def runOne(session_id, json_directory, data_directory, run_CatGT,
catGT_input_json, catGT_output_json, modules, module_input_json,
logFullPath):
if run_CatGT:
print(f'\n--- {session_id}: CatGT... ---')
command = sys.executable + " -W ignore -m ecephys_spike_sorting.modules." + 'catGT_helper' + " --input_json " + catGT_input_json \
+ " --output_json " + catGT_output_json
print(command)
subprocess.check_call(command.split(' '))
print(f'--- {session_id}: CatGT Done! --- \n')
# copy module json file to data directory as record of the input parameters
shutil.copy(module_input_json,
os.path.join(data_directory, session_id + '-input.json'))
for module in modules:
print(f'\n--- {session_id}: {module}... ---')
output_json = os.path.join(json_directory,
session_id + '-' + module + '-output.json')
command = sys.executable + " -W ignore -m ecephys_spike_sorting.modules." + module + " --input_json " + module_input_json \
+ " --output_json " + output_json
print(command)
subprocess.check_call(command.split(' '))
print(f'--- {session_id}: {module} Done! --- \n')
log_from_json.addEntry(modules, json_directory, session_id,
logFullPath) # -*- coding: utf-8 -*-
def runOne(session_id, json_directory, data_directory, run_CatGT,
catGT_input_json, catGT_output_json, modules, module_input_json,
logFullPath):
if run_CatGT:
command = "python -W ignore -m ecephys_spike_sorting.modules." + 'catGT_helper' + " --input_json " + catGT_input_json \
+ " --output_json " + catGT_output_json
subprocess.check_call(command.split(' '))
# copy module json file to data directory as record of the input parameters
shutil.copy(module_input_json,
os.path.join(data_directory, session_id + '-input.json'))
for module in modules:
output_json = os.path.join(json_directory,
session_id + '-' + module + '-output.json')
command = "python -W ignore -m ecephys_spike_sorting.modules." + module + " --input_json " + module_input_json \
+ " --output_json " + output_json
subprocess.check_call(command.split(' '))
log_from_json.addEntry(modules, json_directory, session_id,
logFullPath) # -*- coding: utf-8 -*-
catGT_gfix_edits=gfix_edits[i],
extracted_data_directory=catGT_dest,
event_ex_param_str=event_ex_param_str)
# copy json file to data directory as record of the input parameters (and gfix edit rates)
shutil.copy(input_json,
os.path.join(data_directory, session_id + '-input.json'))
for module in modules:
output_json = os.path.join(
json_directory, session_id + '-' + module + '-output.json')
command = "python -W ignore -m ecephys_spike_sorting.modules." + module + " --input_json " + input_json \
+ " --output_json " + output_json
subprocess.check_call(command.split(' '))
log_from_json.addEntry(modules, json_directory, session_id,
logFullPath)
if runTPrime:
# after loop over probes, run TPrime to create files of
# event times -- edges detected in auxialliary files and spike times
# from each probe -- all aligned to a reference stream.
# create json files for calling TPrime
session_id = spec[0] + '_TPrime'
input_json = os.path.join(json_directory, session_id + '-input.json')
output_json = os.path.join(json_directory, session_id + '-output.json')
info = createInputJson(input_json,
npx_directory=npx_directory,
continuous_file=continuous_file,
spikeGLX_data=True,