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Merge pull request #1 from jdpigeon/master

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Updated lsl-viewer and minor updates to lab7
Esse commit está contido em:
Pierre Karashchuk
2017-07-07 11:49:40 -07:00
commit de GitHub
pai 4a8646a138 372ed9e706
commit ccbed2b55c
10 arquivos alterados com 186 adições e 87 exclusões
Baixar Arquivo de Patch Baixar Arquivo de Diff Expandir todos os arquivos Colapsar todos os arquivos
lab4/lsl-viewer.py
+23 -17
Ver Arquivo
@@ -1,17 +1,15 @@
#!/usr/bin/env python
## code by Alexandre Barachant
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt
from time import time, sleep
from scipy.signal import butter, lfilter, lfilter_zi
from time import sleep
from pylsl import StreamInlet, resolve_byprop
from optparse import OptionParser
import seaborn as sns
from threading import Thread
sns.set(style="whitegrid")
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-w", "--window",
@@ -55,6 +53,7 @@ class LSLViewer():
self.dejitter = dejitter
self.inlet = StreamInlet(stream, max_chunklen=buf)
self.filt = True
info = self.inlet.info()
description = info.desc()
@@ -105,6 +104,9 @@ class LSLViewer():
self.bf, self.af = butter(4, np.array([1, 40])/(self.sfreq/2.),
'bandpass')
zi = lfilter_zi(self.bf, self.af)
self.filt_state = np.tile(zi, (self.n_chan, 1)).transpose()
self.data_f = np.zeros((self.n_samples, self.n_chan))
def update_plot(self):
k = 0
@@ -112,33 +114,37 @@ class LSLViewer():
samples, timestamps = self.inlet.pull_chunk(timeout=1.0,
max_samples=12)
if timestamps:
self.data = np.vstack([self.data, samples])
if self.dejitter:
timestamps = np.float64(np.arange(len(timestamps)))
timestamps /= self.sfreq
timestamps += self.times[-1] + 1./self.sfreq
self.times = np.concatenate([self.times, timestamps])
self.n_samples = int(self.sfreq * self.window)
self.data = self.data[-self.n_samples:]
self.times = self.times[-self.n_samples:]
self.data = np.vstack([self.data, samples])
self.data = self.data[-self.n_samples:]
filt_samples, self.filt_state = lfilter(
self.bf, self.af,
samples,
axis=0, zi=self.filt_state)
self.data_f = np.vstack([self.data_f, filt_samples])
self.data_f = self.data_f[-self.n_samples:]
k += 1
if k == self.display_every:
if self.filt:
data_f = filtfilt(self.bf, self.af, self.data, axis=0)
else:
data_f = self.data
data_f -= data_f.mean(axis=0)
if self.filt:
plot_data = self.data_f
elif not self.filt:
plot_data = self.data - self.data.mean(axis=0)
for ii in range(self.n_chan):
self.lines[ii].set_xdata(self.times[::subsample] -
self.times[-1])
self.lines[ii].set_ydata(data_f[::subsample, ii] /
self.lines[ii].set_ydata(plot_data[::subsample, ii] /
self.scale - ii)
impedances = np.std(plot_data, axis=0)
impedances = np.std(data_f, axis=0)
ticks_labels = ['%s - %.2f' %
(self.ch_names[ii], impedances[ii])
ticks_labels = ['%s - %.2f' % (self.ch_names[ii],
impedances[ii])
for ii in range(self.n_chan)]
self.axes.set_yticklabels(ticks_labels)
self.axes.set_xlim(-self.window, 0)
lab5/lsl-viewer.py
+23 -17
Ver Arquivo
@@ -1,17 +1,15 @@
#!/usr/bin/env python
## code by Alexandre Barachant
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt
from time import time, sleep
from scipy.signal import butter, lfilter, lfilter_zi
from time import sleep
from pylsl import StreamInlet, resolve_byprop
from optparse import OptionParser
import seaborn as sns
from threading import Thread
sns.set(style="whitegrid")
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-w", "--window",
@@ -55,6 +53,7 @@ class LSLViewer():
self.dejitter = dejitter
self.inlet = StreamInlet(stream, max_chunklen=buf)
self.filt = True
info = self.inlet.info()
description = info.desc()
@@ -105,6 +104,9 @@ class LSLViewer():
self.bf, self.af = butter(4, np.array([1, 40])/(self.sfreq/2.),
'bandpass')
zi = lfilter_zi(self.bf, self.af)
self.filt_state = np.tile(zi, (self.n_chan, 1)).transpose()
self.data_f = np.zeros((self.n_samples, self.n_chan))
def update_plot(self):
k = 0
@@ -112,33 +114,37 @@ class LSLViewer():
samples, timestamps = self.inlet.pull_chunk(timeout=1.0,
max_samples=12)
if timestamps:
self.data = np.vstack([self.data, samples])
if self.dejitter:
timestamps = np.float64(np.arange(len(timestamps)))
timestamps /= self.sfreq
timestamps += self.times[-1] + 1./self.sfreq
self.times = np.concatenate([self.times, timestamps])
self.n_samples = int(self.sfreq * self.window)
self.data = self.data[-self.n_samples:]
self.times = self.times[-self.n_samples:]
self.data = np.vstack([self.data, samples])
self.data = self.data[-self.n_samples:]
filt_samples, self.filt_state = lfilter(
self.bf, self.af,
samples,
axis=0, zi=self.filt_state)
self.data_f = np.vstack([self.data_f, filt_samples])
self.data_f = self.data_f[-self.n_samples:]
k += 1
if k == self.display_every:
if self.filt:
data_f = filtfilt(self.bf, self.af, self.data, axis=0)
else:
data_f = self.data
data_f -= data_f.mean(axis=0)
if self.filt:
plot_data = self.data_f
elif not self.filt:
plot_data = self.data - self.data.mean(axis=0)
for ii in range(self.n_chan):
self.lines[ii].set_xdata(self.times[::subsample] -
self.times[-1])
self.lines[ii].set_ydata(data_f[::subsample, ii] /
self.lines[ii].set_ydata(plot_data[::subsample, ii] /
self.scale - ii)
impedances = np.std(plot_data, axis=0)
impedances = np.std(data_f, axis=0)
ticks_labels = ['%s - %.2f' %
(self.ch_names[ii], impedances[ii])
ticks_labels = ['%s - %.2f' % (self.ch_names[ii],
impedances[ii])
for ii in range(self.n_chan)]
self.axes.set_yticklabels(ticks_labels)
self.axes.set_xlim(-self.window, 0)
lab6/lsl-viewer.py
+23 -17
Ver Arquivo
@@ -1,17 +1,15 @@
#!/usr/bin/env python
## code by Alexandre Barachant
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt
from time import time, sleep
from scipy.signal import butter, lfilter, lfilter_zi
from time import sleep
from pylsl import StreamInlet, resolve_byprop
from optparse import OptionParser
import seaborn as sns
from threading import Thread
sns.set(style="whitegrid")
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-w", "--window",
@@ -55,6 +53,7 @@ class LSLViewer():
self.dejitter = dejitter
self.inlet = StreamInlet(stream, max_chunklen=buf)
self.filt = True
info = self.inlet.info()
description = info.desc()
@@ -105,6 +104,9 @@ class LSLViewer():
self.bf, self.af = butter(4, np.array([1, 40])/(self.sfreq/2.),
'bandpass')
zi = lfilter_zi(self.bf, self.af)
self.filt_state = np.tile(zi, (self.n_chan, 1)).transpose()
self.data_f = np.zeros((self.n_samples, self.n_chan))
def update_plot(self):
k = 0
@@ -112,33 +114,37 @@ class LSLViewer():
samples, timestamps = self.inlet.pull_chunk(timeout=1.0,
max_samples=12)
if timestamps:
self.data = np.vstack([self.data, samples])
if self.dejitter:
timestamps = np.float64(np.arange(len(timestamps)))
timestamps /= self.sfreq
timestamps += self.times[-1] + 1./self.sfreq
self.times = np.concatenate([self.times, timestamps])
self.n_samples = int(self.sfreq * self.window)
self.data = self.data[-self.n_samples:]
self.times = self.times[-self.n_samples:]
self.data = np.vstack([self.data, samples])
self.data = self.data[-self.n_samples:]
filt_samples, self.filt_state = lfilter(
self.bf, self.af,
samples,
axis=0, zi=self.filt_state)
self.data_f = np.vstack([self.data_f, filt_samples])
self.data_f = self.data_f[-self.n_samples:]
k += 1
if k == self.display_every:
if self.filt:
data_f = filtfilt(self.bf, self.af, self.data, axis=0)
else:
data_f = self.data
data_f -= data_f.mean(axis=0)
if self.filt:
plot_data = self.data_f
elif not self.filt:
plot_data = self.data - self.data.mean(axis=0)
for ii in range(self.n_chan):
self.lines[ii].set_xdata(self.times[::subsample] -
self.times[-1])
self.lines[ii].set_ydata(data_f[::subsample, ii] /
self.lines[ii].set_ydata(plot_data[::subsample, ii] /
self.scale - ii)
impedances = np.std(plot_data, axis=0)
impedances = np.std(data_f, axis=0)
ticks_labels = ['%s - %.2f' %
(self.ch_names[ii], impedances[ii])
ticks_labels = ['%s - %.2f' % (self.ch_names[ii],
impedances[ii])
for ii in range(self.n_chan)]
self.axes.set_yticklabels(ticks_labels)
self.axes.set_xlim(-self.window, 0)
lab7/analysis/analysis.py
+67
Ver Arquivo
@@ -0,0 +1,67 @@
from scipy import signal, stats
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import argparse
import sys
## sampling rate of ganglion is 200Hz
fs = 200.0
def extract_data(fname):
d = pd.read_csv(fname)
eeg = np.array(d.ix[:, 1:5])
tag = np.array(d.Marker)
start = np.where(tag == 1)[0][0]
end = np.where(tag == 2)[0][0]
eeg = eeg[start:end]
return eeg
## get data
eeg1 = extract_data(sys.argv[1])
eeg2 = extract_data(sys.argv[2])
## data may be off by a few samples, so need to align
N_samp = min(len(eeg1), len(eeg2))
eeg1 = eeg1[:N_samp]
eeg2 = eeg2[:N_samp]
## filter signal to remove noise
b, a = signal.butter(2, (2/(fs/2), 20/(fs/2)), btype='bandpass')
eeg1 = signal.filtfilt(b, a, eeg1, axis=0)
eeg2 = signal.filtfilt(b, a, eeg2, axis=0)
## advance window of 200 samples
## take correlation between signals across each sample
window = 200
step = 25
corr = []
times = []
for start in np.arange(0, N_samp, step):
end = start + window
w1 = eeg1[start:end]
w2 = eeg2[start:end]
## average the correlation across each channel
r = 0
for c in range(w1.shape[1]):
r += stats.pearsonr(w1[:, c], w2[:, c])[0]
r /= w1.shape[1]
mid = (start+end)/2 # middle sample
t = mid / fs # convert middle sample to time
times.append(t)
corr.append(r)
times = np.array(times)
corr = np.array(corr)
plt.figure(figsize=(14,4))
plt.plot(times, np.abs(corr))
plt.xlabel('Time (s)')
plt.ylabel('Correlation')
plt.title('Correlation across brains')
plt.show()
lab7/analysis/cross_brain_correlation.ipynb
+4 -2
Ver Arquivo
@@ -76,7 +76,9 @@
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"## filter signal to remove noise\n",
@@ -181,7 +183,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.0"
"version": "3.6.1"
}
},
"nbformat": 4,
lab7/recording/lsl-viewer.py
+23 -17
Ver Arquivo
@@ -1,17 +1,15 @@
#!/usr/bin/env python
## code by Alexandre Barachant
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt
from time import time, sleep
from scipy.signal import butter, lfilter, lfilter_zi
from time import sleep
from pylsl import StreamInlet, resolve_byprop
from optparse import OptionParser
import seaborn as sns
from threading import Thread
sns.set(style="whitegrid")
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-w", "--window",
@@ -55,6 +53,7 @@ class LSLViewer():
self.dejitter = dejitter
self.inlet = StreamInlet(stream, max_chunklen=buf)
self.filt = True
info = self.inlet.info()
description = info.desc()
@@ -105,6 +104,9 @@ class LSLViewer():
self.bf, self.af = butter(4, np.array([1, 40])/(self.sfreq/2.),
'bandpass')
zi = lfilter_zi(self.bf, self.af)
self.filt_state = np.tile(zi, (self.n_chan, 1)).transpose()
self.data_f = np.zeros((self.n_samples, self.n_chan))
def update_plot(self):
k = 0
@@ -112,33 +114,37 @@ class LSLViewer():
samples, timestamps = self.inlet.pull_chunk(timeout=1.0,
max_samples=12)
if timestamps:
self.data = np.vstack([self.data, samples])
if self.dejitter:
timestamps = np.float64(np.arange(len(timestamps)))
timestamps /= self.sfreq
timestamps += self.times[-1] + 1./self.sfreq
self.times = np.concatenate([self.times, timestamps])
self.n_samples = int(self.sfreq * self.window)
self.data = self.data[-self.n_samples:]
self.times = self.times[-self.n_samples:]
self.data = np.vstack([self.data, samples])
self.data = self.data[-self.n_samples:]
filt_samples, self.filt_state = lfilter(
self.bf, self.af,
samples,
axis=0, zi=self.filt_state)
self.data_f = np.vstack([self.data_f, filt_samples])
self.data_f = self.data_f[-self.n_samples:]
k += 1
if k == self.display_every:
if self.filt:
data_f = filtfilt(self.bf, self.af, self.data, axis=0)
else:
data_f = self.data
data_f -= data_f.mean(axis=0)
if self.filt:
plot_data = self.data_f
elif not self.filt:
plot_data = self.data - self.data.mean(axis=0)
for ii in range(self.n_chan):
self.lines[ii].set_xdata(self.times[::subsample] -
self.times[-1])
self.lines[ii].set_ydata(data_f[::subsample, ii] /
self.lines[ii].set_ydata(plot_data[::subsample, ii] /
self.scale - ii)
impedances = np.std(plot_data, axis=0)
impedances = np.std(data_f, axis=0)
ticks_labels = ['%s - %.2f' %
(self.ch_names[ii], impedances[ii])
ticks_labels = ['%s - %.2f' % (self.ch_names[ii],
impedances[ii])
for ii in range(self.n_chan)]
self.axes.set_yticklabels(ticks_labels)
self.axes.set_xlim(-self.window, 0)
lab7/videos/2-seal-cuddles-with-dog.mp4
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lab7/videos/chicken.mp4
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lab7/videos/first_contact.mp4
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lab9/lsl-viewer.py
+23 -17
Ver Arquivo
@@ -1,17 +1,15 @@
#!/usr/bin/env python
## code by Alexandre Barachant
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt
from time import time, sleep
from scipy.signal import butter, lfilter, lfilter_zi
from time import sleep
from pylsl import StreamInlet, resolve_byprop
from optparse import OptionParser
import seaborn as sns
from threading import Thread
sns.set(style="whitegrid")
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-w", "--window",
@@ -55,6 +53,7 @@ class LSLViewer():
self.dejitter = dejitter
self.inlet = StreamInlet(stream, max_chunklen=buf)
self.filt = True
info = self.inlet.info()
description = info.desc()
@@ -105,6 +104,9 @@ class LSLViewer():
self.bf, self.af = butter(4, np.array([1, 40])/(self.sfreq/2.),
'bandpass')
zi = lfilter_zi(self.bf, self.af)
self.filt_state = np.tile(zi, (self.n_chan, 1)).transpose()
self.data_f = np.zeros((self.n_samples, self.n_chan))
def update_plot(self):
k = 0
@@ -112,33 +114,37 @@ class LSLViewer():
samples, timestamps = self.inlet.pull_chunk(timeout=1.0,
max_samples=12)
if timestamps:
self.data = np.vstack([self.data, samples])
if self.dejitter:
timestamps = np.float64(np.arange(len(timestamps)))
timestamps /= self.sfreq
timestamps += self.times[-1] + 1./self.sfreq
self.times = np.concatenate([self.times, timestamps])
self.n_samples = int(self.sfreq * self.window)
self.data = self.data[-self.n_samples:]
self.times = self.times[-self.n_samples:]
self.data = np.vstack([self.data, samples])
self.data = self.data[-self.n_samples:]
filt_samples, self.filt_state = lfilter(
self.bf, self.af,
samples,
axis=0, zi=self.filt_state)
self.data_f = np.vstack([self.data_f, filt_samples])
self.data_f = self.data_f[-self.n_samples:]
k += 1
if k == self.display_every:
if self.filt:
data_f = filtfilt(self.bf, self.af, self.data, axis=0)
else:
data_f = self.data
data_f -= data_f.mean(axis=0)
if self.filt:
plot_data = self.data_f
elif not self.filt:
plot_data = self.data - self.data.mean(axis=0)
for ii in range(self.n_chan):
self.lines[ii].set_xdata(self.times[::subsample] -
self.times[-1])
self.lines[ii].set_ydata(data_f[::subsample, ii] /
self.lines[ii].set_ydata(plot_data[::subsample, ii] /
self.scale - ii)
impedances = np.std(plot_data, axis=0)
impedances = np.std(data_f, axis=0)
ticks_labels = ['%s - %.2f' %
(self.ch_names[ii], impedances[ii])
ticks_labels = ['%s - %.2f' % (self.ch_names[ii],
impedances[ii])
for ii in range(self.n_chan)]
self.axes.set_yticklabels(ticks_labels)
self.axes.set_xlim(-self.window, 0)