def setUp(self):
_, self.connectivity = DatatypesFactory().create_connectivity()
self.test_user = TestFactory.create_user(username="******")
self.test_project = TestFactory.create_project(self.test_user, "Test")
burst_conf = BurstConfiguration(self.test_project.id)
burst_conf._simulator_configuration = self.CONF_HOPFIELD_HEUN_STOCH_RANGES
burst_conf.prepare_after_load()
burst_conf.simulator_configuration['connectivity'] = {'value': self.connectivity.gid}
self.s_manager = SerializationManager(burst_conf)
self.empty_manager = SerializationManager(BurstConfiguration(None))
def transactional_setup_method(self):
self.test_user = TestFactory.create_user(username="******")
self.test_project = TestFactory.create_project(self.test_user, "Test")
zip_path = path.join(path.dirname(tvb_data.__file__), 'connectivity',
'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path, "John")
self.connectivity = TestFactory.get_entity(self.test_project,
ConnectivityIndex)
sim_conf = Simulator(model=ModelsEnum.HOPFIELD.get_class()(),
integrator=HeunStochastic())
self.s_manager = SerializationManager(sim_conf)
self.empty_manager = SerializationManager(None)
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 submit_model_parameters(self, node_values):
"""
Collects the model parameters values from all the models used for the connectivity nodes.
Assumes that the array indices are consistent with the node order.
"""
dynamic_ids = json.loads(node_values)
dynamics = [dao.get_dynamic(did) for did in dynamic_ids]
for dynamic in dynamics[1:]:
if dynamic.model_class != dynamics[0].model_class:
raise Exception("All dynamics must have the same model type")
model_name = dynamics[0].model_class
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
# update model parameters in burst config
des = SerializationManager(burst_config)
model_parameters = [
dict(json.loads(d.model_parameters)) for d in dynamics
]
des.write_model_parameters(model_name, model_parameters)
# update dynamic ids in burst config
burst_config.dynamic_ids = dynamic_ids
# Update in session BURST configuration for burst-page.
# todo was this needed? as the burst config in session has already been changed
#common.add2session(common.KEY_BURST_CONFIG, burst_config.clone())
raise cherrypy.HTTPRedirect("/burst/")
def submit_model_parameters(self, node_values):
"""
Collects the model parameters values from all the models used for the connectivity nodes.
Assumes that the array indices are consistent with the node order.
"""
dynamic_ids = json.loads(node_values)
dynamics = [dao.get_dynamic(did) for did in dynamic_ids]
for dynamic in dynamics[1:]:
if dynamic.model_class != dynamics[0].model_class:
raise Exception("All dynamics must have the same model type")
model_name = dynamics[0].model_class
burst_config = common.get_from_session(common.KEY_BURST_CONFIG)
simulator_config = common.get_from_session(common.KEY_SIMULATOR_CONFIG)
# update model parameters in burst config
des = SerializationManager(simulator_config)
model_parameters = [
dict(json.loads(d.model_parameters)) for d in dynamics
]
des.write_model_parameters(model_name, model_parameters)
# update dynamic ids in burst config
burst_config.dynamic_ids = json.dumps(dynamic_ids)
# Update in session the simulator configuration and the current form URL in wizzard for burst-page.
common.add2session(common.KEY_BURST_CONFIG, burst_config)
common.add2session(common.KEY_LAST_LOADED_FORM_URL,
SimulatorWizzardURLs.SET_INTEGRATOR_URL)
raise cherrypy.HTTPRedirect("/burst/")
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 get_data_from_burst_configuration(self):
"""
Returns the model and surface instances from the burst configuration.
"""
des = SerializationManager(
common.get_from_session(common.KEY_BURST_CONFIG))
### Read from session current burst-configuration
if des.conf is None:
return None, None
if des.has_model_pse_ranges():
common.set_error_message(
"When configuring model parameters you are not allowed to specify range values."
)
raise cherrypy.HTTPRedirect("/burst/")
try:
model, integrator = des.make_model_and_integrator()
except Exception:
self.logger.exception(
"Some of the provided parameters have an invalid value.")
common.set_error_message(
"Some of the provided parameters have an invalid value.")
raise cherrypy.HTTPRedirect("/burst/")
surface = des.get_surface()
return model, surface
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)
current_project = common.get_current_project()
file_handler = FilesHelper()
conn_path = file_handler.get_project_folder(current_project, str(connectivity.fk_from_operation))
params = ConnectivityViewer.get_connectivity_parameters(connectivity, conn_path)
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 submit(self, node_values):
"""
Submit noise dispersions
:param node_values: A map from state variable names to noise dispersion arrays. Ex {'V': [1,2...74]}
"""
des = SerializationManager(
common.get_from_session(common.KEY_BURST_CONFIG))
des.write_noise_parameters(json.loads(node_values))
raise cherrypy.HTTPRedirect("/burst/")
def submit(self, node_values):
"""
Submit noise dispersions
:param node_values: A map from state variable names to noise dispersion arrays. Ex {'V': [1,2...74]}
"""
des = SerializationManager(self.simulator_context.simulator)
des.write_noise_parameters(json.loads(node_values))
self.simulator_context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_NOISE_PARAMS_URL)
raise cherrypy.HTTPRedirect("/burst/")
def submit(self, node_values):
"""
Submit noise dispersions
:param node_values: A map from state variable names to noise dispersion arrays. Ex {'V': [1,2...74]}
"""
des = SerializationManager(common.get_from_session(common.KEY_SIMULATOR_CONFIG))
des.write_noise_parameters(json.loads(node_values))
common.add2session(common.KEY_LAST_LOADED_FORM_URL, SimulatorWizzardURLs.SET_NOISE_PARAMS_URL)
raise cherrypy.HTTPRedirect("/burst/")
def get_data_from_burst_configuration(self):
"""
Returns the model and surface instances from the burst configuration.
"""
des = SerializationManager(self.simulator_context.simulator)
### Read from session current burst-configuration
if des.conf is None:
return None, None
# if des.has_model_pse_ranges():
# common.set_error_message("When configuring model parameters you are not allowed to specify range values.")
# raise cherrypy.HTTPRedirect("/burst/")
try:
model = des.conf.model
except Exception:
self.logger.exception(
"Some of the provided parameters have an invalid value.")
common.set_error_message(
"Some of the provided parameters have an invalid value.")
raise cherrypy.HTTPRedirect("/burst/")
cortex = des.conf.surface
return model, cortex
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')
