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   "metadata": {},
   "source": [
    "# 1. Data Preparation for Gauss Hermite kinematics\n",
    "\n",
    "This notebook shows how to prepare input kinematic data files from Gauss-Hermite files from the CALIFA and ATLAS-3D surveys.\n",
    "\n",
    "It uses the example script for data preparation ``dynamite/data_prep/generate_kin_input.py`` which works for 4 Gauss-Hermite coefficients out of the box and hence would need to be modified for a different number of coefficients. Also, in case of CALIFA data, the script's ``read_califa(file)`` method forces the errors to fulfil ``dvel ≥ 1``, ``dsig ≥ 1``, ``dh3 ≥ 0.005``, and ``dh4 ≥ 0.005`` and corrects negative sigma values.\n",
    "\n",
    "Run this notebook from the directory ``docs/tutorial_notebooks``.\n",
    "\n",
    "First, import some modules..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2618f546",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import dynamite as dyn"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ecbd021c",
   "metadata": {},
   "source": [
    "## CALIFA \n",
    "\n",
    "Example galaxy: **NGC 6278**. A Schwarzschild model for this galaxy can be found in [Zhu et al. (2018)](https://ui.adsabs.harvard.edu/abs/2018MNRAS.473.3000Z/abstract)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "specified-george",
   "metadata": {},
   "outputs": [],
   "source": [
    "from dynamite.data_prep.generate_kin_input import create_kin_input\n",
    "\n",
    "# Input directory\n",
    "in_dir = 'NGC6278_input/'\n",
    "\n",
    "# The CALIFA stellar kinematic file for NGC 6278 can be found here:\n",
    "in_file = 'NGC6278_input/NGC6278.V1200.rscube_INDOUSv2_SN20_stellar_kin.fits'\n",
    "\n",
    "# The output will be placed here:\n",
    "out_dir = 'NGC6278_input/dynamite_input/'\n",
    "if not os.path.exists(out_dir):\n",
    "    os.makedirs(out_dir)\n",
    "\n",
    "# Convert file to ECSV, fit the kinematic PA,\n",
    "# write aperture.dat and bins.dat files\n",
    "create_kin_input('NGC6278', in_file, out_dir, expr='', \n",
    "                 fit_PA=True, kin_input='CALIFA')\n",
    "\n",
    "# Add the PSF to the header of the kinematic file\n",
    "gh = dyn.kinematics.GaussHermite()\n",
    "gh.add_psf_to_datafile(sigma=[1.06], weight=[1.0],\n",
    "                       datafile=f'{out_dir}/gauss_hermite_kins.ecsv')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "efficient-prairie",
   "metadata": {},
   "source": [
    "The directory `NGC6278_input/dynamite_input` should now contain the following files:\n",
    "\n",
    "- `mge.ecsv` (this file was already present)\n",
    "- `gauss_hermite_kins.ecsv` \n",
    "- `aperture.dat`            \n",
    "- `bins.dat`\n",
    "\n",
    "together with some diagnostic plots. These files are the complete input needed to run DYNAMITE!"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5c1456c8",
   "metadata": {},
   "source": [
    "## ATLAS 3D \n",
    "\n",
    "Example galaxy: **NGC 4570**. Schwarzschild models for this galaxy can be found in [Thater et al. (2019)](https://ui.adsabs.harvard.edu/abs/2019A%26A...625A..62T/abstract)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "blind-hospital",
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "from dynamite.data_prep.generate_kin_input import create_kin_input\n",
    "\n",
    "# Input directory\n",
    "in_dir = 'NGC4570_input/'\n",
    "\n",
    "# For ATLAS3D data, two input/files are needed: the original cube and \n",
    "# the kinematics cube. They can be found here:\n",
    "in_files =[in_dir+'MS_NGC4570_r1_C2D.fits',\n",
    "           in_dir+'NGC4570_4moments_ATLAS3d.fits']\n",
    "\n",
    "# The output will be placed here:\n",
    "out_dir = 'NGC4570_input/dynamite_input/'\n",
    "if not os.path.exists(out_dir):\n",
    "    os.makedirs(out_dir)\n",
    "\n",
    "# Convert file to ECSV, fit the kinematic PA, \n",
    "# write aperture.dat and bins.dat files\n",
    "create_kin_input('NGC4570', in_files, out_dir, expr='',\n",
    "                 fit_PA=True, kin_input='ATLAS3D', ngh=6)\n",
    "\n",
    "# Add the PSF to the header of the kinematic file\n",
    "gh = dyn.kinematics.GaussHermite()\n",
    "gh.add_psf_to_datafile(sigma=[1.5], weight=[1.0],\n",
    "                       datafile=f'{out_dir}/gauss_hermite_kins.ecsv')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "electric-tracy",
   "metadata": {},
   "source": [
    "The directory `NGC4570_input/dynamite_input` should now contain the following files:\n",
    "\n",
    "- `gauss_hermite_kins.ecsv`\n",
    "- `aperture.dat`            \n",
    "- `bins.dat`\n",
    "\n",
    "together with some diagnostic plots. These files are your kinematic input for DYNAMITE. In addition, you will only need a file containing a Multi Gaussian Expansion (MGE) describing the stellar surface density of the galaxy."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db060fcb",
   "metadata": {},
   "source": [
    "## Preparing other Gauss Hermite data files \n",
    "\n",
    "To prepare DYNAMITE input from other surveys, or from your own fits, we recommend looking at the functions defined in `dynamite/data_prep/generate_kin_input.py` and adjusting them to your needs.\n",
    "\n",
    "The file `aperture.dat` contains the spatial extent in arcseconds, the angle (in degrees) `90 - position_angle`, and the size of the grid in pixels:\n",
    "\n",
    "```\n",
    "    #counter_rotation_boxed_aperturefile_version_2\n",
    "          min_x   min_y\n",
    "          max_x   max_y\n",
    "          90.-position_angle\n",
    "          npix_x  n_pix_y\n",
    "```     \n",
    "\n",
    "The file `bins.dat` encodes the spatial (e.g. Voronoi) binning: specifically, it has one header line with the total number of pixels in the grid, followed by the bin ID of each pixel in the grid."
   ]
  }
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