View Preference Test Data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import datetime\n",
    "import glob\n",
    "import os\n",
    "import re\n",
    "import sys\n",
    "\n",
    "# import cv2\n",
    "import ipywidgets as widgets\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import scipy.io.wavfile\n",
    "import traitlets\n",
    "\n",
    "from IPython.display import display, HTML, Audio, Pretty\n",
    "from ipywidgets import interact, interactive\n",
    "from soundsig.sound import spectrogram, plot_spectrogram\n",
    "from collections import deque\n",
    "\n",
    "from pecking_analysis.peck_data import (\n",
    "    load_pecking_days,\n",
    "    get_dates\n",
    ")\n",
    "\n",
    "pd.options.display.float_format = '{:,.4f}'.format"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tell the program where to look for the bird pecking test folders and the stimulus folders"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "DATADIR = \"/home/fet/data/\"\n",
    "STIMULI_DIR = \"/home/fet/stimuli_chubby/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# BIRDS = [\"XXXOra0039F\"]\n",
    "BIRDS = [\n",
    "    os.path.basename(bird)\n",
    "    for bird in sorted(glob.glob(os.path.join(DATADIR, \"*\")), key=os.path.getmtime, reverse=True)\n",
    "    if re.search(r\"^[a-zA-Z]{6}[0-9]{4}[MF]?$\", os.path.basename(bird))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## Helper functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "def cached_load(bird, date):\n",
    "    if (bird, date) not in cached_load._cache:\n",
    "        blocks, stim_blocks = load_pecking_days(\n",
    "            os.path.join(DATADIR, bird, date.strftime(\"%d%m%y\")),\n",
    "            (\"Playback\",)\n",
    "        )\n",
    "        cached_load._cache[(bird, date)] = (blocks, stim_blocks)\n",
    "    return cached_load._cache[(bird, date)]\n",
    "cached_load._cache = {}\n",
    "\n",
    "def get_new_location(datadir, stimulus_path):\n",
    "    \"\"\"Swap out the stimulus directory of a stimulus path with a local one\n",
    "    \"\"\"\n",
    "    rest = stimulus_path.split(\"stimuli/\")[1]\n",
    "    new_path = os.path.join(STIMULI_DIR, rest)\n",
    "    return new_path\n",
    "\n",
    "offsets = deque([], 10)\n",
    "\n",
    "def view_pecking_data(date, bird, trial):\n",
    "    if date is None:\n",
    "        return\n",
    "\n",
    "    # UJpdate the dates dropdown with dates found for this bird.\n",
    "    valid_dates = get_dates(os.path.join(DATADIR, bird))\n",
    "    valid_dates = list(reversed(valid_dates))\n",
    "    date_picker.options = valid_dates\n",
    "    if date not in valid_dates:\n",
    "        date_picker.value = valid_dates[0]\n",
    "        date = valid_dates[0]\n",
    "        return\n",
    "\n",
    "    blocks, stim_blocks = cached_load(bird, date)\n",
    "    \n",
    "    if not blocks:\n",
    "        status_field.value = \"Data for {} does not exist\".format(date)\n",
    "        display(None)\n",
    "    else:\n",
    "        status_field.value = \"Loading {}\".format(date)\n",
    "\n",
    "    for block, stims in zip(blocks, stim_blocks):\n",
    "        if block.date == date:\n",
    "            block.data.index = pd.Series(np.arange(len(block.data)))\n",
    "            stimuli = block.data[[\"Trial\", \"Bird Name\", \"Stimulus\"]]\n",
    "            \n",
    "            slider.max = len(stimuli) - 1\n",
    "            \n",
    "            curr_stim.value = \"Trial {Trial}, Vocalizer {Bird Name}\".format(**stimuli.iloc[trial])\n",
    "            date_dir = os.path.join(DATADIR, bird, block.date.strftime(\"%d%m%y\"))\n",
    "            \n",
    "            t_rec, f_rec, spec_rec, widget_rec = get_playback_trial(\n",
    "                date_dir, \n",
    "                os.path.basename(os.path.splitext(block.annotations[\"filename\"])[0]),\n",
    "                stimuli.iloc[trial][\"Trial\"],\n",
    "            )\n",
    "            t_stim, f_stim, spec_stim, widget_stim = get_stimulus(get_new_location(DATADIR, stimuli.iloc[trial][\"Stimulus\"]))\n",
    "            spec_rec += 1e-12\n",
    "            spec_stim += 1e-12\n",
    "            \n",
    "            # figure out alignmnet\n",
    "            template = spec_stim[(f_stim > 2000) & (f_stim < 5000), :spec_stim.shape[1] // 2]\n",
    "#             convolved = cv2.matchTemplate(\n",
    "#                 spec_rec[(f_rec > 2000) & (f_rec < 5000)].astype(np.float32),\n",
    "#                 template.astype(np.float32),\n",
    "#                 cv2.TM_CCOEFF_NORMED,\n",
    "#             )[0]\n",
    "#             peak = t_rec[np.argmax(convolved[:template.shape[1]])]\n",
    "#             if peak > 1:\n",
    "#                 peak = np.mean(offsets)\n",
    "#             else:\n",
    "#                 offsets.append(peak)\n",
    "#             peak = np.mean(offsets)\n",
    "            peak = 0\n",
    "\n",
    "            fig = plt.figure(figsize=(10, 5))\n",
    "            ax0 = fig.add_axes([0, 0, 1, 0.7])\n",
    "            ax1 = fig.add_axes([0, 0.7, 1, 0.3])\n",
    "            \n",
    "            plot_spectrogram(t_rec - peak, f_rec, spec_rec, ax=ax0, colorbar=False)\n",
    "            ax0.text(0.01, 0.99, 'Recorded', fontsize=14, horizontalalignment='left', verticalalignment='top', transform = ax0.transAxes)\n",
    "            \n",
    "            plot_spectrogram(t_stim, f_stim, spec_stim, ax=ax1, colorbar=False)\n",
    "            ax1.text(0.01, 0.99, 'Stimulus: {}'.format(stimuli.iloc[trial][\"Stimulus\"]), fontsize=14, horizontalalignment='left', verticalalignment='top', transform = ax1.transAxes)\n",
    "            \n",
    "            ax0.set_xlim(-1, 7)\n",
    "            ax1.set_xlim(-1, 7)\n",
    "            ax0.set_ylim(0, 10000)\n",
    "            ax1.set_ylim(0, 10000)\n",
    "\n",
    "            status_field.value = \"\"\n",
    "            plt.show()\n",
    "            plt.close(fig)\n",
    "            \n",
    "            display(widget_stim)\n",
    "            display(widget_rec)\n",
    "            \n",
    "            \n",
    "def get_playback_trial(datedir, session, trial):\n",
    "    stimulus_file = None\n",
    "    recording_file = os.path.join(datedir, \"audio_recordings\", session, \"trial{}.wav\".format(trial))\n",
    "    fs, data = scipy.io.wavfile.read(recording_file)\n",
    "    audio_widget = Audio(recording_file)\n",
    "\n",
    "    t_spec, f_spec, spec, rms = spectrogram(data, fs, 500, 100, cmplx=False)\n",
    "    return t_spec, f_spec, spec, audio_widget\n",
    "\n",
    "\n",
    "def get_stimulus(stim_path):    \n",
    "    fs, data = scipy.io.wavfile.read(stim_path)\n",
    "    t_spec, f_spec, spec, rms = spectrogram(data, fs, 500, 100, cmplx=False)\n",
    "    audio_widget = Audio(stim_path)\n",
    "\n",
    "    return t_spec, f_spec, spec, audio_widget\n",
    "\n",
    "def next_page(x):\n",
    "    slider.value += 1\n",
    "    \n",
    "def prev_page(x):\n",
    "    slider.value -= 1\n",
    "    \n",
    "def first_page(x):\n",
    "    slider.value = slider.min\n",
    "    \n",
    "def last_page(x):\n",
    "    slider.value = slider.max"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run this cell to view preference test trials"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "8ef6876e9b1b412795727b938b6adf4e"
      }
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "first_page_widget = widgets.Button(description='First')\n",
    "last_page_widget = widgets.Button(description=\"Last\")\n",
    "next_page_widget = widgets.Button(description='Next Stim', icon='fa-arrow-right')\n",
    "previous_page_widget = widgets.Button(description='Previous Stim', icon='fa-arrow-left')\n",
    "first_page_widget.on_click(first_page)\n",
    "last_page_widget.on_click(last_page)\n",
    "next_page_widget.on_click(next_page)\n",
    "previous_page_widget.on_click(prev_page)\n",
    "\n",
    "curr_stim = widgets.Label(value=\"\")\n",
    "status_field = widgets.Label(value=\"\")\n",
    "\n",
    "date_picker = widgets.Dropdown(\n",
    "    options=[datetime.date.today() - datetime.timedelta(days=x) for x in range(60)],\n",
    "    value=datetime.date.today() - datetime.timedelta(days=1),\n",
    "    description=\"Date\",\n",
    "    disabled=False,\n",
    ")\n",
    "\n",
    "bird_picker = widgets.Dropdown(\n",
    "    options=BIRDS,\n",
    "    value=BIRDS[0],\n",
    "    description=\"Bird\",\n",
    "    disabled=False,\n",
    ")\n",
    "\n",
    "\n",
    "slider = widgets.IntSlider(\n",
    "    value=0,\n",
    "    min=0,\n",
    "    max=100,\n",
    "    step=1,\n",
    "    description='Trial:',\n",
    "    disabled=False,\n",
    "    continuous_update=False,\n",
    "    orientation='horizontal',\n",
    "    readout=True,\n",
    "    readout_format='d'\n",
    ")\n",
    "\n",
    "out_plot = widgets.interactive_output(\n",
    "    view_pecking_data, \n",
    "    {\n",
    "        \"date\": date_picker,\n",
    "        \"bird\": bird_picker,\n",
    "        \"trial\": slider,\n",
    "    }\n",
    ")\n",
    "\n",
    "widgets.VBox([\n",
    "    status_field,\n",
    "    widgets.HBox([\n",
    "        widgets.VBox([\n",
    "            bird_picker,\n",
    "            date_picker,\n",
    "        ]),\n",
    "    ]),\n",
    "    widgets.VBox([\n",
    "        widgets.HBox([\n",
    "            first_page_widget,\n",
    "            previous_page_widget,\n",
    "            slider,\n",
    "            next_page_widget,\n",
    "            last_page_widget\n",
    "        ])\n",
    "    ]),\n",
    "    out_plot,\n",
    "    curr_stim,\n",
    "])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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