spacetelescope · haticekaratay · Feb 22, 2024 · Feb 22, 2024 · Feb 22, 2024 · Feb 22, 2024
diff --git a/notebooks/COS/AsnFile/AsnFile.ipynb b/notebooks/COS/AsnFile/AsnFile.ipynb
@@ -905,7 +905,7 @@
     "    \"Exposure_type\": rawtag_a_exptypes,\n",
     "    # Date in MJD\n",
     "    \"Exposure_start_date\": rawtag_a_expstart_times,\n",
-    "    \"Seconds_since_first_exposure\":\\\n",
+    "    \"Seconds_since_first_exposure\": \\\n",
     "    # Convert time since the first exposure into seconds\n",
     "    86400*np.subtract(rawtag_a_expstart_times, min(rawtag_a_expstart_times))\n",
     "})"

diff --git a/notebooks/COS/AsnFile/test_asn.py b/notebooks/COS/AsnFile/test_asn.py
@@ -1,23 +1,23 @@
 #!/usr/bin/env python
-#%%[markdown]
-### From here, you can run the `calcos` pipeline on your new association file.
-##### Running `calcos` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
+# From here, you can run the `calcos` pipeline on your new association file.
+# Running `calcos` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
 
-##### In short, to run the `calcos` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
-##### No matter *where* you place these files, you *must* create the lref environment variable.
+# In short, to run the `calcos` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
+# No matter *where* you place these files, you *must* create the lref environment variable.
 # %%
-import os, shutil
+import os
+import shutil
 import calcos
 from astropy.table import Table
 import matplotlib.pyplot as plt
 from pathlib import Path
 # %%
 datadir = Path('./data/')
 outputdir = Path('./output/')
-plotsdir =  Path('./output/plots/')
+plotsdir = Path('./output/plots/')
 # %%
-######### Setting the lref environment variable:
-### YOU LIKELY NEED TO CHANGE THIS LOCATION !
+# Setting the lref environment variable:
+# YOU LIKELY NEED TO CHANGE THIS LOCATION !
 where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
 os.environ['lref'] = where_i_keep_my_ref_files
 assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
@@ -26,7 +26,9 @@
 shutil.copy("./output/ldifcombo_2_asn.fits", "./data/ldifcombo_2_asn.fits")
 
 # Run the CalCOS pipeline on our ldifcombo asn file
-calcos.calcos('./data/ldifcombo_2_asn.fits', verbosity=0, outdir=str(outputdir/"./calcos_processed_1"))
+calcos.calcos('./data/ldifcombo_2_asn.fits',
+              verbosity=0,
+              outdir=str(outputdir/"./calcos_processed_1"))
 
 # %%
 # Read in the processed data
@@ -37,12 +39,14 @@
     wvln, flux = segment["WAVELENGTH", "FLUX"]
     plt.plot(wvln, flux)
 
-plt.xlabel('Wavelength [$\AA$]')
-plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
+plt.xlabel(r'Wavelength [$\AA$]')
+plt.ylabel(r'Flux [ergs/s/$cm^2$/$\AA$]')
 
 plt.title("If this graph looks at all reasonable, your ASN file seems to have worked\n")
 plt.tight_layout()
 plot_path = str(plotsdir/"AsnFile_test.png")
-plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+plt.savefig(plot_path,
+            bbox_inches='tight',
+            dpi=200)
 print(f"Saved plot to: {plot_path}")
 # %%
diff --git a/notebooks/COS/AsnFile/test_removed_exposure_asn.py b/notebooks/COS/AsnFile/test_removed_exposure_asn.py
@@ -1,32 +1,33 @@
 #!/usr/bin/env python3
-#%%[markdown]
-### From here, you can run the `CalCOS` pipeline on your association file where we've removed the empty exposure file.
-##### Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
 
-##### In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
-##### No matter *where* you place these files, you *must* create the lref environment variable.
+# From here, you can run the `CalCOS` pipeline on your association file where we've removed the empty exposure file.
+# Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
+
+# In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
+# No matter *where* you place these files, you *must* create the lref environment variable.
 # %%
-import os, shutil
+import os
 import calcos
 from astropy.table import Table
 import matplotlib.pyplot as plt
 from pathlib import Path
-from astropy.io import fits
 # %%
 datadir = Path('./data/')
 mast_download_dir = datadir / "mastDownload"
 outputdir = Path('./output/')
-plotsdir =  Path('./output/plots/')
+plotsdir = Path('./output/plots/')
 # %%
-######### Setting the lref environment variable:
-### YOU LIKELY NEED TO CHANGE THIS LOCATION !
+# Setting the lref environment variable:
+# YOU LIKELY NEED TO CHANGE THIS LOCATION!
 where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
 os.environ['lref'] = where_i_keep_my_ref_files
 assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
 # %%
 remove_badfile_asn = "data/removed_badfile_asn.fits"
 # Run the CalCOS pipeline on our asn file
-calcos.calcos(remove_badfile_asn, verbosity=0, outdir=str(outputdir/"calcos_processed_remove_badfile/"))
+calcos.calcos(remove_badfile_asn,
+              verbosity=0,
+              outdir=str(outputdir/"calcos_processed_remove_badfile/"))
 # %%
 # Read in the processed data
 processed_data_tab = Table.read(str(outputdir/'calcos_processed_remove_badfile/')+'/ldif01010_x1dsum.fits')
@@ -36,12 +37,12 @@
     wvln, flux = segment["WAVELENGTH", "FLUX"]
     plt.plot(wvln, flux)
 
-plt.xlabel('Wavelength [$\AA$]')
-plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
+plt.xlabel(r'Wavelength [$\AA$]')
+plt.ylabel(r'Flux [ergs/s/$cm^2$/$\AA$]')
 
 plt.title("If this plot looks reasonable, your ASN file seems to have worked\n")
 plt.tight_layout()
 plot_path = str(plotsdir/"remove_badfile_AsnFile_test.png")
-plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+plt.savefig(plot_path, bbox_inches='tight', dpi=200)
 print(f"Saved plot to: {plot_path}")
 # %%
diff --git a/notebooks/COS/AsnFile/test_splitwave_asn.py b/notebooks/COS/AsnFile/test_splitwave_asn.py
@@ -1,43 +1,44 @@
 #!/usr/bin/env python3
-#%%[markdown]
-### From here, you can run the `CalCOS` pipeline on your new association SPLIT wavecal file.
-##### Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
+# From here, you can run the `CalCOS` pipeline on your new association SPLIT wavecal file.
+# Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
 
-##### In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
-##### No matter *where* you place these files, you *must* create the lref environment variable.
-# %%
-import os, shutil
+# In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
+# No matter *where* you place these files, you *must* create the lref environment variable.
+
+import os
+import shutil
 import calcos
 from astropy.table import Table
 import matplotlib.pyplot as plt
 from pathlib import Path
 from astropy.io import fits
-# %%
+
 datadir = Path('./data/')
 mast_download_dir = datadir / "mastDownload"
 lp6_1exp_datadir = datadir / "lp6_1exp_datadir"
 lp6_1exp_datadir.mkdir(exist_ok=True)
 outputdir = Path('./output/')
-plotsdir =  Path('./output/plots/')
+plotsdir = Path('./output/plots/')
 # %%
 # Copy all of the relevant LP6 data files into the lp6_1exp_datadir
 splitwave_rawtags = [
-    shutil.copy(rt, lp6_1exp_datadir / rt.name) \
-        for rt in mast_download_dir.glob("**/*rawtag*fits") \
-            # Only grab the necessary files
-            if fits.getval(rt, "ROOTNAME").upper() in ['LETC01M6Q','LETC01MTQ','LETC01MVQ']
+    shutil.copy(rt, lp6_1exp_datadir / rt.name)
+    for rt in mast_download_dir.glob("**/*rawtag*fits")
+    if fits.getval(rt, "ROOTNAME").upper() in ['LETC01M6Q', 'LETC01MTQ', 'LETC01MVQ']
 ]
 # Copy the LP6 single exposure asn file we made into the directory where we moved all of the relevant exposures' data
 lp6_1exp_asn = shutil.copy('data/letc01mtq_only_asn.fits', lp6_1exp_datadir)
-# %%
-######### Setting the lref environment variable:
-### YOU LIKELY NEED TO CHANGE THIS LOCATION !
+
+# Setting the lref environment variable:
+# YOU LIKELY NEED TO CHANGE THIS LOCATION !
 where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
 os.environ['lref'] = where_i_keep_my_ref_files
 assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
 # %%
 # Run the CalCOS pipeline on our SPLIT wavecal asn file
-calcos.calcos(lp6_1exp_asn, verbosity=0, outdir=str(outputdir/"calcos_processed_lp6_1exp/"))
+calcos.calcos(lp6_1exp_asn,
+              verbosity=0,
+              outdir=str(outputdir/"calcos_processed_lp6_1exp/"))
 # %%
 # Read in the processed data
 processed_data_tab = Table.read(str(outputdir/'calcos_processed_lp6_1exp/')+'/letc01mtq_only_x1dsum.fits')
@@ -47,12 +48,14 @@
     wvln, flux = segment["WAVELENGTH", "FLUX"]
     plt.plot(wvln, flux)
 
-plt.xlabel('Wavelength [$\AA$]')
-plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
+plt.xlabel(r'Wavelength [$\AA$]')
+plt.ylabel(r'Flux [ergs/s/$cm^2$/$\AA$]')
 
 plt.title("If this plot looks reasonable, your ASN file seems to have worked\n")
 plt.tight_layout()
 plot_path = str(plotsdir/"LP6_1exposure_AsnFile_test.png")
-plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+plt.savefig(plot_path,
+            bbox_inches='tight',
+            dpi=200)
 print(f"Saved plot to: {plot_path}")
 # %%
diff --git a/notebooks/COS/CalCOS/CalCOS.ipynb b/notebooks/COS/CalCOS/CalCOS.ipynb
@@ -79,7 +79,7 @@
     "## 1.1. Prerequisites\n",
     "This tutorial assumes some basic knowledge of the command line and was built using a unix style shell. Those using a Windows computer will likely have the best results if working within the [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10).\n",
     "\n",
-    "If you do not already have any distribution of the `conda` tool, see [this page](https://stenv.readthedocs.io/en/latest/getting_started.html#getting-started) for instructions, and install either [`anaconda` (\\~ 3 GB, more beginner friendly, lots of extras you likely won't use)](https://docs.anaconda.com/anaconda/install/), [`miniconda` (\\~ 400 MB, only what you need to make environments)](https://docs.conda.io/en/latest/miniconda.html), or [`mamba` (\\~85 MB, similar to `miniconda` but rewritten in C++).](https://mamba.readthedocs.io/en/latest/installation.html)\n"
+    "If you do not already have any distribution of the `conda` tool, see [this page](https://stenv.readthedocs.io/en/latest/getting_started.html#getting-started) for instructions, and install either [`anaconda` (\\~ 3 GB, more beginner friendly, lots of extras you likely won't use)](https://docs.anaconda.com/anaconda/install/), [`miniconda` (\\~ 400 MB, only what you need to make environments)](https://docs.conda.io/en/latest/miniconda.html), or [`mamba` (\\~85 MB, similar to `miniconda` but rewritten in C++).](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)\n"
    ]
   },
   {
@@ -442,7 +442,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -459,11 +459,8 @@
     "# This command looks up the pmap file, which tells what ref files to download.\n",
     "# It then downloads these to the CRDS_PATH directory.\n",
     "# Make sure you have the latest pmap file, found on the CRDS site.\n",
-    "!crds bestrefs \\\n",
-    "    --files data/*raw*.fits \\\n",
-    "    --sync-references=2 \\\n",
-    "    --update-bestrefs \\\n",
-    "    --new-context 'hst_1071.pmap'"
+    "!crds bestrefs --files data/*raw*.fits --sync-references=2\n",
+    "!crds bestrefs --update-bestrefs --new-context 'hst_1140.pmap'"
    ]
   },
   {
@@ -579,10 +576,10 @@
     "# 1st param specifies which asn file to run the pipeline on\n",
     "try:\n",
     "    calcos.calcos(str(datadir/asn_name),\n",
-    "              # verbosity param\n",
-    "              verbosity=2,\n",
-    "              # Save all resulting files in this subdirectory in our outdir\n",
-    "              outdir=str(outputdir/\"calcos_processed_1\"))\n",
+    "                  # verbosity param\n",
+    "                  verbosity=2,\n",
+    "                  # Save all resulting files in this subdirectory in our outdir\n",
+    "                  outdir=str(outputdir/\"calcos_processed_1\"))\n",
     "except RuntimeError as e:\n",
     "    print('An error occured, ', e)"
    ]
@@ -1096,7 +1093,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/COS/DataDl/DataDl.ipynb b/notebooks/COS/DataDl/DataDl.ipynb
@@ -425,6 +425,11 @@
     "   - Clicking the single dataset download button will attempt to open a \"pop-up\" window, which you must allow in order to download the file. Some browsers will require you to manually allow pop-ups.\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -580,7 +585,7 @@
     "print(col_data[sort_order])\n",
     "\n",
     "chosenObs = col_data[sort_order][-1]  # Grab the last value of the sorted list\n",
-    "print(f\"\\n\\nThe longest COS/FUV exposure with the G160M filter is:\" +\n",
+    "print(\"\\n\\nThe longest COS/FUV exposure with the G160M filter is:\" +\n",
     "      f\"\\n\\n{chosenObs}\")"
    ]
   },

diff --git a/notebooks/COS/LSF/LSF.ipynb b/notebooks/COS/LSF/LSF.ipynb
@@ -297,13 +297,19 @@
     "<font size=\"4 \"><b>Where can you find the LSF files?</b></font>\n",
     "The COS team maintains up-to-date LSF files on the [COS Spectral Resolution page](https://www.stsci.edu/hst/instrumentation/cos/performance/spectral-resolution). Opening up this link leads to a page like that shown in Fig. 1.1, where the LSF files are discussed in detail. The bottom part of this page has links to all the relavent files. The links at the top of the page will take you to the relevant section. In Fig. 1.1, we have circled in black the link to the section pertaining to our data: FUV at the Lifetime Position: 3.\n",
     "\n",
-    "### <center> Fig 1.1: Screenshot of the COS Spectral Resolution Site</center>\n",
-    "<img src=./figures/LSFHomepage.png width =\"900\" title=\"COS Spectral Resolution Site\" alt=\"COS Spectral Resolution Site\">\n",
+    "<div style=\"text-align:center\">\n",
+    "<img src=\"./figures/LSFHomepage.png\" width=\"900\" alt=\"COS Spectral Resolution Site\">\n",
+    "<p>Fig 1.1: Screenshot of the COS Spectral Resolution Site</p>\n",
+    "</div>\n",
+    "\n",
     "\n",
     "Clicking on the circled link takes us to the table of hyperlinks to all the files perataining to data taken with the FUV, Lifetime Postition 3 configutation, shown in Fig. 1.2:\n",
     "\n",
-    "### <center>Fig 1.2: Screenshot of the COS Spectral Resolution Site - Focus on LP-POS 3</center>\n",
-    "<img src=./figures/LSFHomepage2.png width =\"900\" title=\"COS Spectral Resolution Site - Lifetime Position 3\" alt=\"COS Spectral Resolution Site - Lifetime Position 3\">\n",
+    "<div style=\"text-align:center\">\n",
+    "<img src=\"./figures/LSFHomepage2.png\" width=\"900\" alt=\"COS Spectral Resolution Site - Lifetime Position 3\">\n",
+    "<p>Fig 1.2: Screenshot of the COS Spectral Resolution Site - Focus on LP-POS 3</p>\n",
+    "</div>\n",
+    "\n",
     "\n",
     "Circled in solid red is the button to download the LSF file we need for our data with CENWAVE = 1291. Circled in dashed black is the corresponding CDSF.\n",
     "\n",
@@ -1341,7 +1347,7 @@
     "    continuum (array or -1) : if -1, default of continuum of 1, \\\n",
     "        otherwise must be same length as emitspec\n",
     "    \"\"\"\n",
-    "    if type(continuum) == int:\n",
+    "    if type(continuum) is int:\n",
     "        if continuum == -1:\n",
     "            continuum = np.ones(len(emitspec))\n",
     "            \n",

diff --git a/notebooks/COS/README.md b/notebooks/COS/README.md
@@ -19,7 +19,7 @@ If you don't want to run the Notebooks for yourself but just want to see rendere
 
 |Name|Topic|Notebook file (`ipynb`)|Rendered file (`html`)|
 |-|-|-|-|
-|Setup|Setting up an environment to work with COS data|[Setup.ipynb](https://github.com/spacetelescope/hst_notebooks/blob/master/notebooks/COS/Setup/Setup.ipynb)|[Setup.html](https://spacetelescope.github.io/hst_notebooks/notebooks/COS/Setup/Setup.html)|
+|Setup|Setting up an environment to work with COS data|[Setup.ipynb](https://github.com/spacetelescope/hst_notebooks/blob/main/notebooks/COS/Setup/Setup.ipynb)|[Setup.html](https://spacetelescope.github.io/hst_notebooks/notebooks/COS/Setup/Setup.html)|
 |DataDl|Downloading COS Data from the archive|[DataDl.ipynb](https://github.com/spacetelescope/hst_notebooks/blob/master/notebooks/COS/DataDl/DataDl.ipynb)|[DataDl.html](https://spacetelescope.github.io/hst_notebooks/notebooks/COS/DataDl/DataDl.html)|
 |ViewData|Beginning to work with COS data in Python: *plotting, binning, calculating SNR, & evaluating* a spectrum|[ViewData.ipynb](https://github.com/spacetelescope/hst_notebooks/blob/master/notebooks/COS/ViewData/ViewData.ipynb)|[ViewData.html](https://spacetelescope.github.io/hst_notebooks/notebooks/COS/ViewData/ViewData.html)|
 |AsnFile|Modifying or creating an association file|[AsnFile.ipynb](https://github.com/spacetelescope/hst_notebooks/blob/master/notebooks/COS/AsnFile/AsnFile.ipynb)|[AsnFile.html](https://spacetelescope.github.io/hst_notebooks/notebooks/COS/AsnFile/AsnFile.html)|