def test_multicomp_graph(self):
msc = sc.compare_multiple_sorters([self._sorting, self._sorting, self._sorting])
sw.plot_multicomp_graph(msc, edge_cmap='viridis', node_cmap='rainbow', draw_labels=False)
sw.plot_multicomp_agreement(msc)
sw.plot_multicomp_agreement_by_sorter(msc)
fig, axes = plt.subplots(len(msc.sorting_list), 1)
sw.plot_multicomp_agreement_by_sorter(msc, axes=axes)
def auto(recording_folder):
os.chdir(recording_folder)
#If sorter has already been run skip it.
subfolders = [f.name for f in os.scandir(recording_folder) if f.is_dir()]
if ('phy_AGR' in subfolders) or ('phy_MS4' in subfolders):
print('Tetrode ' + recording_folder.split('_')[-1] +
' was previously sorted. Skipping')
return
"""
Adding Matlab-based sorters to path
"""
#IronClust
iron_path = "~/Documents/SpikeSorting/ironclust"
ss.IronClustSorter.set_ironclust_path(os.path.expanduser(iron_path))
ss.IronClustSorter.ironclust_path
#HDSort
#ss.HDSortSorter.set_hdsort_path('/home/adrian/Documents/SpikeSorting/HDsort')
#ss.HDSortSorter.hdsort_path
#Waveclus
#ss.WaveClusSorter.set_waveclus_path('/home/adrian/Documents/SpikeSorting/wave_clus')
#ss.WaveClusSorter.waveclus_path
#Check if the recording has been preprocessed before and load it.
# Else proceed with preprocessing.
arr = os.listdir()
#Load .continuous files
recording = se.OpenEphysRecordingExtractor(recording_folder)
channel_ids = recording.get_channel_ids()
fs = recording.get_sampling_frequency()
num_chan = recording.get_num_channels()
print('Channel ids:', channel_ids)
print('Sampling frequency:', fs)
print('Number of channels:', num_chan)
#!cat tetrode9.prb #Asks for prb file
# os.system('cat /home/adrian/Documents/SpikeSorting/Adrian_test_data/Irene_data/test_without_zero_main_channels/Tetrode_9_CH/tetrode9.prb')
#recording_prb = recording.load_probe_file('/home/adrian/Documents/SpikeSorting/Adrian_test_data/Irene_data/test_without_zero_main_channels/Tetrode_9_CH/tetrode.prb')
recording_prb = recording.load_probe_file('tetrode.prb')
print('Channels after loading the probe file:',
recording_prb.get_channel_ids())
print('Channel groups after loading the probe file:',
recording_prb.get_channel_groups())
#For testing only: Reduce recording.
#recording_prb = se.SubRecordingExtractor(recording_prb, start_frame=100*fs, end_frame=420*fs)
#Bandpass filter
recording_cmr = st.preprocessing.bandpass_filter(recording_prb,
freq_min=300,
freq_max=6000)
recording_cache = se.CacheRecordingExtractor(recording_cmr)
print(recording_cache.get_channel_ids())
print(recording_cache.get_channel_groups())
print(recording_cache.get_num_frames() /
recording_cache.get_sampling_frequency())
#View installed sorters
#ss.installed_sorters()
#mylist = [f for f in glob.glob("*.txt")]
#%% Run all channels. There are only a single tetrode channels anyway.
#Create sub recording to avoid saving whole recording.Requirement from NWB to allow saving sorters data.
recording_sub = se.SubRecordingExtractor(recording_cache,
start_frame=200 * fs,
end_frame=320 * fs)
Sorters2Compare = []
Sorters2CompareLabel = []
SortersCount = []
#Amount of detections per sorter
#Klusta
if 'sorting_KL_all.nwb' in arr:
print('Loading Klusta')
sorting_KL_all = se.NwbSortingExtractor('sorting_KL_all.nwb')
if not (not (sorting_KL_all.get_unit_ids())):
Sorters2Compare.append(sorting_KL_all)
Sorters2CompareLabel.append('KL')
else:
t = time.time()
sorting_KL_all = ss.run_klusta(recording_cache,
output_folder='results_all_klusta',
delete_output_folder=True)
print('Found', len(sorting_KL_all.get_unit_ids()), 'units')
time.time() - t
#Save Klusta
se.NwbRecordingExtractor.write_recording(recording_sub,
'sorting_KL_all.nwb')
se.NwbSortingExtractor.write_sorting(sorting_KL_all,
'sorting_KL_all.nwb')
if not (not (sorting_KL_all.get_unit_ids())):
Sorters2Compare.append(sorting_KL_all)
Sorters2CompareLabel.append('KL')
SortersCount.append(len(sorting_KL_all.get_unit_ids()))
#Ironclust
if 'sorting_IC_all.nwb' in arr:
print('Loading Ironclust')
sorting_IC_all = se.NwbSortingExtractor('sorting_IC_all.nwb')
if not (not (sorting_IC_all.get_unit_ids())):
Sorters2Compare.append(sorting_IC_all)
Sorters2CompareLabel.append('IC')
SortersCount.append(len(sorting_IC_all.get_unit_ids()))
else:
try:
t = time.time()
sorting_IC_all = ss.run_ironclust(recording_cache,
output_folder='results_all_ic',
delete_output_folder=True,
filter=False)
print('Found', len(sorting_IC_all.get_unit_ids()), 'units')
time.time() - t
#Save IC
se.NwbRecordingExtractor.write_recording(recording_sub,
'sorting_IC_all.nwb')
se.NwbSortingExtractor.write_sorting(sorting_IC_all,
'sorting_IC_all.nwb')
if not (not (sorting_IC_all.get_unit_ids())):
Sorters2Compare.append(sorting_IC_all)
Sorters2CompareLabel.append('IC')
SortersCount.append(len(sorting_IC_all.get_unit_ids()))
except:
print('Ironclust has failed')
# #Waveclust
# if 'sorting_waveclus_all.nwb' in arr:
# print('Loading waveclus')
# sorting_waveclus_all=se.NwbSortingExtractor('sorting_waveclus_all.nwb');
# if not(not(sorting_waveclus_all.get_unit_ids())):
# Sorters2Compare.append(sorting_waveclus_all);
# Sorters2CompareLabel.append('Waveclus');
# SortersCount.append(len(sorting_waveclus_all.get_unit_ids()))
# else:
# t = time.time()
# try:
# sorting_waveclus_all = ss.run_waveclus(recording_cache, output_folder='results_all_waveclus',delete_output_folder=True)
# print('Found', len(sorting_waveclus_all.get_unit_ids()), 'units')
# time.time() - t
# #Save waveclus
# se.NwbRecordingExtractor.write_recording(recording_sub, 'sorting_waveclus_all.nwb')
# se.NwbSortingExtractor.write_sorting(sorting_waveclus_all, 'sorting_waveclus_all.nwb')
# if not(not(sorting_waveclus_all.get_unit_ids())):
# Sorters2Compare.append(sorting_waveclus_all);
# Sorters2CompareLabel.append('Waveclus');
# SortersCount.append(len(sorting_waveclus_all.get_unit_ids()))
# except:
# print('Waveclus cannot be run')
#Herdingspikes
if 'sorting_herdingspikes_all.nwb' in arr:
print('Loading herdingspikes')
sorting_herdingspikes_all = se.NwbSortingExtractor(
'sorting_herdingspikes_all.nwb')
if not (not (sorting_herdingspikes_all.get_unit_ids())):
Sorters2Compare.append(sorting_herdingspikes_all)
Sorters2CompareLabel.append('HS')
SortersCount.append(len(sorting_herdingspikes_all.get_unit_ids()))
else:
try:
t = time.time()
sorting_herdingspikes_all = ss.run_herdingspikes(
recording_cache,
output_folder='results_all_herdingspikes',
delete_output_folder=True)
print('Found', len(sorting_herdingspikes_all.get_unit_ids()),
'units')
time.time() - t
#Save herdingspikes
se.NwbRecordingExtractor.write_recording(
recording_sub, 'sorting_herdingspikes_all.nwb')
try:
se.NwbSortingExtractor.write_sorting(
sorting_herdingspikes_all, 'sorting_herdingspikes_all.nwb')
except TypeError:
print("No units detected. Can't save HerdingSpikes")
os.remove("sorting_herdingspikes_all.nwb")
if not (not (sorting_herdingspikes_all.get_unit_ids())):
Sorters2Compare.append(sorting_herdingspikes_all)
Sorters2CompareLabel.append('HS')
SortersCount.append(len(sorting_herdingspikes_all.get_unit_ids()))
except:
print('Herdingspikes has failed')
try:
rmtree("results_all_herdingspikes")
except:
print('Removed leftover herdingspikes files')
try:
rmtree("results_all_herdingspikes")
except:
print('Removed leftover herdingspikes files')
#Mountainsort4
if 'sorting_mountainsort4_all.nwb' in arr:
print('Loading mountainsort4')
sorting_mountainsort4_all = se.NwbSortingExtractor(
'sorting_mountainsort4_all.nwb')
if not (not (sorting_mountainsort4_all.get_unit_ids())):
Sorters2Compare.append(sorting_mountainsort4_all)
Sorters2CompareLabel.append('MS4')
else:
t = time.time()
sorting_mountainsort4_all = ss.run_mountainsort4(
recording_cache,
output_folder='results_all_mountainsort4',
delete_output_folder=True,
filter=False)
print('Found', len(sorting_mountainsort4_all.get_unit_ids()), 'units')
time.time() - t
#Save mountainsort4
se.NwbRecordingExtractor.write_recording(
recording_sub, 'sorting_mountainsort4_all.nwb')
se.NwbSortingExtractor.write_sorting(sorting_mountainsort4_all,
'sorting_mountainsort4_all.nwb')
if not (not (sorting_mountainsort4_all.get_unit_ids())):
Sorters2Compare.append(sorting_mountainsort4_all)
Sorters2CompareLabel.append('MS4')
SortersCount.append(len(sorting_mountainsort4_all.get_unit_ids()))
#Spykingcircus
if 'sorting_spykingcircus_all.nwb' in arr:
print('Loading spykingcircus')
sorting_spykingcircus_all = se.NwbSortingExtractor(
'sorting_spykingcircus_all.nwb')
if not (not (sorting_spykingcircus_all.get_unit_ids())):
Sorters2Compare.append(sorting_spykingcircus_all)
Sorters2CompareLabel.append('SC')
SortersCount.append(len(sorting_spykingcircus_all.get_unit_ids()))
else:
try:
t = time.time()
sorting_spykingcircus_all = ss.run_spykingcircus(
recording_cache,
output_folder='results_all_spykingcircus',
delete_output_folder=True,
filter=False)
print('Found', len(sorting_spykingcircus_all.get_unit_ids()),
'units')
time.time() - t
#Save sorting_spykingcircus
se.NwbRecordingExtractor.write_recording(
recording_sub, 'sorting_spykingcircus_all.nwb')
se.NwbSortingExtractor.write_sorting(
sorting_spykingcircus_all, 'sorting_spykingcircus_all.nwb')
if not (not (sorting_spykingcircus_all.get_unit_ids())):
Sorters2Compare.append(sorting_spykingcircus_all)
Sorters2CompareLabel.append('SC')
SortersCount.append(len(sorting_spykingcircus_all.get_unit_ids()))
except:
print('Spykingcircus has failed')
#Tridesclous
if 'sorting_tridesclous_all.nwb' in arr:
print('Loading tridesclous')
try:
sorting_tridesclous_all = se.NwbSortingExtractor(
'sorting_tridesclous_all.nwb')
except AttributeError:
print("No units detected. Can't load Tridesclous so will run it.")
t = time.time()
sorting_tridesclous_all = ss.run_tridesclous(
recording_cache,
output_folder='results_all_tridesclous',
delete_output_folder=True)
print('Found', len(sorting_tridesclous_all.get_unit_ids()),
'units')
time.time() - t
os.remove("sorting_tridesclous_all.nwb")
#Save sorting_tridesclous
se.NwbRecordingExtractor.write_recording(
recording_sub, 'sorting_tridesclous_all.nwb')
se.NwbSortingExtractor.write_sorting(
sorting_tridesclous_all, 'sorting_tridesclous_all.nwb')
if not (not (sorting_tridesclous_all.get_unit_ids())):
Sorters2Compare.append(sorting_tridesclous_all)
Sorters2CompareLabel.append('TRI')
SortersCount.append(len(sorting_tridesclous_all.get_unit_ids()))
else:
try:
t = time.time()
sorting_tridesclous_all = ss.run_tridesclous(
recording_cache,
output_folder='results_all_tridesclous',
delete_output_folder=True)
print('Found', len(sorting_tridesclous_all.get_unit_ids()),
'units')
time.time() - t
#Save sorting_tridesclous
se.NwbRecordingExtractor.write_recording(
recording_sub, 'sorting_tridesclous_all.nwb')
se.NwbSortingExtractor.write_sorting(
sorting_tridesclous_all, 'sorting_tridesclous_all.nwb')
if not (not (sorting_tridesclous_all.get_unit_ids())):
Sorters2Compare.append(sorting_tridesclous_all)
Sorters2CompareLabel.append('TRI')
SortersCount.append(len(sorting_tridesclous_all.get_unit_ids()))
except:
print('Tridesclous failed')
try:
rmtree("results_all_tridesclous")
except:
print('Removed leftover tridesclous files')
#Consensus based curation.
print(Sorters2CompareLabel)
print('Comparing sorters agreement. Please wait...')
mcmp = sc.compare_multiple_sorters(Sorters2Compare, Sorters2CompareLabel)
w = sw.plot_multicomp_agreement_by_sorter(mcmp)
# plt.show()
plt.savefig('consensus.pdf', bbox_inches='tight')
plt.savefig('consensus.png', bbox_inches='tight')
plt.close()
w = sw.plot_multicomp_agreement(mcmp)
plt.savefig('consensus_spikes.pdf', bbox_inches='tight')
plt.savefig('consensus_spikes.png', bbox_inches='tight')
plt.close()
# #Use amount of sorters which give a value closest to 10 units.
# agreed_units=[];
# for x in [1,2,3,4,5]:
# agreement_sorting = mcmp.get_agreement_sorting(minimum_agreement_count=x)
# agreed_units.append(len(agreement_sorting.get_unit_ids()));
# print(agreed_units)
# print(agreed_units.index(min(agreed_units, key=lambda x:abs(x-10)))+1)
# agreement_sorting = mcmp.get_agreement_sorting(minimum_agreement_count=
# agreed_units.index(min(agreed_units, key=lambda x:abs(x-10)))+1);
# Use units with at least 2 sorters agreeing.
agreement_sorting = mcmp.get_agreement_sorting(minimum_agreement_count=2)
print(agreement_sorting.get_unit_ids())
phy_folder_name = 'phy_AGR'
if not (agreement_sorting.get_unit_ids()): #If there is no agreement.
# print('No consensus. Finding sorter with closest to expected amount of units')
# print(Sorters2CompareLabel[SortersCount.index(min(SortersCount, key=lambda x:abs(x-10)))])
# agreement_sorting=Sorters2Compare[SortersCount.index(min(SortersCount, key=lambda x:abs(x-10)))]
print('No consensus. Using detections from MountainSort4')
agreement_sorting = sorting_mountainsort4_all
phy_folder_name = 'phy_MS4'
st.postprocessing.export_to_phy(recording_cache,
agreement_sorting,
output_folder=phy_folder_name,
grouping_property='group',
verbose=True,
recompute_info=True)
# se.NwbRecordingExtractor.write_recording(recording_sub, 'agreement_sorting.nwb')
# se.NwbSortingExtractor.write_sorting(agreement_sorting, 'agreement_sorting.nwb')
# os.system('phy template-gui phy_AGR/params.py')
# sorting_phy_curated = se.PhySortingExtractor('phy_AGR/', exclude_cluster_groups=['noise']);
# se.NwbRecordingExtractor.write_recording(recording_sub, 'consensus_phy_curated.nwb')
# se.NwbSortingExtractor.write_sorting(sorting_phy_curated, 'consensus_phy_curated.nwb')
w_wf = sw.plot_unit_templates(sorting=agreement_sorting,
recording=recording_cache)
plt.savefig('unit_templates.pdf', bbox_inches='tight')
plt.savefig('unit_templates.png', bbox_inches='tight')
plt.close()
#Access unit ID and firing rate.
os.chdir(phy_folder_name)
spike_times = np.load('spike_times.npy')
spike_clusters = np.load('spike_clusters.npy')
#Create a list with the unit IDs
some_list = np.unique(spike_clusters)
some_list = some_list.tolist()
#Bin data in bins of 25ms
#45 minutes
bins = np.arange(start=0, stop=45 * 60 * fs + 1, step=.025 * fs)
NData = np.zeros([np.unique(spike_clusters).shape[0], bins.shape[0] - 1])
cont = 0
for x in some_list:
ind = (spike_clusters == x)
fi = spike_times[ind]
inds = np.histogram(fi, bins=bins)
inds1 = inds[0]
NData[cont, :] = inds1
cont = cont + 1
#Save activation matrix
os.chdir("..")
a = os.path.split(os.getcwd())[1]
np.save('actmat_auto_' + a.split('_')[1], NData)
np.save('unit_id_auto_' + a.split('_')[1], some_list)
Sorters2label.remove(i)
else:
Sorters2Compare.append(sorting_curated);
#Consensus based curation.
print(Sorters2label)
print('Comparing sorters agreement. Please wait...')
mcmp = sc.compare_multiple_sorters(Sorters2Compare, Sorters2label)
w = sw.plot_multicomp_agreement_by_sorter(mcmp)
plt.savefig('consensus_curation.pdf', bbox_inches='tight');
plt.savefig('consensus_curation.png', bbox_inches='tight');
plt.close()
w = sw.plot_multicomp_agreement(mcmp)
plt.savefig('consensus_curation_spikes.pdf', bbox_inches='tight');
plt.savefig('consensus_curation_spikes.png', bbox_inches='tight');
plt.close()
#Consider at least 2 sorters agreeing.
agreement_sorting=mcmp.get_agreement_sorting(minimum_agreement_count=2);
st.postprocessing.export_to_phy(recording_cache,
agreement_sorting, output_folder='phy_AGR_post',
grouping_property='group', verbose=True, recompute_info=True)
print('Consensus ended. Results saved')
