added read_avi notebook to 000559

000559/dattalab/markowitz_gillis_nature_2023/README.md

@@ -10,4 +10,6 @@ Each notebook provides an example of how to access the critical data and metadat
 
 Note: `reproduce_figure1d.ipynb` and `reproduce_figure_S1.ipynb` use the conda environment defined by the 
 `environment.yaml` file, but `reproduce_figure_S3.ipynb` uses a different environment defined by the 
-`environment_S3.yaml` due to dependency conflicts.
+`environment_S3.yaml` due to dependency conflicts.
+
+This submission also provides a notebook showcasing how to read the raw depth video (.avi) files: `read_avi.ipynb`

000559/dattalab/markowitz_gillis_nature_2023/read_avi.ipynb

@@ -0,0 +1,139 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Read AVI Files"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook showcases how to read the .avi depth video files in the dataset."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from fsspec import filesystem\n",
+    "import cv2\n",
+    "import tempfile\n",
+    "from dandi.dandiapi import DandiAPIClient\n",
+    "from tqdm.notebook import tqdm\n",
+    "\n",
+    "def stream_avifile(DANDISET_ID, file_path, temp_file, num_chunks=None):\n",
+    "    '''Stream .avi file from DANDI archive.\n",
+    "    \n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    DANDISET_ID : str\n",
+    "        Dandiset ID\n",
+    "    file_path : str\n",
+    "        Path to .avi file in DANDI archive\n",
+    "    temp_file : file-like object\n",
+    "        Temporary file to write the .avi file to\n",
+    "    num_chunks : int, optional\n",
+    "        Number of chunks to read from the file. If None, read the whole file.\n",
+    "    '''\n",
+    "    with DandiAPIClient() as client:\n",
+    "        asset = client.get_dandiset(DANDISET_ID, 'draft').get_asset_by_path(file_path)\n",
+    "        s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)\n",
+    "    fs = filesystem(\"http\")\n",
+    "    file_system = fs.open(s3_url, \"rb\")\n",
+    "    file_size = file_system.size\n",
+    "    chunk_size = 10_000_000 # 10 MB\n",
+    "    num_chunks = num_chunks or file_size // chunk_size\n",
+    "    for _ in tqdm(range(num_chunks)):\n",
+    "        chunk = file_system.read(length=chunk_size)\n",
+    "        temp_file.write(chunk)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def show_video(file_path: str):\n",
+    "    '''Show video in a window.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    file_path : str\n",
+    "        Path to video file\n",
+    "    '''\n",
+    "    raw_video = cv2.VideoCapture(file_path)\n",
+    "\n",
+    "    while True:\n",
+    "        # Read a frame from the video\n",
+    "        ret, frame = raw_video.read()\n",
+    "\n",
+    "        # If the frame is not read successfully, the video has ended\n",
+    "        if not ret:\n",
+    "            break\n",
+    "\n",
+    "        frame = frame / frame.max() # Normalize the frame\n",
+    "\n",
+    "        # Display the frame in a window\n",
+    "        cv2.imshow('Frame', frame)\n",
+    "\n",
+    "        # Wait for a key press to exit\n",
+    "        if cv2.waitKey(25) & 0xFF == ord('q'):\n",
+    "            break\n",
+    "\n",
+    "    # Release the video capture and close the window\n",
+    "    raw_video.release()\n",
+    "    cv2.destroyAllWindows()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DANDISET_ID = '000559'\n",
+    "avi_file_path = 'sub-10/sub-10_ses-reinforcement-0e0aca4f-6a99-46eb-9eb8-439f36e66c40_behavior+image+ogen/f9af8a18-7cab-471c-802f-6937edeaec68_external_file_0.avi'\n",
+    "num_chunks = 10 # Use None to read the whole file\n",
+    "\n",
+    "with tempfile.NamedTemporaryFile() as temp:\n",
+    "    stream_avifile(DANDISET_ID, avi_file_path, temp, num_chunks=num_chunks)\n",
+    "    temp.flush()\n",
+    "    show_video(temp.name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "datta_env",
+   "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": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}