def test_read_head_folder_and_write_h5(self):
head = self._prepare_dummy_head()
path = self.writer.write_tvb_to_h5(head, recursive=True)
head2 = Head.from_file(path)
assert np.max(
np.abs(head.connectivity.weights -
head2.connectivity.weights)) < 1e-6
assert np.max(
np.abs(head.connectivity.tract_lengths -
head2.connectivity.tract_lengths)) < 1e-6
assert np.max(
np.abs(head.surface.vertices - head2.surface.vertices)) < 1e-6
assert np.max(
np.abs(head.surface.triangles - head2.surface.triangles)) < 1e-6
assert np.max(
np.abs(head.eeg_sensors.locations -
head2.eeg_sensors.locations)) < 1e-6
assert np.max(
np.abs(head.eeg_projection.projection_data -
head2.eeg_projection.projection_data)) < 1e-6
# The following will not work as long as Head references tvb-scripts classes instead of TVB ones
from tvb.core.neocom import h5
head3 = h5.load(path, with_references=True)
assert np.max(
np.abs(head.connectivity.weights -
head3.connectivity.weights)) < 1e-6
assert np.max(
np.abs(head.connectivity.tract_lengths -
head3.connectivity.tract_lengths)) < 1e-6
assert np.max(
np.abs(head.surface.vertices - head3.surface.vertices)) < 1e-6
assert np.max(
np.abs(head.surface.triangles - head3.surface.triangles)) < 1e-6
assert np.max(
np.abs(head.eeg_sensors.locations -
head3.eeg_sensors.locations)) < 1e-6
assert np.max(
np.abs(head.eeg_projection.projection_data -
head3.eeg_projection.projection_data)) < 1e-6
Demo script on how to use tvb-framework default read/write capabilities
.. moduleauthor:: Lia Domide <*****@*****.**>
"""
from tvb.core.neocom import h5
from tvb.basic.profile import TvbProfile
from tvb.datatypes.connectivity import Connectivity
from tvb.adapters.datatypes.h5.connectivity_h5 import ConnectivityH5
if __name__ == '__main__':
TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)
# Read from a ZIP
conn_ht = Connectivity.from_file()
conn_ht.configure()
# Store in a given folder the HasTraits entity
PATH = "."
h5.store_complete(conn_ht, PATH)
# Reproduce the just written file name containing GUID
file_name = h5.path_for(PATH, ConnectivityH5, conn_ht.gid)
# Load back from a file name a HasTraits instance
conn_back = h5.load(file_name)
# Check that the loaded and written entities are correct
assert conn_ht.number_of_regions == 76
assert conn_ht.number_of_regions == conn_back.number_of_regions
def test_store_load(tmpdir, connectivity_factory):
path = os.path.join(str(tmpdir), 'interface.conn.h5')
connectivity = connectivity_factory(2)
store(connectivity, path)
con2 = load(path)
numpy.testing.assert_equal(connectivity.weights, con2.weights)
operation_gid = tvb_client.launch_operation(project_gid,
algo_dto.module,
algo_dto.classname,
fourier_model)
logger.info(
"Fourier Analyzer operation has launched with gid {}".format(
operation_gid))
logger.info("Download the connectivity file...")
connectivity_path = tvb_client.retrieve_datatype(
connectivity_gid, tvb_client.temp_folder)
logger.info(
"The connectivity file location is: {}".format(connectivity_path))
logger.info("Loading an entire Connectivity datatype in memory...")
connectivity = h5.load(connectivity_path)
logger.info("Info on current Connectivity: {}".format(
connectivity.summary_info()))
logger.info(
"Loading a chuck from the time series H5 file, as this can be very large..."
)
with TimeSeriesH5(time_series_path) as time_series_h5:
data_shape = time_series_h5.read_data_shape()
chunk = time_series_h5.read_data_slice(
tuple([
slice(20),
slice(data_shape[1]),
slice(data_shape[2]),
slice(data_shape[3])
]))