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IDProjectCategoryView StatusDate SubmittedLast Update
0003586Slicer4Core: MRMLpublic2014-02-11 13:402017-06-10 08:51
Reporternicole Assigned Tonicole  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionfixed 
Product Version 
Target VersionSlicer 4.4.0Fixed in VersionSlicer 4.4.0 
Summary0003586: Volume color table nodes have incorrect TableRange
Description

Exploring how some fMRI volumes are displayed with the fMRI color node with window/level tweaks, Steve and I dug into the scalar volume display pipeline. It turns out that the map window level to colors filter does not have a color look up table set, and it produces output data adjusted by the window and level settings with the scalar range of 0-255 (unsigned char).
The next step in the pipeline is map scalars to colors, which uses the look up table (with the table range set) provided by the color node.
The fMRI color node has 43 colors defined, and currently a table range set to 0-43 (ignoring the off by one error). This means that the input scalar values from 0-255 from the map window level to color output are not all used, just those in the 0-43 range, when mapping to the full range of colors defined in the look up table.

Steps To Reproduce

To fix this in python:
fmri = slicer.mrmlScene.GetFirstNodeByName('fMRI')
fmri.GetLookupTable().SetTableRange(0,255)

Additional Information

A user reported[1] unexpected color mapping when viewing an fMRI volume with the fMRI color node when the window level was set to 10 and 0.

[1] http://slicer-users.65878.n3.nabble.com/Volume-Lookup-Table-Windowing-and-fMRI-Functional-Data-td4027002.html

TagsNo tags attached.

Relationships

related to 0003115 closednicole Editor module does not draw with the selected color 

Activities

nicole

nicole

2014-02-11 13:43

administrator   ~0010583

In vtkMRMLColorTableNode, setting the following types uses incorret table range settings:
Iron
fMRI
fMRIPA
The copy method and the color table storage node are also using the number of colors for the table range in places.
nicole

nicole

2014-02-14 09:50

administrator   ~0010593

Fix checked in as svn 22878:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22878
nicole

nicole

2014-02-18 07:29

administrator   ~0010610

Not working with Editor, the drawn colors are not appearing as expected in the label map volumes.
nicole

nicole

2014-02-27 13:45

administrator   ~0010652

Adjust the look up table range in the label map volume display node to match the number of colors in the table.
Restrict the editor to only allowing non procedural color nodes.

svn 22912
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&sortby=date&revision=22912

Related Changesets

Import 2017-06-07 23:51:09: master 718e12e9

2014-02-14 14:48:51

naucoin

Details Diff 		BUG: fix table range on color nodes

Color table range values were being set to the number of entries
in the look up table, rather than the range of scalar values that
are to be mapped through the table. This restricts that mapping (especially
when using them with volumes) to for example scalar values from 0-43
in the fMRI table, rather than allowing mapping of 0-255, the default
that is input to the map scalars to colors filter in the
slice pipeline.

Reset the table ranges on the fMRI, fMRIPA, Iron nodes, as well as
the default range for Copy and the color table storage node, to
allow mapping 0-255 rather than 0-number of colors.

Issue 0003586



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22878 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLColorTableNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLColorTableStorageNode.cxx Diff File

Import 2017-06-07 23:51:09: master 8c978e98

2014-02-14 19:03:53

naucoin

Details Diff 		BUG: back out table range for LUTs from file

Painting in the editor is not showing the correct
colors when the table range is set to 0-255, go back
to using the maxID as the upper range for now.

Issue 0003586



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22881 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLColorTableStorageNode.cxx Diff File

Import 2017-06-07 23:51:09: master c8c39f43

2014-02-27 18:43:52

naucoin

Details Diff 		BUG: reset table range for label map volumes

Label map volumes need to be mapped to colors in the color
look up table. For editing, don't allow procedurally defined
color nodes to be chosen.

Issue 0003586



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22912 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLLabelMapVolumeDisplayNode.cxx Diff File
mod - Modules/Scripted/EditorLib/HelperBox.py Diff File

Issue History

Date Modified Username Field Change
2014-02-11 13:40 nicole New Issue
2014-02-11 13:40 nicole Status new => assigned
2014-02-11 13:40 nicole Assigned To => nicole
2014-02-11 13:43 nicole Note Added: 0010583
2014-02-14 09:50 nicole Note Added: 0010593
2014-02-14 09:50 nicole Status assigned => resolved
2014-02-14 09:50 nicole Fixed in Version => Slicer 4.4.0
2014-02-14 09:50 nicole Resolution open => fixed
2014-02-18 07:29 nicole Note Added: 0010610
2014-02-18 07:29 nicole Status resolved => assigned
2014-02-27 13:45 nicole Note Added: 0010652
2014-02-27 13:45 nicole Status assigned => resolved
2014-03-06 04:59 nicole Relationship added related to 0003115
2014-03-06 05:23 jcfr Status resolved => closed
2017-06-10 08:51 Changeset attached => Slicer master c8c39f43
2017-06-10 08:51 Changeset attached => Slicer master 8c978e98
2017-06-10 08:51 Changeset attached => Slicer master 718e12e9