Merge branch 'main' into fix_all_missing_images

_config.yml

@@ -53,13 +53,11 @@ exclude_patterns: [notebooks/DrizzlePac/align_mosaics/align_mosaics.ipynb,
                    notebooks/WFC3/dash/dash.ipynb,
                    notebooks/WFC3/filter_transformations/filter_transformations.ipynb,
                    notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb,
-                   notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb,
                    notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb,
                    notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.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]
 

_toc.yml

@@ -65,13 +65,13 @@ parts:
       - file: notebooks/WFC3/exception_report/wfc3_exception_report.ipynb
 #      - file: notebooks/WFC3/filter_transformations/filter_transformations.ipynb
 #      - file: notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
-#      - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
+      - file: notebooks/WFC3/image_displayer_analyzer/wfc3_image_displayer_analyzer.ipynb
 #      - file: notebooks/WFC3/ir_ima_visualization/IR_IMA_Visualization_with_an_Example_of_Time_Variable_Background.ipynb
 #      - file: notebooks/WFC3/ir_scattered_light_calwf3_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_Using_calwf3_to_Mask_Bad_Reads.ipynb
 #      - file: notebooks/WFC3/ir_scattered_light_manual_corrections/Correcting_for_Scattered_Light_in_IR_Exposures_by_Manually_Subtracting_Bad_Reads.ipynb
       - 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

notebooks/COS/AsnFile/AsnFile.ipynb

@@ -307,9 +307,7 @@
     "\n",
     "### Figure 1. Comparison of fluxes between the data retrieved from MAST, and the same data reprocessed after removing the bad exposure\n",
     "\n",
-    "<!-- <img src=./figures/compare_fluxes_after_removing_badfile.png width=60% title='Comparison of fluxes' alt='A comparison between the fluxes of our data. One dataset if without our bad exposure removed, and the other is with our bad exposure removed. Both plots are relatively the same, as they should be.'/> -->\n",
-    "\n",
-    "![A comparison between the fluxes of our data. One dataset if without our bad exposure removed, and the other is with our bad exposure removed. Both plots are relatively the same, as they should be.](./figures/compare_fluxes_after_removing_badfile.png \"Comparison of fluxes\")"
+    "<img src=./figures/compare_fluxes_after_removing_badfile.png width=60% title='Comparison of fluxes' alt='A comparison between the fluxes of our data. One dataset if without our bad exposure removed, and the other is with our bad exposure removed. Both plots are relatively the same, as they should be.'>"
    ]
   },
   {
@@ -907,7 +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",
     "})"
@@ -1114,7 +1112,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   },
   "nbdime-conflicts": {
    "local_diff": [

notebooks/COS/CalCOS/CalCOS.ipynb

@@ -420,9 +420,7 @@
     "\n",
     "<font size=\"4 \">Caution!</font>\n",
     "    \n",
-    "<!-- <img src= ./figures/warning.png width =\"60\" title=\"CAUTION!\" alt=\"A warning symbol. Watch out!\">  -->\n",
-    "\n",
-    "![A warning symbol. Watch out!](./figures/warning.png \"CAUTION!\")\n",
+    "<img src= ./figures/warning.png width =\"60\" title=\"CAUTION!\" alt=\"A warning symbol. Watch out!\"> \n",
     "\n",
     "*Note* that as of the time of this Notebook's update, the pipeline context used below was **`hst_1071.pmap`**, but this changes over time. You are running this in the future, and there is certainly a newer context you would be better off working with. Take a minute to consider this, and check the [HST Calibration Reference Data System webpage](http://hst-crds.stsci.edu/) to determine what the **current operational pmap file** is. "
    ]
@@ -1098,7 +1096,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

notebooks/COS/DataDl/DataDl.ipynb

@@ -319,7 +319,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -347,7 +347,7 @@
     "Because we are searching by Dataset ID, we don't need to specify any additional parameters to narrow down the data.\n",
     "\n",
     "### Fig 1.8\n",
-    "<img src =figures/new_search_file_list_small.png width =\"900\" title=\"File Upload Search Form\" alt=\"The image shows the MAST search page, with the top box filled in. The title of this box is 'Object name(s) and/or RA and Dec pair(s). The filled in box is the text file obsId_list.txt. The observations box below it has only the science box checked off.\">"
+    "<img src =figures/new_search_file_list_small.png width =\"900\" title=\"File Upload Search Form\" alt=\"The image shows the MAST search page, with the top box filled in. The title of this box is 'Object name(s) and/or RA and Dec pair(s). The filled in box is the text file obsId_list.txt. The observations box below it has only the science box checked off.\">\n"
    ]
   },
   {
@@ -590,9 +590,7 @@
    "source": [
     "<font size=\"5\">Caution! </font>\n",
     "    \n",
-    "<!-- <img src=./figures/warning.png width =\"60\" title=\"CAUTION\" alt=\"This image is a warning symbol.\">  -->\n",
-    "\n",
-    "![This image is a warning symbol.](figures/warning.png \"CAUTION\")\n",
+    "<img src=./figures/warning.png width =\"60\" title=\"CAUTION\" alt=\"This image is a warning symbol.\"> \n",
     "\n",
     "Please note that these queries are `Astropy` tables and do not always respond as expected for other data structures like `Pandas DataFrames`. For instance, the first way of filtering a table shown below is correct, but the second will consistently produce the *wrong result*. You *must* search and filter these tables by masking them, as in the first example below."
    ]
@@ -647,9 +645,7 @@
     "- Support files such as the spacecraft's pointing data over time (`jit` files).\n",
     "- Intermediate data products such as calibrated TIME-TAG data (`corrtag` or `corrtag_a`/`corrtag_b` files) and extracted 1-dimensional spectra averaged over exposures with a specific `FP-POS` value (`x1dsum` files).\n",
     "\n",
-    "<!-- <img src=./figures/warning.png width =\"60\" title=\"CAUTION\" alt=\"This image is a warning symbol.\"> -->\n",
-    "\n",
-    "![This image is a warning symbol.](figures/warning.png \"CAUTION\")\n",
+    "<img src=./figures/warning.png width =\"60\" title=\"CAUTION\" alt=\"This image is a warning symbol.\">\n",
     "\n",
     "However, use caution with downloading all files, as in this case, setting `mrp_only` to `False` results in the transfer of **7 Gigabytes** of data, which can take a long time to transfer and eat away at your computer's storage! In general, only download the files you need. On the other hand, often researchers will download only the raw data, so that they can process it for themselves. Since here we only need the final `x1dsum` and `asn` files, we only need to download 2 Megabytes."
    ]

notebooks/COS/DayNight/DayNight.ipynb

@@ -524,9 +524,7 @@
     "\n",
     "<font size=\"4 \"> Caution!</font>\n",
     "\n",
-    "<!-- <img src=figures/warning.png width =\"60\" title=\"CAUTION!\"> -->\n",
-    "\n",
-    "![CAUTION!](figures/warning.png \"CAUTION!\")\n",
+    "<img src=figures/warning.png width =\"60\" title=\"CAUTION!\"> \n",
     "\n",
     "**The process in the following two cells can take a long time and strain network resources!** If you have already downloaded *up-to-date* COS reference files, avoid doing so again.\n",
     "    \n",
@@ -552,7 +550,7 @@
     "\n",
     "# The next line depends on your context and pmap file\n",
     "# You can find the latest pmap file at https://hst-crds.stsci.edu\n",
-    "!crds bestrefs --files **/*corrtag*.fits  --sync-references=2 --update-bestrefs --new-context 'hst_1078.pmap'"
+    "!crds bestrefs --files **/*corrtag*.fits  --sync-references=2 --update-bestrefs --new-context 'hst_1123.pmap'"
    ]
   },
   {
@@ -633,7 +631,7 @@
    "outputs": [],
    "source": [
     "# Read in the wvln, flux, flux error of the *UNfiltered* spectrum file\n",
-    "unfilt_tab = Table.read(\"./output/full_data_outs/\"+filename_root+\"_x1dsum.fits\")['WAVELENGTH', 'FLUX', 'ERROR']\n",
+    "unfilt_tab = Table.read(f\"./output/full_data_outs/{filename_root}_x1dsum.fits\")['WAVELENGTH', 'FLUX', 'ERROR']\n",
     "\n",
     "# Read in the wvln, flux, flux error of the *filtered* spectrum file\n",
     "filt_tab = Table.read(\"./output/filtered_data_outs/filtered_x1dsum.fits\")['WAVELENGTH', 'FLUX', 'ERROR']\n",
@@ -822,7 +820,7 @@
     "\n",
     "**Contributors:** Elaine Mae Frazer\n",
     "\n",
-    "**Updated On:** 2023-06-26\n",
+    "**Updated On:** 2023-12-05\n",
     "\n",
     "> *This tutorial was generated to be in compliance with the [STScI style guides](https://github.com/spacetelescope/style-guides) and would like to cite the [Jupyter guide](https://github.com/spacetelescope/style-guides/blob/master/templates/example_notebook.ipynb) in particular.*\n",
     "\n",
@@ -870,7 +868,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,

notebooks/COS/DayNight/requirements.txt

@@ -4,3 +4,4 @@ calcos==3.4.4
 costools==1.2.6
 matplotlib==3.7.0
 numpy==1.23.4
+crds==11.17.13

notebooks/COS/LSF/LSF.ipynb

@@ -1341,7 +1341,7 @@
     "    continuum (array or -1) : if -1, default of continuum of 1, \\\n",
     "        otherwise must be same length as emitspec\n",
     "    \"\"\"\n",
-    "    if type(continuum) is int:\n",
+    "    if type(continuum) == int:\n",
     "        if continuum == -1:\n",
     "            continuum = np.ones(len(emitspec))\n",
     "            \n",
@@ -2201,7 +2201,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

notebooks/COS/Setup/Setup.ipynb

@@ -433,7 +433,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,

notebooks/COS/ViewData/ViewData.ipynb

@@ -458,27 +458,20 @@
     "\n",
     "### Fig. 1.1 from [COS DHB Fig. 1.6](https://hst-docs.stsci.edu/cosdhb/chapter-1-cos-overview/1-2-cos-physical-configuration#id-1.2COSPhysicalConfiguration-Figure1.6)\n",
     "\n",
-    "<!-- <center>\n",
+    "<center>\n",
     "    <img src=figures/cosdhb_fig1p6.jpg width =\"900\" title=\"Layout of the COS FUV detector\">\n",
     "    <figcaption>Layout of the COS FUV detector. Note that FUVB corresponds to shorter wavelengths than FUVA.</figcaption>\n",
-    "</center> -->\n",
-    "\n",
-    "![Layout of the COS FUV detector. Note that FUVB corresponds to shorter wavelengths than FUVA.](figures/cosdhb_fig1p6.jpg \"Layout of the COS FUV detector\")\n",
-    "\n",
-    "Layout of the COS FUV detector. Note that FUVB corresponds to shorter wavelengths than FUVA.\n",
+    "</center>\n",
     "\n",
     "**In the case of the NUV data, we see a similar `astropy` style table of 3 rows** (labeled NUVA, NUVB, and NUVC). These rows contain data from the 3 stripes of the NUV spectrum (see Figure 1.2).\n",
     "\n",
     "### Fig. 1.2 from [COS DHB Fig. 1.10](https://hst-docs.stsci.edu/cosdhb/chapter-1-cos-overview/1-2-cos-physical-configuration#id-1.2COSPhysicalConfiguration-Figure1.10)\n",
     "\n",
-    "<!-- <center>\n",
+    "<center>\n",
     "    <img src=figures/ch1_cos_overview3.10.jpg width =\"900\" title=\"An example COS NUV spectrum\">\n",
     "    <figcaption>An example COS NUV spectrum. The spectrum itself, taken with the Primary Science Aperture, is in the lower three stripes labeled 'PSA'. The upper stripes, labeled 'WCA' are for wavelength calibration.</figcaption>\n",
-    "</center> -->\n",
-    "\n",
-    "![An example COS NUV spectrum. The spectrum itself, taken with the Primary Science Aperture, is in the lower three stripes labeled 'PSA'. The upper stripes, labeled 'WCA' are for wavelength calibration.](figures/ch1_cos_overview3.10.jpg \"An example COS NUV spectrum\")\n",
+    "</center>\n",
     "\n",
-    "An example COS NUV spectrum. The spectrum itself, taken with the Primary Science Aperture, is in the lower three stripes labeled 'PSA'. The upper stripes, labeled 'WCA' are for wavelength calibration.\n",
     "\n",
     "An important thing to note about this *NUV* data in particular is that with the grating used here (G230L), stripe C is actually a 2nd order spectrum with a higher dispersion and ~5% contamination from the 1st order spectrum. See the [COS Data Handbook](https://hst-docs.stsci.edu/cosdhb/chapter-1-cos-overview/1-1-instrument-capabilities-and-design#id-1.1InstrumentCapabilitiesandDesign-NUVSpectroscopyNUVSpectroscopy) for more information."
    ]
@@ -1588,10 +1581,7 @@
     "\n",
     "<font size=\"5\">Caution!</font>\n",
     "\n",
-    "<!-- <img src=figures/warning.png width =\"60\" title=\"CAUTION!\"> -->\n",
-    "\n",
-    "![CAUTION!](figures/warning.png \"CAUTION!\")\n",
-    "\n",
+    "<img src=figures/warning.png width =\"60\" title=\"CAUTION!\"> \n",
     "This simplification may not hold very well if your source is diffuse or faint."
    ]
   },
@@ -2034,7 +2024,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,

notebooks/STIS/CoronagraphyViz/STIS_Coronagraphy_Visualization_v2.ipynb

@@ -41,9 +41,7 @@
     "\n",
     "To this end, the functions and examples in this notebook are meant to be an illustrative guide to visualizing possible aperture+companion+orientation configurations. \n",
     "\n",
-    "<!-- <img src=\"c12_special12.1.png\" alt=\"Positions of STIS supported coronagraphic apertures, including the two WEDGEs and two BARs.\" style=\"width: 500px;\"/> -->\n",
-    "\n",
-    "![Positions of STIS supported coronagraphic apertures, including the two WEDGEs and two BARs.](c12_special12.1.png \"Positions of STIS supported coronagraphic apertures, including the two WEDGEs and two BARs.\")\n",
+    "<img src=\"c12_special12.1.png\" alt=\"Positions of STIS supported coronagraphic apertures, including the two WEDGEs and two BARs.\" style=\"width: 500px;\"/>\n",
     "\n",
     "<span style=\"font-size: larger; font-weight:bold\">Positions of STIS supported coronagraphic apertures, including the two WEDGEs and two BARs. Note that the full STIS field of view is 50\" x 50\".</span>"
    ]
@@ -496,7 +494,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,