View source for Documentation/4.5/HowTo

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{{Infobox
|name         = 3D Slicer {{documentation/version}}
|above        = 3D Slicer
|abovestyle   = 

|image        = [[File:3DSlicer41Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
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|headerstyle  = background:#E7DCC3;
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|datastyle    = 

|header1 = Description
|label1  = 
|data1   =
|header2 =
|label2  = 
|data2   = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3  = 
|data3   = Free and extensible open source package.
|header4 =
|label4  = Multi-platform
|data4   = Linux, MacOSX, Windows
|header5 =
|label5  = Version
|data5   = {{documentation/version}}
|header6 =
|label6  = License
|data6   = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

= Overview =

This document aims at describing the principle and guidelines to consider when writing Slicer user documentation.

The documentation framework has been designed keeping in mind the following principles:
* Single location for editing documentation (either the wiki or the source code), no duplicative editing.
* Smart use of mediawiki templates to enforce consistency and reduce maintenance work.


__TOC__

= Naming conventions =
# The application '''Slicer''' should be referenced with an uppercase '''S'''.
# All documentation should be added as subpages under '''Documentation/X.Y/''' where '''X''' and '''Y''' are respectively the '''major''' and '''minor''' Slicer version.
# Version of Slicer should NOT be written in plain text, {{[[Template:Documentation/version|documentation/version]]}} template should be used instead.
# [[Documentation/{{documentation/version}}/SlicerApplication]] should be the root of all subpages specific to Slicer application.
# [[Documentation/{{documentation/version}}/Modules]] should be the root of all subpages specific to Slicer modules.
# Module subpage should be named after the '''module name''' used in the associated source repository. Assuming the module is named '''Foo''', the corresponding subpage is expected to be '''Documentation/{{documentation/version}}/Modules/Foo'''
# Collaborator names, logos or URLs should be referenced using the convenient [[Template:Collaborator|Collaborator]] template.
## For example: <nowiki>''{{collaborator|longname|namic}}''</nowiki> generates ''{{collaborator|longname|namic}}''
# Email addresses must be wrapped with the '''<nowiki><email></email></nowiki>''' tags

= Documentation version =

In addition to the wiki documentation specific to each release 4.0, 4.1 ... there is also a namespace named "Nightly".

See http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly

* This set of documentation pages applies to the nightly build of Slicer.

* Documentation associated with new features, new modules, new extensions etc .. should be added into the Nightly set.

* If an edit done on Nightly pages also applies to the "{{documentation/currentversion}}" ones, the edit should also be done on the {{documentation/currentversion}} pages.

* When Slicer {{documentation/nextversion}} will be released, the set of "Nightly" pages will be copied into "{{documentation/nextversion}}" then the nightly pages will continue to evolve until the next release.

See [http://slicer-devel.65872.n3.nabble.com/Slicer-wiki-quot-Nightly-quot-documentation-tt4026026.html email sent on the list August 23, 2012].

= Category =
# All subpages should be categorized. See [https://secure.wikimedia.org/wikipedia/mediawiki/wiki/Help:Categories#Adding_a_page_to_a_category]
# The user documentation pages are grouped in the [[:Category:Documentation/{{documentation/version}}/SlicerApplication|Slicer Application]] and [[:Category:Documentation/{{documentation/version}}/Modules|Modules]] categories.

= SlicerApplication page =
# [[Template:Documentation/{{documentation/version}}/slicerapplication-header|slicerapplication-header]] and [[Template:Documentation/{{documentation/version}}/slicerapplication-footer|slicerapplication-footer]] templates should be respectively used at the top and the bottom of the page.

= Module page =
# [[Template:Documentation/{{documentation/version}}/module-header|module-header]] and [[Template:Documentation/{{documentation/version}}/module-footer|module-footer]] templates should be respectively used at the top and the bottom of the page.
# [[Template:Documentation/modulename|modulename]] should be used instead of writing in plain text the name of the module.
# Base your work on either [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME]] or an [[:Category:Documentation/{{documentation/version}}/Modules|existing module]] documentation.
# For CLI modules, the '''SVNREVISION''' revision number is reported on this [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Applications/CLI page]. The module description and the information for developers would be automatically extracted from the corresponding XML description. 
# See [[Documentation/{{documentation/version}}/ModulesMetadata|this page]] to define the revision number. The revision number associated to a module is used to extract module information from the source code directly.

== Documentation for a CLI module ==
The main idea is to re-use the documentation of the CLI parameters in the wiki. When a CLI is added into Slicer, please execute the following steps to create the module online documentation.
# Create a CLI in Slicer4/Modules/CLI
# Add your module in [[Documentation/{{documentation/version}}/ModulesMetadata]]. Adding a module consists of adding a module name+revision pair alphabetically in the list. The revision number must correspond to the most up to date revision number of your module.
# Copy the content of the [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|template]] module and paste it in a page you created with the name of your module: [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME]].
# Edit the wiki code to replace the generic information with the module specific information. You can upload screenshots and tutorials.

== Documentation for a loadable module ==
Creating online documentation for loadable modules is similar to CLI modules. The difference is that loadable modules don't have parameter descriptions, it must be added separately.
# In Slicer4, if it doesn't exist yet
## create a ''Documentation'' subdirectory in your module directory (e.g. ''Slicer4/Modules/Loadable/Transforms/Documentation'').
## Copy and rename the ''YourModuleName.{xml,dox}'' files from an existing module documentation.
# Add description for each [[Documentation/{{documentation/version}}/Developers/Style_Guide/UI#Section|section]] of your module (''YourModuleName.xml'') applying the following pattern:
<pre>
  <parameters>
    <label>Section1 header</label>
    <parameter>
      <label>Parameter1 name</label>
      <description><![CDATA[Parameter1 description]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Section2 header</label>
    <parameter>
      <label>Parameter2 name</label>
      <description><![CDATA[Parameter2 description]]></description>
    </parameter>
    <parameter>
      <label>Parameter3 name</label>
      <description><![CDATA[Parameter3 description]]></description>
    </parameter>
  ...
</pre>

== Documentation for a scripted module ==
The trick used in loadable module documentation is not supported yet for scripted modules. Documentation must be written directly in the created module wiki page.

= Extension page =
# Create an extension page
## [[Template:Documentation/{{documentation/version}}/extension-footer|extension-footer]] template should be at the bottom of the page. Except for page doing a REDIRECT.
## If the extension bundles exactly [[Documentation/{{documentation/version}}/Developers/Tutorials/BundleModulesIntoExtension#Extension_bundles_1_module|one]] module, use [{{fullurl:Documentation/{{documentation/version}}/Extensions/SkullStripper|redirect=no}} this template]
## If the extension bundles [[Documentation/{{documentation/version}}/Developers/Tutorials/BundleModulesIntoExtension#Extension_bundles_N_modules|more]] than one module, use [[Documentation/{{documentation/version}}/Extensions/Plastimatch|this template]].
# Add an extension entry in [[Documentation/{{documentation/version}}/Extensions#Extension_Categories]]
# The extension should now be listed on [[Documentation/{{documentation/version}}]].
# Create a [[#Module_page|regular wiki page]] for each module of the extension using the [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|template]] page. The URLs of the extension modules are the same than the built-in modules.



== Remarks ==

=== Actively maintained and developed extension ===

* If the extension is actively developed and maintained so that the code of the nightly extension is the same as the extension associated with a specific slicer release (i.e {{documentation/currentversion}}), a different approach could be considered.

==== Extension bundles ONE module ====

* In addition to create the following pages:

 Documentation/Nightly/Extensions/YOURMODULENAME
 Documentation/{{documentation/currentversion}}/Extensions/YOURMODULENAME
 Documentation/Nightly/Modules/YOURMODULENAME
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME

* ... and setup the following [http://www.mediawiki.org/wiki/Help:Redirects redirect]:

 Documentation/Nightly/Extensions/YOURMODULENAME  ->   Documentation/Nightly/Modules/YOURMODULENAME

 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME  ->   Documentation/Nightly/Modules/YOURMODULENAME

 Documentation/{{documentation/currentversion}}/Extensions/YOURMODULENAME  ->   Documentation/Nightly/Modules/YOURMODULENAME   # Since [http://www.mediawiki.org/wiki/Help:Redirects#Double_redirects double redirect are not supported]. Version specific extension page redirects to Nightly module page.

* The only page that would be updated would be the Nightly one:

 Documentation/Nightly/Modules/YOURMODULENAME


==== Extension bundles N modules ====

In addition to create the following pages:

 Documentation/Nightly/Modules/YOURMODULENAME_0
 Documentation/Nightly/Modules/YOURMODULENAME_1
 [...]
 Documentation/Nightly/Modules/YOURMODULENAME_N
 
 Documentation/Nightly/Extensions/YOUREXTENSIONNAME
 
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_0
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_1
 [...]
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_N
 
 Documentation/{{documentation/currentversion}}/Extensions/YOUREXTENSIONNAME

* ... and setup the following [http://www.mediawiki.org/wiki/Help:Redirects redirect]:

 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_0 -> Documentation/Nightly/Modules/YOURMODULENAME_0
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_1 -> Documentation/Nightly/Modules/YOURMODULENAME_1
 [...]
 Documentation/{{documentation/currentversion}}/Modules/YOURMODULENAME_N -> Documentation/Nightly/Modules/YOURMODULENAME_N

 Documentation/{{documentation/currentversion}}/Extensions/YOUREXTENSIONNAME -> Documentation/Nightly/Extensions/YOUREXTENSIONNAME


* The only page(s) that would be updated would be the Nightly ones:

 Documentation/Nightly/Modules/YOURMODULENAME_0
 Documentation/Nightly/Modules/YOURMODULENAME_1
 [...]
 Documentation/Nightly/Modules/YOURMODULENAME_N
 
 Documentation/Nightly/Extensions/YOUREXTENSIONNAME


==== Case where a version specific documentation page diverges from the Nightly one ====

* If for some reason the documentation associated with the version specific extension is going to diverge from the Nightly one. Before modifying the Nightly page, *MAKE SURE* to create the associated version-ed page(s) by copying the content of the Nighty module page(s) into their own page(s).

= Miscellaneous =
* High resolution logos are in the [[Logo_Gallery|Logo Gallery]]
* There is a python helper script for SEM compliant tools that can save a significant amount of transcription time:  Slicer/Utilities/Scripts/SEMToMediaWiki.py 
**To use it run "python Slicer/Utilities/Scripts/SEMToMediaWiki.py -x XMLFILE.xml -o OUTPUT.txt" and the mediawiki content will be in OUTPUT.txt