Add WFC3 notebook 'WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays…

….ipynb' (spacetelescope#112) * updated _toc.yml and _config.yml files * WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb: cleared notebook outputs. * updating requirements.txt, some edits to notebook * pep8 corrections and adding a section to the notebook to automatically downlaod necessary files from the WFC3 webpage * PEP8 corrections --------- Co-authored-by: annierose3 <[email protected]>
st-apidgeon · Dec 5, 2023 · 32a780f · 32a780f
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commit 32a780f
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Showing 4 changed files with 38 additions and 67 deletions.
diff --git a/_config.yml b/_config.yml
@@ -59,7 +59,6 @@ exclude_patterns: [notebooks/DrizzlePac/align_mosaics/align_mosaics.ipynb,
                    notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb,
                    notebooks/WFC3/photometry_examples/phot_examples.ipynb,
                    notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb,
-                   notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb,
                    notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb,
                    notebooks/WFC3/zeropoints/zeropoints.ipynb]
 
diff --git a/_toc.yml b/_toc.yml
@@ -72,6 +72,6 @@ parts:
       - file: notebooks/WFC3/persistence/wfc3_ir_persistence.ipynb
 #      - file: notebooks/WFC3/photometry_examples/phot_examples.ipynb
 #      - file: notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb
-#      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
+      - file: notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
 #      - file: notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb
 #      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
diff --git a/notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb b/notebooks/WFC3/uvis_pam_corrections/WFC3_UVIS_Pixel_Area_Map_Corrections_for_Subarrays.ipynb
@@ -86,7 +86,7 @@
     "- *astroquery* for downloading data from MAST\n",
     "- *matplotlib.pyplot* for plotting data\n",
     "- *ginga* for finding min/max outlier pixels\n",
-    "- *shutil* for copying files from one directory to another"
+    "- *urlib* for downloading files from a webpage"
    ]
   },
   {
@@ -100,11 +100,10 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import shutil\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "import urllib.request\n",
     "from astropy.io import fits\n",
-    "from astroquery.mast import Mast\n",
     "from astroquery.mast import Observations\n",
     "from ginga.util.zscale import zscale"
    ]
@@ -305,12 +304,12 @@
    "source": [
     "data_512 = hdu_512[1].data\n",
     "\n",
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_512, vmax_512 = zscale(data_512)\n",
     "\n",
     "im = plt.imshow(data_512, vmin=vmin_512, vmax=vmax_512, origin='lower')\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -369,7 +368,7 @@
     "x1 = int(x0 + scihdr_512['NAXIS1'])\n",
     "y1 = int(y0 + scihdr_512['NAXIS2'])\n",
     "\n",
-    "print (f'(x0, y0, x1, y1) = ({x0}, {y0}, {x1}, {y1})')"
+    "print(f'(x0, y0, x1, y1) = ({x0}, {y0}, {x1}, {y1})')"
    ]
   },
   {
@@ -390,16 +389,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The UVIS CCD has two chips: UVIS1 and UVIS2.\n",
-    "\n",
-    "First, please go to the [WFC3 PAM website](https://www.stsci.edu/hst/instrumentation/wfc3/data-analysis/pixel-area-maps) and download the UVIS1 and UVIS2 PAMs under the \"Download Pixel Area Maps\" header. "
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Now, we will use `shutil.copy` to copy the PAMs from your Downloads directory to the present working directory. "
+    "The UVIS CCD has two chips: UVIS1 and UVIS2. We will download the UVIS1 and UVIS2 PAMs from the [WFC3 PAM website](https://www.stsci.edu/hst/instrumentation/wfc3/data-analysis/pixel-area-maps)."
    ]
   },
   {
@@ -408,35 +398,27 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#Please add the path to your local directory in place of \"pwd\" below\n",
-    "#Please add the path to your Downloads folder in place of \"downloads\" below\n",
-    "downloads = '/Users/yourHomeDirectory/Downloads/'\n",
-    "pwd = '/Users/yourHomeDirectory/PAM_notebook/'"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Copy the content of source to destination\n",
-    "source_1 = downloads + 'UVIS1wfc3_map.fits'\n",
-    "source_2 = downloads + 'UVIS2wfc3_map.fits'\n",
+    "filenames = [\"UVIS1wfc3_map.fits\", \"UVIS2wfc3_map.fits\"]\n",
+    "\n",
+    "try:\n",
+    "    for filename in filenames:\n",
+    "        url = (\"https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/\" + \n",
+    "               \"wfc3/data-analysis/pixel-area-maps/_documents/\")\n",
+    "        url += filename\n",
     "\n",
-    "dest_path1 = shutil.copy(source_1, pwd) \n",
-    "dest_path2 = shutil.copy(source_2, pwd) \n",
+    "        with urllib.request.urlopen(url) as response:\n",
+    "            with open(filename, \"wb\") as out_file:\n",
+    "                out_file.write(response.read())\n",
     "\n",
-    "# Print path of newly created file\n",
-    "print(\"Destination path for the UVIS1 PAM:\", dest_path1)\n",
-    "print(\"Destination path for the UVIS2 PAM:\", dest_path2)"
+    "except Exception as e:\n",
+    "    print(f\"An error occured: {e}\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now we have our WFC3/UVIS PAM files in our working directory."
+    "Now, we should have our WFC3/UVIS PAM files in our working directory."
    ]
   },
   {
@@ -463,14 +445,14 @@
    "outputs": [],
    "source": [
     "if scihdr_512['CCDCHIP'] == 1:\n",
-    "        pam = fits.getdata('UVIS1wfc3_map.fits')\n",
-    "        pamcorr_data_512 = data_512 * pam[y0:y1, x0:x1]\n",
+    "    pam = fits.getdata('UVIS1wfc3_map.fits')\n",
+    "    pamcorr_data_512 = data_512 * pam[y0:y1, x0:x1]\n",
     "\n",
     "elif scihdr_512['CCDCHIP'] == 2:\n",
-    "        pam = fits.getdata('UVIS2wfc3_map.fits')\n",
-    "        pamcorr_data_512 = data_512 * pam[y0:y1, x0:x1]\n",
+    "    pam = fits.getdata('UVIS2wfc3_map.fits')\n",
+    "    pamcorr_data_512 = data_512 * pam[y0:y1, x0:x1]\n",
     "else:\n",
-    "        raise Exception('Chip case not handled.')\n"
+    "    raise Exception('Chip case not handled.')"
    ]
   },
   {
@@ -488,14 +470,13 @@
    "source": [
     "diff_data_512 = (pamcorr_data_512 - data_512)\n",
     "\n",
-    "\n",
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_diff_512, vmax_diff_512 = zscale(diff_data_512)\n",
     "\n",
     "im = plt.imshow(diff_data_512, vmin=vmin_diff_512, vmax=vmax_diff_512, origin='lower')\n",
     "\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -536,14 +517,12 @@
     "    pamcorr_data : array\n",
     "        PAM-corrected data.\n",
     "    \"\"\"\n",
-    "\n",
     "    data = np.copy(data)\n",
     "    x0 = int(np.abs(scihdr['LTV1']))\n",
     "    y0 = int(np.abs(scihdr['LTV2']))\n",
     "    x1 = int(x0 + scihdr['NAXIS1'])\n",
     "    y1 = int(y0 + scihdr['NAXIS2'])\n",
     "    \n",
-    "\n",
     "    if scihdr['CCDCHIP'] == 1:\n",
     "        pam = fits.getdata(pamdir + 'UVIS1wfc3_map.fits')\n",
     "        pamcorr_data = data * pam[y0:y1, x0:x1]\n",
@@ -582,12 +561,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_1024, vmax_1024 = zscale(data_1024)\n",
     "\n",
     "im = plt.imshow(data_1024, vmin=vmin_1024, vmax=vmax_1024, origin='lower')\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -607,13 +586,13 @@
    "source": [
     "diff_data_1024 = (pamcorr_data_1024-data_1024)\n",
     "\n",
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_diff_1024, vmax_diff_1024 = zscale(diff_data_1024)\n",
     "\n",
     "im = plt.imshow(diff_data_1024, vmin=vmin_diff_1024, vmax=vmax_diff_1024, origin='lower')\n",
     "\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -641,12 +620,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_2048, vmax_2048 = zscale(data_2048)\n",
     "\n",
     "im = plt.imshow(data_2048, vmin=vmin_2048, vmax=vmax_2048, origin='lower')\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -666,13 +645,13 @@
    "source": [
     "diff_data_2048 = (pamcorr_data_2048-data_2048)\n",
     "\n",
-    "#We use zcale to find the min and max for plotting\n",
+    "# We use zcale to find the min and max for plotting\n",
     "vmin_diff_2048, vmax_diff_2048 = zscale(diff_data_2048)\n",
     "\n",
     "im = plt.imshow(diff_data_2048, vmin=vmin_diff_2048, vmax=vmax_diff_2048, origin='lower')\n",
     "\n",
     "clb = plt.colorbar(im)\n",
-    "_= clb.ax.set_title('Electrons')"
+    "_ = clb.ax.set_title('Electrons')"
    ]
   },
   {
@@ -738,13 +717,6 @@
     "[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\"/> "
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -763,9 +735,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/notebooks/WFC3/uvis_pam_corrections/requirements.txt b/notebooks/WFC3/uvis_pam_corrections/requirements.txt
@@ -1,5 +1,5 @@
 astropy==5.2.1
 astroquery==0.4.6
-ginga==4.1.1
+ginga==4.0.1
 matplotlib==3.7.0
 numpy==1.23.4