3ba2b1fe6ff138deba0edaedb5de5867

driver_sort_datasets.py

import argparse
import spikeforest as sf
import os

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description = 'Sort the SpikeForest datasets')
    parser.add_argument('command',help='sort, clear_in_process, clear_all, assemble')
    parser.add_argument('study',help='The name of the study')
    args = parser.parse_args()

    spikeforest_password=os.environ.get('SPIKEFOREST_PASSWORD','')
    if not spikeforest_password:
      raise Exception('Environment variable not set: SPIKEFOREST_PASSWORD')
    
    sf.kbucketConfigRemote(
      share_id='spikeforest.spikeforest1',
      write=True,
      password=spikeforest_password
    )

    command=args.command
    study_name=args.study
    if command=='clear_in_process':
      sf.batch.clear_sorting_results(study_name=study_name,in_process_only=True)
    elif command=='clear_all':
      sf.batch.clear_sorting_results(study_name=study_name,in_process_only=False)
    elif command=='sort':
      sf.batch.sort_datasets(study_name=study_name)
    elif command=='assemble':
      sf.batch.assemble_sorting_results(study_name=study_name)
    else:
      raise Exception('Unrecognized command: '+command)

notebook.ipynb

run.sh

#!/bin/bash

set -e

# Set number of cpu's to use for spike sorting
export NUM_WORKERS=2
export MKL_NUM_THREADS=$NUM_WORKERS
export NUMEXPR_NUM_THREADS=$NUM_WORKERS
export OMP_NUM_THREADS=$NUM_WORKERS

#study=magland_synth_noise10_K10_C4
study=magland_synth_noise20_K10_C4

python driver_sort_datasets.py clear_in_process $study

srun -c 2 -n 40 python driver_sort_datasets.py sort $study
#srun -c 2 -n 1 python driver_sort_datasets.py sort $study
#python driver_sort_datasets.py sort $study

python driver_sort_datasets.py assemble $study