def split_big_parcels(parcel_file, output_file, max_size=400):
print 'split_big_parcels ...'
roiMask, roiHeader = read_volume(parcel_file)
roiIds = np.unique(roiMask)
background = roiIds.min()
labels = roiMask[np.where(roiMask>background)].astype(int)
if (np.bincount(labels) <= max_size).all():
pyhrf.verbose(1, 'no parcel to split')
return
graphs = parcels_to_graphs(roiMask, kerMask3D_6n)
for roiId in roiIds:
if roiId != background:
roi_size = (roiMask==roiId).sum()
if roi_size > max_size:
print 'roi %d, size = %d' %(roiId, roi_size)
nparcels = int(np.ceil(roi_size*1./max_size))
print 'split into %d parcels ...' %(nparcels)
split_parcel(labels, graphs, roiId, nparcels, inplace=True,
verbosity=1)
final_roi_mask = np.zeros_like(roiMask)
final_roi_mask[np.where(roiMask>background)] = labels
#print np.bincount(labels)
assert (np.bincount(labels) <= max_size).all()
write_volume(final_roi_mask, output_file, roiHeader)
def _compute_graph(self):
if self.data_type != 'volume':
raise Exception('Can only compute graph for volume data')
pyhrf.verbose(6, 'FmriData._compute_graph() ...')
to_discard = [self.backgroundLabel]
self._graph = parcels_to_graphs(self.roiMask, kerMask3D_6n,
toDiscard=to_discard)
def split_big_parcels(parcel_file, output_file, max_size=400):
print 'split_big_parcels ...'
roiMask, roiHeader = read_volume(parcel_file)
roiIds = np.unique(roiMask)
background = roiIds.min()
labels = roiMask[np.where(roiMask > background)].astype(int)
if (np.bincount(labels) <= max_size).all():
logger.info('no parcel to split')
return
graphs = parcels_to_graphs(roiMask, kerMask3D_6n)
for roiId in roiIds:
if roiId != background:
roi_size = (roiMask == roiId).sum()
if roi_size > max_size:
print 'roi %d, size = %d' % (roiId, roi_size)
nparcels = int(np.ceil(roi_size * 1. / max_size))
print 'split into %d parcels ...' % (nparcels)
split_parcel(labels,
graphs,
roiId,
nparcels,
inplace=True,
verbosity=1)
final_roi_mask = np.zeros_like(roiMask)
final_roi_mask[np.where(roiMask > background)] = labels
assert (np.bincount(labels) <= max_size).all()
write_volume(final_roi_mask, output_file, roiHeader)
def build_graphs(self, force=False):
logger.debug('FmriData.build_graphs (self.graphs is None ? %s ) ...',
str(self.graphs is None))
logger.debug('data_type: %s', self.data_type)
if self.graphs is None or force:
if self.data_type == 'volume':
logger.info('Building graph from volume ...')
to_discard = [self.backgroundLabel]
self.graphs = parcels_to_graphs(self.roiMask,
kerMask3D_6n,
toDiscard=to_discard)
logger.info('Graph built (%d rois)!', len(self.graphs.keys()))
self.edge_lentghs = dict([(i, [[1] * len(nl) for nl in g])
for i, g in self.graphs.items()])
elif self.data_type == 'surface':
if self.graphs is not None:
return self.graphs
else:
raise Exception('Graph is not set for surface data!')
def build_graphs(self, force=False):
logger.debug('FmriData.build_graphs (self.graphs is None ? %s ) ...',
str(self.graphs is None))
logger.debug('data_type: %s', self.data_type)
if self.graphs is None or force:
if self.data_type == 'volume':
logger.info('Building graph from volume ...')
to_discard = [self.backgroundLabel]
self.graphs = parcels_to_graphs(self.roiMask,
kerMask3D_6n,
toDiscard=to_discard)
logger.info('Graph built (%d rois)!', len(self.graphs.keys()))
self.edge_lentghs = dict([(i, [[1] * len(nl) for nl in g])
for i, g in self.graphs.items()])
elif self.data_type == 'surface':
if self.graphs is not None:
return self.graphs
else:
raise Exception('Graph is not set for surface data!')
if (TIME_AXIS == 0 and mshape != b.shape[1:]) or \
(TIME_AXIS == 3 and mshape != b.shape[:-1]):
raise Exception('Error: BOLD shape is different from mask shape')
sessionScans.append(np.arange(lastScan, lastScan+b.shape[TIME_AXIS],
dtype=int))
lastScan += b.shape[TIME_AXIS]
bold = np.concatenate(tuple(bolds), axis=TIME_AXIS)
discard_bad_data(bold, roiMask)
if build_graph:
# Build graph
if len(np.unique(roiMask))==1 or keepBackground:
graphs = parcels_to_graphs(roiMask.astype(int), kerMask3D_6n)
else:
if (roiMask==0).any():
toDiscard = [0]
pyhrf.verbose(1,'Discarding background (label=0)')
else:
toDiscard = None
graphs = parcels_to_graphs(roiMask.astype(int), kerMask3D_6n,
toDiscard=toDiscard)
pyhrf.verbose(1,'Graph built !')
else:
graphs = None
#Split bold into rois:
roiBold = {}
for roiId in np.unique(roiMask):
def setUp(self):
pf = 'subj0_parcellation.nii.gz'
fnm = pyhrf.get_data_file_name(pf)
m, mh = read_volume(fnm)
self.graph = parcels_to_graphs(m.astype(int), kerMask3D_6n,
toDiscard=[0])[1]
if (TIME_AXIS == 0 and mshape != b.shape[1:]) or \
(TIME_AXIS == 3 and mshape != b.shape[:-1]):
raise Exception('Error: BOLD shape is different from mask shape')
sessionScans.append(np.arange(lastScan, lastScan + b.shape[TIME_AXIS],
dtype=int))
lastScan += b.shape[TIME_AXIS]
bold = np.concatenate(tuple(bolds), axis=TIME_AXIS)
discard_bad_data(bold, roiMask)
if build_graph:
# Build graph
if len(np.unique(roiMask)) == 1 or keepBackground:
graphs = parcels_to_graphs(roiMask.astype(int), kerMask3D_6n)
else:
if (roiMask == 0).any():
toDiscard = [0]
logger.info('Discarding background (label=0)')
else:
toDiscard = None
graphs = parcels_to_graphs(roiMask.astype(int), kerMask3D_6n,
toDiscard=toDiscard)
logger.info('Graph built !')
else:
graphs = None
# Split bold into rois:
roiBold = {}
for roiId in np.unique(roiMask):