def reset_transfer_functions(sim):
"""
Reset transfer functions
"""
# Delete all TFs
old_tfs, _ = sim.cle.get_simulation_transfer_functions()
for tf in old_tfs:
sim.cle.delete_simulation_transfer_function(get_tf_name(tf))
experiment_basepath = os.path.join(get_experiment_basepath(),
sim.experiment_conf)
_, bibi_conf = get_experiment_data(str(experiment_basepath))
if bibi_conf is None:
return
# Reset Transfer functions
import_referenced_python_tfs(bibi_conf,
os.path.dirname(experiment_basepath))
for tf in bibi_conf.transferFunction:
tf_code = generate_tf(tf, bibi_conf)
tf_code = correct_indentation(tf_code, 0)
tf_code = tf_code.strip() + "\n"
error_message = sim.cle.add_simulation_transfer_function(
str(tf_code))
if error_message:
raise NRPServicesTransferFunctionException(
"Transfer function patch failed: " + str(error_message) +
"\n" + "Updated source:\n" + str(tf_code))
def reset_state_machines(sim):
"""
Reset states machines
"""
sim.delete_all_state_machines()
sm_base_path = get_experiment_basepath()
experiment_basepath = os.path.join(sm_base_path, sim.experiment_conf)
experiment, _ = get_experiment_data(str(experiment_basepath))
if experiment is None:
return
state_machine_paths = {}
if experiment.experimentControl is not None:
state_machine_paths.update({
sm.id: os.path.join(os.path.dirname(experiment_basepath),
sm.src)
for sm in experiment.experimentControl.stateMachine
if isinstance(sm, exp_conf_api_gen.SMACHStateMachine)
})
if experiment.experimentEvaluation is not None:
state_machine_paths.update({
sm.id: os.path.join(os.path.dirname(experiment_basepath),
sm.src)
for sm in experiment.experimentEvaluation.stateMachine
if isinstance(sm, exp_conf_api_gen.SMACHStateMachine)
})
sim.state_machine_manager.add_all(state_machine_paths, sim.sim_id)
sim.state_machine_manager.initialize_all()
def reset_brain(sim):
"""
Reset populations
:param sim:
"""
experiments_base_path = os.path.join(get_experiment_basepath(),
sim.experiment_conf)
models_base_path = get_model_basepath()
_, bibi_conf = get_experiment_data(str(experiments_base_path))
if bibi_conf is None:
return
neurons_config = get_all_neurons_as_dict(
bibi_conf.brainModel.populations)
# Convert the populations to a JSON dictionary
for (name, s) in neurons_config.iteritems():
v = dict()
v['from'] = s.start
v['to'] = s.stop
if s.step <= 0:
v['step'] = 1
else:
v['step'] = s.step
neurons_config[name] = v
neurons_config = json.dumps(neurons_config)
if 'storage://' in bibi_conf.brainModel.file:
for entry in os.listdir(tempfile.gettempdir()):
if entry.startswith('nrpTemp'):
brain_path = os.path.join(
tempfile.gettempdir(), entry,
os.path.basename(bibi_conf.brainModel.file))
else:
brain_path = os.path.join(models_base_path,
bibi_conf.brainModel.file)
with open(brain_path, 'r') as myfile:
data = myfile.read()
DO_CHANGE_POPULATION = 1
result = sim.cle.set_simulation_brain('py', data, "text",
neurons_config,
DO_CHANGE_POPULATION)
if result.error_message is not "":
# Error in given brain
raise ROSCLEClientException(
'{}, line:{}, column:{}, population_change:{}'.format(
result.error_message, result.error_line,
result.error_column, result.handle_population_change))
def get(self, exp_id):
"""
Get preview image of the experiment specified with experiment ID.
:param exp_id: The experiment ID
:> json image_as_base64: The PNG image as base64
:status 500: {0}
:status 404: {1} or {2}
:status 200: Success. The preview image is returned
"""
# Check experiment
experiment_file_path = os.path.join(get_experiment_basepath(),
get_experiment_rel(exp_id))
if not os.path.isfile(experiment_file_path):
raise NRPServicesClientErrorException(
ErrorMessages.EXPERIMENT_CONF_FILE_NOT_FOUND_404,
error_code=404)
experiment_dir = os.path.split(experiment_file_path)[0]
# Parse the experiment XML and get the thumbnail path
with open(experiment_file_path) as exd_file:
try:
experiment_file = exp_conf_api_gen.CreateFromDocument(
exd_file.read())
preview_file = os.path.join(experiment_dir,
experiment_file.thumbnail)
except ValidationError:
raise NRPServicesClientErrorException(
ErrorMessages.EXPERIMENT_CONF_FILE_INVALID_500,
error_code=500)
# Check thumbnail
if not os.path.isfile(preview_file):
raise NRPServicesClientErrorException(
ErrorMessages.EXPERIMENT_PREVIEW_NOT_FOUND_404, error_code=404)
mime_type = mimetypes.guess_type(preview_file)[
0] # returns tuple (type, encoding)
if not mime_type or not mime_type.startswith('image'):
raise NRPServicesClientErrorException(
ErrorMessages.EXPERIMENT_PREVIEW_INVALID_500, error_code=500)
with open(preview_file, "rb") as _file:
data = _file.read()
# Base64
return dict(image_as_base64=base64.b64encode(data))
def test_get_experiment_basepath_ok(self, mock_os):
mock_os.environ.get.return_value = "/test1"
self.assertEqual("/test1", get_experiment_basepath())