def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1,1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
# print 'labels:'
# print labels
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1+1, labels+1)[0]
self.assertEqual(dist, 0)
def test_ward_spatial_scikit(self):
from pyhrf.parcellation import parcellation_dist, \
parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
X = np.reshape(self.p1, (-1, 1))
graph = graph_from_lattice(np.ones(self.p1.shape), kerMask2D_4n)
labels = parcellation_ward_spatial(X, n_clusters=5, graph=graph)
labels = np.reshape(labels, self.p1.shape)
# +1 because parcellation_dist sees 0 as background
dist = parcellation_dist(self.p1 + 1, labels + 1)[0]
self.assertEqual(dist, 0)
def test_parcellation_distance(self):
from pyhrf.parcellation import parcellation_dist
#dist = 4 (cost method: intersection size)
# print 'p1:'
# print self.p1
# print 'p2:'
# print self.p2
dist, cano_parcellation = parcellation_dist(self.p1, self.p2)
# print 'cano_parcellation:'
# print cano_parcellation
self.assertEqual(dist, 4)
def test_ward_spatial_cmd(self):
from pyhrf.parcellation import parcellation_dist
output_file = op.join(self.tmp_dir, 'parcellation_output_test.nii')
nparcels = 4
cmd = 'pyhrf_parcellate_glm -m %s %s %s -o %s -v %d ' \
'-n %d -t ward_spatial ' \
% (self.mask_fn, self.p1_fn, self.p2_fn, output_file,
logger.getEffectiveLevel(), nparcels)
if os.system(cmd) != 0:
raise Exception('"' + cmd + '" did not execute correctly')
logger.info('cmd: %s', cmd)
labels = xndarray.load(output_file).data
logger.info('labels.dtype:%s', str(labels.dtype))
dist = parcellation_dist(self.p1, labels)[0]
logger.info('dist:%d', dist)
self.assertEqual(dist, 0)
def test_ward_spatial_cmd(self):
from pyhrf.parcellation import parcellation_dist
#pyhrf.verbose.verbosity = 2
output_file = op.join(self.tmp_dir,'parcellation_output_test.nii')
nparcels = 4
cmd = 'pyhrf_parcellate_glm -m %s %s %s -o %s -v %d ' \
'-n %d -t ward_spatial ' \
%(self.mask_fn, self.p1_fn, self.p2_fn, output_file,
pyhrf.verbose.verbosity, nparcels)
if os.system(cmd) != 0 :
raise Exception('"' + cmd + '" did not execute correctly')
pyhrf.verbose(1, 'cmd: %s' %cmd)
labels = xndarray.load(output_file).data
pyhrf.verbose(2, 'labels.dtype:%s' %str(labels.dtype))
dist = parcellation_dist(self.p1, labels)[0]
pyhrf.verbose(2, 'dist:%d' %dist)
self.assertEqual(dist, 0)
def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1, 1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1 + 1, labels + 1)[0]
self.assertEqual(dist, 0)
def test_parcellation_distance(self):
from pyhrf.parcellation import parcellation_dist
dist, cano_parcellation = parcellation_dist(self.p1, self.p2)
self.assertEqual(dist, 4)