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Cython ball tree #316

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Merged
fabianp merged 6 commits into from
Aug 24, 2011
Merged

Cython ball tree #316

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bcc63de
initial commit
jakevdp Aug 22, 2011
414a753
added compiled cython
jakevdp Aug 22, 2011
dfe292b
assure C-ordered on init
jakevdp Aug 22, 2011
5011d3e
fix NeighborsClassifier doctest
jakevdp Aug 22, 2011
e4fd194
make memory allocation more efficient
jakevdp Aug 23, 2011
1ea3c95
documentation clarifications
jakevdp Aug 23, 2011
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4 changes: 2 additions & 2 deletions scikits/learn/neighbors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ class NeighborsClassifier(BaseEstimator, ClassifierMixin):

Examples
--------
>>> samples = [[0, 0, 1], [1, 0, 0]]
>>> samples = [[0, 0, 2], [1, 0, 0]]
>>> labels = [0, 1]
>>> from scikits.learn.neighbors import NeighborsClassifier
>>> neigh = NeighborsClassifier(n_neighbors=1)
Expand Down Expand Up @@ -530,7 +530,7 @@ def radius_neighbors_graph(X, radius, mode='connectivity'):
n_neighbors = np.array([len(a) for a in A_ind])
n_nonzero = np.sum(n_neighbors)
A_ind = np.concatenate(list(A_ind))
A_indptr = np.concatenate((np.zeros(1), np.cumsum(n_neighbors)))
A_indptr = np.concatenate((np.zeros(1, dtype=int), np.cumsum(n_neighbors)))

if A_data is None:
A_data = np.ones(n_nonzero)
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4 changes: 1 addition & 3 deletions scikits/learn/setup.py
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Expand Up @@ -43,9 +43,7 @@ def configuration(parent_package='', top_path=None):
warnings.warn(BlasNotFoundError.__doc__)

config.add_extension('ball_tree',
sources=[join('src', 'ball_tree.cpp')],
depends=[join('src', 'BallTree.h'),
join('src', 'BallTreePoint.h')],
sources=[join('src', 'ball_tree.c')],
include_dirs=[numpy.get_include()])

# the following packages depend on cblas, so they have to be build
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