def load_phy(folder_name):
"""Use spikeinterface to load a phy clustering."""
import spikeinterface.extractors as se
to_exclude = ["mua", "noise"]
return se.PhySortingExtractor(folder_name,
exclude_cluster_groups=to_exclude,
load_waveforms=True,
verbose=True)
def spikeinterface_test(folder_name):
"""An example sorting extractor, which loads from Phy."""
import spikeinterface.extractors as se
to_exclude = ["mua", "noise"]
sorting = se.PhySortingExtractor(folder_name,
exclude_cluster_groups=to_exclude,
load_waveforms=True,
verbose=False)
return sorting
sorter=sorting_tridesclous_all;
#Check if sorter failed
if not sorter:
continue
st.postprocessing.export_to_phy(recording_cache,
sorter, output_folder='phy_'+i,
grouping_property='group', verbose=True, recompute_info=True)
#Open phy interface
os.system('phy template-gui phy_'+i+'/params.py')
#Remove detections curated as noise.
sorting_phy_curated = se.PhySortingExtractor('phy_'+i+'/', exclude_cluster_groups=['noise']);
#Print waveforms of units
w_wf = sw.plot_unit_templates(sorting=sorting_phy_curated, recording=recording_cache)
plt.savefig('manual_'+i+'_unit_templates.pdf', bbox_inches='tight');
plt.savefig('manual_'+i+'_unit_templates.png', bbox_inches='tight');
plt.close()
#Compute agreement matrix wrt consensus-based sorting.
sorting_phy_consensus = se.PhySortingExtractor('phy_AGR/', exclude_cluster_groups=['noise']);
cmp=sc.compare_sorter_to_ground_truth(sorting_phy_curated,sorting_phy_consensus)
sw.plot_agreement_matrix(cmp)
plt.savefig('agreement_matrix_'+i+'.pdf', bbox_inches='tight');
plt.savefig('agreement_matrix_'+i+'.png', bbox_inches='tight');
plt.close()
def manual(recording_folder):
#Folder with tetrode data
#recording_folder='/home/adrian/Documents/SpikeSorting/Adrian_test_data/Irene_data/test_without_zero_main_channels/Tetrode_9_CH';
os.chdir(recording_folder)
"""
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
#If sorter has already been run skip it.
subfolders = [f.name for f in os.scandir(recording_folder) if f.is_dir()]
#if ('phy_KL' in subfolders) & ('phy_IC' in subfolders) & ('phy_Waveclus' in subfolders) & ('phy_SC' in subfolders) & ('phy_MS4' in subfolders) & ('phy_HS' in subfolders) & ('phy_TRI' in subfolders):
if ('phy_KL' in subfolders) & ('phy_IC' in subfolders) & (
'phy_SC' in subfolders) & ('phy_MS4' in subfolders) & (
'phy_HS' in subfolders) & ('phy_TRI' in subfolders):
print('Tetrode ' + recording_folder.split('_')[-1] +
' was previously manually sorted. Skipping')
return
#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(os.getcwd() + '/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 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)
# Sorters2CompareLabel=['KL','IC','Waveclus','HS','MS4','SC','TRI'];
Sorters2CompareLabel = ['KL', 'IC', 'HS', 'MS4', 'SC', 'TRI']
subfolders = [f.name for f in os.scandir(recording_folder) if f.is_dir()]
for num in range(len(Sorters2CompareLabel)):
i = Sorters2CompareLabel[num]
print(i)
if 'phy_' + i in subfolders:
print('Sorter already used for curation. Skipping')
continue
else:
if 'KL' in i:
#Klusta
if 'sorting_KL_all.nwb' in arr:
print('Loading Klusta')
sorting_KL_all = se.NwbSortingExtractor(
'sorting_KL_all.nwb')
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')
print(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')
sorter = sorting_KL_all
if 'IC' in i:
#Ironclust
if 'sorting_IC_all.nwb' in arr:
print('Loading Ironclust')
sorting_IC_all = se.NwbSortingExtractor(
'sorting_IC_all.nwb')
else:
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')
print(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')
sorter = sorting_IC_all
# if 'Waveclus' in i:
# #Waveclust
# if 'sorting_waveclus_all.nwb' in arr:
# print('Loading waveclus')
# sorting_waveclus_all=se.NwbSortingExtractor('sorting_waveclus_all.nwb');
# else:
# t = time.time()
# 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')
# print(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')
# sorter=sorting_waveclus_all;
if 'HS' in i:
#Herdingspikes
if 'sorting_herdingspikes_all.nwb' in arr:
print('Loading herdingspikes')
sorting_herdingspikes_all = se.NwbSortingExtractor(
'sorting_herdingspikes_all.nwb')
sorter = sorting_herdingspikes_all
else:
t = time.time()
try:
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")
sorter = sorting_herdingspikes_all
except:
print('Herdingspikes has failed')
sorter = []
if 'MS4' in i:
#Mountainsort4
if 'sorting_mountainsort4_all.nwb' in arr:
print('Loading mountainsort4')
sorting_mountainsort4_all = se.NwbSortingExtractor(
'sorting_mountainsort4_all.nwb')
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')
print(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')
sorter = sorting_mountainsort4_all
if 'SC' in i:
#Spykingcircus
if 'sorting_spykingcircus_all.nwb' in arr:
print('Loading spykingcircus')
sorting_spykingcircus_all = se.NwbSortingExtractor(
'sorting_spykingcircus_all.nwb', filter=False)
else:
t = time.time()
sorting_spykingcircus_all = ss.run_spykingcircus(
recording_cache,
output_folder='results_all_spykingcircus',
delete_output_folder=True)
print('Found',
len(sorting_spykingcircus_all.get_unit_ids()),
'units')
print(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')
sorter = sorting_spykingcircus_all
if 'TRI' in i:
#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')
else:
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')
sorter = sorting_tridesclous_all
#Check if sorter failed
if not sorter:
continue
st.postprocessing.export_to_phy(recording_cache,
sorter,
output_folder='phy_' + i,
grouping_property='group',
verbose=True,
recompute_info=True)
#Open phy interface
os.system('phy template-gui phy_' + i + '/params.py')
#Remove detections curated as noise.
sorting_phy_curated = se.PhySortingExtractor(
'phy_' + i + '/', exclude_cluster_groups=['noise'])
#Print waveforms of units
w_wf = sw.plot_unit_templates(sorting=sorting_phy_curated,
recording=recording_cache)
plt.savefig('manual_' + i + '_unit_templates.pdf',
bbox_inches='tight')
plt.savefig('manual_' + i + '_unit_templates.png',
bbox_inches='tight')
plt.close()
#Compute agreement matrix wrt consensus-based sorting.
sorting_phy_consensus = se.PhySortingExtractor(
'phy_AGR/', exclude_cluster_groups=['noise'])
cmp = sc.compare_sorter_to_ground_truth(sorting_phy_curated,
sorting_phy_consensus)
sw.plot_agreement_matrix(cmp)
plt.savefig('agreement_matrix_' + i + '.pdf', bbox_inches='tight')
plt.savefig('agreement_matrix_' + i + '.png', bbox_inches='tight')
plt.close()
#Access unit ID and firing rate.
os.chdir('phy_' + i)
spike_times = np.load('spike_times.npy')
spike_clusters = np.load('spike_clusters.npy')
#Find units curated as 'noise'
noise_id = []
with open("cluster_group.tsv") as fd:
rd = csv.reader(fd, delimiter="\t", quotechar='"')
for row in rd:
if row[1] == 'noise':
noise_id.append(int(row[0]))
#Create a list with the unit IDs and remove those labeled as 'noise'
some_list = np.unique(spike_clusters)
some_list = some_list.tolist()
for x in noise_id:
print(x)
some_list.remove(x)
#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] - len(noise_id),
bins.shape[0] - 1
])
cont = 0
for x in some_list:
#print(x)
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_manual_' + i + '_' + a.split('_')[1], NData)
np.save('unit_id_manual_' + i + '_' + a.split('_')[1], some_list)
#End of for loop
print("Stop the code here")
recording_cache = se.CacheRecordingExtractor(recording_cmr);
Sorters2Compare=[];
Sorters2CompareLabel=['KL','IC','Waveclus','HS','MS4','SC','TRI'];
Sorters2label=['KL','IC','Waveclus','HS','MS4','SC','TRI'];
subfolders = [ f.name for f in os.scandir(recording_folder) if f.is_dir() ];
for num in range(len(Sorters2CompareLabel)):
i=Sorters2CompareLabel[num];
# print(i)
if 'phy_'+i in subfolders:
sorting_curated = se.PhySortingExtractor('phy_'+i+'/', exclude_cluster_groups=['noise','mua']);
if not sorting_curated.get_unit_ids():
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');
flag = 1
break
if flag == 1:
continue
# Load recording extractor
print('Loading Recording Extractor...')
recording = se.OpenEphysRecordingExtractor(rec_path)
# recording_prb = recording.load_probe_file(os.path.join(base_dir, '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())
# Load sorting extractor
print('Loading Phy Sorting Extractor...')
sorting = se.PhySortingExtractor(phy_path,
exclude_cluster_groups=['noise'])
print('Units:', len(sorting.get_unit_ids()))
# print('Spikes of first unit:', len(sorting.get_unit_spike_train(1)))
# print('Shared properties:', sorting.get_shared_unit_property_names())
# Get waveforms
# waveforms = st.postprocessing.get_unit_waveforms(recording, sorting, verbose=True)
# Calculate quality metrics
quality_metrics = st.validation.compute_quality_metrics(
sorting,
recording,
metric_names=['isi_violation', 'snr', 'l_ratio'],
as_dataframe=True)
# display(quality_metrics)
#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())
#%%
#sorting_mountainsort4_all = ss.run_mountainsort4(recording_cache, output_folder='results_all_mountainsort4',delete_output_folder=True, filter=False)
#sorting_mountainsort4_all=se.NwbSortingExtractor('sorting_mountainsort4_all.nwb');
#st.postprocessing.export_to_phy(recording_cache,
# sorting_mountainsort4_all, output_folder='phy_MS4',
# grouping_property='group', verbose=True, recompute_info=True)
#%%
sorting_check = se.PhySortingExtractor('phy_AGR/')
st.postprocessing.export_to_phy(recording_cache,
sorting_check,
output_folder='phy_check',
grouping_property='group',
verbose=True,
recompute_info=True)
os.system('phy template-gui phy_check/params.py')
def load_sorting(in_dir, extract_method="phy"):
sorting_curated = None
if extract_method == "phy":
sorting_curated = se.PhySortingExtractor(in_dir)
return sorting_curated