assemblies and CCRs updates

postprocessing/execute.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 1,
    "id": "c37dce82",
    "metadata": {
     "scrolled": true
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 2,
    "id": "a8ea2991",
    "metadata": {},
    "outputs": [
@@ -75,7 +75,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 3,
    "id": "3891b792",
    "metadata": {},
    "outputs": [],
@@ -93,16 +93,16 @@
     "#sessions = get_sessions_list(os.path.join(source, animal), animal)\n",
     "#sessions = get_sessions_list(source, animal)\n",
     "#sessions = [filebase]\n",
-    "sessions = processed_008228 + processed_008229\n",
-    "sessions = [\n",
-    "'008228_hippoSIT_2022-06-01_10-19-39'\n",
-    "]\n",
+    "sessions = processed_008229\n",
+    "#sessions = [\n",
+    "#'008228_hippoSIT_2022-06-01_10-19-39'\n",
+    "#]\n",
     "\n",
     "# FIXME move occupancy outside units\n",
     "# FIXME Move 'processed' into H5NAMES\n",
     "\n",
     "steps = {\n",
-    "    'write_trajectory': True,       # Packing to HDF5 (trajectory, trials, sound events)\n",
+    "    'write_trajectory': False,       # Packing to HDF5 (trajectory, trials, sound events)\n",
     "    'write_units': True,            # Loading units (spikes times, trajectory indices, instantaneous rate)\n",
     "    'write_spiking_metrics': True,  # Spiking metrics (mean firing rate, ISI metrics etc.)\n",
     "    'write_spatial_metrics': True,  # Spatial metrics\n",
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 4,
    "id": "24cd2f6e",
    "metadata": {},
    "outputs": [
@@ -120,7 +120,28 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "session 008228_hippoSIT_2022-06-01_10-19-39 done\n"
+      "session 008229_hippoSIT_2022-05-09_15-55-58 done\n",
+      "session 008229_hippoSIT_2022-05-11_13-55-55 done\n",
+      "session 008229_hippoSIT_2022-05-13_09-48-00 done\n",
+      "session 008229_hippoSIT_2022-05-13_15-17-12 done\n",
+      "session 008229_hippoSIT_2022-05-16_20-36-44 done\n",
+      "session 008229_hippoSIT_2022-05-17_21-44-43 done\n",
+      "session 008229_hippoSIT_2022-05-18_14-36-18 done\n",
+      "session 008229_hippoSIT_2022-05-20_15-54-39 done\n",
+      "session 008229_hippoSIT_2022-05-30_21-40-24 done\n",
+      "session 008229_hippoSIT_2022-05-31_11-00-02 done\n",
+      "session 008229_hippoSIT_2022-05-31_16-38-23 done\n",
+      "session 008229_hippoSIT_2022-06-01_11-08-51 done\n",
+      "session 008229_hippoSIT_2022-06-02_20-42-08 done\n",
+      "session 008229_hippoSIT_2022-06-22_09-15-59 done\n",
+      "session 008229_hippoSIT_2022-06-23_16-12-03 done\n",
+      "session 008229_hippoSIT_2022-06-25_17-49-10 done\n",
+      "session 008229_hippoSIT_2022-06-27_16-20-05 done\n",
+      "session 008229_hippoSIT_2022-06-28_10-12-19 done\n",
+      "session 008229_hippoSIT_2022-06-28_21-03-46 done\n",
+      "session 008229_hippoSIT_2022-06-29_19-47-35 done\n",
+      "session 008229_hippoSIT_2022-06-30_21-51-20 done\n",
+      "session 008229_hippoSIT_2022-07-01_14-07-59 done\n"
      ]
     }
    ],

postprocessing/spiketrain.py

@@ -16,7 +16,7 @@ def instantaneous_rate(spiketrain, time_bins, bin_size=10, k_width=100):
 
     # convolve with gaussian kernel for smoothing
     kernel = signal.gaussian(k_width, std=(k_width) / 7.2)
-    i_rate = np.convolve(spikes_count, kernel, 'same') / kernel.sum()
+    i_rate = np.convolve(spikes_count/(1.0/bin_size), kernel, 'same') / kernel.sum()
     
     # interpolate to match experimental timeline
     lin = interp1d(np.linspace(0, time_bins[-1], len(i_rate)), i_rate)
@@ -31,4 +31,4 @@ def spike_idxs(spiketrain, time_bins):
     s_rate_tl = round(1.0 / np.diff(time_bins).mean())
     spiking_idxs = spiketrain * s_rate_tl
     spiking_idxs = spiking_idxs[spiking_idxs < len(time_bins)]
-    return spiking_idxs.astype(np.int32)
+    return spiking_idxs.astype(np.int32)

session/lists.py

@@ -16,10 +16,16 @@ processed_008228 = [
 processed_008229 = [
     "008229_hippoSIT_2022-05-09_15-55-58",
     "008229_hippoSIT_2022-05-11_13-55-55",
+    "008229_hippoSIT_2022-05-13_09-48-00",
     "008229_hippoSIT_2022-05-13_15-17-12",
     "008229_hippoSIT_2022-05-16_20-36-44",
     "008229_hippoSIT_2022-05-17_21-44-43",
+    "008229_hippoSIT_2022-05-18_14-36-18",
+    "008229_hippoSIT_2022-05-20_15-54-39",
     "008229_hippoSIT_2022-05-30_21-40-24",
+    "008229_hippoSIT_2022-05-31_11-00-02",
+    "008229_hippoSIT_2022-05-31_16-38-23",
+    "008229_hippoSIT_2022-06-01_11-08-51",
     "008229_hippoSIT_2022-06-02_20-42-08",
     "008229_hippoSIT_2022-06-22_09-15-59",
     "008229_hippoSIT_2022-06-23_16-12-03",
@@ -30,4 +36,4 @@ processed_008229 = [
     "008229_hippoSIT_2022-06-29_19-47-35",
     "008229_hippoSIT_2022-06-30_21-51-20",
     "008229_hippoSIT_2022-07-01_14-07-59",
-]
+]