Merge branch 'first_steps' into 'main'

Added docs and assets for ISIS First Steps

Closes #17

See merge request astrogeology/asc-public-docs!14

docs/getting-started/Using ISIS: First Steps/Adding Spice.md

+
+## Adding SPICE
+
+-----
+
+An important capability of ISIS is the ability to geometrically and
+photometrically characterize pixels in raw planetary instrument images.
+Information such as latitude, longitude, phase angle, incidence angle,
+emission angle, local solar time, sun azimuth, and a many other pixel
+characteristics can be computed.
+
+To compute this information, the **SPICE** ( **S** pacecraft and **P**
+lanetary ephemeredes, **I** nstrument **C** -matrix and **E** vent
+kernel) kernels must first be determined for the particular raw
+instrument image. These kernels maintain the spacecraft position and
+orientation over time, as well as the target position and instrument
+specific operating modes.
+
+To add SPICE information to your cube, run
+[**spiceinit**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/spiceinit/spiceinit.html)
+application on the image so that camera/instrument specific applications
+(e.g.,
+[**cam2map**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/cam2map/cam2map.html)
+,
+[**campt**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/campt/campt.html)
+,
+[**qview**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/qview/qview.html)
+) will have the information they need to work properly. Generally, you
+can simply run spiceinit with your input filename and no other
+parameters:
+
+``` 
+  spiceinit FROM=my.cub
+```
+
+### Related ISIS Applications
+
+See the following ISIS documentation for information about the
+applications you will need to use to perform this procedure:
+
+  - [**spiceinit**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/spiceinit/spiceinit.html)
+    : adds SPICE information to the input cube

docs/getting-started/Using ISIS: First Steps/Exporting ISIS Data.md

+
+# Exporting ISIS Data 
+-----
+
+Naturally, once you're finished processing your image data, and you have
+your final product, you'll want to use it in reports, papers, posters,
+web pages, your favorite Geographic Information System (GIS) or image
+analysis package, or simply share it with others. Since many other
+software packages can't read ISIS cube format, you'll want to export
+your cube to a file type appropriate to your needs.
+
+
+### General Purpose: Desktop Applications and Web 
+
+[**isis2std**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2std/isis2std.html)
+(ISIS to Standard formats) exports your cubes to a wide variety of
+popular image formats, such as PNG (Portable Network Graphics) and TIFF
+(Tagged Image File Format). No matter what desktop application you're
+using (Word Perfect, Illustrator, or GIMP, just to name a few), or what
+you're creating (posters, web pages, or a pretty background for your
+desktop), **isis2std** will handle it.
+
+
+### GIS and Image Analysis Applications 
+
+But the icing on the cake is that **isis2std** also exports the
+necessary files for taking your image into GIS\! If your cube has
+mapping labels, **isis2std** will write a **world file** that provides
+GIS software, and other software which can take advantage of a
+geographically registered image, with the necessary information to
+properly display your image. Most applications designed to work with
+remotely sensed and map data (such as Arc products, Envi, and Global
+Mapper) can use TIFF, JPEG, and other images with world files. Several
+geographic software applications even have support for planetary data.
+
+
+### Exporting to FITS
+
+[**isis2fits**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2fits/isis2fits.html)
+(ISIS to FITS format) exports your cubes to Flexible Image Transport
+System (FITS) format, a standard in the astronomical community. There's
+lots of software designed to work with FITS (even a few common
+applications and software libraries , like ImageMagick and GIMP). In
+general, FITS format is useful for mission team members who are working
+with cruise data to analyze instrument calibration, camera pointing, and
+other factors. Since cruise image data frequently contain stars,
+astronomy software comes in quite useful for this type of work.
+
+
+### Exporting to RAW
+
+[**isis2raw**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2raw/isis2raw.html)
+(ISIS to Raw format) exports an individual band in your cube to raw
+image format, a minimal format that contains just the data in the
+bit-type of your choosing. **isis2raw** is a good choice when none of
+the other formats ISIS can export to will work for you. In order to
+import a raw image into another application, you will need to know the
+width (samples), height (rows), bit-type, and endianness of your raw file
+in order to import it correctly, so remember to keep track of the
+parameters you used to export your cube.
+
+
+### Related ISIS Applications 
+
+See the following ISIS documentation for information about the
+applications you will need to use to perform this procedure:
+
+  - [**isis2std**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2std/isis2std.html)
+    : Export a cube to popular image formats, such as TIFF and PNG, with
+    GIS world files
+  - [**isis2fits**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2fits/isis2fits.html)
+    : Export a cube to FITS format, the standard image format of the
+    astronomical community
+  - [**isis2raw**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/isis2raw/isis2raw.html)
+    : Export a cube to raw format

docs/getting-started/Using ISIS: First Steps/Locating and Ingesting Image Data.md

+
+# Locating and Ingesting Image Data 
+-----
+This page provides guidance on locating, downloading, and ingesting planetary
+datasets of interest.
+
+## Planetary Image Atlas 
+-----
+
+Overview of the Planetary Data System [PDS](http://pds.nasa.gov/) Image
+Atlas
+
+Planetary Image Atlas
+
+The internet has greatly improved the ability to locate and download
+planetary data. The Planetary Data System (PDS) Planetary Image Atlas is
+the most comprehensive source for planetary data from current and past
+planetary missions. The web site provides tools to help you find image
+data that covers your area of interest in the vast quantities available.
+
+[Planetary Data System Image Atlas.](http://pdsimg.jpl.nasa.gov/Atlas)
+
+Data can be found for each planet, some example missions and instruments listed below.
+
+
+### Venus 
+
+  - *Magellan* : Synthetic Aperture Radar (SAR)
+
+
+### Moon 
+
+  - *Clementine* : Star Tracker A and B (STAR-A and STAR-B), High
+    Resolution (HIRES), Long Wave Infrared (LWIR), Near Infrared (NIR),
+    and Ultraviolet/Visible (UVVIS)
+
+
+### Mars 
+
+  - *Mars Odyssey* : Thermal Emission Imaging System
+    [THEMIS](http://themis-data.asu.edu/) , and Gamma Ray Spectrometer
+    (GRS)
+  - *Mars Exploration Rovers* : Hazard Cameras (HAZCAM), Navigation
+    Cameras (NAVCAM), Microscopic Imager (MI), and Panorama Cameras
+    (PANCAM),
+  - *Mars Global Surveyor* : Mars Orbiter Camera
+    [MOC](http://ida.wr.usgs.gov/) , and Mars Orbiter Laser Altimeter
+    (MOLA)
+  - *Pathfinder* : Imager for Mars Pathfinder (IMP), Rover (navigation
+    and hazard avoidance system cameras), Alpha Proton X-Ray
+    Spectrometer (APXS), and Meteorology Package (MET)
+  - *Viking Landers* : Lander Camera System (LCS)
+  - *Viking Orbiter* : Visible (VIS A and B)
+
+
+### Outer planets 
+
+  - *Voyager* : Imaging Science Subsystem Narrow Angle (ISS-NA)and Wide
+    Angle (ISS-WA)
+  - *Galileo* : Solid State Imaging (SSI) and Near-Infrared Mapping
+    Spectrometer (NIMS)
+  - *Cassini* : Imaging Science Subsystem (ISS), Visual and
+    Infrared Mapping Spectrometer (VIMS)
+
+
+## Power Tips for the PDS Image Atlas 
+
+-----
+
+Finding exactly the data you want for your project can be challenging.
+The following tips and tools may help to you get the results you want
+and weed out the ones you don't.
+
+  - **Increase the size of the latitude and longitude box for search** .
+    In your initial searches that use latitudes and longitudes to find
+    image coverage, it is a good idea to increase the bounds of your
+    search. This will help you find images where the camera pointing
+    indicates the image is outside your area of interest but are
+    actually within it. For the Viking mission, your data search
+    boundaries should be increased by as much as 5 degrees to account
+    for pointing errors for the camera.
+  - **Use advanced parameters to refine your search, but don't overdo
+    it** . For many data sets, there are other search parameters that can
+    be entered in addition to the basic Quick Search options. Look above
+    the main search form for a toolbar with tabs such as Geometry,
+    Instrument, Features, and Time. Click one of the tabs to access
+    additional search parameters related to that particular category.
+    For example, if you're searching for Microscopic Imager images from
+    the Mars Exploration Rover mission, the [PDS Image Atlas search
+    page](http://pds-imaging.jpl.nasa.gov/search/) has an option under
+    the Instrument tab to search for images with the dust filter open or
+    closed.
+  - **Use the cumulative index to interrogate the collection** .
+    Datasets within the Planetary Data System are not limited to digital
+    image data. For each mission, there are also text files that contain
+    information about the image data. The cumulative index will be
+    covered in more detail later in this lesson.
+
+
+## Using the Cumulative Index and Table 
+
+-----
+
+Use the cumulative index to interrogate the collection. Data sets within
+the Planetary Data System are not limited to digital image data. For
+each mission, there are also text files that contain information about
+the image data. Two files that can prove useful in locating data that
+will meet your needs are the Cumulative Index table and the Cumulative
+Index label. As the name implies, the "table" is added to throughout the
+life of the mission. You will want to find the final volume of the
+collection so that all the products will be represented.
+
+  - **Cumulative Index Table** - This file is a table of text that
+    contains information about all the images for a mission up to some
+    date during the mission. You will probably want to find the final
+    volume of a collection so all the products will be represented in
+    the table. The format of the table allows you to use word processing
+    or spreadsheet programs to view the data. You can also write
+    programs or scripts that can interrogate the values and return
+    results. There are many types of information for each image in the
+    collection. You will find information about the instrument that
+    acquired the image, such as the instrument name and the filter used.
+    You can also obtain information that may prove useful in the
+    calibration of an image. Another useful value is the media volume
+    the image data resides on.
+  - **Cumulative Index Label** - This file is a text file that describes
+    each field in the cumulative index table.
+
+
+#### Where do I find the Cumulative Index and Table files? 
+
+These files are included in the directory structure for a mission's
+[PDS](http://pds.nasa.gov/) data distribution. The data distribution is
+generally designed to be put on CD-ROM, and can be accessed through the
+PDS Image Atlas. On the Image Atlas front page, **click Online Data
+Volumes** for a particular mission. You'll be presented a list of all
+the volumes (effectively, a CD-ROMs worth of data and information).
+Click the last volume on the list to get a file list for that volume:
+you should see a directory named INDEX - this is where the Cumulative
+Index and Table files are stored, as well as the index and table files
+for this specific volume.
+
+!!! Example "Try it\!"
+    - [PDS Image Atlas](http://pdsimg.jpl.nasa.gov/Missions/index.html)
+      click on the Data Volumes Index link on the upper left
+        - [PDS Image Volume](http://pds-imaging.jpl.nasa.gov/volumes/) in
+          the By Mission column, click on the Full Resolution UVVIS
+          Digital Image Model in the Clementine section
+        - [Clementine CD-ROM/Online Data Volumes](http://pdsimg.jpl.nasa.gov/Admin/resources/cd_clementine.html#clmUVVIS)
+          under the Mission to the Moon: Full Resolution Clementine UVVIS
+          Digital Image Model section, find the last volume listed. Click
+          on one of the two volume icons.
+            - [Final Volume - cl\_4078](http://pdsimage.wr.usgs.gov/archive/clem1-l-u-5-dim-uvvis-v1.0/cl_4078/)
+              Click on the index folder.
+            - [Index directory](http://pdsimage.wr.usgs.gov/archive/clem1-l-u-5-dim-uvvis-v1.0/cl_4078/index/)
+                - [Cumulative Index](http://pdsimage.wr.usgs.gov/archive/clem1-l-u-5-dim-uvvis-v1.0/cl_4078/index/cumindex.lbl)
+                - [Cumulative Table](http://pdsimage.wr.usgs.gov/archive/clem1-l-u-5-dim-uvvis-v1.0/cl_4078/index/cumindex.tab)
+
+
+## Other Planetary Image Data Resources 
+
+-----
+
+The following are just a few sites distributing planetary data.
+
+  - The [ASU Mars 2001 Odyssey THEMIS](http://themis-data.asu.edu/) data
+    distribution web site provides another source for THEMIS imagery.
+  - MGS MOC data can be found on [USGS PDS Mars Global Surveyor Mars
+    Orbiter Camera (MOC) Image Collection](http://ida.wr.usgs.gov/) .
+  - [JMARS](http://jmars.asu.edu/)
+
+
+## Introduction to Importing 
+
+-----
+
+The job of ingestion programs is to convert the image from another file
+format to one ISIS3 applications understand (i.e., the ISIS3 cube
+format). Once a file has been imported, you can use ISIS3 programs to
+view and manipulate the data. When ingesting data into ISIS3, there are
+multiple applications in two major categories which can be used to
+import a file -- choose the one that is best for your data set:
+
+  - **General Importers** - are used to convert image files in non-ISIS3
+    cube format such as PDS, JPEG or PNG to standard ISIS3 cube format.
+  - **Mission Data Importers** - are used to convert specific mission
+    image files such as [MOC](http://ida.wr.usgs.gov/) Wide Angle or
+    [THEMIS](http://themis-data.asu.edu/) IR to ISIS3 cube format.
+
+
+## General Importers 
+
+-----
+
+These applications output an ISIS3 formatted cube with an ISIS3 header
+that contains the minimum required basic keywords for general ISIS3
+processing. A few examples of general processing are stretching,
+filters, and generating histograms. It is important to note that these
+import applications neither create the necessary labels for mission
+specific applications such as radiometric calibration and noise removal,
+nor can the cubes created by them be projected.
+
+
+### Planetary Data System (PDS) labeled image files 
+
+**pds2isis**
+
+This application will import a [PDS](http://pds.nasa.gov/) labeled image
+file into an ISIS3 cube. Only a minimal set of label keywords required
+by ISIS3 will be put into the output file. No translation of mission
+specific keywords will be done. Read the help page for
+[**pds2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/pds2isis/pds2isis.html)
+.
+
+*Example command line* :
+
+``` 
+ pds2isis FROM=mars_viking.pds TO=mars_viking.cub
+```
+
+!!! Example "Try it\!"
+    Download a sample PDS file (
+    [Mars\_viking.pds.gz](../../assets/locating_and_ingesting_image_data/Mars_viking.pds.gz) ),
+    convert it to an ISIS3 cube, and view it using qview.
+
+
+## Raw image files 
+
+-----
+
+**raw2isis**
+
+This application imports raw image files into an ISIS3 cube. Bytes can
+be swapped if necessary, and there are options to create special pixels.
+It is very important the *correct number of lines and samples is
+provided* to the application -- incorrect values will result in a
+garbled output image.
+
+
+<figure class="inline" markdown>
+  ![Incorrect](../../assets/locating_and_ingesting_image_data/incorrect.png "Incorrect Raw2Isis")
+  <figcaption>Incorrect use of raw2isis with 1203 samples.</figcaption>
+</figure>
+
+<figure class="inline end" markdown>
+  ![correct.png](../../assets/locating_and_ingesting_image_data/correct.png "Raw2isis")
+  <figcaption>Correct use of raw2isis with 1204 samples.</figcaption>
+</figure>
+-----
+
+You must also know if the incoming raw file has a header and what the
+size of the header is. If the raw file has a header, you must use the
+parameter "skip" to skip over any header information that is in the raw
+file. Read the help page for
+[**raw2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/raw2isis/raw2isis.html)
+for more about the parameters and use of **raw2isis** .
+
+*Example command line:*
+
+    raw2isis FROM=image.raw TO=image.cub
+             samples=1204 lines=1056
+             bittype=UNSIGNEDBYTE skip=2137
+
+!!! Example "Try it\!"
+    Download a sample RAW file (
+    [Mars\_viking.raw.gz](../../assets/locating_and_ingesting_image_data/Mars_viking.raw.gz) ),
+    convert it to an ISIS3 cube, and view it using qview. Hint: the image is
+    1024 lines by 1024 samples, and has a 4019 byte header.
+
+
+### Video Image Communication and Retrieval (VICAR) image files 
+
+**vicar2isis**
+
+This application imports VICAR formatted image files into ISIS3 cubes.
+No translation of mission specific VICAR labels is done. Read the help
+page for
+[**vicar2isis**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/vicar2isis/vicar2isis.html)
+.
+
+*Example command line:*
+
+    vicar2isis FROM=mexpress_vicar.img TO=mexpress_vicar.cub
+
+!!! Example "Try it\!"
+    Download a sample VICAR file (
+    [Mexpress\_vicar.img.gz](../../assets/locating_and_ingesting_image_data/Mexpress_vicar.img.gz)
+    ), convert it to an ISIS3 cube, and view it using qview.
+
+
+## Importing Mission Data 
+
+-----
+
+Mission-specific ingestion applications are used to ingest data
+distributed for specific missions. These applications will output ISIS3
+formatted cube files that have mission-specific keywords in the labels.
+These keywords are required for calibration and projection processing
+tasks. Often, there will be mission specific applications for
+calibrating, correcting, analyzing, and enhancing a mission data set.
+These programs require the keywords from the mission-specific ingestion
+applications and will not work properly if a general ingestion
+application is used.
+
+  - [**ciss2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/ciss2isis/ciss2isis.html)
+    : Import a Cassini ISS VICAR image file into ISIS
+  - [**moc2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/moc2isis/moc2isis.html)
+    : Import [PDS](http://pds.nasa.gov/) formatted
+    [MOC](http://ida.wr.usgs.gov/) image cube into ISIS3 format cube
+  - [**thm2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/thm2isis/thm2isis.html)
+    : Import a [THEMIS](http://themis-data.asu.edu/) IR/VIS RDR or EDR
+  - [**hi2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/hi2isis/hi2isis.html)
+    : Import HiRISE EDR images into ISIS3 cube format
+  - [**vik2isis**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/vik2isis/vik2isis.html)
+    : Import [PDS](http://pds.nasa.gov/) formatted Viking EDR
+    into ISIS3 format cube
+
+!!! Example "Try it\!"
+    - [Find and download a Mars Global Surveyor Mars Orbiter Camera
+      image](http://ida.wr.usgs.gov/graphical.htm) (hint: the "Download
+      Standard Compressed Data Product" link will give you a file ending
+      in .imq - this is a [PDS](http://pds.nasa.gov/) formatted
+      [MOC](http://ida.wr.usgs.gov/) file)
+    - Convert the MOC file to an ISIS3 cube using
+      [**moc2isis**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/moc2isis/moc2isis.html)
+    - View the imported file using
+      [**qview**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/qview/qview.html)
+

docs/how-to-guides/Software Management/Software Support.md

@@ -5,7 +5,7 @@ This document provides information about the software support process, including
 ## Step 1: Scheduling the Support Sprint
 While there is some leeway in the exact timing of each support sprint, the sprints must be scheduled quarterly and should be scheduled roughly 3 months apart. Project scheduling should be coordinated by the project/technical lead and the software lead during routine software scheduling meetings.
 
-After setting up the sprint schedule, the technical lead should create a software support board and communicate the schedule contributors.
+After setting up the sprint schedule, the technical lead should create a software support board and communicate the schedule to contributors.
 
 ## Step 2: Setting up the Project Board
 Immediately after scheduling the support sprint, the technical lead should create a project board to facilitate the tracking, prioritization, and assignment of issues.  This has traditionally taken the form of a GitHub [projects board](https://github.com/orgs/DOI-USGS/teams/astrogeology-developers/projects) or a GitHub [discussion post](https://github.com/DOI-USGS/ISIS3/discussions), both of which provide automated tracking for issues that are hosted on GitHub. 
@@ -13,7 +13,7 @@ Immediately after scheduling the support sprint, the technical lead should creat
 !!! Note "Due to recent changes in permissions and organizational boundaries, project boards can only be created as private (within-organization), which precludes external contributors from viewing or editing the board."
 
 ## Step 3: Notifying the Community
-With a project board, there is now a mechanism to store incoming issues, and the technical lead can notify the community of the upcoming sprint.  There is no "correct" way to notify community members, but the recommended method is via a MS Team calendar event, which allows the host to send an email with an associated meeting invitation.
+With a project board in place, there is now a mechanism to store incoming issues, and the technical lead can notify the community of the upcoming sprint.  There is no "correct" way to notify community members, but the recommended method is via an MS Teams calendar event, which allows the host to send an email with an associated meeting invitation.
 
 This email should include:
 
@@ -44,9 +44,9 @@ Despite community engagement, contributors do not generally produce enough issue
 Prioritization meetings are typically a loosely guided discussion in which the technical lead acts as the facilitator.  Prioritization meetings generally follow a format such as:
 
 1. Ask attendees if there are any last-minute issues that should be added.
-1. Introduce and prioritize issues.  If the issue creator in in attendance, call on them for an issue summary and their perspective on relative importance.  If creator is not in attendance, technical lead should be prepared to offer a summary / context on the issue and ask community about importance of issue.
+1. Introduce and prioritize issues.  If the issue creator is in attendance, call on them for an issue summary and their perspective on relative importance.  If the creator is not in attendance, the technical lead should be prepared to offer a summary / context on the issue and ask the community about the importance of the issue.
 1. When all issues are prioritized, revisit any issues that may need additional discussion.
 1. Ask for any closing remarks
 
 ??? Note "Issue deferral"
-    Deferring an issue generally means "this is a good, important issue, but it requires further discussion." This discussion should not interrupt the flow of prioritization, and discussing deferred issues is usually a good
\ No newline at end of file
+    Deferring an issue generally means "this is a good, important issue, but it requires further discussion." This discussion should not interrupt the flow of prioritization, and discussing deferred issues is usually a good final topic.
\ No newline at end of file

mkdocs.yml

@@ -40,6 +40,10 @@ nav:
     - Home: getting-started/index.md
     - CSM Stack:
       - Generating an ISD, creating a CSM model, and converting coordinates: getting-started/CSM Stack/ImageToGroundTutorial.ipynb
+    - "Using ISIS: First Steps":
+      - Locating and Ingesting Image Data: "getting-started/Using ISIS: First Steps/Locating and Ingesting Image Data.md"
+      - Adding SPICE: "getting-started/Using ISIS: First Steps/Adding Spice.md"
+      - Exporting ISIS Data: "getting-started/Using ISIS: First Steps/Exporting ISIS Data.md"
   - How-To Guides: 
     - Home: how-to-guides/index.md
     - Environment Setup and Maintenance: