def launch(self, **kwargs):
"""
Used for creating a `StimuliRegion` instance
"""
stimuli_region = StimuliRegion(storage_path=self.storage_path)
stimuli_region.connectivity = kwargs['connectivity']
stimuli_region.weight = kwargs['weight']
stimuli_region.temporal = Equation.build_equation_from_dict('temporal', kwargs)
return stimuli_region
def launch(self, **kwargs):
"""
Used for creating a `StimuliRegion` instance
"""
stimuli_region = StimuliRegion(storage_path=self.storage_path)
stimuli_region.connectivity = kwargs['connectivity']
stimuli_region.weight = kwargs['weight']
stimuli_region.temporal = Equation.build_equation_from_dict(
'temporal', kwargs)
return stimuli_region
def launch(self, view_model):
# type: (RegionStimulusCreatorModel) -> [StimuliRegionIndex]
"""
Used for creating a `StimuliRegion` instance
"""
stimuli_region = StimuliRegion()
stimuli_region.connectivity = Connectivity()
stimuli_region.connectivity.gid = view_model.connectivity
stimuli_region.weight = view_model.weight
stimuli_region.temporal = view_model.temporal
self.generic_attributes.user_tag_1 = view_model.display_name
stimuli_region_idx = self.store_complete(stimuli_region)
return stimuli_region_idx
def create_stimulus(self, connectivity):
"""
:param connectivity: Connectivity to create stimuli for its regions
:return: persisted region Stimuli instance
"""
operation, _, storage_path = self.__create_operation()
stimuli_region = StimuliRegion(storage_path=storage_path)
stimuli_region.connectivity = connectivity
stimuli_region.weight = numpy.random.random((connectivity.number_of_regions, 1)).tolist()
stimuli_region.temporal = PulseTrain()
adapter_instance = StoreAdapter([stimuli_region])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
return stimuli_region
def create_stimulus(self, connectivity):
"""
:param connectivity: Connectivity to create stimuli for its regions
:return: persisted region Stimuli instance
"""
operation, _, storage_path = self.__create_operation()
stimuli_region = StimuliRegion(storage_path=storage_path)
stimuli_region.connectivity = connectivity
stimuli_region.weight = numpy.random.random((connectivity.number_of_regions, 1)).tolist()
stimuli_region.temporal = PulseTrain()
adapter_instance = StoreAdapter([stimuli_region])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
return stimuli_region
def launch(self, **kwargs):
"""
Used for creating a StimuliRegion instance
"""
stimuli_region = StimuliRegion(storage_path=self.storage_path)
stimuli_region.connectivity = kwargs['connectivity']
stimuli_region.weight = kwargs['weight']
#spatial_eq = parameters_factory.get_traited_instance_for_name(kwargs['spatial'], equations_data.EquationData,
# {'parameters': kwargs['spatial_parameters'].get('parameters', {})})
temporal_eq = parameters_factory.get_traited_instance_for_name(kwargs['temporal'], equations_data.EquationData,
{'parameters': kwargs['temporal_parameters'].get('parameters', {})})
#stimuli_region.spatial = spatial_eq
stimuli_region.temporal = temporal_eq
return stimuli_region
def launch(self, view_model):
# type: (RegionStimulusCreatorModel) -> [StimuliRegionIndex]
"""
Used for creating a `StimuliRegion` instance
"""
stimuli_region = StimuliRegion()
stimuli_region.connectivity = Connectivity()
stimuli_region.connectivity.gid = view_model.connectivity
stimuli_region.weight = view_model.weight
stimuli_region.temporal = view_model.temporal
stimuli_region_idx = StimuliRegionIndex()
stimuli_region_idx.fill_from_has_traits(stimuli_region)
h5.store_complete(stimuli_region, self.storage_path)
return stimuli_region_idx
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.
"""
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 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 get_input_tree(self):
"""
Returns the input interface for this adapter.
"""
stimuli_region = StimuliRegion()
stimuli_region.trait.bound = interface.INTERFACE_ATTRIBUTES_ONLY
inputList = stimuli_region.interface[interface.INTERFACE_ATTRIBUTES]
return inputList
def create_stimulus(self):
"""
Creates a stimulus from the given data.
"""
context = common.get_from_session(KEY_REGION_CONTEXT)
local_connectivity_creator = self.get_creator_and_interface(
REGION_STIMULUS_CREATOR_MODULE, REGION_STIMULUS_CREATOR_CLASS,
StimuliRegion())[0]
context.equation_kwargs.update(
{'weight': json.dumps(context.get_weights())})
self.flow_service.fire_operation(local_connectivity_creator,
common.get_logged_user(),
common.get_current_project().id,
**context.equation_kwargs)
common.set_important_message(
"The operation for creating the stimulus was successfully launched."
)
def load_region_stimulus(self, region_stimulus_gid, from_step=None):
"""
Loads the interface for the selected region stimulus.
"""
selected_region_stimulus = ABCAdapter.load_entity_by_gid(
region_stimulus_gid)
temporal_eq = selected_region_stimulus.temporal
spatial_eq = selected_region_stimulus.spatial
connectivity = selected_region_stimulus.connectivity
weights = selected_region_stimulus.weight
temporal_eq_type = temporal_eq.__class__.__name__
spatial_eq_type = spatial_eq.__class__.__name__
default_dict = {
'temporal': temporal_eq_type,
'spatial': spatial_eq_type,
'connectivity': connectivity.gid,
'weight': json.dumps(weights)
}
for param in temporal_eq.parameters:
prepared_name = 'temporal_parameters_option_' + str(
temporal_eq_type)
prepared_name = prepared_name + '_parameters_parameters_' + str(
param)
default_dict[prepared_name] = str(temporal_eq.parameters[param])
for param in spatial_eq.parameters:
prepared_name = 'spatial_parameters_option_' + str(
spatial_eq_type) + '_parameters_parameters_' + str(param)
default_dict[prepared_name] = str(spatial_eq.parameters[param])
input_list = self.get_creator_and_interface(
REGION_STIMULUS_CREATOR_MODULE, REGION_STIMULUS_CREATOR_CLASS,
StimuliRegion())[1]
input_list = InputTreeManager.fill_defaults(input_list, default_dict)
context = common.get_from_session(KEY_REGION_CONTEXT)
context.reset()
context.update_from_interface(input_list)
context.equation_kwargs[
DataTypeMetaData.KEY_TAG_1] = selected_region_stimulus.user_tag_1
context.set_active_stimulus(region_stimulus_gid)
return self.do_step(from_step)
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 _get_stimulus_interface(self):
"""
Returns a dictionary which contains the data needed
for creating the interface for a stimulus.
"""
context = common.get_from_session(KEY_REGION_CONTEXT)
input_list = self.get_creator_and_interface(
REGION_STIMULUS_CREATOR_MODULE, REGION_STIMULUS_CREATOR_CLASS,
StimuliRegion())[1]
context.equation_kwargs.update(
{SCALING_PARAMETER: context.get_weights()})
input_list = InputTreeManager.fill_defaults(input_list,
context.equation_kwargs)
input_list, any_scaling = self._remove_scaling(input_list)
template_specification = {
'inputList': input_list,
common.KEY_PARAMETERS_CONFIG: False
}
return self._add_extra_fields_to_interface(
template_specification), any_scaling
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()
