glitter_extract_old_to_new.py

from os import listdir
from os.path import join, splitext
from re import match
import re
import numpy as np
import operator
from glitter.logger import DataLogger

filename_pat = re.compile('Carvone Trial([0-9]+) +([0-9]+)_updated_\\.h5')


def update_files(root):
    logger = DataLogger()
    for fname in listdir(root):
        src = join(root, fname)
        dest = '{}_updated_{}'.format(*splitext(src))
        logger.upgrade_legacy_file(src, dest)


def get_dig_latency(root, pat=filename_pat):
    data = {}
    logger = DataLogger()
    for fname in listdir(root):
        fname_full = join(root, fname)
        m = match(pat, fname)
        if m is None:
            continue

        day, rat = m.groups()
        logger.open_file(fname_full)
        s = logger.t_h5.TrialStart_0
        d = logger.t_h5.DigStart_1
        pts = logger.pts_h5

        vals = []
        for item in (pts, s, d):
            vals.append(np.concatenate(item._f_list_nodes()))

        if len(vals[0]) != len(vals[1]) or len(vals[1]) != len(vals[2]):
            raise Exception('Unequal data sizes')

        pts, s, d = vals
        st, dt = pts[s], pts[d]
        if len(st) != len(dt):
            print(
                "{}: The number of trial start times and digging start times "
                "doesn't match; {}, {}".format(fname, len(st), len(dt)))
            continue

        latency = dt - st
        if not all(map(lambda x: x >= 0, latency)):
            raise Exception('Not all latencies are non-negative')

        data[(fname, day, rat)] = latency
        logger.close_file()

    return data


if __name__ == '__main__':
    root = r'C:\kivy-glitter-build\erin'
    update_files(root)
    data = get_dig_latency(root)
    print('Name,Day,Rat,Count,Trial,Latency')
    for (fname, day, rat), latency in data.items():
        for i, val in enumerate(latency):
            print('{},{},{},{},{},{}'.format(fname, day, rat, len(latency), i + 1, val))