8000 FIX add max_iter, and func uses class (#15120) · NeuroDataDesign/scikit-learn@ac72a48 · GitHub
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FIX add max_iter, and func uses class (scikit-learn#15120)
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‎doc/whats_new/v0.22.rst‎

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@@ -89,6 +89,11 @@ Changelog
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producing Segmentation Fault on large arrays due to integer index overflow.
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:pr:`15057` by :user:`Vladimir Korolev <balodja>`.
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- |Fix| :class:`~cluster.MeanShift` now accepts a :term:`max_iter` with a
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default value of 300 instead of always using the default 300. It also now
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exposes an ``n_iter_`` indicating the maximum number of iterations performed
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on each seed. :pr:`15120` by `Adrin Jalali`_.
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:mod:`sklearn.compose`
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......................
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‎sklearn/cluster/mean_shift_.py‎

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@@ -101,8 +101,9 @@ def _mean_shift_single_seed(my_mean, X, nbrs, max_iter):
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# If converged or at max_iter, adds the cluster
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if (np.linalg.norm(my_mean - my_old_mean) < stop_thresh or
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completed_iterations == max_iter):
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return tuple(my_mean), len(points_within)
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break
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completed_iterations += 1
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return tuple(my_mean), len(points_within), completed_iterations
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def mean_shift(X, bandwidth=None, seeds=None, bin_seeding=False,
@@ -178,72 +179,12 @@ def mean_shift(X, bandwidth=None, seeds=None, bin_seeding=False,
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<sphx_glr_auto_examples_cluster_plot_mean_shift.py>`.
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"""
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if bandwidth is None:
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bandwidth = estimate_bandwidth(X, n_jobs=n_jobs)
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elif bandwidth <= 0:
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raise ValueError("bandwidth needs to be greater than zero or None,"
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" got %f" % bandwidth)
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if seeds is None:
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if bin_seeding:
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seeds = get_bin_seeds(X, bandwidth, min_bin_freq)
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else:
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seeds = X
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n_samples, n_features = X.shape
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center_intensity_dict = {}
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# We use n_jobs=1 because this will be used in nested calls under
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# parallel calls to _mean_shift_single_seed so there is no need for
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# for further parallelism.
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nbrs = NearestNeighbors(radius=bandwidth, n_jobs=1).fit(X)
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# execute iterations on all seeds in parallel
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all_res = Parallel(n_jobs=n_jobs)(
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delayed(_mean_shift_single_seed)
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(seed, X, nbrs, max_iter) for seed in seeds)
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# copy results in a dictionary
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for i in range(len(seeds)):
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if all_res[i] is not None:
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center_intensity_dict[all_res[i][0]] = all_res[i][1]
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if not center_intensity_dict:
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# nothing near seeds
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raise ValueError("No point was within bandwidth=%f of any seed."
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" Try a different seeding strategy \
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or increase the bandwidth."
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% bandwidth)
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# POST PROCESSING: remove near duplicate points
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# If the distance between two kernels is less than the bandwidth,
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# then we have to remove one because it is a duplicate. Remove the
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# one with fewer points.
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sorted_by_intensity = sorted(center_intensity_dict.items(),
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key=lambda tup: (tup[1], tup[0]),
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reverse=True)
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sorted_centers = np.array([tup[0] for tup in sorted_by_intensity])
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unique = np.ones(len(sorted_centers), dtype=np.bool)
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nbrs = NearestNeighbors(radius=bandwidth,
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n_jobs=n_jobs).fit(sorted_centers)
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for i, center in enumerate(sorted_centers):
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if unique[i]:
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neighbor_idxs = nbrs.radius_neighbors([center],
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return_distance=False)[0]
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unique[neighbor_idxs] = 0
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unique[i] = 1 # leave the current point as unique
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cluster_centers = sorted_centers[unique]
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# ASSIGN LABELS: a point belongs to the cluster that it is closest to
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nbrs = NearestNeighbors(n_neighbors=1, n_jobs=n_jobs).fit(cluster_centers)
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labels = np.zeros(n_samples, dtype=np.int)
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distances, idxs = nbrs.kneighbors(X)
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if cluster_all:
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labels = idxs.flatten()
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else:
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labels.fill(-1)
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bool_selector = distances.flatten() <= bandwidth
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labels[bool_selector] = idxs.flatten()[bool_selector]
246-
return cluster_centers, labels
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model = MeanShift(bandwidth=bandwidth, seeds=seeds,
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min_bin_freq=min_bin_freq,
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bin_seeding=bin_seeding,
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cluster_all=cluster_all, n_jobs=n_jobs,
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max_iter=max_iter).fit(X)
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return model.cluster_centers_, model.labels_
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def get_bin_seeds(X, bin_size, min_bin_freq=1):
@@ -347,6 +288,12 @@ class MeanShift(ClusterMixin, BaseEstimator):
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``-1`` means using all processors. See :term:`Glossary <n_jobs>`
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for more details.
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max_iter : int, default=300
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Maximum number of iterations, per seed point before the clustering
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operation terminates (for that seed point), if has not converged yet.
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.. versionadded:: 0.22
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Attributes
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----------
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cluster_centers_ : array, [n_clusters, n_features]
@@ -355,6 +302,11 @@ class MeanShift(ClusterMixin, BaseEstimator):
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labels_ :
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Labels of each point.
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n_iter_ : int
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Maximum number of iterations performed on each seed.
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.. versionadded:: 0.22
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Examples
359311
--------
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>>> from sklearn.cluster import MeanShift
@@ -395,13 +347,14 @@ class MeanShift(ClusterMixin, BaseEstimator):
395347
396348
"""
397349
def __init__(self, bandwidth=None, seeds=None, bin_seeding=False,
398-
min_bin_freq=1, cluster_all=True, n_jobs=None):
350+
min_bin_freq=1, cluster_all=True, n_jobs=None, max_iter=300):
399351
self.bandwidth = bandwidth
400352
self.seeds = seeds
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self.bin_seeding = bin_seeding
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self.cluster_all = cluster_all
403355
self.min_bin_freq = min_bin_freq
404356
self.n_jobs = n_jobs
357+
self.max_iter = max_iter
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406359
def fit(self, X, y=None):
407360
"""Perform clustering.
@@ -415,11 +368,78 @@ def fit(self, X, y=None):
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416369
"""
417370
X = check_array(X)
418-
self.cluster_centers_, self.labels_ = \
419-
mean_shift(X, bandwidth=self.bandwidth, seeds=self.seeds,
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min_bin_freq=self.min_bin_freq,
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bin_seeding=self.bin_seeding,
422-
cluster_all=self.cluster_all, n_jobs=self.n_jobs)
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bandwidth = self.bandwidth
372+
if bandwidth is None:
373+
bandwidth = estimate_bandwidth(X, n_jobs=self.n_jobs)
374+
elif bandwidth <= 0:
375+
raise ValueError("bandwidth needs to be greater than zero or None,"
376+
" got %f" % bandwidth)
377+
378+
seeds = self.seeds
379+
if seeds is None:
380+
if self.bin_seeding:
381+
seeds = get_bin_seeds(X, bandwidth, self.min_bin_freq)
382+
else:
383+
seeds = X
384+
n_samples, n_features = X.shape
385+
center_intensity_dict = {}
386+
387+
# We use n_jobs=1 because this will be used in nested calls under
388+
# parallel calls to _mean_shift_single_seed so there is no need for
389+
# for further parallelism.
390+
nbrs = NearestNeighbors(radius=bandwidth, n_jobs=1).fit(X)
391+
392+
# execute iterations on all seeds in parallel
393+
all_res = Parallel(n_jobs=self.n_jobs)(
394+
delayed(_mean_shift_single_seed)
395+
(seed, X, nbrs, self.max_iter) for seed in seeds)
396+
# copy results in a dictionary
397+
for i in range(len(seeds)):
398+
if all_res[i][1]: # i.e. len(points_within) > 0
399+
center_intensity_dict[all_res[i][0]] = all_res[i][1]
400+
401+
self.n_iter_ = max([x[2] for x in all_res])
402+
403+
if not center_intensity_dict:
404+
# nothing near seeds
405+
raise ValueError("No point was within bandwidth=%f of any seed."
406+
" Try a different seeding strategy \
407+
or increase the bandwidth."
408+
% bandwidth)
409+
410+
# POST PROCESSING: remove near duplicate points
411+
# If the distance between two kernels is less than the bandwidth,
412+
# then we have to remove one because it is a duplicate. Remove the
413+
# one with fewer points.
414+
415+
sorted_by_intensity = sorted(center_intensity_dict.items(),
416+
key=lambda tup: (tup[1], tup[0]),
417+
reverse=True)
418+
sorted_centers = np.array([tup[0] for tup in sorted_by_intensity])
419+
unique = np.ones(len(sorted_centers), dtype=np.bool)
420+
nbrs = NearestNeighbors(radius=bandwidth,
421+
n_jobs=self.n_jobs).fit(sorted_centers)
422+
for i, center in enumerate(sorted_centers):
423+
if unique[i]:
424+
neighbor_idxs = nbrs.radius_neighbors([center],
425+
return_distance=False)[0]
426+
unique[neighbor_idxs] = 0
427+
unique[i] = 1 # leave the current point as unique
428+
cluster_centers = sorted_centers[unique]
429+
430+
# ASSIGN LABELS: a point belongs to the cluster that it is closest to
431+
nbrs = NearestNeighbors(n_neighbors=1,
432+
n_jobs=self.n_jobs).fit(cluster_centers)
433+
labels = np.zeros(n_samples, dtype=np.int)
434+
distances, idxs = nbrs.kneighbors(X)
435+
if self.cluster_all:
436+
labels = idxs.flatten()
437+
else:
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labels.fill(-1)
439+
bool_selector = distances.flatten() <= bandwidth
440+
labels[bool_selector] = idxs.flatten()[bool_selector]
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442+
self.cluster_centers_, self.labels_ = cluster_centers, labels
423443
return self
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425445
def predict(self, X):

‎sklearn/cluster/tests/test_mean_shift.py‎

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Original file line numberDiff line numberDiff line change
@@ -155,3 +155,16 @@ def test_bin_seeds():
155155
cluster_std=0.1, random_state=0)
156156
test_bins = get_bin_seeds(X, 1)
157157
assert_array_equal(test_bins, [[0, 0], [1, 1]])
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@pytest.mark.parametrize('max_iter', [1, 100])
161+
def test_max_iter(max_iter):
162+
clusters1, _ = mean_shift(X, max_iter=max_iter)
163+
ms = MeanShift(max_iter=max_iter).fit(X)
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clusters2 = ms.cluster_centers_
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assert ms.n_iter_ <= ms.max_iter
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assert len(clusters1) == len(clusters2)
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for c1, c2 in zip(clusters1, clusters2):
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assert np.allclose(c1, c2)

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