Merge branch 'master' into master

Author: drewyangdev

ecephys_spike_sorting/modules/kilosort_helper/__main__.py

@@ -40,6 +40,7 @@ def run_kilosort(args):
     # chanMap.mat section
     metaName = (Path(args['ephys_params']['ap_band_file']).parent / Path(args['ephys_params']['ap_band_file']).stem).as_posix()
 
+
     if not args['kilosort_helper_params'].get('chanMap_pregenerated', False):
         # generate and write chanMap.mat file - different implementation for SpikeGLX and Open Ephys
         if args['kilosort_helper_params']['spikeGLX_data']:
@@ -88,7 +89,8 @@ def run_kilosort(args):
                                             os.path.basename(args['ephys_params']['ap_band_file']),
                                             args['kilosort_helper_params']['kilosort_params'])
 
-    elif args['kilosort_helper_params']['kilosort_version'] == 2:
+    elif args['kilosort_helper_params']['kilosort_version'] == 2 \
+         or args['kilosort_helper_params']['kilosort_version'] == 3:
 
         matlab_file_generator.create_config2(args['kilosort_helper_params']['matlab_home_directory'],
                                              output_dir_forward_slash,

ecephys_spike_sorting/modules/kilosort_helper/_schemas.py

@@ -92,4 +92,4 @@ class OutputParameters(OutputSchema):
     mask_channels = NumpyArray()
     nTemplate = Int()
     nTot = Int()
-    
+    

ecephys_spike_sorting/modules/tPrime_helper/__main__.py

@@ -12,7 +12,6 @@
 
 
 def call_TPrime(args):
-
     # Run TPrime on a "standard" multiprobe + NI, using NP 1.0 or 2.0, with run
     # folder and probe folders
     # inputs:
@@ -114,7 +113,7 @@ def call_TPrime(args):
         toStream_path = os.path.join(run_directory, prb_dir, c_name)
 
         # convert events in the toStream to sec; they will not be adjusted
-        ks_outdir = 'imec' + str(toStream_prb) + '_ks2'
+        ks_outdir = 'imec' + str(toStream_prb) + '_ks' + args['kilosort_helper_params']['kilosort2_params']['KSver']
         st_file = os.path.join(run_directory, prb_dir, ks_outdir, 'spike_times.npy')
         # convert to seconds; if bNPY = True, returned file is an npy file
         # otherwise, text.
@@ -151,7 +150,7 @@ def call_TPrime(args):
             from_list.append(os.path.join(run_directory, prb_dir, c_name))
             c_index = len(from_stream_index)
             # build path to spike times npy file
-            ks_outdir = 'imec' + str(c_prb) + '_ks2'
+            ks_outdir = 'imec' + str(c_prb) + '_ks' + args['kilosort_helper_params']['kilosort2_params']['KSver']
             st_file = os.path.join(run_directory, prb_dir, ks_outdir, 'spike_times.npy')
             st_file_sec = spike_times_npy_to_sec(st_file, 0, bNPY)
             events_list.append(st_file_sec)
@@ -236,7 +235,7 @@ def call_TPrime(args):
             from_list.append(os.path.join(run_directory, prb_dir, c_name))
             c_index = len(from_stream_index)
             # build path to spike times npy file
-            ks_outdir = 'imec' + str(c_prb) + '_ks2'
+            ks_outdir = 'imec' + str(c_prb) + '_ks' + args['kilosort_helper_params']['kilosort2_params']['KSver'] 
             st_file = os.path.join(run_directory, prb_dir, ks_outdir, 'spike_times.npy')
             st_file_sec = spike_times_npy_to_sec(st_file, 0, bNPY)
             events_list.append(st_file_sec)
@@ -262,25 +261,27 @@ def call_TPrime(args):
     # Essential in linux where TPrime executable is only callable through runit
     if sys.platform.startswith('win'):
         exe_path = os.path.join(args['tPrime_helper_params']['tPrime_path'], 'runit.bat')
-    elif sys.platform.starstwith('linux'):
+    elif sys.platform.startswith('linux'):
         exe_path = os.path.join(args['tPrime_helper_params']['tPrime_path'], 'runit.sh')
     else:
         print('unknown system, cannot run TPrime')   
 
     # Print out command for help with debugging
-    tcmd = exe_path + ' -syncperiod=' + repr(sync_period) + \
-        ' -tostream=' + toStream_path
+    tcmd = list()
+    tcmd.append(exe_path)
+    tcmd.append(' -syncperiod=' + repr(sync_period))
+    tcmd.append(' -tostream=' + toStream_path)
 
     for i, fp in enumerate(from_list):
-        tcmd = tcmd + ' -fromstream=' + repr(i) + ',' + fp
+        tcmd.append(' -fromstream=' + repr(i) + ',' + fp)
 
     for i, ep in enumerate(events_list):
-        tcmd = tcmd + ' -events=' + repr(from_stream_index[i]) + ',' + ep + ',' + out_list[i]
+        tcmd.append(' -events=' + repr(from_stream_index[i]) + ',' + ep + ',' + out_list[i])
 
     # write out file to record the TPrime command for a record
     bat_path = os.path.join(run_directory, run_name + '_TPrime_cmd.txt')
     with open(bat_path, 'w') as batfile:
-        batfile.write(tcmd)
+        batfile.write(str(tcmd))
 
 
     # make the TPrime call
@@ -347,7 +348,7 @@ def call_TPrime_3A(args):
     # convert events in the toStream to sec; they will not be adjusted
     # search the directory the edges file to get the ks2 output
     # get name of ks2 output dir and convert to sec
-    ks_outdir = fnmatch.filter(file_list, 'imec_*_ks2')[0]
+    ks_outdir = fnmatch.filter(file_list, 'imec_*_ks' + args['kilosort_helper_params']['kilosort2_params']['KSver'])[0]
     st_file = os.path.join(toStream_parent, ks_outdir, 'spike_times.npy')
     toStream_events_sec = spike_times_npy_to_sec(st_file, 0, bNPY)
     # for later data analysis with spike times as sec, also save as npy
@@ -367,7 +368,7 @@ def call_TPrime_3A(args):
             return              
         fS_name = flt_list[0]
         fS_file_list.append(os.path.join(fS_parent,fS_name))
-        ks_outdir = fnmatch.filter(file_list, 'imec_*_ks2')[0]
+        ks_outdir = fnmatch.filter(file_list, 'imec_*_ks' + args['kilosort_helper_params']['kilosort2_params']['KSver'])[0]
         st_file = os.path.join(fS_parent, ks_outdir, 'spike_times.npy')
         st_file_sec = spike_times_npy_to_sec(st_file, 0, bNPY)
         events_list.append(st_file_sec)

ecephys_spike_sorting/modules/tPrime_helper/_schemas.py

@@ -3,6 +3,7 @@
 from argschema.fields import Nested, InputDir, String, Float, Dict, Int, List, Boolean
 from ...common.schemas import EphysParams, Directories
 from ..catGT_helper._schemas import CatGTParams
+from ..kilosort_helper._schemas import KilosortHelperParameters
 
 
 class tPrimeParams(DefaultSchema):
@@ -19,6 +20,7 @@ class tPrimeParams(DefaultSchema):
 class InputParameters(ArgSchema):
     tPrime_helper_params = Nested(tPrimeParams)
     catGT_helper_params = Nested(CatGTParams)
+    kilosort_helper_params = Nested(KilosortHelperParameters)
     directories = Nested(Directories)
     ephys_params = Nested(EphysParams)
 
@@ -31,4 +33,4 @@ class OutputSchema(DefaultSchema):
 class OutputParameters(OutputSchema): 
 
     execution_time = Float()
-    
+    

ecephys_spike_sorting/scripts/create_input_json.py

@@ -396,5 +396,7 @@ def createInputJson(
 
     with io.open(output_file, 'w', encoding='utf-8') as f:
         f.write(json.dumps(dictionary, ensure_ascii=False, sort_keys=True, indent=4))
+    if sys.platform == 'linux':
+        os.chmod(output_file, 0o664)
 
     return dictionary