def step_2(self):
"""
Generate the required template dictionary for the second step.
"""
context = common.get_from_session(KEY_REGION_CONTEXT)
selected_stimulus_gid = context.selected_stimulus
left_side_interface = self.get_select_existent_entities(
'Load Region Stimulus:', StimuliRegion, selected_stimulus_gid)
template_specification = dict(
title="Spatio temporal - Region stimulus")
template_specification[
'mainContent'] = 'spatial/stimulus_region_step2_main'
template_specification[
'next_step_url'] = '/spatial/stimulus/region/step_2_submit'
template_specification[
'existentEntitiesInputList'] = left_side_interface
default_weights = context.get_weights()
if len(default_weights) == 0:
selected_connectivity = ABCAdapter.load_entity_by_gid(
context.get_session_connectivity())
default_weights = StimuliRegion.get_default_weights(
selected_connectivity.number_of_regions)
template_specification['node_weights'] = json.dumps(default_weights)
template_specification[common.KEY_PARAMETERS_CONFIG] = False
template_specification.update(
self.display_connectivity(context.get_session_connectivity()))
return self.fill_default_attributes(template_specification)
def step_2(self):
"""
Generate the required template dictionary for the second step.
"""
current_region_stimulus = common.get_from_session(KEY_REGION_STIMULUS)
region_stim_selector_form = StimulusRegionSelectorForm(
common.get_current_project().id)
region_stim_selector_form.region_stimulus.data = current_region_stimulus.gid.hex
region_stim_selector_form.display_name.data = common.get_from_session(
KEY_REGION_STIMULUS_NAME)
template_specification = dict(
title="Spatio temporal - Region stimulus")
template_specification[
'mainContent'] = 'spatial/stimulus_region_step2_main'
template_specification[
'next_step_url'] = '/spatial/stimulus/region/step_2_submit'
template_specification[
'regionStimSelectorForm'] = region_stim_selector_form
default_weights = current_region_stimulus.weight
if len(default_weights) == 0:
selected_connectivity = ABCAdapter.load_entity_by_gid(
current_region_stimulus.connectivity.hex)
default_weights = StimuliRegion.get_default_weights(
selected_connectivity.number_of_regions)
template_specification['node_weights'] = json.dumps(
default_weights.tolist())
template_specification[common.KEY_PARAMETERS_CONFIG] = False
template_specification.update(
self.display_connectivity(
current_region_stimulus.connectivity.hex))
return self.fill_default_attributes(template_specification)
def set_connectivity(self, **param):
current_region_stim = common.get_from_session(KEY_REGION_STIMULUS)
connectivity_form_field = RegionStimulusCreatorForm(common.get_current_project().id).connectivity
connectivity_form_field.fill_from_post(param)
current_region_stim.connectivity = connectivity_form_field.value
conn_index = ABCAdapter.load_entity_by_gid(connectivity_form_field.value.hex)
current_region_stim.weight = StimuliRegion.get_default_weights(conn_index.number_of_regions)
def step_2(self):
"""
Generate the required template dictionary for the second step.
"""
current_region_stimulus = common.get_from_session(KEY_REGION_STIMULUS)
region_stim_selector_form = StimulusRegionSelectorForm(common.get_current_project().id)
region_stim_selector_form.region_stimulus.data = current_region_stimulus.gid.hex
region_stim_selector_form.display_name.data = common.get_from_session(KEY_REGION_STIMULUS_NAME)
template_specification = dict(title="Spatio temporal - Region stimulus")
template_specification['mainContent'] = 'spatial/stimulus_region_step2_main'
template_specification['next_step_url'] = '/spatial/stimulus/region/step_2_submit'
template_specification['regionStimSelectorForm'] = self.render_adapter_form(region_stim_selector_form)
default_weights = current_region_stimulus.weight
if len(default_weights) == 0:
selected_connectivity = ABCAdapter.load_entity_by_gid(current_region_stimulus.connectivity.hex)
if selected_connectivity is None:
common.set_error_message(self.MSG_MISSING_CONNECTIVITY)
default_weights = numpy.array([])
else:
default_weights = StimuliRegion.get_default_weights(selected_connectivity.number_of_regions)
template_specification['baseUrl'] = self.base_url
self.plotted_equation_prefixes = {
self.DISPLAY_NAME_FIELD: region_stim_selector_form.display_name.name
}
template_specification['fieldsWithEvents'] = json.dumps(self.plotted_equation_prefixes)
template_specification['node_weights'] = json.dumps(default_weights.tolist())
template_specification[common.KEY_PARAMETERS_CONFIG] = False
template_specification.update(self.display_connectivity(current_region_stimulus.connectivity.hex))
return self.fill_default_attributes(template_specification)
def step_2(self):
"""
Generate the required template dictionary for the second step.
"""
context = common.get_from_session(KEY_REGION_CONTEXT)
selected_stimulus_gid = context.selected_stimulus
left_side_interface = self.get_select_existent_entities('Load Region Stimulus:',
StimuliRegion, selected_stimulus_gid)
template_specification = dict(title="Spatio temporal - Region stimulus")
template_specification['mainContent'] = 'spatial/stimulus_region_step2_main'
template_specification['next_step_url'] = '/spatial/stimulus/region/step_2_submit'
template_specification['existentEntitiesInputList'] = left_side_interface
default_weights = context.get_weights()
if len(default_weights) == 0:
selected_connectivity = ABCAdapter.load_entity_by_gid(context.get_session_connectivity())
default_weights = StimuliRegion.get_default_weights(selected_connectivity.number_of_regions)
template_specification['node_weights'] = json.dumps(default_weights)
template_specification[common.KEY_PARAMETERS_CONFIG] = False
template_specification.update(self.display_connectivity(context.get_session_connectivity()))
return self.fill_default_attributes(template_specification)
def configure(self,
dt=2**-3,
model=ModelsEnum.GENERIC_2D_OSCILLATOR.get_class(),
speed=4.0,
coupling_strength=0.00042,
method=HeunDeterministic,
surface_sim=False,
default_connectivity=True,
with_stimulus=False):
"""
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.from_file()
region_mapping = RegionMapping.from_file(
source_file="regionMapping_16k_76.txt")
else:
white_matter = Connectivity.from_file(
source_file="connectivity_192.zip")
region_mapping = RegionMapping.from_file(
source_file="regionMapping_16k_192.txt")
region_mapping.surface = CorticalSurface.from_file()
white_matter_coupling = coupling.Linear(
a=numpy.array([coupling_strength]))
white_matter.speed = numpy.array(
[speed]) # no longer allow scalars to numpy array promotion
dynamics = model()
if issubclass(method, IntegratorStochastic):
hisss = noise.Additive(nsig=numpy.array([2**-11]))
integrator = method(dt=dt, noise=hisss)
else:
integrator = method(dt=dt)
if surface_sim:
local_coupling_strength = numpy.array([2**-10])
default_cortex = Cortex.from_file()
default_cortex.region_mapping_data = region_mapping
default_cortex.coupling_strength = local_coupling_strength
if default_connectivity:
default_cortex.local_connectivity = LocalConnectivity.from_file(
)
else:
default_cortex.local_connectivity = LocalConnectivity()
default_cortex.local_connectivity.surface = default_cortex.region_mapping_data.surface
# TODO stimulus
else:
default_cortex = None
if with_stimulus:
weights = StimuliRegion.get_default_weights(
white_matter.weights.shape[0])
weights[self.stim_nodes] = 1.
stimulus = StimuliRegion(temporal=Linear(parameters={
"a": 0.0,
"b": self.stim_value
}),
connectivity=white_matter,
weight=weights)
# Order of monitors determines order of returned values.
self.sim = simulator.Simulator()
self.sim.surface = default_cortex
self.sim.model = dynamics
self.sim.integrator = integrator
self.sim.connectivity = white_matter
self.sim.coupling = white_matter_coupling
self.sim.monitors = self.monitors
if with_stimulus:
self.sim.stimulus = stimulus
self.sim.configure()
