{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Introduction\n",
    "\n",
    "This notebook demonstrates how to visualize and analyze JWST data cubes, including how to:\n",
    "\n",
    "* Launch [CubeViz](https://jdaviz.readthedocs.io/en/latest/cubeviz/index.html)\n",
    "* [Load data](https://jdaviz.readthedocs.io/en/latest/cubeviz/import_data.html) from a notebook cell\n",
    "* Adjust [display parameters](https://jdaviz.readthedocs.io/en/latest/cubeviz/displaycubes.html#display-settings)\n",
    "* Subtract continuum from a datacube\n",
    "* Select [spectral regions](https://jdaviz.readthedocs.io/en/latest/specviz/displaying.html#spectral-regions) for further analysis \n",
    "* Use the [Moment Maps](https://jdaviz.readthedocs.io/en/latest/cubeviz/plugins.html#moment-maps) plugin to map a spectral feature\n",
    "* Use the Moment Maps plugin to extract a velocity map\n",
    "* [Model fitting](https://jdaviz.readthedocs.io/en/latest/cubeviz/plugins.html#model-fitting) for every spaxel in a cube.\n",
    "* Use a cube model to create feature maps.\n",
    "\n",
    "Updated on June 10, 2022.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Data\n",
    "\n",
    "We use a simulated 4-point dithered observation of a point source produced using [MIRISim](https://www.stsci.edu/jwst/science-planning/proposal-planning-toolbox/mirisim), \n",
    "with the spectrum of active galaxy NGC 5728.  It has been processed with the [JWST pipeline](https://jwst-pipeline.readthedocs.io/en/latest/) (Detector1/Spec2/Spec3).  The output is constructed only for a \n",
    "single MRS channel/band (2C).\n",
    "\n",
    "For the NIRSpec IFU data, a point source (quasar) was simulated using the NIRSpec Instrument Performance Simulator (IPS), then run through the JWST Spec2 and Spec3 pipelines. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Imports "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* [_jdaviz_](https://jdaviz.readthedocs.io/en/latest/) : Cubeviz data visualization tool\n",
    "* [_astropy.io_](https://docs.astropy.org/en/stable/io/fits/index.html) for reading and writing FITS cubes and images\n",
    "* [_astropy.utils_](https://docs.astropy.org/en/stable/utils/index.html) for downloading files from URLs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from jdaviz import Cubeviz\n",
    "from astropy.io import fits\n",
    "from astropy.utils.data import download_file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize a simulated MIRI MRS data cube\n",
    "\n",
    "* Load and display the data\n",
    "* Select a spectral region\n",
    "* Create moment maps\n",
    "\n",
    "Execute the next cell to launch Cubeviz, then follow the instructions for each task enumerated in the cell directly below the Cubeviz app."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "cubeviz = Cubeviz()\n",
    "cubeviz.app"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### UI Instructions:\n",
    "#### Task 1:  Load the cube and view it\n",
    "* Load the MIRI MRS datacube into Cubeviz using the next code cell below\n",
    "* Open the Display menu \n",
    "* In the Layer tab, change the stretch to Logarithmic, 95 percentile to see the target PSF wings.\n",
    "* Scrub through the cube using the Slice slider.\n",
    "\n",
    "#### Task 2: Select a spectral region for further analysis\n",
    "* Select 'No selection (create new)' in the Subsets menu in the Cubeviz top banner.\n",
    "* Select a spectral subset region in spectrum viewer, using the region selection tool under the Tools icon, centered on a spectral feature of interest (e.g., the 10.5 micron PAH feature)\n",
    "\n",
    "#### Task 3: Extract an image of a spectral feature using the Moment Maps plugin\n",
    "* Find the Moment Maps data analysis Plugin by clicking the 'Lego' icon at upper right.\n",
    "* Select a dataset with the Data dropdown (e.g. SCI extension of our cube).\n",
    "* Select a spectral region in the Spectral Region dropdown (e.g. Subset 1).\n",
    "* Enter the Moment (0 for flux, 1 for centroid, 2 for dispersion).\n",
    "* Press 'Calculate' \n",
    "* Use the 2nd cube/image viewer to display the moment 0 image. Click the \"Data\" button, deselect the 'ERR' extension checkbox, and select the 'Moment' dataset that was generated by the previous step. \n",
    "* Adjust the Stretch in the viewer and change the colormap to inferno\n",
    "\n",
    "#### Task 4: Model the continuum + broad dust features (PAHs) \n",
    "* Open the Model Fitting Plugin and resize the tray to make the model parameters readable\n",
    "* Select the dataset (SCI extension of our cube)\n",
    "* Create 3 model components: Linear Model L, Gaussian Model G1, and Gaussian Model G2, with the following starting parameters: \n",
    "L: Leave starting parameter guess as is    \n",
    "G1: ampl = 3.5E5 MJy/sr, stddev = 5e-8 m, mean = 1.05E-5 m = fixed  (10.5 um)\n",
    "G2: ampl = 1.5E6 MJy/sr, stddev = 1e-7 m = fixed, mean = 1.126E-5 m = fixed (11.25 um)\n",
    "* Enter the model to fit in the Model Equation Editor: L + G1 + G2\n",
    "* Enter \"Model\" as the Model Label\n",
    "* Press Fit\n",
    "* Press Apply to Cube\n",
    "* Deselect all data in cube viewer 2, then select Model [Cube] to display the modeled continuum + PAH cube\n",
    "* Scrub through the Model cube\n",
    "\n",
    "#### Task 5: Subtract the continuum + PAH model cube from the data cube \n",
    "* Run the continuum subtraction cell below, which reads in the science data, gets the model cube from the middle viewer, subtracts the continuum, then loads the continuum-subtracted cube into Cubeviz\n",
    "* The continuum-subtracted spectrum appears in the spectrum viewer on loading.\n",
    "\n",
    "#### Task 6: Extract a velocity map from the continuum-subtracted data using the Moment Maps plugin\n",
    "* Open the Moment Maps Plugin\n",
    "* Select the continuum-subtracted dataset (Unknown HDU Object [Sci])\n",
    "* Follow the procedure for Task 3; this time for Moment 1\n",
    "* Use the 3rd cube/image viewer to display the Moment 1 image\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load Science Datacube into Cubeviz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#filename = \"l3_ch2-long_s3d.fits\"\n",
    "filename = \"https://stsci.box.com/shared/static/ezl49sugxn379wbo4tveuromnde8e6lv.fits\"\n",
    "miricube_file = download_file(filename)\n",
    "cubeviz.app.load_data(miricube_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Continuum Subtraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "# Open and inspect the science data with astropy.fits.open\n",
    "with fits.open(miricube_file, memmap=False) as miricube:\n",
    "    miricube.info()\n",
    "    sci = miricube['SCI'].data\n",
    "    #Retrieve the continuum + PAH model cube from middle cube viewer in Cubeviz\n",
    "    modeled_cube = cubeviz.app.get_data_from_viewer(\"uncert-viewer\", \"Model [Cube] 1\")\n",
    "    #Inspect the data dictionary and retrieve the continuum model flux cube\n",
    "    print(modeled_cube)\n",
    "    model_flux = modeled_cube[\"flux\"]\n",
    "    #Subtract the continuum model from the science data\n",
    "    sci_contsub = sci-model_flux\n",
    "    #Load the continuum subtracted data back into Cubeviz\n",
    "    miricube['SCI'].data = sci_contsub\n",
    "    cubeviz.app.load_data(miricube)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Inspect the continuum model parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#c_model = cubeviz.get_models(model_label=\"Model1\")\n",
    "#print(c_model)\n",
    "#print(c_model[\"slope_0\"])\n",
    "cubeviz.get_models()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## NIRSpec IFU"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cubeviz2 = Cubeviz()\n",
    "cubeviz2.app"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Download the cube data from Box\n",
    "filename = \"https://stsci.box.com/shared/static/ff0bj31acot1272x5qq2clbmto3s6v4f.fits\"\n",
    "ifucube_file = download_file(filename, cache=True)\n",
    "cubeviz2.app.load_data(ifucube_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## MANGA IFU"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "cubeviz3 = Cubeviz()\n",
    "cubeviz3.app"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fn = download_file('https://stsci.box.com/shared/static/28a88k1qfipo4yxc4p4d40v4axtlal8y.fits', cache=True)\n",
    "cubeviz3.load_data(fn)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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