Add WFC3 notebook 'uvis_timedep_phot.ipynb' (#113)

* updated _toc.yml and _config.yml files * uvis_timedep_phot.ipynb: cleared notebook outputs. * Refactor file path handling for improved clarity * Fix code style and photutils deprecation * Remove codestyle command --------- Co-authored-by: Hatice Karatay <haticekaraty@gmail.com>
spacetelescope · Jan 8, 2024 · 36e096f · 36e096f
1 parent 14ec9f5
commit 36e096f
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Showing 3 changed files with 41 additions and 40 deletions.
diff --git a/_config.yml b/_config.yml
@@ -59,5 +59,4 @@ 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_time_dependent_photometry/uvis_timedep_phot.ipynb,
                    notebooks/WFC3/zeropoints/zeropoints.ipynb]
diff --git a/_toc.yml b/_toc.yml
@@ -75,5 +75,5 @@ parts:
       - file: notebooks/WFC3/tvb_flattenramp/TVB_flattenramp_notebook.ipynb
       - file: notebooks/WFC3/photometry_examples/phot_examples.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/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb
 #      - file: notebooks/WFC3/zeropoints/zeropoints.ipynb
diff --git a/notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb b/notebooks/WFC3/uvis_time_dependent_photometry/uvis_timedep_phot.ipynb
@@ -84,8 +84,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "\n",
     "import os\n",
     "import glob\n",
     "import shutil\n",
@@ -96,16 +94,13 @@
     "\n",
     "from astropy.io import fits\n",
     "from astropy.stats import sigma_clipped_stats\n",
-    "from astropy.coordinates import SkyCoord\n",
-    "from astropy import wcs\n",
     "from astroquery.mast import Observations\n",
     "\n",
     "from drizzlepac import photeq\n",
     "from drizzlepac import astrodrizzle\n",
     "\n",
-    "from photutils import aperture_photometry, CircularAperture, CircularAnnulus\n",
-    "\n",
-    "from stwcs import updatewcs"
+    "from photutils.aperture import aperture_photometry, CircularAperture, CircularAnnulus\n",
+    "%matplotlib inline"
    ]
   },
   {
@@ -124,16 +119,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_list = Observations.query_criteria(obs_id=['IBCDA4010','ICH3040F0','IDBHA6040'])\n",
-    "                                        \n",
+    "data_list = Observations.query_criteria(obs_id=['IBCDA4010', 'ICH3040F0', 'IDBHA6040'])\n",
+    "\n",
     "Observations.download_products(data_list['obsid'], project='CALWF3',\n",
-    "        mrp_only=False,download_dir='./data',productSubGroupDescription=['FLC','ASN'])\n",
+    "                               mrp_only=False, download_dir='./data', productSubGroupDescription=['FLC', 'ASN'])\n",
     "\n",
     "science_files = glob.glob('data/mastDownload/HST/*/*fits')\n",
     "\n",
     "for im in science_files:\n",
-    "    root = im.split('/')[-1]\n",
-    "    os.rename(im,'./'+root)\n",
+    "    root = os.path.basename(im)\n",
+    "    new_path = os.path.join(\"./\", root)\n",
+    "    os.rename(im, new_path)\n",
     "shutil.rmtree('data/')"
    ]
   },
@@ -151,7 +147,6 @@
    "outputs": [],
    "source": [
     "df = pd.read_csv('GD153_F606W_public.csv')\n",
-    "\n",
     "df"
    ]
   },
@@ -230,14 +225,14 @@
     "    mask = annulus_masks.data\n",
     "    annulus_data_1d = annulus_data[mask > 0]\n",
     "    mean_sigclip, _, _ = sigma_clipped_stats(annulus_data_1d)\n",
-    "    \n",
+    "\n",
     "    apers = [aperture, annulus_aperture]\n",
-    "    phot_table = aperture_photometry(data,apers)\n",
+    "    phot_table = aperture_photometry(data, apers)\n",
     "\n",
     "    background = mean_sigclip * aperture.area\n",
     "    final_sum = phot_table['aperture_sum_0'] - background\n",
     "    phots.append(final_sum[0])\n",
-    "    mjds.append(mjd)    \n",
+    "    mjds.append(mjd)\n",
     "    dates.append(date)"
    ]
   },
@@ -279,7 +274,12 @@
    "outputs": [],
    "source": [
     "EE_r10 = 0.91\n",
-    "df['STMags'] = -21.1 -2.5*np.log10(df['PHOTFLAM']) -2.5*np.log10(df['Countrate']) - 2.5 * np.log10(1./EE_r10)"
+    "df[\"STMags\"] = (\n",
+    "    - 21.1\n",
+    "    - 2.5 * np.log10(df[\"PHOTFLAM\"])\n",
+    "    - 2.5 * np.log10(df[\"Countrate\"])\n",
+    "    - 2.5 * np.log10(1.0 / EE_r10)\n",
+    ")"
    ]
   },
   {
@@ -406,9 +406,9 @@
     "    annulus_data_1d = annulus_data[mask > 0]\n",
     "    mean_sigclip, _, _ = sigma_clipped_stats(annulus_data_1d)\n",
     "    background = mean_sigclip * aperture.area\n",
-    "    \n",
+    "\n",
     "    apers = [aperture, annulus_aperture]\n",
-    "    phot_table = aperture_photometry(data,apers)\n",
+    "    phot_table = aperture_photometry(data, apers)\n",
     "\n",
     "    final_sum = phot_table['aperture_sum_0'] - background\n",
     "    phots.append(final_sum[0])\n",
@@ -490,20 +490,22 @@
    },
    "outputs": [],
    "source": [
-    "for asn in glob.glob('*asn.fits'):\n",
-    "    astrodrizzle.AstroDrizzle(asn,\n",
-    "                skymethod= 'match',\n",
-    "                skystat='mean',\n",
-    "                driz_sep_bits='80',\n",
-    "                combine_type='median',\n",
-    "                combine_nhigh=1,\n",
-    "                driz_cr_snr= '3.5 3.0', \n",
-    "                driz_cr_scale= '2.0 1.5',\n",
-    "                final_bits= '80', \n",
-    "                build=True,\n",
-    "                clean=True,\n",
-    "                preserve=False,\n",
-    "                num_cores=1)"
+    "for asn in glob.glob(\"*asn.fits\"):\n",
+    "    astrodrizzle.AstroDrizzle(\n",
+    "        asn,\n",
+    "        skymethod=\"match\",\n",
+    "        skystat=\"mean\",\n",
+    "        driz_sep_bits=\"80\",\n",
+    "        combine_type=\"median\",\n",
+    "        combine_nhigh=1,\n",
+    "        driz_cr_snr=\"3.5 3.0\",\n",
+    "        driz_cr_scale=\"2.0 1.5\",\n",
+    "        final_bits=\"80\",\n",
+    "        build=True,\n",
+    "        clean=True,\n",
+    "        preserve=False,\n",
+    "        num_cores=1,\n",
+    "    )"
    ]
   },
   {
@@ -537,7 +539,7 @@
     "pfls = []\n",
     "for i, drc in enumerate(drcs):\n",
     "    data = fits.getdata(drc, ext=1)\n",
-    "    \n",
+    "\n",
     "    mjds.append(np.mean(df.query('Epoch == {}'.format(i+1))['MJD']))\n",
     "    pfls.append(df.query('Epoch == {}'.format(i+1))['PHOTFLAM'].values[0])\n",
     "\n",
@@ -550,9 +552,9 @@
     "    annulus_data_1d = annulus_data[mask > 0]\n",
     "    mean_sigclip, _, _ = sigma_clipped_stats(annulus_data_1d)\n",
     "    background = mean_sigclip * aperture.area\n",
-    "    \n",
+    " \n",
     "    apers = [aperture, annulus_aperture]\n",
-    "    phot_table = aperture_photometry(data,apers)\n",
+    "    phot_table = aperture_photometry(data, apers)\n",
     "\n",
     "    final_sum = phot_table['aperture_sum_0'] - background\n",
     "    phots.append(final_sum[0])"
@@ -675,7 +677,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -689,7 +691,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,