Merge pull request #474 from spacetelescope/bjkuhn-patch-1

Update slitlessutils_IR_extraction.ipynb

Author: cshanahan1

notebooks/WFC3/slitlessutils_IR_extraction/slitlessutils_IR_extraction.ipynb

@@ -89,7 +89,7 @@
    "metadata": {},
    "source": [
     "<a id=\"env\"></a>\n",
-    "## 1.1 Environment \n",
+    "### 1.1 Environment \n",
     "\n",
     "This notebook requires users to install the packages listed in the `requirements.txt` file located in the notebook's <br>\n",
     "sub-folder on the GitHub repository. We will use the `conda` package manager to build the necessary virtual environment. <br>\n",
@@ -124,7 +124,7 @@
    },
    "source": [
     "<a id=\"import\"></a>\n",
-    "## 1.2 Imports \n",
+    "### 1.2 Imports \n",
     "    \n",
     "For this notebook we import:\n",
     "\n",
@@ -228,7 +228,7 @@
    "metadata": {},
    "source": [
     "<a id=\"config\"></a>\n",
-    "## 1.3 `Slitlessutils` Configuration \n",
+    "### 1.3 `Slitlessutils` Configuration \n",
     "\n",
     "In order to extract or simulate grism spectra with `slitlessutils`, you must have the necessary reference files. <br>\n",
     "Below, we provide a table of file descriptions, example filenames, and file types for the different reference files <br>\n",
@@ -299,7 +299,9 @@
    "outputs": [],
    "source": [
     "# Initialize configuration \n",
-    "cfg = su.config.Config()"
+    "cfg = su.config.Config()\n",
+    "# Download latest reffile version\n",
+    "cfg.retrieve_reffiles(update=True)"
    ]
   },
   {
@@ -411,9 +413,9 @@
     "    \n",
     "We download G102 `_raw.fits` and F105W  `_flt.fits` images of the galactic planetary nebula, [VY2-2](https://simbad.cds.unistra.fr/simbad/sim-id?Ident=%402707077&Name=PN%20Vy%20%202-2&submit=submit), from CAL<br>\n",
     "program [17687](https://www.stsci.edu/hst-program-info/program/?program=17687). This target is a well-established calibration source routinely used by the WFC3 instrument team to <br>\n",
-    "derive and validate the wavelength solution for the IR grisms (WFC3 ISR [2016-15](https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/wfc3/documentation/instrument-science-reports-isrs/_documents/2016/WFC3-2016-15.pdf)).\n",
-    "After downloading the images, we <br>\n",
-    "move them to a subdirectory within the current working directory. "
+    "derive and validate the wavelength solution for the IR grisms ([WFC3 ISR 2016-15](https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/wfc3/documentation/instrument-science-reports-isrs/_documents/2016/WFC3-2016-15.pdf) (Pirzkal et al.)).\n",
+    "After downloading the <br>\n",
+    "images, we move them to a subdirectory within the current working directory. "
    ]
   },
   {
@@ -1045,9 +1047,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "os.chdir('../output')\n",
@@ -1064,8 +1064,10 @@
     "### 6.1 Display a Region File\n",
     "\n",
     "Below, we display a grism FLT file and the associated region file. The region files are useful for quickly inspecting which part <br>\n",
-    "of the grism image contribute to each object’s spectrum. The 0, <span style=\"color: blue;\">+1</span>, <span style=\"color: orange;\">+2</span>, and <span style=\"color: green;\">+3</span> spectral orders for the observations are outlined <br>\n",
-    "in white, blue, orange, and green, respectively. More information about the `slitlessutils` region files can be found in the <br>[documentation](https://slitlessutils.readthedocs.io/en/latest/regions.html). "
+    "of the grism image contribute to each object’s spectrum. The 0, <span style=\"color: blue;\"><b>+1</b></span>, <span style=\"color: orange;\"><b>+2</b></span>, and <span style=\"color: green;\"><b>+3</b></span> spectral orders for the observations are outlined <br>\n",
+    "in white, blue, orange, and green, respectively. More information about the `slitlessutils` region files can be found in the <br>[documentation](https://slitlessutils.readthedocs.io/en/latest/regions.html). \n",
+    "\n",
+    "<b>Note</b>: if the figure below does not display correctly, try switching to `%matplotlib inline`.  "
    ]
   },
   {
@@ -1074,6 +1076,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# %matplotlib inline\n",
     "i = 0 # which FLT image to display\n",
     "fig, axs = plt.subplots(1, 1, figsize=(9, 9))\n",
     "\n",
@@ -1115,9 +1118,13 @@
     "source and grism image. Those spectra are then combined into a single one-dimensional spectrum for each source and saved as a<br>\n",
     "`x1d.fits` file. In this example, we only have one source, so there is a single spectrum.<br>\n",
     "\n",
-    "The `x1d` file is a binary table with columns for the wavelength (`lamb`), flux (`flam`), uncertainty (`func`), contamination (`cont`), <br>\n",
-    "and number of pixels (`npix`). By default [configuration](https://slitlessutils.readthedocs.io/en/latest/configure.html#global-variables-config), the flux and uncertainty values are in units of <em>erg s<sup>-1</sup> cm<sup>-2</sup> · Å<sup>-1</sup></em> and scaled by <br>\n",
-    "10<sup>-17</sup> (`cfg.fluxunits` and `cfg.fluxscale`).\n"
+    "The `x1d` file is a binary table with columns for the wavelength (`WAVELENGTH`), flux (`FLUX`), uncertainty (`UNCERTAINTY`), contamination<br>\n",
+    "(`CONTAMINATION`), and number of pixels (`NMEASUREMENTS`). By default [configuration](https://slitlessutils.readthedocs.io/en/latest/configure.html#global-variables-config), the flux and uncertainty values are in units of <br>\n",
+    "<em>erg s<sup>-1</sup> cm<sup>-2</sup> · Å<sup>-1</sup></em> and scaled by 10<sup>-17</sup> (`cfg.fluxunits` and `cfg.fluxscale`).\n",
+    "\n",
+    "There are several emission lines in VY2-2's spectrum. A list of emission lines is provided in Table 2 of [WFC3 ISR 2015-10](https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/wfc3/documentation/instrument-science-reports-isrs/_documents/2015/WFC3-2015-10.pdf) (Bohlin et al.), <br>\n",
+    "which has been copied over to this notebook in the cell below.\n",
+    "\n"
    ]
   },
   {
@@ -1143,20 +1150,19 @@
     "\n",
     "# create wavelength mask\n",
     "lrange = (8000, 11550) \n",
-    "wav = (lrange[0] < dat['lamb']) & (dat['lamb'] < lrange[1])\n",
+    "wav = (lrange[0] < dat['WAVELENGTH']) & (dat['WAVELENGTH'] < lrange[1])\n",
     "\n",
     "# plot spectrum\n",
-    "ax.errorbar(dat['lamb'][wav], \n",
-    "            dat['flam'][wav]*cfg.fluxscale/1e-13, \n",
-    "            yerr=dat['func'][wav]*cfg.fluxscale/1e-13, \n",
+    "ax.errorbar(dat['WAVELENGTH'][wav], \n",
+    "            dat['FLUX'][wav]*cfg.fluxscale/1e-13, \n",
+    "            yerr=dat['UNCERTAINTY'][wav]*cfg.fluxscale/1e-13, \n",
     "            marker='.', markersize=5)\n",
     "\n",
-    "# overlay known emission lines (vacuum)\n",
-    "ax.axvline(9069, ls='--', c='k', lw=1)  # [SIII]; S²⁺\n",
-    "ax.axvline(9531, ls='--', c='k', lw=1)  # [SIII]; S²⁺  blended with H I\n",
-    "# ax.axvline(9546, ls='--', c='k', lw=1)  # H I Pε; n = 8 → 3 blended with [SIII] \n",
-    "ax.axvline(10049, ls='--', c='k', lw=1) # H I P7; n = 7 → 3\n",
-    "ax.axvline(10830, ls='--', c='k', lw=1) # He I; 2³S → 2³P\n",
+    "# overlay known emission lines\n",
+    "ax.axvline(9070, ls='--', c='k', lw=1)  # [SIII]; S²⁺\n",
+    "ax.axvline(9535, ls='--', c='k', lw=1)  # [SIII]; S²⁺ blended with H I Pε\n",
+    "ax.axvline(10060, ls='--', c='k', lw=1) # H I P7; n = 7 → 3\n",
+    "ax.axvline(10834, ls='--', c='k', lw=1) # He I; 2³S → 2³P\n",
     "\n",
     "# matplotlib formatting\n",
     "ax.minorticks_on()\n",
@@ -1204,7 +1210,7 @@
     "## About this Notebook \n",
     "\n",
     "**Author:** Benjamin Kuhn, WFC3 Team <br>\n",
-    "**Last Updated:** 2026-03-19<br>\n",
+    "**Last Updated:** 2026-03-25<br>\n",
     "**Created** 2026-01-15\n",
     "\n",
     "<a id=\"cite\"></a>\n",
@@ -1246,7 +1252,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,