notebook updates

AllenInstitute · Jul 2, 2024 · 3d1e202 · 3d1e202
1 parent 3cbca16
commit 3d1e202
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Showing 2 changed files with 25 additions and 14 deletions.
diff --git a/notebooks/compute_single_unit_metrics.ipynb b/notebooks/compute_single_unit_metrics.ipynb
@@ -24,9 +24,24 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "#get all uploaded & annotated ephys sessions\n",
     "ephys_sessions=tuple(s for s in npc_lims.get_session_info(is_ephys=True, is_uploaded=True, is_annotated=True,))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#alternatively, provide a list of session ids:\n",
+    "session_id_list=['712815_2024-05-22','712815_2024-05-20','708016_2024-05-01']\n",
+    "session_list=[]\n",
+    "for ss in session_id_list:\n",
+    "    session_list.append(npc_lims.get_session_info(ss))\n",
+    "ephys_sessions=tuple(session_list)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/notebooks/decoding_example_egm.ipynb b/notebooks/decoding_example_egm.ipynb
@@ -24,8 +24,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#load ephys sessions\n",
-    "ephys_sessions = tuple(s for s in npc_lims.get_session_info(is_ephys=True, is_uploaded=True, is_annotated=True)) #, project='DynamicRouting', project='TempletonPilotSession'))\n"
+    "#get all uploaded & annotated ephys sessions\n",
+    "ephys_sessions = tuple(s for s in npc_lims.get_session_info(is_ephys=True, is_uploaded=True, is_annotated=True))"
    ]
   },
   {
@@ -34,7 +34,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ephys_sessions[35]"
+    "#alternatively, provide a list of session ids:\n",
+    "session_id_list=['712815_2024-05-22','712815_2024-05-20','708016_2024-05-01']\n",
+    "session_list=[]\n",
+    "for ss in session_id_list:\n",
+    "    session_list.append(npc_lims.get_session_info(ss))\n",
+    "ephys_sessions=tuple(session_list)\n",
+    "ephys_sessions"
    ]
   },
   {
@@ -43,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
+    "#set savepath and filename\n",
     "savepath=r'\\\\allen\\programs\\mindscope\\workgroups\\templeton\\TTOC\\decoding results\\new_annotations\\linear_shift_20_units'\n",
     "filename='decoding_results_linear_shift_20_units.pkl'\n",
     "\n",
@@ -58,12 +64,7 @@
     "decoder_time_after=0.1\n",
     "\n",
     "params={\n",
-    "    # 'predict':['block_ids','cr_vs_fa','mouse_response_context'],\n",
-    "    # 'predict':['block_ids'],\n",
-    "    # 'trnum':'all',\n",
-    "    # 'n_units':[5,10,20,50,100,'all'],\n",
     "    'n_units':20,\n",
-    "    # 'u_min':20,\n",
     "    'n_repeats':25, \n",
     "    'input_data_type':'spikes', #spikes or facemap\n",
     "    'vid_angle':'face', #behavior, face, eye\n",
@@ -77,15 +78,12 @@
     "    'decoder_binsize':decoder_binsize,\n",
     "    'decoder_time_before':decoder_time_before,\n",
     "    'decoder_time_after':decoder_time_after,\n",
-    "    # 'balance_labels':0,\n",
     "    'savepath':savepath,\n",
     "    'filename':filename,\n",
     "    'use_structure_probe':True,\n",
     "    'crossval':'5_fold',\n",
-    "    # 'all_areas':True,\n",
     "    'labels_as_index':True,\n",
     "    'decoder_type':'linearSVC', # 'linearSVC' or 'LDA' or 'RandomForest' or 'LogisticRegression'\n",
-    "    # 'generate_labels':False,\n",
     "}\n",
     "\n",
     "\n",
@@ -94,9 +92,7 @@
     "        session = DynamicRoutingSession(ephys_session.id)\n",
     "        print(session.id+' loaded')\n",
     "        if 'structure' in session.electrodes[:].columns:\n",
-    "            # decoding_utils.decode_context_from_units(session,params)\n",
     "            decoding_utils.decode_context_with_linear_shift(session,params)\n",
-    "\n",
     "        else:\n",
     "            print('no structure column found in electrodes table, moving to next recording')\n",
     "        session=[]\n",