def cluster_data(img, thr, xyz_a, k=26):
'''docstring for cluster_data'''
# Import packages
from scipy.sparse import coo_matrix, cs_graph_components
import numpy as np
# Threshold the entire correlation map and find connected components, store this in sparse matrix
val_idx = img > thr # store valid indices
xyz_th = xyz_a[
val_idx] # find the 3D indices corresponding to the above threshold voxels
i, j, d = graph_3d_grid(
xyz_th,
k=k) # find the connected components for the above threshold voxels
nvoxs = xyz_th.shape[
0] # store the number of correlated voxels in entire network
adj = coo_matrix((d, (i, j)), shape=(
nvoxs,
nvoxs)) # and store the connected nodes and weights in sparse matrix
# Identify the connected components (clusters) within the graph
nc, labels = cs_graph_components(adj)
# Copy the node labels to their voxel equivalents
lbl_img = np.zeros(img.shape) # init lbl_img - map to store label data
# add 2 so that labels corresponding to unconnected voxels (-2)
# will be zero in lbl_img, and label==0 will now equal 2
lbl_img[val_idx] = labels + 2
return lbl_img
def tree_information_sparse(forest, n_features):
"""Computes mutual information objective from forest.
Parameters
----------
forest: sparse matrix
graph containing trees representing cluster
n_features: int
dimensionality of input space.
"""
entropy = 0
sym_forest = forest + forest.T
n_components, components = sparse.cs_graph_components(sym_forest)
if np.any(components < 0):
# there is a lonely node
entropy -= 1e10
#n_samples = len(components)
for i in xrange(n_components):
inds = np.where(components == i)[0]
subforest = forest[inds[:, np.newaxis], inds]
L = subforest.sum()
n_samples_c = len(inds)
if L == 0:
warnings.warn("L is zero. This means there are identical points in"
" the dataset")
L = 1e-10
entropy += (n_samples_c * (
(n_features - 1) * np.log(n_samples_c) - n_features * np.log(L)))
return entropy
def plot_clustering(X, y=None, axes=None, three_d=False, forest=None):
if y is None and forest is None:
raise ValueError("give me y or a sparse matrix representing the"
"forest")
if y is None:
_, y = sparse.cs_graph_components(forest + forest.T)
if three_d and X.shape[1] > 3:
X = RandomizedPCA(n_components=3).fit_transform(X)
elif not three_d and X.shape[1] > 2:
X = RandomizedPCA(n_components=2).fit_transform(X)
if axes == None or three_d:
plt.figure()
axes = plt.gca()
if three_d:
axes = plt.gca(axes=axes, projection='3d')
colors = np.array([x for x in 'bgrcmykbgrcmykbgrcmykbgrcmyk'] * 10)
color = colors[y]
if three_d:
axes.scatter(X[:, 0], X[:, 1], X[:, 2], color=color)
else:
axes.scatter(X[:, 0], X[:, 1], color=color, s=10)
if not forest is None:
for edge in np.vstack(forest.nonzero()).T:
i, j = edge
axes.plot([X[i, 0], X[j, 0]], [X[i, 1], X[j, 1]], c=color[i])
axes.set_xticks(())
axes.set_yticks(())
return axes
def clusterByAABB(poly, opts, argv):
aabbs = []
aabbsOut = np.zeros((poly.GetLines().GetNumberOfCells(), 6))
for (i, idl) in enumerate(lineGenerator(poly.GetLines())):
pts = idListToPoints(idl, poly.GetPoints())
aabb = AABB(pts)
aabbs.append(aabb)
aabbsOut[i, :] = aabb.toArray()
overlaps = np.zeros((len(aabbs), len(aabbs)))
for (i1, ab1) in enumerate(aabbs):
for i2 in range(i1, len(aabbs)):
if (i1 == i2):
overlaps[i1, i2] = 1
else:
ab2 = aabbs[i2]
overlaps[i1, i2] = ab1.Intersect(ab2)
overlaps[i2, i1] = overlaps[i1, i2]
threshold = np.vectorize(lambda x: 1 if x > opts.overlap else 0,
otypes=[np.int32])
adjacency = threshold(overlaps)
conComps = scsp.cs_graph_components(adjacency)
addCellIntArray(poly, "VortexCluster", conComps[1])
aabbGlyphs = glyphAABB(aabbs)
addCellIntArray(aabbGlyphs, "VortexCluster", conComps[1])
if (opts.aabbOut != ""):
np.savetxt(opts.aabbOut, aabbsOut)
if (opts.aabbLabels != ""):
np.savetxt(opts.aabbLabels, conComps[1])
return (poly, aabbGlyphs)
def tree_information_sparse(forest, n_features):
"""Computes mutual information objective from forest.
Parameters
----------
forest: sparse matrix
graph containing trees representing cluster
n_features: int
dimensionality of input space.
"""
entropy = 0
sym_forest = forest + forest.T
n_components, components = sparse.cs_graph_components(sym_forest)
if np.any(components < 0):
# there is a lonely node
entropy -= 1e10
#n_samples = len(components)
for i in xrange(n_components):
inds = np.where(components == i)[0]
subforest = forest[inds[:, np.newaxis], inds]
L = subforest.sum()
n_samples_c = len(inds)
if L == 0:
warnings.warn("L is zero. This means there are identical points in"
" the dataset")
L = 1e-10
entropy += (n_samples_c * ((n_features - 1) * np.log(n_samples_c) -
n_features * np.log(L)))
return entropy
def plot_clustering(X, y=None, axes=None, three_d=False, forest=None):
if y is None and forest is None:
raise ValueError("give me y or a sparse matrix representing the"
"forest")
if y is None:
_, y = sparse.cs_graph_components(forest + forest.T)
if three_d and X.shape[1] > 3:
X = RandomizedPCA(n_components=3).fit_transform(X)
elif not three_d and X.shape[1] > 2:
X = RandomizedPCA(n_components=2).fit_transform(X)
if axes == None or three_d:
plt.figure()
axes = plt.gca()
if three_d:
axes = plt.gca(axes=axes, projection='3d')
colors = np.array([x for x in 'bgrcmykbgrcmykbgrcmykbgrcmyk'] * 10)
color = colors[y]
if three_d:
axes.scatter(X[:, 0], X[:, 1], X[:, 2], color=color)
else:
axes.scatter(X[:, 0], X[:, 1], color=color, s=10)
if not forest is None:
for edge in np.vstack(forest.nonzero()).T:
i, j = edge
axes.plot([X[i, 0], X[j, 0]], [X[i, 1], X[j, 1]], c=color[i])
axes.set_xticks(())
axes.set_yticks(())
return axes
def clusterByAABB(poly,opts,argv): aabbs = [] aabbsOut = np.zeros((poly.GetLines().GetNumberOfCells(),6)) for (i,idl) in enumerate(lineGenerator(poly.GetLines())): pts = idListToPoints(idl, poly.GetPoints()) aabb = AABB(pts) aabbs.append(aabb) aabbsOut[i,:] = aabb.toArray() overlaps = np.zeros((len(aabbs), len(aabbs))) for (i1, ab1) in enumerate(aabbs): for i2 in range(i1, len(aabbs)): if (i1 == i2): overlaps[i1,i2] = 1 else: ab2 = aabbs[i2] overlaps[i1,i2] = ab1.Intersect(ab2) overlaps[i2,i1] = overlaps[i1,i2] threshold = np.vectorize(lambda x: 1 if x > opts.overlap else 0, otypes=[np.int32]) adjacency = threshold(overlaps) conComps = scsp.cs_graph_components(adjacency) addCellIntArray(poly, "VortexCluster", conComps[1]) aabbGlyphs = glyphAABB(aabbs) addCellIntArray(aabbGlyphs, "VortexCluster", conComps[1]) if (opts.aabbOut != ""): np.savetxt(opts.aabbOut, aabbsOut) if (opts.aabbLabels != ""): np.savetxt(opts.aabbLabels, conComps[1]) return (poly, aabbGlyphs)
def euclidean_mst(X, neighbors_estimator, verbose=2):
n_neighbors = min(2, X.shape[0])
while True:
# make sure we have a connected minimum spanning tree.
# otherwise we need to consider more neighbors
n_neighbors = 2 * n_neighbors
if verbose > 1:
print("Trying to build mst with %d neighbors." % n_neighbors)
distances = neighbors_estimator.kneighbors_graph(
X, n_neighbors=n_neighbors, mode='distance')
n_components, component_indicators =\
sparse.cs_graph_components(distances + distances.T)
if len(np.unique(component_indicators)) > 1:
continue
distances.sort_indices()
forest = minimum_spanning_tree(distances)
_, inds = sparse.cs_graph_components(forest + forest.T)
assert (len(np.unique(inds)) == 1)
break
return forest
def euclidean_mst(X, neighbors_estimator, verbose=2):
n_neighbors = min(2, X.shape[0])
while True:
# make sure we have a connected minimum spanning tree.
# otherwise we need to consider more neighbors
n_neighbors = 2 * n_neighbors
if verbose > 1:
print("Trying to build mst with %d neighbors." % n_neighbors)
distances = neighbors_estimator.kneighbors_graph(
X, n_neighbors=n_neighbors, mode='distance')
n_components, component_indicators =\
sparse.cs_graph_components(distances + distances.T)
if len(np.unique(component_indicators)) > 1:
continue
distances.sort_indices()
forest = minimum_spanning_tree(distances)
_, inds = sparse.cs_graph_components(forest + forest.T)
assert(len(np.unique(inds)) == 1)
break
return forest
def __init__(self, clf, A=None, n_jobs=-1, copy=True):
if copy and A is not None:
self.A = A.copy()
else:
self.A = A
self.copy = copy
self.clf = clf
self.n_jobs = n_jobs
if A is not None:
self.n_components_A = sparse.cs_graph_components(A)[0]
else:
self.n_components_A = 1
def test_cs_graph_components(self):
import numpy as np
from scipy.sparse import csr_matrix, cs_graph_components
D = np.eye(4, dtype=np.bool)
n_comp, flag = cs_graph_components(csr_matrix(D))
assert_(n_comp == 4)
assert_equal(flag, [0, 1, 2, 3])
D[0,1] = D[1,0] = 1
n_comp, flag = cs_graph_components(csr_matrix(D))
assert_(n_comp == 3)
assert_equal(flag, [0, 0, 1, 2])
# A pathological case...
D[2,2] = 0
n_comp, flag = cs_graph_components(csr_matrix(D))
assert_(n_comp == 2)
assert_equal(flag, [0, 0, -2, 1])
def __init__(self, clf, A=None, n_jobs=-1, copy=True):
if copy and A is not None:
self.A = A.copy()
else:
self.A = A
self.copy = copy
self.clf = clf
self.n_jobs = n_jobs
if A is not None:
self.n_components_A = sparse.cs_graph_components(A)[0]
else:
self.n_components_A = 1
def cc(self):
"""Compte the different connected components of the graph.
Returns
-------
label: array of shape(self.V), labelling of the vertices
"""
try:
from scipy.sparse import cs_graph_components
_, label = cs_graph_components(self.adjacency())
except:
lil = self.to_coo_matrix().tolil().rows.tolist()
label = lil_cc(lil)
return label
def get_from_fiber_graph(self,G):
self.ncc,vertexCC = sp.cs_graph_components(G+G.transpose())
self.n = vertexCC.shape[0]
noniso = np.nonzero(np.not_equal(vertexCC,-2))[0]
cccounter = Counter(vertexCC[noniso])
cc_badLabel,_ = zip(*cccounter.most_common())
cc_dict = dict(zip(cc_badLabel, np.arange(self.ncc)+1))
cc_dict[-2] = 0
self.vertexCC = np.array([cc_dict[v] for v in vertexCC])
self.ccsize = Counter(vertexCC)
def fit(self, X):
self.nearest_neighbors_ = NearestNeighbors(algorithm=self.nearest_neighbor_algorithm)
self.nearest_neighbors_.fit(X)
forest = euclidean_mst(X, self.nearest_neighbors_)
weights = forest.data
inds = np.argsort(weights)[::-1]
edges = np.vstack(forest.nonzero()).T
n_samples = len(edges) + 1
i = 0
while len(forest.nonzero()[0]) > n_samples - self.n_clusters:
e = edges[inds[i]]
forest[e[0], e[1]] = 0
if np.min(sparse.cs_graph_components(forest + forest.T)[1]) < 0:
# only one node in new component. messes up cs_graph_components
forest[e[0], e[1]] = weights[i]
elif (np.min(np.bincount(sparse.cs_graph_components(forest +
forest.T)[1])) <
2):
# disallow small clusters
forest[e[0], e[1]] = weights[i]
i += 1
self.labels_ = sparse.cs_graph_components(forest + forest.T)[1]
return self
def cc(self):
"""Compte the different connected components of the graph.
Returns
-------
label: array of shape(self.V), labelling of the vertices
"""
try:
from scipy.sparse import cs_graph_components
_, label = cs_graph_components(self.adjacency())
except:
pass
lil = self.to_coo_matrix().tolil().rows.tolist()
label = lil_cc(lil)
return label
def get_lcc_idx(G):
"""Determines and sorts the connected components of G
Each vertex in G is assigned a label corresponding to its connected component.
The largest connected component is labelled 0, second largest 1, etc.
**NOTE**: All isolated vertices (ie no incident edges) are put in 1 connected components
"""
ncc,vertexCC = sp.cs_graph_components(G)
cc_size = Counter(vertexCC)
cc_size = sorted(cc_size.iteritems(), key=lambda cc: cc[1],reverse=True)
cc_badLabel,_ = zip(*cc_size)
cc_dict = dict(zip(cc_badLabel, np.arange(ncc+1)))
vertexCC = [cc_dict[vcc] for vcc in vertexCC]
return np.array(vertexCC)
def cluster_data(img, thr, xyz_a, k=26):
"""docstring for cluster_data"""
from scipy.sparse import coo_matrix, cs_graph_components
# Threshold the entire correlation map and find connected components, store this in sparse matrix
val_idx = img > thr # store valid indices
xyz_th = xyz_a[val_idx] # find the 3D indices corresponding to the above threshold voxels
i,j,d = graph_3d_grid(xyz_th, k=k) # find the connected components for the above threshold voxels
nvoxs = xyz_th.shape[0] # store the number of correlated voxels in entire network
adj = coo_matrix((d, (i,j)), shape=(nvoxs,nvoxs)) # and store the connected nodes and weights in sparse matrix
# Identify the connected components (clusters) within the graph
nc, labels = cs_graph_components(adj)
# Copy the node labels to their voxel equivalents
lbl_img = np.zeros(img.shape) # init lbl_img - map to store label data
# add 2 so that labels corresponding to unconnected voxels (-2)
# will be zero in lbl_img, and label==0 will now equal 2
lbl_img[val_idx] = labels + 2
return lbl_img
def build_sym_geom_adjacency(geoms, max_gnn=100):
""" Return the sparsest yet maximally connected symetric geometrical adjacency matrix
"""
global INTERNAL_PARAMETERS
min_gnn = INTERNAL_PARAMETERS['min_geom_neighbors']
assert min_gnn < max_gnn, "Too high minimum number of neighbors"
n_pts = geoms.shape[0]
for n_neighbors in range(min_gnn, max_gnn + 1):
# find the lowest number of NN s.t. the graph is not too disconnected
C = build_geom_neighbor_graph(geoms, n_neighbors)
neighbs = C.indices.reshape((n_pts, n_neighbors))
C = C + C.T
C.data[:] = 1
n_comp, _ = sparse.cs_graph_components(C)
if n_comp == 1:
print "# use n_neighbors=%d" % n_neighbors
break
elif n_comp < 1:
raise ValueError('Bug: n_comp=%d' % n_comp)
if n_comp > 1:
print "# use maximum n_neighbors=%d (%d components)" % (
n_neighbors, n_comp)
return n_comp, C, neighbs
def fit(self, X):
"""
Parameters
----------
X : ndarray, shape (n_samples, n_features)
Input data.
Returns
------
self
"""
n_samples, n_features = X.shape
self.nearest_neighbors_ = NearestNeighbors(algorithm=self.nearest_neighbor_algorithm)
if self.verbose:
print("Fitting neighbors data structure.")
self.nearest_neighbors_.fit(X)
if self.verbose:
print("Datastructure used: %s" % self.nearest_neighbors_._fit_method)
if self.verbose:
print("Bulding minimum spanning tree.")
forest = euclidean_mst(X, self.nearest_neighbors_, verbose=self.verbose)
# the dimensionality of the space can at most be n_samples
if self.infer_dimensionality:
if self.verbose:
print("Estimating dimensionality.")
intrinsic_dimensionality = estimate_dimension(
X, neighbors_estimator=self.nearest_neighbors_)
if self.verbose > 0:
print("Estimated dimensionality: %d" % intrinsic_dimensionality)
elif n_samples < n_features:
warnings.warn("Got dataset with n_samples < n_features. Setting"
"intrinsic dimensionality to n_samples. This is most"
" likely to high, leading to uneven clusters."
" It is recommendet to set infer_dimensionality=True.")
intrinsic_dimensionality = n_samples
else:
intrinsic_dimensionality = n_features
if self.verbose:
print("Cutting spanning tree.")
clusters = [(forest, np.arange(n_samples))]
cut_improvement = [itm_binary(forest.copy(), intrinsic_dimensionality,
return_edge=True)]
# init cluster_infos to anything.
# doesn't matter any way as there is only one component
cluster_infos = [0]
y = np.zeros(n_samples, dtype=np.int)
removed_edges = []
# keep all possible next splits, pick the one with highest gain.
while len(clusters) < self.n_clusters:
if self.verbose > 1:
print("Finding for split %d." % len(clusters))
possible_improvements = (np.array([cut_i[1] * cut_i[0].shape[0] for
cut_i in cut_improvement]) -
np.array(cluster_infos))
i_to_split = np.argmax(possible_improvements)
split, info, edge = cut_improvement.pop(i_to_split)
# get rid of old cluster
cluster_infos.pop(i_to_split)
# need the indices of the nodes in the cluster to keep track
# of where our datapoint went
_, old_inds = clusters.pop(i_to_split)
removed_edges.append((old_inds[list(edge[:2])], edge[2]))
n_split_components, split_components_indicator = \
sparse.cs_graph_components(split + split.T)
assert(n_split_components == 2)
assert(len(np.unique(split_components_indicator)) == 2)
for i in xrange(n_split_components):
inds = np.where(split_components_indicator == i)[0]
clusters.append((split[inds[np.newaxis, :], inds],
old_inds[inds]))
mi = tree_information_sparse(clusters[-1][0], intrinsic_dimensionality)
cluster_infos.append(mi)
imp = itm_binary(clusters[-1][0].copy(), intrinsic_dimensionality,
return_edge=True)
cut_improvement.append(imp)
# correspondence of nodes to datapoints not present in sparse matrices
# but we saved the indices.
c_inds = [c[1] for c in clusters]
y = np.empty(n_samples, dtype=np.int)
assert len(np.hstack(c_inds)) == n_samples
for i, c in enumerate(c_inds):
y[c] = i
# for computing the objective, we don't care about the indices
result = block_diag([c[0] for c in clusters], format='csr')
self.labels_ = y
self.tree_information_ = (tree_information_sparse(result, intrinsic_dimensionality) /
n_samples)
return self