Commit eee00e74 authored by Laura, Jason R's avatar Laura, Jason R
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Updates Wiki URLS for DGEC migration

parent 7238c461
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@@ -14,26 +14,23 @@

-----

  - [Automatic Registration](#Automatic-Registration)
      - [Introduction](#Introduction)
      - [Match Algorithm Definition Files
        (PVL)](#Match-Algorithm-Definition-Files-PVL)
      - [Match Algorithms](#Match-Algorithms)
          - [Maximum Correlation](#Maximum-Correlation)
          - [Minimum Difference](#Minimum-Difference)
      - [Tolerance](#Tolerance)
      - [Chips](#Chips)
          - [Pattern Chip](#Pattern-Chip)
          - [Search Chip](#Search-Chip)
      - [Restricting Input Pixel
        Ranges](#Restricting-Input-Pixel-Ranges)
          - [Valid Minimum/Maximum](#Valid-MinimumMaximum)
          - [Valid Pixel Count
            (ValidPercent)](#Valid-Pixel-Count-ValidPercent)
      - [Fit Chip](#Fit-Chip)
      - [Sub-Pixel Accuracy](#Sub-Pixel-Accuracy)
          - [Surface Modeling](#Surface-Modeling)
      - [AutoRegDefaults](#AutoRegDefaults)
- [Automatic Registration ¶](#automatic-registration-)
  - [Introduction ¶](#introduction-)
  - [Match Algorithm Definition Files (PVL) ¶](#match-algorithm-definition-files-pvl-)
  - [Match Algorithms ¶](#match-algorithms-)
    - [Maximum Correlation ¶](#maximum-correlation-)
    - [Minimum Difference ¶](#minimum-difference-)
  - [Tolerance ¶](#tolerance-)
  - [Chips ¶](#chips-)
    - [Pattern Chip ¶](#pattern-chip-)
    - [Search Chip ¶](#search-chip-)
  - [Restricting Input Pixel Ranges ¶](#restricting-input-pixel-ranges-)
    - [Valid Minimum/Maximum ¶](#valid-minimummaximum-)
    - [Valid Pixel Count (ValidPercent) ¶](#valid-pixel-count-validpercent-)
  - [Fit Chip ¶](#fit-chip-)
  - [Sub-Pixel Accuracy ¶](#sub-pixel-accuracy-)
    - [Surface Modeling ¶](#surface-modeling-)
  - [AutoRegDefaults ¶](#autoregdefaults-)

<span id="Introduction"></span>

@@ -272,7 +269,7 @@ is:
N(search) \>= N(pattern) + 2 and similarly for M. This ensures that the
Pattern Chip spans at least a 3x3 window within the Search Chip. An
important requirement for surface fitting in order to compute sub-pixel
accuracy. (Refer to: [Sub-Pixel\_Definition](https://USGS-Astrogeology.github.io/ISIS3/gh-pages/ISIS_Cube_Format) ).
accuracy. (Refer to: [Sub-Pixel\_Definition](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format) ).

**TIPS:**

@@ -306,13 +303,13 @@ accuracy. (Refer to: [Sub-Pixel\_Definition](https://USGS-Astrogeology.github.io

-----

The validity of the input pixels ( [What\_Are\_Pixels](https://USGS-Astrogeology.github.io/ISIS3/gh-pages/ISIS_Cube_Format)
The validity of the input pixels ( [What\_Are\_Pixels](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format)
) of the [Pattern Chip](fixit.wr.usgs.gov) is the very first test
performed. Prior to the match algorithm being invoked during the walk
process, a simple test is performed to ensure there are enough pixels to
work with. Pixels are deemed valid if they are in the minimum/maximum
range and/or they are not special pixel values. (
[What\_Are\_Special\_Pixels](https://USGS-Astrogeology.github.io/ISIS3/gh-pages/Special_Pixels.html)
[What\_Are\_Special\_Pixels](https://DOI-USGS.github.io/ISIS3/gh-pages/Special_Pixels.html)
).

The Pattern Chip is only checked once. If it does not contain enough
@@ -428,7 +425,7 @@ Chip](fixit.wr.usgs.gov) . The Fit Chip contains the resulting
correlation position between the two chips of a maximum of ONE pixel
accuracy. In many cases, the actual, ultimate registration may lie
somewhere between two pixels. (Refer to:
[Sub-Pixel\_Definition](https://USGS-Astrogeology.github.io/ISIS3/gh-pages/ISIS_Cube_Format) ).
[Sub-Pixel\_Definition](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format) ).

The sub-pixel accuracy can be turned off through the PVL settings as
follows:
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@@ -14,15 +14,14 @@

-----

  - [Camera Geometry](#Camera-Geometry-)
      - [Introduction](#Introduction-)
      - [Camera Geometry](#Camera-Geometry-2-)
      - [Camera Information
        Applications](#Camera-Information-Applications-)
          - [Camstats](#Camstats-)
          - [Mosrange](#Mosrange-)
          - [Campt](#Campt-)
          - [Phocube](#Phocube-)
- [Camera Geometry ¶](#camera-geometry-)
  - [Introduction ¶](#introduction-)
  - [Camera Geometry ¶](#camera-geometry--1)
  - [Camera Information Applications ¶](#camera-information-applications-)
    - [**Camstats** ¶](#camstats-)
    - [**Mosrange** ¶](#mosrange-)
    - [**Campt** ¶](#campt-)
    - [**Phocube** ¶](#phocube-)

<span id="Introduction"></span>

@@ -177,7 +176,7 @@ Example (not all parameters shown):

[**phocube**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/phocube/phocube.html)
will compute and generate a separate output [multi-band ISIS3
cube](https://USGS-Astrogeology.github.io/ISIS3/gh-pages/ISIS_Cube_Format.html) where each band will represent the selected
cube](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format.html) where each band will represent the selected
(parameter=TRUE) geometric and photometric elements. The bands are named
appropriately in the output cube labels: **Group=BandBin** .

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@@ -5,7 +5,7 @@ Documentation for ISIS applications is located within the ISIS source code and w

For many documentation contributions, very little understanding of XML is required. Changes in existing wording or additional information can be added where appropriate in the current documentation without needing to change any of the XML. 

Since the ISIS documentation is located within the source code, the first step is to create a local copy of the ISIS source code to work with. To do the necessary initial setup, first complete the steps in [Getting Started with Github](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github), then move on to [Anaconda and ISIS3 Dependencies](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github). 
Since the ISIS documentation is located within the source code, the first step is to create a local copy of the ISIS source code to work with. To do the necessary initial setup, first complete the steps in [Getting Started with Github](https://github.com/DOI-USGS/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github), then move on to [Anaconda and ISIS3 Dependencies](https://github.com/DOI-USGS/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github). 
 
# Making Your Documentation Change

@@ -21,7 +21,7 @@ a new ISIS build.

### Creating a New ISIS build: 

Building ISIS requires that the anaconda environment you created in [Anaconda and ISIS3 Dependencies](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#anaconda-and-isis3-dependencies) be activated.
Building ISIS requires that the anaconda environment you created in [Anaconda and ISIS3 Dependencies](https://github.com/DOI-USGS/ISIS3/wiki/Developing-ISIS3-with-cmake#anaconda-and-isis3-dependencies) be activated.

Activate your anaconda environment with:

@@ -75,7 +75,7 @@ To view your documentation, open the `index.html` file immediately under the doc
If you see changes that need to be made to the documentation at this point, you can make the changes in your documentation XML files, re-run your documentation build command, and then just refresh the web-page in your browser to view your updated changes. 

# Adding Your Documentation Changes to ISIS
To contribute your documentation changes to ISIS, please put in a pull request containing your documentation changes, following the instructions at [How to Put in a PR](https://github.com/USGS-Astrogeology/ISIS3/wiki/How-to-Start-Contributing#create-a-pull-request). Be sure to read the [Contributing](https://github.com/USGS-Astrogeology/ISIS3/blob/dev/CONTRIBUTING.md) document, and to select the "Documentation change" under "Types of change" in the PR template which will appear when you put in your pull request. Your pull request will be reviewed by the software team at the Astrogeology Science Center. 
To contribute your documentation changes to ISIS, please put in a pull request containing your documentation changes, following the instructions at [How to Put in a PR](https://github.com/DOI-USGS/ISIS3/wiki/How-to-Start-Contributing#create-a-pull-request). Be sure to read the [Contributing](https://github.com/DOI-USGS/ISIS3/blob/dev/CONTRIBUTING.md) document, and to select the "Documentation change" under "Types of change" in the PR template which will appear when you put in your pull request. Your pull request will be reviewed by the software team at the Astrogeology Science Center. 

# Additional Information About User Documentation in ISIS
For a comprehensive overview of ISIS documentation, see the following:
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## This page has moved. Please see https://USGS-Astrogeology.github.io/ISIS3/gh-pages/Core_Base_and_Multiplier.html
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## This page has moved. Please see https://DOI-USGS.github.io/ISIS3/gh-pages/Core_Base_and_Multiplier.html
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## 1. Deprecation Proposal
Those who wish to deprecate functionality in ISIS should propose the deprecation via an issue on the [ISIS repository](https://github.com/USGS-Astrogeology/ISIS3/issues).  This allows for discussion among the developers and the user community.  If a consensus is met that the functionality should be deprecated, then a deprecation warning should be written.
Those who wish to deprecate functionality in ISIS should propose the deprecation via an issue on the [ISIS repository](https://github.com/DOI-USGS/ISIS3/issues).  This allows for discussion among the developers and the user community.  If a consensus is met that the functionality should be deprecated, then a deprecation warning should be written.

## 2. Deprecation Warning
A deprecation warning should be presented to the user whenever the deprecated functionality is used.  Though no standard has yet been agreed upon by the developers or the ISIS user base, previous deprecation warnings have taken the form of a simple message printed via `cout`.  In addition to creating the deprecation warning message, the deprecated functionality should also be noted in the [changelog](https://github.com/USGS-Astrogeology/ISIS3/blob/dev/CHANGELOG.md).  This warning should include a link to the issue that proposed the deprecation.
A deprecation warning should be presented to the user whenever the deprecated functionality is used.  Though no standard has yet been agreed upon by the developers or the ISIS user base, previous deprecation warnings have taken the form of a simple message printed via `cout`.  In addition to creating the deprecation warning message, the deprecated functionality should also be noted in the [changelog](https://github.com/DOI-USGS/ISIS3/blob/dev/CHANGELOG.md).  This warning should include a link to the issue that proposed the deprecation.

## 3. Removal of Deprecated Functionality
No less than 6 months after the release that includes the deprecation notice, a commit containing the removal of the deprecated functionality should be PR'd into the development branch.  This change should also be captured in the changelog.
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