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plot_spikes_details.py
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Fri, May 3, 12:13

plot_spikes_details.py
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# -*- coding: utf-8 -*-
# @Author: Theo
# @Date: 2018-04-04 11:49:07
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-09-28 14:12:50
''' Plot features of detected spikes on charge profiles. '''
import os
import pickle
import logging
import numpy as np
import matplotlib.pyplot as plt
from PySONIC.utils import logger, OpenFilesDialog
from PySONIC.postpro import findPeaks
from PySONIC.constants import *
# Set logging level
logger.setLevel(logging.INFO)
def plotSpikesDetails(filepaths, fs=15, lw=2):
for fpath in filepaths:
# Load charge profile from file
fname = os.path.basename(fpath)
logger.info('Loading data from "%s" file', fname)
with open(fpath, 'rb') as fh:
frame = pickle.load(fh)
df = frame['data']
t = df['t'].values
Qm = df['Qm'].values
dt = t[1] - t[0]
indexes = np.arange(t.size)
mpd = int(np.ceil(SPIKE_MIN_DT / dt))
ipeaks, prominences, widths, ibounds = findPeaks(Qm, mph=SPIKE_MIN_QAMP, mpd=mpd,
mpp=SPIKE_MIN_QPROM)
if ipeaks is not None:
widths *= dt
tleftbounds = np.interp(ibounds[:, 0], indexes, t)
trightbounds = np.interp(ibounds[:, 1], indexes, t)
# Plot results
fig, ax = plt.subplots(figsize=(8, 4))
ax.set_title(os.path.splitext(fname)[0], fontsize=fs)
ax.set_xlabel('time (ms)', fontsize=fs)
ax.set_ylabel('charge\ (nC/cm2)', fontsize=fs)
ax.plot(t * 1e3, Qm * 1e5, color='C0', label='trace', linewidth=lw)
if ipeaks is not None:
ax.scatter(t[ipeaks] * 1e3, Qm[ipeaks] * 1e5 + 3, color='k', label='peaks', marker='v')
for i in range(len(ipeaks)):
ax.plot(np.array([t[ipeaks[i]]] * 2) * 1e3,
np.array([Qm[ipeaks[i]], Qm[ipeaks[i]] - prominences[i]]) * 1e5,
color='C1', label='prominences' if i == 0 else '')
ax.plot(np.array([tleftbounds[i], trightbounds[i]]) * 1e3,
np.array([Qm[ipeaks[i]] - 0.5 * prominences[i]] * 2) * 1e5, color='C2',
label='widths' if i == 0 else '')
ax.legend(frameon=False)
plt.show()
def main():
# Select data files
pkl_filepaths, _ = OpenFilesDialog('pkl')
if not pkl_filepaths:
logger.error('No input file')
return
plotSpikesDetails(pkl_filepaths)
if __name__ == '__main__':
main()

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