nwb files

talmolab · Jul 1, 2024 · 37f941f · 37f941f
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diff --git a/ntbk.ipynb b/ntbk.ipynb
@@ -0,0 +1,153 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sleap_io as sio\n",
+    "import ndx_pose as ndp\n",
+    "from pynwb import NWBFile, NWBHDF5IO\n",
+    "import numpy as np\n",
+    "from pynwb.file import Subject\n",
+    "from ndx_pose import (\n",
+    "    PoseEstimationSeries,\n",
+    "    PoseEstimation,\n",
+    ")\n",
+    "from sleap_io.io.nwb import read_nwb"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/keya/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.7.0 is already loaded.\n",
+      "  return func(args[0], **pargs)\n"
+     ]
+    }
+   ],
+   "source": [
+    "path = \"/Users/keya/salk/io_fork/tests/data/nwb/centered_pair_predictions.nwb\"\n",
+    "labels = read_nwb(path)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "No accelerated colorspace conversion found from yuv420p to bgr24.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[Video(filename=\"/Users/keya/salk/io_fork/tests/data/videos/centered_pair_low_quality.mp4\", shape=(1100, 384, 384, 1), backend=MediaVideo)] \n",
+      " [Skeleton(nodes=[\"head\", \"neck\", \"thorax\", \"abdomen\", \"wingL\", \"wingR\", \"forelegL1\", \"forelegL2\", \"forelegL3\", \"forelegR1\", \"forelegR2\", \"forelegR3\", \"midlegL1\", \"midlegL2\", \"midlegL3\", \"midlegR1\", \"midlegR2\", \"midlegR3\", \"hindlegL1\", \"hindlegL2\", \"hindlegL3\", \"hindlegR1\", \"hindlegR2\", \"hindlegR3\"], edges=[(2, 1), (1, 0), (2, 3), (2, 4), (2, 5), (2, 6), (6, 7), (7, 8), (2, 9), (9, 10), (10, 11), (2, 12), (12, 13), (13, 14), (2, 15), (15, 16), (16, 17), (2, 18), (18, 19), (19, 20), (2, 21), (21, 22), (22, 23)])] \n",
+      " [Track(name='track0'), Track(name='track1'), Track(name='track2'), Track(name='track3'), Track(name='track4'), Track(name='track5'), Track(name='track6'), Track(name='track7'), Track(name='track8'), Track(name='track9'), Track(name='track10'), Track(name='track11'), Track(name='track12'), Track(name='track13'), Track(name='track14'), Track(name='track15'), Track(name='track16'), Track(name='track17'), Track(name='track18'), Track(name='track19'), Track(name='track20'), Track(name='track21'), Track(name='track22'), Track(name='track23'), Track(name='track24'), Track(name='track25'), Track(name='track26')]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(labels.videos, \"\\n\", labels.skeletons, \"\\n\", labels.tracks)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "path2 = \"/Users/keya/salk/io_fork/tests/data/nwb/centered_pair_predictions.slp\"\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "SLEAP_VIDEO_000_centered_pair_small pynwb.base.ProcessingModule at 0x5866207472\n",
+      "Fields:\n",
+      "  data_interfaces: {\n",
+      "    untracked000 <class 'ndx_pose.pose.PoseEstimation'>,\n",
+      "    untracked001 <class 'ndx_pose.pose.PoseEstimation'>\n",
+      "  }\n",
+      "  description: Processed SLEAP pose data for centered_pair_small.mp4 with Skeleton-0 skeleton.\n",
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/keya/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.7.0 is already loaded.\n",
+      "  return func(args[0], **pargs)\n"
+     ]
+    }
+   ],
+   "source": [
+    "path = \"/Users/keya/salk/io_fork/tests/data/slp/minimal_instance_w_prediction.nwb\"\n",
+    "with NWBHDF5IO(path, mode=\"r\") as io:\n",
+    "    read_nwbfile = io.read()\n",
+    "    #print(read_nwbfile)``\n",
+    "    print(read_nwbfile.processing[\"SLEAP_VIDEO_000_centered_pair_small\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/keya/mambaforge3/envs/io_dev/lib/python3.12/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.7.0 is already loaded.\n",
+      "  return func(args[0], **pargs)\n"
+     ]
+    }
+   ],
+   "source": [
+    "path = \"/Users/keya/salk/io_fork/tests/data/slp/minimal_instance_w_prediction.nwb\"\n",
+    "with NWBHDF5IO(path, mode=\"r\") as io:\n",
+    "    read_nwbfile = io.read()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "io_dev",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/tests/data/nwb/centered_pair_predictions.nwb b/tests/data/nwb/centered_pair_predictions.nwb
diff --git a/tests/data/nwb/minimal_instance_w_prediction.nwb b/tests/data/nwb/minimal_instance_w_prediction.nwb