def test_store_load_region_mapping(session, connectivity_factory,
surface_factory, region_mapping_factory,
sensors_factory):
connectivity = connectivity_factory(2)
conn_idx = ConnectivityIndex()
conn_idx.fill_from_has_traits(connectivity)
session.add(conn_idx)
surface = surface_factory(5)
surf_idx = SurfaceIndex()
surf_idx.fill_from_has_traits(surface)
session.add(surf_idx)
region_mapping = region_mapping_factory(surface, connectivity)
rm_idx = RegionMappingIndex()
rm_idx.fill_from_has_traits(region_mapping)
rm_idx.connectivity = conn_idx
rm_idx.surface = surf_idx
session.add(rm_idx)
sensors = sensors_factory("SEEG", 3)
sensors_seeg_idx = SensorsIndex()
sensors_seeg_idx.fill_from_has_traits(sensors)
session.add(sensors_seeg_idx)
sensors_eeg = sensors_factory("EEG", 3)
sensors_eeg_idx = SensorsIndex()
sensors_eeg_idx.fill_from_has_traits(sensors_eeg)
session.add(sensors_eeg_idx)
time_series = TimeSeries(data=numpy.arange(5))
fcd = Fcd(
array_data=numpy.arange(5),
source=time_series,
)
ts_index = TimeSeriesIndex()
ts_index.fill_from_has_traits(time_series)
session.add(ts_index)
fcd_index = FcdIndex()
fcd_index.fill_from_has_traits(fcd)
fcd_index.source = ts_index
session.add(fcd_index)
session.commit()
res = session.query(ConnectivityIndex)
assert res.count() == 1
assert res[0].number_of_regions == 2
assert res[0].number_of_connections == 4
assert res[0].undirected is True
assert res[0].weights_min == 0
res = session.query(SurfaceIndex)
assert res.count() == 1
res = session.query(RegionMappingIndex)
assert res.count() == 1
def test_happy_flow_import(self):
"""
Test that importing a CFF generates at least one DataType in DB.
"""
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_96.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path, subject=TEST_SUBJECT_A)
field = FilterChain.datatype + '.subject'
filters = FilterChain('', [field], [TEST_SUBJECT_A], ['=='])
reference_connectivity_index = TestFactory.get_entity(self.test_project, ConnectivityIndex, filters)
dt_count_before = TestFactory.get_entity_count(self.test_project, ConnectivityIndex())
self._import_csv_test_connectivity(reference_connectivity_index.gid, TEST_SUBJECT_B)
dt_count_after = TestFactory.get_entity_count(self.test_project, ConnectivityIndex())
assert dt_count_before + 1 == dt_count_after
filters = FilterChain('', [field], [TEST_SUBJECT_B], ['like'])
imported_connectivity_index = TestFactory.get_entity(self.test_project, ConnectivityIndex, filters)
# check relationship between the imported connectivity and the reference
assert reference_connectivity_index.number_of_regions == imported_connectivity_index.number_of_regions
assert not reference_connectivity_index.number_of_connections == imported_connectivity_index.number_of_connections
reference_connectivity = h5.load_from_index(reference_connectivity_index)
imported_connectivity = h5.load_from_index(imported_connectivity_index)
assert not (reference_connectivity.weights == imported_connectivity.weights).all()
assert not (reference_connectivity.tract_lengths == imported_connectivity.tract_lengths).all()
assert (reference_connectivity.centres == imported_connectivity.centres).all()
assert (reference_connectivity.orientations == imported_connectivity.orientations).all()
assert (reference_connectivity.region_labels == imported_connectivity.region_labels).all()
def test_happy_flow_import(self):
"""
Test that importing a CFF generates at least one DataType in DB.
"""
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_96.zip')
dt_count_before = TestFactory.get_entity_count(self.test_project, ConnectivityIndex())
TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path, "John")
dt_count_after = TestFactory.get_entity_count(self.test_project, ConnectivityIndex())
assert dt_count_before + 1 == dt_count_after
def setup():
"""
Sets up the environment for running the tests;
creates a test user, a test project, a connectivity and a surface;
imports a CFF data-set
"""
self.test_project = datatype_factory['project']
self.test_user = datatype_factory['user']
zip_path = os.path.join(os.path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project, zip_path);
self.connectivity = TestFactory.get_entity(self.test_project, ConnectivityIndex())
assert self.connectivity is not None
def test_server_get_operations_for_datatype(self):
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_96.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path)
datatypes_in_project = self.get_data_in_project_resource.get(
self.test_project.gid)
assert type(datatypes_in_project) is list
assert len(datatypes_in_project) == 1
assert datatypes_in_project[0].type == ConnectivityIndex().display_type
result = self.get_operations_resource.get(datatypes_in_project[0].gid)
assert type(result) is list
assert len(result) > 3
def transactional_setup_method(self):
"""
Sets up the environment for running the tests;
creates a test user, a test project, a connectivity and a surface;
imports a CFF data-set
"""
self.test_user = TestFactory.create_user('CrossCoherence_User')
self.test_project = TestFactory.create_project(
self.test_user, "CrossCoherence_Project")
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path)
self.connectivity = TestFactory.get_entity(self.test_project,
ConnectivityIndex())
assert self.connectivity is not None
def test_server_retrieve_datatype(self, mocker):
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_96.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path)
datatypes_in_project = self.get_data_in_project_resource.get(
self.test_project.gid)
assert type(datatypes_in_project) is list
assert len(datatypes_in_project) == 1
assert datatypes_in_project[0].type == ConnectivityIndex().display_type
def send_file_dummy(path, as_attachment, attachment_filename):
return (path, as_attachment, attachment_filename)
# Mock flask.send_file to behave like send_file_dummy
mocker.patch('flask.send_file', send_file_dummy)
result = self.retrieve_resource.get(datatypes_in_project[0].gid)
assert type(result) is tuple
assert result[1] is True
assert result[0] == result[2]
def fire_simulation_example(tvb_client_instance):
logger.info("Requesting projects for logged user")
projects_of_user = tvb_client_instance.get_project_list()
assert len(projects_of_user) > 0
logger.info("TVB has {} projects for this user".format(
len(projects_of_user)))
project_gid = projects_of_user[0].gid
logger.info("Requesting datatypes from project {}...".format(project_gid))
data_in_project = tvb_client_instance.get_data_in_project(project_gid)
logger.info("We have {} datatypes".format(len(data_in_project)))
logger.info("Requesting operations from project {}...".format(project_gid))
ops_in_project, _ = tvb_client_instance.get_operations_in_project(
project_gid, 1)
logger.info("Displayname of the first operation is: {}".format(
ops_in_project[0].displayname))
connectivity_gid = None
datatypes_type = []
for datatype in data_in_project:
datatypes_type.append(datatype.type)
if datatype.type == ConnectivityIndex().display_type:
connectivity_gid = datatype.gid
logger.info("The datatypes in project are: {}".format(datatypes_type))
if connectivity_gid:
logger.info("Preparing the simulator...")
simulator = SimulatorAdapterModel()
simulator.connectivity = connectivity_gid
simulator.simulation_length = 100
logger.info("Starting the simulation...")
operation_gid = tvb_client_instance.fire_simulation(
project_gid, simulator)
logger.info("Monitoring the simulation operation...")
monitor_operation(tvb_client_instance, operation_gid)
logger.info("Requesting the results of the simulation...")
simulation_results = tvb_client_instance.get_operation_results(
operation_gid)
datatype_names = []
for datatype in simulation_results:
datatype_names.append(datatype.name)
logger.info("The resulted datatype are: {}".format(datatype_names))
time_series_gid = simulation_results[1].gid
logger.info("Download the time series file...")
time_series_path = tvb_client_instance.retrieve_datatype(
time_series_gid, tvb_client_instance.temp_folder)
logger.info(
"The time series file location is: {}".format(time_series_path))
logger.info("Requesting algorithms to run on time series...")
algos = tvb_client_instance.get_operations_for_datatype(
time_series_gid)
algo_names = [algo.displayname for algo in algos]
logger.info("Possible algorithms are {}".format(algo_names))
logger.info("Launch Fourier Analyzer...")
fourier_model = FFTAdapterModel()
fourier_model.time_series = time_series_gid
fourier_model.window_function = 'hamming'
operation_gid = tvb_client_instance.launch_operation(
project_gid, FourierAdapter, fourier_model)
logger.info(
"Fourier Analyzer operation has launched with gid {}".format(
operation_gid))
logger.info("Download the connectivity file...")
connectivity_path = tvb_client_instance.retrieve_datatype(
connectivity_gid, tvb_client_instance.temp_folder)
logger.info(
"The connectivity file location is: {}".format(connectivity_path))
logger.info("Loading an entire Connectivity datatype in memory...")
connectivity = tvb_client_instance.load_datatype_from_file(
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])
]))
assert chunk.shape[0] == 20
assert chunk.shape[1] == data_shape[1]
assert chunk.shape[2] == data_shape[2]
assert chunk.shape[3] == data_shape[3]
return project_gid, time_series_gid
logger.info("Requesting projects for user {}...".format(username))
projects_of_user = tvb_client.get_project_list(username)
assert len(projects_of_user) > 0
logger.info("TVB has {} projects for this user".format(
len(projects_of_user)))
project_gid = projects_of_user[0].gid
logger.info("Requesting datatypes from project {}...".format(project_gid))
data_in_project = tvb_client.get_data_in_project(project_gid)
logger.info("We have {} datatypes".format(len(data_in_project)))
connectivity_gid = None
datatypes_type = []
for datatype in data_in_project:
datatypes_type.append(datatype.type)
if datatype.type == ConnectivityIndex().display_type:
connectivity_gid = datatype.gid
logger.info("The datatypes in projecct are: {}".format(datatypes_type))
if connectivity_gid:
logger.info("Preparing the simulator...")
simulator = SimulatorAdapterModel()
simulator.connectivity = uuid.UUID(connectivity_gid)
simulator.simulation_length = 100
logger.info("Starting the simulation...")
operation_gid = tvb_client.fire_simulation(project_gid, simulator)
logger.info("Monitoring the simulation operation...")
while True:
status = tvb_client.get_operation_status(operation_gid)