def test_Stage0_parameters(self):
# Mouse spiny
cell_id_spiny = self.mouse_spiny_id
# Create the parameter bounds for the optimization
model_params_handler_spiny = AllActive_Model_Parameters(cell_id_spiny)
param_bounds_file = 'param_bounds_stage0.json'
param_bounds_path = utility.locate_template_file(
os.path.join('parameters', param_bounds_file))
model_params_spiny, model_params_release = model_params_handler_spiny.get_opt_params(
param_bounds_path)
model_mechs_spiny, model_mechs_release = model_params_handler_spiny.get_opt_mechanism(
model_params_spiny, model_params_release, param_bounds_path)
model_params_dict_spiny = convert_model_params_to_dict(
model_params_spiny)
mouse_spiny_stage0_params = os.path.join(self.mouse_spiny_path,
'Stage0_parameters.json')
mouse_spiny_stage0_mechs = os.path.join(self.mouse_spiny_path,
'Stage0_mechanism.json')
model_params_spiny_true = utility.load_json(mouse_spiny_stage0_params)
model_mechs_spiny_true = utility.load_json(mouse_spiny_stage0_mechs)
model_params_spiny_true_dict = convert_model_params_to_dict(
model_params_spiny_true)
self.assertEqual(model_params_spiny_true_dict, model_params_dict_spiny)
self.assertEqual(model_mechs_spiny_true, model_mechs_spiny)
# Mouse aspiny
cell_id_aspiny = self.mouse_aspiny_id
# Create the parameter bounds for the optimization
model_params_handler_aspiny = AllActive_Model_Parameters(
cell_id_aspiny, swc_search_pattern='reconstruction.swc')
param_bounds_file = 'param_bounds_stage0.json'
param_bounds_path = utility.locate_template_file(
os.path.join('parameters', param_bounds_file))
model_params_aspiny, model_params_release = model_params_handler_aspiny.\
get_opt_params(param_bounds_path)
model_mechs_aspiny, model_mechs_release = model_params_handler_aspiny.\
get_opt_mechanism(model_params_aspiny,
model_params_release, param_bounds_path)
model_params_dict_aspiny = convert_model_params_to_dict(
model_params_aspiny)
mouse_aspiny_stage0_params = os.path.join(self.mouse_aspiny_path,
'Stage0_parameters.json')
mouse_aspiny_stage0_mechs = os.path.join(self.mouse_aspiny_path,
'Stage0_mechanism.json')
model_params_aspiny_true = utility.load_json(
mouse_aspiny_stage0_params)
model_mechs_aspiny_true = utility.load_json(mouse_aspiny_stage0_mechs)
model_params_aspiny_true_dict = convert_model_params_to_dict(
model_params_aspiny_true)
self.assertEqual(model_params_aspiny_true_dict,
model_params_dict_aspiny)
self.assertEqual(model_mechs_aspiny_true, model_mechs_aspiny)
def __init__(self,
script_template,
job_config_path,
script_name='chain_job.sh'):
super(ChainSubJob, self).__init__(script_name)
self.script_template = utility.locate_template_file(script_template)
self.job_config_path = job_config_path
def __init__(self,
script_template,
job_config_path,
script_name='batch_job.sh'):
super(PBS_JobModule, self).__init__(script_name)
self.job_config_path = job_config_path
self.script_template = utility.locate_template_file(script_template)
self.submit_cmd = 'qsub'
def test_Stage2_parameters(self):
# Mouse spiny
cell_id_spiny = self.mouse_spiny_id
# Create the parameter bounds for the optimization
prev_params_file = 'Stage1_fit_spiny.json'
model_params_handler_spiny = AllActive_Model_Parameters(
cell_id_spiny, prev_model_pattern=prev_params_file)
param_bounds_file = 'param_bounds_stage2.json'
param_bounds_path = utility.locate_template_file(
os.path.join('parameters', param_bounds_file))
param_rule_func = adjust_param_bounds
model_params_spiny, model_params_release = model_params_handler_spiny.get_opt_params(
param_bounds_path, param_rule_func)
model_mechs_spiny, model_mechs_release = model_params_handler_spiny.get_opt_mechanism(
model_params_spiny, model_params_release, param_bounds_path)
model_params_dict_spiny = convert_model_params_to_dict(
model_params_spiny)
mouse_spiny_stage2_params = os.path.join(self.mouse_spiny_path,
'Stage2_parameters.json')
mouse_spiny_stage2_mechs = os.path.join(self.mouse_spiny_path,
'Stage2_mechanism.json')
model_params_spiny_true = utility.load_json(mouse_spiny_stage2_params)
model_mechs_spiny_true = utility.load_json(mouse_spiny_stage2_mechs)
model_params_spiny_true_dict = convert_model_params_to_dict(
model_params_spiny_true)
self.assertEqual(model_params_spiny_true_dict, model_params_dict_spiny)
for mech_key, mech_val in model_mechs_spiny.items():
self.assertEqual(set(model_mechs_spiny_true[mech_key]),
set(mech_val))
# Mouse aspiny
cell_id_aspiny = self.mouse_aspiny_id
# Create the parameter bounds for the optimization
prev_params_file = 'Stage1_fit_aspiny.json'
model_params_handler_aspiny = AllActive_Model_Parameters(
cell_id_aspiny,
swc_search_pattern='reconstruction.swc',
prev_model_pattern=prev_params_file)
param_bounds_file = 'param_bounds_stage2_mouse_aspiny.json'
param_bounds_path = os.path.join(self.mouse_aspiny_path,
param_bounds_file)
param_rule_func = adjust_param_bounds
model_params_aspiny, model_params_release = model_params_handler_aspiny.\
get_opt_params(param_bounds_path, param_rule_func)
model_mechs_aspiny, model_mechs_release = model_params_handler_aspiny.\
get_opt_mechanism(model_params_aspiny,
model_params_release, param_bounds_path)
model_params_dict_aspiny = convert_model_params_to_dict(
model_params_aspiny)
model_params_dict_aspiny = convert_model_params_to_dict(
model_params_aspiny)
mouse_aspiny_stage2_params = os.path.join(self.mouse_aspiny_path,
'Stage2_parameters.json')
mouse_aspiny_stage2_mechs = os.path.join(self.mouse_aspiny_path,
'Stage2_mechanism.json')
model_params_aspiny_true = utility.load_json(
mouse_aspiny_stage2_params)
model_mechs_aspiny_true = utility.load_json(mouse_aspiny_stage2_mechs)
model_params_aspiny_true_dict = convert_model_params_to_dict(
model_params_aspiny_true)
self.assertEqual(model_params_aspiny_true_dict,
model_params_dict_aspiny)
for mech_key, mech_val in model_mechs_aspiny.items():
self.assertEqual(set(model_mechs_aspiny_true[mech_key]),
set(mech_val))
def test_Stage0_features(self):
# Mouse spiny
cell_id_spiny = self.mouse_spiny_id
nwb_handler_spiny = NwbExtractor(cell_id_spiny,
nwb_search_pattern=cell_id_spiny)
acceptable_stimtypes = ['Long Square']
ephys_dir = os.path.join(self.mouse_spiny_path, 'mouse_spiny_ephys')
ephys_data_path, stimmap_filename = \
nwb_handler_spiny.save_cell_data(acceptable_stimtypes,
ephys_dir=ephys_dir)
feature_path = utility.locate_template_file(
os.path.join('parameters', 'feature_set_stage0.json'))
train_features_spiny, _, _, train_protocols_spiny, _ = \
nwb_handler_spiny.get_ephys_features(feature_path, ephys_data_path,
stimmap_filename, filter_feat_proto_passive)
train_features_dict_spiny = convert_stim_feat_to_dict(
train_features_spiny, 'soma')
train_protocols_dict_spiny = convert_protocols_to_dict(
train_protocols_spiny, 'stimuli')
mouse_spiny_stage0_features = os.path.join(self.mouse_spiny_path,
'Stage0_features.json')
mouse_spiny_stage0_protocols = os.path.join(self.mouse_spiny_path,
'Stage0_protocols.json')
model_features_spiny_true = utility.load_json(
mouse_spiny_stage0_features)
model_protocols_spiny_true = utility.load_json(
mouse_spiny_stage0_protocols)
model_features_spiny_true_dict = convert_stim_feat_to_dict(
model_features_spiny_true, 'soma')
model_protocols_spiny_true_dict = convert_protocols_to_dict(
model_protocols_spiny_true, 'stimuli')
self.assertAlmostEqual(model_features_spiny_true_dict,
train_features_dict_spiny)
self.assertAlmostEqual(model_protocols_spiny_true_dict,
train_protocols_dict_spiny)
# Mouse aspiny
cell_id_aspiny = self.mouse_aspiny_id
nwb_handler_aspiny = NwbExtractor(cell_id_aspiny,
nwb_search_pattern=cell_id_aspiny)
acceptable_stimtypes = ['Long Square']
ephys_dir = os.path.join(self.mouse_aspiny_path, 'mouse_aspiny_ephys')
ephys_data_path, stimmap_filename = \
nwb_handler_aspiny.save_cell_data(acceptable_stimtypes,
ephys_dir=ephys_dir)
feature_path = utility.locate_template_file(
os.path.join('parameters', 'feature_set_stage0.json'))
train_features_aspiny, _, _, train_protocols_aspiny, _ = \
nwb_handler_aspiny.get_ephys_features(feature_path, ephys_data_path,
stimmap_filename, filter_feat_proto_passive)
train_features_dict_aspiny = convert_stim_feat_to_dict(
train_features_aspiny, 'soma')
train_protocols_dict_aspiny = convert_protocols_to_dict(
train_protocols_aspiny, 'stimuli')
mouse_aspiny_stage0_features = os.path.join(self.mouse_aspiny_path,
'Stage0_features.json')
mouse_aspiny_stage0_protocols = os.path.join(self.mouse_aspiny_path,
'Stage0_protocols.json')
model_features_aspiny_true = utility.load_json(
mouse_aspiny_stage0_features)
model_protocols_aspiny_true = utility.load_json(
mouse_aspiny_stage0_protocols)
model_features_aspiny_true_dict = convert_stim_feat_to_dict(
model_features_aspiny_true, 'soma')
model_protocols_aspiny_true_dict = convert_protocols_to_dict(
model_protocols_aspiny_true, 'stimuli')
self.assertAlmostEqual(model_features_aspiny_true_dict,
train_features_dict_aspiny)
self.assertAlmostEqual(model_protocols_aspiny_true_dict,
train_protocols_dict_aspiny)