remove column of row labels from waveform_metrics.csv and metrics.csv

ecephys_spike_sorting/common/utils.py

@@ -2,10 +2,8 @@
 import os
 import numpy as np
 import json
-import glob
 import sys
 import time
-import psutil
 import pathlib
 
 from git import Repo

ecephys_spike_sorting/modules/mean_waveforms/__main__.py

@@ -149,7 +149,7 @@ def calculate_mean_waveforms(args):
            # save new metrics as _version number
            wm_fullpath = os.path.join(pathlib.Path(wm_fullpath).parent, pathlib.Path(wm_fullpath).stem + '_' + repr(clu_version) + '.csv')
 
-        metrics.to_csv(wm_fullpath)
+        metrics.to_csv(wm_fullpath, index=False)
 
 
     else:

ecephys_spike_sorting/modules/quality_metrics/__main__.py

@@ -78,7 +78,7 @@ def calculate_quality_metrics(args):
 
     print("Saving data...")
 
-    metrics.to_csv(output_file)
+    metrics.to_csv(output_file, index=False )
 
     execution_time = time.time() - start
 

ecephys_spike_sorting/scripts/create_input_json.py

@@ -66,6 +66,7 @@ def createInputJson(output_file,
     # location of kilosor respository and kilosort version
 
     kilosort_repository = r'C:\Users\labadmin\Documents\jic\KS3_fork\Kilosort2'
+
     KS2ver = '2.0'      # must equal '3.0', '2.5' or '2.0', and match the kiilosort_repository
 
     # KS 3.0 does not yet output pcs.
@@ -155,7 +156,7 @@ def createInputJson(output_file,
     nrows = np.sqrt((np.square(ks_templateRadius_um) - np.square(hpitch.get(probe_type))))/vpitch.get(probe_type)
     ks_nNeighbors = int(round(2*nrows*nColumn.get(probe_type)))
     if ks_nNeighbors > 64:
-        ks_nNeighbors = 64          #max allowed in CUDA
+        ks_nNeighbors = 64          #max allowed in CUDA for standard KS2
     print('ks_nNeighbors: ' + repr(ks_nNeighbors))
 
     c_waves_radius_sites = int(round(c_Waves_snr_um/vpitch.get(probe_type)))

ecephys_spike_sorting/scripts/sglx_filelist_pipeline.py

@@ -17,7 +17,7 @@
 # -------------------------------
 # Full path to log file
 # If this file exists, new run data is appended to it
-logFullPath = r'E:\SC045\SC045_121520_g0_imec0\pipeline_log.csv'
+logFullPath = r'D:\ecephys_fork\test_data\file_list_test\pipeline_log.csv'
 
 # brain region specific params
 # can add a new brain region by adding the key and value for each param
@@ -39,12 +39,12 @@
 
 # Raw data directory = npx_directory
 # run_specs = name, gate, trigger and probes to process
-npx_directory = r'D:\ecephys_fork\test_data\SC_10trial'
+npx_directory = r'D:\ecephys_fork\test_data\file_list_test'
 
 # for each recording, specfiy a full path the the binary and a brain region
 
 recording_specs = [									
-				[r'E:\SC045\SC045_121520_g0_imec0\SC045_121520_g0_tcat.imec0.ap.bin', ['default'] ]
+				[r'D:\ecephys_fork\test_data\file_list_test\SC024_092319_NP1.0_Midbrain_g0_tcat.imec0.ap.bin', ['default'] ]
 
 ]
 

ecephys_spike_sorting/scripts/sglx_multi_run_pipeline.py

@@ -67,7 +67,7 @@
 # Set to an existing directory; all output will be written here.
 # Output will be in the standard SpikeGLX directory structure:
 # run_folder/probe_folder/*.bin
-catGT_dest = r'D:\ecephys_fork\test_data\SC_10trial\test_depth'
+catGT_dest = r'D:\ecephys_fork\test_data\SC_10trial\test_events'
 
 # ------------
 # CatGT params
@@ -126,7 +126,7 @@
 # extract param string for psth events -- copy the CatGT params used to extract
 # events that should be exported with the phy output for PSTH plots
 # If not using, remove psth_events from the list of modules
-event_ex_param_str = 'XD=-1,1,50'
+event_ex_param_str = 'XD=4,1,50'
 
 # -----------------
 # TPrime parameters
@@ -143,7 +143,8 @@
 modules = [
             'kilosort_helper',
             'kilosort_postprocessing',
-            'noise_templates',          
+            'noise_templates',    
+            'psth_events',
             'mean_waveforms',
             'quality_metrics'
 			]