PPC / HPC analysis updates

analysis/performance - general.ipynb

@@ -3,6 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": 35,
+   "id": "da40959d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -19,6 +20,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "d10de8e7",
    "metadata": {},
    "source": [
     "## Compute performance and write to the file"
@@ -27,6 +29,7 @@
   {
    "cell_type": "code",
    "execution_count": 36,
+   "id": "1672860e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,6 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": 37,
+   "id": "91af3047",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,6 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": 38,
+   "id": "896a0234",
    "metadata": {},
    "outputs": [
     {
@@ -83,6 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
+   "id": "54278299",
    "metadata": {
     "scrolled": true
    },
@@ -140,6 +146,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "72fea9eb",
    "metadata": {},
    "source": [
     "## Plot performance"
@@ -148,6 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
+   "id": "4d1226ea",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -158,6 +166,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
+   "id": "93c94b1d",
    "metadata": {},
    "outputs": [
     {
@@ -204,6 +213,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "9090e619",
    "metadata": {},
    "source": [
     "## Separate periods"
@@ -212,6 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "fc5b694e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,6 +236,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
+   "id": "4e1470d7",
    "metadata": {},
    "outputs": [
     {
@@ -265,6 +277,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "324613ac",
    "metadata": {},
    "source": [
     "## Reward performance in light vs dark"
@@ -273,6 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
+   "id": "904887f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -312,6 +326,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
+   "id": "5a173322",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -329,6 +344,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
+   "id": "162ba711",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -340,6 +356,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
+   "id": "af2f2bb5",
    "metadata": {},
    "outputs": [
     {
@@ -389,6 +406,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
+   "id": "478891a2",
    "metadata": {},
    "outputs": [
     {
@@ -439,6 +457,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "2daf4cf1",
    "metadata": {},
    "source": [
     "### special plot for grant application"
@@ -447,6 +466,7 @@
   {
    "cell_type": "code",
    "execution_count": 27,
+   "id": "f8775ed7",
    "metadata": {},
    "outputs": [
     {
@@ -487,6 +507,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "010dcbc0",
    "metadata": {},
    "source": [
     "## Trial performance"
@@ -495,6 +516,7 @@
   {
    "cell_type": "code",
    "execution_count": 28,
+   "id": "43187d72",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -512,6 +534,7 @@
   {
    "cell_type": "code",
    "execution_count": 33,
+   "id": "f03bace1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -532,6 +555,7 @@
   {
    "cell_type": "code",
    "execution_count": 49,
+   "id": "b856689b",
    "metadata": {
     "scrolled": true
    },
@@ -583,12 +607,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "7f2f88fc",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "markdown",
+   "id": "bfe2b390",
    "metadata": {},
    "source": [
     "## Miltiple island performance"
@@ -597,6 +623,7 @@
   {
    "cell_type": "code",
    "execution_count": 40,
+   "id": "ac11ea2d",
    "metadata": {},
    "outputs": [
     {
@@ -631,6 +658,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
+   "id": "f61cc408",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -643,6 +671,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
+   "id": "233bf271",
    "metadata": {},
    "outputs": [
     {
@@ -668,6 +697,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
+   "id": "fd2b0cbb",
    "metadata": {},
    "outputs": [
     {
@@ -710,6 +740,7 @@
   {
    "cell_type": "code",
    "execution_count": 41,
+   "id": "4dc144ae",
    "metadata": {},
    "outputs": [
     {
@@ -760,6 +791,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "7f2e76c8",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -767,7 +799,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

postprocessing/execute.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 10,
    "id": "c37dce82",
    "metadata": {
     "scrolled": true
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 11,
    "id": "a8ea2991",
    "metadata": {},
    "outputs": [
@@ -75,7 +75,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 12,
    "id": "3891b792",
    "metadata": {},
    "outputs": [],
@@ -95,15 +95,14 @@
     "#sessions = [filebase]\n",
     "sessions = processed_008228 + processed_008229\n",
     "sessions = [\n",
-    "'008229_hippoSIT_2022-05-31_11-00-02',\n",
-    "#'008229_hippoSIT_2022-05-31_16-38-23'\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': False,       # Packing to HDF5 (trajectory, trials, sound events)\n",
+    "    'write_trajectory': True,       # 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",
@@ -113,7 +112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 13,
    "id": "24cd2f6e",
    "metadata": {},
    "outputs": [
@@ -121,7 +120,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "session 008229_hippoSIT_2022-05-31_11-00-02 done\n"
+      "session 008228_hippoSIT_2022-06-01_10-19-39 done\n"
      ]
     }
    ],