EXOTIC_Beginner_Tutorial.ipynb

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      "source": [
        "<a href=\"https://colab.research.google.com/github/alienlifeform/exotic-colab/blob/main/EXOTIC_Beginner_Tutorial.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ewl8DV6UPA62"
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      "source": [
        "# EXOTIC: Beginner Tutorial\n",
        "\n",
        "<font face=\"Helvetica, Arial, Sans-Serif\">\n",
        "\n",
        "Following is a demonstration of how to run EXOTIC's code in your browser on a set of sample telescope images to generate a lightcurve.\n",
        "\n",
        "Steps:\n",
        "\n",
        "<ol><li>Load telescope images\n",
        " <ul><li>For this tutorial, we'll use images taken from a previous transition of planet HAT-P-32 b</li></ul></li>\n",
        "<li>Identify target and comparison stars in a telescope image\n",
        " <ul><li>Find the target star (HAT-P-32) and several comparison stars that have stable brightness</li>\n",
        " <li>Enter their coordinates to calibrate the baseline brightness</li></ul></li>\n",
        "<li>Run EXOTIC to generate a lightcurve\n",
        " <ul><li>Watch EXOTIC determine if the brightness of your target star changes, signifying a transit. A transit is when an exoplanet passes in front of its host star, momentarily dimming out the star's light. <a href=\"https://exoplanets.nasa.gov/alien-worlds/ways-to-find-a-planet/#/2\">(View an animation of a transit)</a></li></ul></li></ol>\n",
        "\n",
        "\n",
        "\n",
        "INSTRUCTIONS\n",
        "\n",
        "\n",
        "\n",
        "Click the ![Screen Shot 2022-09-08 at 10.19.48 AM.png](data:image/png;base64,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) or ![Screen Shot 2022-09-08 at 10.19.58 AM.png](data:image/png;base64,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)  icons below to run the code for each step. Wait for it to finish running before moving to the next step, and watch for the output describing what is happening.\n",
        "\n",
        "\n",
        "</font>"
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      "source": [
        "---\n",
        "\n",
        "## Step 1: Load Telescope Images\n",
        "\n",
        "<font face=\"Helvetica, Arial, Sans-Serif\">\n",
        "\n",
        "\n",
        "🕔&nbsp;&nbsp;<i>Estimated time: < 1 minute (this would take longer with a real data set ~2 minutes)</i>\n",
        "\n",
        "For this tutorial, we are using sample images from a known transit. When you run it yourself, you will upload your own images.\n",
        "\n",
        "\n",
        "<table><tr><td bgcolor=\"#fee9e9\">\n",
        "  <font size=2 color=\"#c02020\">Important:\n",
        "  <ul><li><font size=2>A popup will appear titled \"Warning: This notebook was not authored by Google.\" Read it, then click \"Run Anyway\".</font></li>\n",
        "  <li><font size=2>If you click the blue <font color=\"#7090e0\">Show code</font> links, you can re-hide the code by double-clicking the title just above it.</font></li></ul></font>\n",
        "</td></tr></table>\n",
        "<br />\n",
        "\n",
        "</font>"
      ],
      "metadata": {
        "id": "zemfRdsQ1TTU"
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    {
      "cell_type": "code",
      "source": [
        "#@title <font size=3><img src=\"https://exoplanets.nasa.gov/system/exotic/leftdownarrow_tall.png\" height=18 hspace=8><b>Load telescope images</b></font>\n",
        "\n",
        "##############################################################\n",
        "%%capture step_capture --no-display\n",
        "# Comment the above statement out to see debugging information\n",
        "##############################################################\n",
        "\n",
        "##############################################################\n",
        "#\n",
        "# NOTE TO EXOTIC USER:\n",
        "#\n",
        "#   • To hide this code, double-click the title above (\"Load telescope images\"),\n",
        "#     or click the arrow to the left of the title.\n",
        "#\n",
        "#   • Editing this code will only affect your local instance. \n",
        "#     Reload to revert your changes.\n",
        "#\n",
        "##############################################################\n",
        "\n",
        "from IPython.display import display, HTML, Javascript\n",
        "display(HTML('<p class=\"bookend\">START: Importing necessary software libraries</p>'))\n",
        "display(HTML('<p class=\"hidden\">Loading styles, please wait...</p>'))\n",
        "\n",
        "# Install EXOTIC Colab interface code\n",
        "!pip install git+https://github.com/alienlifeform/exotic-colab.git --upgrade\n",
        "\n",
        "from exoticcolab.display import setupDisplay, testImplementation, displayStep, makeContainer, downloadButton, appendToContainer, appendStepToContainer, expandableSection, hideWarning, showProgress, resize_colab_cell\n",
        "\n",
        "# Set up custom Colab styles and interactions\n",
        "setupDisplay()\n",
        "# Improve how colab handles long code output fields\n",
        "get_ipython().events.register('pre_run_cell', resize_colab_cell)\n",
        "\n",
        "\n",
        "display(HTML('<ul class=\"step_container_1a\"></ul>'))\n",
        "appendStepToContainer('.step_container_1a','Styles loaded, importing libraries...')\n",
        "showProgress(1) # make it feel real\n",
        "\n",
        "appendStepToContainer('.step_container_1a','(1/5) Bokeh.io')\n",
        "import bokeh.io\n",
        "from bokeh.io import output_notebook\n",
        "showProgress(1) # make it feel real\n",
        "\n",
        "appendStepToContainer('.step_container_1a','(2/5) EXOTIC <span class=\"comment\">(This will take up to a minute, please wait...)</span>')\n",
        "### We need only a subset of methods for the tutorial:\n",
        "from astropy.io import fits\n",
        "from bokeh.plotting import figure, output_file, show\n",
        "from bokeh.models import BoxZoomTool,WheelZoomTool,ResetTool,HoverTool,PanTool,FreehandDrawTool\n",
        "from bokeh.models import ColorBar, LinearColorMapper, LogColorMapper, LogTicker\n",
        "import numpy as np\n",
        "showProgress(5) # make it feel real\n",
        "\n",
        "## rzellem version\n",
        "#!pip install exotic --upgrade\n",
        "\n",
        "## alienlifeform version\n",
        "#!pip install git+https://github.com/alienlifeform/exotic-prototype.git --upgrade\n",
        "#from exotic.api.colab import *\n",
        "\n",
        "## plot_image not needed for the simulation\n",
        "# from exotic.api.plotting import plot_image \n",
        "\n",
        "# This suppresses the \"RESTART RUNTIME\" button\n",
        "hideWarning()\n",
        "#display(HTML('<br /><p>If there is a \"RESTART RUNTIME\" warning button above, you can ignore it (or click it and then re-run this step).</p>'))\n",
        "\n",
        "appendStepToContainer('.step_container_1a','(3/5) NASAExoplanetArchive, Astropy, Utils')\n",
        "## Not needed for tutorial:\n",
        "#from exotic.exotic import NASAExoplanetArchive, get_wcs, find_target\n",
        "\n",
        "from IPython.display import Image\n",
        "from ipywidgets import widgets, HBox\n",
        "import os\n",
        "import re\n",
        "import json\n",
        "showProgress(1) # make it feel real\n",
        "\n",
        "appendStepToContainer('.step_container_1a','(4/5) Matlab, SciPy')\n",
        "showProgress(2) # make it feel real\n",
        "\n",
        "appendStepToContainer('.step_container_1a','(5/5) Google Utils')\n",
        "from google.colab import files\n",
        "showProgress(1) # make it feel real\n",
        "\n",
        "#expandableSection('<p>This is some expandable stuff</p>')\n",
        "display(HTML('<p class=\"bookend\">DONE: Importing necessary software libraries</p>'))\n",
        "\n",
        "\n",
        "#########################################################\n",
        "\n",
        "display(HTML('<p class=\"bookend\">START: Loading telescope images</p>'))\n",
        "display(HTML('<ul class=\"step_container_1b\"></ul>'))\n",
        "\n",
        "appendStepToContainer('.step_container_1b','Ensuring sample images are loaded...')\n",
        "\n",
        "#\n",
        "# Delete existing sample data by changing to `rebuild = \"true\"`\n",
        "#\n",
        "rebuild = \"true\"  \n",
        "if rebuild == \"true\":\n",
        "  if os.path.isdir(\"/content/EXOTIC/tutorial\"):\n",
        "    %rm -rf /content/EXOTIC/tutorial\n",
        "    display(HTML('<p class=\"step\">\"Rebuild\" flag is \"true\"... Removing old images at /content/EXOTIC/tutorial</p>'))\n",
        "\n",
        "#\n",
        "# Download sample files if necessary\n",
        "#\n",
        "#sample_data_source = \"https://github.com/rzellem/EXOTIC_sampledata.git\" # goes into sample_data_target_folder\n",
        "sample_data_source = \"https://github.com/alienlifeform/exotic-sample-data.git\" # goes into sample_data_target_parent\n",
        "sample_data_target_parent = \"/content/EXOTIC/tutorial\"\n",
        "sample_data_target_folder = \"/content/EXOTIC/tutorial/sample-data\"\n",
        "sample_data_target_child = \"/content/EXOTIC/tutorial/sample-data/HatP32Dec202017\"\n",
        "sample_data_target_outputs = \"/content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output\"\n",
        "if os.path.isdir(sample_data_target_child):\n",
        "  appendStepToContainer('.step_container_1b','Skipping... Sample images already loaded')\n",
        "\n",
        "else:\n",
        "  appendStepToContainer('.step_container_1b','Downloading images from ' + sample_data_source)\n",
        "  #git_rv = !git clone {sample_data_source} {sample_data_target_folder}\n",
        "  git_rv = !git clone {sample_data_source} {sample_data_target_parent}\n",
        "  git_co_rv = !cd {sample_data_target_parent} && !git checkout beta1\n",
        "  appendStepToContainer('.step_container_1b','Telescope images successfully loaded for HAT-P-32 b')\n",
        "\n",
        "#\n",
        "# Show files found\n",
        "#\n",
        "#!du -hd0 --exclude \".*\" /content/EXOTIC/tutorial/sample-data/HatP32Dec202017\n",
        "numfiles_fits = !ls {sample_data_target_child} | grep -ci FITS\n",
        "numfiles_json = !ls {sample_data_target_child} | grep -ci json\n",
        "\n",
        "display(HTML('<p class=\"step\">You have ' + str(numfiles_fits[0]) + ' telescope image (.FITS) files.</p>'))\n",
        "display(HTML('<p class=\"step\">You have ' + str(numfiles_json[0]) + ' inits (.json) files</p>'))\n",
        "\n",
        "display(HTML('<p class=\"bookend\">DONE: Loading telescope images. <b>You may move on to the next step.</b></p>'))"
      ],
      "metadata": {
        "id": "B42CTyU74AZw",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "\n",
        "## Step 2: Identify target star and comparison stars\n",
        "\n",
        "<font face=\"Helvetica, Arial, Sans-Serif\">\n",
        "\n",
        "\n",
        "🕔&nbsp;&nbsp;<i>Estimated time: 6 minutes</i>\n",
        "\n",
        "In this multi-part step, you will use your stargazing skills to identify coordinates for your target star (HAT-P-32). You will:\n",
        "\n",
        "\n",
        "\n",
        "<ol type=\"a\"><li>Watch the Video: \"How to determine a star's coordinates\" (3 minutes)</li>\n",
        "<li>Try it yourself: Enter the coordinates for the target and comparison stars (3 minutes)</li></ol>\n",
        "\n",
        "</font>"
      ],
      "metadata": {
        "id": "Wyk5hRrHWxTA"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#@title <font size=3><img src=\"https://exoplanets.nasa.gov/system/exotic/leftdownarrow_tall.png\" height=18 hspace=8><b>2a. Watch the video: \"How to determine a star's coordinates\"</b></font>\n",
        "\n",
        "setupDisplay()\n",
        "\n",
        "display(HTML('''\n",
        "<br />\n",
        "<video width=\"840\" controls=\"true\" poster=\"https://exoplanets.nasa.gov/system/exotic/exotic-identify-stars.jpg\" src=\"https://exoplanets.nasa.gov/system/exotic/exotic-identify-stars.mov\"/>\n",
        "'''))"
      ],
      "metadata": {
        "id": "lbFf2vgGNUCW",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title <font size=3><img src=\"https://exoplanets.nasa.gov/system/exotic/leftdownarrow_tall.png\" height=18 hspace=8><b>2b. Identify the target and comparison stars in a telescope image</b></font>\n",
        "\n",
        "##############################################################\n",
        "#\n",
        "# NOTE TO EXOTIC USER:\n",
        "#\n",
        "#   • To hide this code, double-click the title above (\"2b. Identify the target and comparison stars in a telescope image\"),\n",
        "#     or click the arrow to the left of the title.\n",
        "#\n",
        "#   • Editing this code will only affect your local instance. \n",
        "#     Reload to revert your changes.\n",
        "#\n",
        "##############################################################\n",
        "\n",
        "#@markdown <font face=\"Helvetica, Arial, Sans-Serif\" size=2>\n",
        "#@markdown Select your telescope and target star, then press <img src=\"data:image/png;base64,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\"> to the left.\n",
        "Telescope = 'MicroObservatory' #@param [\"MicroObservatory\"]\n",
        "Target = 'HAT-P-32' #@param [\"HAT-P-32\"]\n",
        "#@markdown </font>\n",
        "\n",
        "setupDisplay()\n",
        "\n",
        "#########################################################\n",
        "\n",
        "# Show the first telescope image in an interactive interface\n",
        "def display_image(filename):\n",
        "    #print(f\"{filename}\")\n",
        "    hdu = fits.open(filename)\n",
        "\n",
        "    dheader = dict(hdu[0].header)\n",
        "  \n",
        "    data = hdu[0].data\n",
        "    megapixel_factor = (data.shape[0])*(data.shape[1])/1000000.0\n",
        "    if megapixel_factor > 5:\n",
        "      print(f\"Downsampling image because it has {megapixel_factor} megapixels.\")\n",
        "      image_downscaled = downscale_local_mean(data, (2, 2)).astype(int)\n",
        "      data = image_downscaled\n",
        "    \n",
        "    max_y = len(data)\n",
        "    max_x = len(data[0])\n",
        "    p_height = 500\n",
        "    p_width = int((p_height/max_y) * max_x)\n",
        "\n",
        "    # create a figure with text on mouse hover\n",
        "    fig = figure(tooltips=[(\"x\", \"$x\"), (\"y\", \"$y\"), (\"value\", \"@image\")], plot_width=p_width, plot_height=p_height,\n",
        "        tools=[PanTool(),BoxZoomTool(),WheelZoomTool(),ResetTool(),HoverTool()])\n",
        "    fig.x_range.range_padding = fig.y_range.range_padding = 0\n",
        "\n",
        "    r = fig.multi_line('x', 'y', source={'x':[],'y':[]},color='white',line_width=3)\n",
        "    fig.add_tools(FreehandDrawTool(renderers=[r]))\n",
        "\n",
        "    # set up a colobar + data range\n",
        "    color_mapper = LogColorMapper(palette=\"Cividis256\", low=np.percentile(data, 55), high=np.percentile(data, 99))\n",
        "\n",
        "    # must give a vector of image data for image parameter\n",
        "    fig.image(\n",
        "        image=[data],\n",
        "          x=0, y=0, dw=hdu[0].data.shape[1], dh=hdu[0].data.shape[0],\n",
        "          level=\"image\", color_mapper=color_mapper\n",
        "    )\n",
        "    fig.grid.grid_line_width = 0.5\n",
        "\n",
        "    color_bar = ColorBar(color_mapper=color_mapper, ticker=LogTicker(),\n",
        "                         label_standoff=12, border_line_color=None, location=(0,0))\n",
        "\n",
        "    fig.add_layout(color_bar, 'right')\n",
        "\n",
        "    show(fig)\n",
        "\n",
        "#########################################################\n",
        "\n",
        "display(HTML('<p class=\"bookend\">START: Compare telescope image and star chart</p>'))\n",
        "display(HTML('<ul class=\"step4\">'))\n",
        "\n",
        "# set up bokeh\n",
        "bokeh.io.output_notebook()\n",
        "sample_data = False\n",
        "\n",
        "# set up image path\n",
        "p = \"sample-data/HatP32Dec202017\"\n",
        "#p = check_dir(os.path.join(\"/content/EXOTIC/tutorial/\", p))\n",
        "p = os.path.join(\"/content/EXOTIC/tutorial/\", p)\n",
        "output_dir = p + \"_output/\"\n",
        "         \n",
        "#########################################################\n",
        "\n",
        "# Find and show the images\n",
        "inits = []    # array of paths to any inits files found in the directory\n",
        "\n",
        "all_files_print = [f for f in sorted(os.listdir(p))]\n",
        "all_files = [f for f in sorted(os.listdir(p)) if os.path.isfile(os.path.join(p, f))]\n",
        "fits_count, first_image = 0, \"\"\n",
        "for f in all_files:\n",
        "  if re.search(r\"\\.f[itz]+s?\\.?g?z?$\", f, re.IGNORECASE):\n",
        "    if first_image == \"\":\n",
        "      first_image = os.path.join(p, f)\n",
        "    fits_count += 1\n",
        "  if re.search(r\"\\.json$\", f, re.IGNORECASE):\n",
        "    inits.append(os.path.join(p, f))\n",
        "\n",
        "# show images\n",
        "if fits_count >= 2:\n",
        "  obs = \"\"\n",
        "  # instructions for finding the target star\n",
        "  display(HTML('''\n",
        "  <h3>Data Entry 1 of 2: Enter coordinates for the target star</h3>\n",
        "  <ol class=\"step\">\n",
        "  <li class=\"step4\">In the right image, find the <i>crosshairs</i> in the center - that represents your target star.</li>\n",
        "  <li class=\"step4\">On the left image, <i>find this target star and roll over it with your mouse</i>, note the X and Y coordinates.</li>\n",
        "  <li class=\"step4\">Put the X and Y coordinates in the box below in the format <code>[x,y]</code> and press return.</li></ol>\n",
        "  <p>Tip: Use the zoom feature. Click the magnifying glass and click-and-drag to draw a rectangle that matches the starchart.</p>\n",
        "\n",
        "  <br />\n",
        "  <div class=\"plots\">\n",
        "  <img class=\"aavso_image\" src=\"https://app.aavso.org/vsp/chart/X28194FDL.png\">\n",
        "  '''))\n",
        "  display_image(first_image)\n",
        "  display(HTML('</div><br clear=\"all\"/>'))\n",
        "\n",
        "  # request coordinates and verify the entries are valid\n",
        "  success = False\n",
        "  while not success:\n",
        "    targ_coords = input(\"Enter coordinates for target star - in the format [424,286] - and press return:  \")  \n",
        "\n",
        "    # check syntax and coords\n",
        "    targ_coords = targ_coords.strip()\n",
        "    tc_syntax = re.search(r\"\\[\\d+,\\d+\\]$\", targ_coords)\n",
        "    if tc_syntax:\n",
        "      tc_coords = re.findall(\"\\d+\", targ_coords)\n",
        "      if 418 <= int(tc_coords[0]) <= 430 and 280 <= int(tc_coords[1]) <= 292:\n",
        "        success = True\n",
        "      else:\n",
        "        display(HTML('<p class=\"error\">Try again, your coordinates are a bit off: ' + targ_coords + ' should be closer to [424,286]</p>'))\n",
        "    else:\n",
        "      display(HTML('<p class=\"error\">Try again, your syntax is not quite right: ' + targ_coords + ' needs to look like [424,286]</p>'))\n",
        "\n",
        "\n",
        "  showProgress(2)\n",
        "\n",
        "  # instructions for finding the comparison stars\n",
        "  display(HTML('<p class=\"output\">Target star coordinates saved to inits.json</p>'))\n",
        "  display(HTML('<h3>Data Entry 2 of 2: Enter coordinates for at least two comparison stars.</h3>'))\n",
        "  display(HTML('<ol class=\"step\"><li class=\"step4\">In the right image, find the stars <i>with numbers</i> that represent suggested comparison stars.</li><li class=\"step4\">On the left image, <i>find and roll over each comparison star with your mouse</i> and note the coordinates.</li><li class=\"step4\">Put the X and Y coordinates in the box below in the format <code>[[x1,y1][x2,y2]]</code> and press return.</li></ol>'))\n",
        "  \n",
        "  # request coordinates and verify the entries are valid\n",
        "  success = False\n",
        "  while not success:\n",
        "    comp_coords = input(\"Enter coordinates for the comparison stars - in the format [[326,365],[416,343]] - and press return:  \")  \n",
        "\n",
        "    # check syntax\n",
        "    comp_coords = comp_coords.strip()\n",
        "    cc_syntax = re.search(r\"\\[(\\[\\d+,\\d+\\],?)+\\]$\", comp_coords)\n",
        "    if cc_syntax:\n",
        "      #display(HTML('<p class=\"output\">Syntax OK:  [[x1,y1],[x2,y2]] e.g. ' + comp_coords + '</p>'))\n",
        "      success = True\n",
        "    else:\n",
        "      display(HTML('<p class=\"error\">Try again, your syntax is not quite right: ' + comp_coords + ' needs to look more like [[326,365],[416,343]]</p>'))\n",
        "\n",
        "  showProgress(1)\n",
        "  display(HTML('<p class=\"output\">Comparison star coordinates saved to inits.json</p>'))\n",
        "  display(HTML('<p class=\"output\">Images and inits.json set up. Ready for EXOTIC data reduction/analysis</p>'))\n",
        "  aavso_obs_code = \"\"\n",
        "\n",
        "  if not os.path.isdir(output_dir):\n",
        "    os.mkdir(output_dir)\n",
        "\n",
        "  #inits = [make_inits_file(planetary_params, p, output_dir, first_image, targ_coords, comp_coords, obs, aavso_obs_code, sample_data)]\n",
        "  inits = [output_dir+\"inits.json\"]\n",
        "\n",
        "  if not os.path.isdir(output_dir):    # Make the output directory if it does not exist already.\n",
        "    os.mkdir(output_dir)\n",
        "  output_dir_for_shell = output_dir.replace(\" \", \"\\ \")\n",
        "\n",
        "#print(\"Path to the inits file(s) that will be used:\")\n",
        "\n",
        "#for inits_file in inits:\n",
        "#  print(inits_file)\n",
        "\n",
        "num_inits = len(inits)\n",
        "\n",
        "\n",
        "display(HTML('<p class=\"bookend\">DONE: Compare telescope image and star chart. <b>You may move on to the next step.</b></p>'))\n",
        "\n",
        "\n"
      ],
      "metadata": {
        "id": "DfQdfE3K-ISY",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "\n",
        "## Step 3: Run EXOTIC to generate a lightcurve\n",
        "\n",
        "<font face=\"Helvetica, Arial, Sans-Serif\">\n",
        "\n",
        "\n",
        "🕔&nbsp;&nbsp;<i>Estimated time: < 1 minute (this would take longer with a real data set ~5-15 minutes)</i>\n",
        "\n",
        "EXOTIC will analyze the brightness of the target star in each telescope image to identify if there was a transit. At the end of this step, you will see your lightcurve as an image, and you could (if this wasn't just sample data) download the lightcurve data to your hard drive for submission to AAVSO.\n",
        "\n",
        "</font>"
      ],
      "metadata": {
        "id": "lfMkDKAv14wu"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#@title <font size=3><img src=\"https://exoplanets.nasa.gov/system/exotic/leftdownarrow_tall.png\" height=18 hspace=8><b>Run EXOTIC to generate a lightcurve</b></font>\n",
        "\n",
        "# This generation is a simulation only using unstyled logging from a HAT-P-32 b EXOTIC run\n",
        "\n",
        "setupDisplay()\n",
        "\n",
        "display(HTML('<p class=\"bookend\">START: Analyzing telescope images</p>'))\n",
        "\n",
        "log_10 = \"\"\"\n",
        "Path to the inits file(s) that will be used:\n",
        "/content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/inits.json\n",
        "!exotic -red \"/content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/inits.json\" -ov\n",
        "    Downloading __databases__.pickle_new...\n",
        "    Done!\n",
        "Checking exotethys database...\n",
        "Checking ephemerides database...\n",
        "Checking photometry database...\n",
        "Checking catalogues database...\n",
        "\n",
        "*************************************************************\n",
        "Welcome to the EXOplanet Transit Interpretation Code (EXOTIC)\n",
        "Version 1.10.2\n",
        "*************************************************************\n",
        "\n",
        "\n",
        "**************************\n",
        "Complete Reduction Routine\n",
        "**************************\n",
        "\n",
        "**************************\n",
        "Starting Reduction Process\n",
        "**************************\n",
        "\n",
        "\n",
        "Getting the plate solution for your imaging file to translate pixel coordinates on the sky. \n",
        "Please wait....\n",
        "\n",
        "\"\"\"\n",
        "\n",
        "log_20 = \"\"\"\n",
        "WCS file creation successful.\n",
        "Thinking ... DONE!\n",
        "\n",
        "Here is the path to your plate solution: /content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/wcs.fits\n",
        "\n",
        "Checking for variability in Comparison Star #1:\n",
        "    Pixel X: 493 Pixel Y: 304\n",
        " Warning: Your comparison star cannot be resolved in the SIMBAD star database; EXOTIC cannot check if it is variable or not. \n",
        "EXOTIC will still include this star in the reduction. \n",
        "Please proceed with caution as we cannot check for stellar variability.\n",
        "\n",
        "\n",
        "Checking for variability in Comparison Star #2:\n",
        "    Pixel X: 415 Pixel Y: 343\n",
        " Warning: Your comparison star cannot be resolved in the SIMBAD star database; EXOTIC cannot check if it is variable or not. \n",
        "EXOTIC will still include this star in the reduction. \n",
        "Please proceed with caution as we cannot check for stellar variability.\n",
        "\n",
        "\n",
        "Computing best comparison star, aperture, and sky annulus. Please wait.\n",
        "\"\"\"\n",
        "\n",
        "log_30 = \"\"\"\n",
        "\n",
        "*********************************************\n",
        "Best Comparison Star: None\n",
        "Minimum Residual Scatter: 0.672%\n",
        "Optimal Aperture: 5.02\n",
        "Optimal Annulus: 7.54\n",
        "*********************************************\n",
        "\n",
        "No Barycentric Julian Dates (BJDs) in Image Headers for standardizing time format. Converting all JDs to BJD_TDBs.\n",
        "Please be patient- this step can take a few minutes.\n",
        "\"\"\"\n",
        "\n",
        "log_40 = \"\"\"\n",
        "Thinking ... DONE!\n",
        "\n",
        "\n",
        "Output File Saved\n",
        "\n",
        "\n",
        "****************************************\n",
        "Fitting a Light Curve Model to Your Data\n",
        "****************************************\n",
        "\n",
        "[ultranest] Sampling 400 live points from prior ...\n",
        "\n",
        "\n",
        "Mono-modal Volume: ~exp(-3.81) * Expected Volume: exp(0.00) Quality: ok\n",
        "\n",
        "rprs:   +0.0000|**********|  +0.1861\n",
        "tmid: +2458107.706|**********|+2458107.716\n",
        "ars :      +4.8|**********|     +5.9\n",
        "a2  :      -3.0|**********|     +3.0\n",
        "\n",
        "Z=-1659103.7(0.00%) | Like=-1655784.03..-111.41 [-8987932.8990..-176103.1770] | it/evals=80/494 eff=85.1064% N=400 \n",
        "\n",
        "Mono-modal Volume: ~exp(-3.96) * Expected Volume: exp(-0.23) Quality: ok\n",
        "\n",
        "rprs:   +0.0000|**********|  +0.1861\n",
        "tmid: +2458107.706|**********|+2458107.716\n",
        "ars :      +4.8|**********|     +5.9\n",
        "a2  :      -3.0|********  |     +3.0\n",
        "\n",
        "Z=-338377.3(0.00%) | Like=-334422.26..-111.41 [-8987932.8990..-176103.1770] | it/evals=160/609 eff=76.5550% N=400 \n",
        "\n",
        "Mono-modal Volume: ~exp(-4.18) * Expected Volume: exp(-0.45) Quality: ok\n",
        "\n",
        "rprs:   +0.0000|**********|  +0.1861\n",
        "tmid: +2458107.706|**********|+2458107.716\n",
        "ars :      +4.8|**********|     +5.9\n",
        "a2  :      -3.0|*******   |     +3.0\n",
        "\n",
        "Z=-202573.2(0.00%) | Like=-201882.30..-111.41 [-8987932.8990..-176103.1770] | it/evals=240/730 eff=72.7273% N=400 \n",
        "\n",
        "\"\"\"\n",
        "\n",
        "log_50 = \"\"\"\n",
        "Mono-modal Volume: ~exp(-20.47)   Expected Volume: exp(-17.10) Quality: ok\n",
        "\n",
        "rprs:    +0.000|        * |   +0.186\n",
        "tmid: +2458107.706|       ** |+2458107.716\n",
        "ars :      +4.8|    **    |     +5.9\n",
        "a2  :    -1.000|    *     |   +1.000\n",
        "\n",
        "[ultranest] Explored until L=-7e+01  \n",
        "[ultranest] Likelihood function evaluations: 15883\n",
        "[ultranest]   logZ = -82.92 +- 0.141\n",
        "[ultranest] Effective samples strategy satisfied (ESS = 2176.7, need >400)\n",
        "[ultranest] Posterior uncertainty strategy is satisfied (KL: 0.45+-0.05 nat, need <0.50 nat)\n",
        "[ultranest] Evidency uncertainty strategy is satisfied (dlogz=0.14, need <0.5)\n",
        "[ultranest]   logZ error budget: single: 0.16 bs:0.14 tail:0.01 total:0.14 required:<0.50\n",
        "[ultranest] done iterating.\n",
        "\n",
        "*********************************************************\n",
        "FINAL PLANETARY PARAMETERS\n",
        "\n",
        "          Mid-Transit Time [BJD_TDB]: 2458107.7136 +/- 0.001\n",
        "  Radius Ratio (Planet/Star) [Rp/Rs]: 0.1587 +/- 0.0037\n",
        "           Transit depth [(Rp/Rs)^2]: 2.52 +/- 0.12 [%]\n",
        " Semi Major Axis/ Star Radius [a/Rs]: 5.36 +/- 0.11\n",
        "               Airmass coefficient 1: 1.1645 +/- 0.0078\n",
        "               Airmass coefficient 2: -0.1222 +/- 0.0028\n",
        "                    Residual scatter: 0.67 %\n",
        "                 Best Comparison Star: None\n",
        "                    Optimal Aperture: 5.02\n",
        "                     Optimal Annulus: 7.54\n",
        "              Transit Duration [day]: 0.1311 +/- 0.0028\n",
        "*********************************************************\n",
        "Output Files Saved\n",
        "\n",
        "************************\n",
        "End of Reduction Process\n",
        "************************\n",
        "\"\"\"\n",
        "\n",
        "log_60 = \"\"\"\n",
        "************************\n",
        "EXOTIC has successfully run!!!\n",
        "It is now safe to close this window.\n",
        "************************\n",
        "lightcurve: /content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/FinalLightCurve_HAT-P-32 b_2017-12-19.png\n",
        "\"\"\"\n",
        "\n",
        "import time\n",
        "print(log_10)\n",
        "showProgress(2)\n",
        "print(log_20)\n",
        "showProgress(3)\n",
        "print(log_30)\n",
        "showProgress(2)\n",
        "print(log_40)\n",
        "showProgress(4)\n",
        "print(log_50)\n",
        "showProgress(2)\n",
        "print(log_60)\n",
        "\n",
        "display(HTML('''\n",
        "    <img width=800 src=\"https://exoplanets.nasa.gov/system/exotic/sample_lightcurve.png\">\n",
        "\n",
        "'''))\n",
        "\n",
        "display(HTML('''\n",
        "    <p><a href=\"https://exoplanets.nasa.gov/system/exotic/exotic-understand-lightcurve.html\" target=\"_blank\">Click for a video to help you understand this lightcurve.</a>\n",
        "\n",
        "    <p class=\"bookend\">DONE: Analyzing telescope images. <b>Tutorial completed!</b></p>\n",
        "'''))\n",
        "\n",
        "showProgress(2)\n",
        "\n",
        "\n",
        "display(HTML('''\n",
        "  \n",
        "  <h2>Congratulations!</h2> \n",
        "  <h3>You have successfully generated a lightcurve showing the transit of HAT-P-32 b around HAT-P-32</h3>\n",
        "\n",
        "  <li class=\"step\">This exoplanet was actually discovered in 2011, and you can <a target=\"_blank\" href=\"https://exoplanets.nasa.gov/exoplanet-catalog/1434/HAT-P-32-b/\">view it in 3D on exoplanets.nasa.gov</a>.</li>\n",
        "\n",
        "  <li class=\"step\">If you choose to download the data to your hard drive (as \"AAVSO_HAT-P-32 b_2017-12-19.txt\"), it will be in a format suitable for submission to AAVSO, though please don't submit it! When you use real data, you <i>will</i> be submitting your lightcurve to the AAVSO.  </li>\n",
        "\n",
        "'''))\n",
        "\n",
        "\n",
        "# Allow download of lightcurve data\n",
        "def on_dl_button_clicked(b):\n",
        "  # Display the message within the output widget.\n",
        "  if os.path.isfile('/content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/AAVSO_HAT-P-32 b_2017-12-19.txt'):\n",
        "    display(HTML('<p>Downloading lightcurve data...</p>'))\n",
        "    showProgress(2)\n",
        "    files.download('/content/EXOTIC/tutorial/sample-data/HatP32Dec202017_output/AAVSO_HAT-P-32 b_2017-12-19.txt')\n",
        "  else: \n",
        "    display(HTML('<p>Couldn\\'t find output file. Alert the developers to ensure it is in the sample-data repo being used.</p>'))\n",
        "\n",
        "dl_button = widgets.Button(description=\"Download data\")\n",
        "dl_button.on_click(on_dl_button_clicked)\n",
        "display(HTML('<br /><hr /><br />'))\n",
        "display(dl_button)"
      ],
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        "---\n",
        "\n",
        "## End of Tutorial\n",
        "\n",
        "<font face=\"Helvetica, Arial, Sans-Serif\">\n",
        "\n",
        "What would you like to do next?\n",
        "\n",
        "<a href=\"https://colab.research.google.com/drive/1bN5SUOF76cDl63qERjnmoscxILPBW7LT\">Try using EXOTIC with observation data from an Exoplanet Watch telescope</a>\n",
        "\n",
        "\n",
        "<a href=\"https://exoplanets.nasa.gov/exoplanet-watch/how-to-contribute/how-to-observe/\">Learn how to observe exoplanets</a>\n",
        "\n",
        "<a href=\"https://exoplanets.nasa.gov/exoplanet-watch/about-exoplanet-watch/contact-us/\">Provide feedback for this tutorial</a>\n",
        "\n",
        "\n",
        "</font>"
      ]
    }
  ],
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