new function

talmolab · Jul 8, 2024 · 9bae8b3 · 9bae8b3
1 parent 8582f51
commit 9bae8b3
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diff --git a/io_test.ipynb b/io_test.ipynb
@@ -2,14 +2,27 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 18,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The autoreload extension is already loaded. To reload it, use:\n",
+      "  %reload_ext autoreload\n"
+     ]
+    }
+   ],
    "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
     "import sleap_io as sio\n",
     "import pynwb\n",
+    "import numpy as np\n",
     "from sleap_io import save_file\n",
     "from sleap_io.model.skeleton import Node, Edge, Symmetry, Skeleton\n",
+    "from pynwb.image import ImageSeries\n",
     "from ndx_pose import (\n",
     "    PoseEstimation,\n",
     "    PoseEstimationSeries,\n",
@@ -18,58 +31,51 @@
     "    PoseTraining,\n",
     "    SourceVideos,\n",
     ")\n",
-    "from sleap_io.io.nwb import convert_slp_skeleton_to_nwb"
+    "from sleap_io.io.nwb import slp_skeleton_to_nwb"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 19,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[]\n"
-     ]
-    },
-    {
-     "ename": "ValueError",
-     "evalue": "CustomClassGenerator.set_init.<locals>.__init__: incorrect shape for 'edges' (got '(0,)', expected '[None, 2]')",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[5], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m skel \u001b[38;5;241m=\u001b[39m Skeleton([Node(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mA\u001b[39m\u001b[38;5;124m\"\u001b[39m), Node(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mB\u001b[39m\u001b[38;5;124m\"\u001b[39m)], name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtest\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 2\u001b[0m new_skel \u001b[38;5;241m=\u001b[39m \u001b[43mconvert_slp_skeleton_to_nwb\u001b[49m\u001b[43m(\u001b[49m\u001b[43mskel\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/salk/io_fork/sleap_io/io/nwb.py:149\u001b[0m, in \u001b[0;36mconvert_slp_skeleton_to_nwb\u001b[0;34m(skeleton)\u001b[0m\n\u001b[1;32m    147\u001b[0m     nwb_edges\u001b[38;5;241m.\u001b[39mappend([i, i \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m])\n\u001b[1;32m    148\u001b[0m \u001b[38;5;28mprint\u001b[39m(nwb_edges)\n\u001b[0;32m--> 149\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mNWBSkeleton\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    150\u001b[0m \u001b[43m    \u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mskeleton\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    151\u001b[0m \u001b[43m    \u001b[49m\u001b[43mnodes\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mskeleton\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnode_names\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    152\u001b[0m \u001b[43m    \u001b[49m\u001b[43medges\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43marray\u001b[49m\u001b[43m(\u001b[49m\u001b[43mnwb_edges\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43muint8\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    153\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:667\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    666\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfunc_call\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m--> 667\u001b[0m     pargs \u001b[38;5;241m=\u001b[39m \u001b[43m_check_args\u001b[49m\u001b[43m(\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    668\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(args[\u001b[38;5;241m0\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mpargs)\n",
-      "File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:660\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>._check_args\u001b[0;34m(args, kwargs)\u001b[0m\n\u001b[1;32m    658\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m parse_err:\n\u001b[1;32m    659\u001b[0m         msg \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m%\u001b[39m (func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__qualname__\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(parse_err))\n\u001b[0;32m--> 660\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m ExceptionType(msg)\n\u001b[1;32m    662\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m parsed[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124margs\u001b[39m\u001b[38;5;124m'\u001b[39m]\n",
-      "\u001b[0;31mValueError\u001b[0m: CustomClassGenerator.set_init.<locals>.__init__: incorrect shape for 'edges' (got '(0,)', expected '[None, 2]')"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "skel = Skeleton([Node(\"A\"), Node(\"B\")], name=\"test\")\n",
-    "new_skel = convert_slp_skeleton_to_nwb(skel)"
+    "node_a = Node(\"A\")\n",
+    "node_b = Node(\"B\")\n",
+    "edge = Edge(node_a, node_b)\n",
+    "skel = Skeleton([Node(\"A\"), Node(\"B\")], [edge], name=\"test\")\n",
+    "new_skel = slp_skeleton_to_nwb(skel)\n",
+    "assert new_skel.nodes[0] == \"A\"\n",
+    "assert new_skel.nodes[1] == \"B\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
-     "ename": "AttributeError",
-     "evalue": "'NoneType' object has no attribute 'name'",
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/keya/salk/io_fork/sleap_io/io/nwb.py:115: FutureWarning: CustomClassGenerator.set_init.<locals>.__init__: Using positional arguments for this method is discouraged and will be deprecated in a future major release. Please use keyword arguments to ensure future compatibility.\n",
+      "  training_frame_skeleton_instances = SkeletonInstances(\n"
+     ]
+    },
+    {
+     "ename": "TypeError",
+     "evalue": "CustomClassGenerator.set_init.<locals>.__init__: incorrect type for 'name' (got 'list', expected 'str')",
      "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[3], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m labels_original \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_slp(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtests/data/slp/minimal_instance.pkg.slp\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 2\u001b[0m \u001b[43mlabels_original\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mminimal_instance.pkg.nwb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnwb_training\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m      3\u001b[0m labels_loaded \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_nwb(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mminimal_instance.pkg.nwb\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m labels_original\u001b[38;5;241m.\u001b[39mlabeled_frames \u001b[38;5;241m==\u001b[39m labels_loaded\u001b[38;5;241m.\u001b[39mlabeled_frames\n",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[20], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m labels_original \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_slp(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtests/data/slp/minimal_instance.pkg.slp\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 2\u001b[0m \u001b[43mlabels_original\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mminimal_instance.pkg.nwb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnwb_training\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m      3\u001b[0m labels_loaded \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_nwb(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mminimal_instance.pkg.nwb\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m labels_original\u001b[38;5;241m.\u001b[39mlabeled_frames \u001b[38;5;241m==\u001b[39m labels_loaded\u001b[38;5;241m.\u001b[39mlabeled_frames\n",
       "File \u001b[0;32m~/salk/io_fork/sleap_io/model/labels.py:372\u001b[0m, in \u001b[0;36mLabels.save\u001b[0;34m(self, filename, format, embed, **kwargs)\u001b[0m\n\u001b[1;32m    348\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Save labels to file in specified format.\u001b[39;00m\n\u001b[1;32m    349\u001b[0m \n\u001b[1;32m    350\u001b[0m \u001b[38;5;124;03mArgs:\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    368\u001b[0m \u001b[38;5;124;03m        This argument is only valid for the SLP backend.\u001b[39;00m\n\u001b[1;32m    369\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    370\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msleap_io\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m save_file\n\u001b[0;32m--> 372\u001b[0m \u001b[43msave_file\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43membed\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43membed\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/salk/io_fork/sleap_io/io/main.py:232\u001b[0m, in \u001b[0;36msave_file\u001b[0;34m(labels, filename, format, **kwargs)\u001b[0m\n\u001b[1;32m    230\u001b[0m     save_jabs(labels, pose_version, filename, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m    231\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnwb_training\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m--> 232\u001b[0m     \u001b[43mnwb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert_labels_to_pose_training\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlabels\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    233\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    234\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mUnknown format \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mformat\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m for filename: \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfilename\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
-      "File \u001b[0;32m~/salk/io_fork/sleap_io/io/nwb.py:115\u001b[0m, in \u001b[0;36mconvert_labels_to_pose_training\u001b[0;34m(labels, filename, **kwargs)\u001b[0m\n\u001b[1;32m    110\u001b[0m training_frame_name \u001b[38;5;241m=\u001b[39m name_generator(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtraining_frame\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    111\u001b[0m training_frame_annotator \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mtraining_frame_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    112\u001b[0m training_frame_skeleton_instances \u001b[38;5;241m=\u001b[39m SkeletonInstances(\n\u001b[1;32m    113\u001b[0m     [\n\u001b[1;32m    114\u001b[0m         SkeletonInstance(\n\u001b[0;32m--> 115\u001b[0m             name\u001b[38;5;241m=\u001b[39m\u001b[43minstance\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtrack\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m,\n\u001b[1;32m    116\u001b[0m             skeleton\u001b[38;5;241m=\u001b[39minstance\u001b[38;5;241m.\u001b[39mskeleton,\n\u001b[1;32m    117\u001b[0m             points\u001b[38;5;241m=\u001b[39minstance\u001b[38;5;241m.\u001b[39mpoints,\n\u001b[1;32m    118\u001b[0m             confidence\u001b[38;5;241m=\u001b[39minstance\u001b[38;5;241m.\u001b[39mpoint_scores,\n\u001b[1;32m    119\u001b[0m         )\n\u001b[1;32m    120\u001b[0m         \u001b[38;5;28;01mfor\u001b[39;00m instance \u001b[38;5;129;01min\u001b[39;00m labeled_frame\u001b[38;5;241m.\u001b[39minstances\n\u001b[1;32m    121\u001b[0m     ]\n\u001b[1;32m    122\u001b[0m )\n\u001b[1;32m    123\u001b[0m training_frame_video \u001b[38;5;241m=\u001b[39m labeled_frame\u001b[38;5;241m.\u001b[39mvideo\n\u001b[1;32m    124\u001b[0m training_frame_video_index \u001b[38;5;241m=\u001b[39m labeled_frame\u001b[38;5;241m.\u001b[39mframe_idx\n",
-      "\u001b[0;31mAttributeError\u001b[0m: 'NoneType' object has no attribute 'name'"
+      "File \u001b[0;32m~/salk/io_fork/sleap_io/io/main.py:232\u001b[0m, in \u001b[0;36msave_file\u001b[0;34m(labels, filename, format, **kwargs)\u001b[0m\n\u001b[1;32m    230\u001b[0m     save_jabs(labels, pose_version, filename, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m    231\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnwb_training\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m--> 232\u001b[0m     \u001b[43mnwb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlabels_to_pose_training\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlabels\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    233\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    234\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mUnknown format \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mformat\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m for filename: \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfilename\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
+      "File \u001b[0;32m~/salk/io_fork/sleap_io/io/nwb.py:115\u001b[0m, in \u001b[0;36mlabels_to_pose_training\u001b[0;34m(labels, filename, **kwargs)\u001b[0m\n\u001b[1;32m    113\u001b[0m training_frame_name \u001b[38;5;241m=\u001b[39m name_generator(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtraining_frame\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    114\u001b[0m training_frame_annotator \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mtraining_frame_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 115\u001b[0m training_frame_skeleton_instances \u001b[38;5;241m=\u001b[39m \u001b[43mSkeletonInstances\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    116\u001b[0m \u001b[43m    \u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m    117\u001b[0m \u001b[43m        \u001b[49m\u001b[43minstance_to_skeleton_instance\u001b[49m\u001b[43m(\u001b[49m\u001b[43minstance\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    118\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43minstance\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mlabeled_frame\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minstances\u001b[49m\n\u001b[1;32m    119\u001b[0m \u001b[43m    \u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m    120\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    121\u001b[0m training_frame_video \u001b[38;5;241m=\u001b[39m labeled_frame\u001b[38;5;241m.\u001b[39mvideo\n\u001b[1;32m    122\u001b[0m training_frame_video_index \u001b[38;5;241m=\u001b[39m labeled_frame\u001b[38;5;241m.\u001b[39mframe_idx\n",
+      "File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:667\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    666\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfunc_call\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m--> 667\u001b[0m     pargs \u001b[38;5;241m=\u001b[39m \u001b[43m_check_args\u001b[49m\u001b[43m(\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    668\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(args[\u001b[38;5;241m0\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mpargs)\n",
+      "File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:660\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>._check_args\u001b[0;34m(args, kwargs)\u001b[0m\n\u001b[1;32m    658\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m parse_err:\n\u001b[1;32m    659\u001b[0m         msg \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m%\u001b[39m (func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__qualname__\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(parse_err))\n\u001b[0;32m--> 660\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m ExceptionType(msg)\n\u001b[1;32m    662\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m parsed[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124margs\u001b[39m\u001b[38;5;124m'\u001b[39m]\n",
+      "\u001b[0;31mTypeError\u001b[0m: CustomClassGenerator.set_init.<locals>.__init__: incorrect type for 'name' (got 'list', expected 'str')"
      ]
     }
    ],