Merge pull request #151 from spacetelescope/revert-149-fix_missing_im…

…ages

Revert "Updated syntax used to display images so they properly render in generated HTML pages"

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/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",
@@ -870,7 +868,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

notebooks/COS/LSF/LSF.ipynb

@@ -298,15 +298,12 @@
     "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",
-    "<!-- <center><img src=./figures/LSFHomepage.png width =\"900\" title=\"COS Spectral Resolution Site\"> </center> -->\n",
-    "![COS Spectral Resolution Site](figures/LSFHomepage.png \"COS Spectral Resolution Site\")\n",
+    "<center><img src=./figures/LSFHomepage.png width =\"900\" title=\"COS Spectral Resolution Site\"> </center>\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",
-    "<!-- <center><img src=./figures/LSFHomepage2.png width =\"900\" title=\"COS Spectral Resolution Site - Lifetime Position 3\"> </center> -->\n",
-    "\n",
-    "![COS Spectral Resolution Site - Lifetime Position 3](figures/LSFHomepage2.png \"COS Spectral Resolution Site - Lifetime Position 3\")\n",
+    "<center><img src=./figures/LSFHomepage2.png width =\"900\" title=\"COS Spectral Resolution Site - Lifetime Position 3\"> </center>\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",
@@ -1344,7 +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",
@@ -2204,7 +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

@@ -230,22 +230,17 @@
     "First, we will check the CRDS website to determine what the current context is, as it changes regularly. In your browser, navigate to [the HST CRDS homepage](https://hst-crds.stsci.edu), and you will see a page as in Fig. 3.1:\n",
     "\n",
     "### Fig 3.1\n",
-    "<!-- <center><img src=./figures/crds1.png width =\"900\" title=\"CRDS Homepage\" alt=\"The CRDS homepage. There is a dropdown which lists all Hubble instruments. The table at the bottom of the page lists historical contexts.\"> </center> -->\n",
-    "\n",
-    "![The CRDS homepage. There is a dropdown which lists all Hubble instruments. The table at the bottom of the page lists historical contexts.](figures/crds1.png \"CRDS Homepage\")\n",
+    "<center><img src=./figures/crds1.png width =\"900\" title=\"CRDS Homepage\" alt=\"The CRDS homepage. There is a dropdown which lists all Hubble instruments. The table at the bottom of the page lists historical contexts.\"> </center>\n",
     "\n",
     "At the bottom of this page is a list of recent contexts, titled \"Context History\". Clicking the context listed with the Status \"Operational\" (circled in red in Fig 3.1) will take you to that context's page, as shown in Fig. 3.2:\n",
     "\n",
     "### Fig 3.2\n",
-    "<!-- <center><img src=./figures/crds2.png width =\"900\" title=\"CRDS current 'Historical References' context page\" alt=\"The CRDS Historical References context page on the CRDS site. Each instrument is listed on the dropdown.\"> </center> -->\n",
+    "<center><img src=./figures/crds2.png width =\"900\" title=\"CRDS current 'Historical References' context page\" alt=\"The CRDS Historical References context page on the CRDS site. Each instrument is listed on the dropdown.\"> </center>\n",
     "\n",
-    "![The CRDS Historical References context page on the CRDS site. Each instrument is listed on the dropdown.\"> </center>\n",
-    "By clicking the \"cos\" tab, (circled in red), you will be open up the tab, showing a page similar to Fig. 3.3, where you can find the current COS instrument context file: `hst_cos_<context number>.imap`. This filename is circled in red in Fig. 3.3.](./figures/crds2.png \"CRDS current 'Historical References' context page\")\n",
+    "By clicking the \"cos\" tab, (circled in red), you will be open up the tab, showing a page similar to Fig. 3.3, where you can find the current COS instrument context file: `hst_cos_<context number>.imap`. This filename is circled in red in Fig. 3.3.\n",
     "\n",
     "### Fig 3.3\n",
-    "<!-- <center><img src=./figures/crds3.png width =\"900\" title=\"Current COS context on the CRDS site\" alt=\"Showing the current COS context on the CRDS site. There is a large list of reference files, and the imap file labeled at the top of this list as hst_cos_0320.imap\"> </center> -->\n",
-    "\n",
-    "![Showing the current COS context on the CRDS site. There is a large list of reference files, and the imap file labeled at the top of this list as hst_cos_0320.imap](figures/crds3.png \"Current COS context on the CRDS site\")\n",
+    "<center><img src=./figures/crds3.png width =\"900\" title=\"Current COS context on the CRDS site\" alt=\"Showing the current COS context on the CRDS site. There is a large list of reference files, and the imap file labeled at the top of this list as hst_cos_0320.imap\"> </center>\n",
     "\n",
     "Note down or copy the filename you just found."
    ]
@@ -440,7 +435,7 @@
    "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,

notebooks/STIS/calstis/calstis_2d_ccd.ipynb

@@ -367,11 +367,10 @@
     "The BLEVCORR step is part of basic 2-D image reduction for CCD data only. This step subtracts the electronic bias level for each line of the CCD image and trims the overscan regions off of the input image, leaving only the exposed portions of the image. \n",
     "\n",
     "Because the electronic bias level can vary with time and temperature, its value is determined from the overscan region in the particular exposure being processed. This bias is applied equally to real pixels (main detector and physical overscan) and the virtual overscan region (pixels that don't actually exist, but are recorded when the detector clocks out extra times after reading out all the parallel rows). A raw STIS CCD image in full frame unbinned mode has 19 leading and trailing columns of serial physical overscan in the AXIS1 (x direction), and 20 rows of virtual overscan in the AXIS2 (y direction); therefore the size of the uncalibrated and unbinned full framge CCD image is 1062(serial) $\\times$ 1044(parallel) pixels, with 1024 * 1024 exposed science pixels.\n",
-    "<!-- <center>\n",
-    "    <img src=figures/CCD_overscan.jpg width =\"400\" alt=\"Graph illustrating parallel serial overscan corresponding to wavelength in the x-axis and virtual overscan corresponding to position along slit in the y-axis.\">\n",
-    "</center> -->\n",
     "\n",
-    "![Graph illustrating parallel serial overscan corresponding to wavelength in the x-axis and virtual overscan corresponding to position along slit in the y-axis.](figures/CCD_overscan.jpg \"Graph illustrating parallel serial overscan corresponding to wavelength in the x-axis and virtual overscan corresponding to position along slit in the y-axis.\")"
+    "<center> \n",
+    "    <img src=figures/CCD_overscan.jpg width =\"400\" alt=\"Graph illustrating parallel serial overscan corresponding to wavelength in the x-axis and virtual overscan corresponding to position along slit in the y-axis.\">\n",
+    "</center>"
    ]
   },
   {
@@ -382,11 +381,10 @@
     "The electronic bias level is subtracted line-by-line. An initial value of electronic bias level is determined for each line of the image using the serial and parallel overscans, and a straight line is fitted to the bias as a function of image line. The intial electronic bias for each line is determined by taking the median of a predetermined subset of the trailing serial overscan pixels, which currently includes most trailing overscan region except the first and last three pixels, and pixels flagged with bad data quality flags. The actual overscan bias subtracted from the image is the value of the linear fit at a specific image line. The mean value of all overscan levels is written to the output SCI extension header as MEANBLEV.\n",
     "\n",
     "THE BLEVCORR step also trims the image of overscan. The size of the overscan regions depend on binning and whether the image if full frame or a subimage, and the locations of the overscan regions depend on which amplifier was used for readout. The number of pixels trimmed during CCD bias level correction on each side is given in the following table.\n",
-    "<!-- <center>\n",
-    "    <img src=figures/pixels_trimmed.jpg width =\"400\">\n",
-    "</center> -->\n",
     "\n",
-    "![The number of pixels trimmed during CCD bias level correction on each side](figures/pixels_trimmed.jpg)\n"
+    "<center>\n",
+    "    <img src=figures/pixels_trimmed.jpg width =\"400\">\n",
+    "</center>"
    ]
   },
   {