pipeline_utils.py

import os
import fnmatch
import numpy as np
from sorting.readSGLX import readMeta, SampRate, makeMemMapRaw, ExtractDigital
import scipy.io
import shutil
from pathlib import Path

def find(pattern, path):
    result = []
    for root, dirs, files in os.walk(path):
        for name in files:
            if fnmatch.fnmatch(name, pattern):
                result.append(os.path.join(root, name))
        for name in dirs:
            if fnmatch.fnmatch(name, pattern):
                result.append(os.path.join(root, name))
    return result


def create_config(script_folder, folder):
    shutil.copyfile(script_folder + '/config_template.yaml', folder + '/config.yaml')


def extract_sync(config_kilosort):
    meta = readMeta(Path(config_kilosort['neuropixel']))
    tStart = 0
    tEnd = np.floor(float(meta['fileTimeSecs']))
    sRate = SampRate(meta)
    firstSamp = int(sRate * tStart)
    lastSamp = int(sRate * tEnd)
    rawData = makeMemMapRaw(Path(config_kilosort['neuropixel']), meta)
    sync_data = dict([])
    sync_data['sync'] = ExtractDigital(rawData, firstSamp, lastSamp, 0, [6], meta)
    scipy.io.savemat(config_kilosort['neuropixel_folder'] + '/sync.mat', sync_data, do_compression=True)