def configure(self,
dt=2**-3,
model=models.Generic2dOscillator,
speed=4.0,
coupling_strength=0.00042,
method="HeunDeterministic",
surface_sim=False,
default_connectivity=True):
"""
Create an instance of the Simulator class, by default use the
generic plane oscillator local dynamic model and the deterministic
version of Heun's method for the numerical integration.
"""
self.method = method
if default_connectivity:
white_matter = connectivity.Connectivity(load_default=True)
# NOTE: This is the default region mapping should consider changing the name.
region_mapping = RegionMapping.from_file(
source_file=
"cortex_reg13/region_mapping/o52r00_irp2008_hemisphere_both_subcortical_false_regions_74.txt.bz2"
)
else:
white_matter = connectivity.Connectivity.from_file(
source_file="connectivity_190.zip")
region_mapping = RegionMapping.from_file(
source_file=
"cortex_reg13/region_mapping/o52r00_irp2008_hemisphere_both_subcortical_true_regions_190.txt.bz2"
)
white_matter_coupling = coupling.Linear(a=coupling_strength)
white_matter.speed = speed
dynamics = model()
if method[-10:] == "Stochastic":
hisss = noise.Additive(nsig=numpy.array([2**-11]))
integrator = eval("integrators." + method + "(dt=dt, noise=hisss)")
else:
integrator = eval("integrators." + method + "(dt=dt)")
if surface_sim:
local_coupling_strength = numpy.array([2**-10])
default_cortex = Cortex(load_default=True,
region_mapping_data=region_mapping)
default_cortex.coupling_strength = local_coupling_strength
default_cortex.local_connectivity = LocalConnectivity(
load_default=default_connectivity, surface=default_cortex)
else:
default_cortex = None
# Order of monitors determines order of returned values.
self.sim = simulator.Simulator(model=dynamics,
connectivity=white_matter,
coupling=white_matter_coupling,
integrator=integrator,
monitors=self.monitors,
surface=default_cortex)
self.sim.configure()
def configure(self, dt=2 ** -3, model=models.Generic2dOscillator, speed=4.0,
coupling_strength=0.00042, method="HeunDeterministic",
surface_sim=False,
default_connectivity=True):
"""
Create an instance of the Simulator class, by default use the
generic plane oscillator local dynamic model and the deterministic
version of Heun's method for the numerical integration.
"""
self.method = method
if default_connectivity:
white_matter = Connectivity(load_file="connectivity_76.zip")
region_mapping = RegionMapping(load_file="regionMapping_16k_76.txt")
else:
white_matter = Connectivity(load_file="connectivity_192.zip")
region_mapping = RegionMapping(load_file="regionMapping_16k_192.txt")
white_matter_coupling = coupling.Linear(a=coupling_strength)
white_matter.speed = speed
dynamics = model()
if method[-10:] == "Stochastic":
hisss = noise.Additive(nsig=numpy.array([2 ** -11]))
integrator = eval("integrators." + method + "(dt=dt, noise=hisss)")
else:
integrator = eval("integrators." + method + "(dt=dt)")
if surface_sim:
local_coupling_strength = numpy.array([2 ** -10])
default_cortex = Cortex(region_mapping_data=region_mapping, load_file="cortex_16384.zip")
default_cortex.coupling_strength = local_coupling_strength
default_cortex.local_connectivity = LocalConnectivity(load_file="local_connectivity_16384.mat")
else:
default_cortex = None
# Order of monitors determines order of returned values.
self.sim = simulator.Simulator(model=dynamics,
connectivity=white_matter,
coupling=white_matter_coupling,
integrator=integrator,
monitors=self.monitors,
surface=default_cortex)
self.sim.configure()
def test_cortexdata(self):
dt = Cortex(load_default=True)
assert isinstance(dt, Cortex)
assert dt.region_mapping is not None
## Initialize Local Connectivity, to avoid long computation time.
dt.local_connectivity = LocalConnectivity(load_default=True)
dt.configure()
summary_info = dt.summary_info
assert abs(summary_info['Region area, maximum (mm:math:`^2`)'] -
9333.39) < 0.01
assert abs(summary_info['Region area, mean (mm:math:`^2`)'] -
3038.51) < 0.01
assert abs(summary_info['Region area, minimum (mm:math:`^2`)'] -
540.90) < 0.01
assert dt.get_data_shape('vertices') == (16384, 3)
assert dt.get_data_shape('vertex_normals') == (16384, 3)
assert dt.get_data_shape('triangles') == (32760, 3)
def test_cortexdata(self):
dt = Cortex(load_file="cortex_16384.zip",
region_mapping_data=RegionMapping(
load_file="regionMapping_16k_76.txt"))
assert isinstance(dt, Cortex)
assert dt.region_mapping_data is not None
## Initialize Local Connectivity, to avoid long computation time.
dt.local_connectivity = LocalConnectivity(
load_file="local_connectivity_16384.mat")
dt.configure()
summary_info = dt._find_summary_info()
assert abs(summary_info['Region area, maximum (mm:math:`^2`)'] -
9333.39) < 0.01
assert abs(summary_info['Region area, mean (mm:math:`^2`)'] -
3038.51) < 0.01
assert abs(summary_info['Region area, minimum (mm:math:`^2`)'] -
540.90) < 0.01
assert dt.vertices.shape == (16384, 3)
assert dt.vertex_normals.shape == (16384, 3)
assert dt.triangles.shape == (32760, 3)
def test_cortexdata(self):
dt = Cortex(load_default=True)
self.assertTrue(isinstance(dt, Cortex))
self.assertTrue(dt.region_mapping is not None)
## Initialize Local Connectivity, to avoid long computation time.
dt.local_connectivity = LocalConnectivity(load_default=True)
dt.configure()
summary_info = dt.summary_info
self.assertTrue(
abs(summary_info['Region area, maximum (mm:math:`^2`)'] -
9119.4540365252615) < 0.00000001)
self.assertTrue(
abs(summary_info['Region area, mean (mm:math:`^2`)'] -
3366.2542250541251) < 0.00000001)
self.assertTrue(
abs(summary_info['Region area, minimum (mm:math:`^2`)'] -
366.48271886512993) < 0.00000001)
self.assertEqual(dt.get_data_shape('vertices'), (16384, 3))
self.assertEqual(dt.get_data_shape('vertex_normals'), (16384, 3))
self.assertEqual(dt.get_data_shape('triangles'), (32760, 3))
#Bundle them
what_to_watch = (mon_tavg, mon_savg, mon_eeg)
#Initialise a surface:
#First define the function describing the "local" connectivity.
grey_matter = LocalConnectivity(cutoff=40.0)
grey_matter.equation.parameters['sigma'] = 10.0
grey_matter.equation.parameters['amp'] = 1.0
#then a scaling factor, to adjust the strength of the local connectivity
local_coupling_strength = numpy.array([-0.0115])
#finally, create a default cortex that includes the custom local connectivity.
default_cortex = Cortex(load_default=True)
default_cortex.local_connectivity = grey_matter
default_cortex.coupling_strength = local_coupling_strength
#Initialise Simulator -- Model, Connectivity, Integrator, Monitors, and surface.
sim = simulator.Simulator(model=oscillator,
connectivity=white_matter,
integrator=heunint,
monitors=what_to_watch,
surface=default_cortex)
sim.configure()
LOG.info("Starting simulation...")
#Perform the simulation
tavg_data = []
tavg_time = []
savg_data = []
