chore: update si params in notebook

Author: ttngu207

notebooks/tutorial.ipynb

@@ -2050,7 +2050,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -2151,30 +2151,42 @@
    ],
    "source": [
     "# insert clustering task manually\n",
-    "params_ks = {\n",
-    "    \"fs\": 30000,\n",
-    "    \"fshigh\": 150,\n",
+    "params = {}\n",
+    "params[\"SI_PREPROCESSING_METHOD\"] = \"CatGT\"\n",
+    "params[\"SI_SORTING_PARAMS\"] = {\n",
     "    \"minfr_goodchannels\": 0.1,\n",
-    "    \"Th\": [10, 4],\n",
     "    \"lam\": 10,\n",
     "    \"AUCsplit\": 0.9,\n",
     "    \"minFR\": 0.02,\n",
     "    \"momentum\": [20, 400],\n",
     "    \"sigmaMask\": 30,\n",
-    "    \"ThPr\": 8,\n",
-    "    \"spkTh\": -6,\n",
-    "    \"reorder\": 1,\n",
-    "    \"nskip\": 25,\n",
-    "    \"GPU\": 1,\n",
-    "    \"Nfilt\": 1024,\n",
     "    \"nfilt_factor\": 4,\n",
     "    \"ntbuff\": 64,\n",
-    "    \"whiteningRange\": 32,\n",
-    "    \"nSkipCov\": 25,\n",
     "    \"scaleproc\": 200,\n",
     "    \"nPCs\": 3,\n",
-    "    \"useRAM\": 0,\n",
     "}\n",
+    "params[\"SI_POSTPROCESSING_PARAMS\"] = {\n",
+    "    \"extensions\": {\n",
+    "        \"random_spikes\": {},\n",
+    "        \"waveforms\": {},\n",
+    "        \"templates\": {},\n",
+    "        \"noise_levels\": {},\n",
+    "        # \"amplitude_scalings\": {},\n",
+    "        \"correlograms\": {},\n",
+    "        \"isi_histograms\": {},\n",
+    "        \"principal_components\": {\"n_components\": 5, \"mode\": \"by_channel_local\"},\n",
+    "        \"spike_amplitudes\": {},\n",
+    "        \"spike_locations\": {},\n",
+    "        \"template_metrics\": {\"include_multi_channel_metrics\": True},\n",
+    "        \"template_similarity\": {},\n",
+    "        \"unit_locations\": {},\n",
+    "        \"quality_metrics\": {},\n",
+    "    },\n",
+    "    \"job_kwargs\": {\"n_jobs\": 0.8, \"chunk_duration\": \"1s\"},\n",
+    "    \"export_to_phy\": True,\n",
+    "    \"export_report\": True,\n",
+    "}\n",
+    "\n",
     "ephys.ClusteringParamSet.insert_new_params(\n",
     "    clustering_method=\"kilosort2\",\n",
     "    paramset_idx=0,\n",
@@ -2750,7 +2762,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "element-dlc",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -2764,7 +2776,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.11.12"
   },
   "orig_nbformat": 4
  },