dev notebooks

extraction/1D_Extraction.ipynb

@@ -42,7 +42,6 @@
     "- `astroquery.mast.Observations` for finding and downloading data from the [MAST](https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.html) archive\n",
     "- `os` for managing system paths\n",
     "- `numpy` to handle array functions\n",
-    "- `stistools` for operations on STIS Data\n",
     "- `matplotlib` for plotting data"
    ]
   },
@@ -51,48 +50,26 @@
    "execution_count": 1,
    "id": "bb98f7e5",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/kding/miniconda3/envs/stis/lib/python3.7/site-packages/stsci/tools/nmpfit.py:8: UserWarning: NMPFIT is deprecated - stsci.tools v 3.5 is the last version to contain it.\n",
-      "  warnings.warn(\"NMPFIT is deprecated - stsci.tools v 3.5 is the last version to contain it.\")\n",
-      "/Users/kding/miniconda3/envs/stis/lib/python3.7/site-packages/stsci/tools/gfit.py:18: UserWarning: GFIT is deprecated - stsci.tools v 3.4.12 is the last version to contain it.Use astropy.modeling instead.\n",
-      "  warnings.warn(\"GFIT is deprecated - stsci.tools v 3.4.12 is the last version to contain it.\"\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "The following tasks in the stistools package can be run with TEAL:\n",
-      "   basic2d      calstis     ocrreject     wavecal        x1d          x2d\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Import for: Reading in fits file\n",
     "from astropy.io import fits\n",
     "from astropy.table import Table\n",
     "\n",
-    "# Import for: Downloading necessary files. (Not necessary if you choose to collect data from MAST)\n",
+    "# Import for: Downloading necessary files.\n",
+    "# (Not necessary if you choose to collect data from MAST)\n",
     "from astroquery.mast import Observations\n",
     "\n",
-    "# Import for: Managing system variables and paths\n",
-    "import os\n",
-    "\n",
     "# Import for: Quick Calculation and Data Analysis\n",
     "import numpy as np\n",
     "\n",
-    "# Import for: Operations on STIS Data\n",
-    "import stistools\n",
+    "# Import for: Managing system variables and paths\n",
+    "import os\n",
     "\n",
     "# Import for: Plotting and specifying plotting parameters\n",
-    "import matplotlib\n",
-    "%matplotlib inline\n",
     "from matplotlib import pyplot as plt\n",
-    "from matplotlib.ticker import FixedLocator"
+    "import matplotlib\n",
+    "%matplotlib inline"
    ]
   },
   {
@@ -128,8 +105,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:HST/product/odj102010_x1d.fits to ./mastDownload/HST/odj102010/odj102010_x1d.fits ... [Done]\n",
-      "Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:HST/product/odj102010_flt.fits to ./mastDownload/HST/odj102010/odj102010_flt.fits ... [Done]\n"
+      "INFO: Found cached file ./mastDownload/HST/odj102010/odj102010_x1d.fits with expected size 77760. [astroquery.query]\n",
+      "INFO: Found cached file ./mastDownload/HST/odj102010/odj102010_flt.fits with expected size 10535040. [astroquery.query]\n"
      ]
     }
    ],
@@ -211,7 +188,7 @@
      "data": {
       "text/html": [
        "<i>Table length=1</i>\n",
-       "<table id=\"table140334336153424\" class=\"table-striped table-bordered table-condensed\">\n",
+       "<table id=\"table140575237431120\" class=\"table-striped table-bordered table-condensed\">\n",
        "<thead><tr><th>SPORDER</th><th>WAVELENGTH [1024]</th><th>FLUX [1024]</th><th>EXTRLOCY [1024]</th><th>A2CENTER</th><th>EXTRSIZE</th><th>BK1SIZE</th><th>BK2SIZE</th><th>BK1OFFST</th><th>BK2OFFST</th></tr></thead>\n",
        "<thead><tr><th></th><th>Angstroms</th><th>erg / (Angstrom cm2 s)</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th></tr></thead>\n",
        "<thead><tr><th>int16</th><th>float64</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th></tr></thead>\n",
@@ -233,7 +210,9 @@
     }
    ],
    "source": [
-    "cols = ['SPORDER', 'WAVELENGTH', 'FLUX', 'EXTRLOCY', 'A2CENTER', 'EXTRSIZE','BK1SIZE', 'BK2SIZE', 'BK1OFFST', 'BK2OFFST']\n",
+    "cols = ['SPORDER', 'WAVELENGTH', 'FLUX', 'EXTRLOCY',\n",
+    "        'A2CENTER', 'EXTRSIZE', 'BK1SIZE', 'BK2SIZE',\n",
+    "        'BK1OFFST', 'BK2OFFST']\n",
     "Table.read(x1d_filename)[cols]"
    ]
   },
@@ -267,55 +246,55 @@
    "outputs": [],
    "source": [
     "def show_extraction_regions(x1d_filename, flt_filename, sci_ext=1, row=0, xrange=None, yrange=None):\n",
-    "    \n",
+    "\n",
     "    fig, axes = plt.subplots(1, 2, sharey=True)\n",
     "    fig.tight_layout()\n",
     "    fig.subplots_adjust(wspace=0.2, hspace=0.2, top=0.88)\n",
     "    fig.set_figwidth(10)\n",
     "    fig.set_figheight(5)\n",
     "    fig.suptitle(os.path.basename(x1d_filename))\n",
-    "    \n",
+    "\n",
     "    x1d = fits.getdata(x1d_filename, ext=sci_ext)[row]\n",
     "    flt = fits.getdata(flt_filename, ext=('SCI', sci_ext))\n",
-    "    \n",
+    "\n",
     "    # LEFT & Right PLOTS:\n",
     "    for ax in axes[0:2]:\n",
     "        # Display the 2D FLT spectrum on the left:\n",
-    "        ax.imshow(flt, origin='lower', interpolation='none', aspect='auto', \n",
-    "                   vmin=-6, vmax=15)\n",
+    "        ax.imshow(flt, origin='lower', interpolation='none', aspect='auto',\n",
+    "                  vmin=-6, vmax=15)\n",
     "        ax.set_xlabel('X')\n",
     "        ax.set_ylabel('Y')\n",
     "\n",
     "    # Right PLOT:\n",
     "    axes[1].set_title(f\"A2CENTER={x1d['A2CENTER']:.2f}\")\n",
     "    # Extraction region in red:\n",
-    "    axes[1].plot(np.arange(1024), \n",
+    "    axes[1].plot(np.arange(1024),\n",
     "                 x1d['EXTRLOCY'] - 1, 'r:', alpha=0.6)\n",
-    "    axes[1].plot(np.arange(1024), \n",
+    "    axes[1].plot(np.arange(1024),\n",
     "                 x1d['EXTRLOCY'] - 1 - x1d['EXTRSIZE']//2,\n",
     "                 color='red', alpha=0.6)\n",
-    "    axes[1].plot(np.arange(1024), \n",
+    "    axes[1].plot(np.arange(1024),\n",
     "                 x1d['EXTRLOCY'] - 1 + x1d['EXTRSIZE']//2,\n",
     "                 color='red', alpha=0.6)\n",
     "    # Background regions in orange:\n",
-    "    axes[1].plot(np.arange(1024), \n",
+    "    axes[1].plot(np.arange(1024),\n",
     "                 x1d['EXTRLOCY'] - 1 + x1d['BK1OFFST'] - x1d['BK1SIZE']//2,\n",
     "                 color='orange', alpha=0.6)\n",
-    "    axes[1].plot(np.arange(1024), \n",
+    "    axes[1].plot(np.arange(1024),\n",
     "                 x1d['EXTRLOCY'] - 1 + x1d['BK1OFFST'] + x1d['BK1SIZE']//2,\n",
     "                 color='orange', alpha=0.6)\n",
-    "    axes[1].plot(np.arange(1024), \n",
-    "                 x1d['EXTRLOCY'] - 1 + x1d['BK2OFFST'] - x1d['BK2SIZE']//2, \n",
+    "    axes[1].plot(np.arange(1024),\n",
+    "                 x1d['EXTRLOCY'] - 1 + x1d['BK2OFFST'] - x1d['BK2SIZE']//2,\n",
     "                 color='orange', alpha=0.6)\n",
-    "    axes[1].plot(np.arange(1024), \n",
-    "                 x1d['EXTRLOCY'] - 1 + x1d['BK2OFFST'] + x1d['BK2SIZE']//2, \n",
+    "    axes[1].plot(np.arange(1024),\n",
+    "                 x1d['EXTRLOCY'] - 1 + x1d['BK2OFFST'] + x1d['BK2SIZE']//2,\n",
     "                 color='orange', alpha=0.6)\n",
-    "    \n",
+    "\n",
     "    axes[0].set_xlim(-0.5, 1023.5)\n",
     "    axes[0].set_ylim(-0.5, 1023.5)\n",
     "    axes[1].set_xlim(-0.5, 1023.5)\n",
     "    axes[1].set_ylim(-0.5, 1023.5)\n",
-    "    \n",
+    "\n",
     "    if xrange is not None:\n",
     "        axes[0].set_xlim(xrange[0], xrange[1])\n",
     "        axes[1].set_xlim(xrange[0], xrange[1])\n",
@@ -428,8 +407,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:HST/product/octx01030_x1d.fits to ./mastDownload/HST/octx01030/octx01030_x1d.fits ... [Done]\n",
-      "Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:HST/product/octx01030_flt.fits to ./mastDownload/HST/octx01030/octx01030_flt.fits ... [Done]\n"
+      "INFO: Found cached file ./mastDownload/HST/octx01030/octx01030_x1d.fits with expected size 7629120. [astroquery.query]\n",
+      "INFO: Found cached file ./mastDownload/HST/octx01030/octx01030_flt.fits with expected size 84139200. [astroquery.query]\n"
      ]
     }
    ],
@@ -441,7 +420,9 @@
     "# get a list of files assiciated with that target\n",
     "echelle_list = Observations.get_product_list(target)\n",
     "# Download fits files\n",
-    "result = Observations.download_products(echelle_list, extension=['_flt.fits', '_x1d.fits'], productType=['SCIENCE',])\n",
+    "result = Observations.download_products(echelle_list,\n",
+    "                                        extension=['_flt.fits', '_x1d.fits'],\n",
+    "                                        productType=['SCIENCE'])\n",
     "echelle_flt = os.path.join(f'./mastDownload/HST/{obs_id}/{obs_id}_flt.fits')\n",
     "echelle_x1d = os.path.join(f'./mastDownload/HST/{obs_id}/{obs_id}_x1d.fits')"
    ]
@@ -471,7 +452,7 @@
      "data": {
       "text/html": [
        "<i>Table length=24</i>\n",
-       "<table id=\"table140333506431376\" class=\"table-striped table-bordered table-condensed\">\n",
+       "<table id=\"table140575098642512\" class=\"table-striped table-bordered table-condensed\">\n",
        "<thead><tr><th>SPORDER</th><th>WAVELENGTH [1024]</th><th>FLUX [1024]</th><th>EXTRLOCY [1024]</th><th>EXTRSIZE</th><th>BK1SIZE</th><th>BK2SIZE</th><th>BK1OFFST</th><th>BK2OFFST</th></tr></thead>\n",
        "<thead><tr><th></th><th>Angstroms</th><th>erg / (Angstrom cm2 s)</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th><th>pix</th></tr></thead>\n",
        "<thead><tr><th>int16</th><th>float64</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th></tr></thead>\n",
@@ -591,9 +572,9 @@
     "\n",
     "---\n",
     "## About this Notebook <a class=\"tocSkip\">\n",
-    "**Author:** [Keyi Ding](kding@stsci.edu)\n",
+    "**Author:** Keyi Ding\n",
     "\n",
-    "**Updated On:** 2023-01-05\n",
+    "**Updated On:** 2023-05-18\n",
     "\n",
     "\n",
     "> *This tutorial was generated to be in compliance with the [STScI style guides](https://github.com/spacetelescope/style-guides) and would like to cite the [Jupyter guide](https://github.com/spacetelescope/style-guides/blob/master/templates/example_notebook.ipynb) in particular.*\n",
@@ -602,13 +583,13 @@
     "If you use `astropy`, `matplotlib`, `astroquery`, or `numpy` for published research, please cite the\n",
     "authors. Follow these links for more information about citations:\n",
     "\n",
-    "* [Citing `astropy`/`numpy`/`matplotlib`](https://www.scipy.org/citing.html)\n",
+    "* [Citing `astropy`](https://www.astropy.org/acknowledging.html)/[`numpy`](https://numpy.org/citing-numpy/)/[`matplotlib`](https://matplotlib.org/stable/users/project/citing.html)\n",
     "* [Citing `astroquery`](https://astroquery.readthedocs.io/en/latest/)\n",
     "\n",
     "---\n",
     "\n",
     "[Top of Page](#top)\n",
-    "<img style=\"float: right;\" src=\"https://raw.githubusercontent.com/spacetelescope/notebooks/master/assets/stsci_pri_combo_mark_horizonal_white_bkgd.png\" alt=\"Space Telescope Logo\" width=\"200px\"/> "
+    "<img style=\"float: right;\" src=\"https://raw.githubusercontent.com/spacetelescope/notebooks/master/assets/stsci_pri_combo_mark_horizonal_white_bkgd.png\" alt=\"Space Telescope Logo\" width=\"200px\"/> \n"
    ]
   },
   {