Merge pull request #240 from camipacifici/nbmos

Update and add screenshots in MOS notebook

notebooks/NIRSpec/mos_spectroscopy_advanced/MOSspec_advanced.ipynb

@@ -116,12 +116,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Check versions. Should be:\n",
+    "## Check versions. Latest working environment is:\n",
     "\n",
-    "Numpy:  1.25.2<br>\n",
-    "Astropy:  5.3.2<br>\n",
-    "Specutils:  1.11.0<br>\n",
-    "Jdaviz: 3.7"
+    "Numpy:  2.1.0<br>\n",
+    "Astropy:  6.1.2<br>\n",
+    "Specutils:  1.16.0<br>\n",
+    "Jdaviz: 3.10.3"
    ]
   },
   {
@@ -257,9 +257,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Use Specviz2d to extract a better 1D spectrum\n",
-    "\n",
-    "We open the Spectral Extraction plugin and select the appropriate trace (Polynomial, order 3, on pixel 2), background (Manual, on pixel 8, width 2, statistic average), and extraction (From Plugin, Horne). We then click Extract and inspect the extracted spectrum in the 1D viewer."
+    "## Use Specviz2d to extract a better 1D spectrum"
    ]
   },
   {
@@ -290,6 +288,19 @@
     "This is being worked on."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We open the Spectral Extraction plugin and select the appropriate trace (Polynomial, order 3, on pixel 2), background (Manual, on pixel 8, width 2, statistic average), and extraction (From Plugin, Horne). We then click Extract and inspect the extracted spectrum in the 1D viewer.\n",
+    "\n",
+    "<img src='./trace.png' alt=\"Specviz2d with spectral extraction plugin open showing the trace parameters.\" width=\"500\"/>\n",
+    "\n",
+    "<img src='./background.png' alt=\"Specviz2d with spectral extraction plugin open showing the background parameters.\" width=\"500\"/>\n",
+    "\n",
+    "<img src='./extraction.png' alt=\"Specviz2d with spectral extraction plugin open showing the extraction parameters.\" width=\"500\"/>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -330,7 +341,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "There are still some artifacts in the data, but we can select a subset masking the artifacts and get out a spectrum without unwanted spikes. We can do so using the tool to select a subset with the \"add\" option (in the top bar) to select multiple regions as part of a single subset."
+    "There are still some artifacts in the data, but we can select a subset masking the artifacts and get out a spectrum without unwanted spikes. We can do so using the tool to select a subset with the \"add\" option (in the top bar) to select multiple regions as part of a single subset.\n",
+    "\n",
+    "<img src='./subset_add.png' alt=\"Specviz showing how to select a subset and choose the add option.\" width=\"600\"/>"
    ]
   },
   {
@@ -348,11 +361,11 @@
     "    print(\"There are no subsets selected.\")\n",
     "    region1_exists = False\n",
     "    \n",
-    "# Spectral region for masking artifacts\n",
+    "# Spectral region for masking artifacts just around [OII]\n",
     "if not region1_exists:\n",
     "    sv = specviz.app.get_viewer('spectrum-viewer')\n",
     "    sv.toolbar_active_subset.selected = []\n",
-    "    sv.apply_roi(XRangeROI(1., 1.58))  "
+    "    sv.apply_roi(XRangeROI(1., 1.27))  "
    ]
   },
   {
@@ -421,6 +434,13 @@
     "I can do some analysis on the spectrum using the plugins in the GUI. For reproducibility, I can do the same thing from the API, changing the parameters in the plugins programmatically."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Select regions"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -453,6 +473,15 @@
     "sv.apply_roi(XRangeROI(1.05, 1.25))  "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Line analysis\n",
+    "\n",
+    "<img src='./line_analysis.png' alt=\"Specviz showing the region on the [OII] line and the line analysis plugin.\" width=\"600\"/>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -493,7 +522,7 @@
    "source": [
     "# Input the values for the continuum\n",
     "plugin_la.continuum = 'Surrounding'\n",
-    "plugin_la.width = 7"
+    "plugin_la.continuum_width = 7"
    ]
   },
   {
@@ -506,6 +535,15 @@
     "plugin_la.get_results()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Line lists\n",
+    "\n",
+    "<img src='./line_lists.png' alt=\"Specviz showing the line list plugin and the redshift identified with the [OII] doublet.\" width=\"600\"/>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -540,6 +578,15 @@
     "Open line list plugin. Select the SDSS IV line list. Load the Oxygen II lines and Hb. Go back to line analysis plugin and associate the Oxygen II line with the line we just analyzed."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Model fitting\n",
+    "\n",
+    "<img src='./model_fitting.png' alt=\"Specviz showing a model fit to the continuum and the [OII] line.\" width=\"600\"/>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1104,7 +1151,7 @@
    "metadata": {},
    "source": [
     "Notebook created by Camilla Pacifici (cpacifici@stsci.edu)<br>\n",
-    "Updated on September 14, 2023"
+    "Updated on August 28, 2024"
    ]
   }
  ],
@@ -1124,7 +1171,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,