MaStar Filter MaNGAID Equivalent Width Alpha Line.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://www.sdss.org/dr15/mastar/mastar-tutorials/\n",
    "\n",
    "https://dr15.sdss.org/sas/dr15/manga/spectro/mastar/v2_4_3/v1_0_2/\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "output_type": "error",
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/PIL/ImageFile.py\u001b[0m in \u001b[0;36m_save\u001b[0;34m(im, fp, tile, bufsize)\u001b[0m\n\u001b[1;32m    499\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 500\u001b[0;31m         \u001b[0mfh\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfileno\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    501\u001b[0m         \u001b[0mfp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflush\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: '_idat' object has no attribute 'fileno'",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-2-d49ba2f6285b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m    175\u001b[0m     \u001b[0mplt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxticks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mxLabels\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrotation\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m90\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    176\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 177\u001b[0;31m     plt.savefig('/Users/josephkarpinski/Downloads/MaStar 6563A Halpha Calc/' + 'Slope[' + str(round(slope, 2)) + ']_'  + \n\u001b[0m\u001b[1;32m    178\u001b[0m                 \u001b[0;34m'Idx['\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m']_'\u001b[0m \u001b[0;34m+\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    179\u001b[0m                 \u001b[0;34m'MaNGAID['\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmangaid\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m']'\u001b[0m \u001b[0;34m+\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py\u001b[0m in \u001b[0;36msavefig\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    935\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msavefig\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    936\u001b[0m     \u001b[0mfig\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgcf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 937\u001b[0;31m     \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msavefig\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    938\u001b[0m     \u001b[0mfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcanvas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdraw_idle\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m   \u001b[0;31m# need this if 'transparent=True' to reset colors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    939\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/figure.py\u001b[0m in \u001b[0;36msavefig\u001b[0;34m(self, fname, transparent, **kwargs)\u001b[0m\n\u001b[1;32m   2960\u001b[0m                 \u001b[0mpatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_edgecolor\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'none'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2961\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2962\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcanvas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprint_figure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2963\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2964\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mtransparent\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/backend_bases.py\u001b[0m in \u001b[0;36mprint_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m   2253\u001b[0m                 \u001b[0;31m# force the figure dpi to 72), so we need to set it again here.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2254\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mcbook\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setattr_cm\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfigure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdpi\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdpi\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2255\u001b[0;31m                     result = print_method(\n\u001b[0m\u001b[1;32m   2256\u001b[0m                         \u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2257\u001b[0m                         \u001b[0mfacecolor\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfacecolor\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/backend_bases.py\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m   1667\u001b[0m             \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1668\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1669\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1670\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1671\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mwrapper\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py\u001b[0m in \u001b[0;36mprint_png\u001b[0;34m(self, filename_or_obj, metadata, pil_kwargs, *args)\u001b[0m\n\u001b[1;32m    507\u001b[0m         \"\"\"\n\u001b[1;32m    508\u001b[0m         \u001b[0mFigureCanvasAgg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 509\u001b[0;31m         mpl.image.imsave(\n\u001b[0m\u001b[1;32m    510\u001b[0m             \u001b[0mfilename_or_obj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuffer_rgba\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"png\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0morigin\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"upper\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    511\u001b[0m             dpi=self.figure.dpi, metadata=metadata, pil_kwargs=pil_kwargs)\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/matplotlib/image.py\u001b[0m in \u001b[0;36mimsave\u001b[0;34m(fname, arr, vmin, vmax, cmap, format, origin, dpi, metadata, pil_kwargs)\u001b[0m\n\u001b[1;32m   1614\u001b[0m         \u001b[0mpil_kwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetdefault\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"format\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1615\u001b[0m         \u001b[0mpil_kwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetdefault\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"dpi\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mdpi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdpi\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1616\u001b[0;31m         \u001b[0mimage\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mpil_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1617\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1618\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/PIL/Image.py\u001b[0m in \u001b[0;36msave\u001b[0;34m(self, fp, format, **params)\u001b[0m\n\u001b[1;32m   2170\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2171\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2172\u001b[0;31m             \u001b[0msave_handler\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2173\u001b[0m         \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2174\u001b[0m             \u001b[0;31m# do what we can to clean up\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/PIL/PngImagePlugin.py\u001b[0m in \u001b[0;36m_save\u001b[0;34m(im, fp, filename, chunk, save_all)\u001b[0m\n\u001b[1;32m   1333\u001b[0m         \u001b[0m_write_multiple_frames\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mim\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrawmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1334\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1335\u001b[0;31m         \u001b[0mImageFile\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_save\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mim\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_idat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"zip\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mim\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrawmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1336\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1337\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0minfo\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/PIL/ImageFile.py\u001b[0m in \u001b[0;36m_save\u001b[0;34m(im, fp, tile, bufsize)\u001b[0m\n\u001b[1;32m    512\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    513\u001b[0m                 \u001b[0;32mwhile\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 514\u001b[0;31m                     \u001b[0ml\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0md\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mencode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbufsize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    515\u001b[0m                     \u001b[0mfp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    516\u001b[0m                     \u001b[0;32mif\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "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",
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "\n",
    "os.system('ulimit -n 50000')\n",
    "os.system('ulimit -a')\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",
    "goodspec = fits.open(\"/Users/josephkarpinski/Downloads/mastar-goodspec-v2_4_3-v1_0_2.fits\")[1].data\n",
    "mastarall = fits.open('/Users/josephkarpinski/Downloads/mastarall-v2_4_3-v1_0_2.fits')\n",
    "\n",
    "ksel = np.logical_and(mastarall[1].data[\"INPUT_TEFF\"] >= -9999 , mastarall[1].data[\"INPUT_TEFF\"] < 52000)\n",
    "kstars = mastarall[1].data[ksel]\n",
    "\n",
    "for x in range(0, 3326):\n",
    "#for x in range(0, 25):\n",
    "    visits = goodspec[\"MANGAID\"] == kstars[x][\"MANGAID\"]\n",
    "    wl = goodspec[visits][\"WAVE\"][0]\n",
    "    flux = goodspec[visits][\"FLUX\"][0]\n",
    "    \n",
    "    mangaid = kstars[x][\"MANGAID\"]\n",
    "    logG = kstars[x][\"INPUT_LOGG\"]\n",
    "    teff = kstars[x][\"INPUT_TEFF\"]\n",
    "    feh = kstars[x][\"INPUT_FE_H\"]\n",
    "    \n",
    "    tbl =np.column_stack((wl, flux))\n",
    "    df = pd.DataFrame(tbl, columns=['wl', 'flux'])\n",
    "    \n",
    "    peak = 0\n",
    "    \n",
    "    if teff > 0:\n",
    "        peak = 2.898 / teff * 10000000\n",
    "        teffCalc = 2.898 / peak * 10000000\n",
    "    else:\n",
    "        peak = wl[flux.argmax()]\n",
    "        teffCalc = 2.898 / peak * 10000000\n",
    " \n",
    "    plt.figure(facecolor='white')\n",
    "\n",
    "    plt.plot(wl,flux, color='r', marker='o')\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",
    "    \n",
    "    \n",
    "    plt.title(\"MaNGAID[\" + str(mangaid) + \"] File_\" +  str(x) + \"\\n\" + \n",
    "             \" Teff: \" + str(teff) + \n",
    "             \" LogG: \" + str(logG) + \n",
    "             \" FeH: \" + str(feh) + \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    df1 = df[df['wl'].between(6538, 6555)]\n",
    "    df1Max = float(df1['flux'].max())\n",
    "    \n",
    "    df2 = df[df['wl'].between(6555, 6572)]\n",
    "    yRange = float(df2['flux'].max())\n",
    "    yRangeMin = float(df2['flux'].min())\n",
    "    \n",
    "    numSum = float(df2['flux'].sum())\n",
    "    lenBand = df2.count()\n",
    "    denSum = float(lenBand['flux'] * df1Max)\n",
    "    \n",
    "    if denSum != 0:\n",
    "        idx = round(numSum / denSum, 2)\n",
    "    else:\n",
    "        idx = -9.999\n",
    "        \n",
    "    df1 = df[df['wl'].between(3900, 9000)]\n",
    "    \n",
    "    slope, intercept = np.polyfit(np.log(df1.wl), np.log(df1.flux), 1)\n",
    "    #slope, intercept = np.polyfit(df1.wl, df1.flux, 1)\n",
    "                   \n",
    "    plt.annotate(xy=[6566, yRangeMin + (yRangeMin * .05)], s='H-alpha 6563')\n",
    "    \n",
    "    #ax = plt.axes()\n",
    "    plt.xlim(xmin=6555, xmax=6572)\n",
    "    plt.ylim(ymin=yRangeMin, ymax=yRange)\n",
    "    \n",
    "    plt.xticks([6555, 6555.5, 6556, 6556.5, 6557, 6557.5, 6558, 6558.5, 6559, 6559.5, 6560, 6560.5,\n",
    "    6561, 6561.5, 6562,  6562.5, 6563, 6563.5, 6564, 6564.5, 6565, 6565.5, 6566, 6566.5, 6567, 6567.5,\n",
    "    6568, 6568.5, 6569, 6569.5, 6570, 6570.5, 6571, 6571.5, 6572])\n",
    "    \n",
    "    xLabels = (6555, 6555.5, 6556, 6556.5, 6557, 6557.5, 6558, 6558.5, 6559, 6559.5, 6560, 6560.5,\n",
    "    6561, 6561.5, 6562,  6562.5, 6563, 6563.5, 6564, 6564.5, 6565, 6565.5, 6566, 6566.5, 6567, 6567.5,\n",
    "    6568, 6568.5, 6569, 6569.5, 6570, 6570.5, 6571, 6571.5, 6572)\n",
    "\n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    plt.savefig('/Users/josephkarpinski/Downloads/MaStar 6563A Halpha Calc/' + 'Slope[' + str(round(slope, 2)) + ']_'  + \n",
    "                'Idx[' + str(idx) + ']_' +\n",
    "                'MaNGAID[' + str(mangaid) + ']' +\n",
    "                 '_' + str(x) +  '.png')\n",
    "\n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "    \n",
    "    \n",
    "    \n",
    "    \n",
    "      # create 2nd line plot\n",
    "    plt.figure(facecolor='white')\n",
    "    \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",
    "\n",
    "    plt.title(\"MaNGAID[\" + str(mangaid) + \"] File_\" +  str(x) + \"\\n\" + \n",
    "             \" Teff: \" + str(teff) + \n",
    "             \" LogG: \" + str(logG) + \n",
    "             \" FeH: \" + str(feh) + \"\\n\" +\n",
    "             \" Teff Calc: \" + str(int(teffCalc)) +\n",
    "             \" Peak Wavelength: \" + str(int(peak))\n",
    "             )\n",
    "\n",
    "    plt.grid()\n",
    "    \n",
    "    df2 = df[df['wl'].between(3622, 10354)]\n",
    "    yRange = float(df2['flux'].max())\n",
    "    \n",
    "    plt.annotate(xy=[3839, yRange * .95], s='CN 3839', rotation=-90)\n",
    "    plt.annotate(xy=[3889, yRange * .20], s='H-zeta 3889', rotation=-90)\n",
    "    plt.annotate(xy=[3970, yRange * .20], 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 * .95], 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",
    "    #ax = plt.axes()\n",
    "    plt.xlim(xmin=3622, xmax=10354)\n",
    "    plt.ylim(ymin=0, ymax=yRange)\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, 9250,\n",
    "               9500, 9750, 10000, 10250])\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, 9250,\n",
    "               9500, 9750, 10000, 10250)\n",
    "    \n",
    "    plt.xticks(xLabels, rotation=90)\n",
    "    \n",
    "    plt.savefig('/Users/josephkarpinski/Downloads/MaStar 6563A Halpha Calc/' + 'Slope[' + str(round(slope, 2)) + ']_'  + \n",
    "                'Idx[' + str(idx) + ']_' +\n",
    "                'MaNGAID[' + str(mangaid) + ']' +\n",
    "                 '_' + str(x) +  '_Full.png')\n",
    "    \n",
    "    plt.gcf().clear()\n",
    "    plt.close('all')\n",
    "    \n",
    "    \n",
    "    #####################################################################################################\n",
    "    \n",
    "    \n",
    " \n",
    "    \n",
    "    \n",
    "print(\"Done\")\n",
    "    "
   ]
  },
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