def testResize(self):
numRows = 10
numCols = 10
A = scipy.sparse.rand(numRows, numCols, 0.1, "csr")
B = SparseUtils.resize(A, (5, 5))
self.assertEquals(B.shape, (5, 5))
for i in range(5):
for j in range(5):
self.assertEquals(B[i,j], A[i,j])
B = SparseUtils.resize(A, (15, 15))
self.assertEquals(B.shape, (15, 15))
self.assertEquals(B.nnz, A.nnz)
for i in range(10):
for j in range(10):
self.assertEquals(B[i,j], A[i,j])
def cluster(self, graphIterator, verbose=False):
"""
Find a set of clusters using the graph and list of subgraph indices.
"""
tol = 10**-6
clustersList = []
decompositionTimeList = []
kMeansTimeList = []
boundList = []
numpy.random.seed(self.seed)
iter = 0
for W in graphIterator:
startTime = time.time()
logging.debug("Graph index:" + str(iter))
startTime = time.time()
if iter % self.T != 0:
# --- Figure out the similarity changes in existing edges ---
n = lastW.shape[0]
deltaW = W.copy()
#Vertices are removed
if n > W.shape[0]:
#deltaW = Util.extendArray(deltaW, lastW.shape)
deltaW = SparseUtils.resize(deltaW, lastW.shape)
#Vertices added
elif n < W.shape[0]:
lastWInds = lastW.nonzero()
lastWVal = scipy.zeros(len(lastWInds[0]))
for i,j,k in zip(lastWInds[0], lastWInds[1], range(len(lastWInds[0]))):
lastWVal[k] = lastW[i,j]
lastW = scipy.sparse.csr_matrix((lastWVal, lastWInds), shape=W.shape)
deltaW = deltaW - lastW
# --- Update the decomposition ---
if n < W.shape[0]:
# Q = numpy.r_[Q, numpy.zeros((W.shape[0]-Q.shape[0], Q.shape[1]))]
Q = numpy.r_[Q, numpy.zeros((W.shape[0]-Q.shape[0], Q.shape[1]))]
lmbda, Q = self.__updateEigenSystem(lmbda, Q, deltaW, lastW)
# --- resize the decomposition if the graph is losing vertices ---
if n > W.shape[0]:
Q = Q[0:W.shape[0], :]
else:
logging.debug("Recomputing eigensystem")
# We want to solve the generalized eigen problem $L.v = lambda.D.v$
# with L and D hermitians.
# scipy.sparse.linalg does not solve this problem actualy (it
# solves it, forgetting about hermitian information, from version
# 0.11)
# So we will solve $D^{-1}.L.v = lambda.v$, where $D^{-1}.L$ is
# no more hermitian.
L = GraphUtils.normalisedLaplacianRw(W)
lmbda, Q = scipy.sparse.linalg.eigs(L, min(self.k, L.shape[0]-1), which="SM", ncv = min(20*self.k, L.shape[0]), v0=numpy.random.rand(L.shape[0]))
lmbda = lmbda.real
Q = Q.real
decompositionTimeList.append(time.time()-startTime)
# Now do actual clustering
startTime = time.time()
V = VqUtils.whiten(Q)
centroids, distortion = vq.kmeans(V, self.k, iter=self.kmeansIter)
clusters, distortion = vq.vq(V, centroids)
clustersList.append(clusters)
kMeansTimeList.append(time.time()-startTime)
lastW = W.copy()
iter += 1
if verbose:
return clustersList, numpy.array((decompositionTimeList, kMeansTimeList)).T, boundList
else:
return clustersList
