2013 Project Week:ColorHierarchies

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  Projects List

Key Investigators

• Nicole Aucoin, BWH

Project Description

Objective

• create a color table including color values for both models and model hierarchy groups.
• update the model maker module to output a scene file that has a tree-like model hierarchy (instead of a flat one), with correct colors on the model and the hierarchy display nodes.

Approach, Plan

Approach

• From Marianna:
  • start from the Head and Neck Atlas model hierarchy: http://www.na-mic.org/publications/item/view/2256
  • she will provide a text file with the necessary description of the model hierarchy

Plan:

• create a data structure to save the new color table hierarchy (storable)
  • extend the color table?
• create a new module that will let users build a model hierarchy from a color table
• in the model maker, instead of having to create a new model heirarchy, select for example HeadAndNeckColorTableHierarchy
  • make sure leave the "sample" hierachy available as a base for multiple runs of the model maker
• future plans: create color table hierarchies for all anatomic based color tables
• alternately, craft a sample .mrml file with the desired model hiearchy, using the Model modules GUI, then pass the file to the model maker

Progress

• Head and Neck Atlas 2012 Color Hierarchy text file
• plain color file
• mrml scene
• Discussed this project during the NA-MIC Eng tcon Dec 27th:
  • could think about a realtionship defining node to be the most general
  • could load a scene that defines a hierarchy, then use it for the model maker
    • extend the scene that's passed into the model maker and returned populated with models
  • each label could have a key value, so parent=labelX (could also change the color name to be a key value pair)
  • in the file, enforce leading spaces to show hierarchy?
    • or use JSON?

{
label:100,name:skull,r:128,g:128,b:128,a:255,parent:201
}

• or lump colors together in one:

color:{128,123,200,255}

• extension .json? c++ library? vtk doesn't do it, python might, boost? there's JSON Spirit. or manual parsing (whitespace assumptions)?
  • need a reader and writer
• create the structure through GUI, or write a text file and make a script that converts it to a MRML structure? for end users who want to use a GUI versus edit a text file
• expand the mrml file that's passed to the model maker to include the full hierarchy and then fill it in
  • associate the hierarhcy with a color node so it's saved/restored?
• During Project Week:
  • expanding ModelMaker.xml to accept a .mrml file as a parameter
  • in ModelMaker.cxx import the .mrml file with the extra model hierarchy nodes
    • BUG: the parent node references aren't updated when importing this on top of the mini scene that Slicer passes to the model maker, which has a model hierarchy node with id number 1 while the color hierarchy mrml file has the same id
  • search for model hierarchy nodes with names that match the color names of the models and set the associated node id on them