def create_stimuli(n_nodes, node_idx, node_weights, **params):
weighting = np.zeros(n_nodes)
weighting[node_idx] = node_weights
eqn_t = equations.DiscreteTemporalEquation()
eqn_t.parameters.update(params)
stimulus = patterns.StimuliRegion(temporal=eqn_t,
connectivity=connectome,
weight=weighting
)
return stimulus
def test_stimuliregion(self):
conn = connectivity.Connectivity(load_default=True)
conn.configure()
dt = patterns.StimuliRegion()
dt.connectivity = conn
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.weight = [0 for _ in range(conn.number_of_regions)]
dt.configure_space()
assert dt.summary_info['Type'] == 'StimuliRegion'
assert dt.connectivity is not None
assert dt.space.shape == (76, 1)
assert dt.spatial_pattern.shape == (76, 1)
assert isinstance(dt.temporal, equations.Gaussian)
assert dt.temporal_pattern is None
assert dt.time is None
def test_stimuliregion(self):
conn = connectivity.Connectivity()
conn.configure()
dt = patterns.StimuliRegion()
dt.connectivity = conn
dt.spatial = equations.DiscreteEquation()
dt.temporal = equations.Gaussian()
dt.weight = [0 for _ in range(conn.number_of_regions)]
dt.configure_space()
self.assertEqual(dt.summary_info['Type'], 'StimuliRegion')
self.assertTrue(dt.connectivity is not None)
self.assertEqual(dt.space.shape, (74, 1))
self.assertEqual(dt.spatial_pattern.shape, (74, 1))
self.assertTrue(isinstance(dt.temporal, equations.Gaussian))
self.assertTrue(dt.temporal_pattern is None)
self.assertTrue(dt.time is None)
def test_stimuliregion(self):
conn = connectivity.Connectivity.from_file()
conn.configure()
dt = patterns.StimuliRegion()
dt.connectivity = conn
dt.spatial = DiscreteEquation()
dt.temporal = Gaussian()
dt.weight = numpy.array([0 for _ in range(conn.number_of_regions)])
dt.configure_space()
assert dt.summary_info()['Type'] == 'StimuliRegion'
assert dt.connectivity is not None
assert dt.space.shape == (76, 1)
assert dt.spatial_pattern.shape == (76, 1)
assert isinstance(dt.temporal, Gaussian)
assert dt.temporal_pattern is None
assert dt.time is None
what_to_watch = (momo, mama)
#Define the stimulus
#Specify a weighting for regions to receive stimuli...
white_matter.configure() # Because we want access to number_of_regions
nodes = [0, 7, 13, 33, 42]
weighting = numpy.zeros((white_matter.number_of_regions, )) #1
weighting[nodes] = numpy.array([2.0**-2, 2.0**-3, 2.0**-4, 2.0**-5,
2.0**-6]) # [:, numpy.newaxis]
eqn_t = equations.Gaussian()
eqn_t.parameters["midpoint"] = 15000.0
eqn_t.parameters["sigma"] = 4.0
stimulus = patterns.StimuliRegion(temporal=eqn_t,
connectivity=white_matter,
weight=weighting)
#Initialise Simulator -- Model, Connectivity, Integrator, Monitors, and stimulus.
sim = simulator.Simulator(model=oscilator,
connectivity=white_matter,
coupling=white_matter_coupling,
integrator=heunint,
monitors=what_to_watch,
stimulus=stimulus) # surface=default_cortex,
sim.configure()
LOG.info("Starting simulation...")
#Perform the simulation
tavg_time = []