def run(self, spikesorter, sign = '-', left_sweep = 1*pq.ms, right_sweep = 1*pq.ms,
peak_method = 'biggest_amplitude'):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep*sr).simplified)
swr = int((right_sweep*sr).simplified)
#~ print swl, (left_sweep*sr)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# clean
remove_limit_spikes(spikesorter, swl, swr*3)
# Initialize
spike_waveforms = initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep =swl
sps.right_sweep = swr
# take individual waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
peak_indexes = get_following_peak_multi_channel(indexes, sps.filtered_sigs[:,s], sign,
method = peak_method)
for ind in peak_indexes :
for c in range(len(sps.rcs)):
sig = sps.filtered_sigs[c, s]
spike_waveforms[n,c, :] = sig[ind-swl:ind+swr+1]
n += 1
sps.spike_waveforms = spike_waveforms
def run(self, spikesorter, sign = '-', left_sweep = 1*pq.ms, right_sweep = 1*pq.ms):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep*sr).simplified)
swr = int((right_sweep*sr).simplified)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# clean
remove_limit_spikes(spikesorter, swl, swr)
# Initialize
initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep =swl
sps.right_sweep = swr
# take individual waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
for ind in indexes :
for c in range(len(sps.rcs)):
sig = sps.filtered_sigs[c, s]
sps.spike_waveforms[n,c, :] = sig[ind-swl:ind+swr+1]
n += 1
def run(self,
spikesorter,
left_sweep=1 * pq.ms,
right_sweep=1 * pq.ms,
waveform_from='filtered signals'):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep * sr).simplified)
swr = int((right_sweep * sr).simplified)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# clean
remove_limit_spikes(spikesorter, swl, swr)
# Initialize
spike_waveforms = initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep = swl
sps.right_sweep = swr
# take individual waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
for ind in indexes:
for c in range(len(sps.rcs)):
if waveform_from == 'filtered signals':
sig = sps.filtered_sigs[c, s]
elif waveform_from == 'full band signals':
sig = sps.full_band_sigs[c, s]
spike_waveforms[n, c, :] = sig[ind - swl:ind + swr + 1]
n += 1
sps.spike_waveforms = spike_waveforms
def run(self,
spikesorter,
sign='-',
left_sweep=1 * pq.ms,
right_sweep=1 * pq.ms,
peak_method='biggest_amplitude'):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep * sr).simplified)
swr = int((right_sweep * sr).simplified)
#~ print swl, (left_sweep*sr)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# clean
remove_limit_spikes(spikesorter, swl, swr * 3)
# Initialize
spike_waveforms = initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep = swl
sps.right_sweep = swr
# take individual waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
peak_indexes = get_following_peak_multi_channel(
indexes, sps.filtered_sigs[:, s], sign, method=peak_method)
for ind in peak_indexes:
for c in range(len(sps.rcs)):
sig = sps.filtered_sigs[c, s]
spike_waveforms[n, c, :] = sig[ind - swl:ind + swr + 1]
n += 1
sps.spike_waveforms = spike_waveforms
def run(self, spikesorter, left_sweep = 1*pq.ms, right_sweep = 1*pq.ms,
sweep_factor_for_interpolation = 3,
shift_estimation_method = 'taylor order1',
shift_method = 'sinc',
max_iter= 1,
):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep*sr).simplified)
swr = int((right_sweep*sr).simplified)
#~ print swl, (left_sweep*sr)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# For interpolation we take a larger sweep in a first time.
swl2 = int(sweep_factor_for_interpolation*swl)
swr2 = int(sweep_factor_for_interpolation*swr)
wisze2 = swl2 + swr2 + 1
# clean
remove_limit_spikes(spikesorter, swl2, swr2)
# Initialize
wfs = initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep =swl
sps.right_sweep = swr
# take waveform in signal
trodness = len(spikesorter.rcs)
n_spike = wfs.shape[0]
large_wfs = np.empty((n_spike, trodness, wisze2), dtype = float) # non aligned larger waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
for ind in indexes :
for c in range(len(sps.rcs)):
sig = sps.filtered_sigs[c, s]
wfs[n,c, :] = sig[ind-swl:ind+swr+1]
large_wfs[n,c, :] = sig[ind-swl2:ind+swr2+1]
n += 1
clusters = self.clusters = sps.cluster_names.keys()
self.deltas = deltas = np.zeros(n_spike)
self.all_centers = [ ]
self.all_centers_mad = [ ]
self.all_deltas = [ ]
for iter in range(max_iter):
print iter
# TODO : sctop criterium
flat_wfs = wfs.reshape(n_spike, -1)
centers = { }
mads = { }
for c in clusters:
ind = sps.spike_clusters==c
centers[c] = np.median(flat_wfs[ind,:], axis=0)
mads[c] = np.median(np.abs(flat_wfs[ind,:]-centers[c]), axis=0) / .6745
# for plotting
self.all_centers.append(centers)
self.all_centers_mad.append(mads)
# shift estimation by clusters
new_deltas = np.zeros(n_spike)
for c in clusters:
ind = sps.spike_clusters==c
if shift_estimation_method == 'taylor order1':
center_D = np.r_[0,(centers[c][2:] - centers[c][:-2])/2, 0]#first derivative
new_deltas[ind] = np.sum((flat_wfs[ind]-centers[c])*center_D , axis = 1)/np.sum(center_D**2)
elif shift_estimation_method == 'taylor order2':
center_D = np.r_[0,(centers[c][2:] - centers[c][:-2])/2, 0] #first derivative
center_DD = np.r_[0,(center_D[2:] - center_D[:-2])/2, 0]#second derivative
#~ for i in range(n_spike):
for i in np.where(ind):
def error(delta):
return np.sum((flat_wfs[i,:]-centers[c]-delta*center_D-delta**2*center_DD/2)**2)
res = minimize(error,[0.], method = 'BFGS')
new_deltas[i] = res.x
deltas += new_deltas
self.all_deltas.append(deltas.copy())
base = np.arange(large_wfs.shape[2])
new_base = np.arange(swl2+1-swl,swl2+2+swr)
# apply shift on waveform by interpolation
if shift_method == 'sinc':
for i in range(n_spike):
for c in range(large_wfs.shape[1]):
half = base.size//2
kernel = np.sinc(np.arange(-half, half)-deltas[i]+1)
wfs[i,c,:] = convolve(large_wfs[i,c,:], kernel, mode = 'same')[swl2+1-swl:swl2+2+swr]
elif shift_method == 'spline':
for i in range(n_spike):
for c in range(large_wfs.shape[1]):
interpolator = interp1d(base, large_wfs[i,c,:], kind = 1)
wfs[i,c,:] = interpolator(new_base-deltas[i])
elif shift_method == 'lanczos':
#TODO!!!
pass
spikesorter.spike_waveforms = wfs
def run(
self,
spikesorter,
left_sweep=1 * pq.ms,
right_sweep=1 * pq.ms,
sweep_factor_for_interpolation=3,
shift_estimation_method='taylor order1',
shift_method='sinc',
max_iter=1,
):
sps = spikesorter
sr = sps.sig_sampling_rate
swl = int((left_sweep * sr).simplified)
swr = int((right_sweep * sr).simplified)
#~ print swl, (left_sweep*sr)
wsize = swl + swr + 1
trodness = sps.filtered_sigs.shape[0]
# For interpolation we take a larger sweep in a first time.
swl2 = int(sweep_factor_for_interpolation * swl)
swr2 = int(sweep_factor_for_interpolation * swr)
wisze2 = swl2 + swr2 + 1
# clean
remove_limit_spikes(spikesorter, swl2, swr2)
# Initialize
wfs = initialize_waveform(spikesorter, wsize)
sps.wf_sampling_rate = sps.sig_sampling_rate
sps.left_sweep = swl
sps.right_sweep = swr
# take waveform in signal
trodness = len(spikesorter.rcs)
n_spike = wfs.shape[0]
large_wfs = np.empty((n_spike, trodness, wisze2),
dtype=float) # non aligned larger waveform
n = 0
for s, indexes in enumerate(sps.spike_index_array):
for ind in indexes:
for c in range(len(sps.rcs)):
sig = sps.filtered_sigs[c, s]
wfs[n, c, :] = sig[ind - swl:ind + swr + 1]
large_wfs[n, c, :] = sig[ind - swl2:ind + swr2 + 1]
n += 1
clusters = self.clusters = sps.cluster_names.keys()
self.deltas = deltas = np.zeros(n_spike)
self.all_centers = []
self.all_centers_mad = []
self.all_deltas = []
for iter in range(max_iter):
print iter
# TODO : sctop criterium
flat_wfs = wfs.reshape(n_spike, -1)
centers = {}
mads = {}
for c in clusters:
ind = sps.spike_clusters == c
centers[c] = np.median(flat_wfs[ind, :], axis=0)
mads[c] = np.median(np.abs(flat_wfs[ind, :] - centers[c]),
axis=0) / .6745
# for plotting
self.all_centers.append(centers)
self.all_centers_mad.append(mads)
# shift estimation by clusters
new_deltas = np.zeros(n_spike)
for c in clusters:
ind = sps.spike_clusters == c
if shift_estimation_method == 'taylor order1':
center_D = np.r_[0, (centers[c][2:] - centers[c][:-2]) / 2,
0] #first derivative
new_deltas[ind] = np.sum(
(flat_wfs[ind] - centers[c]) * center_D,
axis=1) / np.sum(center_D**2)
elif shift_estimation_method == 'taylor order2':
center_D = np.r_[0, (centers[c][2:] - centers[c][:-2]) / 2,
0] #first derivative
center_DD = np.r_[0, (center_D[2:] - center_D[:-2]) / 2,
0] #second derivative
#~ for i in range(n_spike):
for i in np.where(ind):
def error(delta):
return np.sum((flat_wfs[i, :] - centers[c] -
delta * center_D -
delta**2 * center_DD / 2)**2)
res = minimize(error, [0.], method='BFGS')
new_deltas[i] = res.x
deltas += new_deltas
self.all_deltas.append(deltas.copy())
base = np.arange(large_wfs.shape[2])
new_base = np.arange(swl2 + 1 - swl, swl2 + 2 + swr)
# apply shift on waveform by interpolation
if shift_method == 'sinc':
for i in range(n_spike):
for c in range(large_wfs.shape[1]):
half = base.size // 2
kernel = np.sinc(
np.arange(-half, half) - deltas[i] + 1)
wfs[i,
c, :] = convolve(large_wfs[i, c, :],
kernel,
mode='same')[swl2 + 1 - swl:swl2 +
2 + swr]
elif shift_method == 'spline':
for i in range(n_spike):
for c in range(large_wfs.shape[1]):
interpolator = interp1d(base,
large_wfs[i, c, :],
kind=1)
wfs[i, c, :] = interpolator(new_base - deltas[i])
elif shift_method == 'lanczos':
#TODO!!!
pass
spikesorter.spike_waveforms = wfs