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+{
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+ "cells": [
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+ {
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+ "cell_type": "code",
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+ "execution_count": 23,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# include controllers to the path\n",
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+ "import sys, os\n",
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+ "sys.path.append(os.getcwd())\n",
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+ "sys.path.append(os.path.join(os.getcwd(), 'controllers'))\n",
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+ "\n",
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+ "# include pipeline repo to compute performance\n",
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+ "sys.path.append(os.path.join(os.getcwd(), '..'))\n",
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+ "sys.path.append(os.path.join(os.getcwd(), '..', 'pipeline'))\n",
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+ "sys.path.append(os.path.join(os.getcwd(), '..', 'pipeline', 'postprocessing'))\n",
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+ "\n",
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+ "import cv2\n",
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+ "import threading\n",
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+ "import math\n",
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+ "import time\n",
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+ "import random\n",
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+ "import json\n",
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+ "import datetime\n",
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+ "import os, shutil\n",
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+ "import numpy as np\n",
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+ "import multiprocess as mp\n",
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+ "\n",
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+ "# controllers\n",
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+ "import nbimporter\n",
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+ "from controllers.situtils import FPSTimes\n",
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+ "from controllers.camera import WebcamStream\n",
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+ "from controllers.video import VideoWriter\n",
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+ "from controllers.microphones import MicrophoneController\n",
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+ "from controllers.position import PositionTrackerSingle, PositionTrackerDouble\n",
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+ "from controllers.sound import SoundController, ContinuousSoundStream\n",
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+ "from controllers.serial import MCSArduino, FakeArduino, SpeakerMotor, CableMotor\n",
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+ "from controllers.display import SITDisplay\n",
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+ "from controllers.island import IslandFactory\n",
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+ "\n",
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+ "from pipeline.postprocessing.pack import pack\n",
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+ "from pipeline.postprocessing.performance import calculate_performance, dump_performance_to_H5"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "## Load experiment settings\n",
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+ "\n",
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+ "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'."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 24,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "cfg_filename = os.path.join('profiles', 'passive.json')"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 25,
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+ "metadata": {
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+ "scrolled": false
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+ },
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+ "outputs": [],
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+ "source": [
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+ "with open(os.path.join('profiles', 'default.json')) as json_file:\n",
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+ " cfg = json.load(json_file)\n",
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+ "with open(cfg_filename) as json_file:\n",
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+ " cfg_local = json.load(json_file)\n",
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+ "\n",
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+ "for key in cfg.keys():\n",
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+ " if key in cfg_local: # only update if the key exists in the local config, otherwise keep default (important for backward compatibility with cfg files before microphones)\n",
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+ " cfg[key].update(cfg_local[key])\n",
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+ "cfg['experiment']['experiment_date'] = datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')\n",
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+ "\n",
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+ "# print loaded settings\n",
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+ "#print(json.dumps(cfg, indent=4))"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "## Initialize session folder\n",
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+ "\n",
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+ "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."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 26,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# This session's protocols will be saved to this folder\n",
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+ "cfg_exp = cfg['experiment']\n",
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+ "experiment_id = \"%s_%s_%s\" % (cfg_exp['subject'], cfg_exp['experiment_type'], cfg_exp['experiment_date'])\n",
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+ "save_to = os.path.join('sessions', experiment_id)\n",
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+ " \n",
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+ "if not os.path.exists(save_to):\n",
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+ " os.makedirs(save_to)\n",
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+ "\n",
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+ "# update paths (assuming this paths are relative to this notebook)\n",
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+ "cfg['video']['file_path'] = os.path.join(save_to, cfg['video']['file_path'])\n",
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+ "cfg['video']['csv_path'] = os.path.join(save_to, cfg['video']['csv_path'])\n",
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+ "cfg['microphones']['file_path'] = os.path.join(save_to, cfg['microphones']['file_path'])\n",
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+ "cfg['microphones']['csv_path'] = os.path.join(save_to, cfg['microphones']['csv_path'])\n",
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+ "cfg['position']['file_path'] = os.path.join(save_to, cfg['position']['file_path'])\n",
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+ "cfg['position']['contour_path'] = os.path.join(save_to, cfg['position']['contour_path'])\n",
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+ "cfg['experiment']['file_path'] = os.path.join(save_to, cfg['experiment']['file_path'])\n",
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+ "cfg['experiment']['islands_path'] = os.path.join(save_to, 'islands.csv')\n",
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+ "cfg['sound']['file_path'] = os.path.join(save_to, cfg['sound']['file_path'])\n",
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+ "cfg['position']['background_light'] = os.path.join('assets', cfg['position']['background_light'])\n",
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+ "cfg['position']['background_dark'] = os.path.join('assets', cfg['position']['background_dark'])\n",
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+ "if 'wav_file' in cfg['sound']:\n",
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+ " cfg['sound']['wav_file'] = os.path.join('assets', cfg['sound']['wav_file'])\n",
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+ "if 'continuous' in cfg['sound']:\n",
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+ " cfg['sound']['continuous']['wav_file'] = os.path.join('assets', cfg['sound']['continuous']['wav_file'])\n",
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+ " \n",
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+ "# Saves all parameters to a JSON file with the user-defined \"Experiment ID\" as filename\n",
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+ "with open(os.path.join(save_to, experiment_id + '.json'), 'w') as f:\n",
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+ " json.dump(cfg, f, indent=4)\n",
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+ " \n",
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+ "with open(cfg['experiment']['file_path'], 'w') as f:\n",
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+ " # state: 0 - trial start, 1 - trial success, 2 - trial fail\n",
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+ " f.write('time, target_x, target_y, target_r, trial, state\\n')\n",
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+ "\n",
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+ "with open(cfg['experiment']['islands_path'], 'w') as f:\n",
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+ " f.write('tgt_x, tgt_y, tgt_r, d1_x, d1_y, d1_r, d2_x, d2_y, d2_r, d3_x, d3_y, d3_r\\n')"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 27,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "def timeout(t_start):\n",
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+ " return time.time() - t_start > cfg_exp['session_duration'] if t_start is not None else False"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 28,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "def log_event(*args): # log start / end of a trial\n",
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+ " with open(cfg_exp['file_path'], 'a') as f:\n",
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+ " f.write(\",\".join([str(x) for x in args]) + \"\\n\")"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 29,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "def log_islands(islands): # log position of the islands\n",
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+ " sorted_islands = sorted(islands, key=lambda x: x.sound_id, reverse=False)\n",
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+ " args = [(i.x, i.y, i.r) for i in sorted_islands]\n",
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+ " to_dump = [x for xs in args for x in xs]\n",
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+ " \n",
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+ " with open(cfg_exp['islands_path'], 'a') as f: \n",
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+ " f.write(\",\".join([str(round(x, 4)) for x in to_dump]) + \"\\n\")"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 30,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "def switch_light(pt, board):\n",
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+ " pt.switch_background()\n",
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+ " board.switch_light()"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "## Start the experiment\n",
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+ "\n",
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+ "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",
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+ "\n",
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+ "- press 's' to start recording\n",
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+ "- press 's' again to stop recording\n",
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+ "- press 'q' to quit\n",
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+ "\n",
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+ "The experiment will stop automatically if the pre-defined session duration is reached."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 31,
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+ "metadata": {
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+ "scrolled": true
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+ },
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "Webcam stream 1024.0:768.0 at 30.00 FPS started\n",
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+ "Position tracker stopped\n",
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+ "Video writer stopped\n",
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+ "Camera released\n"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "# actual sound selector: -1 - noise, 0 - silence, 1 - foraging, 2 - target, 3 - distractor\n",
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+ "sound = mp.Value('i', 1)\n",
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+ "if 'noise_when_idle' in cfg_exp and cfg_exp['noise_when_idle']:\n",
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+ " sound.value = -1\n",
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+ "\n",
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+ "# experiment status: 1 - idle, 2 - running (recording, logging), 0 - stopped\n",
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+ "status = mp.Value('i', 1)\n",
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+ "\n",
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+ "# init the sync with the acquisition system and feeder via Arduino\n",
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+ "if cfg['experiment']['MCSArduinoPort'] == 'fake':\n",
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+ " board = FakeArduino()\n",
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+ "else:\n",
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+ " board = MCSArduino(cfg['experiment']['MCSArduinoPort'])\n",
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+ "\n",
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+ "# init speaker motor control\n",
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+ "if 'motors_port' in cfg['experiment'] and cfg['experiment']['enable_motors']:\n",
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+ " motor_board = SpeakerMotor(cfg['experiment']['motors_port'])\n",
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+ " \n",
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+ "# init ephys cable rotation motor\n",
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+ "if 'cable_motor_port' in cfg['experiment']:\n",
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+ " cable_board = CableMotor(cfg['experiment']['cable_motor_port'])\n",
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+ "\n",
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+ "# init continuous sound, if required\n",
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+ "if 'continuous' in cfg['sound']:\n",
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+ " cst = ContinuousSoundStream(cfg['sound']['continuous'])\n",
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+ " cst.start()\n",
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+ " \n",
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+ "# start the camera stream\n",
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+ "vs = WebcamStream(cfg['camera'])\n",
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+ "vs.start()\n",
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+ "\n",
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+ "# init video recorder\n",
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+ "vw = VideoWriter(status, vs, cfg['video'])\n",
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+ "vw.start()\n",
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+ "\n",
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+ "# init microphone controller, if required\n",
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+ "if cfg['microphones']['record_audio']:\n",
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+ " mc = mp.Process(target=MicrophoneController.run, args=(status,cfg[\"microphones\"]))\n",
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+ " mc.start()\n",
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+ "\n",
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+ "# start position tracking\n",
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+ "pt = PositionTrackerSingle(status, vs, cfg['position']) if cfg['position']['single_agent'] else PositionTrackerDouble(status, vs, cfg['position'])\n",
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+ "pt.start()\n",
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+ "# print(pt.mask.shape)\n",
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+ "# init frame renderer\n",
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+ "dc = SITDisplay(pt, cfg['video'])\n",
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+ "\n",
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+ "# playing sound in a separate process for performance\n",
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+ "sounds = cfg['sound']['sounds']\n",
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+ "commutator = {\n",
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+ " -1: 'noise',\n",
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+ " 0: 'silence'\n",
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+ "}\n",
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+ "\n",
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+ "sound_order = 1\n",
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+ "for s_type in ('F', 'D', 'I', 'L'):\n",
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+ " keys = sorted([key for key in sounds.keys() if key.startswith(s_type)])\n",
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+ " for key in keys:\n",
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+ " commutator[sound_order] = key\n",
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+ " sound_order += 1\n",
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+ "sc = mp.Process(target=SoundController.run, args=(sound, status, cfg['sound'], commutator))\n",
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+ "sc.start()\n",
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+ "\n",
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+ "cfg_pos = cfg['position']\n",
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+ "isl_factory = IslandFactory(cfg_pos['floor_r_in_meters'], cfg_pos['angle_compensation'], cfg['experiment'])\n",
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+ "\n",
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+ "timers = []\n",
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+ "fps = FPSTimes()\n",
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+ "names = ['camera', 'video', 'position', 'main']\n",
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+ "distr_count = cfg['experiment']['distractor_islands']\n",
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+ "trial = 0\n",
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+ "rewards = 0\n",
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+ "t_start = None\n",
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+ "target_since = None\n",
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+ "distractor_since = None\n",
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+ "punishment_since = None\n",
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+ "trial_start = time.time()\n",
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+ "phase = 0 # 0 - idle, 1 - foraging, 2 - inter-trial interval\n",
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+ "cfg_exp = cfg['experiment']\n",
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+ "cfg_pos = cfg['position']\n",
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+ "islands = []\n",
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+ "iti_distance = 0.0\n",
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+ "last_x, last_y = None, None\n",
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+ "cfg_exp['trial_number'] = max([int(key) for key in commutator.keys()]) # equals number of diff sounds\n",
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+ "\n",
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+ "try:\n",
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+ " while trial <= cfg_exp['trial_number'] and not timeout(t_start):\n",
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+ " \n",
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+ " # ---------- rendering logic -----------\n",
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+ " frame = vs.read()\n",
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+ " if frame is None:\n",
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+ " time.sleep(0.1)\n",
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+ " continue # wait for the stream\n",
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+ " \n",
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+ " c_time = time.time()\n",
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+ " fps.count()\n",
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+ " angles, text_infos = [], []\n",
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+ " \n",
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+ " if not cfg_exp['target_angle'] == 'random':\n",
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+ " phi = isl_factory.phi_initial\n",
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+ " angles = [pt.correct_angle(phi), pt.correct_angle(phi) + np.deg2rad(cfg_exp['phi_max'])]\n",
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+ " \n",
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+ " for i, ctrl in enumerate([vs, vw, pt, fps]): # FPS indicators\n",
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+ " text_infos.append('%s: %.2f FPS' % (names[i], ctrl.get_avg_fps()))\n",
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+ " \n",
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+ " if len(islands) > 0: # target island X, Y\n",
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+ " target = [i for i in islands if not i.is_distractor][0]\n",
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+ " text_infos.append('Target: %.3f %.3f' % (target.x, target.y))\n",
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+ "\n",
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+ " text_infos.append('Time: %.2f' % float(c_time - t_start) if t_start is not None else 'Time: Idle') # stopwatch\n",
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+ " text_infos.append('Trial: %.2f' % float(cfg_exp['trial_duration'] - (c_time - trial_start)) if phase == 1 else 'Trial: not started')\n",
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+ " text_infos.append('Trial: %s' % trial)\n",
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+ " text_infos.append('Rewards: %s' % rewards) # rewards\n",
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+ " text_infos.append('In target: %.2f' % float(c_time - target_since) if target_since is not None else 'In target: --')\n",
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+ " text_infos.append('ITI distance: %.2f' % iti_distance if iti_distance > 0 else 'ITI distance: --')\n",
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+ "\n",
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+ " frame, frame_to_save = dc.render(frame, status, islands=islands, angles=angles, text_infos=text_infos)\n",
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+ " \n",
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+ " # assign the frame back to the video stream for other controllers\n",
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+ " vs.frame_with_infos = frame_to_save\n",
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+ " \n",
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|
+ " cv2.imshow('Press (s)-to start/stop, (q)-to end', frame)\n",
|
|
|
+ "\n",
|
|
|
+ " # -------- experiment logic ---------------\n",
|
|
|
+ " \n",
|
|
|
+ " if status.value == 2 and c_time - trial_start > cfg_exp['trial_duration']:\n",
|
|
|
+ " log_event(c_time, 0, 0, 0, trial, 1) # log trial end\n",
|
|
|
+ " trial += 1\n",
|
|
|
+ " if int(sound.value) < cfg_exp['trial_number']:\n",
|
|
|
+ " sound.value += 1\n",
|
|
|
+ " trial_start = c_time\n",
|
|
|
+ " log_event(c_time, 0, 0, 0, trial, 0) # log trial start\n",
|
|
|
+ " \n",
|
|
|
+ " # -------- key press events ---------------\n",
|
|
|
+ " \n",
|
|
|
+ " k = cv2.waitKey(33)\n",
|
|
|
+ " \n",
|
|
|
+ " # light on/off\n",
|
|
|
+ " if k == ord('l'):\n",
|
|
|
+ " switch_light(pt, board)\n",
|
|
|
+ " \n",
|
|
|
+ " # motors\n",
|
|
|
+ " if k == ord('d'):\n",
|
|
|
+ " if cfg['experiment']['enable_motors']:\n",
|
|
|
+ " motor_board.switch_diodes()\n",
|
|
|
+ " \n",
|
|
|
+ " # ephys cable on top\n",
|
|
|
+ " if k == ord('i') and 'cable_motor_port' in cfg['experiment']:\n",
|
|
|
+ " tf = threading.Timer(0, cable_board.turn_CCW, args=[])\n",
|
|
|
+ " tf.start()\n",
|
|
|
+ " if k == ord('o') and 'cable_motor_port' in cfg['experiment']:\n",
|
|
|
+ " tf = threading.Timer(0, cable_board.turn_CW, args=[])\n",
|
|
|
+ " tf.start()\n",
|
|
|
+ " \n",
|
|
|
+ " # feeding\n",
|
|
|
+ " if k == ord('f'):\n",
|
|
|
+ " tf = threading.Timer(0, board.feed, args=[])\n",
|
|
|
+ " tf.start()\n",
|
|
|
+ "\n",
|
|
|
+ " if k == ord('c'):\n",
|
|
|
+ " f_name = cfg_pos['background_light'] if pt.is_light else cfg_pos['background_dark']\n",
|
|
|
+ " cv2.imwrite(f_name, dc.masked_frame)\n",
|
|
|
+ " tf = threading.Timer(0.2, pt.reload_background, args=[])\n",
|
|
|
+ " tf.start() \n",
|
|
|
+ "\n",
|
|
|
+ " # quit the session\n",
|
|
|
+ " if k == ord('q'):\n",
|
|
|
+ " break\n",
|
|
|
+ "\n",
|
|
|
+ " # start the experiment\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 cfg['experiment']['enable_motors']:\n",
|
|
|
+ " if not motor_board.diodes_on:\n",
|
|
|
+ " motor_board.switch_diodes()\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",
|
|
|
+ " sound.value = 1\n",
|
|
|
+ " phase = 1\n",
|
|
|
+ " trial += 1\n",
|
|
|
+ "\n",
|
|
|
+ " # log trial start\n",
|
|
|
+ " log_event(c_time, 0, 0, 0, trial, 0) # log trial 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",
|
|
|
+ " if 'noise_when_idle' in cfg_exp and cfg_exp['noise_when_idle']:\n",
|
|
|
+ " sound.value = -1\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 = -1 if sound.value >= 0 else 0\n",
|
|
|
+ " switch_light(pt, board) # turn lights off \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",
|
|
|
+ " if board.is_light_off:\n",
|
|
|
+ " board.switch_light() # turn light back on\n",
|
|
|
+ " time.sleep(0.1)\n",
|
|
|
+ " board.exit()\n",
|
|
|
+ " \n",
|
|
|
+ " if cfg['experiment']['enable_motors']:\n",
|
|
|
+ " if motor_board.diodes_on:\n",
|
|
|
+ " motor_board.switch_diodes()\n",
|
|
|
+ " motor_board.exit()\n",
|
|
|
+ " if 'cable_motor_port' in cfg['experiment']:\n",
|
|
|
+ " cable_board.exit()\n",
|
|
|
+ " \n",
|
|
|
+ " cv2.destroyAllWindows()\n",
|
|
|
+ " sc.join()\n",
|
|
|
+ " for ctrl in [pt, vw, vs]:\n",
|
|
|
+ " ctrl.stop()\n",
|
|
|
+ "\n",
|
|
|
+ " # stop microphones recording process\n",
|
|
|
+ " if cfg['microphones']['record_audio']:\n",
|
|
|
+ " mc.join()\n",
|
|
|
+ "\n",
|
|
|
+ " if 'continuous' in cfg['sound']:\n",
|
|
|
+ " time.sleep(cfg['sound']['continuous']['end_sleep'])\n",
|
|
|
+ " cst.stop()"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "markdown",
|
|
|
+ "metadata": {},
|
|
|
+ "source": [
|
|
|
+ "### Merge data in HDF5 file"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": 32,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [],
|
|
|
+ "source": [
|
|
|
+ "session_path = save_to\n",
|
|
|
+ "#trial = 5\n",
|
|
|
+ "#session_path = os.path.join('sessions', '2021-07-30_09-24-14') # some particular session\n",
|
|
|
+ "#session_path = 'Y:\\\\Michael\\\\FreeBehaving\\\\SIT_sessions\\\\51_aSIT_2021-12-03_13-31-51'"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": 33,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [
|
|
|
+ {
|
|
|
+ "name": "stderr",
|
|
|
+ "output_type": "stream",
|
|
|
+ "text": [
|
|
|
+ "D:\\runSIT\\..\\pipeline\\postprocessing\\pack.py:59: UserWarning: loadtxt: Empty input file: \"sessions\\000000_hippoSIT_2023-07-11_09-32-45\\islands.csv\"\n",
|
|
|
+ " data = np.loadtxt(filename, delimiter=',', skiprows=1)\n"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "ename": "IndexError",
|
|
|
+ "evalue": "index 0 is out of bounds for axis 0 with size 0",
|
|
|
+ "output_type": "error",
|
|
|
+ "traceback": [
|
|
|
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
|
|
|
+ "\u001b[1;31mIndexError\u001b[0m Traceback (most recent call last)",
|
|
|
+ "\u001b[1;32m<ipython-input-33-df6d003c4298>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[1;31m# do pack data to HDF5\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0mh5name\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mpack\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msession_path\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 6\u001b[0m \u001b[0mtrial\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
|
|
|
+ "\u001b[1;32mD:\\runSIT\\..\\pipeline\\postprocessing\\pack.py\u001b[0m in \u001b[0;36mpack\u001b[1;34m(session_path)\u001b[0m\n\u001b[0;32m 165\u001b[0m \u001b[1;31m# head direction\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 166\u001b[0m \u001b[0mtemp_tl\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcolumn_stack\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mpos_at_freq\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mx_smooth\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0my_smooth\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mspeed\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 167\u001b[1;33m \u001b[0mhd\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mhead_direction\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mtemp_tl\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 168\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 169\u001b[0m \u001b[1;31m# trial numbers\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
|
|
|
+ "\u001b[1;32mD:\\runSIT\\..\\pipeline\\postprocessing\\head_direction.py\u001b[0m in \u001b[0;36mhead_direction\u001b[1;34m(tl, hd_update_speed)\u001b[0m\n\u001b[0;32m 22\u001b[0m \u001b[0mcrit\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwhere\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdiff\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0midle_idxs\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m>\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 23\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 24\u001b[1;33m \u001b[0midle_periods\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0midle_idxs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0midle_idxs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mcrit\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m)\u001b[0m \u001b[1;31m# first idle period\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 25\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mi\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mpoint\u001b[0m \u001b[1;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mcrit\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 26\u001b[0m \u001b[0midx_start\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0midle_idxs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mcrit\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mi\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
|
|
|
+ "\u001b[1;31mIndexError\u001b[0m: index 0 is out of bounds for axis 0 with size 0"
|
|
|
+ ]
|
|
|
+ }
|
|
|
+ ],
|
|
|
+ "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)\n",
|
|
|
+ "trial = 0"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "markdown",
|
|
|
+ "metadata": {},
|
|
|
+ "source": [
|
|
|
+ "### Plot sessions stats"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": null,
|
|
|
+ "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": null,
|
|
|
+ "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": null,
|
|
|
+ "metadata": {
|
|
|
+ "scrolled": false
|
|
|
+ },
|
|
|
+ "outputs": [],
|
|
|
+ "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",
|
|
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+ "\n",
|
|
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+ "ax = fig.add_subplot(222)\n",
|
|
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+ "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",
|
|
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+ "\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",
|
|
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+ "\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",
|
|
|
+ "\n",
|
|
|
+ "s_rate = 100 # Hz\n",
|
|
|
+ "window = 60 # secs\n",
|
|
|
+ "step = 10 # secs\n",
|
|
|
+ "duration = tl[-1][0]\n",
|
|
|
+ "x_vals = np.arange(int(duration/step))\n",
|
|
|
+ "\n",
|
|
|
+ "inst_speed = [tl[x*step*s_rate:(x*step + window)*s_rate][:, 3].mean() for x in x_vals]\n",
|
|
|
+ "ax.plot(x_vals*step, inst_speed)\n",
|
|
|
+ "ax.set_ylabel('Speed, m/s', fontsize=14)\n",
|
|
|
+ "ax.set_xlabel('Time, s', fontsize=14)\n",
|
|
|
+ "ax.set_title('Speed', fontsize=14)"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "markdown",
|
|
|
+ "metadata": {},
|
|
|
+ "source": [
|
|
|
+ "## Performance"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": null,
|
|
|
+ "metadata": {
|
|
|
+ "scrolled": true
|
|
|
+ },
|
|
|
+ "outputs": [],
|
|
|
+ "source": [
|
|
|
+ "h5name = os.path.join(session_path, experiment_id + '.h5')\n",
|
|
|
+ "jsname = os.path.join(session_path, experiment_id + '.json')\n",
|
|
|
+ "\n",
|
|
|
+ "# loading position and trial data\n",
|
|
|
+ "with h5py.File(h5name, 'r') as f:\n",
|
|
|
+ " tl = np.array(f['processed']['timeline']) # time, X, Y, speed\n",
|
|
|
+ " trial_idxs = np.array(f['processed']['trial_idxs']) # idx start, idx end, X, Y, R, trial result (idx to tl)\n",
|
|
|
+ "\n",
|
|
|
+ "# loading session configuration\n",
|
|
|
+ "with open(jsname, 'r') as f:\n",
|
|
|
+ " cfg = json.load(f)\n",
|
|
|
+ "\n",
|
|
|
+ "timepoints = cfg['experiment']['timepoints']\n",
|
|
|
+ "s_duration = cfg['experiment']['session_duration']\n",
|
|
|
+ "if len(timepoints) > 0:\n",
|
|
|
+ " periods = [[0, s_duration], [0, timepoints[0]], [timepoints[1], timepoints[2]], [timepoints[3], s_duration]]\n",
|
|
|
+ "else:\n",
|
|
|
+ " periods = [[0, s_duration]]\n",
|
|
|
+ "\n",
|
|
|
+ "# separate ALL, L, D, L'\n",
|
|
|
+ "ds_names = ['performance_ALL', 'performance_L', 'performance_D', 'performance_Lp']\n",
|
|
|
+ "ds_names = ['performance_ALL'] # only light\n",
|
|
|
+ "\n",
|
|
|
+ "for i, ds_name in enumerate(ds_names):\n",
|
|
|
+ " t_start, t_end = periods[i]\n",
|
|
|
+ " trial_starts = tl[trial_idxs[:, 0].astype(np.int32)][:, 0]\n",
|
|
|
+ " trial_ends = tl[trial_idxs[:, 1].astype(np.int32)][:, 0]\n",
|
|
|
+ " tr_idxs = trial_idxs[(trial_starts >= t_start) & (trial_ends <= t_end)]\n",
|
|
|
+ "\n",
|
|
|
+ " dataset = calculate_performance(tl, tr_idxs, cfg)\n",
|
|
|
+ " dump_performance_to_H5(h5name, ds_name, dataset)"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": null,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [],
|
|
|
+ "source": [
|
|
|
+ "fig = plt.figure(figsize=(4, 4))\n",
|
|
|
+ "\n",
|
|
|
+ "with h5py.File(h5name, 'r') as f:\n",
|
|
|
+ " perf = np.array(f['analysis']['performance_ALL'])\n",
|
|
|
+ " x = perf[:, 6]\n",
|
|
|
+ "\n",
|
|
|
+ "ax = fig.add_subplot(111)\n",
|
|
|
+ "\n",
|
|
|
+ "ax.plot(x, perf[:, 0]) # performance\n",
|
|
|
+ "ax.plot(x, perf[:, 3]) # chance\n",
|
|
|
+ "ax.fill_between(x, perf[:, 0] + perf[:, 1], perf[:, 0] + perf[:, 2], alpha=0.4)\n",
|
|
|
+ "ax.fill_between(x, perf[:, 3] + perf[:, 4], perf[:, 3] + perf[:, 5], alpha=0.4)\n",
|
|
|
+ "ax.set_ylim(0, 110)\n",
|
|
|
+ "ax.set_xlim(0, 65)\n",
|
|
|
+ "ax.grid()\n",
|
|
|
+ "ax.set_title(experiment_id[-19:], fontsize=14)\n",
|
|
|
+ "ax.set_xlabel('Time, s', fontsize=14)\n",
|
|
|
+ "\n",
|
|
|
+ "if i == 0:\n",
|
|
|
+ " ax.set_ylabel('Successful trials, %', fontsize=14)\n",
|
|
|
+ " \n",
|
|
|
+ "fig.tight_layout()"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": null,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [],
|
|
|
+ "source": []
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": null,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [],
|
|
|
+ "source": []
|
|
|
+ }
|
|
|
+ ],
|
|
|
+ "metadata": {
|
|
|
+ "kernelspec": {
|
|
|
+ "display_name": "Python 3",
|
|
|
+ "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": "3.8.8"
|
|
|
+ }
|
|
|
+ },
|
|
|
+ "nbformat": 4,
|
|
|
+ "nbformat_minor": 2
|
|
|
+}
|
