def setUp(self):
"""
Reset the database before each test.
"""
self.test_user = TestFactory.create_user("UserPM")
self.test_project = TestFactory.create_project(self.test_user)
zip_path = os.path.join(os.path.dirname(tvb_data.sensors.__file__),
'eeg_brainstorm_65.txt')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path,
Sensors_Importer.EEG_SENSORS)
zip_path = os.path.join(os.path.dirname(tvb_data.surfaceData.__file__),
'cortex_16384.zip')
TestFactory.import_surface_zip(self.test_user, self.test_project,
zip_path, CORTICAL, True)
self.surface = TestFactory.get_entity(self.test_project,
CorticalSurface())
self.assertTrue(self.surface is not None)
self.sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
self.assertTrue(self.sensors is not None)
self.importer = TestFactory.create_adapter(
'tvb.adapters.uploaders.projection_matrix_importer',
'ProjectionMatrixSurfaceEEGImporter')
def test_launch_EEG(self):
"""
Check that all required keys are present in output from EegSensorViewer launch.
"""
## Import Sensors
zip_path = os.path.join(os.path.dirname(sensors_dataset.__file__), 'EEG_unit_vectors_BrainProducts_62.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path, Sensors_Importer.EEG_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
## Import EEGCap
zip_path = os.path.join(os.path.dirname(surfaces_dataset.__file__), 'eeg_skin_surface.zip')
TestFactory.import_surface_zip(self.test_user, self.test_project, zip_path, EEG_CAP, True)
eeg_cap_surface = TestFactory.get_entity(self.test_project, EEGCap())
viewer = EegSensorViewer()
viewer.current_project_id = self.test_project.id
## Launch with EEG Cap selected
result = viewer.launch(sensors, eeg_cap_surface)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_EEG, result)
for key in ['urlVertices', 'urlTriangles', 'urlLines', 'urlNormals']:
self.assertIsNotNone(result[key], "Value at key %s should not be None" % key)
## Launch without EEG Cap
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_EEG, result)
for key in ['urlVertices', 'urlTriangles', 'urlLines', 'urlNormals']:
self.assertTrue(not result[key] or result[key] == "[]",
"Value at key %s should be None or empty, but is %s" % (key, result[key]))
def test_happy_flow_import(self):
"""
Test that importing a CFF generates at least one DataType in DB.
"""
ConnectivityZipTest.import_test_connectivity96(self.test_user,
self.test_project,
subject=TEST_SUBJECT_A)
field = FilterChain.datatype + '.subject'
filters = FilterChain('', [field], [TEST_SUBJECT_A], ['=='])
reference_connectivity = TestFactory.get_entity(self.test_project, Connectivity(), filters)
dt_count_before = TestFactory.get_entity_count(self.test_project, Connectivity())
self._import_csv_test_connectivity(reference_connectivity.gid, TEST_SUBJECT_B)
dt_count_after = TestFactory.get_entity_count(self.test_project, Connectivity())
self.assertEqual(dt_count_before + 1, dt_count_after)
filters = FilterChain('', [field], [TEST_SUBJECT_B], ['like'])
imported_connectivity = TestFactory.get_entity(self.test_project, Connectivity(), filters)
# check relationship between the imported connectivity and the reference
self.assertTrue((reference_connectivity.centres == imported_connectivity.centres).all())
self.assertTrue((reference_connectivity.orientations == imported_connectivity.orientations).all())
self.assertEqual(reference_connectivity.number_of_regions, imported_connectivity.number_of_regions)
self.assertTrue((reference_connectivity.region_labels == imported_connectivity.region_labels).all())
self.assertFalse((reference_connectivity.weights == imported_connectivity.weights).all())
self.assertFalse((reference_connectivity.tract_lengths == imported_connectivity.tract_lengths).all())
def setUp(self):
"""
Reset the database before each test.
"""
self.test_user = TestFactory.create_user("UserPM")
self.test_project = TestFactory.import_default_project(self.test_user)
self.surface = TestFactory.get_entity(self.test_project,
CorticalSurface())
self.assertTrue(self.surface is not None)
self.sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
self.assertTrue(self.sensors is not None)
def setUp(self):
"""
Reset the database before each test.
"""
self.test_user = TestFactory.create_user("UserPM")
self.test_project = TestFactory.import_default_project(self.test_user)
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
self.assertTrue(self.connectivity is not None)
self.surface = TestFactory.get_entity(self.test_project, CorticalSurface())
self.assertTrue(self.surface is not None)
self.sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
self.assertTrue(self.sensors is not None)
def setUp(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()
self.test_project = TestFactory.import_default_project(self.test_user)
self.surface = TestFactory.get_entity(self.test_project, CorticalSurface())
self.assertTrue(self.surface is not None)
self.region_mapping = TestFactory.get_entity(self.test_project, RegionMapping())
self.assertTrue(self.region_mapping is not None)
def test_import_bold(self):
### Retrieve Adapter instance
importer = TestFactory.create_adapter(
'tvb.adapters.uploaders.mat_timeseries_importer',
'MatTimeSeriesImporter')
args = dict(
data_file=self.bold_path,
dataset_name='QL_20120824_DK_BOLD_timecourse',
structure_path='',
transpose=False,
slice=None,
sampling_rate=1000,
start_time=0,
tstype='region',
tstype_parameters_option_region_connectivity=self.connectivity.gid,
Data_Subject="QL")
### Launch import Operation
FlowService().fire_operation(importer, self.test_user,
self.test_project.id, **args)
tsr = TestFactory.get_entity(self.test_project, TimeSeriesRegion())
self.assertEqual((661, 1, 68, 1), tsr.read_data_shape())
def setUp(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()
self.test_project = TestFactory.import_default_project(self.test_user)
self.surface = TestFactory.get_entity(self.test_project,
CorticalSurface())
self.assertTrue(self.surface is not None)
self.region_mapping = TestFactory.get_entity(self.test_project,
RegionMapping())
self.assertTrue(self.region_mapping is not None)
def setUp(self):
"""
Sets up the environment for running the tests;
creates a test user, a test project, a connectivity, a cortical surface and a face surface;
imports a CFF data-set
"""
self.datatypeFactory = DatatypesFactory()
self.test_user = self.datatypeFactory.get_user()
self.test_project = TestFactory.import_default_project(self.test_user)
self.datatypeFactory.project = self.test_project
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
self.assertTrue(self.connectivity is not None)
self.face_surface = TestFactory.get_entity(self.test_project, FaceSurface())
self.assertTrue(self.face_surface is not None)
self.assertTrue(TestFactory.get_entity(self.test_project, EEGCap()) is not None)
def test_launch(self):
"""
Check that all required keys are present in output from BrainViewer launch.
"""
zip_path = os.path.join(os.path.dirname(sensors_dataset.__file__), 'eeg_unitvector_62.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path, 'EEG Sensors')
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
time_series = self.datatypeFactory.create_timeseries(self.connectivity, 'EEG', sensors)
viewer = EegMonitor()
result = viewer.launch(time_series)
expected_keys = ['tsNames', 'groupedLabels', 'tsModes', 'tsStateVars', 'longestChannelLength',
'label_x', 'entities', 'page_size', 'number_of_visible_points',
'extended_view', 'initialSelection', 'ag_settings', 'ag_settings']
for key in expected_keys:
self.assertTrue(key in result, "key not found %s" % key)
expected_ag_settings = ['channelsPerSet', 'channelLabels', 'noOfChannels', 'translationStep',
'normalizedSteps', 'nan_value_found', 'baseURLS', 'pageSize',
'nrOfPages', 'timeSetPaths', 'totalLength', 'number_of_visible_points',
'extended_view', 'measurePointsSelectionGIDs']
ag_settings = json.loads(result['ag_settings'])
for key in expected_ag_settings:
self.assertTrue(key in ag_settings, "ag_settings should have the key %s" % key)
def test_bad_reference(self):
TestFactory.import_cff(test_user=self.test_user, test_project=self.test_project)
field = FilterChain.datatype + '.subject'
filters = FilterChain('', [field], [TEST_SUBJECT_A], ['!='])
bad_reference_connectivity = TestFactory.get_entity(self.test_project, Connectivity(), filters)
self.assertRaises(OperationException, self._import_csv_test_connectivity,
bad_reference_connectivity.gid, TEST_SUBJECT_A)
def setUp(self):
"""
Reset the database before each test.
"""
self.test_user = TestFactory.create_user("UserPM")
self.test_project = TestFactory.create_project(self.test_user)
zip_path = os.path.join(os.path.dirname(tvb_data.sensors.__file__), "eeg_brainstorm_65.txt")
TestFactory.import_sensors(self.test_user, self.test_project, zip_path, Sensors_Importer.EEG_SENSORS)
zip_path = os.path.join(os.path.dirname(tvb_data.surfaceData.__file__), "cortex_16384.zip")
TestFactory.import_surface_zip(self.test_user, self.test_project, zip_path, CORTICAL, True)
self.surface = TestFactory.get_entity(self.test_project, CorticalSurface())
self.assertTrue(self.surface is not None)
self.sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
self.assertTrue(self.sensors is not None)
def _import_connectivity(self):
importer = TestFactory.create_adapter('tvb.adapters.uploaders.zip_connectivity_importer',
'ZIPConnectivityImporter')
### Launch Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id,
uploaded=self.connectivity_path, Data_Subject='QL')
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
def _import_connectivity(self):
group = dao.find_group('tvb.adapters.uploaders.zip_connectivity_importer', 'ZIPConnectivityImporter')
importer = ABCAdapter.build_adapter(group)
### Launch Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id,
uploaded=self.connectivity_path, Data_Subject='QL')
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
def test_happy_flow_import(self):
"""
Test that importing a CFF generates at least one DataType in DB.
"""
ConnectivityZipTest.import_test_connectivity96(self.test_user,
self.test_project,
subject=TEST_SUBJECT_A)
field = FilterChain.datatype + '.subject'
filters = FilterChain('', [field], [TEST_SUBJECT_A], ['=='])
reference_connectivity = TestFactory.get_entity(
self.test_project, Connectivity(), filters)
dt_count_before = TestFactory.get_entity_count(self.test_project,
Connectivity())
self._import_csv_test_connectivity(reference_connectivity.gid,
TEST_SUBJECT_B)
dt_count_after = TestFactory.get_entity_count(self.test_project,
Connectivity())
self.assertEqual(dt_count_before + 1, dt_count_after)
filters = FilterChain('', [field], [TEST_SUBJECT_B], ['like'])
imported_connectivity = TestFactory.get_entity(self.test_project,
Connectivity(), filters)
# check relationship between the imported connectivity and the reference
self.assertTrue(
(reference_connectivity.centres == imported_connectivity.centres
).all())
self.assertTrue((reference_connectivity.orientations ==
imported_connectivity.orientations).all())
self.assertEqual(reference_connectivity.number_of_regions,
imported_connectivity.number_of_regions)
self.assertTrue((reference_connectivity.region_labels ==
imported_connectivity.region_labels).all())
self.assertFalse(
(reference_connectivity.weights == imported_connectivity.weights
).all())
self.assertFalse((reference_connectivity.tract_lengths ==
imported_connectivity.tract_lengths).all())
def setUp(self):
"""
Sets up the environment for running the tests;
creates a test user, a test project, a connectivity, a cortical surface and a face surface;
imports a CFF data-set
"""
self.datatypeFactory = DatatypesFactory()
self.test_user = self.datatypeFactory.get_user()
self.test_project = TestFactory.import_default_project(self.test_user)
self.datatypeFactory.project = self.test_project
self.connectivity = TestFactory.get_entity(self.test_project,
Connectivity())
self.assertTrue(self.connectivity is not None)
self.face_surface = TestFactory.get_entity(self.test_project,
FaceSurface())
self.assertTrue(self.face_surface is not None)
self.assertTrue(
TestFactory.get_entity(self.test_project, EEGCap()) is not None)
def setUp(self):
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
self.test_user = TestFactory.create_user('Test_User')
self.test_project = TestFactory.create_project(self.test_user,
"Test_Project")
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
"John", zip_path)
self.connectivity = TestFactory.get_entity(self.test_project,
Connectivity())
def test_bad_reference(self):
TestFactory.import_cff(test_user=self.test_user,
test_project=self.test_project)
field = FilterChain.datatype + '.subject'
filters = FilterChain('', [field], [TEST_SUBJECT_A], ['!='])
bad_reference_connectivity = TestFactory.get_entity(
self.test_project, Connectivity(), filters)
self.assertRaises(OperationException,
self._import_csv_test_connectivity,
bad_reference_connectivity.gid, TEST_SUBJECT_A)
def setUp(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.datatypeFactory = DatatypesFactory()
self.test_project = self.datatypeFactory.get_project()
self.test_user = self.datatypeFactory.get_user()
TestFactory.import_cff(test_user=self.test_user, test_project=self.test_project)
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
self.assertTrue(self.connectivity is not None)
def setUp(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.datatypeFactory = DatatypesFactory()
self.test_project = self.datatypeFactory.get_project()
self.test_user = self.datatypeFactory.get_user()
TestFactory.import_cff(test_user=self.test_user, test_project=self.test_project)
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
self.assertTrue(self.connectivity is not None)
def test_launch_eeg(self):
"""
Tests successful launch of a BrainEEG and that all required keys are present in returned template dictionary
"""
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
time_series = self.datatypeFactory.create_timeseries(self.connectivity, 'EEG', sensors)
time_series.configure()
viewer = DualBrainViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(time_series)
for key in BrainViewerTest.EXPECTED_KEYS + BrainViewerTest.EXPECTED_EXTRA_KEYS:
self.assertTrue(key in result and result[key] is not None)
self.assertTrue(result['extended_view'])
def test_launch_internal(self):
"""
Check that all required keys are present in output from InternalSensorViewer launch.
"""
zip_path = os.path.join(os.path.dirname(sensors_dataset.__file__), 'internal_39.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path, Sensors_Importer.INTERNAL_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsInternal())
viewer = InternalSensorViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_INTERNAL, result)
def test_launch_MEG(self):
"""
Check that all required keys are present in output from MEGSensorViewer launch.
"""
zip_path = os.path.join(os.path.dirname(sensors_dataset.__file__), 'meg_channels_reg13.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path, Sensors_Importer.MEG_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsMEG())
viewer = MEGSensorViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_MEG, result)
def test_launch_eeg(self):
"""
Tests successful launch of a BrainEEG and that all required keys are present in returned template dictionary
"""
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
time_series = self.datatypeFactory.create_timeseries(
self.connectivity, 'EEG', sensors)
time_series.configure()
viewer = DualBrainViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(time_series)
for key in BrainViewerTest.EXPECTED_KEYS + BrainViewerTest.EXPECTED_EXTRA_KEYS:
self.assertTrue(key in result and result[key] is not None)
self.assertTrue(result['extended_view'])
def test_launch_EEG(self):
"""
Check that all required keys are present in output from EegSensorViewer launch.
"""
## Import Sensors
zip_path = os.path.join(os.path.dirname(tvb_data.sensors.__file__),
'EEG_unit_vectors_BrainProducts_62.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path,
Sensors_Importer.EEG_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
## Import EEGCap
cap_path = os.path.join(os.path.dirname(tvb_data.obj.__file__),
'eeg_cap.obj')
TestFactory.import_surface_obj(self.test_user, self.test_project,
cap_path, EEG_CAP)
eeg_cap_surface = TestFactory.get_entity(self.test_project, EEGCap())
viewer = SensorsViewer()
viewer.current_project_id = self.test_project.id
## Launch with EEG Cap selected
result = viewer.launch(sensors, eeg_cap_surface)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_EEG, result)
for key in ['urlVertices', 'urlTriangles', 'urlLines', 'urlNormals']:
self.assertIsNotNone(result[key],
"Value at key %s should not be None" % key)
## Launch without EEG Cap
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_EEG, result)
for key in ['urlVertices', 'urlTriangles', 'urlLines', 'urlNormals']:
self.assertTrue(
not result[key] or result[key] == "[]",
"Value at key %s should be None or empty, but is %s" %
(key, result[key]))
def test_launch_internal(self):
"""
Check that all required keys are present in output from InternalSensorViewer launch.
"""
zip_path = os.path.join(os.path.dirname(tvb_data.sensors.__file__),
'internal_39.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path,
Sensors_Importer.INTERNAL_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsInternal())
viewer = SensorsViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_INTERNAL, result)
def test_import_bold(self):
### Retrieve Adapter instance
importer = TestFactory.create_adapter('tvb.adapters.uploaders.mat_timeseries_importer', 'MatTimeSeriesImporter')
args = dict(data_file=self.bold_path, dataset_name='QL_20120824_DK_BOLD_timecourse', structure_path='',
transpose=False, slice=None, sampling_rate=1000, start_time=0,
tstype='region',
tstype_parameters_option_region_connectivity=self.connectivity.gid,
Data_Subject="QL")
### Launch import Operation
FlowService().fire_operation(importer, self.test_user, self.test_project.id, **args)
tsr = TestFactory.get_entity(self.test_project, TimeSeriesRegion())
self.assertEqual((661, 1, 68, 1), tsr.read_data_shape())
def test_launch_MEG(self):
"""
Check that all required keys are present in output from MEGSensorViewer launch.
"""
zip_path = os.path.join(os.path.dirname(tvb_data.sensors.__file__),
'meg_channels_reg13.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path,
Sensors_Importer.MEG_SENSORS)
sensors = TestFactory.get_entity(self.test_project, SensorsMEG())
viewer = SensorsViewer()
viewer.current_project_id = self.test_project.id
result = viewer.launch(sensors)
self.assert_compliant_dictionary(self.EXPECTED_KEYS_MEG, result)
def test_launch_eeg(self):
"""
Tests successful launch of a BrainEEG and that all required keys are present in returned template dictionary
"""
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
time_series = self.datatypeFactory.create_timeseries(self.connectivity, 'EEG', sensors)
time_series.configure()
viewer = BrainEEG()
viewer.current_project_id = self.test_project.id
result = viewer.launch(time_series)
expected_keys = ['urlVertices', 'urlNormals', 'urlTriangles', 'urlMeasurePointsLabels', 'title',
'time_series', 'shelfObject', 'pageSize', 'labelsStateVar', 'labelsModes',
'minActivityLabels', 'minActivity', 'measure_points', 'maxActivity', 'isOneToOneMapping',
'isAdapter', 'extended_view', 'base_activity_url', 'alphas_indices']
for key in expected_keys:
self.assertTrue(key in result and result[key] is not None)
self.assertTrue(result['extended_view'])
def test_launch(self):
"""
Check that all required keys are present in output from BrainViewer launch.
"""
zip_path = os.path.join(os.path.dirname(sensors_dataset.__file__),
'EEG_unit_vectors_BrainProducts_62.txt.bz2')
TestFactory.import_sensors(self.test_user, self.test_project, zip_path,
'EEG Sensors')
sensors = TestFactory.get_entity(self.test_project, SensorsEEG())
time_series = self.datatypeFactory.create_timeseries(
self.connectivity, 'EEG', sensors)
viewer = EegMonitor()
result = viewer.launch(time_series)
expected_keys = [
'tsNames', 'groupedLabels', 'tsModes', 'tsStateVars',
'longestChannelLength', 'label_x', 'entities', 'page_size',
'number_of_visible_points', 'extended_view', 'initialSelection',
'ag_settings', 'ag_settings'
]
for key in expected_keys:
self.assertTrue(key in result, "key not found %s" % key)
expected_ag_settings = [
'channelsPerSet', 'channelLabels', 'noOfChannels',
'translationStep', 'normalizedSteps', 'nan_value_found',
'baseURLS', 'pageSize', 'nrOfPages', 'timeSetPaths', 'totalLength',
'number_of_visible_points', 'extended_view',
'measurePointsSelectionGIDs'
]
ag_settings = json.loads(result['ag_settings'])
for key in expected_ag_settings:
self.assertTrue(key in ag_settings,
"ag_settings should have the key %s" % key)
def setUp(self):
zip_path = os.path.join(os.path.dirname(tvb_data.__file__), 'connectivity', 'connectivity_66.zip')
self.test_user = TestFactory.create_user('Test_User')
self.test_project = TestFactory.create_project(self.test_user, "Test_Project")
TestFactory.import_zip_connectivity(self.test_user,self.test_project, "John", zip_path)
self.connectivity = TestFactory.get_entity(self.test_project, Connectivity())
