def test_qc_extract(self):
# extract a short lf signal RMS
for fbin in Path(self.init_folder).rglob('*.lf.bin'):
ephysqc.extract_rmsmap(fbin, out_folder=self.alf_folder)
rmsmap_lf = alf.load_object(self.alf_folder, '_ibl_ephysRmsMap_lf')
spec_lf = alf.load_object(self.alf_folder, '_ibl_ephysSpectra_lf')
ntimes = rmsmap_lf['times'].shape[0]
nchannels = rmsmap_lf['rms'].shape[1]
nfreqs = spec_lf['frequencies'].shape[0]
# makes sure the dimensions are consistend
self.assertTrue(rmsmap_lf['rms'].shape == (ntimes, nchannels))
self.assertTrue(spec_lf['power'].shape == (nfreqs, nchannels))
from pathlib import Path
import glob, os
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from ibllib.ephys import ephysqc
from ibllib.examples.ibllib import _plot_spectra, _plot_rmsmap
import alf.io
import tkinter.filedialog
# find the correct session to work on
fbinpath = tkinter.filedialog.askdirectory()
os.chdir(fbinpath)
for file in glob.glob("*.lf.bin"):
print(file)
# make sure you send a path for the time being and not a string
ephysqc.extract_rmsmap(os.path.join(fbinpath, file))
_plot_spectra(fbinpath, 'lf')
_plot_rmsmap(fbinpath, 'lf')
axrms.set_ylabel(r'Channel Number')
plt.colorbar(im, cax=axcb)
if typ == 'ap':
im.set_clim(-110, -90)
axrms.set_xlim(100, 0)
elif typ == 'lf':
im.set_clim(-100, -60)
axrms.set_xlim(500, 0)
axim.set_xlim(0, 4000)
axim.set_title(outpath)
if savefig:
plt.savefig(outpath / (typ + '_rms.png'), dpi=150)
# ============================== ###
# FIND THE RIGHT FILES, RUN AS SCRIPT
# ============================== ###
if __name__ == '__main__':
if len(sys.argv) != 2:
print("Please give the folder path as an input argument!")
else:
outpath = Path(sys.argv[1]) # grab from command line input
fbin = glob.glob(os.path.join(outpath, '*.lf.bin'))
assert (len(fbin) > 0)
print('fbin: %s' % fbin)
# make sure you send a path for the time being and not a string
ephysqc.extract_rmsmap(Path(fbin[0]))
_plot_spectra(outpath, 'lf')
_plot_rmsmap(outpath, 'lf')
aspect='auto',
origin='lower',
extent=[
rmsmap['timestamps'][0], rmsmap['timestamps'][-1], 0,
rmsmap['rms'].shape[1]
])
axim.set_xlabel(r'Time (s)')
axim.set_ylabel(r'Channel Number')
plt.colorbar(im, cax=axcb)
if typ == 'ap':
im.set_clim(-110, -90)
axrms.set_xlim(100, 0)
elif typ == 'lf':
im.set_clim(-100, -60)
axrms.set_xlim(500, 0)
axim.set_xlim(0, 4000)
if savefig:
plt.savefig(outpath / (typ + '_rms.png'), dpi=150)
if __name__ == "__main__":
fbin = Path(
'/mnt/s1/Data/Subjects/ZM_1735/2019-08-01/001/raw_ephys_data/probe_left/'
'_iblrig_ephysData.raw_g0_t0.imec.ap.bin')
ephysqc.extract_rmsmap(
fbin) # make sure you send a path for the time being and not a string
typ = 'lf'
outpath = fbin.parent
_plot_spectra(outpath, typ)
_plot_rmsmap(outpath, typ)