{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# PISCES Data Reduction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The data reduction pipeline for PISCES is kept as simple as possible for easing integration with JPL's coronagraph control software. It requires an existing wavelength calibration."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "codefolder = '../../../../crispy' # this is the path to the entire repo (that contains crispy, docs, notebooks)\n",
    "if codefolder not in sys.path: sys.path.append(codefolder)\n",
    "from crispy.PISCESparams import Params\n",
    "par = Params('../../../crispy')\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is simple: load the reduction function, and call it!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "../../../crispy/ReferenceFiles/Calibra_170306/IFS665nm.fits\n",
      "crispy - INFO - Read data from HDU 0 of ../../../crispy/ReferenceFiles/Calibra_170306/IFS665nm.fits\n",
      "crispy - INFO - Read data from HDU 0 of ../../../crispy/ReferenceFiles/Calibra_170306/IFSdark665nm.fits\n",
      "crispy - INFO - Writing data to ../../../crispy/SimResults/test_varia.fits\n",
      "crispy - INFO - Read data from HDU 1 of ../../../crispy/SimResults/test_varia.fits\n",
      "crispy - INFO - Reduced cube will have 26 wavelength bins\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: AstropyDeprecationWarning: \"clobber\" was deprecated in version 1.3 and will be removed in a future version. Use argument \"overwrite\" instead. [astropy.utils.decorators]\n",
      "/Users/mrizzo/anaconda/lib/python2.7/site-packages/numpy/lib/nanfunctions.py:703: RuntimeWarning: Mean of empty slice\n",
      "  warnings.warn(\"Mean of empty slice\", RuntimeWarning)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "crispy - INFO - Writing data to ../../../crispy/SimResults/test_varia_red_optext.fits\n",
      "crispy - INFO - Elapsed time: 18.090558s\n"
     ]
    }
   ],
   "source": [
    "import glob\n",
    "# call the reduction routine with an example image\n",
    "VARIA_ON= glob.glob(par.wavecalDir+'IFS665nm.fits')\n",
    "VARIA_OFF= glob.glob(par.wavecalDir+'IFSdark665nm.fits')\n",
    "print(VARIA_ON[0])\n",
    "from crispy.IFS import reduceIFSMap\n",
    "from crispy.tools.image import Image\n",
    "test_img = Image(data = (Image(VARIA_ON[0]).data - Image(VARIA_OFF[0]).data)).write(par.exportDir+'/test_varia.fits')\n",
    "reduced_cube= reduceIFSMap(par,par.exportDir+'/test_varia.fits')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The wavelengths of the cube slices are the following:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "crispy - INFO - Reduced cube will have 26 wavelength bins\n",
      "('Wavelengths at midpoints (nm): ', array([ 607.10887147,  611.34869295,  615.61812376,  619.91737068,\n",
      "        624.24664194,  628.6061472 ,  632.99609763,  637.41670582,\n",
      "        641.86818589,  646.35075344,  650.86462556,  655.41002088,\n",
      "        659.98715953,  664.59626322,  669.23755516,  673.91126015,\n",
      "        678.61760456,  683.35681631,  688.12912494,  692.9347616 ,\n",
      "        697.77395902,  702.64695159,  707.55397533,  712.49526788,\n",
      "        717.47106857,  722.48161839]))\n",
      "('Wavelengths at endpoints (nm): ', array([ 605.        ,  609.22509391,  613.4796943 ,  617.76400723,\n",
      "        622.0782402 ,  626.42260216,  630.79730352,  635.20255616,\n",
      "        639.63857343,  644.1055702 ,  648.6037628 ,  653.13336909,\n",
      "        657.69460847,  662.28770183,  666.91287165,  671.57034192,\n",
      "        676.26033822,  680.9830877 ,  685.73881911,  690.52776276,\n",
      "        695.3501506 ,  700.2062162 ,  705.09619475,  710.02032308,\n",
      "        714.97883968,  719.97198471,  725.        ]))\n"
     ]
    }
   ],
   "source": [
    "from crispy.tools.reduction import calculateWaveList\n",
    "lam_midpts,lam_endpts = calculateWaveList(par)\n",
    "print('Wavelengths at midpoints (nm): ',lam_midpts)\n",
    "print('Wavelengths at endpoints (nm): ',lam_endpts)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The files are exported in the folder par.exportDir. Look for the introduction documentation page for more details."
   ]
  }
 ],
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