Difference between revisions of "2013 Project Week:ColorHierarchies"
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<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
− | From Marianna: | + | Approach |
+ | |||
+ | *From Marianna: | ||
** start from the Head and Neck Atlas model hierarchy: http://www.na-mic.org/publications/item/view/2256 | ** 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 | ** she will provide a text file with the necessary description of the model hierarchy | ||
+ | |||
Plan: | Plan: | ||
+ | |||
* create a data structure to save the new color table hierarchy (storable) | * create a data structure to save the new color table hierarchy (storable) | ||
** extend the color table? | ** extend the color table? | ||
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** make sure leave the "sample" hierachy available as a base for multiple runs of the model maker | ** 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 | * 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 | |
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* expand the mrml file that's passed to the model maker to include the full hierarchy and then fill it in | * 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? | ** 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 | ||
</div> | </div> | ||
</div> | </div> |
Revision as of 18:19, 8 January 2013
Home < 2013 Project Week:ColorHierarchiesKey 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