def test_read_default_real_data_tiny(self):
mesh_file = pyhrf.get_data_file_name('real_data_surf_tiny_mesh.gii')
bold_file = pyhrf.get_data_file_name('real_data_surf_tiny_bold.gii')
fn = 'real_data_surf_tiny_parcellation.gii'
parcel_file = pyhrf.get_data_file_name(fn)
cor, tri, mesh_gii = pio.read_mesh(mesh_file)
bold, bold_gii = pio.read_texture(bold_file)
parcellation, parcel_gii = pio.read_texture(parcel_file)
def test_read_default_real_data_tiny(self):
mesh_file = pyhrf.get_data_file_name('real_data_surf_tiny_mesh.gii')
bold_file = pyhrf.get_data_file_name('real_data_surf_tiny_bold.gii')
fn = 'real_data_surf_tiny_parcellation.gii'
parcel_file = pyhrf.get_data_file_name(fn)
cor, tri, mesh_gii = pio.read_mesh(mesh_file)
bold, bold_gii = pio.read_texture(bold_file)
parcellation, parcel_gii = pio.read_texture(parcel_file)
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 test_read_default_real_data_tiny(self):
mesh_file = pyhrf.get_data_file_name('real_data_surf_tiny_mesh.gii')
bold_file = pyhrf.get_data_file_name('real_data_surf_tiny_bold.gii')
fn = 'real_data_surf_tiny_parcellation.gii'
parcel_file = pyhrf.get_data_file_name(fn)
cor, tri, mesh_gii = pio.read_mesh(mesh_file)
bold, bold_gii = pio.read_texture(bold_file)
parcellation, parcel_gii = pio.read_texture(parcel_file)
if 0:
print 'cor:', cor.shape, cor.dtype
print 'tri:', tri.shape, tri.dtype
print 'bold:', bold.shape, bold.dtype
print 'parcellation:', parcellation.shape, parcellation.dtype
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 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'))
logger.info('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):
from pyhrf.tools._io import read_mesh, read_texture, discard_bad_data
logger.info('Load mesh: ' + mesh_file)
coords, triangles, coord_sys = read_mesh(mesh_file)
logger.debug('Build graph...')
fgraph = graph_from_mesh(triangles)
assert graph_is_sane(fgraph)
logger.info('Mesh has %d nodes', len(fgraph))
logger.debug('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):
logger.warning('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 roi_id in np.unique(mask):
mroi = np.where(mask == roi_id)
graph, _ = sub_graph(fgraph, mroi[0])
edge_lengths[roi_id] = edges_l[mroi]
graphs[roi_id] = graph
# Load BOLD:
last_scan = 0
session_scans = []
bolds = []
for bold_file in bold_files:
logger.info('load bold: %s', bold_file)
bold, _ = read_texture(bold_file)
logger.info('bold shape: %s', str(bold.shape))
bolds.append(bold)
session_scans.append(np.arange(last_scan, last_scan + bold.shape[0],
dtype=int))
last_scan += bold.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, session_scans, \
graphs, edge_lengths
def load_surf_bold_mask(bold_files, mesh_file, mask_file=None):
from pyhrf.tools._io import read_mesh, read_texture, discard_bad_data
logger.info('Load mesh: ' + mesh_file)
coords, triangles, coord_sys = read_mesh(mesh_file)
logger.debug('Build graph...')
fgraph = graph_from_mesh(triangles)
assert graph_is_sane(fgraph)
logger.info('Mesh has %d nodes', len(fgraph))
logger.debug('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):
logger.warning('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 roi_id in np.unique(mask):
mroi = np.where(mask == roi_id)
graph, _ = sub_graph(fgraph, mroi[0])
edge_lengths[roi_id] = edges_l[mroi]
graphs[roi_id] = graph
# Load BOLD:
last_scan = 0
session_scans = []
bolds = []
for bold_file in bold_files:
logger.info('load bold: %s', bold_file)
bold, _ = read_texture(bold_file)
logger.info('bold shape: %s', str(bold.shape))
bolds.append(bold)
session_scans.append(
np.arange(last_scan, last_scan + bold.shape[0], dtype=int))
last_scan += bold.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, session_scans, \
graphs, edge_lengths