diff --git a/.travis.yml b/.travis.yml index d7e3f7cf..093fc49a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,7 +18,8 @@ before_install: install: - conda install --yes python=$TRAVIS_PYTHON_VERSION atlas numpy=1.7 scipy=0.12 matplotlib nose sphinx pip nose - - pip install . + #- pip install . + - python setup.py build_ext --inplace #--use-mirrors # # command to run tests, e.g. python setup.py test diff --git a/GPy/core/gp.py b/GPy/core/gp.py index 8100cfcc..5ca86d9e 100644 --- a/GPy/core/gp.py +++ b/GPy/core/gp.py @@ -89,7 +89,6 @@ class GP(Model): assert mean_function.output_dim == self.output_dim self.link_parameter(mean_function) - #find a sensible inference method logger.info("initializing inference method") if inference_method is None: @@ -208,6 +207,7 @@ class GP(Model): Kxx = kern.Kdiag(_Xnew) var = Kxx - np.sum(WiKx*Kx, 0) var = var.reshape(-1, 1) + var[var<0.] = 0. #force mu to be a column vector if len(mu.shape)==1: mu = mu[:,None] @@ -229,13 +229,14 @@ class GP(Model): :param Y_metadata: metadata about the predicting point to pass to the likelihood :param kern: The kernel to use for prediction (defaults to the model kern). this is useful for examining e.g. subprocesses. - :returns: (mean, var, lower_upper): + :returns: (mean, var): mean: posterior mean, a Numpy array, Nnew x self.input_dim var: posterior variance, a Numpy array, Nnew x 1 if full_cov=False, Nnew x Nnew otherwise - lower_upper: lower and upper boundaries of the 95% confidence intervals, Numpy arrays, Nnew x self.input_dim If full_cov and self.input_dim > 1, the return shape of var is Nnew x Nnew x self.input_dim. If self.input_dim == 1, the return shape is Nnew x Nnew. This is to allow for different normalizations of the output dimensions. + + Note: If you want the predictive quantiles (e.g. 95% confidence interval) use :py:func:"~GPy.core.gp.GP.predict_quantiles". """ #predict the latent function values mu, var = self._raw_predict(Xnew, full_cov=full_cov, kern=kern) @@ -243,7 +244,7 @@ class GP(Model): mu, var = self.normalizer.inverse_mean(mu), self.normalizer.inverse_variance(var) # now push through likelihood - mean, var = self.likelihood.predictive_values(mu, var, full_cov, Y_metadata) + mean, var = self.likelihood.predictive_values(mu, var, full_cov, Y_metadata=Y_metadata) return mean, var def predict_quantiles(self, X, quantiles=(2.5, 97.5), Y_metadata=None): @@ -255,12 +256,12 @@ class GP(Model): :param quantiles: tuple of quantiles, default is (2.5, 97.5) which is the 95% interval :type quantiles: tuple :returns: list of quantiles for each X and predictive quantiles for interval combination - :rtype: [np.ndarray (Xnew x self.input_dim), np.ndarray (Xnew x self.input_dim)] + :rtype: [np.ndarray (Xnew x self.output_dim), np.ndarray (Xnew x self.output_dim)] """ m, v = self._raw_predict(X, full_cov=False) if self.normalizer is not None: m, v = self.normalizer.inverse_mean(m), self.normalizer.inverse_variance(v) - return self.likelihood.predictive_quantiles(m, v, quantiles, Y_metadata) + return self.likelihood.predictive_quantiles(m, v, quantiles, Y_metadata=Y_metadata) def predictive_gradients(self, Xnew): """ @@ -330,7 +331,7 @@ class GP(Model): :returns: Ysim: set of simulations, a Numpy array (N x samples). """ fsim = self.posterior_samples_f(X, size, full_cov=full_cov) - Ysim = self.likelihood.samples(fsim, Y_metadata) + Ysim = self.likelihood.samples(fsim, Y_metadata=Y_metadata) return Ysim def plot_f(self, plot_limits=None, which_data_rows='all', @@ -395,7 +396,7 @@ class GP(Model): which_data_ycols='all', fixed_inputs=[], levels=20, samples=0, fignum=None, ax=None, resolution=None, plot_raw=False, - linecol=None,fillcol=None, Y_metadata=None, data_symbol='kx'): + linecol=None,fillcol=None, Y_metadata=None, data_symbol='kx', predict_kw=None): """ Plot the posterior of the GP. - In one dimension, the function is plotted with a shaded region identifying two standard deviations. @@ -444,7 +445,7 @@ class GP(Model): which_data_ycols, fixed_inputs, levels, samples, fignum, ax, resolution, plot_raw=plot_raw, Y_metadata=Y_metadata, - data_symbol=data_symbol, **kw) + data_symbol=data_symbol, predict_kw=predict_kw, **kw) def input_sensitivity(self, summarize=True): """ @@ -472,16 +473,51 @@ class GP(Model): self.inference_method.on_optimization_end() raise - def infer_newX(self, Y_new, optimize=True, ): + def infer_newX(self, Y_new, optimize=True): """ - Infer the distribution of X for the new observed data *Y_new*. + Infer X for the new observed data *Y_new*. :param Y_new: the new observed data for inference :type Y_new: numpy.ndarray :param optimize: whether to optimize the location of new X (True by default) :type optimize: boolean :return: a tuple containing the posterior estimation of X and the model that optimize X - :rtype: (:class:`~GPy.core.parameterization.variational.VariationalPosterior` or numpy.ndarray, :class:`~GPy.core.model.Model`) + :rtype: (:class:`~GPy.core.parameterization.variational.VariationalPosterior` and numpy.ndarray, :class:`~GPy.core.model.Model`) """ from ..inference.latent_function_inference.inferenceX import infer_newX return infer_newX(self, Y_new, optimize=optimize) + + def log_predictive_density(self, x_test, y_test, Y_metadata=None): + """ + Calculation of the log predictive density + + .. math: + p(y_{*}|D) = p(y_{*}|f_{*})p(f_{*}|\mu_{*}\\sigma^{2}_{*}) + + :param x_test: test locations (x_{*}) + :type x_test: (Nx1) array + :param y_test: test observations (y_{*}) + :type y_test: (Nx1) array + :param Y_metadata: metadata associated with the test points + """ + mu_star, var_star = self._raw_predict(x_test) + return self.likelihood.log_predictive_density(y_test, mu_star, var_star, Y_metadata=Y_metadata) + + def log_predictive_density_sampling(self, x_test, y_test, Y_metadata=None, num_samples=1000): + """ + Calculation of the log predictive density by sampling + + .. math: + p(y_{*}|D) = p(y_{*}|f_{*})p(f_{*}|\mu_{*}\\sigma^{2}_{*}) + + :param x_test: test locations (x_{*}) + :type x_test: (Nx1) array + :param y_test: test observations (y_{*}) + :type y_test: (Nx1) array + :param Y_metadata: metadata associated with the test points + :param num_samples: number of samples to use in monte carlo integration + :type num_samples: int + """ + mu_star, var_star = self._raw_predict(x_test) + return self.likelihood.log_predictive_density_sampling(y_test, mu_star, var_star, Y_metadata=Y_metadata, num_samples=num_samples) + diff --git a/GPy/core/model.py b/GPy/core/model.py index 937d30e5..c3ad5cbe 100644 --- a/GPy/core/model.py +++ b/GPy/core/model.py @@ -76,7 +76,7 @@ class Model(Parameterized): jobs = [] pool = mp.Pool(processes=num_processes) for i in range(num_restarts): - self.randomize() + if i>0: self.randomize() job = pool.apply_async(opt_wrapper, args=(self,), kwds=kwargs) jobs.append(job) @@ -90,7 +90,7 @@ class Model(Parameterized): for i in range(num_restarts): try: if not parallel: - self.randomize() + if i>0: self.randomize() self.optimize(**kwargs) else: self.optimization_runs.append(jobs[i].get()) diff --git a/GPy/core/parameterization/index_operations.py b/GPy/core/parameterization/index_operations.py index e4803f37..ae04b2ee 100644 --- a/GPy/core/parameterization/index_operations.py +++ b/GPy/core/parameterization/index_operations.py @@ -5,6 +5,7 @@ import numpy from numpy.lib.function_base import vectorize from .lists_and_dicts import IntArrayDict from functools import reduce +from .transformations import Transformation def extract_properties_to_index(index, props): prop_index = dict() diff --git a/GPy/core/parameterization/param.py b/GPy/core/parameterization/param.py index 1838f2bf..91ce9e24 100644 --- a/GPy/core/parameterization/param.py +++ b/GPy/core/parameterization/param.py @@ -38,6 +38,11 @@ class Param(Parameterizable, ObsAr): Fixing parameters will fix them to the value they are right now. If you change the fixed value, it will be fixed to the new value! + Important Note: + Multilevel indexing (e.g. self[:2][1:]) is not supported and might lead to unexpected behaviour. + Try to index in one go, using boolean indexing or the numpy builtin + np.index function. + See :py:class:`GPy.core.parameterized.Parameterized` for more details on constraining etc. """ diff --git a/GPy/core/parameterization/parameter_core.py b/GPy/core/parameterization/parameter_core.py index 1bc6a29e..48c05a8d 100644 --- a/GPy/core/parameterization/parameter_core.py +++ b/GPy/core/parameterization/parameter_core.py @@ -430,23 +430,38 @@ class Indexable(Nameable, Updateable): def log_prior(self): """evaluate the prior""" - if self.priors.size > 0: - x = self.param_array - #py3 fix - #return reduce(lambda a, b: a + b, (p.lnpdf(x[ind]).sum() for p, ind in self.priors.iteritems()), 0) - return reduce(lambda a, b: a + b, (p.lnpdf(x[ind]).sum() for p, ind in self.priors.items()), 0) - return 0. + if self.priors.size == 0: + return 0. + x = self.param_array + #evaluate the prior log densities + log_p = reduce(lambda a, b: a + b, (p.lnpdf(x[ind]).sum() for p, ind in self.priors.items()), 0) + + #account for the transformation by evaluating the log Jacobian (where things are transformed) + log_j = 0. + priored_indexes = np.hstack([i for p, i in self.priors.items()]) + for c,j in self.constraints.items(): + if not isinstance(c, Transformation):continue + for jj in j: + if jj in priored_indexes: + log_j += c.log_jacobian(x[jj]) + return log_p + log_j def _log_prior_gradients(self): """evaluate the gradients of the priors""" - if self.priors.size > 0: - x = self.param_array - ret = np.zeros(x.size) - #py3 fix - #[np.put(ret, ind, p.lnpdf_grad(x[ind])) for p, ind in self.priors.iteritems()] - [np.put(ret, ind, p.lnpdf_grad(x[ind])) for p, ind in self.priors.items()] - return ret - return 0. + if self.priors.size == 0: + return 0. + x = self.param_array + ret = np.zeros(x.size) + #compute derivate of prior density + [np.put(ret, ind, p.lnpdf_grad(x[ind])) for p, ind in self.priors.items()] + #add in jacobian derivatives if transformed + priored_indexes = np.hstack([i for p, i in self.priors.items()]) + for c,j in self.constraints.items(): + if not isinstance(c, Transformation):continue + for jj in j: + if jj in priored_indexes: + ret[jj] += c.log_jacobian_grad(x[jj]) + return ret #=========================================================================== # Tie parameters together diff --git a/GPy/core/parameterization/parameterized.py b/GPy/core/parameterization/parameterized.py index 691bf4a7..96810927 100644 --- a/GPy/core/parameterization/parameterized.py +++ b/GPy/core/parameterization/parameterized.py @@ -9,7 +9,7 @@ from .param import ParamConcatenation from .parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing import logging -from GPy.core.parameterization.index_operations import ParameterIndexOperationsView +from .index_operations import ParameterIndexOperationsView logger = logging.getLogger("parameters changed meta") class ParametersChangedMeta(type): diff --git a/GPy/core/parameterization/priors.py b/GPy/core/parameterization/priors.py index 5dad088a..83c83dfd 100644 --- a/GPy/core/parameterization/priors.py +++ b/GPy/core/parameterization/priors.py @@ -522,16 +522,9 @@ class DGPLVM(Prior): """ domain = _REAL - # _instances = [] - # def __new__(cls, mu, sigma): # Singleton: - # if cls._instances: - # cls._instances[:] = [instance for instance in cls._instances if instance()] - # for instance in cls._instances: - # if instance().mu == mu and instance().sigma == sigma: - # return instance() - # o = super(Prior, cls).__new__(cls, mu, sigma) - # cls._instances.append(weakref.ref(o)) - # return cls._instances[-1]() + + def __new__(cls, sigma2, lbl, x_shape): + return super(Prior, cls).__new__(cls, sigma2, lbl, x_shape) def __init__(self, sigma2, lbl, x_shape): self.sigma2 = sigma2 @@ -730,7 +723,7 @@ class DGPLVM(Prior): # ****************************************** -from parameterized import Parameterized +from .. import Parameterized from .. import Param class DGPLVM_Lamda(Prior, Parameterized): """ @@ -758,12 +751,12 @@ class DGPLVM_Lamda(Prior, Parameterized): self.sigma2 = sigma2 # self.x = x self.lbl = lbl - self.lamda = lamda + self.lamda = lamda self.classnum = lbl.shape[1] self.datanum = lbl.shape[0] self.x_shape = x_shape self.dim = x_shape[1] - self.lamda = Param('lamda', np.diag(lamda)) + self.lamda = Param('lamda', np.diag(lamda)) self.link_parameter(self.lamda) def get_class_label(self, y): @@ -789,7 +782,7 @@ class DGPLVM_Lamda(Prior, Parameterized): M_i = np.zeros((self.classnum, self.dim)) for i in cls: # Mean of each class - class_i = cls[i] + class_i = cls[i] M_i[i] = np.mean(class_i, axis=0) return M_i @@ -899,8 +892,8 @@ class DGPLVM_Lamda(Prior, Parameterized): #!!!!!!!!!!!!!!!!!!!!!!!!!!! #self.lamda.values[:] = self.lamda.values/self.lamda.values.sum() - xprime = x.dot(np.diagflat(self.lamda)) - x = xprime + xprime = x.dot(np.diagflat(self.lamda)) + x = xprime # print x cls = self.compute_cls(x) M_0 = np.mean(x, axis=0) @@ -916,8 +909,8 @@ class DGPLVM_Lamda(Prior, Parameterized): # This function calculates derivative of the log of prior function def lnpdf_grad(self, x): x = x.reshape(self.x_shape) - xprime = x.dot(np.diagflat(self.lamda)) - x = xprime + xprime = x.dot(np.diagflat(self.lamda)) + x = xprime # print x cls = self.compute_cls(x) M_0 = np.mean(x, axis=0) @@ -951,14 +944,14 @@ class DGPLVM_Lamda(Prior, Parameterized): # Because of the GPy we need to transpose our matrix so that it gets the same shape as out matrix (denominator layout!!!) DPxprim_Dx = DPxprim_Dx.T - DPxprim_Dlamda = DPx_Dx.dot(x) + DPxprim_Dlamda = DPx_Dx.dot(x) # Because of the GPy we need to transpose our matrix so that it gets the same shape as out matrix (denominator layout!!!) - DPxprim_Dlamda = DPxprim_Dlamda.T + DPxprim_Dlamda = DPxprim_Dlamda.T - self.lamda.gradient = np.diag(DPxprim_Dlamda) + self.lamda.gradient = np.diag(DPxprim_Dlamda) # print DPxprim_Dx - return DPxprim_Dx + return DPxprim_Dx # def frb(self, x): @@ -1139,8 +1132,8 @@ class DGPLVM_T(Prior): # This function calculates log of our prior def lnpdf(self, x): x = x.reshape(self.x_shape) - xprim = x.dot(self.vec) - x = xprim + xprim = x.dot(self.vec) + x = xprim # print x cls = self.compute_cls(x) M_0 = np.mean(x, axis=0) @@ -1156,11 +1149,11 @@ class DGPLVM_T(Prior): # This function calculates derivative of the log of prior function def lnpdf_grad(self, x): - x = x.reshape(self.x_shape) - xprim = x.dot(self.vec) - x = xprim + x = x.reshape(self.x_shape) + xprim = x.dot(self.vec) + x = xprim # print x - cls = self.compute_cls(x) + cls = self.compute_cls(x) M_0 = np.mean(x, axis=0) M_i = self.compute_Mi(cls) Sb = self.compute_Sb(cls, M_i, M_0) diff --git a/GPy/core/parameterization/transformations.py b/GPy/core/parameterization/transformations.py index 7e15cee9..01a1f44b 100644 --- a/GPy/core/parameterization/transformations.py +++ b/GPy/core/parameterization/transformations.py @@ -31,6 +31,16 @@ class Transformation(object): raise NotImplementedError def finv(self, model_param): raise NotImplementedError + def log_jacobian(self, model_param): + """ + compute the log of the jacobian of f, evaluated at f(x)= model_param + """ + raise NotImplementedError + def log_jacobian_grad(self, model_param): + """ + compute the drivative of the log of the jacobian of f, evaluated at f(x)= model_param + """ + raise NotImplementedError def gradfactor(self, model_param, dL_dmodel_param): """ df(opt_param)_dopt_param evaluated at self.f(opt_param)=model_param, times the gradient dL_dmodel_param, @@ -74,9 +84,33 @@ class Logexp(Transformation): if np.any(f < 0.): print("Warning: changing parameters to satisfy constraints") return np.abs(f) + def log_jacobian(self, model_param): + return np.where(model_param>_lim_val, model_param, np.log(np.exp(model_param+1e-20) - 1.)) - model_param + def log_jacobian_grad(self, model_param): + return 1./(np.exp(model_param)-1.) def __str__(self): return '+ve' +class Exponent(Transformation): + domain = _POSITIVE + def f(self, x): + return np.where(x<_lim_val, np.where(x>-_lim_val, np.exp(x), np.exp(-_lim_val)), np.exp(_lim_val)) + def finv(self, x): + return np.log(x) + def gradfactor(self, f, df): + return np.einsum('i,i->i', df, f) + def initialize(self, f): + if np.any(f < 0.): + print("Warning: changing parameters to satisfy constraints") + return np.abs(f) + def log_jacobian(self, model_param): + return np.log(model_param) + def log_jacobian_grad(self, model_param): + return 1./model_param + def __str__(self): + return '+ve' + + class NormalTheta(Transformation): "Do not use, not officially supported!" @@ -417,22 +451,6 @@ class LogexpClipped(Logexp): def __str__(self): return '+ve_c' -class Exponent(Transformation): - # TODO: can't allow this to go to zero, need to set a lower bound. Similar with negative Exponent below. See old MATLAB code. - domain = _POSITIVE - def f(self, x): - return np.where(x<_lim_val, np.where(x>-_lim_val, np.exp(x), np.exp(-_lim_val)), np.exp(_lim_val)) - def finv(self, x): - return np.log(x) - def gradfactor(self, f, df): - return np.einsum('i,i->i', df, f) - def initialize(self, f): - if np.any(f < 0.): - print("Warning: changing parameters to satisfy constraints") - return np.abs(f) - def __str__(self): - return '+ve' - class NegativeExponent(Exponent): domain = _NEGATIVE def f(self, x): diff --git a/GPy/core/parameterization/variational.py b/GPy/core/parameterization/variational.py index ab196b98..f33e7715 100644 --- a/GPy/core/parameterization/variational.py +++ b/GPy/core/parameterization/variational.py @@ -36,8 +36,9 @@ class NormalPrior(VariationalPrior): variational_posterior.variance.gradient -= (1. - (1. / (variational_posterior.variance))) * 0.5 class SpikeAndSlabPrior(VariationalPrior): - def __init__(self, pi=None, learnPi=False, variance = 1.0, name='SpikeAndSlabPrior', **kw): - super(SpikeAndSlabPrior, self).__init__(name=name, **kw) + def __init__(self, pi=None, learnPi=False, variance = 1.0, group_spike=False, name='SpikeAndSlabPrior', **kw): + super(SpikeAndSlabPrior, self).__init__(name=name, **kw) + self.group_spike = group_spike self.variance = Param('variance',variance) self.learnPi = learnPi if learnPi: @@ -50,7 +51,10 @@ class SpikeAndSlabPrior(VariationalPrior): def KL_divergence(self, variational_posterior): mu = variational_posterior.mean S = variational_posterior.variance - gamma = variational_posterior.gamma.values + if self.group_spike: + gamma = variational_posterior.gamma.values[0] + else: + gamma = variational_posterior.gamma.values if len(self.pi.shape)==2: idx = np.unique(variational_posterior.gamma._raveled_index()/gamma.shape[-1]) pi = self.pi[idx] @@ -65,14 +69,21 @@ class SpikeAndSlabPrior(VariationalPrior): def update_gradients_KL(self, variational_posterior): mu = variational_posterior.mean S = variational_posterior.variance - gamma = variational_posterior.gamma.values + if self.group_spike: + gamma = variational_posterior.gamma.values[0] + else: + gamma = variational_posterior.gamma.values if len(self.pi.shape)==2: idx = np.unique(variational_posterior.gamma._raveled_index()/gamma.shape[-1]) pi = self.pi[idx] else: pi = self.pi - variational_posterior.binary_prob.gradient -= np.log((1-pi)/pi*gamma/(1.-gamma))+((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. + if self.group_spike: + dgamma = np.log((1-pi)/pi*gamma/(1.-gamma))/variational_posterior.num_data + else: + dgamma = np.log((1-pi)/pi*gamma/(1.-gamma)) + variational_posterior.binary_prob.gradient -= dgamma+((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. mu.gradient -= gamma*mu/self.variance S.gradient -= (1./self.variance - 1./S) * gamma /2. if self.learnPi: @@ -154,13 +165,31 @@ class SpikeAndSlabPosterior(VariationalPosterior): ''' The SpikeAndSlab distribution for variational approximations. ''' - def __init__(self, means, variances, binary_prob, name='latent space'): + def __init__(self, means, variances, binary_prob, group_spike=False, sharedX=False, name='latent space'): """ binary_prob : the probability of the distribution on the slab part. """ super(SpikeAndSlabPosterior, self).__init__(means, variances, name) - self.gamma = Param("binary_prob",binary_prob,Logistic(0.,1.)) - self.link_parameter(self.gamma) + self.group_spike = group_spike + self.sharedX = sharedX + if sharedX: + self.mean.fix(warning=False) + self.variance.fix(warning=False) + if group_spike: + self.gamma_group = Param("binary_prob_group",binary_prob.mean(axis=0),Logistic(1e-10,1.-1e-10)) + self.gamma = Param("binary_prob",binary_prob, __fixed__) + self.link_parameters(self.gamma_group,self.gamma) + else: + self.gamma = Param("binary_prob",binary_prob,Logistic(1e-10,1.-1e-10)) + self.link_parameter(self.gamma) + + def propogate_val(self): + if self.group_spike: + self.gamma.values[:] = self.gamma_group.values + + def collate_gradient(self): + if self.group_spike: + self.gamma_group.gradient = self.gamma.gradient.reshape(self.gamma.shape).sum(axis=0) def set_gradients(self, grad): self.mean.gradient, self.variance.gradient, self.gamma.gradient = grad @@ -179,15 +208,15 @@ class SpikeAndSlabPosterior(VariationalPosterior): n.parameters[dc['variance']._parent_index_] = dc['variance'] n.parameters[dc['binary_prob']._parent_index_] = dc['binary_prob'] n._gradient_array_ = None - oversize = self.size - self.mean.size - self.variance.size - n.size = n.mean.size + n.variance.size + oversize + oversize = self.size - self.mean.size - self.variance.size - self.gamma.size + n.size = n.mean.size + n.variance.size + n.gamma.size + oversize n.ndim = n.mean.ndim n.shape = n.mean.shape n.num_data = n.mean.shape[0] n.input_dim = n.mean.shape[1] if n.ndim != 1 else 1 return n else: - return super(VariationalPrior, self).__getitem__(s) + return super(SpikeAndSlabPosterior, self).__getitem__(s) def plot(self, *args, **kwargs): """ diff --git a/GPy/core/sparse_gp.py b/GPy/core/sparse_gp.py index f8d458ce..c7c99be6 100644 --- a/GPy/core/sparse_gp.py +++ b/GPy/core/sparse_gp.py @@ -132,14 +132,14 @@ class SparseGP(GP): if self.posterior.woodbury_inv.ndim == 2: var = Kxx - np.dot(Kx.T, np.dot(self.posterior.woodbury_inv, Kx)) elif self.posterior.woodbury_inv.ndim == 3: - var = Kxx[:,:,None] - np.tensordot(np.dot(np.atleast_3d(self.posterior.woodbury_inv).T, Kx).T, Kx, [1,0]).swapaxes(1,2) + var = np.empty((Kxx.shape[0],Kxx.shape[1],self.posterior.woodbury_inv.shape[2])) + for i in range(var.shape[2]): + var[:, :, i] = (Kxx - mdot(Kx.T, self.posterior.woodbury_inv[:, :, i], Kx)) var = var else: Kxx = kern.Kdiag(Xnew) if self.posterior.woodbury_inv.ndim == 2: - var = (Kxx - np.sum(np.dot(np.atleast_3d(self.posterior.woodbury_inv).T, Kx) * Kx[None,:,:], 1)).T - #For plot_latent, the below code doesn't work! - #var = Kxx - np.sum(np.dot(self.posterior.woodbury_inv.T, Kx) * Kx, 0) + var = (Kxx - np.sum(np.dot(self.posterior.woodbury_inv.T, Kx) * Kx, 0))[:,None] elif self.posterior.woodbury_inv.ndim == 3: var = np.empty((Kxx.shape[0],self.posterior.woodbury_inv.shape[2])) for i in range(var.shape[1]): @@ -149,9 +149,9 @@ class SparseGP(GP): if self.mean_function is not None: mu += self.mean_function.f(Xnew) else: - psi0_star = self.kern.psi0(self.Z, Xnew) - psi1_star = self.kern.psi1(self.Z, Xnew) - #psi2_star = self.kern.psi2(self.Z, Xnew) # Only possible if we get NxMxM psi2 out of the code. + psi0_star = kern.psi0(self.Z, Xnew) + psi1_star = kern.psi1(self.Z, Xnew) + #psi2_star = kern.psi2(self.Z, Xnew) # Only possible if we get NxMxM psi2 out of the code. la = self.posterior.woodbury_vector mu = np.dot(psi1_star, la) # TODO: dimensions? @@ -163,7 +163,7 @@ class SparseGP(GP): for i in range(Xnew.shape[0]): _mu, _var = Xnew.mean.values[[i]], Xnew.variance.values[[i]] - psi2_star = self.kern.psi2(self.Z, NormalPosterior(_mu, _var)) + psi2_star = kern.psi2(self.Z, NormalPosterior(_mu, _var)) tmp = (psi2_star[:, :] - psi1_star[[i]].T.dot(psi1_star[[i]])) var_ = mdot(la.T, tmp, la) diff --git a/GPy/core/svgp.py b/GPy/core/svgp.py index 06a9749c..c5eb3374 100644 --- a/GPy/core/svgp.py +++ b/GPy/core/svgp.py @@ -9,7 +9,7 @@ from ..inference.latent_function_inference import SVGP as svgp_inf class SVGP(SparseGP): - def __init__(self, X, Y, Z, kernel, likelihood, mean_function=None, name='SVGP', Y_metadata=None, batchsize=None): + def __init__(self, X, Y, Z, kernel, likelihood, mean_function=None, name='SVGP', Y_metadata=None, batchsize=None, num_latent_functions=None): """ Stochastic Variational GP. @@ -41,8 +41,12 @@ class SVGP(SparseGP): SparseGP.__init__(self, X_batch, Y_batch, Z, kernel, likelihood, mean_function=mean_function, inference_method=inf_method, name=name, Y_metadata=Y_metadata, normalizer=False) - self.m = Param('q_u_mean', np.zeros((self.num_inducing, Y.shape[1]))) - chol = choleskies.triang_to_flat(np.tile(np.eye(self.num_inducing)[:,:,None], (1,1,Y.shape[1]))) + #assume the number of latent functions is one per col of Y unless specified + if num_latent_functions is None: + num_latent_functions = Y.shape[1] + + self.m = Param('q_u_mean', np.zeros((self.num_inducing, num_latent_functions))) + chol = choleskies.triang_to_flat(np.tile(np.eye(self.num_inducing)[None,:,:], (num_latent_functions, 1,1))) self.chol = Param('q_u_chol', chol) self.link_parameter(self.chol) self.link_parameter(self.m) diff --git a/GPy/core/verbose_optimization.py b/GPy/core/verbose_optimization.py index a5fb019e..08c5e2dd 100644 --- a/GPy/core/verbose_optimization.py +++ b/GPy/core/verbose_optimization.py @@ -5,9 +5,10 @@ from __future__ import print_function import numpy as np import sys import time +import datetime def exponents(fnow, current_grad): - exps = [np.abs(np.float(fnow)), current_grad] + exps = [np.abs(np.float(fnow)), 1 if current_grad is np.nan else current_grad] return np.sign(exps) * np.log10(exps).astype(int) class VerboseOptimization(object): @@ -23,6 +24,7 @@ class VerboseOptimization(object): self.model.add_observer(self, self.print_status) self.status = 'running' self.clear = clear_after_finish + self.deltat = .2 self.update() @@ -44,25 +46,25 @@ class VerboseOptimization(object): self.hor_align = FlexBox(children = [left_col, right_col], width='100%', orientation='horizontal') display(self.hor_align) - + try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) - + right_col.set_css({ 'padding': '2px', }) - + self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') - + left_col.add_class("box-flex1") right_col.add_class('box-flex0') @@ -74,16 +76,31 @@ class VerboseOptimization(object): else: self.exps = exponents(self.fnow, self.current_gradient) print('Running {} Code:'.format(self.opt_name)) - print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format("i", "f", "|g|", "secs", mi=self.len_maxiters)) + print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format("i", "f", "|g|", "runtime", mi=self.len_maxiters)) def __enter__(self): self.start = time.time() return self - def print_out(self): + def print_out(self, seconds): + if seconds<60: + ms = (seconds%1)*100 + self.timestring = "{s:0>2d}s{ms:0>2d}".format(s=int(seconds), ms=int(ms)) + else: + m, s = divmod(seconds, 60) + if m>59: + h, m = divmod(m, 60) + if h>23: + d, h = divmod(h, 24) + self.timestring = '{d:0>2d}d{h:0>2d}h{m:0>2d}'.format(m=int(m), h=int(h), d=int(d)) + else: + self.timestring = '{h:0>2d}h{m:0>2d}m{s:0>2d}'.format(m=int(m), s=int(s), h=int(h)) + else: + ms = (seconds%1)*100 + self.timestring = '{m:0>2d}m{s:0>2d}s{ms:0>2d}'.format(m=int(m), s=int(s), ms=int(ms)) if self.ipython_notebook: names_vals = [['optimizer', "{:s}".format(self.opt_name)], - ['runtime [s]', "{:> g}".format(time.time()-self.start)], + ['runtime', "{:>s}".format(self.timestring)], ['evaluation', "{:>0{l}}".format(self.iteration, l=self.len_maxiters)], ['objective', "{: > 12.3E}".format(self.fnow)], ['||gradient||', "{: >+12.3E}".format(float(self.current_gradient))], @@ -120,14 +137,18 @@ class VerboseOptimization(object): if b: self.exps = n_exps print('\r', end=' ') - print('{3:> 7.2g} {0:>0{mi}g} {1:> 12e} {2:> 12e}'.format(self.iteration, float(self.fnow), float(self.current_gradient), time.time()-self.start, mi=self.len_maxiters), end=' ') # print 'Iteration:', iteration, ' Objective:', fnow, ' Scale:', beta, '\r', + print('{3:} {0:>0{mi}g} {1:> 12e} {2:> 12e}'.format(self.iteration, float(self.fnow), float(self.current_gradient), "{:>8s}".format(self.timestring), mi=self.len_maxiters), end=' ') # print 'Iteration:', iteration, ' Objective:', fnow, ' Scale:', beta, '\r', sys.stdout.flush() def print_status(self, me, which=None): self.update() + seconds = time.time()-self.start #sys.stdout.write(" "*len(self.message)) - self.print_out() + self.deltat += seconds + if self.deltat > .2: + self.print_out(seconds) + self.deltat = 0 self.iteration += 1 @@ -141,17 +162,24 @@ class VerboseOptimization(object): def finish(self, opt): self.status = opt.status + if self.verbose and self.ipython_notebook: + if 'conv' in self.status.lower(): + self.progress.bar_style = 'success' + elif self.iteration >= self.maxiters: + self.progress.bar_style = 'warning' + else: + self.progress.bar_style = 'danger' def __exit__(self, type, value, traceback): if self.verbose: self.stop = time.time() self.model.remove_observer(self) - self.print_out() + self.print_out(self.stop - self.start) if not self.ipython_notebook: print() - print('Optimization finished in {0:.5g} Seconds'.format(self.stop-self.start)) - print('Optimization status: {0}'.format(self.status)) + print('Runtime: {}'.format("{:>9s}".format(self.timestring))) + print('Optimization status: {0}'.format(self.status)) print() elif self.clear: self.hor_align.close() diff --git a/GPy/defaults.cfg b/GPy/defaults.cfg index 306543ed..aa68a421 100644 --- a/GPy/defaults.cfg +++ b/GPy/defaults.cfg @@ -25,3 +25,6 @@ MKL = False [weave] #if true, try to use weave, and fall back to numpy. if false, just use numpy. working = True + +[cython] +working = True diff --git a/GPy/examples/classification.py b/GPy/examples/classification.py index d4518f24..3aa022e0 100644 --- a/GPy/examples/classification.py +++ b/GPy/examples/classification.py @@ -217,9 +217,8 @@ def crescent_data(model_type='Full', num_inducing=10, seed=default_seed, kernel= elif model_type == 'FITC': m = GPy.models.FITCClassification(data['X'], Y, kernel=kernel, num_inducing=num_inducing) m['.*len'] = 3. - if optimize: - m.pseudo_EM() + m.optimize() if plot: m.plot() diff --git a/GPy/examples/dimensionality_reduction.py b/GPy/examples/dimensionality_reduction.py index 46107a71..745c2c24 100644 --- a/GPy/examples/dimensionality_reduction.py +++ b/GPy/examples/dimensionality_reduction.py @@ -215,6 +215,7 @@ def ssgplvm_oil(optimize=True, verbose=1, plot=True, N=200, Q=7, num_inducing=40 return m def _simulate_matern(D1, D2, D3, N, num_inducing, plot_sim=False): + """Simulate some data drawn from a matern covariance and a periodic exponential for use in MRD demos.""" Q_signal = 4 import GPy import numpy as np @@ -254,6 +255,7 @@ def _simulate_matern(D1, D2, D3, N, num_inducing, plot_sim=False): return slist, [S1, S2, S3], Ylist def _simulate_sincos(D1, D2, D3, N, num_inducing, plot_sim=False): + """Simulate some data drawn from sine and cosine for use in demos of MRD""" _np.random.seed(1234) x = _np.linspace(0, 4 * _np.pi, N)[:, None] @@ -353,13 +355,13 @@ def ssgplvm_simulation(optimize=True, verbose=1, Y = Ylist[0] k = kern.Linear(Q, ARD=True) # + kern.white(Q, _np.exp(-2)) # + kern.bias(Q) # k = kern.RBF(Q, ARD=True, lengthscale=10.) - m = SSGPLVM(Y, Q, init="pca", num_inducing=num_inducing, kernel=k) + m = SSGPLVM(Y, Q, init="rand", num_inducing=num_inducing, kernel=k, group_spike=True) m.X.variance[:] = _np.random.uniform(0, .01, m.X.shape) - m.likelihood.variance = .1 + m.likelihood.variance = .01 if optimize: print("Optimizing model:") - m.optimize('scg', messages=verbose, max_iters=max_iters, + m.optimize('bfgs', messages=verbose, max_iters=max_iters, gtol=.05) if plot: m.X.plot("SSGPLVM Latent Space 1D") @@ -402,7 +404,8 @@ def mrd_simulation(optimize=True, verbose=True, plot=True, plot_sim=True, **kw): from GPy.models import MRD D1, D2, D3, N, num_inducing, Q = 60, 20, 36, 60, 6, 5 - _, _, Ylist = _simulate_matern(D1, D2, D3, N, num_inducing, plot_sim) + _, _, Ylist = _simulate_sincos(D1, D2, D3, N, num_inducing, plot_sim) + # Ylist = [Ylist[0]] k = kern.Linear(Q, ARD=True) @@ -585,6 +588,7 @@ def robot_wireless(optimize=True, verbose=True, plot=True): return m def stick_bgplvm(model=None, optimize=True, verbose=True, plot=True): + """Interactive visualisation of the Stick Man data from Ohio State University with the Bayesian GPLVM.""" from GPy.models import BayesianGPLVM from matplotlib import pyplot as plt import numpy as np @@ -613,7 +617,8 @@ def stick_bgplvm(model=None, optimize=True, verbose=True, plot=True): data_show = GPy.plotting.matplot_dep.visualize.stick_show(y, connect=data['connect']) dim_select = GPy.plotting.matplot_dep.visualize.lvm_dimselect(m.X.mean[:1, :].copy(), m, data_show, latent_axes=latent_axes, sense_axes=sense_axes) fig.canvas.draw() - fig.canvas.show() + # Canvas.show doesn't work on OSX. + #fig.canvas.show() raw_input('Press enter to finish') return m diff --git a/GPy/inference/latent_function_inference/exact_gaussian_inference.py b/GPy/inference/latent_function_inference/exact_gaussian_inference.py index 76b10f08..343387a7 100644 --- a/GPy/inference/latent_function_inference/exact_gaussian_inference.py +++ b/GPy/inference/latent_function_inference/exact_gaussian_inference.py @@ -52,7 +52,7 @@ class ExactGaussianInference(LatentFunctionInference): K = kern.K(X) Ky = K.copy() - diag.add(Ky, likelihood.gaussian_variance(Y_metadata)) + diag.add(Ky, likelihood.gaussian_variance(Y_metadata)+1e-8) Wi, LW, LWi, W_logdet = pdinv(Ky) alpha, _ = dpotrs(LW, YYT_factor, lower=1) diff --git a/GPy/inference/latent_function_inference/inferenceX.py b/GPy/inference/latent_function_inference/inferenceX.py index f68f17cb..19013b06 100644 --- a/GPy/inference/latent_function_inference/inferenceX.py +++ b/GPy/inference/latent_function_inference/inferenceX.py @@ -27,12 +27,19 @@ def infer_newX(model, Y_new, optimize=True, init='L2'): class InferenceX(Model): """ - The class for inference of new X with given new Y. (do_test_latent) + The model class for inference of new X with given new Y. (replacing the "do_test_latent" in Bayesian GPLVM) + It is a tiny inference model created from the original GP model. The kernel, likelihood (only Gaussian is supported at the moment) + and posterior distribution are taken from the original model. + For Regression models and GPLVM, a point estimate of the latent variable X will be inferred. + For Bayesian GPLVM, the variational posterior of X will be inferred. + X is inferred through a gradient optimization of the inference model. :param model: the GPy model used in inference :type model: GPy.core.Model :param Y: the new observed data for inference :type Y: numpy.ndarray + :param init: the distance metric of Y for initializing X with the nearest neighbour. + :type init: 'L2', 'NCC' and 'rand' """ def __init__(self, model, Y, name='inferenceX', init='L2'): if np.isnan(Y).any() or getattr(model, 'missing_data', False): @@ -45,17 +52,23 @@ class InferenceX(Model): super(InferenceX, self).__init__(name) self.likelihood = model.likelihood.copy() self.kern = model.kern.copy() - if model.kern.useGPU: - from ...models import SSGPLVM - if isinstance(model, SSGPLVM): - self.kern.GPU_SSRBF(True) - else: - self.kern.GPU(True) +# if model.kern.useGPU: +# from ...models import SSGPLVM +# if isinstance(model, SSGPLVM): +# self.kern.GPU_SSRBF(True) +# else: +# self.kern.GPU(True) from copy import deepcopy self.posterior = deepcopy(model.posterior) if hasattr(model, 'variational_prior'): self.uncertain_input = True - self.variational_prior = model.variational_prior.copy() + from ...models.ss_gplvm import IBPPrior + from ...models.ss_mrd import IBPPrior_SSMRD + if isinstance(model.variational_prior, IBPPrior) or isinstance(model.variational_prior, IBPPrior_SSMRD): + from ...core.parameterization.variational import SpikeAndSlabPrior + self.variational_prior = SpikeAndSlabPrior(pi=05,learnPi=False, group_spike=False) + else: + self.variational_prior = model.variational_prior.copy() else: self.uncertain_input = False if hasattr(model, 'inducing_inputs'): @@ -147,9 +160,9 @@ class InferenceX(Model): from ...core.parameterization.variational import SpikeAndSlabPrior if isinstance(self.variational_prior, SpikeAndSlabPrior): # Update Log-likelihood - KL_div = self.variational_prior.KL_divergence(self.X, N=self.Y.shape[0]) + KL_div = self.variational_prior.KL_divergence(self.X) # update for the KL divergence - self.variational_prior.update_gradients_KL(self.X, N=self.Y.shape[0]) + self.variational_prior.update_gradients_KL(self.X) else: # Update Log-likelihood KL_div = self.variational_prior.KL_divergence(self.X) diff --git a/GPy/inference/latent_function_inference/laplace.py b/GPy/inference/latent_function_inference/laplace.py index aefc82ac..902d5fff 100644 --- a/GPy/inference/latent_function_inference/laplace.py +++ b/GPy/inference/latent_function_inference/laplace.py @@ -139,10 +139,6 @@ class Laplace(LatentFunctionInference): f_hat, Ki_fhat = self.rasm_mode(K, Y, likelihood, Ki_f_init, Y_metadata=Y_metadata) - self.f_hat = f_hat - #self.Ki_fhat = Ki_fhat - #self.K = K.copy() - #Compute hessian and other variables at mode log_marginal, woodbury_inv, dL_dK, dL_dthetaL = self.mode_computations(f_hat, Ki_fhat, K, Y, likelihood, kern, Y_metadata) @@ -298,6 +294,11 @@ class Laplace(LatentFunctionInference): else: dL_dthetaL = np.zeros(likelihood.size) + #Cache some things for speedy LOO + self.Ki_W_i = Ki_W_i + self.K = K + self.W = W + self.f_hat = f_hat return log_marginal, K_Wi_i, dL_dK, dL_dthetaL def _compute_B_statistics(self, K, W, log_concave, *args, **kwargs): diff --git a/GPy/inference/latent_function_inference/svgp.py b/GPy/inference/latent_function_inference/svgp.py index bad73a71..b04ca609 100644 --- a/GPy/inference/latent_function_inference/svgp.py +++ b/GPy/inference/latent_function_inference/svgp.py @@ -3,25 +3,27 @@ from ...util import linalg from ...util import choleskies import numpy as np from .posterior import Posterior +from scipy.linalg.blas import dgemm, dsymm, dtrmm class SVGP(LatentFunctionInference): def inference(self, q_u_mean, q_u_chol, kern, X, Z, likelihood, Y, mean_function=None, Y_metadata=None, KL_scale=1.0, batch_scale=1.0): - num_inducing = Z.shape[0] - num_data, num_outputs = Y.shape + num_data, _ = Y.shape + num_inducing, num_outputs = q_u_mean.shape #expand cholesky representation L = choleskies.flat_to_triang(q_u_chol) - S = np.einsum('ijk,ljk->ilk', L, L) #L.dot(L.T) + + + S = np.empty((num_outputs, num_inducing, num_inducing)) + [np.dot(L[i,:,:], L[i,:,:].T, S[i,:,:]) for i in range(num_outputs)] #Si,_ = linalg.dpotri(np.asfortranarray(L), lower=1) Si = choleskies.multiple_dpotri(L) - logdetS = np.array([2.*np.sum(np.log(np.abs(np.diag(L[:,:,i])))) for i in range(L.shape[-1])]) + logdetS = np.array([2.*np.sum(np.log(np.abs(np.diag(L[i,:,:])))) for i in range(L.shape[0])]) if np.any(np.isinf(Si)): raise ValueError("Cholesky representation unstable") - #S = S + np.eye(S.shape[0])*1e-5*np.max(np.max(S)) - #Si, Lnew, _,_ = linalg.pdinv(S) #compute mean function stuff if mean_function is not None: @@ -31,26 +33,31 @@ class SVGP(LatentFunctionInference): prior_mean_u = np.zeros((num_inducing, num_outputs)) prior_mean_f = np.zeros((num_data, num_outputs)) - #compute kernel related stuff Kmm = kern.K(Z) - Knm = kern.K(X, Z) + Kmn = kern.K(Z, X) Knn_diag = kern.Kdiag(X) - Kmmi, Lm, Lmi, logdetKmm = linalg.pdinv(Kmm) + Lm = linalg.jitchol(Kmm) + logdetKmm = 2.*np.sum(np.log(np.diag(Lm))) + Kmmi, _ = linalg.dpotri(Lm) #compute the marginal means and variances of q(f) - A = np.dot(Knm, Kmmi) - mu = prior_mean_f + np.dot(A, q_u_mean - prior_mean_u) - v = Knn_diag[:,None] - np.sum(A*Knm,1)[:,None] + np.sum(A[:,:,None] * np.einsum('ij,jkl->ikl', A, S),1) + A, _ = linalg.dpotrs(Lm, Kmn) + mu = prior_mean_f + np.dot(A.T, q_u_mean - prior_mean_u) + v = np.empty((num_data, num_outputs)) + for i in range(num_outputs): + tmp = dtrmm(1.0,L[i].T, A, lower=0, trans_a=0) + v[:,i] = np.sum(np.square(tmp),0) + v += (Knn_diag - np.sum(A*Kmn,0))[:,None] #compute the KL term Kmmim = np.dot(Kmmi, q_u_mean) - KLs = -0.5*logdetS -0.5*num_inducing + 0.5*logdetKmm + 0.5*np.einsum('ij,ijk->k', Kmmi, S) + 0.5*np.sum(q_u_mean*Kmmim,0) + KLs = -0.5*logdetS -0.5*num_inducing + 0.5*logdetKmm + 0.5*np.sum(Kmmi[None,:,:]*S,1).sum(1) + 0.5*np.sum(q_u_mean*Kmmim,0) KL = KLs.sum() #gradient of the KL term (assuming zero mean function) dKL_dm = Kmmim.copy() - dKL_dS = 0.5*(Kmmi[:,:,None] - Si) - dKL_dKmm = 0.5*num_outputs*Kmmi - 0.5*Kmmi.dot(S.sum(-1)).dot(Kmmi) - 0.5*Kmmim.dot(Kmmim.T) + dKL_dS = 0.5*(Kmmi[None,:,:] - Si) + dKL_dKmm = 0.5*num_outputs*Kmmi - 0.5*Kmmi.dot(S.sum(0)).dot(Kmmi) - 0.5*Kmmim.dot(Kmmim.T) if mean_function is not None: #adjust KL term for mean function @@ -75,14 +82,20 @@ class SVGP(LatentFunctionInference): dF_dthetaL = dF_dthetaL.sum(1).sum(1)*batch_scale #derivatives of expected likelihood, assuming zero mean function - Adv = A.T[:,:,None]*dF_dv[None,:,:] # As if dF_Dv is diagonal - Admu = A.T.dot(dF_dmu) - AdvA = np.dstack([np.dot(A.T, Adv[:,:,i].T) for i in range(num_outputs)]) - tmp = np.einsum('ijk,jlk->il', AdvA, S).dot(Kmmi) - dF_dKmm = -Admu.dot(Kmmim.T) + AdvA.sum(-1) - tmp - tmp.T + Adv = A[None,:,:]*dF_dv.T[:,None,:] # As if dF_Dv is diagonal, D, M, N + Admu = A.dot(dF_dmu) + Adv = np.ascontiguousarray(Adv) # makes for faster operations later...(inc dsymm) + AdvA = np.dot(Adv.reshape(-1, num_data),A.T).reshape(num_outputs, num_inducing, num_inducing ) + tmp = np.sum([np.dot(a,s) for a, s in zip(AdvA, S)],0).dot(Kmmi) + dF_dKmm = -Admu.dot(Kmmim.T) + AdvA.sum(0) - tmp - tmp.T dF_dKmm = 0.5*(dF_dKmm + dF_dKmm.T) # necessary? GPy bug? - tmp = 2.*(np.einsum('ij,jlk->ilk', Kmmi,S) - np.eye(num_inducing)[:,:,None]) - dF_dKmn = np.einsum('ijk,jlk->il', tmp, Adv) + Kmmim.dot(dF_dmu.T) + tmp = S.reshape(-1, num_inducing).dot(Kmmi).reshape(num_outputs, num_inducing , num_inducing ) + tmp = 2.*(tmp - np.eye(num_inducing)[None, :,:]) + + dF_dKmn = Kmmim.dot(dF_dmu.T) + for a,b in zip(tmp, Adv): + dF_dKmn += np.dot(a.T, b) + dF_dm = Admu dF_dS = AdvA @@ -98,11 +111,11 @@ class SVGP(LatentFunctionInference): log_marginal = F.sum() - KL dL_dm, dL_dS, dL_dKmm, dL_dKmn = dF_dm - dKL_dm, dF_dS- dKL_dS, dF_dKmm- dKL_dKmm, dF_dKmn - dL_dchol = np.dstack([2.*np.dot(dL_dS[:,:,i], L[:,:,i]) for i in range(num_outputs)]) + dL_dchol = 2.*np.array([np.dot(a,b) for a, b in zip(dL_dS, L) ]) dL_dchol = choleskies.triang_to_flat(dL_dchol) grad_dict = {'dL_dKmm':dL_dKmm, 'dL_dKmn':dL_dKmn, 'dL_dKdiag': dF_dv.sum(1), 'dL_dm':dL_dm, 'dL_dchol':dL_dchol, 'dL_dthetaL':dF_dthetaL} if mean_function is not None: grad_dict['dL_dmfZ'] = dF_dmfZ - dKL_dmfZ grad_dict['dL_dmfX'] = dF_dmfX - return Posterior(mean=q_u_mean, cov=S, K=Kmm, prior_mean=prior_mean_u), log_marginal, grad_dict + return Posterior(mean=q_u_mean, cov=S.T, K=Kmm, prior_mean=prior_mean_u), log_marginal, grad_dict diff --git a/GPy/inference/optimization/optimization.py b/GPy/inference/optimization/optimization.py index fd140688..48bdd809 100644 --- a/GPy/inference/optimization/optimization.py +++ b/GPy/inference/optimization/optimization.py @@ -142,7 +142,7 @@ class opt_lbfgsb(Optimizer): #a more helpful error message is available in opt_result in the Error case if opt_result[2]['warnflag']==2: - self.status = 'Error' + opt_result[2]['task'] + self.status = 'Error' + str(opt_result[2]['task']) class opt_simplex(Optimizer): def __init__(self, *args, **kwargs): diff --git a/GPy/kern/__init__.py b/GPy/kern/__init__.py index 2bd55617..f479c387 100644 --- a/GPy/kern/__init__.py +++ b/GPy/kern/__init__.py @@ -19,5 +19,5 @@ from ._src.splitKern import SplitKern,DEtime from ._src.splitKern import DEtime as DiffGenomeKern -from _src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel +from ._src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel diff --git a/GPy/kern/_src/basis_funcs.py b/GPy/kern/_src/basis_funcs.py index 5225ff10..a6c1f36c 100644 --- a/GPy/kern/_src/basis_funcs.py +++ b/GPy/kern/_src/basis_funcs.py @@ -121,7 +121,7 @@ class LinearSlopeBasisFuncKernel(BasisFuncKernel): class ChangePointBasisFuncKernel(BasisFuncKernel): def __init__(self, input_dim, changepoint, variance=1., active_dims=None, ARD=False, name='changepoint'): - self.changepoint = changepoint + self.changepoint = np.array(changepoint) super(ChangePointBasisFuncKernel, self).__init__(input_dim, variance, active_dims, ARD, name) @Cache_this(limit=3, ignore_args=()) @@ -136,3 +136,48 @@ class DomainKernel(LinearSlopeBasisFuncKernel): def _phi(self, X): phi = np.where((X>self.start)*(Xq', dL_dK, phi1, dphi1_dl) + else: + self.slope.gradient = self.variance * 2 * (dL_dK * phi1.dot(dphi1_dl.T)).sum() + else: + phi1 = self.phi(X) + phi2 = self.phi(X2) + if phi1.ndim != 2: + phi1 = phi1[:, None] + phi2 = phi2[:, None] + dphi1_dl = (phi1**2) * (np.exp(-((X-self.centers)*self.slope)) * (X-self.centers)) + dphi2_dl = (phi2**2) * (np.exp(-((X2-self.centers)*self.slope)) * (X2-self.centers)) + if self.ARD_slope: + self.slope.gradient = (self.variance * np.einsum('ij,iq,jq->q', dL_dK, phi1, dphi2_dl) + np.einsum('ij,iq,jq->q', dL_dK, phi2, dphi1_dl)) + else: + self.slope.gradient = self.variance * (dL_dK * phi1.dot(dphi2_dl.T)).sum() + (dL_dK * phi2.dot(dphi1_dl.T)).sum() + self.slope.gradient = np.where(np.isnan(self.slope.gradient), 0, self.slope.gradient) diff --git a/GPy/kern/_src/coregionalize.py b/GPy/kern/_src/coregionalize.py index 5b91de1c..3d71c99f 100644 --- a/GPy/kern/_src/coregionalize.py +++ b/GPy/kern/_src/coregionalize.py @@ -5,12 +5,8 @@ from .kern import Kern import numpy as np from ...core.parameterization import Param from ...core.parameterization.transformations import Logexp -from ...util.config import config # for assesing whether to use weave - -try: - from scipy import weave -except ImportError: - config.set('weave', 'working', 'False') +from ...util.config import config # for assesing whether to use cython +from . import coregionalize_cython class Coregionalize(Kern): """ @@ -61,13 +57,8 @@ class Coregionalize(Kern): self.B = np.dot(self.W, self.W.T) + np.diag(self.kappa) def K(self, X, X2=None): - if config.getboolean('weave', 'working'): - try: - return self._K_weave(X, X2) - except: - print("\n Weave compilation failed. Falling back to (slower) numpy implementation\n") - config.set('weave', 'working', 'False') - return self._K_numpy(X, X2) + if config.getboolean('cython', 'working'): + return self._K_cython(X, X2) else: return self._K_numpy(X, X2) @@ -80,36 +71,10 @@ class Coregionalize(Kern): index2 = np.asarray(X2, dtype=np.int) return self.B[index,index2.T] - def _K_weave(self, X, X2=None): - """compute the kernel function using scipy.weave""" - index = np.asarray(X, dtype=np.int) - + def _K_cython(self, X, X2=None): if X2 is None: - target = np.empty((X.shape[0], X.shape[0]), dtype=np.float64) - code=""" - for(int i=0;i +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? 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PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#endif +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__GPy__kern___src__coregionalize_cython +#define __PYX_HAVE_API__GPy__kern___src__coregionalize_cython +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "GPy/kern/_src/coregionalize_cython.pyx", + "__init__.pxd", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; 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+ +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; 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r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +static void __Pyx_RaiseBufferIndexError(int axis); + +#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) +#define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + + +/* Module declarations from 'cython' */ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'GPy.kern._src.coregionalize_cython' */ +static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_double_t = { "double_t", NULL, sizeof(__pyx_t_5numpy_double_t), { 0 }, 0, 'R', 0, 0 }; +#define __Pyx_MODULE_NAME "GPy.kern._src.coregionalize_cython" +int __pyx_module_is_main_GPy__kern___src__coregionalize_cython = 0; + +/* Implementation of 'GPy.kern._src.coregionalize_cython' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_pf_3GPy_4kern_4_src_20coregionalize_cython_K_symmetric(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_B, PyArrayObject *__pyx_v_X); /* proto */ +static PyObject *__pyx_pf_3GPy_4kern_4_src_20coregionalize_cython_2K_asymmetric(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_B, PyArrayObject *__pyx_v_X, PyArrayObject *__pyx_v_X2); /* proto */ +static PyObject *__pyx_pf_3GPy_4kern_4_src_20coregionalize_cython_4gradient_reduce(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_D, PyArrayObject *__pyx_v_dL_dK, PyArrayObject *__pyx_v_index, PyArrayObject *__pyx_v_index2); /* 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 char __pyx_k_B[] = "B"; +static char __pyx_k_D[] = "D"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_K[] = "K"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_M[] = "M"; +static char __pyx_k_N[] = "N"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_X[] = "X"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_j[] = "j"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_m[] = "m"; +static char __pyx_k_n[] = "n"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_X2[] = "X2"; 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"" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static void __Pyx_RaiseBufferIndexError(int axis) { + PyErr_Format(PyExc_IndexError, + "Out of bounds on buffer access (axis %d)", axis); +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/GPy/kern/_src/coregionalize_cython.pyx b/GPy/kern/_src/coregionalize_cython.pyx new file mode 100644 index 00000000..ede21edf --- /dev/null +++ b/GPy/kern/_src/coregionalize_cython.pyx @@ -0,0 +1,34 @@ +#cython: boundscheck=True +#cython: wraparound=True +import cython +import numpy as np +cimport numpy as np + +def K_symmetric(np.ndarray[double, ndim=2] B, np.ndarray[np.int64_t, ndim=1] X): + cdef int N = X.size + cdef np.ndarray[np.double_t, ndim=2] K = np.empty((N, N)) + for n in range(N): + for m in range(N): + K[n,m] = B[X[n],X[m]] + return K + +def K_asymmetric(np.ndarray[double, ndim=2] B, np.ndarray[np.int64_t, ndim=1] X, np.ndarray[np.int64_t, ndim=1] X2): + cdef int N = X.size + cdef int M = X2.size + cdef np.ndarray[np.double_t, ndim=2] K = np.empty((N, M)) + for n in range(N): + for m in range(M): + K[n,m] = B[X[n],X2[m]] + return K + +def gradient_reduce(int D, np.ndarray[double, ndim=2] dL_dK, np.ndarray[np.int64_t, ndim=1] index, np.ndarray[np.int64_t, ndim=1] index2): + cdef np.ndarray[np.double_t, ndim=2] dL_dK_small = np.zeros((D, D)) + cdef int N = index.size + cdef int M = index2.size + for i in range(N): + for j in range(M): + dL_dK_small[index2[j],index[i]] += dL_dK[i,j]; + return dL_dK_small + + + diff --git a/GPy/kern/_src/independent_outputs.py b/GPy/kern/_src/independent_outputs.py index 6f8b7be1..9ebb5711 100644 --- a/GPy/kern/_src/independent_outputs.py +++ b/GPy/kern/_src/independent_outputs.py @@ -105,7 +105,7 @@ class IndependentOutputs(CombinationKernel): if X2 is None: # TODO: make use of index_to_slices # FIXME: Broken as X is already sliced out - print "Warning, gradients_X may not be working, I believe X has already been sliced out by the slicer!" + print("Warning, gradients_X may not be working, I believe X has already been sliced out by the slicer!") values = np.unique(X[:,self.index_dim]) slices = [X[:,self.index_dim]==i for i in values] [target.__setitem__(s, kern.gradients_X(dL_dK[s,s],X[s],None)) diff --git a/GPy/kern/_src/mlp.py b/GPy/kern/_src/mlp.py index 4488ea82..e319b8b4 100644 --- a/GPy/kern/_src/mlp.py +++ b/GPy/kern/_src/mlp.py @@ -78,7 +78,7 @@ class MLP(Kern): *((vec1[:, None]+vec2[None, :])*self.weight_variance + 2*self.bias_variance + 2.))*base_cov_grad).sum() - def update_gradients_diag(self, X): + def update_gradients_diag(self, dL_dKdiag, X): self._K_diag_computations(X) self.variance.gradient = np.sum(self._K_diag_dvar*dL_dKdiag) diff --git a/GPy/kern/_src/rbf.py b/GPy/kern/_src/rbf.py index c6998370..73f2d0a4 100644 --- a/GPy/kern/_src/rbf.py +++ b/GPy/kern/_src/rbf.py @@ -20,7 +20,6 @@ class RBF(Stationary): _support_GPU = True def __init__(self, input_dim, variance=1., lengthscale=None, ARD=False, active_dims=None, name='rbf', useGPU=False): super(RBF, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name, useGPU=useGPU) - self.psicomp = PSICOMP_RBF() if self.useGPU: self.psicomp = PSICOMP_RBF_GPU() else: @@ -36,6 +35,7 @@ class RBF(Stationary): dc = super(RBF, self).__getstate__() if self.useGPU: dc['psicomp'] = PSICOMP_RBF() + dc['useGPU'] = False return dc def __setstate__(self, state): diff --git a/GPy/kern/_src/stationary.py b/GPy/kern/_src/stationary.py index 6bc4b304..e69e316b 100644 --- a/GPy/kern/_src/stationary.py +++ b/GPy/kern/_src/stationary.py @@ -9,13 +9,15 @@ from ...util.linalg import tdot from ... import util import numpy as np from scipy import integrate -from ...util.config import config # for assesing whether to use weave +from ...util.config import config # for assesing whether to use cython from ...util.caching import Cache_this try: - from scipy import weave + from . import stationary_cython except ImportError: - config.set('weave', 'working', 'False') + print('warning in sationary: failed to import cython module: falling back to numpy') + config.set('cython', 'working', 'false') + class Stationary(Kern): """ @@ -153,28 +155,18 @@ class Stationary(Kern): (dL_dK), compute the gradient wrt the parameters of this kernel, and store in the parameters object as e.g. self.variance.gradient """ - self.variance.gradient = np.einsum('ij,ij,i', self.K(X, X2), dL_dK, 1./self.variance) + self.variance.gradient = np.sum(self.K(X, X2)* dL_dK)/self.variance #now the lengthscale gradient(s) dL_dr = self.dK_dr_via_X(X, X2) * dL_dK if self.ARD: - #rinv = self._inv_dis# this is rather high memory? Should we loop instead?t(X, X2) - #d = X[:, None, :] - X2[None, :, :] - #x_xl3 = np.square(d) - #self.lengthscale.gradient = -((dL_dr*rinv)[:,:,None]*x_xl3).sum(0).sum(0)/self.lengthscale**3 + tmp = dL_dr*self._inv_dist(X, X2) if X2 is None: X2 = X - - - if config.getboolean('weave', 'working'): - try: - self.lengthscale.gradient = self.weave_lengthscale_grads(tmp, X, X2) - except: - print("\n Weave compilation failed. Falling back to (slower) numpy implementation\n") - config.set('weave', 'working', 'False') - self.lengthscale.gradient = np.array([np.einsum('ij,ij,...', tmp, np.square(X[:,q:q+1] - X2[:,q:q+1].T), -1./self.lengthscale[q]**3) for q in range(self.input_dim)]) + if config.getboolean('cython', 'working'): + self.lengthscale.gradient = self._lengthscale_grads_cython(tmp, X, X2) else: - self.lengthscale.gradient = np.array([np.einsum('ij,ij,...', tmp, np.square(X[:,q:q+1] - X2[:,q:q+1].T), -1./self.lengthscale[q]**3) for q in range(self.input_dim)]) + self.lengthscale.gradient = self._lengthscale_grads_pure(tmp, X, X2) else: r = self._scaled_dist(X, X2) self.lengthscale.gradient = -np.sum(dL_dr*r)/self.lengthscale @@ -189,43 +181,27 @@ class Stationary(Kern): dist = self._scaled_dist(X, X2).copy() return 1./np.where(dist != 0., dist, np.inf) - def weave_lengthscale_grads(self, tmp, X, X2): - """Use scipy.weave to compute derivatives wrt the lengthscales""" + def _lengthscale_grads_pure(self, tmp, X, X2): + return -np.array([np.sum(tmp * np.square(X[:,q:q+1] - X2[:,q:q+1].T)) for q in range(self.input_dim)])/self.lengthscale**3 + + def _lengthscale_grads_cython(self, tmp, X, X2): N,M = tmp.shape - Q = X.shape[1] - if hasattr(X, 'values'):X = X.values - if hasattr(X2, 'values'):X2 = X2.values + Q = self.input_dim + X, X2 = np.ascontiguousarray(X), np.ascontiguousarray(X2) grads = np.zeros(self.input_dim) - code = """ - double gradq; - for(int q=0; q - #include - """ - weave_options = {'headers' : [''], - 'extra_compile_args': ['-fopenmp -O3'], # -march=native'], - 'extra_link_args' : ['-lgomp']} - weave.inline(code, ['ret', 'N', 'D', 'M', 'tmp', 'X', 'X2'], type_converters=weave.converters.blitz, support_code=support_code, **weave_options) - return ret/self.lengthscale**2 + X, X2 = np.ascontiguousarray(X), np.ascontiguousarray(X2) + grad = np.zeros(X.shape) + stationary_cython.grad_X(X.shape[0], X.shape[1], X2.shape[0], X, X2, tmp, grad) + return grad/self.lengthscale**2 def gradients_X_diag(self, dL_dKdiag, X): return np.zeros(X.shape) @@ -290,6 +237,9 @@ class Stationary(Kern): def input_sensitivity(self, summarize=True): return self.variance*np.ones(self.input_dim)/self.lengthscale**2 + + + class Exponential(Stationary): def __init__(self, input_dim, variance=1., lengthscale=None, ARD=False, active_dims=None, name='Exponential'): super(Exponential, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name) diff --git a/GPy/kern/_src/stationary_cython.c b/GPy/kern/_src/stationary_cython.c new file mode 100644 index 00000000..36a782a9 --- /dev/null +++ b/GPy/kern/_src/stationary_cython.c @@ -0,0 +1,20141 @@ +/* Generated by Cython 0.21 */ + +#define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_21" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#endif +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__GPy__kern___src__stationary_cython +#define __PYX_HAVE_API__GPy__kern___src__stationary_cython +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "stationary_utils.h" +#include "pythread.h" +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "GPy/kern/_src/stationary_cython.pyx", + "__init__.pxd", + "GPy/kern/_src/stringsource", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; + +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && MSC_VER + #include + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using MSVC atomics" + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview) \ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview) \ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; + +/* "GPy/kern/_src/stationary_cython.pyx":8 + * from cython.parallel import prange + * + * ctypedef np.float64_t DTYPE_t # <<<<<<<<<<<<<< + * + * cdef extern from "stationary_utils.h": + */ +typedef __pyx_t_5numpy_float64_t __pyx_t_3GPy_4kern_4_src_17stationary_cython_DTYPE_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_array_obj; +struct __pyx_MemviewEnum_obj; +struct __pyx_memoryview_obj; +struct __pyx_memoryviewslice_obj; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* "View.MemoryView":99 + * + * @cname("__pyx_array") + * cdef class array: # <<<<<<<<<<<<<< + * + * cdef: + */ +struct __pyx_array_obj { + PyObject_HEAD + char *data; + Py_ssize_t len; + char *format; + int ndim; + Py_ssize_t *_shape; + Py_ssize_t *_strides; + Py_ssize_t itemsize; + PyObject *mode; + PyObject *_format; + void (*callback_free_data)(void *); + int free_data; 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+ if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +static CYTHON_INLINE int __Pyx_div_int(int, int); /* proto */ + +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) + +static CYTHON_INLINE int __Pyx_mod_int(int, int); /* proto */ + +#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d +#define __Pyx_MEMVIEW_DIRECT 1 +#define __Pyx_MEMVIEW_PTR 2 +#define __Pyx_MEMVIEW_FULL 4 +#define __Pyx_MEMVIEW_CONTIG 8 +#define __Pyx_MEMVIEW_STRIDED 16 +#define __Pyx_MEMVIEW_FOLLOW 32 +#define __Pyx_IS_C_CONTIG 1 +#define __Pyx_IS_F_CONTIG 2 +static int __Pyx_init_memviewslice( + struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference); 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+ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +#include + +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ + +static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_memoryview_transpose(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview__get__base(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_shape(PyObject *__pyx_v_self); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +static PyObject *__pyx_memoryview_get_strides(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_suboffsets(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ + +static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_double(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim); + +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'GPy.kern._src.stationary_cython' */ +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3GPy_4kern_4_src_17stationary_cython_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3GPy_4kern_4_src_17stationary_cython_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; +#define __Pyx_MODULE_NAME "GPy.kern._src.stationary_cython" +int __pyx_module_is_main_GPy__kern___src__stationary_cython = 0; + +/* Implementation of 'GPy.kern._src.stationary_cython' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_xrange; +static PyObject *__pyx_builtin_id; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_pf_3GPy_4kern_4_src_17stationary_cython_grad_X(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_N, int __pyx_v_D, int __pyx_v_M, PyArrayObject *__pyx_v__X, PyArrayObject *__pyx_v__X2, PyArrayObject *__pyx_v__tmp, PyArrayObject *__pyx_v__grad); /* proto */ +static PyObject *__pyx_pf_3GPy_4kern_4_src_17stationary_cython_2grad_X_cython(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED int __pyx_v_N, int __pyx_v_D, int __pyx_v_M, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_X2, __Pyx_memviewslice __pyx_v_tmp, __Pyx_memviewslice __pyx_v_grad); /* proto */ +static PyObject *__pyx_pf_3GPy_4kern_4_src_17stationary_cython_4lengthscale_grads_in_c(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_N, int __pyx_v_M, int __pyx_v_Q, PyArrayObject *__pyx_v__tmp, PyArrayObject *__pyx_v__X, PyArrayObject *__pyx_v__X2, PyArrayObject *__pyx_v__grad); /* proto */ +static PyObject *__pyx_pf_3GPy_4kern_4_src_17stationary_cython_6lengthscale_grads(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_N, int __pyx_v_M, int __pyx_v_Q, __Pyx_memviewslice __pyx_v_tmp, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_X2, __Pyx_memviewslice __pyx_v_grad); /* 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 int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static char __pyx_k_B[] = "B"; +static char __pyx_k_D[] = "D"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_M[] = "M"; +static char __pyx_k_N[] = "N"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_X[] = "_X"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_c[] = "c"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_m[] = "m"; +static char __pyx_k_n[] = "n"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_X2[] = "_X2"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_id[] = "id"; +static char __pyx_k_nd[] = "nd"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_X_2[] = "X"; +static char __pyx_k_obj[] = "obj"; +static char __pyx_k_tmp[] = "_tmp"; +static char __pyx_k_X2_2[] = "X2"; +static char __pyx_k_base[] = "base"; +static char __pyx_k_dist[] = "dist"; +static char __pyx_k_grad[] = "_grad"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_mode[] = "mode"; +static char __pyx_k_name[] = "name"; +static char __pyx_k_ndim[] = "ndim"; +static char __pyx_k_pack[] = "pack"; +static char __pyx_k_size[] = "size"; +static char __pyx_k_step[] = "step"; +static char __pyx_k_stop[] = "stop"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_class[] = "__class__"; +static char __pyx_k_error[] = "error"; +static char __pyx_k_flags[] = "flags"; +static char __pyx_k_gradq[] = "gradq"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_shape[] = "shape"; +static char __pyx_k_start[] = "start"; +static char __pyx_k_tmp_2[] = "tmp"; +static char __pyx_k_format[] = "format"; +static char __pyx_k_grad_2[] = "grad"; +static char __pyx_k_grad_X[] = "grad_X"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_name_2[] = "__name__"; +static char __pyx_k_struct[] = "struct"; +static char __pyx_k_unpack[] = "unpack"; +static char __pyx_k_xrange[] = "xrange"; +static char __pyx_k_fortran[] = "fortran"; +static char __pyx_k_memview[] = "memview"; +static char __pyx_k_Ellipsis[] = "Ellipsis"; +static char __pyx_k_itemsize[] = "itemsize"; +static char __pyx_k_TypeError[] = "TypeError"; +static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_IndexError[] = "IndexError"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static char __pyx_k_MemoryError[] = "MemoryError"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_grad_X_cython[] = "grad_X_cython"; +static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static char __pyx_k_lengthscale_grads[] = "lengthscale_grads"; +static char __pyx_k_strided_and_direct[] = ""; +static char __pyx_k_strided_and_indirect[] = ""; +static char __pyx_k_contiguous_and_direct[] = ""; +static char __pyx_k_MemoryView_of_r_object[] = ""; +static char __pyx_k_lengthscale_grads_in_c[] = "lengthscale_grads_in_c"; +static char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static char __pyx_k_contiguous_and_indirect[] = ""; +static char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static char __pyx_k_getbuffer_obj_view_flags[] = "getbuffer(obj, view, flags)"; +static char __pyx_k_Dimension_d_is_not_direct[] = "Dimension %d is not direct"; +static char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)"; +static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)"; +static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static char __pyx_k_strided_and_direct_or_indirect[] = ""; +static char __pyx_k_GPy_kern__src_stationary_cython[] = "GPy.kern._src.stationary_cython"; +static char __pyx_k_home_james_work_GPy_GPy_kern__s[] = "/home/james/work/GPy/GPy/kern/_src/stationary_cython.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; +static char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static char __pyx_k_Cannot_transpose_memoryview_with[] = "Cannot transpose memoryview with indirect dimensions"; +static char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_n_s_D; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +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_kern__src_stationary_cython; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_M; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_n_s_N; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_Q; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_X; +static PyObject *__pyx_n_s_X2; +static PyObject *__pyx_n_s_X2_2; +static PyObject *__pyx_n_s_X_2; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_d; +static PyObject *__pyx_n_s_dist; +static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_flags; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_fortran; +static PyObject *__pyx_n_u_fortran; +static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; +static PyObject *__pyx_n_s_grad; +static PyObject *__pyx_n_s_grad_2; +static PyObject *__pyx_n_s_grad_X; +static PyObject *__pyx_n_s_grad_X_cython; +static PyObject *__pyx_n_s_gradq; +static PyObject *__pyx_kp_s_home_james_work_GPy_GPy_kern__s; +static PyObject *__pyx_n_s_id; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_itemsize; +static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_lengthscale_grads; +static PyObject *__pyx_n_s_lengthscale_grads_in_c; +static PyObject *__pyx_n_s_m; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_memview; +static PyObject *__pyx_n_s_mode; +static PyObject *__pyx_n_s_n; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_n_s_nd; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_pack; +static PyObject *__pyx_n_s_pyx_getbuffer; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_q; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_size; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_step; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_kp_s_strided_and_direct; +static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; +static PyObject *__pyx_kp_s_strided_and_indirect; +static PyObject *__pyx_n_s_struct; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_tmp; +static PyObject *__pyx_n_s_tmp_2; +static PyObject *__pyx_kp_s_unable_to_allocate_array_data; +static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_n_s_xrange; +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_neg_1; +static PyObject *__pyx_tuple_; +static PyObject *__pyx_tuple__2; +static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; +static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__7; +static PyObject *__pyx_tuple__8; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_slice__14; +static PyObject *__pyx_slice__15; +static PyObject *__pyx_slice__16; +static PyObject *__pyx_tuple__10; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__17; +static PyObject *__pyx_tuple__18; +static PyObject *__pyx_tuple__20; +static PyObject *__pyx_tuple__22; +static PyObject *__pyx_tuple__24; +static PyObject *__pyx_tuple__26; +static PyObject *__pyx_tuple__27; +static PyObject *__pyx_tuple__28; +static PyObject *__pyx_tuple__29; +static PyObject *__pyx_tuple__30; +static PyObject *__pyx_codeobj__19; +static PyObject *__pyx_codeobj__21; +static PyObject *__pyx_codeobj__23; +static PyObject *__pyx_codeobj__25; + +/* "GPy/kern/_src/stationary_cython.pyx":16 + * void _lengthscale_grads "_lengthscale_grads" (int N, int M, int Q, double* tmp, double* X, double* X2, double* grad) + * + * def grad_X(int N, int D, int M, # <<<<<<<<<<<<<< + * np.ndarray[DTYPE_t, ndim=2] _X, + * np.ndarray[DTYPE_t, ndim=2] _X2, + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_3GPy_4kern_4_src_17stationary_cython_1grad_X(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_3GPy_4kern_4_src_17stationary_cython_1grad_X = {"grad_X", (PyCFunction)__pyx_pw_3GPy_4kern_4_src_17stationary_cython_1grad_X, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_3GPy_4kern_4_src_17stationary_cython_1grad_X(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + int __pyx_v_N; + int __pyx_v_D; + int __pyx_v_M; + PyArrayObject *__pyx_v__X = 0; + PyArrayObject *__pyx_v__X2 = 0; + PyArrayObject *__pyx_v__tmp = 0; + PyArrayObject *__pyx_v__grad = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("grad_X (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_N,&__pyx_n_s_D,&__pyx_n_s_M,&__pyx_n_s_X,&__pyx_n_s_X2,&__pyx_n_s_tmp,&__pyx_n_s_grad,0}; + PyObject* values[7] = {0,0,0,0,0,0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); + case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); + case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); 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goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_1 = (__pyx_t_9 != Py_None); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_v_have_step = __pyx_t_1; + + /* "View.MemoryView":725 + * have_step = index.step is not None + * + * slice_memviewslice( # <<<<<<<<<<<<<< + * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], + * dim, new_ndim, p_suboffset_dim, + */ + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":731 + * have_start, have_stop, have_step, + * True) + * new_ndim += 1 # <<<<<<<<<<<<<< + * + * if 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suboffset_dim = -1, dim + * cdef bint negative_step + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("View.MemoryView.memview_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_memviewsliceobj); + __Pyx_XDECREF(__pyx_v_index); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":764 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, Py_ssize_t __pyx_v_shape, Py_ssize_t __pyx_v_stride, Py_ssize_t __pyx_v_suboffset, int __pyx_v_dim, int __pyx_v_new_ndim, int *__pyx_v_suboffset_dim, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_stop, Py_ssize_t __pyx_v_step, int __pyx_v_have_start, int __pyx_v_have_stop, int __pyx_v_have_step, int __pyx_v_is_slice) { + Py_ssize_t __pyx_v_new_shape; + int __pyx_v_negative_step; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "View.MemoryView":784 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ + __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":786 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ + __pyx_t_1 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":787 + * + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + goto __pyx_L4; + } + __pyx_L4:; + + /* "View.MemoryView":788 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ + __pyx_t_1 = (0 <= __pyx_v_start); + if (__pyx_t_1) { + __pyx_t_1 = (__pyx_v_start < __pyx_v_shape); + } + __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":789 + * start += shape + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< + * else: + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L5; + } + __pyx_L5:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":792 + * else: + * + * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< + * + * if have_step and step == 0: + */ + __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); + if (__pyx_t_1) { + goto __pyx_L7_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L6_bool_binop_done; + } + __pyx_L7_next_and:; + __pyx_t_1 = ((__pyx_v_step < 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L6_bool_binop_done:; + __pyx_v_negative_step = __pyx_t_2; + + /* "View.MemoryView":794 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ + __pyx_t_1 = (__pyx_v_have_step != 0); + if (__pyx_t_1) { + goto __pyx_L10_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L9_bool_binop_done; + } + __pyx_L10_next_and:; + __pyx_t_1 = ((__pyx_v_step == 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L9_bool_binop_done:; + if (__pyx_t_2) { + + /* "View.MemoryView":795 + * + * if have_step and step == 0: + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L8; + } + __pyx_L8:; + + /* "View.MemoryView":798 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + __pyx_t_2 = (__pyx_v_have_start != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":799 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":800 + * if have_start: + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if start < 0: + * start = 0 + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":801 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":802 + * start += shape + * if start < 0: + * start = 0 # <<<<<<<<<<<<<< + * elif start >= shape: + * if negative_step: + */ + __pyx_v_start = 0; + goto __pyx_L13; + } + __pyx_L13:; + goto __pyx_L12; + } + + /* "View.MemoryView":803 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":804 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":805 + * elif start >= shape: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = shape + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L14; + } + /*else*/ { + + /* "View.MemoryView":807 + * start = shape - 1 + * else: + * start = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_start = __pyx_v_shape; + } + __pyx_L14:; + goto __pyx_L12; + } + __pyx_L12:; + goto __pyx_L11; + } + /*else*/ { + + /* "View.MemoryView":809 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":810 + * else: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = 0 + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L15; + } + /*else*/ { + + /* "View.MemoryView":812 + * start = shape - 1 + * else: + * start = 0 # <<<<<<<<<<<<<< + * + * if have_stop: + */ + __pyx_v_start = 0; + } + __pyx_L15:; + } + __pyx_L11:; + + /* "View.MemoryView":814 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + __pyx_t_2 = (__pyx_v_have_stop != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":815 + * + * if have_stop: + * if stop < 0: # 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<<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + goto __pyx_L17; + } + __pyx_L17:; + goto __pyx_L16; + } + /*else*/ { + + /* "View.MemoryView":822 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":823 + * else: + * if negative_step: + * stop = -1 # <<<<<<<<<<<<<< + * else: + * stop = shape + */ + __pyx_v_stop = -1; + goto __pyx_L19; + } + /*else*/ { + + /* "View.MemoryView":825 + * stop = -1 + * else: + * stop = shape # <<<<<<<<<<<<<< + * + * if not have_step: + */ + __pyx_v_stop = __pyx_v_shape; + } + __pyx_L19:; + } + __pyx_L16:; + + /* "View.MemoryView":827 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":828 + * + * if not have_step: + * step = 1 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_step = 1; + goto __pyx_L20; + } + __pyx_L20:; + + /* "View.MemoryView":832 + * + * with cython.cdivision(True): + * new_shape = (stop - start) // step # <<<<<<<<<<<<<< + * + * if (stop - start) - step * new_shape: + */ + __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); + + /* "View.MemoryView":834 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":835 + * + * if (stop - start) - step * new_shape: + * new_shape += 1 # <<<<<<<<<<<<<< + * + * if new_shape < 0: + */ + __pyx_v_new_shape = (__pyx_v_new_shape + 1); + goto __pyx_L21; + } + __pyx_L21:; + + /* "View.MemoryView":837 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":838 + * + * 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* else: + */ + __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":847 + * + * if suboffset_dim[0] < 0: + * dst.data += start * stride # <<<<<<<<<<<<<< + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride + */ + __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + goto __pyx_L23; + } + /*else*/ { + + /* "View.MemoryView":849 + * dst.data += start * stride + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< + * + * if suboffset >= 0: + */ + __pyx_t_3 = (__pyx_v_suboffset_dim[0]); + (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); + } + __pyx_L23:; + + /* "View.MemoryView":851 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ + __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":852 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memview).to_dtype_func + * else: + */ + __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; + __pyx_v_to_object_func = __pyx_t_3; + + /* "View.MemoryView":1049 + * if isinstance(memview, _memoryviewslice): + * to_object_func = (<_memoryviewslice> memview).to_object_func + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< + * else: + * to_object_func = NULL + */ + __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; + __pyx_v_to_dtype_func = __pyx_t_4; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1051 + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func + * else: + * to_object_func = NULL # <<<<<<<<<<<<<< + * to_dtype_func = NULL + * + */ + __pyx_v_to_object_func = NULL; + + /* "View.MemoryView":1052 + * else: + * to_object_func = NULL + * to_dtype_func = NULL # <<<<<<<<<<<<<< + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + */ + __pyx_v_to_dtype_func = NULL; + } + __pyx_L3:; + + /* "View.MemoryView":1054 + * to_dtype_func = NULL + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< + * to_object_func, to_dtype_func, + * memview.dtype_is_object) + */ + __Pyx_XDECREF(__pyx_r); + + /* "View.MemoryView":1056 + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + * to_object_func, to_dtype_func, + * memview.dtype_is_object) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "View.MemoryView":1040 + * + * @cname('__pyx_memoryview_copy_object_from_slice') + * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< + * """ + * Create a new memoryview object from a given memoryview object and slice. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_from_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + +static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { + Py_ssize_t __pyx_r; + int __pyx_t_1; + + /* "View.MemoryView":1063 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + __pyx_t_1 = ((__pyx_v_arg < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1064 + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: + * return -arg # <<<<<<<<<<<<<< + * else: + * return arg + */ + __pyx_r = (-__pyx_v_arg); + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1066 + * return -arg + * else: + * return arg # <<<<<<<<<<<<<< + * + * @cname('__pyx_get_best_slice_order') + */ + __pyx_r = __pyx_v_arg; + goto __pyx_L0; + } + + /* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + +static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_c_stride; + Py_ssize_t __pyx_v_f_stride; + char __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1074 + * """ + * cdef int i + * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< + * cdef Py_ssize_t f_stride = 0 + * + */ + __pyx_v_c_stride = 0; + + /* "View.MemoryView":1075 + * cdef int i + * cdef Py_ssize_t c_stride = 0 + * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_f_stride = 0; + + /* "View.MemoryView":1077 + * cdef Py_ssize_t f_stride = 0 + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1078 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1079 + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1080 + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + goto __pyx_L4_break; + } + } + __pyx_L4_break:; + + /* "View.MemoryView":1082 + * break + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + */ + __pyx_t_1 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1083 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1084 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1085 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1087 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1088 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1090 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + +static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; + Py_ssize_t __pyx_v_dst_extent; + Py_ssize_t __pyx_v_src_stride; + Py_ssize_t __pyx_v_dst_stride; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + + /* "View.MemoryView":1100 + * + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + */ + __pyx_v_src_extent = (__pyx_v_src_shape[0]); + + /* "View.MemoryView":1101 + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1102 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1103 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1105 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1106 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L6_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L6_next_and:; + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L7_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L7_next_and:; + + /* "View.MemoryView":1107 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + if (__pyx_t_1) { + + /* "View.MemoryView":1108 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); + goto __pyx_L4; + } + /*else*/ { + + /* "View.MemoryView":1110 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1111 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); + + /* "View.MemoryView":1112 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1113 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1115 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1116 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1120 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1121 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1126 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1133 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1135 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1136 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1138 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1141 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1150 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1151 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_idx = __pyx_t_3; + + /* "View.MemoryView":1152 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1153 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + 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__pyx_L12:; + + /* "View.MemoryView":1272 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_2 = (__pyx_v_direct_copy != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1274 + * if direct_copy: + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1275 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); + + /* "View.MemoryView":1276 + * 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__pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_7 = (__pyx_t_2 != 0); + if (__pyx_t_7) { + + /* "View.MemoryView":1283 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1284 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L14; + } + __pyx_L14:; + + /* "View.MemoryView":1286 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1287 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1288 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1290 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1291 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1222 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + + /* "View.MemoryView":1298 + * int ndim_other) nogil: + * cdef int i + * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); + + /* "View.MemoryView":1300 + * cdef int offset = ndim_other - ndim + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1301 + * + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<< + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] + */ + (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]); + + /* "View.MemoryView":1302 + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<< + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + */ + (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]); + + /* "View.MemoryView":1303 + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<< + * + * for i in range(offset): + */ + (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]); + } + + /* "View.MemoryView":1305 + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + * for i in range(offset): # <<<<<<<<<<<<<< + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + */ + __pyx_t_1 = __pyx_v_offset; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1306 + * + * for i in range(offset): + * slice.shape[i] = 1 # <<<<<<<<<<<<<< + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 + */ + (__pyx_v_slice->shape[__pyx_v_i]) = 1; + + /* "View.MemoryView":1307 + * for i in range(offset): + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] # <<<<<<<<<<<<<< + * slice.suboffsets[i] = -1 + * + */ + (__pyx_v_slice->strides[__pyx_v_i]) = (__pyx_v_slice->strides[0]); + + /* "View.MemoryView":1308 + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_slice->suboffsets[__pyx_v_i]) = -1; + } + + /* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1316 + * + * @cname('__pyx_memoryview_refcount_copying') + * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< + * int ndim, bint inc) nogil: + * + */ + +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { + int __pyx_t_1; + + /* "View.MemoryView":1320 + * + * + * if dtype_is_object: # <<<<<<<<<<<<<< + * refcount_objects_in_slice_with_gil(dst.data, dst.shape, + * dst.strides, ndim, inc) + */ + __pyx_t_1 = (__pyx_v_dtype_is_object != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1321 + * + * if dtype_is_object: + * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< + * dst.strides, ndim, inc) + * + */ + __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); + goto __pyx_L3; + } + __pyx_L3:; + + /* 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*__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + Py_ssize_t __pyx_t_2; + int __pyx_t_3; + __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); + + /* "View.MemoryView":1335 + * cdef Py_ssize_t i + * + * for i in range(shape[0]): # <<<<<<<<<<<<<< + * if ndim == 1: + * if inc: + */ + __pyx_t_1 = (__pyx_v_shape[0]); + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1336 + * + * for i in range(shape[0]): + * if ndim == 1: # <<<<<<<<<<<<<< + * if inc: + * Py_INCREF(( data)[0]) + */ + __pyx_t_3 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1337 + * for i in range(shape[0]): + * if ndim == 1: + * if inc: # <<<<<<<<<<<<<< + * Py_INCREF(( data)[0]) + * else: + */ + __pyx_t_3 = (__pyx_v_inc != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1338 + * if ndim == 1: + * if inc: + * Py_INCREF(( data)[0]) # 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/* "View.MemoryView":1355 + * bint dtype_is_object) nogil: + * refcount_copying(dst, dtype_is_object, ndim, False) + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); + + /* "View.MemoryView":1357 + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * + */ + __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1351 + * + * @cname('__pyx_memoryview_slice_assign_scalar') + * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< + * size_t itemsize, void *item, + * bint dtype_is_object) nogil: + */ + + /* function exit code */ +} + +/* 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__pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1373 + * data += stride + * else: + * for i in range(extent): # <<<<<<<<<<<<<< + * _slice_assign_scalar(data, shape + 1, strides + 1, + * ndim - 1, itemsize, item) + */ + __pyx_t_2 = __pyx_v_extent; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1374 + * else: + * for i in range(extent): + * _slice_assign_scalar(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< + * ndim - 1, itemsize, item) + * data += stride + */ + __pyx_memoryview__slice_assign_scalar(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize, __pyx_v_item); + + /* "View.MemoryView":1376 + * _slice_assign_scalar(data, shape + 1, strides + 1, + * ndim - 1, itemsize, item) + * data += stride # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_data = (__pyx_v_data + __pyx_v_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1361 + * + * @cname('__pyx_memoryview__slice_assign_scalar') + * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< + * Py_ssize_t *strides, int ndim, + * size_t itemsize, void *item) nogil: + */ + + /* function exit code */ +} + +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_array_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_array_obj *)o); + p->mode = ((PyObject*)Py_None); Py_INCREF(Py_None); + p->_format = ((PyObject*)Py_None); Py_INCREF(Py_None); + if (unlikely(__pyx_array___cinit__(o, a, k) < 0)) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_array(PyObject *o) { + struct __pyx_array_obj *p = (struct __pyx_array_obj *)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; + } + #endif + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_array___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->mode); + Py_CLEAR(p->_format); + (*Py_TYPE(o)->tp_free)(o); +} +static PyObject *__pyx_sq_item_array(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_array(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_array___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_tp_getattro_array(PyObject *o, PyObject *n) { + PyObject *v = PyObject_GenericGetAttr(o, n); + if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Clear(); + v = __pyx_array___getattr__(o, n); + } + return v; +} + +static PyObject *__pyx_getprop___pyx_array_memview(PyObject *o, CYTHON_UNUSED void *x) { + return get_memview(o); +} + +static PyMethodDef __pyx_methods_array[] = { + {"__getattr__", (PyCFunction)__pyx_array___getattr__, METH_O|METH_COEXIST, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_array[] = { + {(char *)"memview", __pyx_getprop___pyx_array_memview, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_array = { + 0, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_array, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_array = { + 0, /*mp_length*/ + __pyx_array___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_array, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_array = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_array_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_array = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.kern._src.stationary_cython.array", /*tp_name*/ + sizeof(struct __pyx_array_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_array, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_array, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_array, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + __pyx_tp_getattro_array, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_array, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + 0, /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_array, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_array, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_array, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; + +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_MemviewEnum_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_MemviewEnum_obj *)o); + p->name = Py_None; Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_Enum(PyObject *o) { + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->name); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_Enum(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + if (p->name) { + e = (*v)(p->name, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_Enum(PyObject *o) { + PyObject* tmp; + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + tmp = ((PyObject*)p->name); + p->name = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_Enum[] = { + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_MemviewEnum = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.kern._src.stationary_cython.Enum", /*tp_name*/ + sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_Enum, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + __pyx_MemviewEnum___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 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_Enum, /*tp_traverse*/ + __pyx_tp_clear_Enum, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_Enum, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_MemviewEnum___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_Enum, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; + +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryview_obj *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryview_obj *)o); + p->__pyx_vtab = __pyx_vtabptr_memoryview; + p->obj = Py_None; Py_INCREF(Py_None); + p->_size = Py_None; Py_INCREF(Py_None); + p->_array_interface = Py_None; Py_INCREF(Py_None); + p->view.obj = NULL; + if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_memoryview(PyObject *o) { + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryview___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->obj); + Py_CLEAR(p->_size); + Py_CLEAR(p->_array_interface); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + if (p->obj) { + e = (*v)(p->obj, a); if (e) return e; + } + if (p->_size) { + e = (*v)(p->_size, a); if (e) return e; + } + if (p->_array_interface) { + e = (*v)(p->_array_interface, a); if (e) return e; + } + if (p->view.obj) { + e = (*v)(p->view.obj, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_memoryview(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + tmp = ((PyObject*)p->obj); + p->obj = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_size); + p->_size = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_array_interface); + p->_array_interface = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + Py_CLEAR(p->view.obj); + return 0; +} +static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_memoryview___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_transpose(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview__get__base(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_shape(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_strides(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_suboffsets(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_ndim(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_itemsize(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_nbytes(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_size(o); +} + +static PyMethodDef __pyx_methods_memoryview[] = { + {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, + {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, + {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, + {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, 0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, 0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, 0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, 0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, 0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, 0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, 0, 0}, + {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, 0, 0}, + {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_memoryview = { + __pyx_memoryview___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_memoryview, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_memoryview = { + __pyx_memoryview___len__, /*mp_length*/ + __pyx_memoryview___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_memoryview = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.kern._src.stationary_cython.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*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_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryviewslice__get__base(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.kern._src.stationary_cython._memoryviewslice", /*tp_name*/ + sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___repr__, /*tp_repr*/ + #else + 0, /*tp_repr*/ + #endif + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___str__, /*tp_str*/ + #else + 0, /*tp_str*/ + #endif + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 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*/ + "Internal class for passing memoryview slices to Python", /*tp_doc*/ + __pyx_tp_traverse__memoryviewslice, /*tp_traverse*/ + __pyx_tp_clear__memoryviewslice, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, 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__pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_memoryview_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + PyType_Modified(__pyx_memoryview_type); + + /* "View.MemoryView":953 + * return self.from_object + * + * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + PyType_Modified(__pyx_memoryviewslice_type); + + /* "View.MemoryView":1361 + * + * @cname('__pyx_memoryview__slice_assign_scalar') + * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< + * Py_ssize_t *strides, int ndim, + * size_t itemsize, void *item) nogil: + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init GPy.kern._src.stationary_cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + Py_DECREF(__pyx_d); __pyx_d = 0; + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init GPy.kern._src.stationary_cython"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if PY_MAJOR_VERSION < 3 + return; + #else + return __pyx_m; + #endif +} + +/* Runtime support code */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +static CYTHON_INLINE int __Pyx_div_int(int a, int b) { + int q = a / b; + int r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +static CYTHON_INLINE int __Pyx_mod_int(int a, int b) { + int r = a % b; + r += ((r != 0) & ((r ^ b) < 0)) * b; + return r; +} + +static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { + va_list vargs; + char msg[200]; + va_start(vargs, fmt); +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + Py_FatalError(msg); + va_end(vargs); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + Py_ssize_t q = a / b; + Py_ssize_t r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_COMPILING_IN_CPYTHON +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + length = strlen(cstring); + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; +#else + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); +#endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} + +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else + return NULL; + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +static CYTHON_INLINE long __Pyx_div_long(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 2, + &__Pyx_TypeInfo_double, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_double(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 1, + &__Pyx_TypeInfo_double, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs->memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs->suboffsets[index] >= 0 || mvs->strides[index] != itemsize) + return 0; + itemsize *= mvs->shape[index]; + } + return 1; +} + +static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(char) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x)) + } else if (sizeof(char) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(char, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/GPy/kern/_src/stationary_cython.pyx b/GPy/kern/_src/stationary_cython.pyx new file mode 100644 index 00000000..c550fc91 --- /dev/null +++ b/GPy/kern/_src/stationary_cython.pyx @@ -0,0 +1,59 @@ +#cython: boundscheck=False +#cython: nonecheck=False +#cython: wraparound=False +import numpy as np +cimport numpy as np +from cython.parallel import prange + +ctypedef np.float64_t DTYPE_t + +cdef extern from "stationary_utils.h": + void _grad_X "_grad_X" (int N, int D, int M, double* X, double* X2, double* tmp, double* grad) + +cdef extern from "stationary_utils.h": + void _lengthscale_grads "_lengthscale_grads" (int N, int M, int Q, double* tmp, double* X, double* X2, double* grad) + +def grad_X(int N, int D, int M, + np.ndarray[DTYPE_t, ndim=2] _X, + np.ndarray[DTYPE_t, ndim=2] _X2, + np.ndarray[DTYPE_t, ndim=2] _tmp, + np.ndarray[DTYPE_t, ndim=2] _grad): + cdef double *X = _X.data + cdef double *X2 = _X2.data + cdef double *tmp = _tmp.data + cdef double *grad = _grad.data + _grad_X(N, D, M, X, X2, tmp, grad) # return nothing, work in place. + +def grad_X_cython(int N, int D, int M, double[:,:] X, double[:,:] X2, double[:,:] tmp, double[:,:] grad): + cdef int n,d,nd,m + for nd in prange(N*D, nogil=True): + n = nd/D + d = nd%D + grad[n,d] = 0.0 + for m in range(M): + grad[n,d] += tmp[n,m]*(X[n,d]-X2[m,d]) + + + +def lengthscale_grads_in_c(int N, int M, int Q, + np.ndarray[DTYPE_t, ndim=2] _tmp, + np.ndarray[DTYPE_t, ndim=2] _X, + np.ndarray[DTYPE_t, ndim=2] _X2, + np.ndarray[DTYPE_t, ndim=1] _grad): + cdef double *tmp = _tmp.data + cdef double *X = _X.data + cdef double *X2 = _X2.data + cdef double *grad = _grad.data + _lengthscale_grads(N, M, Q, tmp, X, X2, grad) # return nothing, work in place. + +def lengthscale_grads(int N, int M, int Q, double[:,:] tmp, double[:,:] X, double[:,:] X2, double[:] grad): + cdef int q, n, m + cdef double gradq, dist + for q in range(Q): + grad[q] = 0.0 + for n in range(N): + for m in range(M): + dist = X[n,q] - X2[m,q] + grad[q] += tmp[n,m]*dist*dist + + diff --git a/GPy/kern/_src/stationary_utils.c b/GPy/kern/_src/stationary_utils.c new file mode 100644 index 00000000..1ae1ff33 --- /dev/null +++ b/GPy/kern/_src/stationary_utils.c @@ -0,0 +1,54 @@ +void _grad_X(int N, int D, int M, double* X, double* X2, double* tmp, double* grad){ +double retnd; +int n,d,nd,m; +#pragma omp parallel for private(nd,n,d, retnd, m) +for(nd=0;nd<(D*N);nd++){ + n = nd/D; + d = nd%D; + retnd = 0.0; + for(m=0;m +void _grad_X(int N, int D, int M, double*X, double* X2, double* tmp, double* grad); +void _lengthscale_grads(int N, int D, int M, double* X, double* X2, double* tmp, double* grad); diff --git a/GPy/likelihoods/likelihood.py b/GPy/likelihoods/likelihood.py index 5388526e..67a6a3a3 100644 --- a/GPy/likelihoods/likelihood.py +++ b/GPy/likelihoods/likelihood.py @@ -41,6 +41,14 @@ class Likelihood(Parameterized): self.log_concave = False self.not_block_really = False + def request_num_latent_functions(self, Y): + """ + The likelihood should infer how many latent functions are needed for the likelihood + + Default is the number of outputs + """ + return Y.shape[1] + def _gradients(self,partial): return np.zeros(0) @@ -118,22 +126,57 @@ class Likelihood(Parameterized): """Generate a function which can be integrated to give p(Y*|Y) = int p(Y*|f*)p(f*|Y) df*""" def f(fi_star): - #exponent = np.exp(-(1./(2*v))*np.square(m-f_star)) + #exponent = np.exp(-(1./(2*vi))*np.square(mi-fi_star)) #from GPy.util.misc import safe_exp #exponent = safe_exp(exponent) - #return self.pdf(f_star, y, y_m)*exponent + #res = safe_exp(self.logpdf(fi_star, yi, yi_m))*exponent #More stable in the log space - return np.exp(self.logpdf(fi_star, yi, yi_m) + res = np.exp(self.logpdf(fi_star, yi, yi_m) - 0.5*np.log(2*np.pi*vi) - - 0.5*np.square(mi-fi_star)/vi) + - 0.5*np.square(fi_star-mi)/vi) + if not np.isfinite(res): + import ipdb; ipdb.set_trace() # XXX BREAKPOINT + return res + return f p_ystar, _ = zip(*[quad(integral_generator(yi, mi, vi, yi_m), -np.inf, np.inf) for yi, mi, vi, yi_m in zipped_values]) - p_ystar = np.array(p_ystar).reshape(-1, 1) + p_ystar = np.array(p_ystar).reshape(*y_test.shape) return np.log(p_ystar) + def log_predictive_density_sampling(self, y_test, mu_star, var_star, Y_metadata=None, num_samples=1000): + """ + Calculation of the log predictive density via sampling + + .. math: + log p(y_{*}|D) = log 1/num_samples prod^{S}_{s=1} p(y_{*}|f_{*s}) + f_{*s} ~ p(f_{*}|\mu_{*}\\sigma^{2}_{*}) + + :param y_test: test observations (y_{*}) + :type y_test: (Nx1) array + :param mu_star: predictive mean of gaussian p(f_{*}|mu_{*}, var_{*}) + :type mu_star: (Nx1) array + :param var_star: predictive variance of gaussian p(f_{*}|mu_{*}, var_{*}) + :type var_star: (Nx1) array + :param num_samples: num samples of p(f_{*}|mu_{*}, var_{*}) to take + :type num_samples: int + """ + assert y_test.shape==mu_star.shape + assert y_test.shape==var_star.shape + assert y_test.shape[1] == 1 + + #Take samples of p(f*|y) + #fi_samples = np.random.randn(num_samples)*np.sqrt(var_star) + mu_star + fi_samples = np.random.normal(mu_star, np.sqrt(var_star), size=(mu_star.shape[0], num_samples)) + + from scipy.misc import logsumexp + log_p_ystar = -np.log(num_samples) + logsumexp(self.logpdf(fi_samples, y_test, Y_metadata=Y_metadata), axis=1) + log_p_ystar = np.array(log_p_ystar).reshape(*y_test.shape) + return log_p_ystar + + def _moments_match_ep(self,obs,tau,v): """ Calculation of moments using quadrature @@ -170,9 +213,9 @@ class Likelihood(Parameterized): #only compute gh points if required __gh_points = None - def _gh_points(self): + def _gh_points(self, T=20): if self.__gh_points is None: - self.__gh_points = np.polynomial.hermite.hermgauss(20) + self.__gh_points = np.polynomial.hermite.hermgauss(T) return self.__gh_points def variational_expectations(self, Y, m, v, gh_points=None, Y_metadata=None): @@ -211,9 +254,11 @@ class Likelihood(Parameterized): #d2logp_dx2 = np.clip(d2logp_dx2,-1e9,1e9) #average over the gird to get derivatives of the Gaussian's parameters - F = np.dot(logp, gh_w) - dF_dm = np.dot(dlogp_dx, gh_w) - dF_dv = np.dot(d2logp_dx2, gh_w)/2. + #division by pi comes from fact that for each quadrature we need to scale by 1/sqrt(pi) + F = np.dot(logp, gh_w)/np.sqrt(np.pi) + dF_dm = np.dot(dlogp_dx, gh_w)/np.sqrt(np.pi) + dF_dv = np.dot(d2logp_dx2, gh_w)/np.sqrt(np.pi) + dF_dv /= 2. if np.any(np.isnan(dF_dv)) or np.any(np.isinf(dF_dv)): stop @@ -221,8 +266,8 @@ class Likelihood(Parameterized): stop if self.size: - dF_dtheta = self.dlogpdf_dtheta(X, Y[:,None]) # Ntheta x (orig size) x N_{quad_points} - dF_dtheta = np.dot(dF_dtheta, gh_w) + dF_dtheta = self.dlogpdf_dtheta(X, Y[:,None], Y_metadata=Y_metadata) # Ntheta x (orig size) x N_{quad_points} + dF_dtheta = np.dot(dF_dtheta, gh_w)/np.sqrt(np.pi) dF_dtheta = dF_dtheta.reshape(self.size, shape[0], shape[1]) else: dF_dtheta = None # Not yet implemented @@ -253,13 +298,8 @@ class Likelihood(Parameterized): return self.conditional_mean(f)*p scaled_mean = [quad(int_mean, fmin, fmax,args=(mj,s2j))[0] for mj,s2j in zip(mu,variance)] mean = np.array(scaled_mean)[:,None] / np.sqrt(2*np.pi*(variance)) - return mean - def _conditional_mean(self, f): - """Quadrature calculation of the conditional mean: E(Y_star|f)""" - raise NotImplementedError("implement this function to make predictions") - def predictive_variance(self, mu,variance, predictive_mean=None, Y_metadata=None): """ Approximation to the predictive variance: V(Y_star) @@ -563,23 +603,30 @@ class Likelihood(Parameterized): :param full_cov: whether to use the full covariance or just the diagonal :type full_cov: Boolean """ - - pred_mean = self.predictive_mean(mu, var, Y_metadata) - pred_var = self.predictive_variance(mu, var, pred_mean, Y_metadata) + try: + pred_mean = self.predictive_mean(mu, var, Y_metadata=Y_metadata) + pred_var = self.predictive_variance(mu, var, pred_mean, Y_metadata=Y_metadata) + except NotImplementedError: + print "Finding predictive mean and variance via sampling rather than quadrature" + Nf_samp = 300 + Ny_samp = 1 + s = np.random.randn(mu.shape[0], Nf_samp)*np.sqrt(var) + mu + ss_y = self.samples(s, Y_metadata, samples=Ny_samp) + pred_mean = np.mean(ss_y, axis=1)[:, None] + pred_var = np.var(ss_y, axis=1)[:, None] return pred_mean, pred_var def predictive_quantiles(self, mu, var, quantiles, Y_metadata=None): #compute the quantiles by sampling!!! - N_samp = 500 - s = np.random.randn(mu.shape[0], N_samp)*np.sqrt(var) + mu - #ss_f = s.flatten() - #ss_y = self.samples(ss_f, Y_metadata) - #ss_y = self.samples(s, Y_metadata, samples=100) - ss_y = self.samples(s, Y_metadata) - #ss_y = ss_y.reshape(mu.shape[0], N_samp) + Nf_samp = 300 + Ny_samp = 1 + s = np.random.randn(mu.shape[0], Nf_samp)*np.sqrt(var) + mu + ss_y = self.samples(s, Y_metadata, samples=Ny_samp) + #ss_y = ss_y.reshape(mu.shape[0], mu.shape[1], Nf_samp*Ny_samp) - return [np.percentile(ss_y ,q, axis=1)[:,None] for q in quantiles] + pred_quantiles = [np.percentile(ss_y, q, axis=1)[:,None] for q in quantiles] + return pred_quantiles def samples(self, gp, Y_metadata=None, samples=1): """ diff --git a/GPy/likelihoods/student_t.py b/GPy/likelihoods/student_t.py index b66d4c0f..79745ff6 100644 --- a/GPy/likelihoods/student_t.py +++ b/GPy/likelihoods/student_t.py @@ -10,6 +10,7 @@ from scipy.special import gammaln, gamma from .likelihood import Likelihood from ..core.parameterization import Param from ..core.parameterization.transformations import Logexp +from scipy.special import psi as digamma class StudentT(Likelihood): """ @@ -28,16 +29,13 @@ class StudentT(Likelihood): super(StudentT, self).__init__(gp_link, name='Student_T') # sigma2 is not a noise parameter, it is a squared scale. self.sigma2 = Param('t_scale2', float(sigma2), Logexp()) - self.v = Param('deg_free', float(deg_free)) + self.v = Param('deg_free', float(deg_free), Logexp()) self.link_parameter(self.sigma2) self.link_parameter(self.v) - self.v.constrain_fixed() + #self.v.constrain_fixed() self.log_concave = False - #def parameters_changed(self): - #self.variance = (self.v / float(self.v - 2)) * self.sigma2 - def update_gradients(self, grads): """ Pull out the gradients, be careful as the order must match the order @@ -224,20 +222,46 @@ class StudentT(Likelihood): ) return d2logpdf_dlink2_dvar + def dlogpdf_link_dv(self, inv_link_f, y, Y_metadata=None): + e = y - inv_link_f + e2 = np.square(e) + df = float(self.v[:]) + s2 = float(self.sigma2[:]) + dlogpdf_dv = 0.5*digamma(0.5*(df+1)) - 0.5*digamma(0.5*df) - 1.0/(2*df) + dlogpdf_dv += 0.5*(df+1)*e2/(df*(e2 + s2*df)) + dlogpdf_dv -= 0.5*np.log1p(e2/(s2*df)) + return dlogpdf_dv + + def dlogpdf_dlink_dv(self, inv_link_f, y, Y_metadata=None): + e = y - inv_link_f + e2 = np.square(e) + df = float(self.v[:]) + s2 = float(self.sigma2[:]) + dlogpdf_df_dv = e*(e2 - self.sigma2)/(e2 + s2*df)**2 + return dlogpdf_df_dv + + def d2logpdf_dlink2_dv(self, inv_link_f, y, Y_metadata=None): + e = y - inv_link_f + e2 = np.square(e) + df = float(self.v[:]) + s2 = float(self.sigma2[:]) + e2_s2v = e**2 + s2*df + d2logpdf_df2_dv = (-s2*(df+1) + e2 - s2*df)/e2_s2v**2 - 2*s2*(df+1)*(e2 - s2*df)/e2_s2v**3 + return d2logpdf_df2_dv + def dlogpdf_link_dtheta(self, f, y, Y_metadata=None): dlogpdf_dvar = self.dlogpdf_link_dvar(f, y, Y_metadata=Y_metadata) - dlogpdf_dv = np.zeros_like(dlogpdf_dvar) #FIXME: Not done yet + dlogpdf_dv = self.dlogpdf_link_dv(f, y, Y_metadata=Y_metadata) return np.array((dlogpdf_dvar, dlogpdf_dv)) def dlogpdf_dlink_dtheta(self, f, y, Y_metadata=None): dlogpdf_dlink_dvar = self.dlogpdf_dlink_dvar(f, y, Y_metadata=Y_metadata) - dlogpdf_dlink_dv = np.zeros_like(dlogpdf_dlink_dvar) #FIXME: Not done yet + dlogpdf_dlink_dv = self.dlogpdf_dlink_dv(f, y, Y_metadata=Y_metadata) return np.array((dlogpdf_dlink_dvar, dlogpdf_dlink_dv)) def d2logpdf_dlink2_dtheta(self, f, y, Y_metadata=None): d2logpdf_dlink2_dvar = self.d2logpdf_dlink2_dvar(f, y, Y_metadata=Y_metadata) - d2logpdf_dlink2_dv = np.zeros_like(d2logpdf_dlink2_dvar) #FIXME: Not done yet - + d2logpdf_dlink2_dv = self.d2logpdf_dlink2_dv(f, y, Y_metadata=Y_metadata) return np.array((d2logpdf_dlink2_dvar, d2logpdf_dlink2_dv)) def predictive_mean(self, mu, sigma, Y_metadata=None): diff --git a/GPy/mappings/__init__.py b/GPy/mappings/__init__.py index 5193a232..39568c9f 100644 --- a/GPy/mappings/__init__.py +++ b/GPy/mappings/__init__.py @@ -6,4 +6,5 @@ from .linear import Linear from .mlp import MLP from .additive import Additive from .compound import Compound +from .constant import Constant diff --git a/GPy/mappings/constant.py b/GPy/mappings/constant.py new file mode 100644 index 00000000..958be943 --- /dev/null +++ b/GPy/mappings/constant.py @@ -0,0 +1,40 @@ +# Copyright (c) 2015, James Hensman, Alan Saul +import numpy as np +from ..core.mapping import Mapping +from ..core.parameterization import Param + +class Constant(Mapping): + """ + A Linear mapping. + + .. math:: + + F(\mathbf{x}) = c + + + :param input_dim: dimension of input. + :type input_dim: int + :param output_dim: dimension of output. + :type output_dim: int + :param: value the value of this constant mapping + + """ + + def __init__(self, input_dim, output_dim, value=0., name='constmap'): + Mapping.__init__(self, input_dim=input_dim, output_dim=output_dim, name=name) + value = np.atleast_1d(value) + if not len(value.shape) ==1: + raise ValueError("bad constant values: pass a float or flat vectoor") + elif value.size==1: + value = np.ones(self.output_dim)*value + self.C = Param('C', value) + self.link_parameter(self.C) + + def f(self, X): + return np.tile(self.C.values[None,:], (X.shape[0], 1)) + + def update_gradients(self, dL_dF, X): + self.C.gradient = dL_dF.sum(0) + + def gradients_X(self, dL_dF, X): + return np.zeros_like(X) diff --git a/GPy/models/bayesian_gplvm_minibatch.py b/GPy/models/bayesian_gplvm_minibatch.py index 71f69eb2..7a7bb0e8 100644 --- a/GPy/models/bayesian_gplvm_minibatch.py +++ b/GPy/models/bayesian_gplvm_minibatch.py @@ -64,9 +64,6 @@ class BayesianGPLVMMiniBatch(SparseGPMiniBatch): self.logger.debug("creating inference_method var_dtc") inference_method = VarDTC(limit=1 if not missing_data else Y.shape[1]) - if kernel.useGPU and isinstance(inference_method, VarDTC_GPU): - kernel.psicomp.GPU_direct = True - super(BayesianGPLVMMiniBatch,self).__init__(X, Y, Z, kernel, likelihood=likelihood, name=name, inference_method=inference_method, normalizer=normalizer, diff --git a/GPy/models/dpgplvm.py b/GPy/models/dpgplvm.py index 1c5dccd0..7f947c53 100644 --- a/GPy/models/dpgplvm.py +++ b/GPy/models/dpgplvm.py @@ -3,7 +3,7 @@ import numpy as np from .. import kern -from bayesian_gplvm import BayesianGPLVM +from .bayesian_gplvm import BayesianGPLVM from ..core.parameterization.variational import NormalPosterior, NormalPrior class DPBayesianGPLVM(BayesianGPLVM): @@ -15,5 +15,5 @@ class DPBayesianGPLVM(BayesianGPLVM): name='bayesian gplvm', mpi_comm=None, normalizer=None, missing_data=False, stochastic=False, batchsize=1): super(DPBayesianGPLVM,self).__init__(Y=Y, input_dim=input_dim, X=X, X_variance=X_variance, init=init, num_inducing=num_inducing, Z=Z, kernel=kernel, inference_method=inference_method, likelihood=likelihood, mpi_comm=mpi_comm, normalizer=normalizer, missing_data=missing_data, stochastic=stochastic, batchsize=batchsize, name='dp bayesian gplvm') - self.X.mean.set_prior(X_prior) + self.X.mean.set_prior(X_prior) self.link_parameter(X_prior) diff --git a/GPy/models/gp_regression.py b/GPy/models/gp_regression.py index 7b8fb63f..7266ae92 100644 --- a/GPy/models/gp_regression.py +++ b/GPy/models/gp_regression.py @@ -16,6 +16,7 @@ class GPRegression(GP): :param Y: observed values :param kernel: a GPy kernel, defaults to rbf :param Norm normalizer: [False] + :param noise_var: the noise variance for Gaussian likelhood, defaults to 1. Normalize Y with the norm given. If normalizer is False, no normalization will be done @@ -25,12 +26,12 @@ class GPRegression(GP): """ - def __init__(self, X, Y, kernel=None, Y_metadata=None, normalizer=None): + def __init__(self, X, Y, kernel=None, Y_metadata=None, normalizer=None, noise_var=1.): if kernel is None: kernel = kern.RBF(X.shape[1]) - - likelihood = likelihoods.Gaussian() + + likelihood = likelihoods.Gaussian(variance=noise_var) super(GPRegression, self).__init__(X, Y, kernel, likelihood, name='GP regression', Y_metadata=Y_metadata, normalizer=normalizer) diff --git a/GPy/models/gp_var_gauss.py b/GPy/models/gp_var_gauss.py index cd688360..729b6bb8 100644 --- a/GPy/models/gp_var_gauss.py +++ b/GPy/models/gp_var_gauss.py @@ -9,13 +9,14 @@ from ..core.parameterization import ObsAr from .. import kern from ..core.parameterization.param import Param from ..util.linalg import pdinv +from ..likelihoods import Gaussian log_2_pi = np.log(2*np.pi) class GPVariationalGaussianApproximation(Model): """ - The Variational Gaussian Approximation revisited implementation for regression + The Variational Gaussian Approximation revisited @article{Opper:2009, title = {The Variational Gaussian Approximation Revisited}, @@ -25,44 +26,29 @@ class GPVariationalGaussianApproximation(Model): pages = {786--792}, } """ - def __init__(self, X, Y, kernel=None): - Model.__init__(self,'Variational GP classification') + def __init__(self, X, Y, kernel, likelihood=None, Y_metadata=None): + Model.__init__(self,'Variational GP') + if likelihood is None: + likelihood = Gaussian() # accept the construction arguments self.X = ObsAr(X) - if kernel is None: - kernel = kern.RBF(X.shape[1]) + kern.White(X.shape[1], 0.01) - self.kern = kernel - self.link_parameter(self.kern) + self.Y = Y self.num_data, self.input_dim = self.X.shape + self.Y_metadata = Y_metadata - self.alpha = Param('alpha', np.zeros(self.num_data)) + self.kern = kernel + self.likelihood = likelihood + self.link_parameter(self.kern) + self.link_parameter(self.likelihood) + + self.alpha = Param('alpha', np.zeros((self.num_data,1))) # only one latent fn for now. self.beta = Param('beta', np.ones(self.num_data)) self.link_parameter(self.alpha) self.link_parameter(self.beta) - self.gh_x, self.gh_w = np.polynomial.hermite.hermgauss(20) - self.Ysign = np.where(Y==1, 1, -1).flatten() - def log_likelihood(self): - """ - Marginal log likelihood evaluation - """ return self._log_lik - def likelihood_quadrature(self, m, v): - """ - Perform Gauss-Hermite quadrature over the log of the likelihood, with a fixed weight - """ - # assume probit for now. - X = self.gh_x[None, :]*np.sqrt(2.*v[:, None]) + (m*self.Ysign)[:, None] - p = stats.norm.cdf(X) - N = stats.norm.pdf(X) - F = np.log(p).dot(self.gh_w) - NoverP = N/p - dF_dm = (NoverP*self.Ysign[:,None]).dot(self.gh_w) - dF_dv = -0.5*(NoverP**2 + NoverP*X).dot(self.gh_w) - return F, dF_dm, dF_dv - def parameters_changed(self): K = self.kern.K(self.X) m = K.dot(self.alpha) @@ -71,13 +57,14 @@ class GPVariationalGaussianApproximation(Model): A = np.eye(self.num_data) + BKB Ai, LA, _, Alogdet = pdinv(A) Sigma = np.diag(self.beta**-2) - Ai/self.beta[:, None]/self.beta[None, :] # posterior coavairance: need full matrix for gradients - var = np.diag(Sigma) + var = np.diag(Sigma).reshape(-1,1) - F, dF_dm, dF_dv = self.likelihood_quadrature(m, var) + F, dF_dm, dF_dv, dF_dthetaL = self.likelihood.variational_expectations(self.Y, m, var, Y_metadata=self.Y_metadata) + self.likelihood.gradient = dF_dthetaL.sum(1).sum(1) dF_da = np.dot(K, dF_dm) SigmaB = Sigma*self.beta - dF_db = -np.diag(Sigma.dot(np.diag(dF_dv)).dot(SigmaB))*2 - KL = 0.5*(Alogdet + np.trace(Ai) - self.num_data + m.dot(self.alpha)) + dF_db = -np.diag(Sigma.dot(np.diag(dF_dv.flatten())).dot(SigmaB))*2 + KL = 0.5*(Alogdet + np.trace(Ai) - self.num_data + np.sum(m*self.alpha)) dKL_da = m A_A2 = Ai - Ai.dot(Ai) dKL_db = np.diag(np.dot(KB.T, A_A2)) @@ -86,12 +73,12 @@ class GPVariationalGaussianApproximation(Model): self.beta.gradient = dF_db - dKL_db # K-gradients - dKL_dK = 0.5*(self.alpha[None, :]*self.alpha[:, None] + self.beta[:, None]*self.beta[None, :]*A_A2) + dKL_dK = 0.5*(self.alpha*self.alpha.T + self.beta[:, None]*self.beta[None, :]*A_A2) tmp = Ai*self.beta[:, None]/self.beta[None, :] - dF_dK = self.alpha[:, None]*dF_dm[None, :] + np.dot(tmp*dF_dv, tmp.T) + dF_dK = self.alpha*dF_dm.T + np.dot(tmp*dF_dv, tmp.T) self.kern.update_gradients_full(dF_dK - dKL_dK, self.X) - def predict(self, Xnew): + def _raw_predict(self, Xnew): """ Predict the function(s) at the new point(s) Xnew. @@ -105,4 +92,4 @@ class GPVariationalGaussianApproximation(Model): Kxx = self.kern.Kdiag(Xnew) var = Kxx - np.sum(WiKux*Kux, 0) - return 0.5*(1+erf(mu/np.sqrt(2.*(var+1)))) + return mu, var.reshape(-1,1) diff --git a/GPy/models/gradient_checker.py b/GPy/models/gradient_checker.py index c2cde834..728f3e23 100644 --- a/GPy/models/gradient_checker.py +++ b/GPy/models/gradient_checker.py @@ -228,14 +228,14 @@ class HessianChecker(GradientChecker): if verbose: if block_indices: - print "\nBlock {}".format(block_indices) + print("\nBlock {}".format(block_indices)) else: - print "\nAll blocks" + print("\nAll blocks") header = ['Checked', 'Max-Ratio', 'Min-Ratio', 'Min-Difference', 'Max-Difference'] header_string = map(lambda x: ' | '.join(header), [header]) separator = '-' * len(header_string[0]) - print '\n'.join([header_string[0], separator]) + print('\n'.join([header_string[0], separator])) min_r = '%.6f' % float(numpy.min(ratio)) max_r = '%.6f' % float(numpy.max(ratio)) max_d = '%.6f' % float(numpy.max(difference)) @@ -248,7 +248,7 @@ class HessianChecker(GradientChecker): checked = "\033[91m False \033[0m" grad_string = "{} | {} | {} | {} | {} ".format(checked, cols[0], cols[1], cols[2], cols[3]) - print grad_string + print(grad_string) if plot: import pylab as pb @@ -348,7 +348,7 @@ class SkewChecker(HessianChecker): numeric_hess_partial = nd.Jacobian(self._df, vectorized=True) numeric_hess = numeric_hess_partial(x) - print "Done making numerical hessian" + print("Done making numerical hessian") if analytic_hess.dtype is np.dtype('object'): #Blockify numeric_hess aswell blocksizes, pagesizes = get_block_shapes_3d(analytic_hess) @@ -365,7 +365,7 @@ class SkewChecker(HessianChecker): #Unless super_plot is set, just plot the first one p = True if (plot and block_ind == numeric_hess.shape[2]-1) or super_plot else False if verbose: - print "Checking derivative of hessian wrt parameter number {}".format(block_ind) + print("Checking derivative of hessian wrt parameter number {}".format(block_ind)) check_passed[block_ind] = self.checkgrad_block(analytic_hess[:,:,block_ind], numeric_hess[:,:,block_ind], verbose=verbose, step=step, tolerance=tolerance, block_indices=block_indices, plot=p) current_index += current_size diff --git a/GPy/models/ss_gplvm.py b/GPy/models/ss_gplvm.py index 0f3b8fdd..3e2aa552 100644 --- a/GPy/models/ss_gplvm.py +++ b/GPy/models/ss_gplvm.py @@ -5,11 +5,95 @@ import numpy as np from ..core.sparse_gp_mpi import SparseGP_MPI from .. import kern +from ..core.parameterization import Param from ..likelihoods import Gaussian -from ..core.parameterization.variational import SpikeAndSlabPrior, SpikeAndSlabPosterior +from ..core.parameterization.variational import SpikeAndSlabPrior, SpikeAndSlabPosterior,VariationalPrior from ..inference.latent_function_inference.var_dtc_parallel import update_gradients, VarDTC_minibatch from ..kern._src.psi_comp.ssrbf_psi_gpucomp import PSICOMP_SSRBF_GPU +class IBPPosterior(SpikeAndSlabPosterior): + ''' + The SpikeAndSlab distribution for variational approximations. + ''' + def __init__(self, means, variances, binary_prob, tau=None, sharedX=False, name='latent space'): + """ + binary_prob : the probability of the distribution on the slab part. + """ + from ..core.parameterization.transformations import Logexp + super(IBPPosterior, self).__init__(means, variances, binary_prob, group_spike=True, name=name) + self.sharedX = sharedX + if sharedX: + self.mean.fix(warning=False) + self.variance.fix(warning=False) + self.tau = Param("tau_", np.ones((self.gamma_group.shape[0],2)), Logexp()) + self.link_parameter(self.tau) + + def set_gradients(self, grad): + self.mean.gradient, self.variance.gradient, self.gamma.gradient, self.tau.gradient = grad + + def __getitem__(self, s): + if isinstance(s, (int, slice, tuple, list, np.ndarray)): + import copy + n = self.__new__(self.__class__, self.name) + dc = self.__dict__.copy() + dc['mean'] = self.mean[s] + dc['variance'] = self.variance[s] + dc['binary_prob'] = self.binary_prob[s] + dc['tau'] = self.tau + dc['parameters'] = copy.copy(self.parameters) + n.__dict__.update(dc) + n.parameters[dc['mean']._parent_index_] = dc['mean'] + n.parameters[dc['variance']._parent_index_] = dc['variance'] + n.parameters[dc['binary_prob']._parent_index_] = dc['binary_prob'] + n.parameters[dc['tau']._parent_index_] = dc['tau'] + n._gradient_array_ = None + oversize = self.size - self.mean.size - self.variance.size - self.gamma.size - self.tau.size + n.size = n.mean.size + n.variance.size + n.gamma.size+ n.tau.size + oversize + n.ndim = n.mean.ndim + n.shape = n.mean.shape + n.num_data = n.mean.shape[0] + n.input_dim = n.mean.shape[1] if n.ndim != 1 else 1 + return n + else: + return super(IBPPosterior, self).__getitem__(s) + +class IBPPrior(VariationalPrior): + def __init__(self, input_dim, alpha =2., name='IBPPrior', **kw): + super(IBPPrior, self).__init__(name=name, **kw) + from ..core.parameterization.transformations import Logexp, __fixed__ + self.input_dim = input_dim + self.variance = 1. + self.alpha = Param('alpha', alpha, __fixed__) + self.link_parameter(self.alpha) + + def KL_divergence(self, variational_posterior): + mu, S, gamma, tau = variational_posterior.mean.values, variational_posterior.variance.values, variational_posterior.gamma_group.values, variational_posterior.tau.values + + var_mean = np.square(mu)/self.variance + var_S = (S/self.variance - np.log(S)) + part1 = (gamma* (np.log(self.variance)-1. +var_mean + var_S)).sum()/2. + + ad = self.alpha/self.input_dim + from scipy.special import betaln,digamma + part2 = (gamma*np.log(gamma)).sum() + ((1.-gamma)*np.log(1.-gamma)).sum() + betaln(ad,1.)*self.input_dim \ + -betaln(tau[:,0], tau[:,1]).sum() + ((tau[:,0]-gamma-ad)*digamma(tau[:,0])).sum() + \ + ((tau[:,1]+gamma-2.)*digamma(tau[:,1])).sum() + ((2.+ad-tau[:,0]-tau[:,1])*digamma(tau.sum(axis=1))).sum() + + return part1+part2 + + def update_gradients_KL(self, variational_posterior): + mu, S, gamma, tau = variational_posterior.mean.values, variational_posterior.variance.values, variational_posterior.gamma_group.values, variational_posterior.tau.values + + variational_posterior.mean.gradient -= gamma*mu/self.variance + variational_posterior.variance.gradient -= (1./self.variance - 1./S) * gamma /2. + from scipy.special import digamma,polygamma + dgamma = (np.log(gamma/(1.-gamma))+ digamma(tau[:,1])-digamma(tau[:,0]))/variational_posterior.num_data + variational_posterior.binary_prob.gradient -= dgamma+((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. + ad = self.alpha/self.input_dim + common = (ad+2-tau[:,0]-tau[:,1])*polygamma(1,tau.sum(axis=1)) + variational_posterior.tau.gradient[:,0] = -((tau[:,0]-gamma-ad)*polygamma(1,tau[:,0])+common) + variational_posterior.tau.gradient[:,1] = -((tau[:,1]+gamma-2)*polygamma(1,tau[:,1])+common) + class SSGPLVM(SparseGP_MPI): """ Spike-and-Slab Gaussian Process Latent Variable Model @@ -23,9 +107,11 @@ class SSGPLVM(SparseGP_MPI): """ def __init__(self, Y, input_dim, X=None, X_variance=None, Gamma=None, init='PCA', num_inducing=10, - Z=None, kernel=None, inference_method=None, likelihood=None, name='Spike_and_Slab GPLVM', group_spike=False, mpi_comm=None, pi=None, learnPi=True,normalizer=False, **kwargs): + Z=None, kernel=None, inference_method=None, likelihood=None, name='Spike_and_Slab GPLVM', group_spike=False, IBP=False, alpha=2., tau=None, mpi_comm=None, pi=None, learnPi=False,normalizer=False, sharedX=False, variational_prior=None,**kwargs): self.group_spike = group_spike + self.init = init + self.sharedX = sharedX if X == None: from ..util.initialization import initialize_latent @@ -33,8 +119,6 @@ class SSGPLVM(SparseGP_MPI): else: fracs = np.ones(input_dim) - self.init = init - if X_variance is None: # The variance of the variational approximation (S) X_variance = np.random.uniform(0,.1,X.shape) @@ -64,17 +148,16 @@ class SSGPLVM(SparseGP_MPI): if pi is None: pi = np.empty((input_dim)) pi[:] = 0.5 - self.variational_prior = SpikeAndSlabPrior(pi=pi,learnPi=learnPi) # the prior probability of the latent binary variable b - - X = SpikeAndSlabPosterior(X, X_variance, gamma) - + + if IBP: + self.variational_prior = IBPPrior(input_dim=input_dim, alpha=alpha) if variational_prior is None else variational_prior + X = IBPPosterior(X, X_variance, gamma, tau=tau,sharedX=sharedX) + else: + self.variational_prior = SpikeAndSlabPrior(pi=pi,learnPi=learnPi, group_spike=group_spike) if variational_prior is None else variational_prior + X = SpikeAndSlabPosterior(X, X_variance, gamma, group_spike=group_spike,sharedX=sharedX) + super(SSGPLVM,self).__init__(X, Y, Z, kernel, likelihood, variational_prior=self.variational_prior, inference_method=inference_method, name=name, mpi_comm=mpi_comm, normalizer=normalizer, **kwargs) -# self.X.unfix() -# self.X.variance.constrain_positive() self.link_parameter(self.X, index=0) - - if self.group_spike: - [self.X.gamma[:,i].tie('tieGamma'+str(i)) for i in range(self.X.gamma.shape[1])] # Tie columns together def set_X_gradients(self, X, X_grad): """Set the gradients of the posterior distribution of X in its specific form.""" @@ -84,9 +167,15 @@ class SSGPLVM(SparseGP_MPI): """Get the gradients of the posterior distribution of X in its specific form.""" return X.mean.gradient, X.variance.gradient, X.binary_prob.gradient + def _propogate_X_val(self): + pass + def parameters_changed(self): + self.X.propogate_val() + if self.sharedX: self._highest_parent_._propogate_X_val() super(SSGPLVM,self).parameters_changed() if isinstance(self.inference_method, VarDTC_minibatch): + self.X.collate_gradient() return self._log_marginal_likelihood -= self.variational_prior.KL_divergence(self.X) @@ -95,6 +184,7 @@ class SSGPLVM(SparseGP_MPI): # update for the KL divergence self.variational_prior.update_gradients_KL(self.X) + self.X.collate_gradient() def input_sensitivity(self): if self.kern.ARD: diff --git a/GPy/models/ss_mrd.py b/GPy/models/ss_mrd.py index bd2efce0..41289d3f 100644 --- a/GPy/models/ss_mrd.py +++ b/GPy/models/ss_mrd.py @@ -2,33 +2,256 @@ The Maniforld Relevance Determination model with the spike-and-slab prior """ +import numpy as np from ..core import Model from .ss_gplvm import SSGPLVM +from ..core.parameterization.variational import SpikeAndSlabPrior,NormalPosterior,VariationalPrior +from ..util.misc import param_to_array +from ..kern import RBF +from ..core import Param +from numpy.linalg.linalg import LinAlgError class SSMRD(Model): - def __init__(self, Ylist, input_dim, X=None, X_variance=None, - initx = 'PCA', initz = 'permute', - num_inducing=10, Z=None, kernel=None, - inference_method=None, likelihoods=None, name='ss_mrd', Ynames=None): + def __init__(self, Ylist, input_dim, X=None, X_variance=None, Gammas=None, initx = 'PCA_concat', initz = 'permute', + num_inducing=10, Zs=None, kernels=None, inference_methods=None, likelihoods=None, group_spike=True, + pi=0.5, name='ss_mrd', Ynames=None, mpi_comm=None, IBP=False, alpha=2., taus=None, ): super(SSMRD, self).__init__(name) + self.mpi_comm = mpi_comm + self._PROPAGATE_ = False - self.updates = False - self.models = [SSGPLVM(y, input_dim, X=X, X_variance=X_variance, num_inducing=num_inducing,Z=Z,init=initx, - kernel=kernel.copy() if kernel else None,inference_method=inference_method,likelihood=likelihoods, - name='model_'+str(i)) for i,y in enumerate(Ylist)] - self.add_parameters(*(self.models)) + # initialize X for individual models + X, X_variance, Gammas, fracs = self._init_X(Ylist, input_dim, X, X_variance, Gammas, initx) + self.X = NormalPosterior(means=X, variances=X_variance) - [[[self.models[m].X.mean[i,j:j+1].tie('mean_'+str(i)+'_'+str(j)) for m in range(len(self.models))] for j in range(self.models[0].X.mean.shape[1])] - for i in range(self.models[0].X.mean.shape[0])] - [[[self.models[m].X.variance[i,j:j+1].tie('var_'+str(i)+'_'+str(j)) for m in range(len(self.models))] for j in range(self.models[0].X.variance.shape[1])] - for i in range(self.models[0].X.variance.shape[0])] + if kernels is None: + kernels = [RBF(input_dim, lengthscale=1./fracs, ARD=True) for i in xrange(len(Ylist))] + if Zs is None: + Zs = [None]* len(Ylist) + if likelihoods is None: + likelihoods = [None]* len(Ylist) + if inference_methods is None: + inference_methods = [None]* len(Ylist) - self.updates = True + if IBP: + self.var_priors = [IBPPrior_SSMRD(len(Ylist),input_dim,alpha=alpha) for i in xrange(len(Ylist))] + else: + self.var_priors = [SpikeAndSlabPrior_SSMRD(nModels=len(Ylist),pi=pi,learnPi=False, group_spike=group_spike) for i in xrange(len(Ylist))] + self.models = [SSGPLVM(y, input_dim, X=X.copy(), X_variance=X_variance.copy(), Gamma=Gammas[i], num_inducing=num_inducing,Z=Zs[i], learnPi=False, group_spike=group_spike, + kernel=kernels[i],inference_method=inference_methods[i],likelihood=likelihoods[i], variational_prior=self.var_priors[i], IBP=IBP, tau=None if taus is None else taus[i], + name='model_'+str(i), mpi_comm=mpi_comm, sharedX=True) for i,y in enumerate(Ylist)] + self.link_parameters(*(self.models+[self.X])) + + def _propogate_X_val(self): + if self._PROPAGATE_: return + for m in self.models: + m.X.mean.values[:] = self.X.mean.values + m.X.variance.values[:] = self.X.variance.values + varp_list = [m.X for m in self.models] + [vp._update_inernal(varp_list) for vp in self.var_priors] + self._PROPAGATE_=True + + def _collate_X_gradient(self): + self._PROPAGATE_ = False + self.X.mean.gradient[:] = 0 + self.X.variance.gradient[:] = 0 + for m in self.models: + self.X.mean.gradient += m.X.mean.gradient + self.X.variance.gradient += m.X.variance.gradient def parameters_changed(self): - super(SSMRD, self).parameters_changed() + super(SSMRD, self).parameters_changed() + [m.parameters_changed() for m in self.models] self._log_marginal_likelihood = sum([m._log_marginal_likelihood for m in self.models]) + self._collate_X_gradient() def log_likelihood(self): return self._log_marginal_likelihood + + def _init_X(self, Ylist, input_dim, X=None, X_variance=None, Gammas=None, initx='PCA_concat'): + + # Divide latent dimensions + idx = np.empty((input_dim,),dtype=np.int) + residue = (input_dim)%(len(Ylist)) + for i in xrange(len(Ylist)): + if i < residue: + size = input_dim/len(Ylist)+1 + idx[i*size:(i+1)*size] = i + else: + size = input_dim/len(Ylist) + idx[i*size+residue:(i+1)*size+residue] = i + + if X is None: + if initx == 'PCA_concat': + X = np.empty((Ylist[0].shape[0],input_dim)) + fracs = np.empty((input_dim,)) + from ..util.initialization import initialize_latent + for i in xrange(len(Ylist)): + Y = Ylist[i] + dim = (idx==i).sum() + if dim>0: + x, fr = initialize_latent('PCA', dim, Y) + X[:,idx==i] = x + fracs[idx==i] = fr + elif initx=='PCA_joint': + y = np.hstack(Ylist) + from ..util.initialization import initialize_latent + X, fracs = initialize_latent('PCA', input_dim, y) + else: + X = np.random.randn(Ylist[0].shape[0], input_dim) + fracs = np.ones(input_dim) + else: + fracs = np.ones(input_dim) + + + if X_variance is None: # The variance of the variational approximation (S) + X_variance = np.random.uniform(0,.1,X.shape) + + if Gammas is None: + Gammas = [] + for x in X: + gamma = np.empty_like(X) # The posterior probabilities of the binary variable in the variational approximation + gamma[:] = 0.5 + 0.1 * np.random.randn(X.shape[0], input_dim) + gamma[gamma>1.-1e-9] = 1.-1e-9 + gamma[gamma<1e-9] = 1e-9 + Gammas.append(gamma) + return X, X_variance, Gammas, fracs + + @Model.optimizer_array.setter + def optimizer_array(self, p): + if self.mpi_comm != None: + if self._IN_OPTIMIZATION_ and self.mpi_comm.rank==0: + self.mpi_comm.Bcast(np.int32(1),root=0) + self.mpi_comm.Bcast(p, root=0) + Model.optimizer_array.fset(self,p) + + def optimize(self, optimizer=None, start=None, **kwargs): + self._IN_OPTIMIZATION_ = True + if self.mpi_comm==None: + super(SSMRD, self).optimize(optimizer,start,**kwargs) + elif self.mpi_comm.rank==0: + super(SSMRD, self).optimize(optimizer,start,**kwargs) + self.mpi_comm.Bcast(np.int32(-1),root=0) + elif self.mpi_comm.rank>0: + x = self.optimizer_array.copy() + flag = np.empty(1,dtype=np.int32) + while True: + self.mpi_comm.Bcast(flag,root=0) + if flag==1: + try: + self.optimizer_array = x + self._fail_count = 0 + except (LinAlgError, ZeroDivisionError, ValueError): + if self._fail_count >= self._allowed_failures: + raise + self._fail_count += 1 + elif flag==-1: + break + else: + self._IN_OPTIMIZATION_ = False + raise Exception("Unrecognizable flag for synchronization!") + self._IN_OPTIMIZATION_ = False + + +class SpikeAndSlabPrior_SSMRD(SpikeAndSlabPrior): + def __init__(self, nModels, pi=0.5, learnPi=False, group_spike=True, variance = 1.0, name='SSMRDPrior', **kw): + self.nModels = nModels + self._b_prob_all = 0.5 + super(SpikeAndSlabPrior_SSMRD, self).__init__(pi=pi,learnPi=learnPi,group_spike=group_spike,variance=variance, name=name, **kw) + + def _update_inernal(self, varp_list): + """Make an update of the internal status by gathering the variational posteriors for all the individual models.""" + # The probability for the binary variable for the same latent dimension of any of the models is on. + if self.group_spike: + self._b_prob_all = 1.-param_to_array(varp_list[0].gamma_group) + [np.multiply(self._b_prob_all, 1.-vp.gamma_group, self._b_prob_all) for vp in varp_list[1:]] + else: + self._b_prob_all = 1.-param_to_array(varp_list[0].binary_prob) + [np.multiply(self._b_prob_all, 1.-vp.binary_prob, self._b_prob_all) for vp in varp_list[1:]] + + def KL_divergence(self, variational_posterior): + mu = variational_posterior.mean + S = variational_posterior.variance + if self.group_spike: + gamma = variational_posterior.binary_prob[0] + else: + gamma = variational_posterior.binary_prob + if len(self.pi.shape)==2: + idx = np.unique(gamma._raveled_index()/gamma.shape[-1]) + pi = self.pi[idx] + else: + pi = self.pi + + var_mean = np.square(mu)/self.variance + var_S = (S/self.variance - np.log(S)) + var_gamma = (gamma*np.log(gamma/pi)).sum()+((1-gamma)*np.log((1-gamma)/(1-pi))).sum() + return var_gamma +((1.-self._b_prob_all)*(np.log(self.variance)-1. +var_mean + var_S)).sum()/(2.*self.nModels) + + def update_gradients_KL(self, variational_posterior): + mu = variational_posterior.mean + S = variational_posterior.variance + N = variational_posterior.num_data + if self.group_spike: + gamma = variational_posterior.binary_prob.values[0] + else: + gamma = variational_posterior.binary_prob.values + if len(self.pi.shape)==2: + idx = np.unique(gamma._raveled_index()/gamma.shape[-1]) + pi = self.pi[idx] + else: + pi = self.pi + + if self.group_spike: + tmp = self._b_prob_all/(1.-gamma) + variational_posterior.binary_prob.gradient -= np.log((1-pi)/pi*gamma/(1.-gamma))/N +tmp*((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. + else: + variational_posterior.binary_prob.gradient -= np.log((1-pi)/pi*gamma/(1.-gamma))+((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. + mu.gradient -= (1.-self._b_prob_all)*mu/(self.variance*self.nModels) + S.gradient -= (1./self.variance - 1./S) * (1.-self._b_prob_all) /(2.*self.nModels) + if self.learnPi: + raise 'Not Supported!' + +class IBPPrior_SSMRD(VariationalPrior): + def __init__(self, nModels, input_dim, alpha =2., tau=None, name='IBPPrior', **kw): + super(IBPPrior_SSMRD, self).__init__(name=name, **kw) + from ..core.parameterization.transformations import Logexp, __fixed__ + self.nModels = nModels + self._b_prob_all = 0.5 + self.input_dim = input_dim + self.variance = 1. + self.alpha = Param('alpha', alpha, __fixed__) + self.link_parameter(self.alpha) + + def _update_inernal(self, varp_list): + """Make an update of the internal status by gathering the variational posteriors for all the individual models.""" + # The probability for the binary variable for the same latent dimension of any of the models is on. + self._b_prob_all = 1.-param_to_array(varp_list[0].gamma_group) + [np.multiply(self._b_prob_all, 1.-vp.gamma_group, self._b_prob_all) for vp in varp_list[1:]] + + def KL_divergence(self, variational_posterior): + mu, S, gamma, tau = variational_posterior.mean.values, variational_posterior.variance.values, variational_posterior.gamma_group.values, variational_posterior.tau.values + + var_mean = np.square(mu)/self.variance + var_S = (S/self.variance - np.log(S)) + part1 = ((1.-self._b_prob_all)* (np.log(self.variance)-1. +var_mean + var_S)).sum()/(2.*self.nModels) + + ad = self.alpha/self.input_dim + from scipy.special import betaln,digamma + part2 = (gamma*np.log(gamma)).sum() + ((1.-gamma)*np.log(1.-gamma)).sum() + (betaln(ad,1.)*self.input_dim -betaln(tau[:,0], tau[:,1]).sum())/self.nModels \ + + (( (tau[:,0]-ad)/self.nModels -gamma)*digamma(tau[:,0])).sum() + \ + (((tau[:,1]-1.)/self.nModels+gamma-1.)*digamma(tau[:,1])).sum() + (((1.+ad-tau[:,0]-tau[:,1])/self.nModels+1.)*digamma(tau.sum(axis=1))).sum() + return part1+part2 + + def update_gradients_KL(self, variational_posterior): + mu, S, gamma, tau = variational_posterior.mean.values, variational_posterior.variance.values, variational_posterior.gamma_group.values, variational_posterior.tau.values + + variational_posterior.mean.gradient -= (1.-self._b_prob_all)*mu/(self.variance*self.nModels) + variational_posterior.variance.gradient -= (1./self.variance - 1./S) * (1.-self._b_prob_all) /(2.*self.nModels) + from scipy.special import digamma,polygamma + tmp = self._b_prob_all/(1.-gamma) + dgamma = (np.log(gamma/(1.-gamma))+ digamma(tau[:,1])-digamma(tau[:,0]))/variational_posterior.num_data + variational_posterior.binary_prob.gradient -= dgamma+tmp*((np.square(mu)+S)/self.variance-np.log(S)+np.log(self.variance)-1.)/2. + ad = self.alpha/self.input_dim + common = ((1.+ad-tau[:,0]-tau[:,1])/self.nModels+1.)*polygamma(1,tau.sum(axis=1)) + variational_posterior.tau.gradient[:,0] = -(((tau[:,0]-ad)/self.nModels -gamma)*polygamma(1,tau[:,0])+common) + variational_posterior.tau.gradient[:,1] = -(((tau[:,1]-1.)/self.nModels+gamma-1.)*polygamma(1,tau[:,1])+common) diff --git a/GPy/plotting/matplot_dep/models_plots.py b/GPy/plotting/matplot_dep/models_plots.py index 0cda12f1..9f841372 100644 --- a/GPy/plotting/matplot_dep/models_plots.py +++ b/GPy/plotting/matplot_dep/models_plots.py @@ -11,13 +11,14 @@ from base_plots import gpplot, x_frame1D, x_frame2D from ...models.gp_coregionalized_regression import GPCoregionalizedRegression from ...models.sparse_gp_coregionalized_regression import SparseGPCoregionalizedRegression from scipy import sparse +from ...core.parameterization.variational import VariationalPosterior def plot_fit(model, plot_limits=None, which_data_rows='all', which_data_ycols='all', fixed_inputs=[], levels=20, samples=0, fignum=None, ax=None, resolution=None, plot_raw=False, linecol=Tango.colorsHex['darkBlue'],fillcol=Tango.colorsHex['lightBlue'], Y_metadata=None, data_symbol='kx', - apply_link=False, samples_f=0, plot_uncertain_inputs=True): + apply_link=False, samples_f=0, plot_uncertain_inputs=True, predict_kw=None): """ Plot the posterior of the GP. - In one dimension, the function is plotted with a shaded region identifying two standard deviations. @@ -76,6 +77,9 @@ def plot_fit(model, plot_limits=None, which_data_rows='all', if hasattr(model, 'Z'): Z = model.Z + if predict_kw is None: + predict_kw = {} + #work out what the inputs are for plotting (1D or 2D) fixed_dims = np.array([i for i,v in fixed_inputs]) free_dims = np.setdiff1d(np.arange(model.input_dim),fixed_dims) @@ -92,7 +96,7 @@ def plot_fit(model, plot_limits=None, which_data_rows='all', #make a prediction on the frame and plot it if plot_raw: - m, v = model._raw_predict(Xgrid) + m, v = model._raw_predict(Xgrid, **predict_kw) if apply_link: lower = model.likelihood.gp_link.transf(m - 2*np.sqrt(v)) upper = model.likelihood.gp_link.transf(m + 2*np.sqrt(v)) @@ -103,11 +107,13 @@ def plot_fit(model, plot_limits=None, which_data_rows='all', upper = m + 2*np.sqrt(v) else: if isinstance(model,GPCoregionalizedRegression) or isinstance(model,SparseGPCoregionalizedRegression): - meta = {'output_index': Xgrid[:,-1:].astype(np.int)} - else: - meta = None - m, v = model.predict(Xgrid, full_cov=False, Y_metadata=meta) - lower, upper = model.predict_quantiles(Xgrid, Y_metadata=meta) + extra_data = Xgrid[:,-1:].astype(np.int) + if Y_metadata is None: + Y_metadata = {'output_index': extra_data} + else: + Y_metadata['output_index'] = extra_data + m, v = model.predict(Xgrid, full_cov=False, Y_metadata=Y_metadata, **predict_kw) + lower, upper = model.predict_quantiles(Xgrid, Y_metadata=Y_metadata) for d in which_data_ycols: @@ -116,7 +122,9 @@ def plot_fit(model, plot_limits=None, which_data_rows='all', #optionally plot some samples if samples: #NOTE not tested with fixed_inputs - Ysim = model.posterior_samples(Xgrid, samples) + Ysim = model.posterior_samples(Xgrid, samples, Y_metadata=Y_metadata) + print Ysim.shape + print Xnew.shape for yi in Ysim.T: plots['posterior_samples'] = ax.plot(Xnew, yi[:,None], Tango.colorsHex['darkBlue'], linewidth=0.25) #ax.plot(Xnew, yi[:,None], marker='x', linestyle='--',color=Tango.colorsHex['darkBlue']) #TODO apply this line for discrete outputs. @@ -178,13 +186,15 @@ def plot_fit(model, plot_limits=None, which_data_rows='all', #predict on the frame and plot if plot_raw: - m, _ = model._raw_predict(Xgrid) + m, _ = model._raw_predict(Xgrid, **predict_kw) else: if isinstance(model,GPCoregionalizedRegression) or isinstance(model,SparseGPCoregionalizedRegression): - meta = {'output_index': Xgrid[:,-1:].astype(np.int)} - else: - meta = None - m, v = model.predict(Xgrid, full_cov=False, Y_metadata=meta) + extra_data = Xgrid[:,-1:].astype(np.int) + if Y_metadata is None: + Y_metadata = {'output_index': extra_data} + else: + Y_metadata['output_index'] = extra_data + m, v = model.predict(Xgrid, full_cov=False, Y_metadata=Y_metadata, **predict_kw) for d in which_data_ycols: m_d = m[:,d].reshape(resolution, resolution).T plots['contour'] = ax.contour(x, y, m_d, levels, vmin=m.min(), vmax=m.max(), cmap=pb.cm.jet) @@ -216,7 +226,7 @@ def plot_fit_f(model, *args, **kwargs): kwargs['plot_raw'] = True plot_fit(model,*args, **kwargs) -def fixed_inputs(model, non_fixed_inputs, fix_routine='median'): +def fixed_inputs(model, non_fixed_inputs, fix_routine='median', as_list=True, X_all=False): """ Convenience function for returning back fixed_inputs where the other inputs are fixed using fix_routine @@ -226,18 +236,30 @@ def fixed_inputs(model, non_fixed_inputs, fix_routine='median'): :type non_fixed_inputs: list :param fix_routine: fixing routine to use, 'mean', 'median', 'zero' :type fix_routine: string + :param as_list: if true, will return a list of tuples with (dimension, fixed_val) otherwise it will create the corresponding X matrix + :type as_list: boolean """ f_inputs = [] if hasattr(model, 'has_uncertain_inputs') and model.has_uncertain_inputs(): X = model.X.mean.values.copy() - else: + elif isinstance(model.X, VariationalPosterior): X = model.X.values.copy() + else: + if X_all: + X = model.X_all.copy() + else: + X = model.X.copy() for i in range(X.shape[1]): if i not in non_fixed_inputs: if fix_routine == 'mean': f_inputs.append( (i, np.mean(X[:,i])) ) if fix_routine == 'median': f_inputs.append( (i, np.median(X[:,i])) ) - elif fix_routine == 'zero': + else: # set to zero zero f_inputs.append( (i, 0) ) - return f_inputs + if not as_list: + X[:,i] = f_inputs[-1][1] + if as_list: + return f_inputs + else: + return X diff --git a/GPy/plotting/matplot_dep/visualize.py b/GPy/plotting/matplot_dep/visualize.py index b57b7dfc..b17900db 100644 --- a/GPy/plotting/matplot_dep/visualize.py +++ b/GPy/plotting/matplot_dep/visualize.py @@ -408,12 +408,13 @@ class mocap_data_show_vpython(vpython_show): class mocap_data_show(matplotlib_show): """Base class for visualizing motion capture data.""" - def __init__(self, vals, axes=None, connect=None): + def __init__(self, vals, axes=None, connect=None, color='b'): if axes==None: fig = plt.figure() axes = fig.add_subplot(111, projection='3d', aspect='equal') matplotlib_show.__init__(self, vals, axes) + self.color = color self.connect = connect self.process_values() self.initialize_axes() @@ -423,7 +424,7 @@ class mocap_data_show(matplotlib_show): self.axes.figure.canvas.draw() def draw_vertices(self): - self.points_handle = self.axes.scatter(self.vals[:, 0], self.vals[:, 1], self.vals[:, 2]) + self.points_handle = self.axes.scatter(self.vals[:, 0], self.vals[:, 1], self.vals[:, 2], color=self.color) def draw_edges(self): self.line_handle = [] @@ -442,7 +443,7 @@ class mocap_data_show(matplotlib_show): z.append(self.vals[i, 2]) z.append(self.vals[j, 2]) z.append(np.NaN) - self.line_handle = self.axes.plot(np.array(x), np.array(y), np.array(z), 'b-') + self.line_handle = self.axes.plot(np.array(x), np.array(y), np.array(z), '-', color=self.color) def modify(self, vals): self.vals = vals.copy() @@ -450,7 +451,7 @@ class mocap_data_show(matplotlib_show): self.initialize_axes_modify() self.draw_vertices() self.initialize_axes() - self.finalize_axes_modify() + #self.finalize_axes_modify() self.draw_edges() self.axes.figure.canvas.draw() @@ -469,12 +470,20 @@ class mocap_data_show(matplotlib_show): self.line_handle[0].remove() def finalize_axes(self): - self.axes.set_xlim(self.x_lim) - self.axes.set_ylim(self.y_lim) - self.axes.set_zlim(self.z_lim) - self.axes.auto_scale_xyz([-1., 1.], [-1., 1.], [-1., 1.]) +# self.axes.set_xlim(self.x_lim) +# self.axes.set_ylim(self.y_lim) +# self.axes.set_zlim(self.z_lim) +# self.axes.auto_scale_xyz([-1., 1.], [-1., 1.], [-1., 1.]) -# self.axes.set_aspect('equal') + extents = np.array([getattr(self.axes, 'get_{}lim'.format(dim))() for dim in 'xyz']) + sz = extents[:,1] - extents[:,0] + centers = np.mean(extents, axis=1) + maxsize = max(abs(sz)) + r = maxsize/2 + for ctr, dim in zip(centers, 'xyz'): + getattr(self.axes, 'set_{}lim'.format(dim))(ctr - r, ctr + r) + +# self.axes.set_aspect('equal') # self.axes.autoscale(enable=False) def finalize_axes_modify(self): @@ -494,7 +503,7 @@ class stick_show(mocap_data_show): class skeleton_show(mocap_data_show): """data_show class for visualizing motion capture data encoded as a skeleton with angles.""" - def __init__(self, vals, skel, axes=None, padding=0): + def __init__(self, vals, skel, axes=None, padding=0, color='b'): """data_show class for visualizing motion capture data encoded as a skeleton with angles. :param vals: set of modeled angles to use for printing in the axis when it's first created. :type vals: np.array @@ -506,7 +515,7 @@ class skeleton_show(mocap_data_show): self.skel = skel self.padding = padding connect = skel.connection_matrix() - mocap_data_show.__init__(self, vals, axes=axes, connect=connect) + mocap_data_show.__init__(self, vals, axes=axes, connect=connect, color=color) def process_values(self): """Takes a set of angles and converts them to the x,y,z coordinates in the internal prepresentation of the class, ready for plotting. diff --git a/GPy/testing/cython_tests.py b/GPy/testing/cython_tests.py new file mode 100644 index 00000000..f88f12f3 --- /dev/null +++ b/GPy/testing/cython_tests.py @@ -0,0 +1,65 @@ +import numpy as np +import scipy as sp +from GPy.util import choleskies +import GPy + +""" +These tests make sure that the opure python and cython codes work the same +""" + +class CythonTestChols(np.testing.TestCase): + def setUp(self): + self.flat = np.random.randn(45,5) + self.triang = np.array([np.eye(20) for i in range(3)]) + def test_flat_to_triang(self): + L1 = choleskies._flat_to_triang_pure(self.flat) + L2 = choleskies._flat_to_triang_cython(self.flat) + np.testing.assert_allclose(L1, L2) + def test_triang_to_flat(self): + A1 = choleskies._triang_to_flat_pure(self.triang) + A2 = choleskies._triang_to_flat_cython(self.triang) + np.testing.assert_allclose(A1, A2) + +class test_stationary(np.testing.TestCase): + def setUp(self): + self.k = GPy.kern.RBF(10) + self.X = np.random.randn(300,10) + self.Z = np.random.randn(20,10) + self.dKxx = np.random.randn(300,300) + self.dKzz = np.random.randn(20,20) + self.dKxz = np.random.randn(300,20) + + def test_square_gradX(self): + g1 = self.k._gradients_X_cython(self.dKxx, self.X) + g2 = self.k._gradients_X_pure(self.dKxx, self.X) + np.testing.assert_allclose(g1, g2) + + def test_rect_gradx(self): + g1 = self.k._gradients_X_cython(self.dKxz, self.X, self.Z) + g2 = self.k._gradients_X_pure(self.dKxz, self.X, self.Z) + np.testing.assert_allclose(g1, g2) + + def test_square_lengthscales(self): + g1 = self.k._lengthscale_grads_pure(self.dKxx, self.X, self.X) + g2 = self.k._lengthscale_grads_cython(self.dKxx, self.X, self.X) + np.testing.assert_allclose(g1, g2) + + def test_rect_lengthscales(self): + g1 = self.k._lengthscale_grads_pure(self.dKxz, self.X, self.Z) + g2 = self.k._lengthscale_grads_cython(self.dKxz, self.X, self.Z) + np.testing.assert_allclose(g1, g2) + +class test_choleskies_backprop(np.testing.TestCase): + def setUp(self): + self.dL, self.L = np.random.randn(2, 100, 100) + def test(self): + r1 = GPy.util.choleskies._backprop_gradient_pure(self.dL, self.L) + r2 = GPy.util.choleskies.choleskies_cython.backprop_gradient(self.dL, self.L) + np.testing.assert_allclose(r1, r2) + + + + + + + diff --git a/GPy/testing/kernel_tests.py b/GPy/testing/kernel_tests.py index f3d82216..043d5e9a 100644 --- a/GPy/testing/kernel_tests.py +++ b/GPy/testing/kernel_tests.py @@ -366,9 +366,9 @@ class KernelTestsNonContinuous(unittest.TestCase): X2 = self.X2[self.X2[:,-1]!=2] self.assertTrue(check_kernel_gradient_functions(kern, X=X, X2=X2, verbose=verbose, fixed_X_dims=-1)) -class Coregionalize_weave_test(unittest.TestCase): +class Coregionalize_cython_test(unittest.TestCase): """ - Make sure that the coregionalize kernel work with and without weave enabled + Make sure that the coregionalize kernel work with and without cython enabled """ def setUp(self): self.k = GPy.kern.Coregionalize(1, output_dim=12) @@ -378,36 +378,42 @@ class Coregionalize_weave_test(unittest.TestCase): def test_sym(self): dL_dK = np.random.randn(self.N1, self.N1) - GPy.util.config.config.set('weave', 'working', 'True') - K_weave = self.k.K(self.X) + GPy.util.config.config.set('cython', 'working', 'True') + K_cython = self.k.K(self.X) self.k.update_gradients_full(dL_dK, self.X) - grads_weave = self.k.gradient.copy() + grads_cython = self.k.gradient.copy() - GPy.util.config.config.set('weave', 'working', 'False') + GPy.util.config.config.set('cython', 'working', 'False') K_numpy = self.k.K(self.X) self.k.update_gradients_full(dL_dK, self.X) grads_numpy = self.k.gradient.copy() - self.assertTrue(np.allclose(K_numpy, K_weave)) - self.assertTrue(np.allclose(grads_numpy, grads_weave)) + self.assertTrue(np.allclose(K_numpy, K_cython)) + self.assertTrue(np.allclose(grads_numpy, grads_cython)) + + #reset the cython state for any other tests + GPy.util.config.config.set('cython', 'working', 'true') def test_nonsym(self): dL_dK = np.random.randn(self.N1, self.N2) - GPy.util.config.config.set('weave', 'working', 'True') - K_weave = self.k.K(self.X, self.X2) + GPy.util.config.config.set('cython', 'working', 'True') + K_cython = self.k.K(self.X, self.X2) + self.k.gradient = 0. self.k.update_gradients_full(dL_dK, self.X, self.X2) - grads_weave = self.k.gradient.copy() + grads_cython = self.k.gradient.copy() - GPy.util.config.config.set('weave', 'working', 'False') + GPy.util.config.config.set('cython', 'working', 'False') K_numpy = self.k.K(self.X, self.X2) + self.k.gradient = 0. self.k.update_gradients_full(dL_dK, self.X, self.X2) grads_numpy = self.k.gradient.copy() - self.assertTrue(np.allclose(K_numpy, K_weave)) - self.assertTrue(np.allclose(grads_numpy, grads_weave)) + self.assertTrue(np.allclose(K_numpy, K_cython)) + self.assertTrue(np.allclose(grads_numpy, grads_cython)) + + #reset the cython state for any other tests + GPy.util.config.config.set('cython', 'working', 'true') - #reset the weave state for any other tests - GPy.util.config.config.set('weave', 'working', 'False') class KernelTestsProductWithZeroValues(unittest.TestCase): diff --git a/GPy/testing/likelihood_tests.py b/GPy/testing/likelihood_tests.py index 7fa5886f..27b27892 100644 --- a/GPy/testing/likelihood_tests.py +++ b/GPy/testing/likelihood_tests.py @@ -93,6 +93,9 @@ def dparam_checkgrad(func, dfunc, params, params_names, args, constraints=None, if not grad.checkgrad(verbose=True): gradchecking = False + if not grad.checkgrad(verbose=True): + gradchecking = False + return gradchecking @@ -116,6 +119,7 @@ class TestNoiseModels(object): self.integer_Y = np.where(tmp > 0, tmp, 0) self.var = 0.2 + self.deg_free = 4.0 #Make a bigger step as lower bound can be quite curved self.step = 1e-4 @@ -135,7 +139,7 @@ class TestNoiseModels(object): } """ self.noise_models = {"Student_t_default": { - "model": GPy.likelihoods.StudentT(deg_free=5, sigma2=self.var), + "model": GPy.likelihoods.StudentT(deg_free=self.deg_free, sigma2=self.var), "grad_params": { "names": [".*t_scale2"], "vals": [self.var], @@ -143,8 +147,17 @@ class TestNoiseModels(object): }, "laplace": True }, + #"Student_t_deg_free": { + #"model": GPy.likelihoods.StudentT(deg_free=self.deg_free, sigma2=self.var), + #"grad_params": { + #"names": [".*deg_free"], + #"vals": [self.deg_free], + #"constraints": [(".*t_scale2", self.constrain_fixed), (".*deg_free", self.constrain_positive)] + #}, + #"laplace": True + #}, "Student_t_1_var": { - "model": GPy.likelihoods.StudentT(deg_free=5, sigma2=self.var), + "model": GPy.likelihoods.StudentT(deg_free=self.deg_free, sigma2=self.var), "grad_params": { "names": [".*t_scale2"], "vals": [1.0], @@ -162,7 +175,7 @@ class TestNoiseModels(object): "laplace": True }, "Student_t_small_var": { - "model": GPy.likelihoods.StudentT(deg_free=5, sigma2=self.var), + "model": GPy.likelihoods.StudentT(deg_free=self.deg_free, sigma2=self.var), "grad_params": { "names": [".*t_scale2"], "vals": [0.001], @@ -171,7 +184,7 @@ class TestNoiseModels(object): "laplace": True }, "Student_t_large_var": { - "model": GPy.likelihoods.StudentT(deg_free=5, sigma2=self.var), + "model": GPy.likelihoods.StudentT(deg_free=self.deg_free, sigma2=self.var), "grad_params": { "names": [".*t_scale2"], "vals": [10.0], diff --git a/GPy/testing/linalg_test.py b/GPy/testing/linalg_test.py index 8e103795..ec3aca5a 100644 --- a/GPy/testing/linalg_test.py +++ b/GPy/testing/linalg_test.py @@ -1,6 +1,7 @@ import numpy as np import scipy as sp -from ..util.linalg import jitchol +from GPy.util.linalg import jitchol +import GPy class LinalgTests(np.testing.TestCase): def setUp(self): @@ -35,3 +36,25 @@ class LinalgTests(np.testing.TestCase): return False except sp.linalg.LinAlgError: return True + + def test_einsum_ijk_jlk_to_il(self): + A = np.random.randn(50, 150, 5) + B = np.random.randn(150, 100, 5) + pure = np.einsum('ijk,jlk->il', A, B) + quick = GPy.util.linalg.ijk_jlk_to_il(A, B) + np.testing.assert_allclose(pure, quick) + + def test_einsum_ij_jlk_to_ilk(self): + A = np.random.randn(15, 150, 5) + B = np.random.randn(150, 50, 5) + pure = np.einsum('ijk,jlk->il', A, B) + quick = GPy.util.linalg.ijk_jlk_to_il(A,B) + np.testing.assert_allclose(pure, quick) + + def test_einsum_ijk_ljk_to_ilk(self): + A = np.random.randn(150, 20, 5) + B = np.random.randn(150, 20, 5) + #B = A.copy() + pure = np.einsum('ijk,ljk->ilk', A, B) + quick = GPy.util.linalg.ijk_ljk_to_ilk(A,B) + np.testing.assert_allclose(pure, quick) diff --git a/GPy/testing/link_function_tests.py b/GPy/testing/link_function_tests.py index fb8fba99..e8cbbf66 100644 --- a/GPy/testing/link_function_tests.py +++ b/GPy/testing/link_function_tests.py @@ -49,7 +49,7 @@ class LinkFunctionTests(np.testing.TestCase): self.assertTrue(grad3.checkgrad(verbose=True)) if test_lim: - print "Testing limits" + print("Testing limits") #Remove some otherwise we are too close to the limit for gradcheck to work effectively lim_of_inf = lim_of_inf - 1e-4 grad = GradientChecker(link_func.transf, link_func.dtransf_df, x0=lim_of_inf) diff --git a/GPy/util/block_matrices.py b/GPy/util/block_matrices.py index e1e04aaa..8c0de67d 100644 --- a/GPy/util/block_matrices.py +++ b/GPy/util/block_matrices.py @@ -100,10 +100,10 @@ def block_dot(A, B, diagonal=False): Dshape = D.shape if diagonal and (len(Cshape) == 1 or len(Dshape) == 1\ or C.shape[0] != C.shape[1] or D.shape[0] != D.shape[1]): - print "Broadcasting, C: {} D:{}".format(C.shape, D.shape) + print("Broadcasting, C: {} D:{}".format(C.shape, D.shape)) return C*D else: - print "Dotting, C: {} C:{}".format(C.shape, D.shape) + print("Dotting, C: {} C:{}".format(C.shape, D.shape)) return np.dot(C,D) dot = np.vectorize(f, otypes = [np.object]) return dot(A,B) diff --git a/GPy/util/choleskies.py b/GPy/util/choleskies.py index 37ac7211..f079cabd 100644 --- a/GPy/util/choleskies.py +++ b/GPy/util/choleskies.py @@ -1,14 +1,11 @@ -# Copyright James Hensman and Max Zwiessele 2014 +# Copyright James Hensman and Max Zwiessele 2014, 2015 # Licensed under the GNU GPL version 3.0 import numpy as np from . import linalg from .config import config -try: - from scipy import weave -except ImportError: - config.set('weave', 'working', 'False') +from . import choleskies_cython def safe_root(N): i = np.sqrt(N) @@ -17,125 +14,72 @@ def safe_root(N): raise ValueError("N is not square!") return j -def _flat_to_triang_weave(flat): - """take a matrix N x D and return a M X M x D array where - - N = M(M+1)/2 - - the lower triangluar portion of the d'th slice of the result is filled by the d'th column of flat. - This is the weave implementation - """ - N, D = flat.shape - M = (-1 + safe_root(8*N+1))/2 - ret = np.zeros((M, M, D)) - flat = np.ascontiguousarray(flat) - - code = """ - int count = 0; - for(int m=0; milk', Ki, LL) - #self._loglik = np.sum([np.sum(np.log(np.abs(np.diag()))) for i in range(self.L.shape[-1])]) -# +if config.getboolean('cython', 'working'): + triang_to_flat = _triang_to_flat_cython + flat_to_triang = _flat_to_triang_cython + backprop_gradient = choleskies_cython.backprop_gradient_par_c +else: + backprop_gradient = _backprop_gradient_pure + triang_to_flat = _triang_to_flat_pure + flat_to_triang = _flat_to_triang_pure diff --git a/GPy/util/choleskies_cython.c b/GPy/util/choleskies_cython.c new file mode 100644 index 00000000..21492a88 --- /dev/null +++ b/GPy/util/choleskies_cython.c @@ -0,0 +1,21096 @@ +/* Generated by Cython 0.21 */ + +#define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else 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PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#endif +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__GPy__util__choleskies_cython +#define __PYX_HAVE_API__GPy__util__choleskies_cython +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "cholesky_backprop.h" +#include "pythread.h" +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "GPy/util/choleskies_cython.pyx", + "__init__.pxd", + "GPy/util/stringsource", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; + +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && MSC_VER + #include + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using MSVC atomics" + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview) \ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview) \ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_array_obj; +struct __pyx_MemviewEnum_obj; +struct __pyx_memoryview_obj; +struct __pyx_memoryviewslice_obj; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; 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+ if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +#define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) +#define __Pyx_BufPtrStrided3d(type, buf, i0, s0, i1, s1, i2, s2) (type)((char*)buf + i0 * s0 + i1 * s1 + i2 * s2) +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d +#define __Pyx_MEMVIEW_DIRECT 1 +#define __Pyx_MEMVIEW_PTR 2 +#define __Pyx_MEMVIEW_FULL 4 +#define __Pyx_MEMVIEW_CONTIG 8 +#define __Pyx_MEMVIEW_STRIDED 16 +#define __Pyx_MEMVIEW_FOLLOW 32 +#define __Pyx_IS_C_CONTIG 1 +#define __Pyx_IS_F_CONTIG 2 +static int __Pyx_init_memviewslice( + struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference); +static CYTHON_INLINE int __pyx_add_acquisition_count_locked( + __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); +static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( + __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); +#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) +#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) +#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) +#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) +static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +#include + +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ + +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) + +static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_memoryview_transpose(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview__get__base(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_shape(PyObject *__pyx_v_self); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +static PyObject *__pyx_memoryview_get_strides(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_suboffsets(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback); + +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static PyObject *__pyx_memview_get_double(const char *itemp); +static int __pyx_memview_set_double(const char *itemp, PyObject *obj); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim); + +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'GPy.util.choleskies_cython' */ +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; +#define __Pyx_MODULE_NAME "GPy.util.choleskies_cython" +int __pyx_module_is_main_GPy__util__choleskies_cython = 0; + +/* Implementation of 'GPy.util.choleskies_cython' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_xrange; +static PyObject *__pyx_builtin_id; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_flat_to_triang(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_flat, int __pyx_v_M); /* proto */ +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_2triang_to_flat(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_L); /* proto */ +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_4backprop_gradient(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_dL, PyArrayObject *__pyx_v_L); /* proto */ +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_6backprop_gradient_par(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_dL, __Pyx_memviewslice __pyx_v_L); /* proto */ +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_8backprop_gradient_par_c(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_dL, PyArrayObject *__pyx_v_L); /* proto */ +static PyObject *__pyx_pf_3GPy_4util_17choleskies_cython_10backprop_gradient_par_c_old(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_dL, PyArrayObject *__pyx_v_L); /* 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 int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static char __pyx_k_B[] = "B"; +static char __pyx_k_D[] = "D"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_M[] = "M"; +static char __pyx_k_N[] = "N"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_c[] = "c"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_j[] = "j"; +static char __pyx_k_k[] = "k"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_m[] = "m"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_dL[] = "dL"; +static char __pyx_k_id[] = "id"; +static char __pyx_k_mm[] = "mm"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_obj[] = "obj"; +static char __pyx_k_ret[] = "ret"; +static char __pyx_k_base[] = "base"; +static char __pyx_k_copy[] = "copy"; +static char __pyx_k_flat[] = "flat"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_mode[] = "mode"; +static char __pyx_k_name[] = "name"; +static char __pyx_k_ndim[] = "ndim"; +static char __pyx_k_pack[] = "pack"; +static char __pyx_k_size[] = "size"; +static char __pyx_k_step[] = "step"; +static char __pyx_k_stop[] = "stop"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_tril[] = "tril"; +static char __pyx_k_class[] = "__class__"; +static char __pyx_k_count[] = "count"; +static char __pyx_k_dL_dK[] = "dL_dK"; +static char __pyx_k_empty[] = "empty"; +static char __pyx_k_error[] = "error"; +static char __pyx_k_flags[] = "flags"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_shape[] = "shape"; +static char __pyx_k_start[] = "start"; +static char __pyx_k_zeros[] = "zeros"; +static char __pyx_k_format[] = "format"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_name_2[] = "__name__"; +static char __pyx_k_struct[] = "struct"; +static char __pyx_k_unpack[] = "unpack"; +static char __pyx_k_xrange[] = "xrange"; +static char __pyx_k_fortran[] = "fortran"; +static char __pyx_k_memview[] = "memview"; +static char __pyx_k_Ellipsis[] = "Ellipsis"; +static char __pyx_k_itemsize[] = "itemsize"; +static char __pyx_k_TypeError[] = "TypeError"; +static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_IndexError[] = "IndexError"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static char __pyx_k_MemoryError[] = "MemoryError"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static char __pyx_k_flat_to_triang[] = "flat_to_triang"; +static char __pyx_k_triang_to_flat[] = "triang_to_flat"; +static char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static char __pyx_k_backprop_gradient[] = "backprop_gradient"; +static char __pyx_k_strided_and_direct[] = ""; +static char __pyx_k_strided_and_indirect[] = ""; +static char __pyx_k_backprop_gradient_par[] = "backprop_gradient_par"; +static char __pyx_k_contiguous_and_direct[] = ""; +static char __pyx_k_MemoryView_of_r_object[] = ""; +static char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static char __pyx_k_backprop_gradient_par_c[] = "backprop_gradient_par_c"; +static char __pyx_k_contiguous_and_indirect[] = ""; +static char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static char __pyx_k_getbuffer_obj_view_flags[] = "getbuffer(obj, view, flags)"; +static char __pyx_k_Dimension_d_is_not_direct[] = "Dimension %d is not direct"; +static char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static char __pyx_k_GPy_util_choleskies_cython[] = "GPy.util.choleskies_cython"; +static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)"; +static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)"; +static char __pyx_k_backprop_gradient_par_c_old[] = "backprop_gradient_par_c_old"; +static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static char __pyx_k_strided_and_direct_or_indirect[] = ""; +static char __pyx_k_home_james_work_GPy_GPy_util_ch[] = "/home/james/work/GPy/GPy/util/choleskies_cython.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; +static char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static char __pyx_k_Cannot_transpose_memoryview_with[] = "Cannot transpose memoryview with indirect dimensions"; +static char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_n_s_D; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +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_util_choleskies_cython; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_L; +static PyObject *__pyx_n_s_M; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_n_s_N; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_backprop_gradient; +static PyObject *__pyx_n_s_backprop_gradient_par; +static PyObject *__pyx_n_s_backprop_gradient_par_c; +static PyObject *__pyx_n_s_backprop_gradient_par_c_old; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_copy; +static PyObject *__pyx_n_s_count; +static PyObject *__pyx_n_s_d; +static PyObject *__pyx_n_s_dL; +static PyObject *__pyx_n_s_dL_dK; 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suboffset_dim = -1, dim + * cdef bint negative_step + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("View.MemoryView.memview_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_memviewsliceobj); + __Pyx_XDECREF(__pyx_v_index); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":764 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, Py_ssize_t __pyx_v_shape, Py_ssize_t __pyx_v_stride, Py_ssize_t __pyx_v_suboffset, int __pyx_v_dim, int __pyx_v_new_ndim, int *__pyx_v_suboffset_dim, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_stop, Py_ssize_t __pyx_v_step, int __pyx_v_have_start, int __pyx_v_have_stop, int __pyx_v_have_step, int __pyx_v_is_slice) { + Py_ssize_t __pyx_v_new_shape; + int __pyx_v_negative_step; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "View.MemoryView":784 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ + __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":786 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ + __pyx_t_1 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":787 + * + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + goto __pyx_L4; + } + __pyx_L4:; + + /* "View.MemoryView":788 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ + __pyx_t_1 = (0 <= __pyx_v_start); + if (__pyx_t_1) { + __pyx_t_1 = (__pyx_v_start < __pyx_v_shape); + } + __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":789 + * start += shape + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< + * else: + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L5; + } + __pyx_L5:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":792 + * else: + * + * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< + * + * if have_step and step == 0: + */ + __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); + if (__pyx_t_1) { + goto __pyx_L7_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L6_bool_binop_done; + } + __pyx_L7_next_and:; + __pyx_t_1 = ((__pyx_v_step < 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L6_bool_binop_done:; + __pyx_v_negative_step = __pyx_t_2; + + /* "View.MemoryView":794 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ + __pyx_t_1 = (__pyx_v_have_step != 0); + if (__pyx_t_1) { + goto __pyx_L10_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L9_bool_binop_done; + } + __pyx_L10_next_and:; + __pyx_t_1 = ((__pyx_v_step == 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L9_bool_binop_done:; + if (__pyx_t_2) { + + /* "View.MemoryView":795 + * + * if have_step and step == 0: + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L8; + } + __pyx_L8:; + + /* "View.MemoryView":798 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + __pyx_t_2 = (__pyx_v_have_start != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":799 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":800 + * if have_start: + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if start < 0: + * start = 0 + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":801 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":802 + * start += shape + * if start < 0: + * start = 0 # <<<<<<<<<<<<<< + * elif start >= shape: + * if negative_step: + */ + __pyx_v_start = 0; + goto __pyx_L13; + } + __pyx_L13:; + goto __pyx_L12; + } + + /* "View.MemoryView":803 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":804 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":805 + * elif start >= shape: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = shape + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L14; + } + /*else*/ { + + /* "View.MemoryView":807 + * start = shape - 1 + * else: + * start = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_start = __pyx_v_shape; + } + __pyx_L14:; + goto __pyx_L12; + } + __pyx_L12:; + goto __pyx_L11; + } + /*else*/ { + + /* "View.MemoryView":809 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":810 + * else: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = 0 + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L15; + } + /*else*/ { + + /* "View.MemoryView":812 + * start = shape - 1 + * else: + * start = 0 # <<<<<<<<<<<<<< + * + * if have_stop: + */ + __pyx_v_start = 0; + } + __pyx_L15:; + } + __pyx_L11:; + + /* "View.MemoryView":814 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + __pyx_t_2 = (__pyx_v_have_stop != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":815 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":816 + * if have_stop: + * if stop < 0: + * stop += shape # <<<<<<<<<<<<<< + * if stop < 0: + * stop = 0 + */ + __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); + + /* "View.MemoryView":817 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":818 + * stop += shape + * if stop < 0: + * stop = 0 # <<<<<<<<<<<<<< + * elif stop > shape: + * stop = shape + */ + __pyx_v_stop = 0; + goto __pyx_L18; + } + __pyx_L18:; + goto __pyx_L17; + } + + /* "View.MemoryView":819 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":820 + * stop = 0 + * elif stop > shape: + * stop = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + goto __pyx_L17; + } + __pyx_L17:; + goto __pyx_L16; + } + /*else*/ { + + /* "View.MemoryView":822 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":823 + * else: + * if negative_step: + * stop = -1 # <<<<<<<<<<<<<< + * else: + * stop = shape + */ + __pyx_v_stop = -1; + goto __pyx_L19; + } + /*else*/ { + + /* "View.MemoryView":825 + * stop = -1 + * else: + * stop = shape # <<<<<<<<<<<<<< + * + * if not have_step: + */ + __pyx_v_stop = __pyx_v_shape; + } + __pyx_L19:; + } + __pyx_L16:; + + /* "View.MemoryView":827 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":828 + * + * if not have_step: + * step = 1 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_step = 1; + goto __pyx_L20; + } + __pyx_L20:; + + /* "View.MemoryView":832 + * + * with cython.cdivision(True): + * new_shape = (stop - start) // step # <<<<<<<<<<<<<< + * + * if (stop - start) - step * new_shape: + */ + __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); + + /* "View.MemoryView":834 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":835 + * + * if (stop - start) - step * new_shape: + * new_shape += 1 # <<<<<<<<<<<<<< + * + * if new_shape < 0: + */ + __pyx_v_new_shape = (__pyx_v_new_shape + 1); + goto __pyx_L21; + } + __pyx_L21:; + + /* "View.MemoryView":837 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":838 + * + * if new_shape < 0: + * new_shape = 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_new_shape = 0; + goto __pyx_L22; + } + __pyx_L22:; + + /* "View.MemoryView":841 + * + * + * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset + */ + (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); + + /* "View.MemoryView":842 + * + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< + * dst.suboffsets[new_ndim] = suboffset + * + */ + (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; + + /* "View.MemoryView":843 + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; + } + __pyx_L3:; + + /* "View.MemoryView":846 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ + __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":847 + * + * if suboffset_dim[0] < 0: + * dst.data += start * stride # <<<<<<<<<<<<<< + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride + */ + __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + goto __pyx_L23; + } + /*else*/ { + + /* "View.MemoryView":849 + * dst.data += start * stride + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< + * + * if suboffset >= 0: + */ + __pyx_t_3 = (__pyx_v_suboffset_dim[0]); + (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); + } + __pyx_L23:; + + /* "View.MemoryView":851 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ + __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":852 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset + */ + __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":853 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ + __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":854 + * if not is_slice: + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " + */ + __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); + goto __pyx_L26; + } + /*else*/ { + + /* "View.MemoryView":856 + * dst.data = ( dst.data)[0] + suboffset + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< + * "must be indexed and not sliced", dim) + * else: + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L26:; + goto __pyx_L25; + } + /*else*/ { + + /* "View.MemoryView":859 + * "must be indexed and not sliced", dim) + * else: + * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< + * + * return 0 + */ + (__pyx_v_suboffset_dim[0]) = __pyx_v_new_ndim; + } + __pyx_L25:; + goto __pyx_L24; + } + __pyx_L24:; + + /* "View.MemoryView":861 + * suboffset_dim[0] = new_ndim + * + * return 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":764 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.slice_memviewslice", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":867 + * + * @cname('__pyx_pybuffer_index') + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 + */ + +static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, Py_ssize_t __pyx_v_index, Py_ssize_t __pyx_v_dim) { + Py_ssize_t __pyx_v_shape; + Py_ssize_t __pyx_v_stride; + Py_ssize_t __pyx_v_suboffset; + Py_ssize_t __pyx_v_itemsize; + char *__pyx_v_resultp; + char *__pyx_r; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("pybuffer_index", 0); + + /* "View.MemoryView":869 + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< + * cdef Py_ssize_t itemsize = view.itemsize + * cdef char *resultp + */ + __pyx_v_suboffset = -1; + + /* "View.MemoryView":870 + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 + * cdef Py_ssize_t itemsize = view.itemsize # <<<<<<<<<<<<<< + * cdef char *resultp + * + */ + __pyx_t_1 = __pyx_v_view->itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "View.MemoryView":873 + * cdef char *resultp + * + * if view.ndim == 0: # <<<<<<<<<<<<<< + * shape = view.len / itemsize + * stride = itemsize + */ + __pyx_t_2 = ((__pyx_v_view->ndim == 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":874 + * + * if view.ndim == 0: + * shape = view.len / itemsize # <<<<<<<<<<<<<< + * stride = itemsize + * else: + */ + if (unlikely(__pyx_v_itemsize == 0)) { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + else if (sizeof(Py_ssize_t) == sizeof(long) && unlikely(__pyx_v_itemsize == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_v_shape = __Pyx_div_Py_ssize_t(__pyx_v_view->len, __pyx_v_itemsize); + + /* "View.MemoryView":875 + * if view.ndim == 0: + * shape = view.len / itemsize + * stride = itemsize # <<<<<<<<<<<<<< + * else: + * shape = view.shape[dim] + */ + __pyx_v_stride = __pyx_v_itemsize; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":877 + * stride = itemsize + * else: + * shape = view.shape[dim] # <<<<<<<<<<<<<< + * stride = view.strides[dim] + * if view.suboffsets != NULL: + */ + __pyx_v_shape = (__pyx_v_view->shape[__pyx_v_dim]); + + /* "View.MemoryView":878 + * else: + * shape = view.shape[dim] + * stride = view.strides[dim] # <<<<<<<<<<<<<< + * if view.suboffsets != NULL: + * suboffset = view.suboffsets[dim] + */ + __pyx_v_stride = (__pyx_v_view->strides[__pyx_v_dim]); + + /* "View.MemoryView":879 + * shape = view.shape[dim] + * stride = view.strides[dim] + * if view.suboffsets != NULL: # <<<<<<<<<<<<<< + * suboffset = view.suboffsets[dim] + * + */ + __pyx_t_2 = ((__pyx_v_view->suboffsets != NULL) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":880 + * stride = view.strides[dim] + * if view.suboffsets != NULL: + * suboffset = view.suboffsets[dim] # <<<<<<<<<<<<<< + * + * if index < 0: + */ + __pyx_v_suboffset = (__pyx_v_view->suboffsets[__pyx_v_dim]); + goto __pyx_L4; + } + __pyx_L4:; + } + __pyx_L3:; + + /* "View.MemoryView":882 + * suboffset = view.suboffsets[dim] + * + * if index < 0: # <<<<<<<<<<<<<< + * index += view.shape[dim] + * if index < 0: + */ + __pyx_t_2 = ((__pyx_v_index < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":883 + * + * if index < 0: + * index += view.shape[dim] # <<<<<<<<<<<<<< + * if index < 0: + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + */ + __pyx_v_index = (__pyx_v_index + (__pyx_v_view->shape[__pyx_v_dim])); + + /* "View.MemoryView":884 + * if index < 0: + * index += view.shape[dim] + * if index < 0: # <<<<<<<<<<<<<< + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + * + */ + 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memview).to_dtype_func + * else: + */ + __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; + __pyx_v_to_object_func = __pyx_t_3; + + /* "View.MemoryView":1049 + * if isinstance(memview, _memoryviewslice): + * to_object_func = (<_memoryviewslice> memview).to_object_func + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< + * else: + * to_object_func = NULL + */ + __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; + __pyx_v_to_dtype_func = __pyx_t_4; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1051 + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func + * else: + * to_object_func = NULL # <<<<<<<<<<<<<< + * to_dtype_func = NULL + * + */ + __pyx_v_to_object_func = NULL; + + /* "View.MemoryView":1052 + * else: + * to_object_func = NULL + * to_dtype_func = NULL # <<<<<<<<<<<<<< + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + */ + __pyx_v_to_dtype_func = NULL; + } + __pyx_L3:; + + /* "View.MemoryView":1054 + * to_dtype_func = NULL + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< + * to_object_func, to_dtype_func, + * memview.dtype_is_object) + */ + __Pyx_XDECREF(__pyx_r); + + /* "View.MemoryView":1056 + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + * to_object_func, to_dtype_func, + * memview.dtype_is_object) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "View.MemoryView":1040 + * + * @cname('__pyx_memoryview_copy_object_from_slice') + * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< + * """ + * Create a new memoryview object from a given memoryview object and slice. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_from_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + +static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { + Py_ssize_t __pyx_r; + int __pyx_t_1; + + /* "View.MemoryView":1063 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + __pyx_t_1 = ((__pyx_v_arg < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1064 + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: + * return -arg # <<<<<<<<<<<<<< + * else: + * return arg + */ + __pyx_r = (-__pyx_v_arg); + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1066 + * return -arg + * else: + * return arg # <<<<<<<<<<<<<< + * + * @cname('__pyx_get_best_slice_order') + */ + __pyx_r = __pyx_v_arg; + goto __pyx_L0; + } + + /* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + +static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_c_stride; + Py_ssize_t __pyx_v_f_stride; + char __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1074 + * """ + * cdef int i + * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< + * cdef Py_ssize_t f_stride = 0 + * + */ + __pyx_v_c_stride = 0; + + /* "View.MemoryView":1075 + * cdef int i + * cdef Py_ssize_t c_stride = 0 + * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_f_stride = 0; + + /* "View.MemoryView":1077 + * cdef Py_ssize_t f_stride = 0 + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1078 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1079 + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1080 + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + goto __pyx_L4_break; + } + } + __pyx_L4_break:; + + /* "View.MemoryView":1082 + * break + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + */ + __pyx_t_1 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1083 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1084 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1085 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1087 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1088 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1090 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + +static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; + Py_ssize_t __pyx_v_dst_extent; + Py_ssize_t __pyx_v_src_stride; + Py_ssize_t __pyx_v_dst_stride; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + + /* "View.MemoryView":1100 + * + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + */ + __pyx_v_src_extent = (__pyx_v_src_shape[0]); + + /* "View.MemoryView":1101 + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1102 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1103 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1105 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1106 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L6_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L6_next_and:; + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L7_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L7_next_and:; + + /* "View.MemoryView":1107 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + if (__pyx_t_1) { + + /* "View.MemoryView":1108 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); + goto __pyx_L4; + } + /*else*/ { + + /* "View.MemoryView":1110 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1111 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); + + /* "View.MemoryView":1112 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1113 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1115 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1116 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1120 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1121 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1126 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1133 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1135 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1136 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1138 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1141 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1150 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1151 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_idx = __pyx_t_3; + + /* "View.MemoryView":1152 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1153 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + 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__pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1261; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_tmpdata = __pyx_t_6; + + /* "View.MemoryView":1262 + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + * src = tmp # <<<<<<<<<<<<<< + * + * if not broadcasting: + */ + __pyx_v_src = __pyx_v_tmp; + goto __pyx_L9; + } + __pyx_L9:; + + /* "View.MemoryView":1264 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1267 + * + * + * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1268 + * + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<< + * elif slice_is_contig(&src, 'F', ndim): + * direct_copy = slice_is_contig(&dst, 'F', ndim) + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim); + goto __pyx_L12; + } + + /* "View.MemoryView":1269 + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1270 + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<< + * + * if direct_copy: + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim); + goto __pyx_L12; + } + __pyx_L12:; + + /* "View.MemoryView":1272 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_2 = (__pyx_v_direct_copy != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1274 + * if direct_copy: + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1275 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); + + /* "View.MemoryView":1276 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * free(tmpdata) + * return 0 + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1277 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1278 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + } + goto __pyx_L11; + } + __pyx_L11:; + + /* "View.MemoryView":1280 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (__pyx_v_order == 'F'); + if (__pyx_t_2) { + __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_7 = (__pyx_t_2 != 0); + if (__pyx_t_7) { + + /* "View.MemoryView":1283 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1284 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L14; + } + __pyx_L14:; + + /* "View.MemoryView":1286 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1287 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1288 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1290 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1291 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1222 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + + /* "View.MemoryView":1298 + * int ndim_other) nogil: + * cdef int i + * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); + + /* "View.MemoryView":1300 + * cdef int offset = ndim_other - ndim + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1301 + * + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<< + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] + */ + (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]); + + /* "View.MemoryView":1302 + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<< + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + */ + (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]); + + /* "View.MemoryView":1303 + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<< + * + * for i in range(offset): + */ + (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]); + } + + /* "View.MemoryView":1305 + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + * for i in range(offset): # <<<<<<<<<<<<<< + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + */ + __pyx_t_1 = __pyx_v_offset; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1306 + * + * for i in range(offset): + * slice.shape[i] = 1 # <<<<<<<<<<<<<< + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 + */ + (__pyx_v_slice->shape[__pyx_v_i]) = 1; + + /* "View.MemoryView":1307 + * for i in range(offset): + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] # <<<<<<<<<<<<<< + * slice.suboffsets[i] = -1 + * + */ + (__pyx_v_slice->strides[__pyx_v_i]) = (__pyx_v_slice->strides[0]); + + /* "View.MemoryView":1308 + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_slice->suboffsets[__pyx_v_i]) = -1; + } + + /* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + + /* function 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*__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + Py_ssize_t __pyx_t_2; + int __pyx_t_3; + __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); + + /* "View.MemoryView":1335 + * cdef Py_ssize_t i + * + * for i in range(shape[0]): # <<<<<<<<<<<<<< + * if ndim == 1: + * if inc: + */ + __pyx_t_1 = (__pyx_v_shape[0]); + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1336 + * + * for i in range(shape[0]): + * if ndim == 1: # <<<<<<<<<<<<<< + * if inc: + * Py_INCREF(( data)[0]) + */ + __pyx_t_3 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1337 + * for i in range(shape[0]): + * if ndim == 1: + * if inc: # <<<<<<<<<<<<<< + * Py_INCREF(( data)[0]) + * else: + */ + __pyx_t_3 = (__pyx_v_inc != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1338 + * if ndim == 1: + * if inc: + * Py_INCREF(( data)[0]) # 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/* "View.MemoryView":1355 + * bint dtype_is_object) nogil: + * refcount_copying(dst, dtype_is_object, ndim, False) + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); + + /* "View.MemoryView":1357 + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * + */ + __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1351 + * + * @cname('__pyx_memoryview_slice_assign_scalar') + * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< + * size_t itemsize, void *item, + * bint dtype_is_object) nogil: + */ + + /* function exit code */ +} + +/* 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__pyx_methods_memoryview[] = { + {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, + {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, + {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, + {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, 0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, 0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, 0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, 0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, 0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, 0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, 0, 0}, + {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, 0, 0}, + {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_memoryview = { + __pyx_memoryview___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_memoryview, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_memoryview = { + __pyx_memoryview___len__, /*mp_length*/ + __pyx_memoryview___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_memoryview = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.util.choleskies_cython.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*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_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryviewslice__get__base(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "GPy.util.choleskies_cython._memoryviewslice", /*tp_name*/ + sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___repr__, /*tp_repr*/ + #else + 0, /*tp_repr*/ + #endif + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___str__, /*tp_str*/ + #else + 0, /*tp_str*/ + #endif + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 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*/ + "Internal class for passing memoryview slices to Python", /*tp_doc*/ + __pyx_tp_traverse__memoryviewslice, /*tp_traverse*/ + __pyx_tp_clear__memoryviewslice, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, 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__Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +static CYTHON_INLINE long __Pyx_div_long(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { + va_list vargs; + char msg[200]; + va_start(vargs, fmt); +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + Py_FatalError(msg); + va_end(vargs); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + Py_ssize_t q = a / b; + Py_ssize_t r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_COMPILING_IN_CPYTHON +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + length = strlen(cstring); + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; +#else + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); +#endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} + +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else + return NULL; + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +} + +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 2, + &__Pyx_TypeInfo_double, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static PyObject *__pyx_memview_get_double(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(double *) itemp); +} +static int __pyx_memview_set_double(const char *itemp, PyObject *obj) { + double value = __pyx_PyFloat_AsDouble(obj); + if ((value == (double)-1) && PyErr_Occurred()) + return 0; + *(double *) itemp = value; + return 1; +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs->memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs->suboffsets[index] >= 0 || mvs->strides[index] != itemsize) + return 0; + itemsize *= mvs->shape[index]; + } + return 1; +} + +static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(char) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x)) + } else if (sizeof(char) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(char, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/GPy/util/choleskies_cython.pyx b/GPy/util/choleskies_cython.pyx new file mode 100644 index 00000000..d85b19cf --- /dev/null +++ b/GPy/util/choleskies_cython.pyx @@ -0,0 +1,107 @@ +#cython: wraparaound=False +#cython: boundscheck=False +#cython: nonecheck=False + +# Copyright James Hensman and Alan Saul 2015 + +import numpy as np +from cython.parallel import prange, parallel +cimport numpy as np + +def flat_to_triang(np.ndarray[double, ndim=2] flat, int M): + """take a matrix N x D and return a D X M x M array where + + N = M(M+1)/2 + + the lower triangluar portion of the d'th slice of the result is filled by the d'th column of flat. + """ + cdef int D = flat.shape[1] + cdef int N = flat.shape[0] + cdef int count = 0 + cdef np.ndarray[double, ndim=3] ret = np.zeros((D, M, M)) + cdef int d, m, mm + for d in range(D): + count = 0 + for m in range(M): + for mm in range(m+1): + ret[d, m, mm] = flat[count,d] + count += 1 + return ret + +def triang_to_flat(np.ndarray[double, ndim=3] L): + cdef int D = L.shape[0] + cdef int M = L.shape[1] + cdef int N = M*(M+1)/2 + cdef int count = 0 + cdef np.ndarray[double, ndim=2] flat = np.empty((N, D)) + cdef int d, m, mm + for d in range(D): + count = 0 + for m in range(M): + for mm in range(m+1): + flat[count,d] = L[d, m, mm] + count += 1 + return flat + + +def backprop_gradient(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2] L): + cdef np.ndarray[double, ndim=2] dL_dK = np.tril(dL).copy() + cdef int N = L.shape[0] + cdef int k, j, i + for k in range(N - 1, -1, -1): + for j in range(k + 1, N): + for i in range(j, N): + dL_dK[i, k] -= dL_dK[i, j] * L[j, k] + dL_dK[j, k] -= dL_dK[i, j] * L[i, k] + for j in range(k + 1, N): + dL_dK[j, k] /= L[k, k] + dL_dK[k, k] -= L[j, k] * dL_dK[j, k] + dL_dK[k, k] /= (2. * L[k, k]) + return dL_dK + +def backprop_gradient_par(double[:,:] dL, double[:,:] L): + cdef double[:,:] dL_dK = np.tril(dL).copy() + cdef int N = L.shape[0] + cdef int k, j, i + for k in range(N - 1, -1, -1): + with nogil, parallel(): + for i in prange(k + 1, N): + for j in range(k+1, i+1): + dL_dK[i, k] -= dL_dK[i, j] * L[j, k] + for j in range(i, N): + dL_dK[i, k] -= dL_dK[j, i] * L[j, k] + for j in range(k + 1, N): + dL_dK[j, k] /= L[k, k] + dL_dK[k, k] -= L[j, k] * dL_dK[j, k] + dL_dK[k, k] /= (2. * L[k, k]) + return dL_dK + +#here's a pure C version... +cdef extern from "cholesky_backprop.h" nogil: + void chol_backprop(int N, double* dL, double* L) + +def backprop_gradient_par_c(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2] L): + cdef np.ndarray[double, ndim=2] dL_dK = np.tril(dL) # makes a copy, c-contig + cdef int N = L.shape[0] + with nogil: + chol_backprop(N, dL_dK.data, L.data) + return dL_dK + +cdef extern from "cholesky_backprop.h" nogil: + void old_chol_backprop(int N, double* dL, double* L) + +def backprop_gradient_par_c_old(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2] L): + cdef np.ndarray[double, ndim=2] dL_dK = np.tril(dL) # makes a copy, c-contig + cdef int N = L.shape[0] + with nogil: + old_chol_backprop(N, dL_dK.data, L.data) + return dL_dK + + + + + + + + + diff --git a/GPy/util/cholesky_backprop.c b/GPy/util/cholesky_backprop.c new file mode 100644 index 00000000..0a4a2f03 --- /dev/null +++ b/GPy/util/cholesky_backprop.c @@ -0,0 +1,51 @@ +#include +void chol_backprop(int N, double* dL, double* L){ + //at the input to this fn, dL is df_dL. after this fn is complet, dL is df_dK + int i,k; + + dL[N*N - 1] /= (2. * L[N*N - 1]); + for(k=N-2;k>(-1);k--){ + cblas_dsymv(CblasRowMajor, CblasLower, + N-k-1, -1, + &dL[(N*(k+1) + k+1)],N, + &L[k*N+k+1],1, + 1, &dL[N*(k+1)+k], N); + for(i=0;i<(N-k-1); i++){ + dL[N*(k+1+i)+k] -= dL[N*(k+1)+k+i*(N+1)+1] * L[k*N+k+1+i]; + } + + cblas_dscal(N-k-1, 1.0/L[k*N+k], &dL[(k+1)*N+k], N); + dL[k*N + k] -= cblas_ddot(N-k-1, &dL[(k+1)*N+k], N, &L[k*N+k+1], 1); + dL[k*N + k] /= (2.0 * L[k*N + k]); + } +} + +double mydot(int n, double* a, int stride_a, double* b, int stride_b){ + double ret = 0; + for(int i=0; i(-1);k--){ + kN = k*N; + #pragma omp parallel for private(i,iN) + for(i=k+1; i + +void dsymv(int N, double*A, double*b, double*y); +double mydot(int n, double* a, int stride_a, double* b, int stride_b); +void chol_backprop(int N, double* dL, double* L); diff --git a/GPy/util/linalg.py b/GPy/util/linalg.py index 26c4b774..ed73d133 100644 --- a/GPy/util/linalg.py +++ b/GPy/util/linalg.py @@ -15,11 +15,7 @@ import warnings import os from .config import config import logging - -try: - from scipy import weave -except ImportError: - config.set('weave', 'working', 'False') +from . import linalg_cython _scipyversion = np.float64((scipy.__version__).split('.')[:2]) @@ -422,114 +418,33 @@ def DSYR(*args, **kwargs): def symmetrify(A, upper=False): """ - Take the square matrix A and make it symmetrical by copting elements from the lower half to the upper + Take the square matrix A and make it symmetrical by copting elements from + the lower half to the upper works IN PLACE. - note: tries to use weave, falls back to a slower numpy version + note: tries to use cython, falls back to a slower numpy version """ - if config.getboolean('weave', 'working'): - try: - symmetrify_weave(A, upper) - except: - print("\n Weave compilation failed. Falling back to (slower) numpy implementation\n") - config.set('weave', 'working', 'False') - symmetrify_numpy(A, upper) + if config.getboolean('cython', 'working'): + _symmetrify_cython(A, upper) else: - symmetrify_numpy(A, upper) + _symmetrify_numpy(A, upper) -def symmetrify_weave(A, upper=False): - """ - Take the square matrix A and make it symmetrical by copting elements from the lower half to the upper +def _symmetrify_cython(A, upper=False): + return linalg_cython.symmetrify(A, upper) - works IN PLACE. - - - """ - N, M = A.shape - assert N == M - - c_contig_code = """ - int iN; - for (int i=1; i -# """ -# code = """ -# double r,c,s; -# int j,i; -# for(j=0; jilk' + """ + return A.dot(B.reshape(B.shape[0], -1)).reshape(A.shape[0], B.shape[1], B.shape[2]) + +def ijk_jlk_to_il(A, B): + """ + Faster version of einsum einsum('ijk,jlk->il', A,B) + """ + res = np.zeros((A.shape[0], B.shape[1])) + [np.add(np.dot(A[:,:,k], B[:,:,k]), res, out=res) for k in range(B.shape[-1])] + return res + +def ijk_ljk_to_ilk(A, B): + """ + Faster version of einsum np.einsum('ijk,ljk->ilk', A, B) + + I.e A.dot(B.T) for every dimension + """ + res = np.zeros((A.shape[-1], A.shape[0], B.shape[0])) + [np.dot(A[:,:,i], B[:,:,i].T, out=res[i,:,:]) for i in range(A.shape[-1])] + res = res.swapaxes(0, 2).swapaxes(0,1) + return res diff --git a/GPy/util/linalg_cython.c b/GPy/util/linalg_cython.c new file mode 100644 index 00000000..1374b233 --- /dev/null +++ b/GPy/util/linalg_cython.c @@ -0,0 +1,6191 @@ +/* Generated by Cython 0.21 */ + +#define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_21" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#endif +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__GPy__util__linalg_cython +#define __PYX_HAVE_API__GPy__util__linalg_cython +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "pythread.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "GPy/util/linalg_cython.pyx", + "__init__.pxd", + "type.pxd", + "bool.pxd", + "complex.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; 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+ +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; 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}} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) +#else + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannyFinishContext() + #define __Pyx_INCREF(r) Py_INCREF(r) + #define __Pyx_DECREF(r) Py_DECREF(r) + #define __Pyx_GOTREF(r) + #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) + #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) +#endif +#define __Pyx_XDECREF_SET(r, v) do { \ + PyObject *tmp = (PyObject *) r; \ + r = v; __Pyx_XDECREF(tmp); \ + } while (0) +#define __Pyx_DECREF_SET(r, v) do { \ + PyObject *tmp = (PyObject *) r; \ + r = v; __Pyx_DECREF(tmp); \ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); 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+typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_symmetrify, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "GPy/util/linalg_cython.pyx":22 + * @cython.wraparound(False) + * @cython.nonecheck(False) + * def cholupdate(np.ndarray[double, ndim=1] x, np.ndarray[double, ndim=2] L, int N): # <<<<<<<<<<<<<< + * cdef double r + * cdef double c + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3GPy_4util_13linalg_cython_3cholupdate, NULL, __pyx_n_s_GPy_util_linalg_cython); 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 (PyDict_SetItem(__pyx_d, __pyx_n_s_cholupdate, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "GPy/util/linalg_cython.pyx":1 + * cimport numpy as np # <<<<<<<<<<<<<< + * from cpython cimport bool + * import cython + */ + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + 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; + + /* "../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init GPy.util.linalg_cython", __pyx_clineno, __pyx_lineno, __pyx_filename); + Py_DECREF(__pyx_d); __pyx_d = 0; + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init GPy.util.linalg_cython"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if PY_MAJOR_VERSION < 3 + return; + #else + return __pyx_m; + #endif +} + +/* Runtime support code */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/GPy/util/linalg_cython.pyx b/GPy/util/linalg_cython.pyx new file mode 100644 index 00000000..72252bd9 --- /dev/null +++ b/GPy/util/linalg_cython.pyx @@ -0,0 +1,34 @@ +cimport numpy as np +from cpython cimport bool +import cython + +@cython.boundscheck(False) +@cython.wraparound(False) +@cython.nonecheck(False) +def symmetrify(np.ndarray[double, ndim=2] A, bool upper): + cdef int N = A.shape[0] + if not upper: + for i in xrange(N): + for j in xrange(i): + A[j, i] = A[i, j] + else: + for j in xrange(N): + for i in xrange(j): + A[j, i] = A[i, j] + +@cython.boundscheck(False) +@cython.wraparound(False) +@cython.nonecheck(False) +def cholupdate(np.ndarray[double, ndim=1] x, np.ndarray[double, ndim=2] L, int N): + cdef double r + cdef double c + cdef double s + for j in xrange(N): + r = np.sqrt(L[j,j]*L[j,j] + x[j]*x[j]) + c = r / L[j,j] + s = x[j] / L[j,j] + L[j,j] = r + for i in xrange(j): + L[i,j] = (L[i,j] + s*x[i])/c + x[i] = c*x[i] - s*L[i,j]; + r = np.sqrt(L[j,j]) diff --git a/GPy/util/misc.py b/GPy/util/misc.py index ddc29fa0..8bef929c 100644 --- a/GPy/util/misc.py +++ b/GPy/util/misc.py @@ -42,9 +42,6 @@ def chain_1(df_dg, dg_dx): """ if np.all(dg_dx==1.): return df_dg - if len(df_dg) > 1 and len(df_dg.shape)>1 and df_dg.shape[-1] > 1: - #import ipdb; ipdb.set_trace() # XXX BREAKPOINT - raise NotImplementedError('Not implemented for matricies yet') return df_dg * dg_dx def chain_2(d2f_dg2, dg_dx, df_dg, d2g_dx2): @@ -56,8 +53,6 @@ def chain_2(d2f_dg2, dg_dx, df_dg, d2g_dx2): """ if np.all(dg_dx==1.) and np.all(d2g_dx2 == 0): return d2f_dg2 - if len(d2f_dg2) > 1 and len(d2f_dg2.shape)>1 and d2f_dg2.shape[-1] > 1: - raise NotImplementedError('Not implemented for matricies yet') dg_dx_2 = np.clip(dg_dx, -np.inf, _lim_val_square)**2 #dg_dx_2 = dg_dx**2 return d2f_dg2*(dg_dx_2) + df_dg*d2g_dx2 @@ -71,11 +66,7 @@ def chain_3(d3f_dg3, dg_dx, d2f_dg2, d2g_dx2, df_dg, d3g_dx3): """ if np.all(dg_dx==1.) and np.all(d2g_dx2==0) and np.all(d3g_dx3==0): return d3f_dg3 - if ( (len(d2f_dg2) > 1 and d2f_dg2.shape[-1] > 1) - or (len(d3f_dg3) > 1 and d3f_dg3.shape[-1] > 1)): - raise NotImplementedError('Not implemented for matricies yet') dg_dx_3 = np.clip(dg_dx, -np.inf, _lim_val_cube)**3 - #dg_dx_3 = dg_dx**3 return d3f_dg3*(dg_dx_3) + 3*d2f_dg2*dg_dx*d2g_dx2 + df_dg*d3g_dx3 def opt_wrapper(m, **kwargs): @@ -133,10 +124,11 @@ def kmm_init(X, m = 10): ### make a parameter to its corresponding array: def param_to_array(*param): """ -Convert an arbitrary number of parameters to :class:ndarray class objects. This is for -converting parameter objects to numpy arrays, when using scipy.weave.inline routine. -In scipy.weave.blitz there is no automatic array detection (even when the array inherits -from :class:ndarray)""" + Convert an arbitrary number of parameters to :class:ndarray class objects. + This is for converting parameter objects to numpy arrays, when using + scipy.weave.inline routine. In scipy.weave.blitz there is no automatic + array detection (even when the array inherits from :class:ndarray) + """ import warnings warnings.warn("Please use param.values, as this function will be deprecated in the next release.", DeprecationWarning) assert len(param) > 0, "At least one parameter needed" diff --git a/GPy/util/warping_functions.py b/GPy/util/warping_functions.py index 8f9d232f..a56f8c27 100644 --- a/GPy/util/warping_functions.py +++ b/GPy/util/warping_functions.py @@ -2,7 +2,7 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) import numpy as np -from GPy.core.parameterization import Parameterized, Param +from ..core.parameterization import Parameterized, Param from ..core.parameterization.transformations import Logexp class WarpingFunction(Parameterized): diff --git a/MANIFEST.in b/MANIFEST.in index bcbf3583..1800fa52 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -6,3 +6,6 @@ include *.cfg recursive-include doc *.cfg include *.json recursive-include doc *.json +recursive-include GPy *.c +recursive-include GPy *.so +recursive-include GPy *.pyx diff --git a/README.md b/README.md index 60dcbe24..07a65cc6 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,6 @@ Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GP ### Python 3 Compatibility Work is underway to make GPy run on Python 3. -* Python 2.x compatibility is currently broken in this fork * All tests in the testsuite now run on Python3. To see this for yourself, in Ubuntu 14.04, you can do @@ -21,12 +20,17 @@ To see this for yourself, in Ubuntu 14.04, you can do git clone https://github.com/mikecroucher/GPy.git cd GPy git checkout devel + python3 setup.py build_ext --inplace nosetests3 GPy/testing nosetests3 is Ubuntu's way of reffering to the Python 3 version of nosetests. You install it with sudo apt-get install python3-nose +The command `python3 setup.py build_ext --inplace` builds the Cython extensions. IF it doesn't work, you may need to install this: + + sudo apt-get install python3-dev + * Test coverage is less than 100% so it is expected that there is still more work to be done. We need more tests and examples to try out. * All weave functions not covered by the test suite are *simply commented out*. Can add equivalents later as test functions become available * A set of benchmarks would be useful! diff --git a/setup.py b/setup.py index 0562c9d8..8025cd5d 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,8 @@ # -*- coding: utf-8 -*- import os -from setuptools import setup +from setuptools import setup, Extension +import numpy as np # Version number version = '0.6.1' @@ -10,6 +11,28 @@ version = '0.6.1' def read(fname): return open(os.path.join(os.path.dirname(__file__), fname)).read() +#compile_flags = ["-march=native", '-fopenmp', '-O3', ] +compile_flags = [ '-fopenmp', '-O3', ] + +ext_mods = [Extension(name='GPy.kern._src.stationary_cython', + sources=['GPy/kern/_src/stationary_cython.c','GPy/kern/_src/stationary_utils.c'], + include_dirs=[np.get_include()], + extra_compile_args=compile_flags, + extra_link_args = ['-lgomp']), + Extension(name='GPy.util.choleskies_cython', + sources=['GPy/util/choleskies_cython.c', 'GPy/util/cholesky_backprop.c'], + include_dirs=[np.get_include()], + extra_link_args = ['-lgomp', '-lblas'], + extra_compile_args=compile_flags+['-std=c99']), + Extension(name='GPy.util.linalg_cython', + sources=['GPy/util/linalg_cython.c'], + include_dirs=[np.get_include()], + extra_compile_args=compile_flags), + Extension(name='GPy.kern._src.coregionalize_cython', + sources=['GPy/kern/_src/coregionalize_cython.c'], + include_dirs=[np.get_include()], + extra_compile_args=compile_flags)] + setup(name = 'GPy', version = version, author = read('AUTHORS.txt'), @@ -18,6 +41,7 @@ setup(name = 'GPy', license = "BSD 3-clause", keywords = "machine-learning gaussian-processes kernels", url = "http://sheffieldml.github.com/GPy/", + ext_modules = ext_mods, packages = ["GPy.models", "GPy.inference.optimization", "GPy.inference.mcmc",