def test_abf(rootdir):
"""Test loading of abf"""
config = json.load(open(os.path.join(rootdir, 'configs', 'abf1.json')))
config['path'] = os.path.join(rootdir, config['path'])
extractor = bpefe.Extractor('testtype_abf', config, use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features(threshold=-30)
extractor.mean_features()
extractor.plt_features()
extractor.feature_config_cells()
extractor.feature_config_all()
def extr_features(self):
with open(self.config_file, "r") as file:
config = json.load(file)
extractor = bpefe.Extractor('test_run', config)
extractor.create_dataset()
extractor.create_metadataset()
#extractor.plt_traces()
extractor.extract_features(threshold=-20)
extractor.mean_features()
#extractor.analyse_threshold()
#extractor.plt_features()
extractor.feature_config_cells(version='legacy')
extractor.feature_config_all(version='legacy')
def test_config(rootdir, config_path):
"""Test config"""
config = json.load(open(config_path))
config['path'] = os.path.join(rootdir, config['path'])
extractor = bpefe.Extractor('test_run', config, use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features(threshold=-30)
extractor.mean_features()
# extractor.analyse_threshold()
extractor.plt_features()
extractor.feature_config_cells()
extractor.feature_config_all()
extractor.plt_features_dist()
'''
def test_ibf_json(rootdir):
"""Test ibf json"""
config_str = """
{
"cells": {
"970509hp2": {
"etype": "etype",
"exclude": [
[
-1.8
],
[
-1.8
]
],
"experiments": {
"step": {
"files": [
"rattus-norvegicus____hippocampus____ca1____interneuron____cac____970509hp2____97509008",
"rattus-norvegicus____hippocampus____ca1____interneuron____cac____970509hp2____97509009"
],
"location": "soma"
}
},
"ljp": 0,
"v_corr": 0
}
},
"comment": [],
"features": {
"step": [
"time_to_last_spike",
"time_to_second_spike",
"voltage",
"voltage_base"
]
},
"format": "ibf_json",
"options": {
"delay": 500,
"logging": false,
"nanmean": false,
"relative": false,
"target": [
"all"
],
"tolerance": 0.02
},
"path": "./data_ibf_json/eg_json_data/traces"
}
"""
config = json.loads(config_str)
json.dump(config, open(os.path.join(rootdir, 'configs', 'ibf_json1.json'),
'w'), sort_keys=True, indent=4)
config['path'] = os.path.join(rootdir, config['path'])
import bluepyefe as bpefe
extractor = bpefe.Extractor(
'temptype_ibf', config)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features(threshold=-30)
extractor.mean_features()
extractor.plt_features()
extractor.feature_config_cells(version='legacy')
extractor.feature_config_all(version='legacy')
def test_config(rootdir):
"""Test config"""
config_str = """
{
"comment": [
"v_corr: normalize membrane potential to this value",
"ljp: set so to 14mV",
"etype: was defined individually by eye from plotted traces"
],
"features": {
"IDthresh": [
"adaptation_index2",
"mean_frequency",
"time_to_first_spike",
"ISI_log_slope",
"ISI_log_slope_skip",
"time_to_last_spike",
"inv_time_to_first_spike",
"inv_first_ISI",
"inv_second_ISI",
"inv_third_ISI",
"inv_fourth_ISI",
"inv_fifth_ISI",
"inv_last_ISI",
"voltage_deflection",
"voltage_deflection_begin",
"steady_state_voltage",
"decay_time_constant_after_stim",
"AP_amplitude"
]
},
"format": "igor",
"cells": {
"C060109A2-SR-C1": {
"ljp": 14,
"v_corr": false,
"experiments": {
"IDthresh": {
"files": [
{
"ordinal": "348",
"i_unit": "A",
"v_file": "C060109A2-SR-C1/X_IDthresh_ch1_348.ibw",
"t_unit": "s",
"i_file": "C060109A2-SR-C1/X_IDthresh_ch0_348.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "349",
"i_unit": "A",
"v_file": "C060109A2-SR-C1/X_IDthresh_ch1_349.ibw",
"t_unit": "s",
"i_file": "C060109A2-SR-C1/X_IDthresh_ch0_349.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "350",
"i_unit": "A",
"v_file": "C060109A2-SR-C1/X_IDthresh_ch1_350.ibw",
"t_unit": "s",
"i_file": "C060109A2-SR-C1/X_IDthresh_ch0_350.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "351",
"i_unit": "A",
"v_file": "C060109A2-SR-C1/X_IDthresh_ch1_351.ibw",
"t_unit": "s",
"i_file": "C060109A2-SR-C1/X_IDthresh_ch0_351.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "352",
"i_unit": "A",
"v_file": "C060109A2-SR-C1/X_IDthresh_ch1_352.ibw",
"t_unit": "s",
"i_file": "C060109A2-SR-C1/X_IDthresh_ch0_352.ibw",
"v_unit": "V",
"dt": 0.00025
}
],
"location": "soma.v"
}
}
},
"C060109A1-SR-C1": {
"ljp": 14,
"v_corr": false,
"experiments": {
"IDthresh": {
"files": [
{
"ordinal": "349",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_349.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_349.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "350",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_350.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_350.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "351",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_351.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_351.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "352",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_352.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_352.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "353",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_353.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_353.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "354",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_354.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_354.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "355",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_355.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_355.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "356",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_356.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_356.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "357",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_357.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_357.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "362",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_362.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_362.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "363",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_363.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_363.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "364",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_364.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_364.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "365",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_365.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_365.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "366",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_366.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_366.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "367",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_367.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_367.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "368",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_368.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_368.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "369",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_369.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_369.ibw",
"v_unit": "V",
"dt": 0.00025
},
{
"ordinal": "370",
"i_unit": "A",
"v_file": "C060109A1-SR-C1/X_IDthresh_ch1_370.ibw",
"t_unit": "s",
"i_file": "C060109A1-SR-C1/X_IDthresh_ch0_370.ibw",
"v_unit": "V",
"dt": 0.00025
}
],
"location": "soma.v"
}
}
}
},
"path": "./data/",
"options": {
"expthreshold": [
"IDrest",
"IDthresh"
],
"relative": true,
"delay": 0,
"nanmean": false,
"target": [
-20,
"noinput",
50,
100,
120,
"all"
],
"tolerance": [
5,
false,
5,
5,
5,
false
],
"nangrace": 0,
"spike_threshold": 1,
"amp_min": 0,
"strict_stiminterval": {
"SpikeRec": false,
"base": true
},
"onoff": {
"TesteCode": [
100.0,
600.0
],
"APWaveform": [
5.0,
55.0
],
"IV": [
20.0,
1020.0
],
"IDrest": [
700.0,
2700.0
],
"SpontAPs": [
100.0,
10100.0
],
"APDrop": [
10.0,
15.0
],
"IRhyperpol": [
500.0,
700.0
],
"Spontaneous": [
100.0,
10100.0
],
"IDthresh": [
700.0,
2700.0
],
"APThreshold": [
0.0,
2000.0
],
"SpikeRec": [
10.0,
13.5
],
"IDdepol": [
700.0,
2700.0
],
"Step": [
700.0,
2700.0
],
"Delta": [
10.0,
60.0
],
"IRdepol": [
500.0,
700.0
]
},
"logging": true,
"boxcox": false
}
}
"""
config = json.loads(config_str)
json.dump(config,
open(os.path.join(rootdir, 'configs', 'ibw1.json'), 'w'),
sort_keys=True,
indent=4)
config['path'] = os.path.join(rootdir, config['path'])
extractor = bpefe.Extractor('testtype_legacy', config, use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features(threshold=-30)
extractor.mean_features()
extractor.analyse_threshold()
extractor.plt_features()
extractor.feature_config_cells(version='legacy')
extractor.feature_config_all(version='legacy')
extractor = bpefe.Extractor('testtype', config, use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features(threshold=-30)
extractor.mean_features()
extractor.analyse_threshold()
extractor.plt_features()
extractor.feature_config_cells()
extractor.feature_config_all()
extractor.plt_features_dist()
def test_csv(rootdir):
"""Test loading from csv"""
config_str = """
{
"features": {
"step": [
"ISI_log_slope",
"mean_frequency",
"adaptation_index2",
"ISI_CV",
"AP_height",
"AHP_depth_abs",
"AHP_depth_abs_slow",
"AHP_slow_time",
"AP_width",
"AP_amplitude",
"AP1_amp",
"AP2_amp",
"APlast_amp",
"AP_duration_half_width",
"AHP_depth",
"fast_AHP",
"AHP_time_from_peak",
"voltage_deflection",
"voltage_deflection_begin",
"voltage_base",
"steady_state_voltage",
"Spikecount",
"time_to_last_spike",
"time_to_first_spike",
"inv_time_to_first_spike",
"inv_first_ISI",
"inv_second_ISI",
"inv_third_ISI",
"inv_fourth_ISI",
"inv_fifth_ISI",
"inv_last_ISI",
"decay_time_constant_after_stim",
"AP_begin_voltage",
"AP_rise_time",
"AP_fall_time",
"AP_rise_rate",
"AP_fall_rate"
]
},
"path": "./data_csv/",
"format": "csv_lccr",
"comment": [
"cells named using name of first trace file belonging to this cell",
"v_corr: normalize membrane potential to this value
(given in UCL excel sheet)",
"ljp: set so that RMP (UCL) - 10mV ljp = RMP (Golding 2001) -14mV ljp",
"etype: was defined individually by eye from plotted traces"
],
"cells": {
"TEST_CELL": {
"v_corr": false,
"ljp": 14.4,
"experiments": {
"step": {
"location": "soma",
"files": [
"s150420-0403_ch1_cols",
"s150420-0404_ch1_cols"
],
"dt": 0.2,
"startstop": [
200,
1000
],
"amplitudes": [
0.01,
-0.01,
0.02,
-0.02,
0.03,
-0.03,
0.04,
-0.04,
0.05,
-0.05,
0.06,
-0.06,
0.07,
-0.07,
0.08,
-0.08,
0.09,
-0.09,
0.1,
-0.1,
0.15,
0.2,
0.25,
0.3,
0.4,
0.5,
0.6
],
"hypamp": 0.0,
"ton": 200,
"toff": 1000
}
}
}
},
"options": {
"relative": false,
"tolerance": 0.01,
"target": [
0.02,
-0.02,
0.04,
-0.04,
0.06,
-0.06,
0.08,
-0.08,
0.1,
-0.1,
0.2,
0.3,
0.4,
0.5,
0.6
],
"delay": 200,
"nanmean": false
}
}
"""
config = json.loads(config_str)
json.dump(config,
open(os.path.join(rootdir, 'configs', 'csv1.json'), 'w'),
sort_keys=True,
indent=4)
config['path'] = os.path.join(rootdir, config['path'])
import bluepyefe as bpefe
extractor = bpefe.Extractor('testtype_csv', config, use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features()
extractor.mean_features()
# extractor.analyse_threshold()
extractor.feature_config_cells()
extractor.feature_config_all()
extractor.plt_features()
def extract_features(request):
# if not ctx exit the application
if "ctx" not in request.session:
return render(request, 'efelg/overview.html')
selected_traces_rest_json = request.session['selected_traces_rest_json']
global_parameters_json = request.session['global_parameters_json']
allfeaturesnames = efel.getFeatureNames()
username = request.session['username']
time_info = request.session['time_info']
# conf_dir = request.session['main_json_dir']
conf_dir = EfelStorage.getMainJsonDir()
# traces_files_dir = request.session['user_files_dir']
traces_files_dir = EfelStorage.getTracesDir()
# user_files_dir = request.session['user_files_dir']
user_files_dir = EfelStorage.getUserFilesDir(username, time_info)
# user_results_dir = request.session['user_results_dir']
user_results_dir = EfelStorage.getResultsDir(username, time_info)
selected_features = request.session["selected_features"]
cell_dict = {}
for k in selected_traces_rest_json:
path_to_file = os.path.join(user_files_dir, k + '.json')
if k + '.json' not in os.listdir(user_files_dir):
shutil.copy2(os.path.join(traces_files_dir, k + '.json'),
path_to_file)
with open(path_to_file) as f:
crr_file_dict = json.loads(f.read())
crr_file_all_stim = list(crr_file_dict['traces'].keys())
crr_file_sel_stim = selected_traces_rest_json[k]['stim']
if "stimulus_unit" in crr_file_dict:
crr_file_amp_unit = crr_file_dict["stimulus_unit"]
elif "amp_unit" in crr_file_dict:
crr_file_amp_unit = crr_file_dict["amp_unit"]
else:
raise Exception("stimulus_unit not found!")
if "cell_id" in crr_file_dict:
crr_cell_name = crr_file_dict["cell_id"]
elif "name" in crr_file_dict:
crr_cell_name = crr_file_dict["name"]
else:
raise Exception("cell_id not found!")
new_keys = [("animal_species", "species"), ("brain_structure", "area"),
("cell_soma_location", "region"), ("cell_type", "type"),
("etype", "etype"), ("cell_id", "name")]
keys = [
crr_file_dict[t[0]]
if t[0] in crr_file_dict else crr_file_dict[t[1]] for t in new_keys
]
keys2 = []
for kk2 in keys:
if not type(kk2) == list:
keys2.append(kk2)
else:
for kkk in kk2:
keys2.append(kkk)
crr_key = '____'.join(keys2)
"""
if crr_key in cell_dict:
print("here")
cell_dict[crr_key]['stim'].append(crr_file_sel_stim)
cell_dict[crr_key]['files'].append(k)
cell_dict[crr_key]['v_corr'] = crr_vcorr
else:
"""
cell_dict[crr_key] = {}
cell_dict[crr_key]['stim'] = [crr_file_sel_stim]
cell_dict[crr_key]['files'] = [k]
cell_dict[crr_key]['cell_name'] = crr_cell_name
cell_dict[crr_key]['all_stim'] = crr_file_all_stim
cell_dict[crr_key]['v_corr'] = [
int(selected_traces_rest_json[k]['v_corr'])
]
target = []
final_cell_dict = {}
final_exclude = []
for key in cell_dict:
crr_el = cell_dict[key]
for c_stim_el in crr_el['stim']:
[
target.append(float(i)) for i in c_stim_el
if float(i) not in target
]
exc_stim_lists = [
list(set(crr_el['all_stim']) - set(sublist))
for sublist in crr_el['stim']
]
crr_exc = []
for crr_list in exc_stim_lists:
crr_stim_val = [float(i) for i in crr_list]
crr_exc.append(crr_stim_val)
final_cell_dict[cell_dict[key]['cell_name']] = \
{
'v_corr': crr_el['v_corr'],
'ljp': 0,
'experiments': {
'step': {
'location': 'soma',
'files': [str(i) for i in crr_el['files']]
}
},
'etype': 'etype',
'exclude': crr_exc,
'exclude_unit': [crr_file_amp_unit for i in range(len(crr_exc))]
}
# build configuration dictionary
config = {}
config['features'] = {'step': [str(i) for i in selected_features]}
config['path'] = user_files_dir
config['format'] = 'ibf_json'
config['comment'] = []
config['cells'] = final_cell_dict
config['options'] = {
# 'featconffile': './pt_conf.json',
# 'featzerotonan': False,
'zero_to_nan': {
'flag':
bool(global_parameters_json['zero_to_nan']),
'value':
global_parameters_json['value'],
'mean_features_no_zeros':
global_parameters_json['mean_features_no_zeros']
},
'relative': False,
'tolerance': 0.02,
'target': target,
'target_unit': 'nA',
'delay': 500,
'nanmean': True,
'logging': True,
'nangrace': 0,
# 'spike_threshold': 1,
'amp_min': -1e22,
'zero_std': bool(global_parameters_json['zero_std']),
'trace_check': False,
'strict_stiminterval': {
'base': True
},
'print_table': {
'flag': True,
'num_events': int(global_parameters_json['num_events']),
}
}
try:
main_results_folder = os.path.join(user_results_dir,
time_info + "_nfe_results")
extractor = bpefe.Extractor(main_results_folder, config)
extractor.create_dataset()
extractor.plt_traces()
if global_parameters_json['threshold'] != '':
extractor.extract_features(
threshold=int(global_parameters_json['threshold']))
else:
extractor.extract_features(threshold=-20)
extractor.mean_features()
extractor.plt_features()
extractor.feature_config_cells(version="legacy")
extractor.feature_config_all(version="legacy")
except ValueError as e:
print('SOME ERROR OCCURED')
print(e)
conf_cit = os.path.join(conf_dir, 'citation_list.json')
final_cit_file = os.path.join(main_results_folder, 'HOWTOCITE.txt')
resources.print_citations(selected_traces_rest_json, conf_cit,
final_cit_file)
zip_name = time_info + '_nfe_results.zip'
zip_path = os.path.join(user_results_dir, zip_name)
request.session['nfe_result_file_zip'] = zip_path
request.session['nfe_result_file_zip_name'] = zip_name
for k in selected_traces_rest_json:
f = os.path.join(user_results_dir, k + ".json")
if os.path.exists(f):
os.remove(f)
#parent_folder = os.path.dirname(full_crr_result_folder)
contents = os.walk(main_results_folder)
try:
zip_file = zipfile.ZipFile(zip_path, 'w', zipfile.ZIP_DEFLATED)
for root, folders, files in contents:
for folder_name in folders:
absolute_path = os.path.join(root, folder_name)
relative_path = absolute_path.replace(
main_results_folder + os.sep, '')
zip_file.write(absolute_path, relative_path)
for file_name in files:
absolute_path = os.path.join(root, file_name)
relative_path = absolute_path.replace(
main_results_folder + os.sep, '')
zip_file.write(absolute_path, relative_path)
except IOError as message:
print(message)
sys.exit(1)
except OSError as message:
print(message)
sys.exit(1)
except zip_file.BadZipfile as message:
print(message)
sys.exit(1)
finally:
zip_file.close()
# accesslogger.info(resources.string_for_log('extract_features', request, page_spec_string='___'.join(check_features)))
return HttpResponse(json.dumps({"status": "OK"}))
def extract_features(request):
# if not ctx exit the application
if not "ctx" in request.session:
return render(request, 'efelg/hbp_redirect.html')
data_dir = request.session['data_dir']
json_dir = request.session['json_dir']
selected_traces_rest_json = request.session['selected_traces_rest_json']
allfeaturesnames = efel.getFeatureNames()
crr_user_folder = request.session['time_info']
full_crr_result_folder = request.session['u_crr_res_r_dir']
full_crr_uploaded_folder = request.session['u_up_dir']
full_crr_data_folder = request.session['u_crr_res_d_dir']
full_crr_user_folder = request.session['user_crr_res_dir']
check_features = request.session["check_features"]
request.session['selected_features'] = check_features
cell_dict = {}
selected_traces_rest = []
for k in selected_traces_rest_json:
#crr_vcorr = selected_traces_rest_json[k]['vcorr']
crr_file_rest_name = k + '.json'
crr_name_split = k.split('____')
crr_cell_name = crr_name_split[5]
crr_sample_name = crr_name_split[6]
crr_key = crr_name_split[0] + '____' + crr_name_split[1] + '____' + \
crr_name_split[2] + '____' + crr_name_split[3] + '____' + \
crr_name_split[4] + '____' + crr_name_split[5]
if os.path.isfile(os.path.join(json_dir, crr_file_rest_name)):
crr_json_file = os.path.join(json_dir, crr_file_rest_name)
elif os.path.isfile(os.path.join(full_crr_uploaded_folder, \
crr_file_rest_name)):
crr_json_file = os.path.join(full_crr_uploaded_folder, \
crr_file_rest_name)
else:
continue
with open(crr_json_file) as f:
crr_file_dict_read = f.read()
crr_file_dict = json.loads(crr_file_dict_read)
crr_file_all_stim = crr_file_dict['traces'].keys()
crr_file_sel_stim = selected_traces_rest_json[k]['stim']
crr_cell_data_folder = os.path.join(full_crr_data_folder,
crr_cell_name)
crr_cell_data_folder = full_crr_data_folder
if not os.path.exists(crr_cell_data_folder):
os.makedirs(crr_cell_data_folder)
shutil.copy2(crr_json_file, crr_cell_data_folder)
#
if crr_key in cell_dict:
cell_dict[crr_key]['stim'].append(crr_file_sel_stim)
cell_dict[crr_key]['files'].append(k)
#cell_dict[crr_key]['vcorr'].append(float(crr_vcorr))
else:
cell_dict[crr_key] = {}
cell_dict[crr_key]['stim'] = [crr_file_sel_stim]
cell_dict[crr_key]['files'] = [k]
cell_dict[crr_key]['cell_name'] = crr_cell_name
cell_dict[crr_key]['all_stim'] = crr_file_all_stim
#cell_dict[crr_key]['vcorr'] = [float(crr_vcorr)]
target = []
final_cell_dict = {}
final_exclude = []
for key in cell_dict:
crr_el = cell_dict[key]
#v_corr = crr_el['vcorr']
v_corr = 0
for c_stim_el in crr_el['stim']:
[
target.append(float(i)) for i in c_stim_el
if float(i) not in target
]
exc_stim_lists = [list(set(crr_el['all_stim']) - set(sublist)) for \
sublist in crr_el['stim']]
crr_exc = []
for crr_list in exc_stim_lists:
crr_stim_val = [float(i) for i in crr_list]
crr_exc.append(crr_stim_val)
final_cell_dict[cell_dict[key]['cell_name']] = {'v_corr':v_corr, \
'ljp':0, 'experiments':{'step': {'location':'soma', 'files': \
[str(i) for i in crr_el['files']]}}, 'etype':'etype', \
'exclude':crr_exc}
# build configuration dictionary
config = {}
config['features'] = {'step': [str(i) for i in check_features]}
config['path'] = crr_cell_data_folder
config['format'] = 'ibf_json'
config['comment'] = []
config['cells'] = final_cell_dict
config['options'] = {'relative': False, 'tolerance': 0.02, \
'target': target, 'delay': 500, 'nanmean': False, 'logging':False, \
'nangrace': 0, 'spike_threshold': 1, 'amp_min': 0,
'strict_stiminterval': {'base': True}}
try:
extractor = bpefe.Extractor(full_crr_result_folder,
config,
use_git=False)
extractor.create_dataset()
extractor.plt_traces()
extractor.extract_features()
extractor.mean_features()
extractor.plt_features()
extractor.feature_config_cells(version="legacy")
extractor.feature_config_all(version="legacy")
except:
return render(request, 'efelg/hbp_redirect.html', {"status":"KO", \
"message": "An error occured while extracting the features. \
Either you selected too many data or the traces were corrupted." })
conf_dir = request.session['conf_dir']
conf_cit = os.path.join(conf_dir, 'citation_list.json')
final_cit_file = os.path.join(full_crr_result_folder, 'HOWTOCITE.txt')
resources.print_citations(selected_traces_rest_json, conf_cit,
final_cit_file)
crr_result_folder = request.session['time_info']
output_path = os.path.join(full_crr_user_folder, crr_user_folder + \
'_results.zip')
request.session['result_file_zip'] = output_path
request.session['result_file_zip_name'] = crr_user_folder + '_results.zip'
parent_folder = os.path.dirname(full_crr_result_folder)
contents = os.walk(full_crr_result_folder)
try:
zip_file = zipfile.ZipFile(output_path, 'w', zipfile.ZIP_DEFLATED)
for root, folders, files in contents:
for folder_name in folders:
absolute_path = os.path.join(root, folder_name)
relative_path = absolute_path.replace(parent_folder + \
os.sep, '')
zip_file.write(absolute_path, relative_path)
for file_name in files:
absolute_path = os.path.join(root, file_name)
relative_path = absolute_path.replace(parent_folder + \
os.sep, '')
zip_file.write(absolute_path, relative_path)
except IOError as message:
print(message)
sys.exit(1)
except OSError as message:
print(message)
sys.exit(1)
except zip_file.BadZipfile as message:
print(message)
sys.exit(1)
finally:
zip_file.close()
accesslogger.info(resources.string_for_log('extract_features', \
request, page_spec_string = '___'.join(check_features)))
return HttpResponse(json.dumps({"status": "OK"}))