SDSS DR16 FITS Spectra Analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": [
      "\nDone!\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import random\n",
    "import matplotlib.pyplot as plt\n",
    "import os\n",
    "import glob\n",
    "from astropy.table import Table\n",
    "from astropy.io import fits\n",
    "from os import listdir\n",
    "from glob import glob\n",
    "from os import getcwd, chdir\n",
    "\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "\n",
    "\n",
    "print(\"\\nDone!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "t = \"\"\"\n",
    "ImportError: \n",
    "The plotly.plotly module is deprecated,\n",
    "please install the chart-studio package and use the\n",
    "chart_studio.plotly module instead. \n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def list_files(directory, extension):\n",
    "    saved = getcwd()\n",
    "    chdir(directory)\n",
    "    it = glob('*.' + extension)\n",
    "    chdir(saved)\n",
    "    return it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": [
      "Number of files: 20\n"
     ]
    },
    {
     "output_type": "display_data",
     "data": {
      "text/plain": "<Figure size 432x288 with 0 Axes>"
     },
     "metadata": {}
    }
   ],
   "source": [
    "\n",
    "targetdir = \"/Users/josephkarpinski/Downloads\"\n",
    "\n",
    "\n",
    "selected_files = list_files(targetdir + '/eBOSS FITS New Test', 'fits')\n",
    "\n",
    "selected_file = int(len(selected_files))\n",
    "print(\"Number of files: \" + str(selected_file))\n",
    "\n",
    "os.system('ulimit -n 50000')\n",
    "os.system('ulimit -a')\n",
    "\n",
    "fig = plt.figure(facecolor='white')\n",
    "\n",
    "fig_size = plt.rcParams[\"figure.figsize\"]\n",
    "fig_size[0] = 15\n",
    "fig_size[1] = 9\n",
    "plt.rcParams[\"figure.figsize\"] = fig_size\n",
    "\n",
    "yInit = 0\n",
    "modelWavelengthShift = 0\n",
    "\n",
    "yRange = 0\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": [
      "Done\n"
     ]
    }
   ],
   "source": [
    "for x in range(0, selected_file):\n",
    "    #table = Table.read('/Users/josephkarpinski/Downloads/eBOSS FITS New Test/' + selected_files[x], hdu=1)\n",
    "    table = Table.read(targetdir + '/eBOSS FITS New Test/' + selected_files[x], hdu=1)\n",
    "    df0 = table.to_pandas() \n",
    "    \n",
    "    #hdulist = fits.open('/Users/josephkarpinski/Downloads/eBOSS FITS New Test/' + selected_files[x])\n",
    "    hdulist = fits.open(targetdir + '/eBOSS FITS New Test/' + selected_files[x])\n",
    "    hdu2 = hdulist[2].data\n",
    "    \n",
    "    wl = np.power(10, df0[\"LOGLAM\"])\n",
    "    flux = df0['MODEL']\n",
    "    \n",
    "    tbl =np.column_stack((wl, flux))\n",
    "    df = pd.DataFrame(tbl, columns=['wl', 'flux'])\n",
    "\n",
    "    \n",
    "    peak = 0\n",
    "    \n",
    "    peak = wl[flux.argmax()]\n",
    "    teffCalc = 2.898 / peak * 10000000\n",
    "\n",
    "     # create line plot\n",
    "    plt.plot(df['wl'].astype(int),df['flux'].astype(float), color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "    \n",
    "    \n",
    "    plt.grid()\n",
    "    \n",
    "    df2 = df[df['wl'].between(3833, 9200)]\n",
    "\n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[3839,  yRange * 0.8], s='CN 3839', rotation=-90)\n",
    "    plt.annotate(xy=[3889, yRange * .20], s='H-zeta 3889', rotation=-90)\n",
    "    plt.annotate(xy=[3970, yRange * 0.8], s='H-epsilon 3970', rotation=-90)\n",
    "    plt.annotate(xy=[4101, yRange * .20], s='H-delta 4101', rotation=-90)\n",
    "    plt.annotate(xy=[4340, yRange * .20], s='H-gamma 4340', rotation=-90)\n",
    "    plt.annotate(xy=[4472, yRange * .20], s='He I 4471.7', rotation=-90)\n",
    "    plt.annotate(xy=[4861, yRange * .20], s='H-beta 4861', rotation=-90)\n",
    "    plt.annotate(xy=[5175, yRange * .20], s='Mg I 5175', rotation=-90)\n",
    "    plt.annotate(xy=[5270, yRange * .20], s='Fe I 5270', rotation=-90)\n",
    "    plt.annotate(xy=[5411, yRange * .20], s='He II 5411', rotation=-90)\n",
    "    plt.annotate(xy=[5755, yRange * .20], s='N II 5755', rotation=-90)\n",
    "    plt.annotate(xy=[5895, yRange * .20], s='D1 Na I 5895', rotation=-90)\n",
    "    plt.annotate(xy=[6302, yRange * .20], s='OI 6302', rotation=-90)\n",
    "    plt.annotate(xy=[6365, yRange * .20], s='OI 6365.5', rotation=-90)\n",
    "    plt.annotate(xy=[6562, yRange * .20], s='H-alpha 6562', rotation=-90)\n",
    "    plt.annotate(xy=[6890, yRange * .20], s='CN 6890', rotation=-90)\n",
    "    plt.annotate(xy=[7135, yRange * .20], s='Ar III 7135', rotation=-90)\n",
    "    plt.annotate(xy=[7775, yRange * .20], s='O I 7775', rotation=-90)\n",
    "    plt.annotate(xy=[8498, yRange * .25], s='Ca II 8498', rotation=-90)\n",
    "    plt.annotate(xy=[8542, yRange * .20], s='Ca II 8542', rotation=-90)\n",
    "    plt.annotate(xy=[8662, yRange * .20], s='Ca II 8662.1', rotation=-90)\n",
    "\n",
    "    plt.xlim(xmin=3833, xmax=9200)\n",
    "\n",
    "    plt.xticks([3839, 3889, 3970, 4101, 4340, 4472, 4861, 5175, 5270, 5411, 5755, 5895, 6302,\n",
    "               6365, 6562, 6562, 6890, 7135, 7500, 7775, 8000, 8498, 8542, 8662, 9000, 9200])\n",
    "    \n",
    "    xLabels = (3839, 3889, 3970, 4101, 4340, 4472, 4861, 5175, 5270, 5411, 5755, 5895, 6302,\n",
    "               6365, 6562, 6562, 6890, 7135, 7500, 7775, 8000, 8498, 8542, 8662, 9000, 9200)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate 3833A-9200A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "\n",
    "    #plt.show()\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "    \n",
    "    \n",
    "    \n",
    "    #####################################################################################################\n",
    "    \n",
    "    \n",
    "    # Filter u\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    plt.xticks([3835, 3889, 3934, 3968, 4000])\n",
    "    xLabels =     (3835, 3889, 3934, 3968, 4000)\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(3833, 4000)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "    \n",
    "    plt.annotate(xy=[3835, yRange * .20], s='H9-eta 3835', rotation=-90)\n",
    "    plt.annotate(xy=[3889, yRange * .20], s='H8-zeta 3889', rotation=-90)\n",
    "    plt.annotate(xy=[3934,yRange * .20], s='K Ca II 3933.6', rotation=-90)\n",
    "    plt.annotate(xy=[3968,yRange * .20], s='H Ca II 3968', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=3833, xmax=4000)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter U 3833A-4000A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all') \n",
    "    \n",
    "    #####################################################################################################\n",
    "    \n",
    "     # Filter g-1\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    plt.xticks([4006, 4026, 4031, 4046, 4064, 4077, 4101, 4132, 4142, 4152, 4172, 4202, 4226, 4246, \n",
    "                   4266, 4286, 4305, 4340, 4364, 4380, 4394, 4404, 4414, 4424, 4434, 4444, 4454, 4464, \n",
    "                   4471, 4486, 4500])\n",
    "    xLabels =     (4006, 4026, 4031, 4046, 4064, 4077, 4101, 4132, 4142, 4152, 4172, 4202, 4226, 4246,\n",
    "                   4266, 4286, 4305, 4340, 4364, 4380, 4394, 4404, 4414, 4424, 4434, 4444, 4454, 4464, \n",
    "                   4471, 4486, 4500)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90) \n",
    "    \n",
    "    df2 = df[df['wl'].between(4000, 4500)]\n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "    \n",
    "    plt.annotate(xy=[4026,yRange * .20], s='He I 4026', rotation=-90)\n",
    "    plt.annotate(xy=[4031,yRange * .45], s='Mn I 4031-36', rotation=-90)\n",
    "    plt.annotate(xy=[4077,yRange * .20], s='Sr II 4077', rotation=-90)\n",
    "    plt.annotate(xy=[4101,yRange * .20], s='H-delta 4101', rotation=-90)\n",
    "    plt.annotate(xy=[4172,yRange * .45], s='FeII/TiII 4172-73', rotation=-90)\n",
    "    plt.annotate(xy=[4226,yRange * .20], s='Ca I 4226', rotation=-90)\n",
    "    plt.annotate(xy=[4305,yRange * .45], s='G 4229-4313', rotation=-90)\n",
    "    plt.annotate(xy=[4340,yRange * .20], s='H-gamma 4340', rotation=-90)\n",
    "    plt.annotate(xy=[4364,yRange * .20], s='O III 4364', rotation=-90)\n",
    "    plt.annotate(xy=[4471,yRange * .20], s='He I 4471', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=4000, xmax=4500)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter G1 4000A-4500A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "\n",
    "\n",
    "    #####################################################################################################\n",
    "    # Filter g-2\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    \n",
    "    plt.xticks([4520, 4550, 4554, 4585, 4666, 4708, 4754, 4863, 4923, 4957, 4983])\n",
    "    xLabels =     (4520, 4550, 4554, 4585, 4666, 4708, 4754, 4863, 4923, 4957, 4983)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(4500, 5000)]\n",
    "\n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[4520,yRange * .45], s='FeI/TiII 4520-34', rotation=-90)\n",
    "    plt.annotate(xy=[4550,yRange * .45], s='Ti II 4550-56', rotation=-90)\n",
    "    plt.annotate(xy=[4554,yRange * .20], s='Ba 4554', rotation=-90)\n",
    "    plt.annotate(xy=[4585,yRange * .45], s='FeII/CrII 4585-88', rotation=-90)\n",
    "    plt.annotate(xy=[4666,yRange * .45], s='FeII/ScII 4666-70', rotation=-90)\n",
    "    plt.annotate(xy=[4708,yRange * .20], s='Ti II 4708', rotation=-90)\n",
    "    plt.annotate(xy=[4754,yRange * .20], s='Mn I 4754', rotation=-90)\n",
    "    plt.annotate(xy=[4863,yRange * .20], s='H-beta 4863', rotation=-90)\n",
    "    plt.annotate(xy=[4923,yRange * .20], s='Fe II 4923', rotation=-90)\n",
    "    plt.annotate(xy=[4957,yRange * .20], s='Fe I 4957', rotation=-90)\n",
    "    plt.annotate(xy=[4983,yRange * .20], s='Fe I 4983', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=4500, xmax=5000)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax)\n",
    "    \n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter G2 4500A-5000A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "    \n",
    "\n",
    "    #####################################################################################################\n",
    "    \n",
    "\n",
    "     # Filter r-1\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "\n",
    "    plt.xticks([5018, 5041, 5079, 5167, 5176,5183, 5210, 5227, 5270, 5328, 5404, 5500])\n",
    "    xLabels =     (5018, 5041, 5079, 5167, 5176,5183, 5210, 5227, 5270, 5328, 5404, 5500)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(5000, 5500)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[5018,yRange * .20], s='Fe II 5018', rotation=-90)\n",
    "    plt.annotate(xy=[5041,yRange * .20], s='Fe I 5041', rotation=-90)\n",
    "    plt.annotate(xy=[5079,yRange * .35], s='FeI/NiI 5079-81', rotation=-90)\n",
    "    plt.annotate(xy=[5167,yRange * .20], s='Mg I 5167', rotation=-90)\n",
    "    plt.annotate(xy=[5176,yRange * .35], s='Mg 5176', rotation=-90)\n",
    "    plt.annotate(xy=[5183,yRange * .20], s='Mg I 5183', rotation=-90)\n",
    "    plt.annotate(xy=[5210,yRange * .20], s='MgH 5210', rotation=-90)\n",
    "    plt.annotate(xy=[5227,yRange * .35], s='FeI/TiII 5227', rotation=-90)\n",
    "    plt.annotate(xy=[5270,yRange * .20], s='FeI/CaI 5270', rotation=-90)\n",
    "    plt.annotate(xy=[5328,yRange * .20], s='Fe I 5328', rotation=-90)\n",
    "    plt.annotate(xy=[5404,yRange * .20], s='Fe I 5404', rotation=-90)\n",
    "    \n",
    "    \n",
    "    plt.xlim(xmin=5000, xmax=5500)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter R1 5000A-5500A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "\n",
    "\n",
    "    #####################################################################################################\n",
    "    \n",
    "     # Filter r-2\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    \n",
    "    plt.xticks([5500, 5587, 5597, 5668, 5700, 5760, 5814, 5847, 5889, 5895, 5968, 5998, \n",
    "                   6159, 6180, 6200, 6268,6358, 6365, 6384, 6386, 6478, 6500])\n",
    "    xLabels =     (5500, 5587, 5597, 5668, 5700, 5760, 5814, 5847, 5889, 5895, 5968, 5998, \n",
    "                   6159, 6180, 6200, 6268,6358, 6365, 6384, 6386, 6478, 6500)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(5500, 6500)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[5587,yRange * .35], s='CaI/FeI 5587-90', rotation=-90)\n",
    "    plt.annotate(xy=[5597,yRange * .10], s='TiO 5597-03', rotation=-90)\n",
    "    plt.annotate(xy=[5668,yRange * .20], s='TiO 5668', rotation=-90)\n",
    "    plt.annotate(xy=[5760,yRange * .20], s='TiO 5760', rotation=-90)\n",
    "    plt.annotate(xy=[5814,yRange * .20], s='TiO 5814', rotation=-90)\n",
    "    plt.annotate(xy=[5847,yRange * .20], s='TiO 5847', rotation=-90)\n",
    "    plt.annotate(xy=[5889,yRange * .20], s='Na I 5889', rotation=-90)\n",
    "    plt.annotate(xy=[5895,yRange * .35], s='Na I 5895', rotation=-90)\n",
    "    plt.annotate(xy=[5968,yRange * .20], s='TiO 5968', rotation=-90)\n",
    "    plt.annotate(xy=[5998,yRange * .20], s='TiO 5998', rotation=-90)\n",
    "    plt.annotate(xy=[6159,yRange * .20], s='TiO 6159', rotation=-90)\n",
    "    plt.annotate(xy=[6180,yRange * .20], s='TiO 6180', rotation=-90)\n",
    "    plt.annotate(xy=[6268,yRange * .20], s='TiO 6268', rotation=-90)\n",
    "    plt.annotate(xy=[6358,yRange * .35], s='TiO 6358', rotation=-90)\n",
    "    plt.annotate(xy=[6365,yRange * .20], s='     OI 6365', rotation=-90)\n",
    "    plt.annotate(xy=[6384,yRange * .10], s='TiO 6384', rotation=-90)\n",
    "    plt.annotate(xy=[6386,yRange * .35], s='CaH1 6386.7', rotation=-90)\n",
    "    plt.annotate(xy=[6478,yRange * .20], s='TiO 6478', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=5500, xmax=6500)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "    \n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter R2 5500A-6500A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "\n",
    "\n",
    "    #####################################################################################################\n",
    "    \n",
    "     # Filter r-3\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    \n",
    "    plt.xticks([6500, 6548, 6563, 6569, 6585, 6651, 6678, 6681, 6715, 6730, 6782, 6788, 6815, \n",
    "                   6831, 6890, 6903, 6908, 6927, 6976])\n",
    "    xLabels =     (6500, 6548, 6563, 6569, 6585, 6651, 6678, 6681, 6715, 6730, 6782, 6788, 6815, \n",
    "                   6831, 6890, 6903, 6908, 6927, 6976)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(6500, 7000)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[6563,yRange * .35], s='H-alpha 6563', rotation=-90)\n",
    "    plt.annotate(xy=[6569,yRange * .15], s='TiO 6569', rotation=-90)\n",
    "    plt.annotate(xy=[6651,yRange * .20], s='TiO 6651', rotation=-90)\n",
    "    plt.annotate(xy=[6678,yRange * .35], s='He 6678', rotation=-90)\n",
    "    plt.annotate(xy=[6681,yRange * .20], s='TiO 6681', rotation=-90)\n",
    "    plt.annotate(xy=[6715,yRange * .20], s='TiO 6715', rotation=-90)\n",
    "    plt.annotate(xy=[6782,yRange * .20], s='TiO 6782', rotation=-90)\n",
    "    plt.annotate(xy=[6788,yRange * .35], s='CaH 6788', rotation=-90)\n",
    "    plt.annotate(xy=[6815,yRange * .20], s='TiO 6815', rotation=-90)\n",
    "    plt.annotate(xy=[6831,yRange * .35], s='CaH2 6831.9', rotation=-90)\n",
    "    plt.annotate(xy=[6890,yRange * .20], s='CN 6890', rotation=-90)\n",
    "    plt.annotate(xy=[6903,yRange * .20], s='CaH 6903', rotation=-90)\n",
    "    plt.annotate(xy=[6908,yRange * .35], s='CaH 6908', rotation=-90)\n",
    "    plt.annotate(xy=[6927,yRange * .20], s='CaH 6927', rotation=-90)\n",
    "    plt.annotate(xy=[6976,yRange * .35], s='CaH3 6976.9', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=6500, xmax=7000)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter R3 6500A-7000A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "\n",
    "\n",
    "    #####################################################################################################\n",
    "    \n",
    "    \n",
    "     # Filter i\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    \n",
    "    plt.xticks([7000, 7054, 7088, 7126, 7134, 7164, 7209, 7300, 7400, 7500, 7664, 7688, 7775, 7900, 8000])\n",
    "    xLabels =     (7000, 7054, 7088, 7126, 7134, 7164, 7209, 7300, 7400, 7500, 7664, 7688, 7775, 7900, 8000)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    df2 = df[df['wl'].between(7000, 8000)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "\n",
    "    plt.annotate(xy=[7054,yRange * .20], s='TiO 7054', rotation=-90)\n",
    "    plt.annotate(xy=[7088,yRange * .20], s='TiO 7088', rotation=-90)\n",
    "    plt.annotate(xy=[7126,yRange * .20], s='TiO 7126', rotation=-90)\n",
    "    plt.annotate(xy=[7134,yRange * .35], s='TiO5 7134', rotation=-90)\n",
    "    plt.annotate(xy=[7209,yRange * .20], s='TiO 7209', rotation=-90)\n",
    "    plt.annotate(xy=[7688,yRange * .20], s='K I 7688', rotation=-90)\n",
    "    plt.annotate(xy=[7775,yRange * .20], s='O I triplet 7775', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=7000, xmax=8000)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter I 7000A-8000A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "\n",
    "\n",
    "    #####################################################################################################\n",
    "    \n",
    "    \n",
    "     # Filter z\n",
    "    plt.plot(wl,flux, color='r')\n",
    "    plt.ylabel(\"flux (1e-17 erg/s/cm$^2$/Angstrom\")\n",
    "    plt.xlabel(\"wavelength (Angstroms)\")\n",
    "    \n",
    "    plt.title(str(hdu2['SUBCLASS']).strip('[\\]')+ \" Spectrum \"  + \"\\n\" + \n",
    "             \" Plate: \" + str(hdu2['PLATE']).strip(\"[\\]\") + \n",
    "             \" MJD: \" + str(hdu2['MJD']).strip(\"[\\]\") + \n",
    "             \" Fiber: \" + str(hdu2['FIBERID']).strip(\"[\\]\") + \"\\n\" +\n",
    "             \" Teff \" + str(hdu2['ELODIE_TEFF']).strip(\"[\\]\") +\n",
    "             \" FeH \" + str(hdu2['ELODIE_FEH']).strip(\"[\\]\") +\n",
    "             \" LogG \" + str(hdu2['ELODIE_LOGG']).strip(\"[\\]\")+ \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "        \n",
    "    \n",
    "    plt.xticks([8000, 8080, 8190, 8300, 8400, 8457, 8498, 8542,8598, 8662, 8751, 8860, 9010, \n",
    "                   9046, 9200])\n",
    "    xLabels =     (8000, 8080, 8190, 8300, 8400, 8457, 8498, 8542,8598, 8662, 8751, 8860, 9010, \n",
    "                   9046, 9200)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "\n",
    "    df2 = df[df['wl'].between(8000, 9000)]\n",
    "    \n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    yRangeMax = float(df2['flux'].max())\n",
    "    yRange = yRangeMax\n",
    "    \n",
    "    plt.annotate(xy=[8190, yRange * .20], s='NaI 8190.2', rotation=-90)\n",
    "    plt.annotate(xy=[8457, yRange * .20], s='TiO8 8457.3', rotation=-90)\n",
    "    plt.annotate(xy=[8498, yRange * .20], s='CaII 8498.5', rotation=-90)\n",
    "    plt.annotate(xy=[8542, yRange * .20], s='CaII 8542', rotation=-90)\n",
    "    plt.annotate(xy=[8598, yRange * .20], s='Paschen 8598', rotation=-90)\n",
    "    plt.annotate(xy=[8662, yRange * .20], s='CaII 8662', rotation=-90)\n",
    "    plt.annotate(xy=[8751, yRange * .20], s='Paschen 8751', rotation=-90)\n",
    "    #plt.annotate(xy=[10049, yRange * .20], s='Paschen 10049', rotation=-90)\n",
    "    \n",
    "    plt.xlim(xmin=8000, xmax=9200)\n",
    "    plt.ylim(ymin=0, ymax=yRangeMax) \n",
    "    \n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    plt.savefig(targetdir + '/Prefixed By Plate Filter Z 8000A-9200A/' + selected_files[x][0:20] +  '.png',\n",
    "        facecolor=fig.get_facecolor(), edgecolor='none')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "    \n",
    "print(\"Done\")\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "\n",
    "    \n",
    "    "
   ]
  }
 ],
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