def test_monitor_stereoeeg(self): """ This has to be verified. """ monitor = monitors.iEEG() monitor.sensors = sensors.SensorsInternal(load_default=True) assert monitor.period == self.default_period
def test_set_seeg_monitor_params(self): region_mapping = self.set_region_mapping() seeg_file = path.join(path.dirname(tvb_data.sensors.__file__), 'seeg_39.txt') seeg_sensors = TestFactory.import_sensors( self.test_user, self.test_project, seeg_file, SensorsImporterModel.OPTIONS['Internal Sensors']) self.sess_mock['_period'] = '0.75' self.sess_mock['_variables_of_interest'] = '[0, 1]' self.sess_mock['_region_mapping'] = region_mapping.gid self.sess_mock['_projection'] = seeg_sensors.gid self.sess_mock['_sigma'] = "1.0" self.sess_mock['_sensors'] = seeg_sensors.gid self.session_stored_simulator.monitors = [iEEG()] with patch('cherrypy.session', self.sess_mock, create=True): common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator) self.simulator_controller.set_monitor_params( **self.sess_mock._data) assert self.session_stored_simulator.monitors[ 0].period == 0.75, "Period was not set correctly." assert (self.session_stored_simulator.monitors[0].variables_of_interest == [0, 1]).all(), \ "Variables of interest where not set correctly." assert self.session_stored_simulator.monitors[0].region_mapping.gid.hex == region_mapping.gid, \ "Region Mapping wasn't set and stored correctly." assert self.session_stored_simulator.monitors[0].sensors.gid.hex == seeg_sensors.gid, \ "Region Mapping wasn't set and stored correctly." assert self.session_stored_simulator.monitors[0].projection.gid is not None, \ "Projection wasn't stored correctly."
def test_monitor_stereoeeg(self): """ This has to be verified. """ monitor = monitors.iEEG() monitor.sensors = sensors.SensorsInternal(load_file="seeg_39.txt.bz2") assert monitor.period == self.default_period
def setup_method(self): self.sim = simulator.Simulator( connectivity=connectivity.Connectivity.from_file( 'connectivity_192.zip'), monitors=(monitors.iEEG( sensors=SensorsInternal(load_default=True), region_mapping=RegionMapping.from_file( 'regionMapping_16k_192.txt')))).configure()
def setup_method(self): self.sim = simulator.Simulator( connectivity=connectivity.Connectivity( load_file='connectivity_192.zip'), monitors=(monitors.iEEG( sensors=SensorsInternal(load_file="seeg_39.txt.bz2"), region_mapping=RegionMapping( load_file='regionMapping_16k_192.txt')))).configure()
def test_set_seeg_monitor_params(self): region_mapping = self.set_region_mapping() seeg_sensors_file = path.join(path.dirname(tvb_data.sensors.__file__), 'seeg_588.txt') seeg_sensors = TestFactory.import_sensors( self.test_user, self.test_project, seeg_sensors_file, SensorsImporterModel.OPTIONS['Internal Sensors']) surface_file = path.join(path.dirname(tvb_data.surfaceData.__file__), 'cortex_16384.zip') surface = TestFactory.import_surface_zip(self.test_user, self.test_project, surface_file, CORTICAL, True) seeg_projection_file = path.join( path.dirname(tvb_data.projectionMatrix.__file__), 'projection_seeg_588_surface_16k.npy') seeg_projections = TestFactory.import_projection_matrix( self.test_user, self.test_project, seeg_projection_file, seeg_sensors.gid, surface.gid) self.session_stored_simulator.model.variables_of_interest = ('V', 'W', 'V - W') variable_of_interest_indexes = {'W': 1, 'V - W': 2} self.sess_mock['variables_of_interest'] = list( variable_of_interest_indexes.keys()) self.sess_mock['period'] = '0.75' self.sess_mock['region_mapping'] = region_mapping.gid self.sess_mock['projection'] = seeg_projections.gid self.sess_mock['sigma'] = "1.0" self.sess_mock['sensors'] = seeg_sensors.gid self.session_stored_simulator.monitors = [iEEG()] with patch('cherrypy.session', self.sess_mock, create=True): common.add2session(common.KEY_SIMULATOR_CONFIG, self.session_stored_simulator) common.add2session(common.KEY_BURST_CONFIG, BurstConfiguration(self.test_project.id)) self.simulator_controller.set_monitor_params( 'iEEG', **self.sess_mock._data) assert self.session_stored_simulator.monitors[ 0].period == 0.75, "Period was not set correctly." assert list(self.session_stored_simulator.monitors[0].variables_of_interest) == \ list(variable_of_interest_indexes.values()), "Variables of interest were not set correctly." assert self.session_stored_simulator.monitors[0].region_mapping.gid.hex == region_mapping.gid, \ "Region Mapping wasn't set and stored correctly." assert self.session_stored_simulator.monitors[0].sensors.gid.hex == seeg_sensors.gid, \ "Region Mapping wasn't set and stored correctly." assert self.session_stored_simulator.monitors[0].projection.gid is not None, \ "Projection wasn't stored correctly."
def test_gain_size(self): sim = simulator.Simulator( connectivity=connectivity.Connectivity.from_file('connectivity_192.zip'), monitors=(monitors.iEEG( sensors=SensorsInternal.from_file(), region_mapping=RegionMapping.from_file('regionMapping_16k_192.txt') ),) ).configure() ieeg = sim.monitors[0] # type: SensorsInternal n_sens, n_reg = ieeg.gain.shape assert ieeg.sensors.locations.shape[0] == n_sens assert sim.connectivity.number_of_regions == n_reg
def setup_method(self): oscillator = models.Generic2dOscillator() white_matter = connectivity.Connectivity(load_file='connectivity_' + str(self.n_regions) + '.zip') white_matter.speed = numpy.array([self.speed]) white_matter_coupling = coupling.Difference(a=self.coupling_a) heunint = integrators.HeunStochastic( dt=2**-4, noise=noise.Additive(nsig=numpy.array([ 2**-10, ]))) mons = ( monitors.EEG(projection=ProjectionMatrix( load_file='projection_eeg_65_surface_16k.npy'), sensors=SensorsEEG(load_file="eeg_brainstorm_65.txt"), period=self.period), monitors.MEG( projection=ProjectionMatrix( load_file='projection_meg_276_surface_16k.npy'), sensors=SensorsMEG(load_file='meg_brainstorm_276.txt'), period=self.period), monitors.iEEG(projection=ProjectionMatrix( load_file='projection_seeg_588_surface_16k.npy'), sensors=SensorsInternal(load_file='seeg_588.txt'), period=self.period), ) local_coupling_strength = numpy.array([2**-10]) region_mapping = RegionMapping(load_file='regionMapping_16k_' + str(self.n_regions) + '.txt') default_cortex = Cortex( region_mapping_data=region_mapping, load_file="cortex_16384.zip" ) #region_mapping_file="regionMapping_16k_192.txt") default_cortex.coupling_strength = local_coupling_strength self.sim = simulator.Simulator(model=oscillator, connectivity=white_matter, coupling=white_matter_coupling, integrator=heunint, monitors=mons, surface=default_cortex) self.sim.configure()