def test_good_events():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 2)
#~ peak_pos = peak_pos[:100]
#~ print(peak_pos)
waveforms = extract_peak_waveforms(sigs, peak_pos, peak_pos, -30,50)
keep = good_events(waveforms,upper_thr=5.,lower_thr=-5.)
#~ print(keep)
goods_wf = waveforms[keep]
bads_wf = waveforms[~keep]
fig, ax = pyplot.subplots()
#~ goods_wf.transpose().plot(ax =ax, color = 'g', lw = .3)
bads_wf.transpose().plot(ax =ax,color = 'r', lw = .3)
med = waveforms.median(axis=0)
mad = np.median(np.abs(waveforms-med),axis=0)*1.4826
limit1 = med+5*mad
limit2 = med-5*mad
med.plot(ax = ax, color = 'm', lw = 2)
limit1.plot(ax = ax, color = 'm')
limit2.plot(ax = ax, color = 'm')
def test_clustering():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
#peak
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 2)
#waveforms
waveformextractor = WaveformExtractor(peakdetector, n_left=-30, n_right=50)
limit_left, limit_right = waveformextractor.find_good_limits(mad_threshold = 1.1)
short_wf = waveformextractor.get_ajusted_waveforms()
print(short_wf.shape)
#clustering
clustering = Clustering(short_wf)
#PCA
features = clustering.project(method = 'pca', n_components = 5)
clustering.plot_projection(plot_density = True)
#Kmean
labels = clustering.find_clusters(7)
clustering.plot_projection(plot_density = True)
#ùake catalogue
catalogue = clustering.construct_catalogue()
clustering.plot_derivatives()
clustering.plot_catalogue()
clustering.merge_cluster(1,2)
clustering.split_cluster(1, 2)
def test_rectify_signals():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
retified_sigs = rectify_signals(normalize_signals(sigs), threshold = -4)
fig, ax = pyplot.subplots()
retified_sigs[3.14:3.22].plot(ax = ax)
ax.set_ylim(-20, 10)
def test_peakdetector():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs, seg_num=0)
peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 2)
print(peakdetector.peak_pos.size)
peakdetector.detect_peaks(threshold=-5, peak_sign = '-', n_span = 5)
print(peakdetector.peak_pos.size)
def test_peeler():
dataio = DataIO(dirname = 'datatest')
#~ dataio = DataIO(dirname = 'datatest_neo')
sigs = dataio.get_signals(seg_num=0)
#peak
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 5)
#waveforms
waveformextractor = WaveformExtractor(peakdetector, n_left=-30, n_right=50)
limit_left, limit_right = waveformextractor.find_good_limits(mad_threshold = 1.1)
#~ print(limit_left, limit_right)
short_wf = waveformextractor.get_ajusted_waveforms()
#~ print(short_wf.shape)
#clustering
clustering = Clustering(short_wf)
features = clustering.project(method = 'pca', n_components = 4)
clustering.find_clusters(8, order_clusters = True)
catalogue = clustering.construct_catalogue()
#~ clustering.plot_catalogue(sameax = False)
#~ clustering.plot_catalogue(sameax = True)
#~ clustering.merge_cluster(1, 2)
catalogue = clustering.construct_catalogue()
clustering.plot_catalogue(sameax = False)
#~ clustering.plot_catalogue(sameax = True)
#peeler
signals = peakdetector.normed_sigs
peeler = Peeler(signals, catalogue, limit_left, limit_right,
threshold=-5., peak_sign = '-', n_span = 5)
prediction0, residuals0 = peeler.peel()
prediction1, residuals1 = peeler.peel()
spiketrains = peeler.get_spiketrains()
print(spiketrains)
fig, axs = pyplot.subplots(nrows = 6, sharex = True)#, sharey = True)
axs[0].plot(signals)
axs[1].plot(prediction0)
axs[2].plot(residuals0)
axs[3].plot(prediction1)
axs[4].plot(residuals1)
for i in range(5):
axs[i].set_ylim(-25, 10)
peeler.plot_spiketrains(ax = axs[5])
def test_extract_noise_waveforms():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 2)
waveforms = extract_noise_waveforms(sigs, peak_pos, -30,50, size = 500)
print(waveforms.shape)
fig, ax = pyplot.subplots()
waveforms.median(axis=0).plot(ax =ax)
def test_filter():
dataio = DataIO(dirname = 'datatest_neo')
sigs = dataio.get_signals(seg_num=0, signal_type = 'unfiltered')
filter = SignalFilter(sigs, highpass_freq = 300.)
filterred_sigs = filter.get_filtered_data()
filter2 = SignalFilter(sigs, highpass_freq = 300., box_smooth = 3)
filterred_sigs2 = filter2.get_filtered_data()
fig, axs = pyplot.subplots(nrows=3, sharex = True)
sigs[0:.5].plot(ax=axs[0])
filterred_sigs[0:.5].plot(ax=axs[1])
filterred_sigs2[0:.5].plot(ax=axs[2])
def test_extract_peak_waveforms():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 2)
peak_index = sigs.index[peak_pos]
waveforms = extract_peak_waveforms(sigs, peak_pos,peak_index, -30,50)
print(waveforms.shape)
fig, ax = pyplot.subplots()
waveforms.median(axis=0).plot(ax =ax)
normed_waveforms = extract_peak_waveforms(peakdetector.normed_sigs, peak_pos, peak_index, -15,50)
fig, ax = pyplot.subplots()
normed_waveforms.median(axis=0).plot(ax =ax)
def test_waveform_extractor():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs)
peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 5)
waveformextractor = WaveformExtractor(peakdetector, n_left=-30, n_right=50)
limit_left, limit_right = waveformextractor.find_good_limits(mad_threshold = 1.1)
print(limit_left, limit_right)
long_wf = waveformextractor.long_waveforms
short_wf = waveformextractor.get_ajusted_waveforms()
assert long_wf.shape[1]>short_wf.shape[1]
waveformextractor.plot_good_limit()
def test_peeler():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
#peak
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 5)
#waveforms
waveformextractor = WaveformExtractor(peakdetector, n_left=-30, n_right=50)
limit_left, limit_right = waveformextractor.find_good_limits(mad_threshold = 1.1)
#~ print(limit_left, limit_right)
short_wf = waveformextractor.get_ajusted_waveforms(margin=2)
#~ print(short_wf.shape)
#clustering
clustering = Clustering(short_wf)
features = clustering.project(method = 'pca', n_components = 5)
clustering.find_clusters(7)
catalogue = clustering.construct_catalogue()
clustering.plot_catalogue()
#peeler
signals = peakdetector.normed_sigs
peeler = Peeler(signals, catalogue, limit_left, limit_right,
threshold=-4, peak_sign = '-', n_span = 5)
prediction0, residuals0 = peeler.peel()
prediction1, residuals1 = peeler.peel()
fig, axs = pyplot.subplots(nrows = 6, sharex = True)#, sharey = True)
axs[0].plot(signals)
axs[1].plot(prediction0)
axs[2].plot(residuals0)
axs[3].plot(prediction1)
axs[4].plot(residuals1)
colors = sns.color_palette('husl', len(catalogue))
spiketrains = peeler.get_spiketrains()
i = 0
for k , pos in spiketrains.items():
axs[5].plot(pos, np.ones(pos.size)*k, ls = 'None', marker = '|', markeredgecolor = colors[i], markersize = 10, markeredgewidth = 2)
i += 1
axs[5].set_ylim(0, len(catalogue))
def plot_interpolation():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
#peak
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 5)
#waveforms
waveformextractor = WaveformExtractor(peakdetector, n_left=-30, n_right=50)
limit_left, limit_right = waveformextractor.find_good_limits(mad_threshold = 1.1)
#~ print(limit_left, limit_right)
short_wf = waveformextractor.get_ajusted_waveforms(margin=2)
#~ print(short_wf.shape)
#clustering
clustering = Clustering(short_wf)
features = clustering.project(method = 'pca', n_components = 5)
clustering.find_clusters(7)
catalogue = clustering.construct_catalogue()
k = list(catalogue.keys())[1]
w0 = catalogue[k]['center']
w1 = catalogue[k]['centerD']
w2 = catalogue[k]['centerDD']
fig, ax = pyplot.subplots()
t = np.arange(w0.size)
colors = sns.color_palette('husl', 12)
all = []
jitters = np.arange(-.5,.5,.1)
for i, jitter in enumerate(jitters):
pred = w0 + jitter*w1 + jitter**2/2.*w2
all.append(pred)
ax.plot(t+jitter, pred, marker = 'o', label = str(jitter), color = colors[i], linestyle = 'None')
ax.plot(t, w0, marker = '*', markersize = 4, label = 'w0', lw = 1, color = 'k')
all = np.array(all)
interpolated = all.transpose().flatten()
t2 = np.arange(interpolated.size)/all.shape[0] + jitters[0]
ax.plot(t2, interpolated, label = 'interp', lw = 1, color = 'm')
def test_detect_peak_method_span():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
normed_sigs = normalize_signals(sigs)
retified_sigs = rectify_signals(normed_sigs, threshold = -4)
peaks_pos = detect_peak_method_span(retified_sigs, peak_sign='-', n_span = 5)
peaks_index = sigs.index[peaks_pos]
fig, ax = pyplot.subplots()
chunk = retified_sigs[3.14:3.22]
chunk.plot(ax = ax)
peaks_value = retified_sigs.loc[peaks_index]
peaks_value[3.14:3.22].plot(marker = 'o', linestyle = 'None', ax = ax, color = 'k')
ax.set_ylim(-20, 10)
fig, ax = pyplot.subplots()
chunk = normed_sigs[3.14:3.22]
chunk.plot(ax = ax)
peaks_value = normed_sigs.loc[peaks_index]
peaks_value[3.14:3.22].plot(marker = 'o', linestyle = 'None', ax = ax, color = 'k')
ax.set_ylim(-20, 10)
def test_find_good_limits():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
peakdetector = PeakDetector(sigs)
peak_pos = peakdetector.detect_peaks(threshold=-4, peak_sign = '-', n_span = 5)
peak_index = sigs.index[peak_pos]
normed_waveforms = extract_peak_waveforms(peakdetector.normed_sigs, peak_pos, peak_index, -25,50)
normed_med = normed_waveforms.median(axis=0)
normed_mad = np.median(np.abs(normed_waveforms-normed_med),axis=0)*1.4826
normed_mad = normed_mad.reshape(4,-1)
fig, ax = pyplot.subplots()
ax.plot(normed_mad.transpose())
ax.axhline(1.1)
l1, l2 = find_good_limits(normed_mad)
print(l1,l2)
ax.axvline(l1)
ax.axvline(l2)
def test_normalize_signals():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
normed_sigs = normalize_signals(sigs)
normed_sigs[3.14:3.22].plot()
def test_derivative_signals():
dataio = DataIO(dirname = 'datatest')
sigs = dataio.get_signals(seg_num=0)
deriv_sigs = derivative_signals(sigs)
deriv_sigs[3.14:3.22].plot()