2011 Slicer4-Documentation-Sprint

The meeting in full swing

What

Slicer 4 Documentation Sprint. The purpose of this event is to jump start the documentation for Slicer 4 in preparation for the RSNA release.

Who

Module creators

Where

1249 Boylston Street

When

October 20, starting at 8am

Background

JC has been working on a design which is supposed to accomplish two objectives:

• Single location for editing documentation (either the wiki or the source code), no duplicative editing.
• As much automation as possible

List of Features & Modules

List of Slicer functionality that we are planning to use at RSNA. All of them should be fully documented and contain proper acknowledgements.

Slicer Features

• Application Layout (Wendy)
• Menu Items
• Tool Bars (Wendy)
• Slice Viewer (Wendy)
  • Mouse/Key Bindings (Steve)
  • Pop Up Controllers (J2)
  • Linking Behavior (Jim)
  • Compare Viewer (Jim)
• 3D Viewer (Wendy)
  • Mouse/Key Bindings
  • Pop Up Controllers (Wendy)
• Data Probe (Steve)
• Load Data Dialogs
• Save Data Dialog (Wendy)

Modules

• Data (Julien)
• Welcome to Slicer (Wendy)
• Volumes (Julien)
• Models (Nicole)
• Scene Views (Nicole)
• Annotations (Nicole)
• Volume Rendering (Julien)
• Editor (Steve)
• Model Maker (Nicole)
• Diffusion Tensor Estimation (Demian)
• Diffusion Tensor Scalar Measurements (Alex)
• Tractography Labelmap Seeding (Demian)
• Tractography Fiducial Seeding (Demian)
• Tractography Display (Demian)
• Change Tracker (Andrey)
• N4 bias correction (Andrey)
• Crop tool (Andrey)
• DICOM (Steve)
• EMSegmenter
• BRAINSTools (Hans)

Extensions:

• ABC
• Plastimatch
• Skullstripper

Naming conventions

• For matter of consistency, both example pages have been renamed:
  • Module:EndUserDocumentationTemplate-Documentation-4.0 -> Documentation/4.0/Modules/YOURMODULENAME
  • Modules:GradientAnisotropicFilter-Documentation-4.0 -> Documentation/4.0/Modules/GradientAnisotropicDiffusion
• The main documentation page has also been renamed from "Documentation-4.0" to Documentation/4.0
• All module documentation pages for a given version of Slicer Y.Z should be named according to the following pattern: Documentation/X.Y/Modules/MODULENAME

Category

The following link will list all modules belonging to the Documentation/4.0/Modules category: http://wiki.slicer.org/slicerWiki/index.php?title=Category:Documentation/4.0/Modules

• The template "Documentation/4.0/module-footer" takes care of including the documentation page in the appropriate category. See [3]
• The following page will list all element from the given category: http://wiki.slicer.org/slicerWiki/index.php/Category:Documentation-4.0-Modules
• "category" is a parameter of the "module-footer" template.
• For CLI module, as explained on the template itself [1], it's recommended to use the template "Documentation/4.0/module-cli-category" that can extract the category from the XML module description. See [4].
• Using the provided module category, the module will also be added to the category "Documentation/4.0/Modules/<MainCategory" and "Documentation/4.0/Modules/<MainCategory.SubCategory>". For example:
  • Documentation/4.0/Modules/Filtering see [5]
  • Documentation/4.0/Modules/Filtering.Denoising see [6].
• Ideally, it would be great if the category associated with loadable module (interactive module) could also be extracted from a unique location. Doing so would avoid to maintain the category attribute both in the source and in the documentation.

Versioning

• All pages and template associated with version X.Y of Slicer are located under the page prefix: Documentation/X.Y
• From any documentation page or template, doing so allows to easily extract the current version using the template Template:Documentation/version. See [7]
  • In other words, assuming the current page is "Documentation/4.2" adding {{documentation/version}} in the source will return 4.2.

• Following each release of Slicer, this approach will allow us to:
  • minimize the work required after a documentation set is duplicated
  • easily reference the different documentation sets
  • automate the duplication of these pages. Let's note that the mediawiki extensions like "Duplicator" [8] or "Multiplicator" [9] could be useful.

• "Long life" of past documentation will also be ensured. Indeed, each time the documentation will be duplicated, a complete set of category, template and documentation page will be created. You will find below what the list of pages and templates could like after 4.2 is released:

      [...]
      Documentation/4.0/Modules/Add
      Documentation/4.0/Modules/GradientAnisotropicDiffusion
      Documentation/4.0/Modules/Threshold
      Documentation/4.0/Modules/YOURMODULENAME
      [...]
      Documentation/4.2/Modules/Add
      Documentation/4.2/Modules/GradientAnisotropicDiffusion
      Documentation/4.2/Modules/Threshold
      Documentation/4.2/Modules/YOURMODULENAME
      [...]
      Category:Documentation/4.0/Modules
      Category:Documentation/4.0/Modules/Filtering
      Category:Documentation/4.0/Modules/Filtering.Denoising
      [...]
      Category:Documentation/4.2/Modules
      Category:Documentation/4.2/Modules/Filtering
      Category:Documentation/4.2/Modules/Filtering.Denoising
      [...]
      Template:Documentation/4.0/module-cli-description
      Template:Documentation/4.0/module-header
      Template:Documentation/4.0/module-footer
      [...]
      Template:Documentation/4.2/module-cli-description
      Template:Documentation/4.2/module-header
      Template:Documentation/4.2/module-footer

Separation of information and representation

• This could be done with the help of a few convenient custom templates:
  • See http://wiki.slicer.org/slicerWiki/index.php?title=Category:Templates:Documentation/4.0
• It allows to tune / update how the documentation looks like for a given documentation set.

Developer information

• For each module, the list of bugs, associated tests, list of classes, developer notes etc. should be collected automatically. This could be achieved with the help of the "module-developerinfo" template.
• Every module should include the template "Documentation/X.Y/module-developerinfo". See [10]
• As of today, this template is a placeholder/stub. As soon as, functionality will be implemented all module including that template will automatically display the wanted information.
• This implies:
  • In mantis, bugs should be assigned to a category / tag and product version
  • In CDash, tests should be labeled with both the ModuleName and the Slicer version. Then, using the webapi we should be able to obtain the list of tests, coverage, etc ...
  • Status of the "Ron rules" could be semi-automatically generated: coverage, number of test, amount of documentation, style, ...

Categorizing

• The list of category is currently manually generated. This is not sustainable. Given the new page structure. These lists could be automatically generated.

• Mediawiki offers some nice feature to manage category. Let's use them.

Documentation packaging in Slicer

• Since a template "module-section" has been introduced, there is now a placeholder that will allow to refine how sections are identified and will ease the integration in a future Slicer Assistant module.
  • See http://wiki.slicer.org/slicerWiki/index.php/Template:Documentation/4.0/module-section

Critical details

• A module should be identified consistently in both the source and the documentation. GradientAnisotropicFilter != GradientAnisotropicDiffusion
• If a name is incorrect, it should be fixed/updated at the source ! Not just in the documentation.

ToDo

• Look at wiki like "http://techbase.kde.org" .. I think we could be inspired from what they did and improve the "user friendliness" of slicer wiki
• Add "EmailObfuscator"[11] or "EmailAddressImage"[12] extension to mediawiki that will be used inside the "contact" template [13] Done - EmailAddressImage added
• Setup a mechanism so that current "Documentation Set" follow Slicer source trunk could be duplicated and "frozen"
• Implement "developerinfo"
• Please, review both the template [1] and GradientAnisotropicDiffusion [2] documentation.

Links

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/YOURMODULENAME

[2] http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/GradientAnisotropicDiffusion

[3] http://wiki.slicer.org/slicerWiki/index.php?title=Template:Documentation/4.0/module-footer&action=edit

[4] http://wiki.slicer.org/slicerWiki/index.php/Template:Documentation/4.0/module-cli-category

[5] http://wiki.slicer.org/slicerWiki/index.php?title=Category:Documentation/4.0/Modules/Filtering

[6] http://wiki.slicer.org/slicerWiki/index.php?title=Category:Documentation/4.0/Modules/Filtering.Denoising

[7] http://wiki.slicer.org/slicerWiki/index.php/Template:Documentation/version

[8] http://www.mediawiki.org/wiki/Extension:Duplicator

[9] http://www.mediawiki.org/wiki/Extension:Multiplicator

[10] http://wiki.slicer.org/slicerWiki/index.php/Template:Documentation/4.0/module-developerinfo

[11] http://www.mediawiki.org/wiki/Extension:EmailObfuscator

[12] http://www.mediawiki.org/wiki/Extension:EmailAddressImage

[13] http://wiki.slicer.org/slicerWiki/index.php/Template:Documentation/4.0/contact

Logos

A ready source of logos can be found here.

Participants

1. Ron Kikinis
2. Steve Pieper
3. Julien Finet
4. Jean-Christophe Fillion-Robin
5. Nicole Aucoin