calculate site spacing for npx 2.0 compatibility

ecephys_spike_sorting/common/utils.py

@@ -313,6 +313,26 @@ def load_kilosort_data(folder,
     else:
         return spike_times, spike_clusters, spike_templates, amplitudes, unwhitened_temps, channel_map, cluster_ids, cluster_quality, pc_features, pc_feature_ind
 
+def load_channel_positions(folder):
+    """
+    Loads Kilosort output files from a directory
+
+    Inputs:
+    -------
+    folder : String
+        Location of Kilosort output directory
+
+    Outputs:
+    --------
+    channel_positions : numpy.ndarray 
+        x,y positions of each channel
+    """
+
+    channel_positions = np.squeeze(load(folder,'channel_positions.npy'))
+
+    return channel_positions
+
+
 
 def get_spike_depths(spike_templates, pc_features, pc_feature_ind):
 

ecephys_spike_sorting/modules/mean_waveforms/__main__.py

@@ -6,7 +6,7 @@
 import numpy as np
 import pandas as pd
 
-from ...common.utils import load_kilosort_data
+from ...common.utils import load_kilosort_data,load_channel_positions
 
 from .extract_waveforms import extract_waveforms, writeDataAsNpy
 from .waveform_metrics import calculate_waveform_metrics
@@ -26,6 +26,8 @@ def calculate_mean_waveforms(args):
             load_kilosort_data(args['directories']['kilosort_output_directory'], \
                 args['ephys_params']['sample_rate'], \
                 convert_to_seconds = False)
+
+    channel_positions = load_channel_positions(args['directories']['kilosort_output_directory'])
 
     print("Calculating mean waveforms...")
 
@@ -34,6 +36,7 @@ def calculate_mean_waveforms(args):
                 spike_templates,
                 templates,
                 channel_map,
+                channel_positions,
                 args['ephys_params']['bit_volts'], \
                 args['ephys_params']['sample_rate'], \
                 args['ephys_params']['vertical_site_spacing'], \

ecephys_spike_sorting/modules/mean_waveforms/extract_waveforms.py

@@ -16,7 +16,8 @@ def extract_waveforms(raw_data,
                       spike_clusters, 
                       spike_templates,
                       templates, 
-                      channel_map, 
+                      channel_map,
+                      channel_positions,
                       bit_volts, 
                       sample_rate, 
                       site_spacing, 
@@ -130,6 +131,7 @@ def extract_waveforms(raw_data,
                                                                          cluster_id, 
                                                                          peak_channels[target_template_id], 
                                                                          channel_map,
+                                                                         channel_positions,
                                                                          sample_rate, 
                                                                          upsampling_factor,
                                                                          spread_threshold,

ecephys_spike_sorting/modules/mean_waveforms/waveform_metrics.py

@@ -9,6 +9,7 @@ def calculate_waveform_metrics(waveforms,
                                cluster_id, 
                                peak_channel, 
                                channel_map, 
+                               channel_positions,
                                sample_rate, 
                                upsampling_factor, 
                                spread_threshold,
@@ -75,7 +76,7 @@ def calculate_waveform_metrics(waveforms,
         mean_1D_waveform, timestamps)
     recovery_slope = calculate_waveform_recovery_slope(
         mean_1D_waveform, timestamps)
-
+    site_spacing = (channel_positions[2,1] - channel_positions[0,1])/2 * 10e-7 # calculate site spacing, compatible for both npx 1.0 and npx 2.0
     amplitude, spread, velocity_above, velocity_below = calculate_2D_features(
         mean_2D_waveform, timestamps, local_peak, spread_threshold, site_range, site_spacing)