def get_connectivity_parameters(input_connectivity, surface_data=None):
"""
Returns a dictionary which contains all the needed data for drawing a connectivity.
"""
viewer = ConnectivityViewer()
global_params, global_pages = viewer.compute_connectivity_global_params(input_connectivity, surface_data)
global_params.update(global_pages)
global_params['selectedConnectivityGid'] = input_connectivity.gid
return global_params
def test_launch(self):
"""
Check that all required keys are present in output from BrainViewer launch.
"""
viewer = ConnectivityViewer()
result = viewer.launch(self.connectivity)
expected_keys = ['weightsMin', 'weightsMax', 'urlWeights', 'urlVertices',
'urlTriangles', 'urlTracts', 'urlPositions', 'urlNormals',
'rightHemisphereJson', 'raysArray', 'rayMin', 'rayMax', 'positions',
'leftHemisphereJson', 'connectivity_entity', 'bothHemisphereJson']
for key in expected_keys:
self.assertTrue(key in result)
def test_launch(self):
"""
Check that all required keys are present in output from BrainViewer launch.
"""
viewer = ConnectivityViewer()
view_model = viewer.get_view_model_class()()
view_model.connectivity = UUID(self.connectivity_index.gid)
result = viewer.launch(view_model)
expected_keys = ['weightsMin', 'weightsMax', 'urlWeights', 'urlVertices',
'urlTriangles', 'urlTracts', 'urlPositions', 'urlNormals',
'rightHemisphereJson', 'raysArray', 'rayMin', 'rayMax', 'positions',
'leftHemisphereJson', 'connectivity_entity', 'bothHemisphereJson']
for key in expected_keys:
assert key in result
def index(self):
current_user_id = common.get_logged_user().id
# In case the number of dynamics gets big we should add a filter in the ui.
dynamics = dao.get_dynamics_for_user(current_user_id)
if not dynamics:
return self.no_dynamics_page()
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
des = SerializationManager(burst_config)
connectivity = des.get_connectivity()
params = ConnectivityViewer.get_connectivity_parameters(connectivity)
params.update({
'title':
'Model parameters',
'mainContent':
'burst/model_param_region',
'isSingleMode':
True,
'submit_parameters_url':
'/burst/modelparameters/regions/submit_model_parameters',
'dynamics':
dynamics,
'dynamics_json':
self._dynamics_json(dynamics),
'initial_dynamic_ids':
json.dumps(burst_config.dynamic_ids)
})
return self.fill_default_attributes(params, 'regionmodel')
def index(self):
current_user_id = common.get_logged_user().id
# In case the number of dynamics gets big we should add a filter in the ui.
dynamics = dao.get_dynamics_for_user(current_user_id)
if not dynamics:
return self.no_dynamics_page()
sim_config = common.get_from_session(common.KEY_SIMULATOR_CONFIG)
connectivity = sim_config.connectivity
if connectivity is None:
msg = 'You have to select a connectivity before setting up the region Model. '
common.set_error_message(msg)
raise ValueError(msg)
current_project = common.get_current_project()
file_handler = FilesHelper()
conn_idx = dao.get_datatype_by_gid(connectivity.hex)
conn_path = file_handler.get_project_folder(current_project, str(conn_idx.fk_from_operation))
params = ConnectivityViewer.get_connectivity_parameters(conn_idx, conn_path)
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
params.update({
'title': 'Model parameters',
'mainContent': 'burst/model_param_region',
'isSingleMode': True,
'submit_parameters_url': '/burst/modelparameters/regions/submit_model_parameters',
'dynamics': dynamics,
'dynamics_json': self._dynamics_json(dynamics),
'initial_dynamic_ids': burst_config.dynamic_ids
})
return self.fill_default_attributes(params, 'regionmodel')
def index(self):
des = SerializationManager(self.simulator_context.simulator)
conn_idx = load.load_entity_by_gid(des.conf.connectivity)
model = des.conf.model
integrator = des.conf.integrator
state_vars = model.state_variables
noise_values = self.init_noise_config_values(model, integrator,
conn_idx)
initial_noise = self.group_noise_array_by_state_var(
noise_values, state_vars, conn_idx.number_of_regions)
current_project = common.get_current_project()
file_handler = FilesHelper()
conn_path = file_handler.get_project_folder(
current_project, str(conn_idx.fk_from_operation))
params = ConnectivityViewer.get_connectivity_parameters(
conn_idx, conn_path)
params.update({
'title': 'Noise configuration',
'mainContent': 'burst/noise',
'isSingleMode': True,
'submit_parameters_url': '/burst/noise/submit',
'stateVars': state_vars,
'stateVarsJson': json.dumps(state_vars),
'noiseInputValues': initial_noise[0],
'initialNoiseValues': json.dumps(initial_noise)
})
return self.fill_default_attributes(params, 'regionmodel')
def index(self):
current_user_id = common.get_logged_user().id
# In case the number of dynamics gets big we should add a filter in the ui.
dynamics = dao.get_dynamics_for_user(current_user_id)
if not dynamics:
return self.no_dynamics_page()
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
des = SerializationManager(burst_config)
connectivity = des.get_connectivity()
params = ConnectivityViewer.get_connectivity_parameters(connectivity)
params.update(
{
"title": "Model parameters",
"mainContent": "burst/model_param_region",
"isSingleMode": True,
"submit_parameters_url": "/burst/modelparameters/regions/submit_model_parameters",
"dynamics": dynamics,
"dynamics_json": self._dynamics_json(dynamics),
"initial_dynamic_ids": json.dumps(burst_config.dynamic_ids),
}
)
return self.fill_default_attributes(params, "regionmodel")
def index(self):
current_user_id = self.simulator_context.logged_user.id
# In case the number of dynamics gets big we should add a filter in the ui.
dynamics = dao.get_dynamics_for_user(current_user_id)
if not dynamics:
return self.no_dynamics_page()
sim_config = self.simulator_context.simulator
connectivity = sim_config.connectivity
if connectivity is None:
msg = 'You have to select a connectivity before setting up the region Model. '
common.set_error_message(msg)
raise ValueError(msg)
current_project = common.get_current_project()
conn_idx = load.load_entity_by_gid(connectivity)
params = ConnectivityViewer.get_connectivity_parameters(conn_idx, current_project.name,
str(conn_idx.fk_from_operation))
burst_config = self.simulator_context.burst_config
params.update({
'title': 'Model parameters',
'mainContent': 'burst/model_param_region',
'isSingleMode': True,
'submit_parameters_url': '/burst/modelparameters/regions/submit_model_parameters',
'dynamics': dynamics,
'dynamics_json': self._dynamics_json(dynamics),
'initial_dynamic_ids': burst_config.dynamic_ids
})
return self.fill_default_attributes(params, 'regionmodel')
def index(self):
current_user_id = common.get_logged_user().id
# In case the number of dynamics gets big we should add a filter in the ui.
dynamics = dao.get_dynamics_for_user(current_user_id)
if not dynamics:
return self.no_dynamics_page()
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
des = SerializationManager(burst_config)
connectivity = des.get_connectivity()
if connectivity is None:
msg = 'You have to select a connectivity before setting up the region Model. '
common.set_error_message(msg)
raise ValueError(msg)
params = ConnectivityViewer.get_connectivity_parameters(connectivity)
params.update({
'title': 'Model parameters',
'mainContent': 'burst/model_param_region',
'isSingleMode': True,
'submit_parameters_url': '/burst/modelparameters/regions/submit_model_parameters',
'dynamics': dynamics,
'dynamics_json': self._dynamics_json(dynamics),
'initial_dynamic_ids': json.dumps(burst_config.dynamic_ids)
})
return self.fill_default_attributes(params, 'regionmodel')
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(connectivity)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(
connectivity)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
if connectivity is None:
raise MissingDataException(RegionStimulusController.MSG_MISSING_CONNECTIVITY + "!!")
current_project = common.get_current_project()
conn_path = FilesHelper().get_project_folder(current_project, str(connectivity.fk_from_operation))
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(connectivity, conn_path)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def display_connectivity(connectivity_gid):
"""
Generates the html for displaying the connectivity matrix.
"""
connectivity = ABCAdapter.load_entity_by_gid(connectivity_gid)
current_project = common.get_current_project()
file_handler = FilesHelper()
conn_path = file_handler.get_project_folder(current_project, str(connectivity.fk_from_operation))
connectivity_viewer_params = ConnectivityViewer.get_connectivity_parameters(connectivity, conn_path)
template_specification = dict()
template_specification['isSingleMode'] = True
template_specification.update(connectivity_viewer_params)
return template_specification
def index(self):
des = SerializationManager(common.get_from_session(common.KEY_BURST_CONFIG))
connectivity = des.get_connectivity()
model, integrator = des.make_model_and_integrator()
state_vars = model.state_variables
noise_values = self.init_noise_config_values(model, integrator, connectivity)
initial_noise = self.group_noise_array_by_state_var(noise_values, state_vars, connectivity.number_of_regions)
params = ConnectivityViewer.get_connectivity_parameters(connectivity)
params.update({
'title': 'Noise configuration',
'mainContent': 'burst/noise',
'isSingleMode': True,
'submit_parameters_url': '/burst/noise/submit',
'stateVars': state_vars,
'stateVarsJson' : json.dumps(state_vars),
'noiseInputValues' : initial_noise[0],
'initialNoiseValues': json.dumps(initial_noise)
})
return self.fill_default_attributes(params, 'regionmodel')
def index(self):
des = SerializationManager(
common.get_from_session(common.KEY_BURST_CONFIG))
connectivity = des.get_connectivity()
model, integrator = des.make_model_and_integrator()
state_vars = model.state_variables
noise_values = self.init_noise_config_values(model, integrator,
connectivity)
initial_noise = self.group_noise_array_by_state_var(
noise_values, state_vars, connectivity.number_of_regions)
params = ConnectivityViewer.get_connectivity_parameters(connectivity)
params.update({
'title': 'Noise configuration',
'mainContent': 'burst/noise',
'isSingleMode': True,
'submit_parameters_url': '/burst/noise/submit',
'stateVars': state_vars,
'stateVarsJson': json.dumps(state_vars),
'noiseInputValues': initial_noise[0],
'initialNoiseValues': json.dumps(initial_noise)
})
return self.fill_default_attributes(params, 'regionmodel')