def load_and_get_fdata_params(self):
pyhrf.verbose(1,'Load mask from: %s' %self.mask_file)
if self.data_type == 'surface':
pyhrf.verbose(2,'Read mesh from: %s' %self.mesh_file)
p = {'mask' : xndarray.load(self.mask_file).data}
pyhrf.verbose(1, 'Mask shape %s' %str(p['mask'].shape))
if self.data_type == 'surface':
p['graph'] = graph_from_mesh(read_mesh(self.mesh_file))
return p
def extract_sub_mesh_with_files(input_mesh, center_node, radius,
output_mesh=None):
from nibabel import gifti
from nibabel.gifti import GiftiImage, GiftiDataArray
from pyhrf.tools.io import read_mesh
cor, tri, coord_sys = read_mesh(input_mesh)
sub_cor, sub_tri = extract_sub_mesh(cor, tri, center_node, radius)
#nimg = GiftiImage_fromTriangles(sub_cor, sub_tri)
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_cor,intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_tri,intent))
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_sub'))
pyhrf.verbose(1, 'Saving extracted mesh to %s' %output_mesh)
gifti.write(nimg, output_mesh)
return sub_cor, sub_tri, coord_sys
def load_surf_bold_mask(bold_files, mesh_file, mask_file=None):
pyhrf.verbose(1, 'Load mesh: ' + mesh_file)
coords,triangles,coord_sys = read_mesh(mesh_file)
pyhrf.verbose(2, 'Build graph ... ')
fgraph = graph_from_mesh(triangles)
assert graph_is_sane(fgraph)
pyhrf.verbose(1, 'Mesh has %d nodes' %len(fgraph))
pyhrf.verbose(2, 'Compute length of edges ... ')
edges_l = np.array([np.array([distance(coords[i],
coords[n],
coord_sys.xform) \
for n in nl]) \
for i,nl in enumerate(fgraph)],dtype=object)
if mask_file is None or not op.exists(mask_file):
pyhrf.verbose(1,'Mask file %s does not exist. Taking '\
' all nodes ...' %mask_file)
mask = np.ones(len(fgraph))
mask_meta_obj = None
mask_loaded_from_file = False
else:
mask, mask_meta_obj = read_texture(mask_file)
mask_loaded_from_file = True
if not (np.round(mask) == mask).all():
raise Exception("Mask is not n-ary")
if len(mask) != len(fgraph):
raise Exception('Size of mask (%d) is different from size '\
'of graph (%d)' %(len(mask),len(fgraph)))
mask = mask.astype(np.int32)
if mask.min() == -1:
mask += 1
#Split graph into rois:
graphs = {}
edge_lengths = {}
for roiId in np.unique(mask):
mroi = np.where(mask==roiId)
g, nm = sub_graph(fgraph, mroi[0])
edge_lengths[roiId] = edges_l[mroi]
graphs[roiId] = g
#Load BOLD:
lastScan = 0
sessionScans = []
bolds = []
for boldFile in bold_files:
pyhrf.verbose(1, 'load bold: ' + boldFile)
b,_ = read_texture(boldFile)
pyhrf.verbose(1, 'bold shape: ' + str(b.shape))
bolds.append(b)
sessionScans.append(np.arange(lastScan, lastScan+b.shape[0],
dtype=int))
lastScan += b.shape[0]
bold = np.concatenate(tuple(bolds))
if len(fgraph) != bold.shape[1]:
raise Exception('Nb positions not consistent between BOLD (%d) '\
'and mesh (%d)' %(bold.shape[1],len(fgraph)))
# discard bad data (bold with var=0 and nan values):
discard_bad_data(bold, mask, time_axis=0)
return mask, mask_meta_obj, mask_loaded_from_file, bold, sessionScans, \
graphs, edge_lengths
