def setup_method(self):
oscillator = models.Generic2dOscillator()
white_matter = connectivity.Connectivity.from_file(
'connectivity_%d.zip' % (self.n_regions, ))
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.from_file(period=self.period),
monitors.MEG.from_file(period=self.period),
monitors.iEEG.from_file(period=self.period),
)
local_coupling_strength = numpy.array([2**-10])
region_mapping = RegionMapping.from_file('regionMapping_16k_%d.txt' %
(self.n_regions, ))
default_cortex = Cortex(region_mapping_data=region_mapping,
load_default=True)
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()
def test_g2d(self):
"""
Default parameters:
---------------------------
| EXCITABLE CONFIGURATION |
---------------------------
|Parameter | Value |
-----------------------------
| a | -2.0 |
| b | -10.0 |
| c | 0.0 |
| d | 0.02 |
| I | 0.0 |
-----------------------------
|* limit cylce if a = 2.0 |
-----------------------------
"""
model = models.Generic2dOscillator()
history_shape = (1, model._nvar, 1, model.number_of_modes)
model_ic = model.initial(dt, history_shape)
self.assertEqual(model._nvar, 2)
self.assertTrue(ArrayAlmostEqual(model_ic, numpy.array([[[[ 1.70245989]],
[[ 0.2765286 ]]]])) is None)
def test_g2d_voi(self):
model = models.Generic2dOscillator(
variables_of_interest = ['W', 'W - V']
)
(V, W), (voi_W, voi_WmV) = self._validate_initialization(model, 2)
numpy.testing.assert_allclose(voi_W, W)
numpy.testing.assert_allclose(voi_WmV, W - V)
def __init__(self,
connectivity,
default_model=None,
default_integrator=None,
compute_phase_plane_params=True):
self.logger = get_logger(self.__class__.__module__)
self.default_model = default_model
self.default_integrator = default_integrator
self.connectivity = connectivity
self.connectivity_models = dict()
if self.default_model is None:
self.default_model = models_module.Generic2dOscillator()
if self.default_integrator is None:
self.default_integrator = integrators_module.RungeKutta4thOrderDeterministic(
)
self.model_parameter_names = deepcopy(
self.default_model.ui_configurable_parameters)
if not len(self.model_parameter_names):
self.logger.warning(
"The 'ui_configurable_parameters' list of the current model is empty!"
)
self.prepared_model_parameter_names = self._prepare_parameter_names(
self.model_parameter_names)
model = self._get_model_for_region(0)
if compute_phase_plane_params:
self._phase_plane = PhasePlaneInteractive(
deepcopy(model), deepcopy(self.default_integrator))
self.phase_plane_params = self._phase_plane.draw_phase_plane()
def test_g2d(self):
"""
Default parameters:
+---------------------------+
| SanzLeonetAl 2013 |
+--------------+------------+
|Parameter | Value |
+==============+============+
| a | - 0.5 |
+--------------+------------+
| b | -10.0 |
+--------------+------------+
| c | 0.0 |
+--------------+------------+
| d | 0.02 |
+--------------+------------+
| I | 0.0 |
+--------------+------------+
|* excitable regime if |
|* intrinsic frequency is |
| approx 10 Hz |
+---------------------------+
"""
model = models.Generic2dOscillator()
state, obser = self._validate_initialization(model, 2)
numpy.testing.assert_allclose(obser[0], state[0])
def test_expr_pre(self):
sim, ys = self._run_sim(5, models.Generic2dOscillator(),
Raw(pre_expr='V;W;V**2;W-V', post_expr=''))
self.assertTrue(hasattr(sim.monitors[0], '_transforms'))
v, w, v2, wmv = ys.transpose((1, 0, 2, 3))
self.assertTrue(numpy.allclose(v**2, v2))
self.assertTrue(numpy.allclose(w - v, wmv))
def test_g2d(self):
"""
Default parameters:
+---------------------------+
| SanzLeonetAl 2013 |
+--------------+------------+
|Parameter | Value |
+==============+============+
| a | - 0.5 |
+--------------+------------+
| b | -10.0 |
+--------------+------------+
| c | 0.0 |
+--------------+------------+
| d | 0.02 |
+--------------+------------+
| I | 0.0 |
+--------------+------------+
|* excitable regime if |
|* intrinsic frequency is |
| approx 10 Hz |
+---------------------------+
"""
model = models.Generic2dOscillator()
history_shape = (1, model._nvar, 1, model.number_of_modes)
model_ic = model.initial(dt, history_shape)
self.assertEqual(model._nvar, 2)
assert_array_almost_equal(
model_ic, numpy.array([[[[0.97607082]], [[-0.03384097]]]]))
def test_expr_post(self):
sim, ys = self._run_sim(
5, models.Generic2dOscillator(),
Raw(pre_expr='V;W;V;W', post_expr=';;mon**2; exp(mon)'))
self.assertTrue(hasattr(sim.monitors[0], '_transforms'))
v, w, v2, ew = ys.transpose((1, 0, 2, 3))
self.assertTrue(numpy.allclose(v**2, v2))
self.assertTrue(numpy.allclose(numpy.exp(w), ew))
def test_surface_sim_with_projections(self):
# Setup Simulator obj
oscillator = models.Generic2dOscillator()
white_matter = connectivity.Connectivity.from_file('connectivity_%d.zip' % (self.n_regions,))
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.from_file(period=self.period),
monitors.MEG.from_file(period=self.period),
# monitors.iEEG.from_file(period=self.period),
# SEEG projection data is not part of tvb-data on Pypi, thus this can not work generic
)
local_coupling_strength = numpy.array([2 ** -10])
region_mapping = RegionMapping.from_file('regionMapping_16k_%d.txt' % (self.n_regions,))
region_mapping.surface = CorticalSurface.from_file()
default_cortex = Cortex.from_file()
default_cortex.region_mapping_data = region_mapping
default_cortex.coupling_strength = local_coupling_strength
sim = simulator.Simulator(model=oscillator, connectivity=white_matter, coupling=white_matter_coupling,
integrator=heunint, monitors=mons, surface=default_cortex)
sim.configure()
# check configured simulation connectivity attribute
conn = sim.connectivity
assert conn.number_of_regions == self.n_regions
assert conn.speed == self.speed
# test monitor properties
lc_n_node = sim.surface.local_connectivity.matrix.shape[0]
for mon in sim.monitors:
assert mon.period == self.period
n_sens, g_n_node = mon.gain.shape
assert g_n_node == sim.number_of_nodes
assert n_sens == mon.sensors.number_of_sensors
assert lc_n_node == g_n_node
# check output shape
ys = {}
mons = 'eeg meg seeg'.split()
for key in mons:
ys[key] = []
for data in sim(simulation_length=3.0):
for key, dat in zip(mons, data):
if dat:
_, y = dat
ys[key].append(y)
for mon, key in zip(sim.monitors, mons):
ys[key] = numpy.array(ys[key])
assert ys[key].shape[2] == mon.gain.shape[0]
def __init__(self, model=None, integrator=None):
if model is None:
model = models.Generic2dOscillator()
if integrator is None:
integrator = integrators.HeunDeterministic()
model.configure()
self.model = model
self.integrator = integrator
# Only one instance should exist for a browser page.
# To achieve something close to that we store it here
self.phase_plane = phase_space_d3(model, integrator)
def __init__(self, connectivity, default_model = None, default_integrator = None):
self.logger = get_logger(self.__class__.__module__)
self.default_model = default_model
self.default_integrator = default_integrator
self.connectivity = connectivity
self.connectivity_models = dict()
if self.default_model is None:
self.default_model = models_module.Generic2dOscillator()
if self.default_integrator is None:
self.default_integrator = integrators_module.RungeKutta4thOrderDeterministic()
self.model_parameter_names = deepcopy(self.default_model.ui_configurable_parameters)
if not len(self.model_parameter_names):
self.logger.warning("The 'ui_configurable_parameters' list of the current model is empty!")
def setUp(self):
"""
Reset the database before each test.
"""
self.flow_service = FlowService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(self.test_user)
TestFactory.import_cff(test_user=self.test_user,
test_project=self.test_project)
self.default_model = models_module.Generic2dOscillator()
all_connectivities = self.flow_service.get_available_datatypes(
self.test_project.id, Connectivity)
self.connectivity = ABCAdapter.load_entity_by_gid(
all_connectivities[0][2])
self.connectivity.number_of_regions = 74
self.context_model_param = ContextModelParameters(
self.connectivity, self.default_model)
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()
def test_period_handling(self):
"""Test that expression application working for monitors with a period."""
sim, ys = self._run_sim(5, models.Generic2dOscillator(),
TemporalAverage(pre_expr='V+W'))
class Simulator(HasTraits):
"""A Simulator assembles components required to perform simulations."""
connectivity = Attr(
field_type=connectivity.Connectivity,
label="Long-range connectivity",
default=None,
required=True,
doc="""A tvb.datatypes.Connectivity object which contains the
structural long-range connectivity data (i.e., white-matter tracts). In
combination with the ``Long-range coupling function`` it defines the inter-regional
connections. These couplings undergo a time delay via signal propagation
with a propagation speed of ``Conduction Speed``""")
conduction_speed = Float(
label="Conduction Speed",
default=3.0,
required=False,
# range=basic.Range(lo=0.01, hi=100.0, step=1.0),
doc="""Conduction speed for ``Long-range connectivity`` (mm/ms)""")
coupling = Attr(
field_type=coupling.Coupling,
label="Long-range coupling function",
default=coupling.Linear(),
required=True,
doc="""The coupling function is applied to the activity propagated
between regions by the ``Long-range connectivity`` before it enters the local
dynamic equations of the Model. Its primary purpose is to 'rescale' the
incoming activity to a level appropriate to Model.""")
surface = Attr(field_type=cortex.Cortex,
label="Cortical surface",
default=None,
required=False,
doc="""By default, a Cortex object which represents the
cortical surface defined by points in the 3D physical space and their
neighborhood relationship. In the current TVB version, when setting up a
surface-based simulation, the option to configure the spatial spread of
the ``Local Connectivity`` is available.""")
stimulus = Attr(
field_type=patterns.SpatioTemporalPattern,
label="Spatiotemporal stimulus",
default=None,
required=False,
doc=
"""A ``Spatiotemporal stimulus`` can be defined at the region or surface level.
It's composed of spatial and temporal components. For region defined stimuli
the spatial component is just the strength with which the temporal
component is applied to each region. For surface defined stimuli, a
(spatial) function, with finite-support, is used to define the strength
of the stimuli on the surface centred around one or more focal points.
In the current version of TVB, stimuli are applied to the first state
variable of the ``Local dynamic model``.""")
model = Attr(
field_type=models.Model,
label="Local dynamic model",
default=models.Generic2dOscillator(),
required=True,
doc="""A tvb.simulator.Model object which describe the local dynamic
equations, their parameters, and, to some extent, where connectivity
(local and long-range) enters and which state-variables the Monitors
monitor. By default the 'Generic2dOscillator' model is used. Read the
Scientific documentation to learn more about this model.""")
integrator = Attr(field_type=integrators.Integrator,
label="Integration scheme",
default=integrators.HeunDeterministic(),
required=True,
doc="""A tvb.simulator.Integrator object which is
an integration scheme with supporting attributes such as
integration step size and noise specification for stochastic
methods. It is used to compute the time courses of the model state
variables.""")
initial_conditions = NArray(
label="Initial Conditions",
required=False,
doc="""Initial conditions from which the simulation will begin. By
default, random initial conditions are provided. Needs to be the same shape
as simulator 'history', ie, initial history function which defines the
minimal initial state of the network with time delays before time t=0.
If the number of time points in the provided array is insufficient the
array will be padded with random values based on the 'state_variables_range'
attribute.""")
monitors = List(
of=monitors.Monitor,
label="Monitor(s)",
default=(monitors.TemporalAverage(), ),
doc="""A tvb.simulator.Monitor or a list of tvb.simulator.Monitor
objects that 'know' how to record relevant data from the simulation. Two
main types exist: 1) simple, spatial and temporal, reductions (subsets
or averages); 2) physiological measurements, such as EEG, MEG and fMRI.
By default the Model's specified variables_of_interest are returned,
temporally downsampled from the raw integration rate to a sample rate of
1024Hz.""")
simulation_length = Float(
label="Simulation Length (ms, s, m, h)",
default=1000.0, # ie 1 second
required=True,
doc="""The length of a simulation (default in milliseconds).""")
history = None # type: SparseHistory
@property
def good_history_shape(self):
"""Returns expected history shape."""
n_reg = self.connectivity.number_of_regions
shape = self.horizon, len(
self.model.state_variables), n_reg, self.model.number_of_modes
return shape
calls = 0
current_step = 0
number_of_nodes = None
_memory_requirement_guess = None
_memory_requirement_census = None
_storage_requirement = None
_runtime = None
# methods consist of
# 1) generic configure
# 2) component specific configure
# 3) loop preparation
# 4) loop step
# 5) estimations
@property
def is_surface_simulation(self):
if self.surface:
return True
return False
def _configure_integrator_boundaries(self):
if self.model.state_variable_boundaries is not None:
indices = []
boundaries = []
for sv, sv_bounds in self.model.state_variable_boundaries.items():
indices.append(self.model.state_variables.index(sv))
boundaries.append(sv_bounds)
sort_inds = numpy.argsort(indices)
self.integrator.bounded_state_variable_indices = numpy.array(
indices)[sort_inds]
self.integrator.state_variable_boundaries = numpy.array(
boundaries).astype("float64")[sort_inds]
else:
self.integrator.bounded_state_variable_indices = None
self.integrator.state_variable_boundaries = None
def preconfigure(self):
"""Configure just the basic fields, so that memory can be estimated."""
self.connectivity.configure()
if self.surface:
self.surface.configure()
if self.stimulus:
self.stimulus.configure()
self.coupling.configure()
self.model.configure()
self.integrator.configure()
self._configure_integrator_boundaries()
# monitors needs to be a list or tuple, even if there is only one...
if not isinstance(self.monitors, (list, tuple)):
self.monitors = [self.monitors]
# Configure monitors
for monitor in self.monitors:
monitor.configure()
# "Nodes" refers to either regions or vertices + non-cortical regions.
if self.surface is None:
self.number_of_nodes = self.connectivity.number_of_regions
self.log.info('Region simulation with %d ROI nodes',
self.number_of_nodes)
else:
rm = self.surface.region_mapping
unmapped = self.connectivity.unmapped_indices(rm)
self._regmap = numpy.r_[rm, unmapped]
self.number_of_nodes = self._regmap.shape[0]
self.log.info(
'Surface simulation with %d vertices + %d non-cortical, %d total nodes',
rm.size, unmapped.size, self.number_of_nodes)
self._guesstimate_memory_requirement()
def configure(self, full_configure=True):
"""Configure simulator and its components.
The first step of configuration is to run the configure methods of all
the Simulator's components, ie its traited attributes.
Configuration of a Simulator primarily consists of calculating the
attributes, etc, which depend on the combinations of the Simulator's
traited attributes (keyword args).
Converts delays from physical time units into integration steps
and updates attributes that depend on combinations of the 6 inputs.
Returns
-------
sim: Simulator
The configured Simulator instance.
"""
if full_configure:
# When run from GUI, preconfigure is run separately, and we want to avoid running that part twice
self.preconfigure()
# Make sure spatialised model parameters have the right shape (number_of_nodes, 1)
# todo: this exclusion list is fragile, consider excluding declarative attrs that are not arrays
excluded_params = ("state_variable_range", "state_variable_boundaries",
"variables_of_interest", "noise", "psi_table",
"nerf_table", "gid")
spatial_reshape = self.model.spatial_param_reshape
for param in type(self.model).declarative_attrs:
if param in excluded_params:
continue
# If it's a surface sim and model parameters were provided at the region level
region_parameters = getattr(self.model, param)
if self.surface is not None:
if region_parameters.size == self.connectivity.number_of_regions:
new_parameters = region_parameters[
self.surface.region_mapping].reshape(spatial_reshape)
setattr(self.model, param, new_parameters)
region_parameters = getattr(self.model, param)
if region_parameters.size == self.number_of_nodes:
new_parameters = region_parameters.reshape(spatial_reshape)
setattr(self.model, param, new_parameters)
# Configure spatial component of any stimuli
self._configure_stimuli()
# Set delays, provided in physical units, in integration steps.
self.connectivity.set_idelays(self.integrator.dt)
self.horizon = self.connectivity.idelays.max() + 1
# Reshape integrator.noise.nsig, if necessary.
if isinstance(self.integrator, integrators.IntegratorStochastic):
self._configure_integrator_noise()
# Setup history
self._configure_history(self.initial_conditions)
# Configure Monitors to work with selected Model, etc...
self._configure_monitors()
# Estimate of memory usage.
self._census_memory_requirement()
# Allow user to chain configure to another call or assignment.
return self
def _handle_random_state(self, random_state):
if random_state is not None:
if isinstance(self.integrator, integrators.IntegratorStochastic):
self.integrator.noise.random_stream.set_state(random_state)
msg = "random_state supplied with seed %s"
self.log.info(
msg,
self.integrator.noise.random_stream.get_state()[1][0])
else:
self.log.warn(
"random_state supplied for non-stochastic integration")
def _prepare_local_coupling(self):
if self.surface is None:
local_coupling = 0.0
else:
if self.surface.coupling_strength.size == 1:
local_coupling = (self.surface.coupling_strength[0] *
self.surface.local_connectivity.matrix)
elif self.surface.coupling_strength.size == self.surface.number_of_vertices:
ind = numpy.arange(self.number_of_nodes, dtype=numpy.intc)
vec_cs = numpy.zeros((self.number_of_nodes, ))
vec_cs[:self.surface.
number_of_vertices] = self.surface.coupling_strength
sp_cs = scipy.sparse.csc_matrix(
(vec_cs, (ind, ind)),
shape=(self.number_of_nodes, self.number_of_nodes))
local_coupling = sp_cs * self.surface.local_connectivity.matrix
if local_coupling.shape[1] < self.number_of_nodes:
# must match unmapped indices handling in preconfigure
from scipy.sparse import csr_matrix, vstack, hstack
nn = self.number_of_nodes
npad = nn - local_coupling.shape[0]
rpad = csr_matrix((local_coupling.shape[0], npad))
bpad = csr_matrix((npad, nn))
local_coupling = vstack([hstack([local_coupling, rpad]), bpad])
return local_coupling
def _prepare_stimulus(self):
if self.stimulus is None:
stimulus = 0.0
else:
time = numpy.r_[0.0:self.simulation_length:self.integrator.dt]
self.stimulus.configure_time(time.reshape((1, -1)))
stimulus = numpy.zeros((self.model.nvar, self.number_of_nodes, 1))
self.log.debug("stimulus shape is: %s", stimulus.shape)
return stimulus
def _loop_compute_node_coupling(self, step):
"""Compute delayed node coupling values."""
coupling = self.coupling(step, self.history)
if self.surface is not None:
coupling = coupling[:, self._regmap]
return coupling
def _loop_update_stimulus(self, step, stimulus):
"""Update stimulus values for current time step."""
if self.stimulus is not None:
# TODO stim_step != current step
stim_step = step - (self.current_step + 1)
stimulus[self.model.stvar, :, :] = self.stimulus(
stim_step).reshape((1, -1, 1))
def _loop_update_history(self, step, n_reg, state):
"""Update history."""
if self.surface is not None and state.shape[
1] > self.connectivity.number_of_regions:
region_state = numpy.zeros(
(n_reg, state.shape[0],
state.shape[2])) # temp (node, cvar, mode)
numpy_add_at(region_state, self._regmap, state.transpose(
(1, 0, 2))) # sum within region
region_state /= numpy.bincount(self._regmap).reshape(
(-1, 1, 1)) # div by n node in region
state = region_state.transpose((1, 0, 2)) # (cvar, node, mode)
self.history.update(step, state)
def _loop_monitor_output(self, step, state):
observed = self.model.observe(state)
output = [monitor.record(step, observed) for monitor in self.monitors]
if any(outputi is not None for outputi in output):
return output
def __call__(self, simulation_length=None, random_state=None):
"""
Return an iterator which steps through simulation time, generating monitor outputs.
See the run method for a convenient way to collect all output in one call.
:param simulation_length: Length of the simulation to perform in ms.
:param random_state: State of NumPy RNG to use for stochastic integration.
:return: Iterator over monitor outputs.
"""
self.calls += 1
if simulation_length is not None:
self.simulation_length = float(simulation_length)
# intialization
self._guesstimate_runtime()
self._calculate_storage_requirement()
self._handle_random_state(random_state)
n_reg = self.connectivity.number_of_regions
local_coupling = self._prepare_local_coupling()
stimulus = self._prepare_stimulus()
state = self.current_state
# integration loop
n_steps = int(math.ceil(self.simulation_length / self.integrator.dt))
for step in range(self.current_step + 1,
self.current_step + n_steps + 1):
# needs implementing by hsitory + coupling?
node_coupling = self._loop_compute_node_coupling(step)
self._loop_update_stimulus(step, stimulus)
state = self.integrator.scheme(state, self.model.dfun,
node_coupling, local_coupling,
stimulus)
self._loop_update_history(step, n_reg, state)
output = self._loop_monitor_output(step, state)
if output is not None:
yield output
self.current_state = state
self.current_step = self.current_step + n_steps
def _configure_history(self, initial_conditions):
"""
Set initial conditions for the simulation using either the provided
initial_conditions or, if none are provided, the model's initial()
method. This method is called durin the Simulator's __init__().
Any initial_conditions that are provided as an argument are expected
to have dimensions 1, 2, and 3 with shapse corresponding to the number
of state_variables, nodes and modes, respectively. If the provided
inital_conditions are shorter in time (dim=0) than the required history
the model's initial() method is called to make up the difference.
"""
rng = numpy.random
if hasattr(self.integrator, 'noise'):
rng = self.integrator.noise.random_stream
# Default initial conditions
if initial_conditions is None:
n_time, n_svar, n_node, n_mode = self.good_history_shape
self.log.info(
'Preparing initial history of shape %r using model.initial()',
self.good_history_shape)
if self.surface is not None:
n_node = self.number_of_nodes
history = self.model.initial(self.integrator.dt,
(n_time, n_svar, n_node, n_mode), rng)
# ICs provided
else:
# history should be [timepoints, state_variables, nodes, modes]
self.log.info('Using provided initial history of shape %r',
initial_conditions.shape)
n_time, n_svar, n_node, n_mode = ic_shape = initial_conditions.shape
nr = self.connectivity.number_of_regions
if self.surface is not None and n_node == nr:
initial_conditions = initial_conditions[:, :, self._regmap]
return self._configure_history(initial_conditions)
elif ic_shape[1:] != self.good_history_shape[1:]:
raise ValueError(
"Incorrect history sample shape %s, expected %s" %
(ic_shape[1:], self.good_history_shape[1:]))
else:
if ic_shape[0] >= self.horizon:
self.log.debug("Using last %d time-steps for history.",
self.horizon)
history = initial_conditions[
-self.horizon:, :, :, :].copy()
else:
self.log.debug(
'Padding initial conditions with model.initial')
history = self.model.initial(self.integrator.dt,
self.good_history_shape, rng)
shift = self.current_step % self.horizon
history = numpy.roll(history, -shift, axis=0)
history[:ic_shape[0], :, :, :] = initial_conditions
history = numpy.roll(history, shift, axis=0)
self.current_step += ic_shape[0] - 1
if self.integrator.state_variable_boundaries is not None:
self.integrator.bound_state(numpy.swapaxes(history, 0, 1))
self.log.info('Final initial history shape is %r', history.shape)
# create initial state from history
self.current_state = history[self.current_step % self.horizon].copy()
self.log.debug('initial state has shape %r' %
(self.current_state.shape, ))
if self.surface is not None and history.shape[
2] > self.connectivity.number_of_regions:
n_reg = self.connectivity.number_of_regions
(nt, ns, _, nm), ax = history.shape, (2, 0, 1, 3)
region_history = numpy.zeros((nt, ns, n_reg, nm))
numpy_add_at(region_history.transpose(ax), self._regmap,
history.transpose(ax))
region_history /= numpy.bincount(self._regmap).reshape((-1, 1))
history = region_history
# create history query implementation
self.history = SparseHistory(self.connectivity.weights,
self.connectivity.idelays,
self.model.cvar,
self.model.number_of_modes)
# initialize its buffer
self.history.initialize(history)
def _configure_integrator_noise(self):
"""
This enables having noise to be state variable specific and/or to enter
only via specific brain structures, for example it we only want to
consider noise as an external input entering the brain via appropriate
thalamic nuclei.
Support 3 possible shapes:
1) number_of_nodes;
2) number_of_state_variables; and
3) (number_of_state_variables, number_of_nodes).
"""
noise = self.integrator.noise
if self.integrator.noise.ntau > 0.0:
self.integrator.noise.configure_coloured(
self.integrator.dt, self.good_history_shape[1:])
else:
self.integrator.noise.configure_white(self.integrator.dt,
self.good_history_shape[1:])
if self.surface is not None:
if self.integrator.noise.nsig.size == self.connectivity.number_of_regions:
self.integrator.noise.nsig = self.integrator.noise.nsig[
self.surface.region_mapping]
elif self.integrator.noise.nsig.size == self.model.nvar * self.connectivity.number_of_regions:
self.integrator.noise.nsig = self.integrator.noise.nsig[:,
self.
surface
.
region_mapping]
good_nsig_shape = (self.model.nvar, self.number_of_nodes,
self.model.number_of_modes)
nsig = self.integrator.noise.nsig
self.log.debug("Given noise shape is %s", nsig.shape)
if nsig.shape in (good_nsig_shape, (1, )):
return
elif nsig.shape == (self.model.nvar, ):
nsig = nsig.reshape((self.model.nvar, 1, 1))
elif nsig.shape == (self.number_of_nodes, ):
nsig = nsig.reshape((1, self.number_of_nodes, 1))
elif nsig.shape == (self.model.nvar, self.number_of_nodes):
nsig = nsig.reshape((self.model.nvar, self.number_of_nodes, 1))
else:
msg = "Bad Simulator.integrator.noise.nsig shape: %s"
self.log.error(msg % str(nsig.shape))
self.log.debug("Corrected noise shape is %s", nsig.shape)
self.integrator.noise.nsig = nsig
def _configure_monitors(self):
""" Configure the requested Monitors for this Simulator """
# Coerce to list if required
if not isinstance(self.monitors, (list, tuple)):
self.monitors = [self.monitors]
# Configure monitors
for monitor in self.monitors:
monitor.config_for_sim(self)
def _configure_stimuli(self):
""" Configure the defined Stimuli for this Simulator """
if self.stimulus is not None:
if self.surface:
self.stimulus.configure_space(self.surface.region_mapping)
else:
self.stimulus.configure_space()
# used by simulator adaptor
def memory_requirement(self):
"""
Return an estimated of the memory requirements (Bytes) for this
simulator's current configuration.
"""
self._guesstimate_memory_requirement()
return self._memory_requirement_guess
# appears to be unused
def runtime(self, simulation_length):
"""
Return an estimated run time (seconds) for the simulator's current
configuration and a specified simulation length.
"""
self.simulation_length = simulation_length
self._guesstimate_runtime()
return self._runtime
# used by simulator adaptor
def storage_requirement(self):
"""
Return an estimated storage requirement (Bytes) for the simulator's
current configuration and a specified simulation length.
"""
self._calculate_storage_requirement()
return self._storage_requirement
def _guesstimate_memory_requirement(self):
"""
guesstimate the memory required for this simulator.
Guesstimate is based on the shape of the dominant arrays, and as such
can operate before configuration.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
if self.surface:
number_of_nodes = self.surface.number_of_vertices
else:
number_of_nodes = self.connectivity.number_of_regions
number_of_regions = self.connectivity.number_of_regions
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
bits_64 = 8.0 # Bytes
bits_32 = 4.0 # Bytes
# NOTE: The speed hack for getting the first element of hist shape should
# partially resolves calling of this method with a non-configured
# connectivity, there remains the less common issue if no tract_lengths...
hist_shape = (
self.connectivity.tract_lengths.max() /
(self.conduction_speed or self.connectivity.speed or 3.0) /
self.integrator.dt, self.model.nvar, number_of_nodes,
self.model.number_of_modes)
self.log.debug("Estimated history shape is %r", hist_shape)
memreq = numpy.prod(hist_shape) * bits_64
if self.surface:
memreq += self.surface.number_of_triangles * 3 * bits_32 * 2 # normals
memreq += self.surface.number_of_vertices * 3 * bits_64 * 2 # normals
memreq += number_of_nodes * number_of_regions * bits_64 * 4 # region_mapping, region_average, region_sum
# ???memreq += self.surface.local_connectivity.matrix.nnz * 8
if not hasattr(self.monitors, '__len__'):
self.monitors = [self.monitors]
for monitor in self.monitors:
if not isinstance(monitor, monitors.Bold):
stock_shape = (monitor.period / self.integrator.dt,
len(self.model.variables_of_interest),
number_of_nodes, self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
if hasattr(monitor, "sensors"):
try:
memreq += number_of_nodes * monitor.sensors.number_of_sensors * bits_64 # projection_matrix
except AttributeError:
self.log.debug(
"No sensors specified, guessing memory based on default EEG."
)
memreq += number_of_nodes * 62.0 * bits_64
else:
stock_shape = (monitor.hrf_length * monitor._stock_sample_rate,
len(self.model.variables_of_interest),
number_of_nodes, self.model.number_of_modes)
interim_stock_shape = (1.0 / (2.0**-2 * self.integrator.dt),
len(self.model.variables_of_interest),
number_of_nodes,
self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
memreq += numpy.prod(interim_stock_shape) * bits_64
if psutil and memreq > psutil.virtual_memory().total:
self.log.warning(
"There may be insufficient memory for this simulation.")
self._memory_requirement_guess = magic_number * memreq
msg = "Memory requirement estimate: simulation will need about %.1f MB"
self.log.info(msg, self._memory_requirement_guess / 2**20)
def _census_memory_requirement(self):
"""
Guesstimate the memory required for this simulator.
Guesstimate is based on a census of the dominant arrays after the
simulator has been configured.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
memreq = self.history.nbytes
try:
memreq += self.surface.triangles.nbytes * 2
memreq += self.surface.vertices.nbytes * 2
memreq += self.surface.region_mapping.nbytes * self.number_of_nodes * 8. * 4 # region_average, region_sum
memreq += self.surface.local_connectivity.matrix.nnz * 8
except AttributeError:
pass
for monitor in self.monitors:
memreq += monitor._stock.nbytes
if isinstance(monitor, monitors.Bold):
memreq += monitor._interim_stock.nbytes
if psutil and memreq > psutil.virtual_memory().total:
self.log.warning("Memory estimate exceeds total available RAM.")
self._memory_requirement_census = magic_number * memreq
# import pdb; pdb.set_trace()
msg = "Memory requirement census: simulation will need about %.1f MB"
self.log.info(msg % (self._memory_requirement_census / 1048576.0))
def _guesstimate_runtime(self):
"""
Estimate the runtime for this simulator.
Spread in parallel executions of larger arrays means this will be an over-estimation,
or rather a single threaded estimation...
Different choice of integrators and monitors has an additional effect,
on the magic number though relatively minor
"""
magic_number = 6.57e-06 # seconds
self._runtime = (magic_number * self.number_of_nodes *
self.model.nvar * self.model.number_of_modes *
self.simulation_length / self.integrator.dt)
msg = "Simulation runtime should be about %0.3f seconds"
self.log.info(msg, self._runtime)
def _calculate_storage_requirement(self):
"""
Calculate the storage requirement for the simulator, configured with
models, monitors, etc being run for a particular simulation length.
While this is only approximate, it is far more reliable/accurate than
the memory and runtime guesstimates.
"""
self.log.info("Calculating storage requirement for ...")
strgreq = 0
for monitor in self.monitors:
# Avoid division by zero for monitor not yet configured
# (in framework this is executed, when only preconfigure has been called):
current_period = monitor.period or self.integrator.dt
strgreq += (TvbProfile.current.MAGIC_NUMBER *
self.simulation_length * self.number_of_nodes *
self.model.nvar * self.model.number_of_modes /
current_period)
self.log.info("Calculated storage requirement for simulation: %d " %
int(strgreq))
self._storage_requirement = int(strgreq)
def run(self, **kwds):
"""Convenience method to call the simulator with **kwds and collect output data."""
ts, xs = [], []
for _ in self.monitors:
ts.append([])
xs.append([])
wall_time_start = time.time()
for data in self(**kwds):
for tl, xl, t_x in zip(ts, xs, data):
if t_x is not None:
t, x = t_x
tl.append(t)
xl.append(x)
elapsed_wall_time = time.time() - wall_time_start
self.log.info("%.3f s elapsed, %.3fx real time", elapsed_wall_time,
elapsed_wall_time * 1e3 / self.simulation_length)
for i in range(len(ts)):
ts[i] = numpy.array(ts[i])
xs[i] = numpy.array(xs[i])
return list(zip(ts, xs))
import tvb.simulator.coupling as coupling
import tvb.simulator.integrators as integrators
import tvb.simulator.monitors as monitors
import tvb.datatypes.connectivity as connectivity
import tvb.datatypes.equations as equations
import tvb.datatypes.patterns as patterns
##----------------------------------------------------------------------------##
##- Perform the simulation -##
##----------------------------------------------------------------------------##
LOG.info("Configuring...")
#Initialise a Model, Coupling, and Connectivity.
oscilator = models.Generic2dOscillator() #ReducedSetHindmarshRose() #
white_matter = connectivity.Connectivity()
white_matter.speed = numpy.array([4.0])
white_matter_coupling = coupling.Linear(a=0.0126)
#Initialise an Integrator
heunint = integrators.HeunDeterministic(dt=2**-4)
#Initialise some Monitors with period in physical time
momo = monitors.TemporalAverage(period=1.0) #1000Hz
mama = monitors.Bold(period=500) #defaults to one data point every 2s
#Bundle them
what_to_watch = (momo, mama)
self.pp_ax.scatter(x, y, s=42, c='g', marker='o', edgecolor=None)
self.pp_ax.plot(traj[:, svx_ind, 0, self.mode],
traj[:, svy_ind, 0, self.mode])
#Plot the selected state variable trajectories as a function of time
self.pp_splt.plot(numpy.arange(TRAJ_STEPS+1) * self.integrator.dt,
traj[:, :, 0, self.mode])
pylab.draw()
def click_trajectory(self, event):
"""
This method captures mouse clicks on the phase-plane and then uses the
plot_trajectory() method to generate a sample trajectory.
"""
if event.inaxes is self.pp_ax:
x, y = event.xdata, event.ydata
LOG.info('trajectory starting at (%f, %f)', x, y)
self.plot_trajectory(x, y)
if __name__ == "__main__":
# Do some stuff that tests or makes use of this module...
LOG.info("Testing %s module..." % __file__)
MODEL = models_module.Generic2dOscillator()
ppi_fig = PhasePlaneInteractive(model = MODEL)
ppi_fig.show()
class PhasePlaneInteractive(HasTraits):
"""
The GUI for the interactive phase-plane viewer provides sliders for setting:
- The value of all parameters of the Model.
- The extent of the axes.
- A fixed value for the state-variables which aren't currently selected.
- The noise strength, if a stocahstic integrator is specified.
and radio buttons for selecting:
- Which state-variables to show on each axis.
- Which mode to show, if the Model has them.
Clicking on the phase-plane will generate a sample trajectory, originating
from where you clicked.
"""
model = Attr(
field_type=models_module.Model,
label="Model",
default=models_module.Generic2dOscillator(),
doc="""An instance of the local dynamic model to be investigated with
PhasePlaneInteractive.""")
integrator = Attr(
field_type=integrators_module.Integrator,
label="Integrator",
default=integrators_module.RungeKutta4thOrderDeterministic(),
doc="""The integration scheme used to for generating sample
trajectories on the phase-plane. NOTE: This is not used for generating
the phase-plane itself, ie the vector field and nulclines.""")
exclude_sliders = List(of=str)
def __init__(self, **kwargs):
"""
Initialise based on provided keywords or their traited defaults. Also,
initialise the place-holder attributes that aren't filled until the
show() method is called.
"""
super(PhasePlaneInteractive, self).__init__(**kwargs)
LOG.debug(str(kwargs))
#figure
self.ipp_fig = None
#phase-plane
self.pp_ax = None
self.X = None
self.Y = None
self.U = None
self.V = None
self.UVmag = None
self.nullcline_x = None
self.nullcline_y = None
self.pp_quivers = None
#Current state
self.svx = None
self.svy = None
self.default_sv = None
self.no_coupling = None
self.mode = None
#Selectors
self.state_variable_x = None
self.state_variable_y = None
self.mode_selector = None
#Sliders
self.param_sliders = None
self.axes_range_sliders = None
self.sv_sliders = None
self.noise_slider = None
#Reset buttons
self.reset_param_button = None
self.reset_sv_button = None
self.reset_axes_button = None
self.reset_noise_button = None
self.reset_seed_button = None
def show(self):
""" Generate the interactive phase-plane figure. """
model_name = self.model.__class__.__name__
msg = "Generating an interactive phase-plane plot for %s"
LOG.info(msg % model_name)
#Make sure the model is fully configured...
self.model.configure()
#Setup the inital(current) state
try:
self.svx = self.model.state_variables[
0] #x-axis: 1st state variable
self.svy = self.model.state_variables[
1] #y-axis: 2nd state variable
except:
import pdb
pdb.set_trace()
self.svx = self.model.state_variables[
'S1'] #x-axis: 1st state variable
self.svy = self.model.state_variables[
'S2'] #y-axis: 2nd state variable
self.mode = 0
self.set_state_vector()
#Make the figure:
self.create_figure()
#Selectors
self.add_state_variable_selector()
self.add_mode_selector()
#Sliders
self.add_axes_range_sliders()
self.add_state_variable_sliders()
self.add_param_sliders()
if isinstance(self.integrator,
integrators_module.IntegratorStochastic):
if self.integrator.noise.ntau > 0.0:
self.integrator.noise.configure_coloured(
self.integrator.dt,
(1, self.model.nvar, 1, self.model.number_of_modes))
else:
self.integrator.noise.configure_white(
self.integrator.dt,
(1, self.model.nvar, 1, self.model.number_of_modes))
self.add_noise_slider()
self.add_reset_noise_button()
self.add_reset_seed_button()
#Reset buttons
self.add_reset_param_button()
self.add_reset_sv_button()
self.add_reset_axes_button()
#Calculate the phase plane
self.set_mesh_grid()
self.calc_phase_plane()
#Plot phase plane
self.plot_phase_plane()
# add mouse handler for trajectory clicking
self.ipp_fig.canvas.mpl_connect('button_press_event',
self.click_trajectory)
#import pdb; pdb.set_trace()
pylab.show()
##------------------------------------------------------------------------##
##----------------- Functions for building the figure --------------------##
##------------------------------------------------------------------------##
def create_figure(self):
""" Create the figure and phase-plane axes. """
#Figure and main phase-plane axes
model_name = self.model.__class__.__name__
integrator_name = self.integrator.__class__.__name__
figsize = 10, 5
try:
figure_window_title = "Interactive phase-plane: " + model_name
figure_window_title += " -- %s" % integrator_name
self.ipp_fig = pylab.figure(num=figure_window_title,
figsize=figsize,
facecolor=BACKGROUNDCOLOUR,
edgecolor=EDGECOLOUR)
except ValueError:
LOG.info("My life would be easier if you'd update your PyLab...")
self.ipp_fig = pylab.figure(num=42,
figsize=figsize,
facecolor=BACKGROUNDCOLOUR,
edgecolor=EDGECOLOUR)
self.pp_ax = self.ipp_fig.add_axes([0.265, 0.2, 0.5, 0.75])
self.pp_splt = self.ipp_fig.add_subplot(212)
self.ipp_fig.subplots_adjust(left=0.265,
bottom=0.02,
right=0.765,
top=0.3,
wspace=0.1,
hspace=None)
self.pp_splt.set_prop_cycle(color=get_color(self.model.nvar))
self.pp_splt.plot(
numpy.arange(TRAJ_STEPS + 1) * self.integrator.dt,
numpy.zeros((TRAJ_STEPS + 1, self.model.nvar)))
if hasattr(self.pp_splt, 'autoscale'):
self.pp_splt.autoscale(enable=True, axis='y', tight=True)
self.pp_splt.legend(self.model.state_variables)
def add_state_variable_selector(self):
"""
Generate radio selector buttons to set which state variable is displayed
on the x and y axis of the phase-plane plot.
"""
svx_ind = self.model.state_variables.index(self.svx)
svy_ind = self.model.state_variables.index(self.svy)
#State variable for the x axis
pos_shp = [0.07, 0.05, 0.065, 0.12 + 0.006 * self.model.nvar]
rax = self.ipp_fig.add_axes(pos_shp,
facecolor=AXCOLOUR,
title="x-axis")
self.state_variable_x = widgets.RadioButtons(
rax, tuple(self.model.state_variables), active=svx_ind)
self.state_variable_x.on_clicked(self.update_svx)
#State variable for the y axis
pos_shp = [0.14, 0.05, 0.065, 0.12 + 0.006 * self.model.nvar]
rax = self.ipp_fig.add_axes(pos_shp,
facecolor=AXCOLOUR,
title="y-axis")
self.state_variable_y = widgets.RadioButtons(
rax, tuple(self.model.state_variables), active=svy_ind)
self.state_variable_y.on_clicked(self.update_svy)
def add_mode_selector(self):
"""
Add a radio button to the figure for selecting which mode of the model
should be displayed.
"""
pos_shp = [0.02, 0.07, 0.04, 0.1 + 0.002 * self.model.number_of_modes]
rax = self.ipp_fig.add_axes(pos_shp, facecolor=AXCOLOUR, title="Mode")
mode_tuple = tuple(range(self.model.number_of_modes))
self.mode_selector = widgets.RadioButtons(rax, mode_tuple, active=0)
self.mode_selector.on_clicked(self.update_mode)
def add_axes_range_sliders(self):
"""
Add sliders to the figure to allow the phase-planes axes to be set.
"""
self.axes_range_sliders = dict()
default_range_x = (self.model.state_variable_range[self.svx][1] -
self.model.state_variable_range[self.svx][0])
default_range_y = (self.model.state_variable_range[self.svy][1] -
self.model.state_variable_range[self.svy][0])
min_val_x = self.model.state_variable_range[
self.svx][0] - 4.0 * default_range_x
max_val_x = self.model.state_variable_range[
self.svx][1] + 4.0 * default_range_x
min_val_y = self.model.state_variable_range[
self.svy][0] - 4.0 * default_range_y
max_val_y = self.model.state_variable_range[
self.svy][1] + 4.0 * default_range_y
sax = self.ipp_fig.add_axes([0.04, 0.835, 0.125, 0.025],
facecolor=AXCOLOUR)
sl_x_min = widgets.Slider(
sax,
"xlo",
min_val_x,
max_val_x,
valinit=self.model.state_variable_range[self.svx][0])
sl_x_min.on_changed(self.update_range)
sax = self.ipp_fig.add_axes([0.04, 0.8, 0.125, 0.025],
facecolor=AXCOLOUR)
sl_x_max = widgets.Slider(
sax,
"xhi",
min_val_x,
max_val_x,
valinit=self.model.state_variable_range[self.svx][1])
sl_x_max.on_changed(self.update_range)
sax = self.ipp_fig.add_axes([0.04, 0.765, 0.125, 0.025],
facecolor=AXCOLOUR)
sl_y_min = widgets.Slider(
sax,
"ylo",
min_val_y,
max_val_y,
valinit=self.model.state_variable_range[self.svy][0])
sl_y_min.on_changed(self.update_range)
sax = self.ipp_fig.add_axes([0.04, 0.73, 0.125, 0.025],
facecolor=AXCOLOUR)
sl_y_max = widgets.Slider(
sax,
"yhi",
min_val_y,
max_val_y,
valinit=self.model.state_variable_range[self.svy][1])
sl_y_max.on_changed(self.update_range)
self.axes_range_sliders["sl_x_min"] = sl_x_min
self.axes_range_sliders["sl_x_max"] = sl_x_max
self.axes_range_sliders["sl_y_min"] = sl_y_min
self.axes_range_sliders["sl_y_max"] = sl_y_max
def add_state_variable_sliders(self):
"""
Add sliders to the figure to allow default values for the models state
variable to be set.
"""
msv_range = self.model.state_variable_range
offset = 0.0
self.sv_sliders = dict()
for sv in range(self.model.nvar):
offset += 0.035
pos_shp = [0.04, 0.6 - offset, 0.125, 0.025]
sax = self.ipp_fig.add_axes(pos_shp, facecolor=AXCOLOUR)
sv_str = self.model.state_variables[sv]
self.sv_sliders[sv_str] = widgets.Slider(
sax,
sv_str,
msv_range[sv_str][0],
msv_range[sv_str][1],
valinit=self.default_sv[sv, 0, 0])
self.sv_sliders[sv_str].on_changed(self.update_state_variables)
# Traited paramaters as sliders
def add_param_sliders(self):
"""
Add sliders to the figure to allow the models parameters to be set.
"""
offset = 0.0
self.param_sliders = dict()
# import pdb; pdb.set_trace()
for param_name in type(self.model).declarative_attrs:
if self.exclude_sliders is not None and param_name in self.exclude_sliders:
continue
param_def = getattr(type(self.model), param_name)
if not isinstance(param_def,
NArray) or not param_def.dtype == numpy.float:
continue
param_range = param_def.domain
if param_range is None:
continue
offset += 0.035
sax = self.ipp_fig.add_axes([0.825, 0.865 - offset, 0.125, 0.025],
facecolor=AXCOLOUR)
param_value = getattr(self.model, param_name)[0]
self.param_sliders[param_name] = widgets.Slider(
sax,
param_name,
param_range.lo,
param_range.hi,
valinit=param_value)
self.param_sliders[param_name].on_changed(self.update_parameters)
def add_noise_slider(self):
"""
Add a slider to the figure to allow the integrators noise strength to
be set.
"""
pos_shp = [0.825, 0.1, 0.125, 0.025]
sax = self.ipp_fig.add_axes(pos_shp, facecolor=AXCOLOUR)
self.noise_slider = widgets.Slider(sax,
"Log Noise",
-9.0,
1.0,
valinit=self.integrator.noise.nsig)
self.noise_slider.on_changed(self.update_noise)
def add_reset_param_button(self):
"""
Add a button to the figure for reseting the model parameter values to
their original values.
"""
bax = self.ipp_fig.add_axes([0.825, 0.865, 0.125, 0.04])
self.reset_param_button = widgets.Button(bax,
'Reset parameters',
color=BUTTONCOLOUR,
hovercolor=HOVERCOLOUR)
def reset_parameters(event):
for param_slider in self.param_sliders:
self.param_sliders[param_slider].reset()
self.reset_param_button.on_clicked(reset_parameters)
def add_reset_sv_button(self):
"""
Add a button to the figure for reseting the model state variables to
their default values.
"""
bax = self.ipp_fig.add_axes([0.04, 0.60, 0.125, 0.04])
self.reset_sv_button = widgets.Button(bax,
'Reset state-variables',
color=BUTTONCOLOUR,
hovercolor=HOVERCOLOUR)
def reset_state_variables(event):
for svsl in self.sv_sliders.values():
svsl.reset()
self.reset_sv_button.on_clicked(reset_state_variables)
def add_reset_noise_button(self):
"""
Add a button to the figure for reseting the noise to its default value.
"""
bax = self.ipp_fig.add_axes([0.825, 0.135, 0.125, 0.04])
self.reset_noise_button = widgets.Button(bax,
'Reset noise strength',
color=BUTTONCOLOUR,
hovercolor=HOVERCOLOUR)
def reset_noise(event):
self.noise_slider.reset()
self.reset_noise_button.on_clicked(reset_noise)
def add_reset_seed_button(self):
"""
Add a button to the figure for reseting the random number generator to
its intial state. For reproducible noise...
"""
bax = self.ipp_fig.add_axes([0.825, 0.05, 0.125, 0.04])
self.reset_seed_button = widgets.Button(bax,
'Reset random stream',
color=BUTTONCOLOUR,
hovercolor=HOVERCOLOUR)
def reset_seed(event):
self.integrator.noise.trait["random_stream"].reset()
self.reset_seed_button.on_clicked(reset_seed)
def add_reset_axes_button(self):
"""
Add a button to the figure for reseting the phase-plane axes to their
default ranges.
"""
bax = self.ipp_fig.add_axes([0.04, 0.87, 0.125, 0.04])
self.reset_axes_button = widgets.Button(bax,
'Reset axes',
color=BUTTONCOLOUR,
hovercolor=HOVERCOLOUR)
def reset_ranges(event):
self.axes_range_sliders["sl_x_min"].reset()
self.axes_range_sliders["sl_x_max"].reset()
self.axes_range_sliders["sl_y_min"].reset()
self.axes_range_sliders["sl_y_max"].reset()
self.reset_axes_button.on_clicked(reset_ranges)
##------------------------------------------------------------------------##
##------------------- Functions for updating the figure ------------------##
##------------------------------------------------------------------------##
#NOTE: All the ax.set_xlim, poly.xy, etc, garbage below is fragile. It works
# at the moment, but there are currently bugs in Slider and the hackery
# below takes these into account... If the bugs are fixed/changed then
# this could break. As an example, the Slider doc says poly is a
# Rectangle, but it's actually a Polygon. The Slider set_val method
# assumes a Rectangle even though this is not the case, so the array
# Slider.poly.xy is corrupted by that method. The corruption isn't
# visible in the plot, which is probably why it hasn't been fixed...
def update_xrange_sliders(self):
"""
A hacky update of the x-axis range sliders that is called when the
state-variable selected for the x-axis is changed.
"""
default_range_x = (self.model.state_variable_range[self.svx][1] -
self.model.state_variable_range[self.svx][0])
min_val_x = self.model.state_variable_range[
self.svx][0] - 4.0 * default_range_x
max_val_x = self.model.state_variable_range[
self.svx][1] + 4.0 * default_range_x
self.axes_range_sliders[
"sl_x_min"].valinit = self.model.state_variable_range[self.svx][0]
self.axes_range_sliders["sl_x_min"].valmin = min_val_x
self.axes_range_sliders["sl_x_min"].valmax = max_val_x
self.axes_range_sliders["sl_x_min"].ax.set_xlim(min_val_x, max_val_x)
self.axes_range_sliders["sl_x_min"].poly.axes.set_xlim(
min_val_x, max_val_x)
self.axes_range_sliders["sl_x_min"].poly.xy[[0, 1], 0] = min_val_x
self.axes_range_sliders["sl_x_min"].vline.set_data(([
self.axes_range_sliders["sl_x_min"].valinit,
self.axes_range_sliders["sl_x_min"].valinit
], [0, 1]))
self.axes_range_sliders[
"sl_x_max"].valinit = self.model.state_variable_range[self.svx][1]
self.axes_range_sliders["sl_x_max"].valmin = min_val_x
self.axes_range_sliders["sl_x_max"].valmax = max_val_x
self.axes_range_sliders["sl_x_max"].ax.set_xlim(min_val_x, max_val_x)
self.axes_range_sliders["sl_x_max"].poly.axes.set_xlim(
min_val_x, max_val_x)
self.axes_range_sliders["sl_x_max"].poly.xy[[0, 1], 0] = min_val_x
self.axes_range_sliders["sl_x_max"].vline.set_data(([
self.axes_range_sliders["sl_x_max"].valinit,
self.axes_range_sliders["sl_x_max"].valinit
], [0, 1]))
self.axes_range_sliders["sl_x_min"].reset()
self.axes_range_sliders["sl_x_max"].reset()
def update_yrange_sliders(self):
"""
A hacky update of the y-axis range sliders that is called when the
state-variable selected for the y-axis is changed.
"""
#svy_ind = self.model.state_variables.index(self.svy)
default_range_y = (self.model.state_variable_range[self.svy][1] -
self.model.state_variable_range[self.svy][0])
min_val_y = self.model.state_variable_range[
self.svy][0] - 4.0 * default_range_y
max_val_y = self.model.state_variable_range[
self.svy][1] + 4.0 * default_range_y
self.axes_range_sliders[
"sl_y_min"].valinit = self.model.state_variable_range[self.svy][0]
self.axes_range_sliders["sl_y_min"].valmin = min_val_y
self.axes_range_sliders["sl_y_min"].valmax = max_val_y
self.axes_range_sliders["sl_y_min"].ax.set_xlim(min_val_y, max_val_y)
self.axes_range_sliders["sl_y_min"].poly.axes.set_xlim(
min_val_y, max_val_y)
self.axes_range_sliders["sl_y_min"].poly.xy[[0, 1], 0] = min_val_y
self.axes_range_sliders["sl_y_min"].vline.set_data(([
self.axes_range_sliders["sl_y_min"].valinit,
self.axes_range_sliders["sl_y_min"].valinit
], [0, 1]))
self.axes_range_sliders[
"sl_y_max"].valinit = self.model.state_variable_range[self.svy][1]
self.axes_range_sliders["sl_y_max"].valmin = min_val_y
self.axes_range_sliders["sl_y_max"].valmax = max_val_y
self.axes_range_sliders["sl_y_max"].ax.set_xlim(min_val_y, max_val_y)
self.axes_range_sliders["sl_y_max"].poly.axes.set_xlim(
min_val_y, max_val_y)
self.axes_range_sliders["sl_y_max"].poly.xy[[0, 1], 0] = min_val_y
self.axes_range_sliders["sl_y_max"].vline.set_data(([
self.axes_range_sliders["sl_y_max"].valinit,
self.axes_range_sliders["sl_y_max"].valinit
], [0, 1]))
self.axes_range_sliders["sl_y_min"].reset()
self.axes_range_sliders["sl_y_max"].reset()
def update_svx(self, label):
"""
Update state variable used for x-axis based on radio buttton selection.
"""
self.svx = label
self.update_xrange_sliders()
self.set_mesh_grid()
self.calc_phase_plane()
self.update_phase_plane()
def update_svy(self, label):
"""
Update state variable used for y-axis based on radio buttton selection.
"""
self.svy = label
self.update_yrange_sliders()
self.set_mesh_grid()
self.calc_phase_plane()
self.update_phase_plane()
def update_mode(self, label):
""" Update the visualised mode based on radio button selection. """
self.mode = label
self.update_phase_plane()
def update_parameters(self, val):
"""
Update model parameters based on the current parameter slider values.
NOTE: Haven't figured out how to update independantly, so just update
everything.
"""
#TODO: Grab caller and use val directly, ie independent parameter update.
#import pdb; pdb.set_trace()
for param in self.param_sliders:
setattr(self.model, param,
numpy.array([self.param_sliders[param].val]))
self.model.update_derived_parameters()
self.calc_phase_plane()
self.update_phase_plane()
def update_noise(self, nsig):
""" Update integrator noise based on the noise slider value. """
self.integrator.noise.nsig = numpy.array([
10**nsig,
])
def update_range(self, val):
"""
Update the axes ranges based on the current axes slider values.
NOTE: Haven't figured out how to update independantly, so just update
everything.
"""
#TODO: Grab caller and use val directly, ie independent range update.
self.axes_range_sliders["sl_x_min"].ax.set_facecolor(AXCOLOUR)
self.axes_range_sliders["sl_x_max"].ax.set_facecolor(AXCOLOUR)
self.axes_range_sliders["sl_y_min"].ax.set_facecolor(AXCOLOUR)
self.axes_range_sliders["sl_y_max"].ax.set_facecolor(AXCOLOUR)
if (self.axes_range_sliders["sl_x_min"].val >=
self.axes_range_sliders["sl_x_max"].val):
LOG.error("X-axis min must be less than max...")
self.axes_range_sliders["sl_x_min"].ax.set_facecolor("Red")
self.axes_range_sliders["sl_x_max"].ax.set_facecolor("Red")
return
if (self.axes_range_sliders["sl_y_min"].val >=
self.axes_range_sliders["sl_y_max"].val):
LOG.error("Y-axis min must be less than max...")
self.axes_range_sliders["sl_y_min"].ax.set_facecolor("Red")
self.axes_range_sliders["sl_y_max"].ax.set_facecolor("Red")
return
msv_range = self.model.state_variable_range
msv_range[self.svx][0] = self.axes_range_sliders["sl_x_min"].val
msv_range[self.svx][1] = self.axes_range_sliders["sl_x_max"].val
msv_range[self.svy][0] = self.axes_range_sliders["sl_y_min"].val
msv_range[self.svy][1] = self.axes_range_sliders["sl_y_max"].val
self.set_mesh_grid()
self.calc_phase_plane()
self.update_phase_plane()
def update_phase_plane(self):
""" Clear the axes and redraw the phase-plane. """
self.pp_ax.clear()
self.pp_splt.clear()
self.pp_splt.set_prop_cycle('color', get_color(self.model.nvar))
self.pp_splt.plot(
numpy.arange(TRAJ_STEPS + 1) * self.integrator.dt,
numpy.zeros((TRAJ_STEPS + 1, self.model.nvar)))
if hasattr(self.pp_splt, 'autoscale'):
self.pp_splt.autoscale(enable=True, axis='y', tight=True)
self.pp_splt.legend(self.model.state_variables)
self.plot_phase_plane()
def update_state_variables(self, val):
"""
Update the default state-variable values, used for non-visualised state
variables, based of the current slider values.
"""
for sv in self.sv_sliders:
k = self.model.state_variables.index(sv)
self.default_sv[k] = self.sv_sliders[sv].val
self.calc_phase_plane()
self.update_phase_plane()
def set_mesh_grid(self):
"""
Generate the phase-plane gridding based on currently selected
state-variables and their range values.
"""
xlo = self.model.state_variable_range[self.svx][0]
xhi = self.model.state_variable_range[self.svx][1]
ylo = self.model.state_variable_range[self.svy][0]
yhi = self.model.state_variable_range[self.svy][1]
self.X = numpy.mgrid[xlo:xhi:(NUMBEROFGRIDPOINTS * 1j)]
self.Y = numpy.mgrid[ylo:yhi:(NUMBEROFGRIDPOINTS * 1j)]
def set_state_vector(self):
"""
Set up a vector containing the default state-variable values and create
a filler(all zeros) for the coupling arg of the Model's dfun method.
This method is called once at initialisation (show()).
"""
#import pdb; pdb.set_trace()
sv_mean = numpy.array([
self.model.state_variable_range[key].mean()
for key in self.model.state_variables
])
sv_mean = sv_mean.reshape((self.model.nvar, 1, 1))
self.default_sv = sv_mean.repeat(self.model.number_of_modes, axis=2)
self.no_coupling = numpy.zeros(
(self.model.nvar, 1, self.model.number_of_modes))
def calc_phase_plane(self):
""" Calculate the vector field. """
svx_ind = self.model.state_variables.index(self.svx)
svy_ind = self.model.state_variables.index(self.svy)
#Calculate the vector field discretely sampled at a grid of points
grid_point = self.default_sv.copy()
self.U = numpy.zeros((NUMBEROFGRIDPOINTS, NUMBEROFGRIDPOINTS,
self.model.number_of_modes))
self.V = numpy.zeros((NUMBEROFGRIDPOINTS, NUMBEROFGRIDPOINTS,
self.model.number_of_modes))
for ii in range(NUMBEROFGRIDPOINTS):
grid_point[svy_ind] = self.Y[ii]
for jj in range(NUMBEROFGRIDPOINTS):
#import pdb; pdb.set_trace()
grid_point[svx_ind] = self.X[jj]
d = self.model.dfun(grid_point, self.no_coupling)
for kk in range(self.model.number_of_modes):
self.U[ii, jj, kk] = d[svx_ind, 0, kk]
self.V[ii, jj, kk] = d[svy_ind, 0, kk]
#Colours for the vector field quivers
#self.UVmag = numpy.sqrt(self.U**2 + self.V**2)
#import pdb; pdb.set_trace()
if numpy.isnan(self.U).any() or numpy.isnan(self.V).any():
LOG.error("NaN")
def plot_phase_plane(self):
""" Plot the vector field and its nullclines. """
# Set title and axis labels
model_name = self.model.__class__.__name__
self.pp_ax.set(title=model_name + " mode " + str(self.mode))
self.pp_ax.set(xlabel="State Variable " + self.svx)
self.pp_ax.set(ylabel="State Variable " + self.svy)
#import pdb; pdb.set_trace()
#Plot a discrete representation of the vector field
if numpy.all(self.U[:, :, self.mode] + self.V[:, :, self.mode] == 0):
self.pp_ax.set(title=model_name + " mode " + str(self.mode) +
": NO MOTION IN THIS PLANE")
X, Y = numpy.meshgrid(self.X, self.Y)
self.pp_quivers = self.pp_ax.scatter(X, Y, s=8, marker=".", c="k")
else:
self.pp_quivers = self.pp_ax.quiver(
self.X,
self.Y,
self.U[:, :, self.mode],
self.V[:, :, self.mode],
#self.UVmag[:, :, self.mode],
width=0.001,
headwidth=8)
#Plot the nullclines
self.nullcline_x = self.pp_ax.contour(self.X,
self.Y,
self.U[:, :, self.mode], [0],
colors="r")
self.nullcline_y = self.pp_ax.contour(self.X,
self.Y,
self.V[:, :, self.mode], [0],
colors="g")
pylab.draw()
def plot_trajectory(self, x, y):
"""
Plot a sample trajectory, starting at the position x,y in the
phase-plane. This method is called as a result of a mouse click on the
phase-plane.
"""
svx_ind = self.model.state_variables.index(self.svx)
svy_ind = self.model.state_variables.index(self.svy)
print(svx_ind)
#Calculate an example trajectory
state = self.default_sv.copy()
self.integrator.clamped_state_variable_indices = numpy.setdiff1d(
numpy.r_[:len(self.model.state_variables)], numpy.r_[svx_ind,
svy_ind])
self.integrator.clamped_state_variable_values = self.default_sv[
self.integrator.clamped_state_variable_indices]
state[svx_ind] = x
state[svy_ind] = y
scheme = self.integrator.scheme
traj = numpy.zeros(
(TRAJ_STEPS + 1, self.model.nvar, 1, self.model.number_of_modes))
traj[0, :] = state
for step in range(TRAJ_STEPS):
#import pdb; pdb.set_trace()
state = scheme(state, self.model.dfun, self.no_coupling, 0.0, 0.0)
traj[step + 1, :] = state
self.pp_ax.scatter(x, y, s=42, c='g', marker='o', edgecolor=None)
self.pp_ax.plot(traj[:, svx_ind, 0, self.mode], traj[:, svy_ind, 0,
self.mode])
#Plot the selected state variable trajectories as a function of time
self.pp_splt.plot(
numpy.arange(TRAJ_STEPS + 1) * self.integrator.dt, traj[:, :, 0,
self.mode])
pylab.draw()
def click_trajectory(self, event):
"""
This method captures mouse clicks on the phase-plane and then uses the
plot_trajectory() method to generate a sample trajectory.
"""
if event.inaxes is self.pp_ax:
x, y = event.xdata, event.ydata
LOG.info('trajectory starting at (%f, %f)', x, y)
self.plot_trajectory(x, y)
import tvb.simulator.coupling as coupling
import tvb.simulator.integrators as integrators
import tvb.simulator.monitors as monitors
import tvb.datatypes.connectivity as connectivity
import tvb.datatypes.surfaces as surfaces
import tvb.datatypes.equations as equations
import tvb.datatypes.patterns as patterns
##----------------------------------------------------------------------------##
##- Perform the simulation -##
##----------------------------------------------------------------------------##
LOG.info("Configuring...")
#Initialise a Model, Coupling, and Connectivity.
oscilator = models.Generic2dOscillator()
white_matter = connectivity.Connectivity()
white_matter.speed = 4.0
white_matter_coupling = coupling.Linear(a=-2**-9)
#Initialise an Integrator
heunint = integrators.HeunDeterministic(dt=2**-4)
#Initialise some Monitors with period in physical time
mon_tavg = monitors.TemporalAverage(period=2**-2)
mon_savg = monitors.SpatialAverage(period=2**-2)
mon_eeg = monitors.EEG(period=2**-2)
#Bundle them
what_to_watch = (mon_tavg, mon_savg, mon_eeg)
class Simulator(HasTraits):
"""A Simulator assembles components required to perform simulations."""
connectivity = Attr(
field_type=connectivity.Connectivity,
label="Long-range connectivity",
default=None,
required=True,
doc="""A tvb.datatypes.Connectivity object which contains the
structural long-range connectivity data (i.e., white-matter tracts). In
combination with the ``Long-range coupling function`` it defines the inter-regional
connections. These couplings undergo a time delay via signal propagation
with a propagation speed of ``Conduction Speed``""")
conduction_speed = Float(
label="Conduction Speed",
default=3.0,
required=False,
# range=basic.Range(lo=0.01, hi=100.0, step=1.0),
doc="""Conduction speed for ``Long-range connectivity`` (mm/ms)""")
coupling = Attr(
field_type=coupling.Coupling,
label="Long-range coupling function",
default=coupling.Linear(),
required=True,
doc="""The coupling function is applied to the activity propagated
between regions by the ``Long-range connectivity`` before it enters the local
dynamic equations of the Model. Its primary purpose is to 'rescale' the
incoming activity to a level appropriate to Model.""")
surface: cortex.Cortex = Attr(
field_type=cortex.Cortex,
label="Cortical surface",
default=None,
required=False,
doc="""By default, a Cortex object which represents the
cortical surface defined by points in the 3D physical space and their
neighborhood relationship. In the current TVB version, when setting up a
surface-based simulation, the option to configure the spatial spread of
the ``Local Connectivity`` is available.""")
stimulus = Attr(
field_type=patterns.SpatioTemporalPattern,
label="Spatiotemporal stimulus",
default=None,
required=False,
doc=
"""A ``Spatiotemporal stimulus`` can be defined at the region or surface level.
It's composed of spatial and temporal components. For region defined stimuli
the spatial component is just the strength with which the temporal
component is applied to each region. For surface defined stimuli, a
(spatial) function, with finite-support, is used to define the strength
of the stimuli on the surface centred around one or more focal points.
In the current version of TVB, stimuli are applied to the first state
variable of the ``Local dynamic model``.""")
model: Model = Attr(
field_type=models.Model,
label="Local dynamic model",
default=models.Generic2dOscillator(),
required=True,
doc="""A tvb.simulator.Model object which describe the local dynamic
equations, their parameters, and, to some extent, where connectivity
(local and long-range) enters and which state-variables the Monitors
monitor. By default the 'Generic2dOscillator' model is used. Read the
Scientific documentation to learn more about this model.""")
integrator = Attr(field_type=integrators.Integrator,
label="Integration scheme",
default=integrators.HeunDeterministic(),
required=True,
doc="""A tvb.simulator.Integrator object which is
an integration scheme with supporting attributes such as
integration step size and noise specification for stochastic
methods. It is used to compute the time courses of the model state
variables.""")
initial_conditions = NArray(
label="Initial Conditions",
required=False,
doc="""Initial conditions from which the simulation will begin. By
default, random initial conditions are provided. Needs to be the same shape
as simulator 'history', ie, initial history function which defines the
minimal initial state of the network with time delays before time t=0.
If the number of time points in the provided array is insufficient the
array will be padded with random values based on the 'state_variables_range'
attribute.""")
monitors = List(
of=monitors.Monitor,
label="Monitor(s)",
default=(monitors.TemporalAverage(), ),
doc="""A tvb.simulator.Monitor or a list of tvb.simulator.Monitor
objects that 'know' how to record relevant data from the simulation. Two
main types exist: 1) simple, spatial and temporal, reductions (subsets
or averages); 2) physiological measurements, such as EEG, MEG and fMRI.
By default the Model's specified variables_of_interest are returned,
temporally downsampled from the raw integration rate to a sample rate of
1024Hz.""")
simulation_length = Float(
label="Simulation Length (ms, s, m, h)",
default=1000.0, # ie 1 second
required=True,
doc="""The length of a simulation (default in milliseconds).""")
backend = ReferenceBackend()
history = None # type: SparseHistory
@property
def good_history_shape(self):
"""Returns expected history shape."""
n_reg = self.connectivity.number_of_regions
shape = self.connectivity.horizon, len(
self.model.state_variables), n_reg, self.model.number_of_modes
return shape
calls = 0
current_step = 0
number_of_nodes = None
_memory_requirement_guess = None
_memory_requirement_census = None
_storage_requirement = None
_runtime = None
integrate_next_step = None
# methods consist of
# 1) generic configure
# 2) component specific configure
# 3) loop preparation
# 4) loop step
# 5) estimations
@property
def is_surface_simulation(self):
if self.surface:
return True
return False
def configure_integration_for_model(self):
self.integrator.configure_boundaries(self.model)
if self.model.has_nonint_vars:
self.integrate_next_step = self.integrator.integrate_with_update
self.integrator. \
reconfigure_boundaries_and_clamping_for_integration_state_variables(self.model)
else:
self.integrate_next_step = self.integrator.integrate
def preconfigure(self):
"""Configure just the basic fields, so that memory can be estimated."""
self.connectivity.configure()
if self.surface:
self.surface.configure()
if self.stimulus:
self.stimulus.configure()
self.coupling.configure()
# ------- Keep this order of configurations ----
self.model.configure() # 1
self.integrator.configure() # 2
# Configure integrators' next step computation
# and state variables' boundaries and clamping,
# based on model attributes # 3
self.configure_integration_for_model()
# ----------------------------------------------
# monitors needs to be a list or tuple, even if there is only one...
if not isinstance(self.monitors, (list, tuple)):
self.monitors = [self.monitors]
# Configure monitors
for monitor in self.monitors:
monitor.configure()
self._set_number_of_nodes()
self._guesstimate_memory_requirement()
def _set_number_of_nodes(self):
# "Nodes" refers to either regions or vertices + non-cortical regions.
if self.surface is None:
self.number_of_nodes = self.connectivity.number_of_regions
self.log.info('Region simulation with %d ROI nodes',
self.number_of_nodes)
else:
self._regmap, nc, nsc = self.backend.full_region_map(
self.surface, self.connectivity)
self.number_of_nodes = nc + nsc
self.log.info(
'Surface simulation with %d vertices + %d non-cortical, %d total nodes',
nc, nsc, self.number_of_nodes)
def configure(self, full_configure=True):
"""Configure simulator and its components.
The first step of configuration is to run the configure methods of all
the Simulator's components, ie its traited attributes.
Configuration of a Simulator primarily consists of calculating the
attributes, etc, which depend on the combinations of the Simulator's
traited attributes (keyword args).
Converts delays from physical time units into integration steps
and updates attributes that depend on combinations of the 6 inputs.
Returns
-------
sim: Simulator
The configured Simulator instance.
"""
if full_configure:
# When run from GUI, preconfigure is run separately, and we want to avoid running that part twice
self.preconfigure()
self.model._spatialize_model_parameters(sim=self)
# Configure spatial component of any stimuli
self._configure_stimuli()
# Set delays, provided in physical units, in integration steps.
self.connectivity.set_idelays(self.integrator.dt)
# Reshape integrator.noise.nsig, if necessary.
if isinstance(self.integrator, integrators.IntegratorStochastic):
self._configure_integrator_noise()
# create history
# TODO refactor history impl to backend
self._configure_history()
# Configure Monitors to work with selected Model, etc...
self._configure_monitors()
# Estimate of memory usage.
self._census_memory_requirement()
# Allow user to chain configure to another call or assignment.
return self
def _prepare_local_coupling(self):
if self.surface is None:
return 0.0
return self.surface.prepare_local_coupling(self.number_of_nodes)
def _loop_compute_node_coupling(self, step):
"""Compute delayed node coupling values."""
coupling = self.coupling(step, self.history)
if self.surface is not None:
coupling = coupling[:, self._regmap]
return coupling
def _prepare_stimulus(self):
if self.stimulus is None:
stimulus = 0.0
else:
# TODO time grid wrong for continuations
time = numpy.r_[0.0:self.simulation_length:self.integrator.dt]
self.stimulus.configure_time(time.reshape((1, -1)))
stimulus = numpy.zeros((self.model.nvar, self.number_of_nodes, 1))
self.log.debug("stimulus shape is: %s", stimulus.shape)
return stimulus
def _loop_update_stimulus(self, step, stimulus):
"""Update stimulus values for current time step."""
if self.stimulus is not None:
# TODO stim_step != current step
stim_step = step - (self.current_step + 1)
stimulus[self.model.stvar, :, :] = self.stimulus(
stim_step).reshape((1, -1, 1))
def _loop_update_history(self, step, state):
"""Update history."""
if self.surface is not None and state.shape[
1] > self.connectivity.number_of_regions:
state = self.backend.surface_state_to_rois(
self._regmap, self.connectivity.number_of_regions, state)
self.history.update(step, state)
def _loop_monitor_output(self, step, state, node_coupling):
observed = self.model.observe(state)
output = [
monitor.record(
step, node_coupling if isinstance(
monitor, monitors.AfferentCoupling) else observed)
for monitor in self.monitors
]
if any(outputi is not None for outputi in output):
return output
def __call__(self,
simulation_length=None,
random_state=None,
n_steps=None):
"""
Return an iterator which steps through simulation time, generating monitor outputs.
See the run method for a convenient way to collect all output in one call.
:param simulation_length: Length of the simulation to perform in ms.
:param random_state: State of NumPy RNG to use for stochastic integration.
:param n_steps: Length of the simulation to perform in integration steps. Overrides simulation_length.
:return: Iterator over monitor outputs.
"""
self.calls += 1
if simulation_length is not None:
self.simulation_length = float(simulation_length)
# initialization
self._guesstimate_runtime()
self._calculate_storage_requirement()
# TODO a provided random_state should be used for history init
self.integrator.set_random_state(random_state)
local_coupling = self._prepare_local_coupling()
stimulus = self._prepare_stimulus()
state = self.current_state
start_step = self.current_step + 1
node_coupling = self._loop_compute_node_coupling(start_step)
# integration loop
if n_steps is None:
n_steps = int(
math.ceil(self.simulation_length / self.integrator.dt))
else:
if not numpy.issubdtype(type(n_steps), numpy.integer):
raise TypeError(
"Incorrect type for n_steps: %s, expected integer" %
type(n_steps))
for step in range(start_step, start_step + n_steps):
self._loop_update_stimulus(step, stimulus)
state = self.integrate_next_step(state, self.model, node_coupling,
local_coupling, stimulus)
self._loop_update_history(step, state)
node_coupling = self._loop_compute_node_coupling(step + 1)
output = self._loop_monitor_output(step, state, node_coupling)
if output is not None:
yield output
self.current_state = state
self.current_step = self.current_step + n_steps
def _configure_history(self, initial_conditions=None):
self.history = SparseHistory.from_simulator(self, initial_conditions)
def _configure_integrator_noise(self):
"""
This enables having noise to be state variable specific and/or to enter
only via specific brain structures, for example it we only want to
consider noise as an external input entering the brain via appropriate
thalamic nuclei.
Support 3 possible shapes:
1) number_of_nodes;
2) number_of_state_variables or number_of_integrated_state_variables; and
3) (number_of_state_variables or number_of_integrated_state_variables, number_of_nodes).
"""
# Noise has to have a shape corresponding to only the integrated state variables!
good_history_shape = list(self.good_history_shape[1:])
good_history_shape[0] = self.model.nintvar
if self.integrator.noise.ntau > 0.0:
self.integrator.noise.configure_coloured(self.integrator.dt,
tuple(good_history_shape))
else:
self.integrator.noise.configure_white(self.integrator.dt,
tuple(good_history_shape))
if self.surface is not None:
if self.integrator.noise.nsig.size == self.connectivity.number_of_regions:
self.integrator.noise.nsig = self.integrator.noise.nsig[
self.surface.region_mapping]
elif self.integrator.noise.nsig.size == self.model.nvar * self.connectivity.number_of_regions:
self.integrator.noise.nsig = \
self.integrator.noise.nsig[self.model.state_variable_mask][:, self.surface.region_mapping]
elif self.integrator.noise.nsig.size == self.model.nintvar * self.connectivity.number_of_regions:
self.integrator.noise.nsig = self.integrator.noise.nsig[:,
self.
surface
.
region_mapping]
good_nsig_shape = (self.model.nintvar, self.number_of_nodes,
self.model.number_of_modes)
nsig = self.integrator.noise.nsig
self.log.debug("Given noise shape is %s", nsig.shape)
if nsig.shape in (good_nsig_shape, (1, )):
return
elif nsig.shape == (self.model.nvar, ):
nsig = nsig[self.model.state_variable_mask].reshape(
(self.model.nintvar, 1, 1))
elif nsig.shape == (self.model.nintvar, ):
nsig = nsig.reshape((self.model.nintvar, 1, 1))
elif nsig.shape == (self.number_of_nodes, ):
nsig = nsig.reshape((1, self.number_of_nodes, 1))
elif nsig.shape == (self.model.nvar, self.number_of_nodes):
nsig = nsig[self.model.state_variable_mask].reshape(
(self.n_intvar, self.number_of_nodes, 1))
elif nsig.shape == (self.model.nintvar, self.number_of_nodes):
nsig = nsig.reshape((self.model.nintvar, self.number_of_nodes, 1))
else:
msg = "Bad Simulator.integrator.noise.nsig shape: %s"
self.log.error(msg % str(nsig.shape))
self.log.debug("Corrected noise shape is %s", nsig.shape)
self.integrator.noise.nsig = nsig
def _configure_monitors(self):
""" Configure the requested Monitors for this Simulator """
# Coerce to list if required
if not isinstance(self.monitors, (list, tuple)):
self.monitors = [self.monitors]
# Configure monitors
for monitor in self.monitors:
monitor.config_for_sim(self)
def _configure_stimuli(self):
""" Configure the defined Stimuli for this Simulator """
if self.stimulus is not None:
if self.surface:
# NOTE the region mapping of the stimuli should also include the subcortical areas
self.stimulus.configure_space(region_mapping=numpy.r_[
self.surface.region_mapping,
self.connectivity.unmapped_indices(self.surface.
region_mapping)])
else:
self.stimulus.configure_space()
# used by simulator adaptor
def memory_requirement(self):
"""
Return an estimated of the memory requirements (Bytes) for this
simulator's current configuration.
"""
self._guesstimate_memory_requirement()
return self._memory_requirement_guess
# appears to be unused
def runtime(self, simulation_length):
"""
Return an estimated run time (seconds) for the simulator's current
configuration and a specified simulation length.
"""
self.simulation_length = simulation_length
self._guesstimate_runtime()
return self._runtime
# used by simulator adaptor
def storage_requirement(self):
"""
Return an estimated storage requirement (Bytes) for the simulator's
current configuration and a specified simulation length.
"""
self._calculate_storage_requirement()
return self._storage_requirement
def _guesstimate_memory_requirement(self):
"""
guesstimate the memory required for this simulator.
Guesstimate is based on the shape of the dominant arrays, and as such
can operate before configuration.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
if self.surface:
number_of_nodes = self.surface.number_of_vertices
else:
number_of_nodes = self.connectivity.number_of_regions
number_of_regions = self.connectivity.number_of_regions
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
bits_64 = 8.0 # Bytes
bits_32 = 4.0 # Bytes
# NOTE: The speed hack for getting the first element of hist shape should
# partially resolves calling of this method with a non-configured
# connectivity, there remains the less common issue if no tract_lengths...
hist_shape = (
self.connectivity.tract_lengths.max() /
(self.conduction_speed or self.connectivity.speed or 3.0) /
self.integrator.dt, self.model.nvar, number_of_nodes,
self.model.number_of_modes)
self.log.debug("Estimated history shape is %r", hist_shape)
memreq = numpy.prod(hist_shape) * bits_64
if self.surface:
memreq += self.surface.number_of_triangles * 3 * bits_32 * 2 # normals
memreq += self.surface.number_of_vertices * 3 * bits_64 * 2 # normals
memreq += number_of_nodes * number_of_regions * bits_64 * 4 # region_mapping, region_average, region_sum
# ???memreq += self.surface.local_connectivity.matrix.nnz * 8
if not hasattr(self.monitors, '__len__'):
self.monitors = [self.monitors]
for monitor in self.monitors:
if not isinstance(monitor, monitors.Bold):
stock_shape = (monitor.period / self.integrator.dt,
len(self.model.variables_of_interest),
number_of_nodes, self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
if hasattr(monitor, "sensors"):
try:
memreq += number_of_nodes * monitor.sensors.number_of_sensors * bits_64 # projection_matrix
except AttributeError:
self.log.debug(
"No sensors specified, guessing memory based on default EEG."
)
memreq += number_of_nodes * 62.0 * bits_64
else:
stock_shape = (monitor.hrf_length * monitor._stock_sample_rate,
len(self.model.variables_of_interest),
number_of_nodes, self.model.number_of_modes)
interim_stock_shape = (1.0 / (2.0**-2 * self.integrator.dt),
len(self.model.variables_of_interest),
number_of_nodes,
self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
memreq += numpy.prod(interim_stock_shape) * bits_64
if psutil and memreq > psutil.virtual_memory().total:
self.log.warning(
"There may be insufficient memory for this simulation.")
self._memory_requirement_guess = magic_number * memreq
msg = "Memory requirement estimate: simulation will need about %.1f MB"
self.log.info(msg, self._memory_requirement_guess / 2**20)
def _census_memory_requirement(self):
"""
Guesstimate the memory required for this simulator.
Guesstimate is based on a census of the dominant arrays after the
simulator has been configured.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
memreq = self.history.nbytes
try:
memreq += self.surface.triangles.nbytes * 2
memreq += self.surface.vertices.nbytes * 2
memreq += self.surface.region_mapping.nbytes * self.number_of_nodes * 8. * 4 # region_average, region_sum
memreq += self.surface.local_connectivity.matrix.nnz * 8
except AttributeError:
pass
for monitor in self.monitors:
memreq += monitor._stock.nbytes
if isinstance(monitor, monitors.Bold):
memreq += monitor._interim_stock.nbytes
if psutil and memreq > psutil.virtual_memory().total:
self.log.warning("Memory estimate exceeds total available RAM.")
self._memory_requirement_census = magic_number * memreq
# import pdb; pdb.set_trace()
msg = "Memory requirement census: simulation will need about %.1f MB"
self.log.info(msg % (self._memory_requirement_census / 1048576.0))
def _guesstimate_runtime(self):
"""
Estimate the runtime for this simulator.
Spread in parallel executions of larger arrays means this will be an over-estimation,
or rather a single threaded estimation...
Different choice of integrators and monitors has an additional effect,
on the magic number though relatively minor
"""
magic_number = 6.57e-06 # seconds
self._runtime = (magic_number * self.number_of_nodes *
self.model.nvar * self.model.number_of_modes *
self.simulation_length / self.integrator.dt)
msg = "Simulation runtime should be about %0.3f seconds"
self.log.info(msg, self._runtime)
def _calculate_storage_requirement(self):
"""
Calculate the storage requirement for the simulator, configured with
models, monitors, etc being run for a particular simulation length.
While this is only approximate, it is far more reliable/accurate than
the memory and runtime guesstimates.
"""
self.log.info("Calculating storage requirement for ...")
strgreq = 0
for monitor in self.monitors:
# Avoid division by zero for monitor not yet configured
# (in framework this is executed, when only preconfigure has been called):
current_period = monitor.period or self.integrator.dt
strgreq += (TvbProfile.current.MAGIC_NUMBER *
self.simulation_length * self.number_of_nodes *
self.model.nvar * self.model.number_of_modes /
current_period)
self.log.info("Calculated storage requirement for simulation: %d " %
int(strgreq))
self._storage_requirement = int(strgreq)
def run(self, **kwds):
"""Convenience method to call the simulator with **kwds and collect output data."""
ts, xs = [], []
for _ in self.monitors:
ts.append([])
xs.append([])
wall_time_start = time.time()
for data in self(**kwds):
for tl, xl, t_x in zip(ts, xs, data):
if t_x is not None:
t, x = t_x
tl.append(t)
xl.append(x)
elapsed_wall_time = time.time() - wall_time_start
self.log.info("%.3f s elapsed, %.3fx real time", elapsed_wall_time,
elapsed_wall_time * 1e3 / self.simulation_length)
for i in range(len(ts)):
ts[i] = numpy.array(ts[i])
xs[i] = numpy.array(xs[i])
return list(zip(ts, xs))