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()
