{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# include controllers to the path\n",
    "import sys, os\n",
    "sys.path.append(os.getcwd())\n",
    "sys.path.append(os.path.join(os.getcwd(), 'controllers'))\n",
    "\n",
    "import cv2\n",
    "import threading\n",
    "import math\n",
    "import time\n",
    "import random\n",
    "import json\n",
    "import datetime\n",
    "import os, shutil\n",
    "import numpy as np\n",
    "import multiprocess as mp\n",
    "\n",
    "# controllers\n",
    "import nbimporter\n",
    "from controllers.situtils import FPSTimes\n",
    "from controllers.camera import WebcamStream\n",
    "from controllers.video import VideoWriter\n",
    "from controllers.position import PositionTracker\n",
    "from controllers.sound import SoundController\n",
    "from controllers.serial import MCSArduino, FakeArduino, Feeder\n",
    "from postprocessing import pack"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load experiment settings\n",
    "\n",
    "For every experimental cofiguration you can copy the original 'settings.json' file, build your own specific experimental preset, save it in this folder as e.g. 'settings_elena.json' and load it here instead of 'settings.json'."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "cfg_filename = os.path.join('profiles', 'andrey_hippoSIT_006865.json')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "with open(cfg_filename) as json_file:\n",
    "    cfg = json.load(json_file)\n",
    "cfg['experiment']['experiment_date'] = datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')\n",
    "\n",
    "# print loaded settings\n",
    "#print(json.dumps(cfg, indent=4))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# check if the sound interface is there\n",
    "import sounddevice as sd\n",
    "asio = [x for x in sd.query_devices() if x['name'].find('ASIO') > 0]\n",
    "#if len(asio) == 0:\n",
    "#    raise SystemExit('The sound interface is not found. Please restart the computer')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Initialize session folder\n",
    "\n",
    "Run the upcoming cell, to create a session folder and to save the chosen experimetal parameters to a JSON-file (\"experiment_id_parameters.json\"). The session folder will be created here where this notebook is located."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# This session's protocols will be saved to this folder\n",
    "cfg_exp = cfg['experiment']\n",
    "experiment_id = \"%s_%s_%s\" % (cfg_exp['subject'], cfg_exp['experiment_type'], cfg_exp['experiment_date'])\n",
    "save_to = os.path.join('sessions', experiment_id)\n",
    "             \n",
    "if not os.path.exists(save_to):\n",
    "    os.makedirs(save_to)\n",
    "\n",
    "# update paths (assuming this paths are relative to this notebook)\n",
    "cfg['video']['file_path'] = os.path.join(save_to, 'video.avi')\n",
    "cfg['position']['file_path'] = os.path.join(save_to, 'positions.csv')\n",
    "cfg['experiment']['file_path'] = os.path.join(save_to, 'events.csv')\n",
    "cfg['sound']['file_path'] = os.path.join(save_to, 'sounds.csv')\n",
    "cfg['position']['background_light'] = os.path.join('assets', cfg['position']['background_light'])\n",
    "cfg['position']['background_dark'] = os.path.join('assets', cfg['position']['background_dark'])\n",
    "    \n",
    "# Saves all parameters to a JSON file with the user-defined \"Experiment ID\" as filename\n",
    "with open(os.path.join(save_to, experiment_id + '.json'), 'w') as f:\n",
    "    json.dump(cfg, f, indent=4)\n",
    "    \n",
    "with open(cfg['experiment']['file_path'], 'w') as f:\n",
    "    # state: 0 - trial start, 1 - trial success, 2 - trial fail\n",
    "    f.write('time, target_x, target_y, target_r, trial, state\\n')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "class Island:    \n",
    "    def __init__(self, x, y, radius, sound_id, is_distractor=False):\n",
    "        self.x = x  # in meters\n",
    "        self.y = y  # in meters\n",
    "        self.r = radius  # in meters\n",
    "        self.sound_id = sound_id\n",
    "        self.is_distractor = is_distractor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_island_position(time_from_start, phi_initial, phi_max, timepoints=[600, 1200, 1800, 2400]):\n",
    "    # returns the angle of the island (in polar coordinates)\n",
    "    # all angles are in radians\n",
    "    \n",
    "    # no change during light periods\n",
    "    if time_from_start <= timepoints[0] or time_from_start >= timepoints[-1]:\n",
    "        return phi_initial\n",
    "    \n",
    "    # max anglular conflict in the middle of the dark\n",
    "    if time_from_start >= timepoints[1] and time_from_start <= timepoints[2]:\n",
    "        return phi_initial + phi_max\n",
    "    \n",
    "    # raising phase\n",
    "    if time_from_start < timepoints[1]:\n",
    "        p_dur = timepoints[1] - timepoints[0]\n",
    "        t_in_p = time_from_start - timepoints[0]\n",
    "        return phi_initial + phi_max * (t_in_p/p_dur)\n",
    "        \n",
    "    # falling phase\n",
    "    p_dur = timepoints[3] - timepoints[2]\n",
    "    t_in_p = time_from_start - timepoints[2]\n",
    "    return phi_initial + phi_max * (1 - (t_in_p/p_dur))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def timeout(t_start):\n",
    "    return time.time() - t_start > cfg_exp['session_duration'] if t_start is not None else False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def log_event(*args):  # log start / end of a trial\n",
    "    with open(cfg_exp['file_path'], 'a') as f:\n",
    "        f.write(\",\".join([str(x) for x in args]) + \"\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "def switch_light(pt, board):\n",
    "    pt.switch_background()\n",
    "    board.switch_light()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Start the experiment\n",
    "\n",
    "This cell contains code for animal tracking. We hope that the comments provided in the code suffice to understand the individual steps and to adjust them to your own setup and needs, if necessary.\n",
    "\n",
    "- press 's' to start recording\n",
    "- press 's' again to stop recording\n",
    "- press 'q' to quit\n",
    "\n",
    "The experiment will stop automatically if the pre-defined session duration is reached."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Webcam stream 1024.0:768.0 at 20.00 FPS started\n",
      "Position tracker stopped\n",
      "Video writer stopped\n",
      "Camera released\n"
     ]
    }
   ],
   "source": [
    "# actual sound selector: 0 - silence, 1 - foraging, 2 - target, 3 - distractor\n",
    "sound = mp.Value('i', 1)\n",
    "\n",
    "# experiment status: 1 - idle, 2 - running (recording, logging), 0 - stopped\n",
    "status = mp.Value('i', 1)\n",
    "\n",
    "# init the sync with the acquisition system via Arduino\n",
    "if cfg['experiment']['MCSArduinoPort'] == 'fake':\n",
    "    board = FakeArduino()\n",
    "else:\n",
    "    board = MCSArduino(cfg['experiment']['MCSArduinoPort'])\n",
    "\n",
    "# init the feeder\n",
    "feeder = Feeder(cfg['experiment']['feeder_port'])\n",
    "    \n",
    "# start the camera stream\n",
    "vs = WebcamStream(cfg['camera'])\n",
    "vs.start()\n",
    "\n",
    "# init video recorder\n",
    "vw = VideoWriter(status, vs, cfg['video'])\n",
    "vw.start()\n",
    "\n",
    "# start position tracking\n",
    "pt = PositionTracker(status, vs, cfg['position'])\n",
    "pt.start()\n",
    "\n",
    "# playing sound in a separate process for performance\n",
    "sc = mp.Process(target=SoundController.run, args=(sound, status, cfg['sound']))\n",
    "sc.start()\n",
    "\n",
    "timers = []\n",
    "fps = FPSTimes()\n",
    "names = ['camera', 'video', 'position', 'main']\n",
    "trial = 0\n",
    "rewards = 0\n",
    "t_start = None\n",
    "target_since = None\n",
    "punishment_since = None\n",
    "trial_start = time.time()\n",
    "phase = 0  # 0 - idle, 1 - foraging, 2 - inter-trial interval\n",
    "cfg_exp = cfg['experiment']\n",
    "cfg_pos = cfg['position']\n",
    "\n",
    "COLORS = {\n",
    "    'red': (0,0,255), 'green': (127,255,0), 'blue': (255,127,0), 'yellow': (0,127,255), \\\n",
    "    'black': (0,0,0), 'white': (255,255,255)\n",
    "}\n",
    "islands = []\n",
    "\n",
    "# initial position of the island\n",
    "phi_initial = np.random.rand() * 2 * np.pi if cfg_exp['target_angle'] == 'random' else np.deg2rad(int(cfg_exp['target_angle']))\n",
    "rho = pt.cfg['floor_radius'] * pt.pixel_size - cfg_exp['target_radius']  # constant, in meters\n",
    "iti_distance = 0.0\n",
    "last_x, last_y = None, None\n",
    "\n",
    "# inaudible island trial profiles\n",
    "max_trials = 200\n",
    "p0 = np.array([0 for x in range(max_trials)])                          # never\n",
    "p1 = np.array([0 if (x+1) % 4 > 0 else 1 for x in range(max_trials)])  # every 4-th trial\n",
    "p2 = np.array([0 if (x+1) % 2 > 0 else 1 for x in range(max_trials)])  # every 2-nd trial\n",
    "p3 = np.array([1 if x % 4 > 0 else 0 for x in range(max_trials)])      # always except every 4-th trial\n",
    "unaudible_trials = np.vstack([p0, p1, p2, p3])\n",
    "\n",
    "try:\n",
    "    while trial <= cfg_exp['trial_number'] and not timeout(t_start):\n",
    "        frame = vs.read()\n",
    "        if frame is None:\n",
    "            time.sleep(0.1)\n",
    "            continue # wait for the stream\n",
    "            \n",
    "        c_time = time.time()\n",
    "        fps.count()\n",
    "        status_color = COLORS['green'] if status.value == 1 else COLORS['red']\n",
    "\n",
    "        # -------- prepare the video frame ---------------\n",
    "        \n",
    "        # mask space outside arena\n",
    "        #frame = cv2.subtract(pt.background, frame)\n",
    "        #frame = cv2.absdiff(frame, pt.background)\n",
    "        #frame = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)\n",
    "        frame = cv2.bitwise_and(src1=frame, src2=pt.mask)\n",
    "\n",
    "        # draw position center and contours\n",
    "        if pt.x_in_px is not None:\n",
    "            cv2.circle(frame, (pt.x_in_px, pt.y_in_px), 10, status_color, -1)\n",
    "            cv2.drawContours(frame, [pt.contour], 0, status_color, 1, cv2.LINE_AA)            \n",
    "\n",
    "        # add FPS indicators\n",
    "        for i, ctrl in enumerate([vs, vw, pt, fps]):\n",
    "            cv2.putText(frame, '%s: %.2f FPS' % (names[i], ctrl.get_avg_fps()), \n",
    "                     (10, 30 + 20*(i+1)), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "\n",
    "        # size of the arena and status indicator\n",
    "        cv2.circle(frame, (cfg_pos['arena_x'], cfg_pos['arena_y']), cfg_pos['arena_radius'], COLORS['red'], 2)\n",
    "        cv2.circle(frame, (cfg_pos['arena_x'], cfg_pos['arena_y']), cfg_pos['floor_radius'], COLORS['red'], 2)\n",
    "        cv2.circle(frame, (20,20), 10, status_color, -6)\n",
    "\n",
    "        # draw islands\n",
    "        if len(islands) > 0:\n",
    "            for island in islands:\n",
    "                clr = COLORS['red'] if island.is_distractor else COLORS['green']\n",
    "                x, y = pt.meters_to_px(island.x, island.y)\n",
    "                cv2.circle(frame, (x, y), int(island.r/pt.pixel_size), clr, 2)\n",
    "\n",
    "        # positions of animal and target\n",
    "        if pt.x_in_px is not None:\n",
    "            cv2.putText(frame, 'Animal: %.3f %.3f' % (pt.x_in_m, pt.y_in_m), (10, 550), \\\n",
    "                        cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "            cv2.putText(frame, '%.2f %.2f' % (pt.x_in_m, pt.y_in_m), (pt.x_in_px + 10, pt.y_in_px + 10), \\\n",
    "                        cv2.FONT_HERSHEY_DUPLEX, .3, COLORS['white'])\n",
    "            \n",
    "        if len(islands) > 0:\n",
    "            target = [i for i in islands if not i.is_distractor][0]\n",
    "            cv2.putText(frame, 'Target: %.3f %.3f' % (target.x, target.y), (10, 570), \\\n",
    "                        cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "            \n",
    "        # stopwatch\n",
    "        stopwatch = 'Time: %.2f' % float(c_time - t_start) if t_start is not None else 'Time: Idle'\n",
    "        cv2.putText(frame, stopwatch, (10, 590), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "\n",
    "        # trial countdown (TODO add island countdown)\n",
    "        if phase == 1:\n",
    "            text = 'Trial: %.2f' % float(cfg_exp['trial_duration'] - (c_time - trial_start))\n",
    "            cv2.putText(frame, text, (10, 610), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "        cv2.putText(frame, 'Trial: %s' % trial, (10, 630), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "\n",
    "        # rewards\n",
    "        cv2.putText(frame, 'Rewards: %s' % rewards, (10, 650), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "        \n",
    "        # time since in target\n",
    "        if target_since is not None:\n",
    "            cv2.putText(frame, 'In target: %.2f' % float(c_time - target_since), (10, 670), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])\n",
    "\n",
    "        # light or dark period\n",
    "        cv2.putText(frame, 'Light' if pt.is_light else 'Dark', (10, 690), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])            \n",
    "\n",
    "        if iti_distance > 0:  # TODO change red / white color\n",
    "            cv2.putText(frame, 'ITI distance: %.2f' % iti_distance, (10, 710), cv2.FONT_HERSHEY_DUPLEX, .5, COLORS['white'])            \n",
    "            \n",
    "        # indicators of the initial / conflicting anges\n",
    "        p_rho, p_phi = pt.cfg['floor_radius']*pt.pixel_size, pt.correct_angle(phi_initial)\n",
    "        x_init, y_init = pt.meters_to_px(p_rho * np.sin(p_phi), p_rho * np.cos(p_phi))\n",
    "        cv2.circle(frame, (x_init, y_init), 10, COLORS['blue'], -1)\n",
    "        \n",
    "        p_phi = pt.correct_angle(phi_initial + np.deg2rad(cfg_exp['phi_max']))\n",
    "        x_init, y_init = pt.meters_to_px(p_rho * np.sin(p_phi), p_rho * np.cos(p_phi))\n",
    "        cv2.circle(frame, (x_init, y_init), 10, COLORS['yellow'], -1)\n",
    "            \n",
    "        # assign the frame back to the video stream for other controllers\n",
    "        vs.frame_with_infos = frame\n",
    "        \n",
    "        cv2.imshow('Press (s)-to start/stop, (q)-to end', frame)\n",
    "\n",
    "        # -------- experiment logic ---------------\n",
    "        \n",
    "        # animals is either foraging (phase == 1) or in the inter-trial-interval (phase == 2)\n",
    "        if phase == 1: # foraging\n",
    "            if pt.x_in_m is not None and len(islands) > 0:\n",
    "                # check if animal in the island and for how long\n",
    "                tgt = [i for i in islands if not i.is_distractor][0]\n",
    "                distractors = [i for i in islands if i.is_distractor]\n",
    "                \n",
    "                if (pt.x_in_m - tgt.x)**2 + (pt.y_in_m - tgt.y)**2 <= cfg_exp['target_radius']**2:\n",
    "                    if target_since is None:  # just entered target\n",
    "                        target_since = c_time\n",
    "                        if unaudible_trials[cfg_exp['unaudible_profile']][trial - 1] == 0:\n",
    "                            sound.value = 2\n",
    "\n",
    "                    elif c_time - target_since > cfg_exp['target_duration']: # successful trial\n",
    "                        log_event(c_time, round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4), trial, 1) # log trial success\n",
    "                        feeder.feed()\n",
    "                        \n",
    "                        # init inter-trial interval and new trial\n",
    "                        trial_start = c_time + 20 + 5 * np.random.rand()  # random b/w 10-15 sec\n",
    "                        sound.value = 0  # silence\n",
    "                        islands = []\n",
    "                        phase = 2\n",
    "                        rewards += 1\n",
    "                        target_since = None\n",
    "                        \n",
    "                elif c_time - trial_start > cfg_exp['trial_duration']:  # trial failed and animal is not in the target\n",
    "                    log_event(c_time, round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4), trial, 2) # log trial failed\n",
    "\n",
    "                    trial_start = c_time + 20 + 5 * np.random.rand()  # random b/w 10-15 sec\n",
    "                    sound.value = -1  # punishment\n",
    "                    punishment_since = c_time\n",
    "                    islands = []\n",
    "                    phase = 2\n",
    "                \n",
    "                else:\n",
    "                    target_since = None\n",
    "                    in_distractor = False\n",
    "                    \n",
    "                    for isl in distractors:  # maybe animal is in one of the distractors\n",
    "                        if (pt.x_in_m - isl.x)**2 + (pt.y_in_m - isl.y)**2 <= cfg_exp['target_radius']**2:\n",
    "                            sound.value = isl.sound_id\n",
    "                            in_distractor = True\n",
    "                    \n",
    "                    if not in_distractor:  # outside of the islands\n",
    "                        sound.value = 1\n",
    "            \n",
    "        elif phase == 2:  # inter-trial-interval\n",
    "            # count distance between trials\n",
    "            if last_x is None:\n",
    "                last_x, last_y = pt.x_in_m, pt.y_in_m\n",
    "            else:\n",
    "                x, y = pt.x_in_m, pt.y_in_m\n",
    "                iti_distance += np.sqrt((x - last_x)**2 + (y - last_y)**2)\n",
    "                last_x, last_y = x, y\n",
    "            \n",
    "            if punishment_since is not None and c_time - punishment_since > 10:  # max 10 sec of punishment\n",
    "                sound.value = 0\n",
    "                punishment_since = None\n",
    "\n",
    "            phi = get_island_position(c_time - t_start, phi_initial, np.deg2rad(cfg_exp['phi_max']), cfg_exp['timepoints'])\n",
    "            phi = pt.correct_angle(phi)  # correct for the camera orientation\n",
    "            x_tgt, y_tgt = rho * np.sin(phi), rho * np.cos(phi)\n",
    "\n",
    "            if c_time > trial_start and iti_distance > cfg_exp['iti_distance'] and \\\n",
    "                  (pt.x_in_m - x_tgt)**2 + (pt.y_in_m - y_tgt)**2 >= cfg_exp['target_radius']**2:\n",
    "                # init_new_trial\n",
    "                islands = [Island(x_tgt, y_tgt, cfg_exp['target_radius'], 2)]\n",
    "                sound.value = 1\n",
    "                phase = 1\n",
    "                trial += 1\n",
    "                \n",
    "                # reset ITI distance and trial_start\n",
    "                iti_distance = 0\n",
    "                trial_start = c_time\n",
    "                \n",
    "                # log trial start\n",
    "                tgt = [i for i in islands if not i.is_distractor][0]\n",
    "                log_event(c_time, round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4), trial, 0)\n",
    "        \n",
    "        # -------- key press events ---------------\n",
    "        \n",
    "        k = cv2.waitKey(33)\n",
    "        \n",
    "        if k == ord('l'):\n",
    "            switch_light(pt, board)\n",
    "        \n",
    "        if k == ord('q'):\n",
    "            break\n",
    "\n",
    "        if k == ord('s'):\n",
    "            board.start_or_stop()  # start/stop data acquisition\n",
    "            c_time = time.time()   # more accurate time\n",
    "\n",
    "            if status.value == 1: # start the session\n",
    "                if t_start is None:\n",
    "                    t_start = c_time\n",
    "                trial_start = c_time\n",
    "                status.value = 2\n",
    "                \n",
    "                # init_new_trial\n",
    "                phi = get_island_position(c_time - t_start, phi_initial, np.deg2rad(cfg_exp['phi_max']), cfg_exp['timepoints'])\n",
    "                phi = pt.correct_angle(phi)  # correct for the camera orientation\n",
    "                x_tgt, y_tgt = rho * np.sin(phi), rho * np.cos(phi)\n",
    "                islands = [Island(x_tgt, y_tgt, cfg_exp['target_radius'], 2)]\n",
    "                sound.value = 1\n",
    "                phase = 1\n",
    "                trial += 1\n",
    "\n",
    "                # log trial start\n",
    "                tgt = [i for i in islands if not i.is_distractor][0]\n",
    "                log_event(c_time, round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4), trial, 0)\n",
    "                \n",
    "                # init light events\n",
    "                timers = []\n",
    "                for event_t in cfg_exp['light_events']:\n",
    "                    timers.append(threading.Timer(event_t, switch_light, args=(pt, board)))                \n",
    "                for t in timers:\n",
    "                    t.start()\n",
    "                \n",
    "            elif status.value == 2:  # pause the session\n",
    "                if len(islands) > 0:\n",
    "                    tgt = [i for i in islands if not i.is_distractor][0]\n",
    "                    x, y, r = round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4)\n",
    "                else:\n",
    "                    x, y, r = 0, 0, 0\n",
    "                log_event(c_time, x, y, r, trial, -1)  # log experiment break\n",
    "                \n",
    "                status.value = 1\n",
    "                phase = 0\n",
    "                islands = []\n",
    "                for t in timers:\n",
    "                    t.cancel()\n",
    "                    \n",
    "        if k == ord('a'):\n",
    "            sound.value = 0 if sound.value == 1 else 1\n",
    "\n",
    "finally:\n",
    "    if status.value == 2:  # stop data acquisition, in case exited via timeout\n",
    "        board.start_or_stop()\n",
    "        if len(islands) > 0:\n",
    "            tgt = [i for i in islands if not i.is_distractor][0]\n",
    "            x, y, r = round(tgt.x, 4), round(tgt.y, 4), round(tgt.r, 4)\n",
    "        else:  \n",
    "            x, y, r = 0, 0, 0\n",
    "        log_event(c_time, x, y, r, trial, -1)  # log experiment end\n",
    "        \n",
    "    status.value = 0\n",
    "    time.sleep(0.01)\n",
    "    for t in timers:\n",
    "        t.cancel()\n",
    "    \n",
    "    feeder.exit()\n",
    "    if board.is_light_off:\n",
    "        board.switch_light()  # turn light back on\n",
    "        time.sleep(0.1)\n",
    "    board.exit()\n",
    "    cv2.destroyAllWindows()\n",
    "    sc.join()\n",
    "    for ctrl in [pt, vw, vs]:\n",
    "        ctrl.stop()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Merge data in HDF5 file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "session_path = save_to\n",
    "#session_path = os.path.join('sessions', '2021-07-30_09-24-14')  # some particular session\n",
    "#session_path = 'Y:\\\\Michael\\\\FreeBehaving\\\\SIT_sessions\\\\50_aSIT_2021-10-25_10-32-19'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "#if not trial > 0:\n",
    "#    raise SystemExit('Nothing recorded. No sense to continue.')\n",
    "\n",
    "# do pack data to HDF5\n",
    "h5name = pack(session_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Plot sessions stats"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import h5py\n",
    "import numpy as np\n",
    "from scipy import signal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "arena_r = 0.4  # in meters\n",
    "\n",
    "with h5py.File(h5name, 'r') as f:\n",
    "    tl = np.array(f['processed']['timeline'])\n",
    "    trial_idxs = np.array(f['processed']['trial_idxs'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 1.0, 'Speed')"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "[encoded data, 246784 characters]\n",
      "text/plain": [
       "<Figure size 864x864 with 4 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig = plt.figure(figsize=(12, 12))\n",
    "\n",
    "# trajectory and islands\n",
    "ax = fig.add_subplot(221)\n",
    "ax.scatter(tl[:, 1], tl[:, 2], s=1, alpha=0.1)  # positions\n",
    "scat = ax.scatter(trial_idxs[:, 2], trial_idxs[:, 3], s=1000, facecolors='none', edgecolors='r')  # islands, radius approx.\n",
    "ax.add_patch(plt.Circle((0, 0), arena_r, color='r', fill=False))\n",
    "ax.set_aspect('equal')\n",
    "ax.set_xlabel('X, m', fontsize=14)\n",
    "ax.set_ylabel('Y, m', fontsize=14)\n",
    "ax.set_title('Running', fontsize=14)\n",
    "ax.grid()\n",
    "\n",
    "# occupancy\n",
    "sigma = 0.1\n",
    "lin_profile = np.linspace(-15, 15, 20)\n",
    "bump = np.exp(-sigma * lin_profile**2)\n",
    "bump /= np.trapz(bump)  # normalize to 1\n",
    "kernel = bump[:, np.newaxis] * bump[np.newaxis, :]\n",
    "occupancy_map, _, _ = np.histogram2d(tl[:, 1], tl[:, 2], bins=[40, 40], range=np.array([[-0.5, 0.5], [-0.5, 0.5]]))\n",
    "occupancy_map = signal.convolve2d(occupancy_map, kernel, mode='same')\n",
    "\n",
    "ax = fig.add_subplot(222)\n",
    "ax.imshow(occupancy_map.T, origin='lower', extent=(-0.5, 0.5, -0.5, 0.5), cmap='Blues')\n",
    "ax.add_patch(plt.Circle((0, 0), arena_r, color='r', fill=False))\n",
    "ax.set_xlabel('X, m', fontsize=14)\n",
    "ax.set_title('Occupancy', fontsize=14)\n",
    "ax.grid()\n",
    "\n",
    "# trials\n",
    "durations = tl[trial_idxs[:, 1].astype(int)][:, 0] - tl[trial_idxs[:, 0].astype(int)][:, 0]\n",
    "colors = ['red' if x == 1 else 'grey' for x in trial_idxs[:, 5]]\n",
    "\n",
    "ax = fig.add_subplot(223)\n",
    "ax.barh(np.arange(len(trial_idxs)), durations, color=colors, align='center')\n",
    "ax.set_xlabel('Time, s', fontsize=14)\n",
    "ax.set_ylabel('Trial, #', fontsize=14)\n",
    "ax.set_title('Trials', fontsize=14)\n",
    "\n",
    "# speed\n",
    "ax = fig.add_subplot(224)\n",
    "ax.hist(tl[:, 3], bins=50, ec='black')\n",
    "ax.set_xlabel('Speed, m/s', fontsize=14)\n",
    "ax.set_title('Speed', fontsize=14)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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