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[subbarray] logging

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This commit is contained in:
mzwiessele 2014-06-27 15:17:12 -07:00
parent 83e2df838d
commit 06ee090a50
2 changed files with 10 additions and 6 deletions
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4
GPy/inference/latent_function_inference/var_dtc.py
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@ -221,9 +221,11 @@ class VarDTCMissingData(LatentFunctionInference):
inan = self._inan inan = self._inan
has_none = True has_none = True
if has_none: if has_none:
print "caching missing data slices, this can take several minutes..."
from ...util.subarray_and_sorting import common_subarrays from ...util.subarray_and_sorting import common_subarrays
self._subarray_indices = [] self._subarray_indices = []
for v,ind in common_subarrays(inan, 1).iteritems(): csa = common_subarrays(inan, 1)
for v,ind in csa.iteritems():
if not np.all(v): if not np.all(v):
v = ~np.array(v, dtype=bool) v = ~np.array(v, dtype=bool)
ind = np.array(ind, dtype=int) ind = np.array(ind, dtype=int)

12
GPy/util/subarray_and_sorting.py
View file

@ -16,13 +16,13 @@ def common_subarrays(X, axis=0):
for the subarray in X, where index is the index to the remaining axis. for the subarray in X, where index is the index to the remaining axis.
:param :class:`np.ndarray` X: 2d array to check for common subarrays in :param :class:`np.ndarray` X: 2d array to check for common subarrays in
:param int axis: axis to apply subarray detection over. :param int axis: axis to apply subarray detection over.
When the index is 0, compare rows -- columns, otherwise. When the index is 0, compare rows -- columns, otherwise.
Examples: Examples:
========= =========
In a 2d array: In a 2d array:
>>> import numpy as np >>> import numpy as np
>>> X = np.zeros((3,6), dtype=bool) >>> X = np.zeros((3,6), dtype=bool)
>>> X[[1,1,1],[0,4,5]] = 1; X[1:,[2,3]] = 1 >>> X[[1,1,1],[0,4,5]] = 1; X[1:,[2,3]] = 1
@ -48,6 +48,8 @@ def common_subarrays(X, axis=0):
assert X.ndim == 2 and axis in (0,1), "Only implemented for 2D arrays" assert X.ndim == 2 and axis in (0,1), "Only implemented for 2D arrays"
subarrays = defaultdict(list) subarrays = defaultdict(list)
cnt = count() cnt = count()
if axis == 0: size = X.shape[0]
else: size = X.shape[1]
logger = logging.getLogger("common_subarrays") logger = logging.getLogger("common_subarrays")
def accumulate(x, s, c): def accumulate(x, s, c):
logger.debug("creating tuple") logger.debug("creating tuple")
@ -55,7 +57,7 @@ def common_subarrays(X, axis=0):
logger.debug("tuple done") logger.debug("tuple done")
col = c.next() col = c.next()
iadd(s[t], [col]) iadd(s[t], [col])
logger.debug("added col {}".format(col)) logger.info("added col {} {:.2%}".format(col, col/float(size)))
return None return None
if axis == 0: [accumulate(x, subarrays, cnt) for x in X] if axis == 0: [accumulate(x, subarrays, cnt) for x in X]
else: [accumulate(x, subarrays, cnt) for x in X.T] else: [accumulate(x, subarrays, cnt) for x in X.T]
@ -63,4 +65,4 @@ def common_subarrays(X, axis=0):
if __name__ == '__main__': if __name__ == '__main__':
import doctest import doctest
doctest.testmod() doctest.testmod()