sw.plot_unit_probe_map(we, unit_ids=unit_ids) ############################################################################## # plot_unit_waveform_density_map() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # This is your best friend to check over merge unit_ids = sorting.unit_ids[:4] sw.plot_unit_waveform_density_map(we, unit_ids=unit_ids, max_channels=5) ############################################################################## # plot_amplitudes_distribution() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sw.plot_amplitudes_distribution(we) ############################################################################## # plot_amplitudes_timeseres() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~ sw.plot_amplitudes_timeseries(we) ############################################################################## # plot_units_depth_vs_amplitude() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sw.plot_units_depth_vs_amplitude(we) plt.show()
def test_amplitudes_distribution(self):
sw.plot_amplitudes_distribution(self._we)
sw.plot_amplitudes_distribution(self._we, amplitudes=self._amplitudes)
def visualize_units(recording, recording_f, sorting, wf, templates,
num_channels, file_name):
wf2 = st.postprocessing.get_unit_waveforms(recording,
sorting,
ms_before=4,
ms_after=0,
verbose=True)
color = cm.rainbow(np.linspace(0, 1, len(wf)))
output_dir = "waveform_visualization/" + file_name + "/"
if not os.path.exists(output_dir):
os.mkdir(output_dir)
fig, axs = plt.subplots(3, 2, constrained_layout=True)
axe = axs.ravel()
sw.plot_timeseries(recording_f, ax=axe[0])
for i in range(len(wf)):
normalized = preprocessing.normalize(np.array(templates)[i][:, :])
axe[1].plot(normalized.T, label=i + 1, color=color[i])
sw.plot_rasters(sorting, ax=axe[2])
sw.plot_pca_features(recording,
sorting,
colormap='rainbow',
nproj=3,
max_spikes_per_unit=100,
axes=axe[3:6])
legend = axe[1].legend(loc='lower right')
fig.set_size_inches((8.5, 11), forward=False)
# name = file_name.split("_")
# # acc_1_04052016_kurocoppola_pre
fig.suptitle(file_name)
fig.savefig(output_dir + '_full_info.png', dpi=500)
for idx in range(len(wf)):
for j in range(num_channels):
fig, axs = plt.subplots(4, 3, constrained_layout=True)
axe = axs.ravel()
normalized = preprocessing.normalize(wf[idx][:, j, :])
axe[2].plot(normalized.T, lw=0.3, alpha=0.3)
normalized = preprocessing.normalize(
np.array(templates)[idx][:, :])
axe[2].plot(normalized.T, lw=0.8, color='black')
axe[0].plot(templates[idx].T, lw=0.8)
for i in range(len(wf)):
normalized = preprocessing.normalize(
np.array(templates)[i][:, :])
if idx == i:
axe[1].plot(normalized.T, label=i + 1)
else:
axe[1].plot(normalized.T, label=i + 1, alpha=0.3)
values = randint(0, len(wf), 3)
for i, val in enumerate(values):
axe[3 + i].plot(wf2[idx][val, j, :].T)
sw.plot_pca_features(recording,
sorting,
colormap='binary',
figure=fig,
nproj=3,
axes=axe[6:9],
max_spikes_per_unit=100)
sw.plot_pca_features(recording,
sorting,
unit_ids=[idx],
figure=fig,
nproj=3,
axes=axe[6:9],
max_spikes_per_unit=100)
sw.plot_isi_distribution(sorting,
unit_ids=[idx + 1],
bins=100,
window=1,
axes=axe[9:11])
sw.plot_amplitudes_distribution(recording,
sorting,
max_spikes_per_unit=300,
unit_ids=[idx + 1],
axes=axe[10:12])
sp = sorting.get_unit_spike_train(unit_id=idx + 1)
axe[11].plot(sp)
legend = axe[1].legend(loc='lower right', shadow=True)
axe[0].set_title('Template')
axe[2].set_title('Waveforms, template')
axe[3].set_title('Random waveforms')
axe[6].set_title('PCA component analysis')
axe[9].set_title('ISI distribution')
axe[10].set_title('Amplitude distribution')
axe[11].set_title('Spike frame')
fig.set_size_inches((8.5, 11), forward=False)
fig.suptitle("File name: " + file_name + '\nChannel: ' +
str(j + 1).zfill(2) + '\nUnit: ' +
str(idx + 1).zfill(2))
fig.savefig(output_dir + file_name + '_ch' + str(j + 1).zfill(2) +
'_u' + str(idx + 1).zfill(2) + '.png',
dpi=500)
plt.close('all')
def export_report(waveform_extractor,
output_folder,
remove_if_exists=False,
format="png",
show_figures=False,
peak_sign='neg',
**job_kwargs):
"""
Exports a SI spike sorting report. The report includes summary figures of the spike sorting output
(e.g. amplitude distributions, unit localization and depth VS amplitude) as well as unit-specific reports,
that include waveforms, templates, template maps, ISI distributions, and more.
Parameters
----------
waveform_extractor: a WaveformExtractor or None
If WaveformExtractor is provide then the compute is faster otherwise
output_folder: str
The output folder where the report files are saved
remove_if_exists: bool
If True and the output folder exists, it is removed
format: str
'png' (default) or 'pdf' or any format handled by matplotlib
peak_sign: 'neg' or 'pos'
used to compute amplitudes and metrics
show_figures: bool
If True, figures are shown. If False (default), figures are closed after saving.
{}
"""
we = waveform_extractor
sorting = we.sorting
unit_ids = sorting.unit_ids
# lets matplotlib do this check svg is also cool
# assert format in ["png", "pdf"], "'format' can be 'png' or 'pdf'"
if we.is_extension('spike_amplitudes'):
sac = we.load_extension('spike_amplitudes')
amplitudes = sac.get_amplitudes(outputs='by_unit')
else:
amplitudes = st.compute_spike_amplitudes(we,
peak_sign=peak_sign,
outputs='by_unit',
**job_kwargs)
output_folder = Path(output_folder).absolute()
if output_folder.is_dir():
if remove_if_exists:
shutil.rmtree(output_folder)
else:
raise FileExistsError(f'{output_folder} already exists')
output_folder.mkdir(parents=True, exist_ok=True)
# unit list
units = pd.DataFrame(
index=unit_ids) # , columns=['max_on_channel_id', 'amplitude'])
units.index.name = 'unit_id'
units['max_on_channel_id'] = pd.Series(
st.get_template_extremum_channel(we, peak_sign='neg', outputs='id'))
units['amplitude'] = pd.Series(
st.get_template_extremum_amplitude(we, peak_sign='neg'))
units.to_csv(output_folder / 'unit list.csv', sep='\t')
# metrics
if we.is_extension('quality_metrics'):
qmc = we.load_extension('quality_metrics')
metrics = qmc._metrics
else:
# compute principal_components if not done
if not we.is_extension('principal_components'):
pca = st.compute_principal_components(we,
load_if_exists=True,
n_components=5,
mode='by_channel_local')
metrics = st.compute_quality_metrics(we)
metrics.to_csv(output_folder / 'quality metrics.csv')
unit_colors = sw.get_unit_colors(sorting)
# global figures
fig = plt.figure(figsize=(20, 10))
w = sw.plot_unit_localization(we, figure=fig, unit_colors=unit_colors)
fig.savefig(output_folder / f'unit_localization.{format}')
if not show_figures:
plt.close(fig)
fig, ax = plt.subplots(figsize=(20, 10))
sw.plot_units_depth_vs_amplitude(we, ax=ax, unit_colors=unit_colors)
fig.savefig(output_folder / f'units_depth_vs_amplitude.{format}')
if not show_figures:
plt.close(fig)
fig = plt.figure(figsize=(20, 10))
sw.plot_amplitudes_distribution(we, figure=fig, unit_colors=unit_colors)
fig.savefig(output_folder / f'amplitudes_distribution.{format}')
if not show_figures:
plt.close(fig)
# units
units_folder = output_folder / 'units'
units_folder.mkdir()
for unit_id in unit_ids:
fig = plt.figure(
constrained_layout=False,
figsize=(15, 7),
)
sw.plot_unit_summary(we, unit_id, figure=fig)
fig.suptitle(f'unit {unit_id}')
fig.savefig(units_folder / f'{unit_id}.{format}')
if not show_figures:
plt.close(fig)
import spikeinterface.widgets as sw ############################################################################## # First, let's create a toy example with the `extractors` module: recording, sorting = se.example_datasets.toy_example(duration=10, num_channels=4, seed=0) ############################################################################## # plot_unit_waveforms() # ~~~~~~~~~~~~~~~~~~~~~~~~ w_wf = sw.plot_unit_waveforms(recording, sorting, max_num_waveforms=100) ############################################################################## # plot_amplitudes_distribution() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ w_ampd = sw.plot_amplitudes_distribution(recording, sorting, max_num_waveforms=300) ############################################################################## # plot_amplitudes_timeseres() # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ w_ampt = sw.plot_amplitudes_timeseries(recording, sorting, max_num_waveforms=300) ############################################################################## # plot_features() # ~~~~~~~~~~~~~~~~~~~~~~~~ w_feat = sw.plot_features(recording, sorting, colormap='rainbow', nproj=3, max_num_waveforms=100)
recording, sorting = se.example_datasets.toy_example(duration=10,
num_channels=4,
seed=0)
##############################################################################
# plot_unit_waveforms()
# ~~~~~~~~~~~~~~~~~~~~~~~~
w_wf = sw.plot_unit_waveforms(recording, sorting, max_spikes_per_unit=100)
##############################################################################
# plot_amplitudes_distribution()
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
w_ampd = sw.plot_amplitudes_distribution(recording,
sorting,
max_spikes_per_unit=300)
##############################################################################
# plot_amplitudes_timeseres()
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
w_ampt = sw.plot_amplitudes_timeseries(recording,
sorting,
max_spikes_per_unit=300)
##############################################################################
# plot_pca_features()
# ~~~~~~~~~~~~~~~~~~~~~~~~
w_feat = sw.plot_pca_features(recording,