0003573: Model scalar display: lookup table scalar range option

ID	Project	Category	View Status	Date Submitted	Last Update

0003573	Slicer4	Core: MRML	public	2014-01-29 11:58	2017-06-10 08:51

Reporter	johan.andruejol	Assigned To	nicole
Priority	normal	Severity	feature	Reproducibility	N/A
Status	closed	Resolution	fixed
Product Version
Target Version	Slicer 4.4.0	Fixed in Version	Slicer 4.4.0

Summary	0003573: Model scalar display: lookup table scalar range option
Description	Copy-paste from my e-mail to the developer's list: I am currently looking at the display of scalars arrays on models. When displaying a model and its associated scalar array, I realized that the look-up table used for display is always scaled to the scalar array's range. For example, let's say that I have a model with an array called 'Struct" that lists different anatomical structures. It ranges from 3 to 15. If I try to display my model with the array and the GenericAnatomyColors color node, all the model's point with a "Struct" value of 3 will be displayed with the GenericAnatomyColors' color of label 0. The points with "Struct" value of 15 will be displayed with the GenericAnatomyColors' color of the GenericAnatomyColors maximum label. I think it would make sense to have an option that would prevent this sort of scaling. With this option on and my example from above, all the points with a "Struct" value of 3 would be displayed with the GenericAnatomyColors' label 3. This especially make sense when the model array's corresponds to an anatomical color table.
Additional Information	Original discussion here: http://massmail.spl.harvard.edu/public-archives/slicer-devel/2014/014539.html
Tags	No tags attached.

nicole 2014-03-03 10:30 administrator ~0010661	Working on a github topic branch to provide more options for scalar range in color mapping.

nicole 2014-04-11 12:12 administrator ~0011579	Working on integrating this branch: https://github.com/naucoin/Slicer/commits/3573-model-scalar-display-rebase

nicole 2014-04-11 14:00 administrator ~0011582	Fixed as of svn 23084: http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23084 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23083 (this one adds the ScalarRangeFlag) http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23082

2014-04-16 05:51	3573.PNG (221,821 bytes) 3573.PNG (221,821 bytes)

johan.andruejol 2014-04-16 05:54 manager ~0011596	It's great thanks ! I tried it with my data and I was able to change the scalar range appropriately. However, I could only see the colors in the slices views and not in the 3D view (see enclosed screenshot). I used this model: http://packages.kitware.com/download/item/4983/man-arm-2mm-merged-padded-tetmesh-v2.vtk. Is my data the issue ?

nicole 2014-04-16 07:41 administrator ~0011597	I think it's the scalar overlay, the "Active Scalar Range" calculation is failing on the the MaterialId overlay. It looks like most of the other overlays are defined from 0-1 or so, and are mapping properly, but the MaterialId scalar array is different. Digging into the .vtk, turns out that MaterialId and MaterialParameters are defined as Cell Data not Point Data. The latter is assumed for the 3D rendering of the overlays, and there is a bug open about enabling Cell Data: http://na-mic.org/Mantis/view.php?id=2947 For now, the hint that it won't work in 3D is that the "Active Scalar Range" is blank.

johan.andruejol 2014-04-16 07:43 manager ~0011598	Thanks for the answers. Resolving the issue.

jcfr 2014-09-17 23:01 administrator ~0012554	Closing resolved issues that have not been updated in more than 3 months.

Import 2017-06-07 23:51:09: master a22c49ca 2014-04-11 17:44:58 naucoin Details Diff	ENH: Expand scalar range options Add the ScalarRangeFlag on the display node, test it, use it in the Model display node. Provide a GUI interface for it in the Models Scalars GUI. Use it in the model displayable manager. Separate out the auto scalar range setting from updating the poly data in the model display node. This expands the options from just using the scalar range of the data to allowing the user to select using the scalar range defined on the display node, the range on the color node, or the range of the data type (use this last with caution, TBD: readjusting the minimum and maximum values allowed on the range slider). Keeps the default behaviour of AutoScalarRange and Data. The interaction of Auto/Manual and the range flags might need some tweaking. Also keeps the deep copy of the color look up table in the model displayable manager - monitor for performance issues. Expands the model displayable manager to work with procedural color nodes, this required copying the color transfer function to a look up table to support setting the range. Using a table with 256 entries for now. UI full change due to having to run dos2unix on it to get it commited to git without whitespace errors. Issue 0003573 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23083 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - Libs/MRML/Core/vtkMRMLCoreTestingMacros.h	Diff File
	mod - Libs/MRML/Core/vtkMRMLDisplayNode.cxx	Diff File
	mod - Libs/MRML/Core/vtkMRMLDisplayNode.h	Diff File
	mod - Libs/MRML/Core/vtkMRMLModelDisplayNode.cxx	Diff File
	mod - Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx	Diff File
	mod - Modules/Loadable/Models/Widgets/Resources/UI/qMRMLModelDisplayNodeWidget.ui	Diff File
	mod - Modules/Loadable/Models/Widgets/qMRMLModelDisplayNodeWidget.cxx	Diff File
	mod - Modules/Loadable/Models/Widgets/qMRMLModelDisplayNodeWidget.h	Diff File
Import 2017-06-07 23:51:09: master 8edcb92e 2014-04-11 17:51:08 naucoin Details Diff	ENH: Add procedural color storage node and GUI support Add a new storage node, register it, test it. Added support for copying procedural nodes so that users can copy an existing one and then save it to disk. LoadColorFile expanded to work with both color table and procedural color node loading. TBD: add support for .cxml Added support in the Colors gui to display and edit color transfer functions (Continuous frame, with a ctkVTKScalarsToColorsWidget). As well as allowing the scalar bar widget to be set from a procedural color node. Issue 0003573 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23084 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - Libs/MRML/Core/CMakeLists.txt	Diff File
	mod - Libs/MRML/Core/Testing/CMakeLists.txt	Diff File
	add - Libs/MRML/Core/Testing/vtkMRMLProceduralColorStorageNodeTest1.cxx	Diff File
	mod - Libs/MRML/Core/vtkMRMLColorTableStorageNode.cxx	Diff File
	mod - Libs/MRML/Core/vtkMRMLProceduralColorNode.cxx	Diff File
	mod - Libs/MRML/Core/vtkMRMLProceduralColorNode.h	Diff File
	add - Libs/MRML/Core/vtkMRMLProceduralColorStorageNode.cxx	Diff File
	add - Libs/MRML/Core/vtkMRMLProceduralColorStorageNode.h	Diff File
	mod - Libs/MRML/Core/vtkMRMLScene.cxx	Diff File
	mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLColorLogicTest1.cxx	Diff File
	mod - Libs/MRML/Logic/vtkMRMLColorLogic.cxx	Diff File
	mod - Libs/MRML/Logic/vtkMRMLColorLogic.h	Diff File
	mod - Modules/Loadable/Colors/Logic/vtkSlicerColorLogic.cxx	Diff File
	mod - Modules/Loadable/Colors/Resources/UI/qSlicerColorsModuleWidget.ui	Diff File
	mod - Modules/Loadable/Colors/Testing/Cxx/qSlicerColorsModuleWidgetTest1.cxx	Diff File
	mod - Modules/Loadable/Colors/qSlicerColorsModuleWidget.cxx	Diff File
	mod - Modules/Loadable/Colors/qSlicerColorsReader.cxx	Diff File
Import 2017-06-07 23:51:09: master 66cbdfe1 2014-04-13 22:09:53 naucoin Details Diff	COMP: memory allocation on windows Issue 0003573 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23094 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx	Diff File
Import 2017-06-07 23:51:09: master a0f86c3d 2014-05-01 17:14:01 naucoin Details Diff	BUG: disable alternate color editors The color module was just collapsing the color table and continuous color transfer viewer/editors when the other type of node was active. User feedback showed this to be confusing as valid looking data was visible if the sections were expanded. This change disables the invalid editor on selection of a color node. Issue 0003573 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23117 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - Modules/Loadable/Colors/qSlicerColorsModuleWidget.cxx	Diff File
Import 2017-06-07 23:51:09: master d0bffb09 2014-05-02 17:10:43 naucoin Details Diff	BUG: fix fiber bundle color display Check for fiber bundle display nodes and use the old method, igoring the new scalar range options for models. Fixes bug introduced with issue 0003573 in svn revision 23083 Issue 0003672 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23118 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx	Diff File
Import 2017-06-07 23:51:09: master daeeacad 2014-05-21 17:21:14 naucoin Details Diff	ENH: Update copy color icon User feedback on the customisation of color tables suggested that a more clear icon be used for the copy to edit functionality. Issue 0003573 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23225 3bd1e089-480b-0410-8dfb-8563597acbee
	add - Modules/Loadable/Colors/Resources/Icons/SlicerCopyColor.png	Diff File
	mod - Modules/Loadable/Colors/Resources/qSlicerColorsModule.qrc	Diff File
	mod - Modules/Loadable/Colors/qSlicerColorsModuleWidget.cxx	Diff File

Date Modified	Username	Field	Change
2014-01-29 11:58	johan.andruejol	New Issue
2014-01-29 11:58	johan.andruejol	Status	new => assigned
2014-01-29 11:58	johan.andruejol	Assigned To	=> alexy
2014-01-29 12:04	jcfr	Assigned To	alexy => nicole
2014-01-29 12:04	jcfr	Target Version	=> Slicer 4.4.0
2014-01-29 12:05	jcfr	Severity	minor => feature
2014-01-29 12:05	jcfr	Reproducibility	have not tried => N/A
2014-03-03 10:30	nicole	Relationship added	related to 0001918
2014-03-03 10:30	nicole	Note Added: 0010661
2014-04-11 12:12	nicole	Note Added: 0011579
2014-04-11 14:00	nicole	Note Added: 0011582
2014-04-11 14:00	nicole	Status	assigned => resolved
2014-04-11 14:00	nicole	Fixed in Version	=> Slicer 4.4.0
2014-04-11 14:00	nicole	Resolution	open => fixed
2014-04-16 05:51	johan.andruejol	File Added: 3573.PNG
2014-04-16 05:54	johan.andruejol	Note Added: 0011596
2014-04-16 05:54	johan.andruejol	Status	resolved => feedback
2014-04-16 05:54	johan.andruejol	Resolution	fixed => reopened
2014-04-16 07:41	nicole	Relationship added	related to 0002947
2014-04-16 07:41	nicole	Note Added: 0011597
2014-04-16 07:43	johan.andruejol	Note Added: 0011598
2014-04-16 07:43	johan.andruejol	Status	feedback => resolved
2014-04-16 07:43	johan.andruejol	Resolution	reopened => fixed
2014-08-01 16:33	finetjul	Relationship added	parent of 0003783
2014-09-17 22:59	jcfr	Status	resolved => closed
2014-09-17 23:01	jcfr	Note Added: 0012554
2017-06-10 08:51		Changeset attached	=> Slicer master daeeacad
2017-06-10 08:51		Changeset attached	=> Slicer master d0bffb09
2017-06-10 08:51		Changeset attached	=> Slicer master a0f86c3d
2017-06-10 08:51		Changeset attached	=> Slicer master 66cbdfe1
2017-06-10 08:51		Changeset attached	=> Slicer master 8edcb92e
2017-06-10 08:51		Changeset attached	=> Slicer master a22c49ca

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Issue History

related to	0001918	closed	mehrtash	Color scale
parent of	0003783	closed	nicole	Force color to children checkbox does not work
related to	0002947	closed	alexy	Color models by cell field arrays