def read_head(self, path):
"""
:param path: Path towards a custom head folder
:return: Head object
"""
self.logger.info("Starting to read Head from: %s" % path)
conn = self.read_connectivity(
os.path.join(path, self.connectivity_filename))
srf = self.read_surface(
os.path.join(path, self.cortical_surface_filename))
rm = self.read_region_mapping(
os.path.join(path, self.region_mapping_filename))
vm = self.read_volume_mapping(
os.path.join(path, self.volume_mapping_filename))
t1 = self.read_t1(os.path.join(path, self.structural_mri_filename))
sensorsSEEG, sensorsEEG, sensorsMEG = self.read_sensors(path)
head = Head(conn,
srf,
rm,
vm,
t1,
path,
sensorsSEEG=sensorsSEEG,
sensorsEEG=sensorsEEG,
sensorsMEG=sensorsMEG)
self.logger.info("Successfully read Head from: %s" % path)
return head
def _prepare_dummy_head(self):
reader = H5Reader()
connectivity = reader.read_connectivity(
os.path.join(self.config.input.HEAD, "Connectivity.h5"))
cort_surface = Surface([], [])
seeg_sensors = Sensors(numpy.array(["sens1", "sens2"]),
numpy.array([[0, 0, 0], [0, 1, 0]]))
head = Head(connectivity, cort_surface, sensorsSEEG=seeg_sensors)
return head
def read_head(
self,
root_folder,
name='',
connectivity_file="connectivity.zip",
surface_file="surface.zip",
region_mapping_file="region_mapping.txt",
eeg_sensors_files=[("eeg_brainstorm_65.txt",
"gain_matrix_eeg_65_surface_16k.npy")],
meg_sensors_files=[("meg_brainstorm_276.txt",
"gain_matrix_meg_276_surface_16k.npy")],
seeg_sensors_files=[("seeg_588.txt",
"gain_matrix_seeg_588_surface_16k.npy")],
):
conn = self.read_connectivity(
os.path.join(root_folder, connectivity_file))
srf = self.read_cortical_surface(
os.path.join(root_folder, surface_file))
rm = self.read_region_mapping(
os.path.join(root_folder, region_mapping_file))
vm = None
t1 = None
sensorsSEEG = []
for s_files in ensure_list(seeg_sensors_files):
sensorsSEEG.append(
self.read_sensors(s_files, root_folder, Sensors.TYPE_SEEG))
sensorsEEG = []
for s_files in ensure_list(eeg_sensors_files):
sensorsEEG.append(
self.read_sensors(s_files, root_folder, Sensors.TYPE_EEG))
sensorsMEG = []
for s_files in ensure_list(meg_sensors_files):
sensorsMEG.append(
self.read_sensors(s_files, root_folder, Sensors.TYPE_MEG))
return Head(conn,
srf,
rm,
vm,
t1,
name,
sensorsSEEG=sensorsSEEG,
sensorsEEG=sensorsEEG,
sensorsMEG=sensorsMEG)
def _prepare_dummy_head_from_dummy_attrs(self):
return Head(self.dummy_connectivity,
self.dummy_surface,
sensorsSEEG=[self.dummy_sensors])