Python getFile Examples

Example #1

# -*- coding: utf-8 -*-
"""
Created on Mon Sep 17 12:43:05 2018

@author: svc_ccg
"""
import fileIO
import pandas as pd
import cv2
import os
import numpy as np

imageDictPickleFile = fileIO.getFile()
imageDict = pd.read_pickle(imageDictPickleFile)

saveDir = fileIO.getDir()

downSampleFactor = 9
for image in imageDict:
    im = imageDict[image][image]
    im_thumb = cv2.resize(im,
                          tuple(np.array(im.shape)[::-1] / downSampleFactor),
                          interpolation=cv2.INTER_AREA)

    cv2.imwrite(os.path.join(saveDir, image + ".jpg"), im)
    cv2.imwrite(os.path.join(saveDir, image + "_thumbnail.jpg"), im_thumb)

Example #2

File: plotPerformanceOverTime.py Project: cstrawder/Masking-EDA

# -*- coding: utf-8 -*-
"""
Created on Mon Aug 12 12:36:41 2019

@author: svc_ccg
"""
"""
Script that plots the performance of individual mice over time.  
For the position task, Produces 2 separate plots:  1 includes percent correct by side and no-gos.  
The other has no response trials and the direction turned for no-go trials.

For the orientation task, returns a single plot with all information (no no-go trials)

"""


import h5py
import fileIO
import numpy as np
from performanceData import performance_data

f = fileIO.getFile(rootDir=r'\\allen\programs\braintv\workgroups\nc-ophys\corbettb\Masking')
d = h5py.File(f)

performance_data(mouse='477210', ignoreRepeats=True)

Example #3

File: ultra_analysis.py Project: corbennett/ephys_behavior

#ymin = rawData[channelsToPlot,samplesToPlot].min()
#ymax = rawData[channelsToPlot,samplesToPlot].max()
#for i,ch in enumerate(channelsToPlot):
#    ax = fig.add_subplot(len(channelsToPlot),1,i+1)
#    ax.plot(rawData[ch,samplesToPlot],'k')
#    for side in ('right','top'):
#        ax.spines[side].set_visible(False)
#    ax.set_ylim([ymin,ymax])
#    ax.set_ylabel('uV')
#    if i==len(channelsToPlot)-1:
#        ax.set_xlabel('Sample')
#    ax.set_title('ch '+str(ch))
#plt.tight_layout()

# sync data
syncFile = fileIO.getFile('select sync file')
syncDataset = sync.Dataset(syncFile)

probeEventsDir = os.path.join(
    os.path.join(probeDataDir, 'events',
                 'Neuropix-PXI-' + pxiDict[probeLabel]), 'TTL_1')

# get barcodes from sync file
bRising, bFalling = get_sync_line_data(syncDataset, 'barcode')
bs_t, bs = ecephys.extract_barcodes_from_times(bRising, bFalling)

# get barcodes from ephys data
channel_states = np.load(os.path.join(probeEventsDir, 'channel_states.npy'))
event_times = np.load(os.path.join(probeEventsDir, 'event_timestamps.npy'))

beRising = event_times[channel_states > 0] / 30000.