def get_data_lims(cell_id):
lr = lims.LimsReader()
os.mkdir(data_dir)
nwb_path = os.path.join(data_dir, f'{cell_id}.nwb')
swc_path = os.path.join(data_dir, f'{cell_id}.swc')
nwb_lims = lr.get_nwb_path_from_lims(cell_id)
swc_lims = lr.get_swc_path_from_lims(cell_id)
shutil.copy(nwb_lims, nwb_path)
shutil.copy(swc_lims, swc_path)
return {"nwb_path": nwb_path, "swc_path": swc_path}
def get_efeatures(cell_id):
from ateamopt.nwb_extractor import NwbExtractor
from ateamopt.optim_config_rules import correct_voltage_feat_std
from ateam.data import lims
import os
from ateamopt.utils import utility
import shutil
acceptable_stimtypes = ['Long Square']
feature_names_path = 'feature_set_all.json'
ephys_dir_origin = 'ephys_ttype'
efel_feature_path = 'eFEL_features_ttype'
lr = lims.LimsReader()
cell_efeatures_dir = os.path.join(efel_feature_path, cell_id)
cell_protocols_filename = os.path.join(cell_efeatures_dir,
'protocols.json')
cell_features_filename = os.path.join(efel_feature_path, cell_id,
'features.json')
efeature_filenames = [cell_protocols_filename, cell_features_filename]
if not all(os.path.exists(filename_) for filename_ in efeature_filenames):
utility.create_filepath(cell_protocols_filename)
nwb_path = lr.get_nwb_path_from_lims(int(cell_id),
get_sdk_version=True)
cell_ephys_dir = os.path.join(ephys_dir_origin, cell_id)
nwb_handler = NwbExtractor(cell_id, nwb_path)
ephys_data_path, stimmap_filename = nwb_handler.save_cell_data_web(
acceptable_stimtypes, ephys_dir=cell_ephys_dir)
protocol_dict, feature_dict = nwb_handler.get_efeatures_all(
feature_names_path, ephys_data_path, stimmap_filename)
feature_dict = correct_voltage_feat_std(feature_dict)
utility.save_json(cell_protocols_filename, protocol_dict)
utility.save_json(cell_features_filename, feature_dict)
shutil.move(stimmap_filename, cell_efeatures_dir)
shutil.rmtree(cell_ephys_dir, ignore_errors=True)
def get_morph_path(cell_id):
lr = lims.LimsReader()
morph_path = lr.get_swc_path_from_lims(int(cell_id))
return morph_path
def main():
# Read sensitivity analysis config file
sens_config_file = sys.argv[-1]
sens_config_dict = utility.load_json(sens_config_file)
cell_id = sens_config_dict['Cell_id']
cpu_count = sens_config_dict['cpu_count'] if 'cpu_count'\
in sens_config_dict.keys() else mp.cpu_count()
perisomatic_sa = sens_config_dict.get('run_peri_analysis',False)
# Parameters to vary (All-active)
select_aa_param_path = sens_config_dict['select_aa_param_path'] # knobs
# Parameters to vary (Perisomatic)
if perisomatic_sa:
select_peri_param_path = sens_config_dict['select_peri_param_path'] # knobs
select_feature_path = sens_config_dict['select_feature_path'] # knobs
param_mod_range = sens_config_dict.get('param_mod_range',.1) # knobs
mechanism_path = sens_config_dict['mechanism']
# config files with all the paths for Bluepyopt sim
lr = lims.LimsReader()
morph_path = lr.get_swc_path_from_lims(int(cell_id))
model_base_path='/allen/aibs/mat/ateam_shared/' \
'Mouse_Model_Fit_Metrics/{}'.format(cell_id)
opt_config_file = os.path.join(model_base_path,'config_file.json')
if not os.path.exists(opt_config_file):
opt_config = {
"morphology": "",
"parameters": "config/{}/parameters.json".format(cell_id),
"mechanism": "config/{}/mechanism.json".format(cell_id),
"protocols": "config/{}/protocols.json".format(cell_id),
"all_protocols": "config/{}/all_protocols.json".format(cell_id),
"features": "config/{}/features.json".format(cell_id),
"peri_parameters": "config/{}/peri_parameters.json".format(cell_id),
"peri_mechanism": "config/{}/peri_mechanism.json".format(cell_id)
}
opt_config_file = os.path.join(os.getcwd(),'config_file.json')
utility.save_json(opt_config_file,opt_config)
# optimized parameters around which select parameters are varied
optim_param_path_aa = '/allen/aibs/mat/ateam_shared/Mouse_Model_Fit_Metrics/'\
'{cell_id}/fitted_params/optim_param_unformatted_{cell_id}.json'.\
format(cell_id = cell_id)
if not os.path.exists(optim_param_path_aa):
optim_param_path_aa = '/allen/aibs/mat/ateam_shared/Mouse_Model_Fit_Metrics/'\
'{cell_id}/fitted_params/optim_param_{cell_id}_bpopt.json'.\
format(cell_id = cell_id)
SA_obj_aa = SA_helper(optim_param_path_aa,select_aa_param_path,param_mod_range,
opt_config_file)
_,protocol_path,mech_path,feature_path,\
param_bound_path = SA_obj_aa.load_config(model_base_path)
# Make sure to get the parameter bounds big enough for BluePyOpt sim
sens_param_bound_write_path_aa = "param_sensitivity_aa.json"
optim_param_aa = SA_obj_aa.create_sa_bound(param_bound_path,
sens_param_bound_write_path_aa)
param_dict_uc_aa = SA_obj_aa.create_sens_param_dict()
parameters_aa ={key:optim_param_aa[val] for key,val in param_dict_uc_aa.items()}
eval_handler_aa = Bpopt_Evaluator(protocol_path, feature_path,
morph_path, sens_param_bound_write_path_aa,
mech_path,
ephys_dir=None,
timed_evaluation = False)
evaluator_aa = eval_handler_aa.create_evaluator()
opt_aa = bpopt.optimisations.DEAPOptimisation(evaluator=evaluator_aa)
stim_protocols = utility.load_json(protocol_path)
stim_protocols = {key:val for key,val in stim_protocols.items() \
if 'LongDC' in key}
stim_dict = {key:val['stimuli'][0]['amp'] \
for key,val in stim_protocols.items()}
sorted_stim_tuple= sorted(stim_dict.items(), key=operator.itemgetter(1))
stim_name= sorted_stim_tuple[-1][0] # knobs (the max amp)
# Copy compiled modfiles
if not os.path.isdir('x86_64'):
raise Exception('Compiled modfiles do not exist')
efel_features = utility.load_json(select_feature_path)
un_features = un.EfelFeatures(features_to_run=efel_features)
un_parameters_aa = un.Parameters(parameters_aa)
un_parameters_aa.set_all_distributions(un.uniform(param_mod_range))
un_model_aa = un.Model(run=nrnsim_bpopt, interpolate=True,
labels=["Time (ms)", "Membrane potential (mV)"],
opt=opt_aa,stim_protocols =stim_protocols,
param_dict_uc = param_dict_uc_aa,
stim_name=stim_name,
optim_param=optim_param_aa)
# Perform the uncertainty quantification
UQ_aa = un.UncertaintyQuantification(un_model_aa,
parameters=un_parameters_aa,
features=un_features)
data_folder = 'sensitivity_data'
sa_filename_aa = 'sa_allactive_%s.h5'%cell_id
sa_filename_aa_csv = 'sa_allactive_%s.csv'%cell_id
sa_data_path_aa = os.path.join(data_folder,sa_filename_aa)
sa_aa_csv_path = os.path.join(data_folder,sa_filename_aa_csv)
UQ_aa.quantify(seed=0,CPUs=cpu_count,data_folder=data_folder,
filename= sa_filename_aa)
_ = SA_obj_aa.save_analysis_data(sa_data_path_aa,
filepath=sa_aa_csv_path)
cell_data_aa = un.Data(sa_data_path_aa)
SA_obj_aa.plot_sobol_analysis(cell_data_aa,analysis_path = \
'figures/sa_analysis_aa_%s.pdf'%cell_id,
palette='Set1')
# Perisomatic model
if perisomatic_sa:
try:
optim_param_path_peri = None
SA_obj_peri = SA_helper(optim_param_path_peri,select_peri_param_path,param_mod_range,
opt_config_file)
_,_,mech_path_peri,_,\
param_bound_path_peri = SA_obj_peri.load_config(model_base_path,
perisomatic=True)
sens_param_bound_write_path_peri = "param_sensitivity_peri.json"
optim_param_peri = SA_obj_peri.create_sa_bound_peri(param_bound_path_peri,
sens_param_bound_write_path_peri)
param_dict_uc_peri = SA_obj_peri.create_sens_param_dict()
parameters_peri ={key:optim_param_peri[val] for key,val in param_dict_uc_peri.items()}
eval_handler_peri = Bpopt_Evaluator(protocol_path, feature_path,
morph_path, sens_param_bound_write_path_peri,
mech_path_peri,
ephys_dir=None,
timed_evaluation = False)
evaluator_peri = eval_handler_peri.create_evaluator()
opt_peri = bpopt.optimisations.DEAPOptimisation(evaluator=evaluator_peri)
un_parameters_peri= un.Parameters(parameters_peri)
un_parameters_peri.set_all_distributions(un.uniform(param_mod_range))
un_model_peri = un.Model(run=nrnsim_bpopt, interpolate=True,
labels=["Time (ms)", "Membrane potential (mV)"],
opt=opt_peri,stim_protocols =stim_protocols,
param_dict_uc = param_dict_uc_peri,
stim_name=stim_name,
optim_param=optim_param_peri)
UQ_peri = un.UncertaintyQuantification(un_model_peri,
parameters=un_parameters_peri,
features=un_features)
sa_filename_peri = 'sa_perisomatic_%s.h5'%cell_id
sa_filename_peri_csv = 'sa_perisomatic_%s.csv'%cell_id
sa_data_path_peri = os.path.join(data_folder,sa_filename_peri)
sa_peri_csv_path = os.path.join(data_folder,sa_filename_peri_csv)
UQ_peri.quantify(seed=0,CPUs=cpu_count,data_folder=data_folder,
filename= sa_filename_peri)
_ = SA_obj_peri.save_analysis_data(sa_data_path_peri,
filepath=sa_peri_csv_path)
cell_data_peri = un.Data(sa_data_path_peri)
SA_obj_peri.plot_sobol_analysis(cell_data_peri,analysis_path = \
'figures/sa_analysis_peri_%s.pdf'%cell_id,
palette='Set2')
except Exception as e:
print(e)