# if the directory animal name_date does not yet exist, create it
catGT_dest = os.path.join(catGT_dest_parent, session_id)
if not os.path.exists(catGT_dest):
os.mkdir(catGT_dest)
# probe list == probe label list for 3A
prb_list = spec[4]
# inputs for tPrime
fromStream_list = list()
# build path to the first probe folder; look into that folder
# to determine the range of trials if the user specified t limits as
# start and end
runFolder = os.path.join(npx_directory, prb_list[0], spec[0], spec[1])
first_trig, last_trig = SpikeGLX_utils.ParseTrigStr(
spec[3], '', spec[2], runFolder)
trigger_str = repr(first_trig) + ',' + repr(last_trig)
# loop over all probes in hte run to build json files of input parameters
# initalize lists for input and output json files
catGT_input_json = []
catGT_output_json = []
module_input_json = []
module_output_json = []
session_id = []
data_directory = []
# first loop over probes creates json files containing parameters for
# both preprocessing (CatGt) and sorting + postprocessing
for i, prb in enumerate(prb_list):
for spec in run_specs:
session_id = spec[0]
# Run CatGT
input_json = os.path.join(json_directory, session_id + '-input.json')
output_json = os.path.join(json_directory, session_id + '-output.json')
# Make list of probes from the probe string
prb_list = SpikeGLX_utils.ParseProbeStr(spec[3])
# build path to the first probe folder
run_folder_name = spec[0] + '_g' + spec[1]
prb0_fld_name = run_folder_name + '_imec' + prb_list[0]
prb0_fld = os.path.join(npx_directory, run_folder_name, prb0_fld_name)
first_trig, last_trig = SpikeGLX_utils.ParseTrigStr(spec[2], prb0_fld)
trigger_str = repr(first_trig) + ',' + repr(last_trig)
print('Creating json file for preprocessing')
info = createInputJson(input_json,
npx_directory=npx_directory,
continuous_file=None,
spikeGLX_data='True',
kilosort_output_directory=catGT_dest,
catGT_run_name=session_id,
gate_string=spec[1],
trigger_string=trigger_str,
probe_string=spec[3],
catGT_stream_string=catGT_stream_string,
catGT_cmd_string=catGT_cmd_string,
extracted_data_directory=catGT_dest)