measurement + + A = 1.0 + Q = 2.0 + dA= np.zeros((state_dim,state_dim,param_num)) + dQ = np.zeros((state_dim,state_dim,param_num)); dQ[0,0,0] = 1.0 + + # measurement related parameters (subject to change) -> + H = np.ones((measurement_dim,state_dim )) + R = 0.5 * np.eye(measurement_dim) + dH = np.zeros((measurement_dim,state_dim,param_num)) + dR = np.zeros((measurement_dim,measurement_dim,param_num)); dR[:,:,1] = np.eye(measurement_dim) + # measurement related parameters (subject to change) <- + + # 1D measurement, 1 ts_no -> + data = generate_random_y_data(10, 1, 1) # np.array((samples, dim, ts_no)) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=True, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:]+H*f_var[1:]*H), 'b--') + plt.plot( np.squeeze(f_mean[1:]-H*f_var[1:]*H), 'b--') +# plt.plot( np.squeeze(M_sm[1:]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:]+H*P_sm[1:]*H), 'r--') +# plt.plot( np.squeeze(M_sm[1:]-H*P_sm[1:]*H), 'r--') + plt.legend() + plt.title("1D state-space, 1D measurements, 1 ts_no") + plt.show() + # plotting <- + # 1D measurement, 1 ts_no <- + + + # 1D measurement, 3 ts_no -> + data = generate_random_y_data(10, 1, 3) # np.array((samples, dim, ts_no)) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=True, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + #import pdb; pdb.set_trace() + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data[:,:,1]), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:,0,1]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:,0,1])+np.squeeze(H*f_var[1:]*H), 'b--') + plt.plot( np.squeeze(f_mean[1:,0,1])-np.squeeze(H*f_var[1:]*H), 'b--') +# plt.plot( np.squeeze(M_sm[1:,0,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,0,1])+H*np.squeeze(P_sm[1:])*H, 'r--') +# plt.plot( np.squeeze(M_sm[1:,0,1])-H*np.squeeze(P_sm[1:])*H, 'r--') + plt.legend() + plt.title("1D state-space, 1D measurements, 3 ts_no. 2-nd ts ploted") + plt.show() + # plotting <- + # 1D measurement, 3 ts_no <- + measurement_dim = 2 # dimensionality of measurement + + H = np.ones((measurement_dim,state_dim)) + R = 0.5 * np.eye(measurement_dim) + dH = np.zeros((measurement_dim,state_dim,param_num)) + dR = np.zeros((measurement_dim,measurement_dim,param_num)); dR[:,:,1] = np.eye(measurement_dim) + # measurement related parameters (subject to change) < + + data = generate_random_y_data(10, 2, 3) # np.array((samples, dim, ts_no)) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + +# (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, +# mean_compare_decimal=16, +# m_init=None, P_init=None, dA=dA,dQ=dQ, +# dH=dH,dR=dR, use_cython=True, +# kalman_filter_type='svd', +# calc_log_likelihood=True, +# calc_grad_log_likelihood=True) + + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data[:,0,1]), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:,0,1]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:,0,1])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot( np.squeeze(f_mean[1:,0,1])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,0,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,0,1])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,0,1])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("1D state-space, 2D measurements, 3 ts_no. 1-st measurement, 2-nd ts ploted") + plt.show() + # plotting <- + # 2D measurement, 3 ts_no <- + + def test_discrete_ss_2D(self,plot=False): + """ + This function tests Kalman filter and smoothing when the state + dimensionality is two dimensional. + """ + + np.random.seed(234) # seed the random number generator + + # 1D ss model + state_dim = 2; + param_num = 3 # sigma_Q, sigma_R, one parameters in A - parameters + measurement_dim = 1 # dimensionality od measurement + + A = np.eye(state_dim); A[0,0] = 0.5 + Q = np.ones((state_dim,state_dim)); + dA = np.zeros((state_dim,state_dim,param_num)); dA[1,1,2] = 1 + dQ = np.zeros((state_dim,state_dim,param_num)); dQ[:,:,1] = np.eye(measurement_dim) + + # measurement related parameters (subject to change) -> + H = np.ones((measurement_dim,state_dim)) + R = 0.5 * np.eye(measurement_dim) + dH = np.zeros((measurement_dim,state_dim,param_num)) + dR = np.zeros((measurement_dim,measurement_dim,param_num)); dR[:,:,1] = np.eye(measurement_dim) + # measurement related parameters (subject to change) <- + + # 1D measurement, 1 ts_no -> + data = generate_random_y_data(10, 1, 1) # np.array((samples, dim, ts_no)) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=True, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:,0]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:,0])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot( np.squeeze(f_mean[1:,0])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,0]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,0])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,0])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("2D state-space, 1D measurements, 1 ts_no") + plt.show() + # plotting <- + # 1D measurement, 1 ts_no <- + + # 1D measurement, 3 ts_no -> + data = generate_random_y_data(10, 1, 3) # np.array((samples, dim, ts_no)) + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=True, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data[:,:,1]), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:,0,1]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:,0,1])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot( np.squeeze(f_mean[1:,0,1])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,0,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,0,1])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,0,1])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("2D state-space, 1D measurements, 3 ts_no. 2-nd ts ploted") + plt.show() + # plotting <- + # 1D measurement, 3 ts_no <- + + # 2D measurement, 3 ts_no -> + # measurement related parameters (subject to change) -> + measurement_dim = 2 # dimensionality od measurement + + H = np.ones((measurement_dim,state_dim)) + R = 0.5 * np.eye(measurement_dim) + dH = np.zeros((measurement_dim,state_dim,param_num)) + dR = np.zeros((measurement_dim,measurement_dim,param_num)); dR[:,:,1] = np.eye(measurement_dim) + # measurement related parameters (subject to change) < + + data = generate_random_y_data(10, 2, 3) # np.array((samples, dim, ts_no)) + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + + (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, + mean_compare_decimal=16, + m_init=None, P_init=None, dA=dA,dQ=dQ, + dH=dH,dR=dR, use_cython=False, + kalman_filter_type='svd', + calc_log_likelihood=True, + calc_grad_log_likelihood=True) + +# (f_mean, f_var) = self.run_descr_model(data, A,Q,H,R, true_states=None, +# mean_compare_decimal=16, +# m_init=None, P_init=None, dA=dA,dQ=dQ, +# dH=dH,dR=dR, use_cython=True, +# kalman_filter_type='svd', +# calc_log_likelihood=True, +# calc_grad_log_likelihood=True) + + if plot: + # plotting -> + plt.figure() + plt.plot( np.squeeze(data[:,0,1]), 'g.-', label='measurements') + plt.plot( np.squeeze(f_mean[1:,0,1]), 'b.-',label='Kalman filter estimates') + plt.plot( np.squeeze(f_mean[1:,0,1])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot( np.squeeze(f_mean[1:,0,1])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,0,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,0,1])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,0,1])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("2D state-space, 2D measurements, 3 ts_no. 1-st measurement, 2-nd ts ploted") + plt.show() + # plotting <- + # 2D measurement, 3 ts_no <- + + def test_continuos_ss(self,plot=False): + """ + This function tests the continuos state-space model. + """ + + # 1D measurements, 1 ts_no -> + measurement_dim = 1 # dimensionality of measurement + + X_data = generate_x_points(points_num=10, x_interval = (0, 20), random=True) + Y_data = generate_random_y_data(10, 1, 1) # np.array((samples, dim, ts_no)) + + try: + import GPy + except ImportError as e: + return None + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + (F,L,Qc,H,P_inf,P0, dFt,dQct,dP_inft,dP0) = periodic_kernel.sde() + + state_dim = dFt.shape[0]; + param_num = dFt.shape[2] + + + grad_calc_params = {} + grad_calc_params['dP_inf'] = dP_inft + grad_calc_params['dF'] = dFt + grad_calc_params['dQc'] = dQct + grad_calc_params['dR'] = np.zeros((measurement_dim,measurement_dim,param_num)) + grad_calc_params['dP_init'] = dP0 + # dH matrix is None + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='rbc', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=True, + kalman_filter_type='rbc', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + if plot: + # plotting -> + plt.figure() + plt.plot( X_data, np.squeeze(Y_data[:,0]), 'g.-', label='measurements') + plt.plot( X_data, np.squeeze(f_mean[1:,15]), 'b.-',label='Kalman filter estimates') + plt.plot( X_data, np.squeeze(f_mean[1:,15])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot( X_data, np.squeeze(f_mean[1:,15])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + # plt.plot( np.squeeze(M_sm[1:,15]), 'r.-',label='Smoother Estimates') + # plt.plot( np.squeeze(M_sm[1:,15])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + # plt.plot( np.squeeze(M_sm[1:,15])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("1D measurements, 1 ts_no") + plt.show() + # plotting <- + # 1D measurements, 1 ts_no <- + + # 1D measurements, 3 ts_no -> + measurement_dim = 1 # dimensionality od measurement + + X_data = generate_x_points(points_num=10, x_interval = (0, 20), random=True) + Y_data = generate_random_y_data(10, 1, 3) # np.array((samples, dim, ts_no)) + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + (F,L,Qc,H,P_inf,P0, dFt,dQct,dP_inft,dP0) = periodic_kernel.sde() + + state_dim = dFt.shape[0]; + param_num = dFt.shape[2] + + grad_calc_params = {} + grad_calc_params['dP_inf'] = dP_inft + grad_calc_params['dF'] = dFt + grad_calc_params['dQc'] = dQct + grad_calc_params['dR'] = np.zeros((measurement_dim,measurement_dim,param_num)) + grad_calc_params['dP_init'] = dP0 + # dH matrix is None + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='rbc', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, 1.5, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=True, + kalman_filter_type='rbc', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + if plot: + # plotting -> + plt.figure() + plt.plot(X_data, np.squeeze(Y_data[:,0,1]), 'g.-', label='measurements') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1]), 'b.-',label='Kalman filter estimates') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,15,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,15,1])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,15,1])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("1D measurements, 3 ts_no. 2-nd ts ploted") + plt.show() + # plotting <- + # 1D measurements, 3 ts_no <- + + + # 2D measurements, 3 ts_no -> + measurement_dim = 2 # dimensionality od measurement + + X_data = generate_x_points(points_num=10, x_interval = (0, 20), random=True) + Y_data = generate_random_y_data(10, 2, 3) # np.array((samples, dim, ts_no)) + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + (F,L,Qc,H,P_inf,P0, dFt,dQct,dP_inft,dP0) = periodic_kernel.sde() + H = np.vstack((H,H)) # make 2D measurements + R = 1.5 * np.eye(measurement_dim) + + state_dim = dFt.shape[0]; + param_num = dFt.shape[2] + + + grad_calc_params = {} + grad_calc_params['dP_inf'] = dP_inft + grad_calc_params['dF'] = dFt + grad_calc_params['dQc'] = dQct + grad_calc_params['dR'] = np.zeros((measurement_dim,measurement_dim,param_num)) + grad_calc_params['dP_init'] = dP0 + # dH matrix is None + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, R, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='regular', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + + (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, R, P_inf, X_data, Y_data, index = None, + m_init=None, P_init=P0, use_cython=False, + kalman_filter_type='rbc', + calc_log_likelihood=True, + calc_grad_log_likelihood=True, + grad_params_no=param_num, grad_calc_params=grad_calc_params) + +# (f_mean, f_var) = self.run_continuous_model(F, L, Qc, H, R, P_inf, X_data, Y_data, index = None, +# m_init=None, P_init=P0, use_cython=True, +# kalman_filter_type='rbc', +# calc_log_likelihood=True, +# calc_grad_log_likelihood=True, +# grad_params_no=param_num, grad_calc_params=grad_calc_params) + + if plot: + # plotting -> + plt.figure() + plt.plot(X_data, np.squeeze(Y_data[:,0,1]), 'g.-', label='measurements') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1]), 'b.-',label='Kalman filter estimates') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1])+np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') + plt.plot(X_data, np.squeeze(f_mean[1:,15,1])-np.einsum('ij,ajk,kl', H, f_var[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_sm[1:,15,1]), 'r.-',label='Smoother Estimates') +# plt.plot( np.squeeze(M_sm[1:,15,1])+np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') +# plt.plot( np.squeeze(M_sm[1:,15,1])-np.einsum('ij,ajk,kl', H, P_sm[1:], H.T)[:,0,0], 'r--') + plt.legend() + plt.title("1D measurements, 3 ts_no. 2-nd ts ploted") + plt.show() + # plotting <- + # 2D measurements, 3 ts_no <- + +#def test_EM_gradient(plot=False): +# """ +# Test EM gradient calculation. This method works (the formulas are such) +# that it works only for time invariant matrices A, Q, H, R. For the continuous +# model it means that time intervals are the same. +# """ +# +# np.random.seed(234) # seed the random number generator +# +# # 1D measurements, 1 ts_no -> +# measurement_dim = 1 # dimensionality of measurement +# +# x_data = generate_x_points(points_num=10, x_interval = (0, 20), random=False) +# data = generate_random_y_data(10, 1, 1) # np.array((samples, dim, ts_no)) +# +# import GPy +# #periodic_kernel = GPy.kern.sde_Matern32(1,active_dims=[0,]) +# periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) +# (F,L,Qc,H,P_inf,P0, dFt,dQct,dP_inft,dP0t) = periodic_kernel.sde() +# +# state_dim = dFt.shape[0]; +# param_num = dFt.shape[2] +# +# grad_calc_params = {} +# grad_calc_params['dP_inf'] = dP_inft +# grad_calc_params['dF'] = dFt +# grad_calc_params['dQc'] = dQct +# grad_calc_params['dR'] = np.zeros((measurement_dim,measurement_dim,param_num)) +# grad_calc_params['dP_init'] = dP0t +# # dH matrix is None +# +# +# #(F,L,Qc,H,P_inf,dF,dQc,dP_inf) = ssm.balance_ss_model(F,L,Qc,H,P_inf,dF,dQc,dP_inf) +# # Use the Kalman filter to evaluate the likelihood +# +# #import pdb; pdb.set_trace() +# (M_kf, P_kf, log_likelihood, +# grad_log_likelihood,SmootherMatrObject) = ss.ContDescrStateSpace.cont_discr_kalman_filter(F, +# L, Qc, H, 1.5, P_inf, x_data, data, m_init=None, +# P_init=P0, calc_log_likelihood=True, +# calc_grad_log_likelihood=True, +# grad_params_no=param_num, +# grad_calc_params=grad_calc_params) +# +# if plot: +# # plotting -> +# plt.figure() +# plt.plot( np.squeeze(data[:,0]), 'g.-', label='measurements') +# plt.plot( np.squeeze(M_kf[1:,15]), 'b.-',label='Kalman filter estimates') +# plt.plot( np.squeeze(M_kf[1:,15])+np.einsum('ij,ajk,kl', H, P_kf[1:], H.T)[:,0,0], 'b--') +# plt.plot( np.squeeze(M_kf[1:,15])-np.einsum('ij,ajk,kl', H, P_kf[1:], H.T)[:,0,0], 'b--') +# plt.title("1D measurements, 1 ts_no") +# plt.show() +# # plotting <- +# # 1D measurements, 1 ts_no <- + +if __name__ == '__main__': + print("Running state-space inference tests...") + unittest.main() + + #tt = StateSpaceKernelsTests('test_discrete_ss_first') + #res = tt.test_discrete_ss_first(plot=True) + #res = tt.test_discrete_ss_1D(plot=True) + #res = tt.test_discrete_ss_2D(plot=False) + #res = tt.test_continuos_ss(plot=True) + + \ No newline at end of file