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 "cells": [
  {
   "cell_type": "markdown",
   "id": "header",
   "metadata": {},
   "source": [
    "# Sound production in philodoptera\n",
    "\n",
    "Stridulation in crickets (e.g. [Pholidoptera littoralis](https://www.orthoptera.ch/wiki/arten/ensifera/tettigoniinae/item/pholidoptera-littoralis)) is a great animal model to study motor control/ sound production. Below is a tutorial on how we can create a `trials.nc`. Note that we have a video, audio and DeepLabCut pose file, meaning we can look at **movement** and **sound** features in the GUI!"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7160e4af",
   "metadata": {},
   "source": [
    "<img src=\"assets/cricket1.png\" width=\"900\">\n",
    "<img src=\"assets/cricket2.png\" width=\"900\">\n",
    "\n",
    "Made in Slovenia, 2025."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "imports",
   "metadata": {},
   "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",
    "\n",
    "import pandas as pd\n",
    "from pathlib import Path\n",
    "from audioio import AudioLoader\n",
    "from movement.io import load_poses\n",
    "from movement.kinematics import compute_velocity, compute_speed, compute_acceleration\n",
    "\n",
    "import ethograph as eto\n",
    "from ethograph.utils.download import download_example_dataset\n",
    "from ethograph.io.nwb_alignment import align_media_per_trial"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "093c813f",
   "metadata": {},
   "source": [
    "### Download example data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "download",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading philodoptera.nc... (1/4)\n",
      "Downloading philodoptera.mp4... (2/4)\n",
      "Downloading philodoptera.wav... (3/4)\n",
      "  philodoptera.csv (4/4)\n",
      "\n",
      "data_folder: d:\\Akseli\\Code\\ethograph\\data\\philodoptera\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    _here = Path(__vsc_ipynb_file__).parent\n",
    "except NameError:\n",
    "    _here = Path().resolve()\n",
    "\n",
    "data_folder = _here.parent / \"data\" / \"philodoptera\"\n",
    "download_example_dataset(\"philodoptera\", data_folder)\n",
    "print(f\"\\ndata_folder: {data_folder}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2350b3f0",
   "metadata": {},
   "source": [
    "### Build NWB alignment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "build_alignment",
   "metadata": {},
   "outputs": [],
   "source": [
    "video_path = data_folder / \"philodoptera.mp4\"\n",
    "audio_path = data_folder / \"philodoptera.wav\"\n",
    "poses_csv_path = data_folder / \"philodoptera.csv\"\n",
    "fps = 240\n",
    "\n",
    "# Probe audio sample rate from file\n",
    "with AudioLoader(str(audio_path)) as f:\n",
    "    audio_sr = f.rate\n",
    "\n",
    "# Single-session dataset: one row in the session table\n",
    "session_table = pd.DataFrame({\n",
    "    \"trial\":   [\"session\"],\n",
    "    \"video_0\": [str(video_path)],\n",
    "    \"audio_0\": [str(audio_path)],\n",
    "    \"pose_0\":  [str(poses_csv_path)],\n",
    "})\n",
    "\n",
    "nwb_path = data_folder / \".ethograph\" / \"alignment.nwb\"\n",
    "align_media_per_trial(\n",
    "    trial_table=session_table,\n",
    "    stream_rates={\"video\": float(fps), \"audio\": float(audio_sr), \"pose\": float(fps)},\n",
    "    output_path=nwb_path,\n",
    "    pose_fps=float(fps),\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "create_ds_header",
   "metadata": {},
   "source": [
    "### Create dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "create_ds",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saved to d:\\Akseli\\Code\\ethograph\\data\\philodoptera\\philodoptera.nc\n"
     ]
    }
   ],
   "source": [
    "# Load pose data and compute kinematics\n",
    "ds = load_poses.from_dlc_file(poses_csv_path, fps=fps)\n",
    "ds[\"velocity\"] = compute_velocity(ds.position)\n",
    "ds[\"speed\"] = compute_speed(ds.position)\n",
    "ds[\"acceleration\"] = compute_acceleration(ds.position)\n",
    "\n",
    "ds[\"individuals\"] = [\"Pholidoptera_littoralis_1\"]\n",
    "ds.attrs[\"Recording info\"] = (\n",
    "    \"This cricket species Pholidoptera littoralis was recorded on a field trip \"\n",
    "    \"in Slovenia in 2025. The video was recorded with an iPhone and the audio \"\n",
    "    \"with a Zoom recorder. Synchronization may not be perfect.\"\n",
    ")\n",
    "\n",
    "\n",
    "ds.to_netcdf(data_folder / \"philodoptera.nc\")\n",
    "print(f\"Saved to {data_folder / 'philodoptera.nc'}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "75e603c9",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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