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Model hierarchy within subject hierarchy #4

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cpinter opened this Issue Oct 30, 2018 · 2 comments

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cpinter commented Oct 30, 2018

In order to label the existing atlases in Slicer properly, we need a way to assign standard terminologies to models in a hierarchy. Instead of fixing the current model hierarchy (which is quite buggy and that's part of the reason SH is not based on the original MRML scene model), we can achieve this within subject hierarchy:

  • Add a new column for color
    • Proposed design: new function in abstract plugin which SH plugins can implement if makes sense to show one color (models, segments, fiducials, ?)
    • Add option to SH tree view to whitelist/blacklist plugins. This will be done with two QLists that, if not empty, will specify which plugins are used for populating the context menu
    • On double-click on color, the terminology selector will pop up, which sets the color and writes the terminology in the proper place (the relevant SH plugins would do this).
    • Add a remove button to terminology selector (in segments it's mandatory but in other nodes it's not)
  • Add opacity SH plugin that has a slider in a sub-menu of the action (similarly to slice spacing in slice view controller)
  • Add color information to folder items, allow them to override branch color

@cpinter cpinter added the enhancement label Oct 30, 2018

@cpinter cpinter self-assigned this Oct 30, 2018

@cpinter cpinter referenced this issue Oct 30, 2018

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Hierarchical organization of segments #2

0 of 3 tasks complete

cpinter added a commit to cpinter/Slicer that referenced this issue Nov 23, 2018

ENH: Add color column and improve transform column in subject hierarchy
- Add new column for color between visibility and transform columns. It shows the color for segments, models, and markup fiducials (selected color)
- Double-clicking the color brings up terminology selector where terminology and color can be selected. Terminology information is stored in segments as before (segment attributes), and for models and markups it is stored in MRML node attributes. When selecting a terminology type, color is overwritten but name is not by default
Re PerkLab/SlicerOpenAnatomy#4

- Transform column now shows icon instead of the first few letters of the transform name. There is a separate icon for linear and deformable transforms
- Double-clicking the icon brings up a menu instead of a node selector that had to be clicked again
- Subject hierarchy reference highlights are now updated immediately after selecting a transforms, so the highlighted transform node is always correct
Re https://issues.slicer.org/view.php?id=4401

slicerbot pushed a commit to Slicer/Slicer that referenced this issue Nov 26, 2018

cpinter
ENH: Add color column and improve transform column in subject hierarchy
- Add new column for color between visibility and transform columns. It shows the color for segments, models, and markup fiducials (selected color)
- Double-clicking the color brings up terminology selector where terminology and color can be selected. Terminology information is stored in segments as before (segment attributes), and for models and markups it is stored in MRML node attributes. When selecting a terminology type, color is overwritten but name is not by default
Re PerkLab/SlicerOpenAnatomy#4

- Transform column now shows icon instead of the first few letters of the transform name. There is a separate icon for linear and deformable transforms
- Double-clicking the icon brings up a menu instead of a node selector that had to be clicked again
- Subject hierarchy reference highlights are now updated immediately after selecting a transforms, so the highlighted transform node is always correct
Re https://issues.slicer.org/view.php?id=4401

git-svn-id: http://svn.slicer.org/Slicer4/trunk@27571 3bd1e089-480b-0410-8dfb-8563597acbee

slicerbot pushed a commit to Slicer/Slicer that referenced this issue Nov 30, 2018

cpinter
ENH: Implement whitelist and blacklist for SH plugins
It is now possible to determine a subset of enabled subject hierarchy plugins for each subject hierarchy tree and combobox.
- Whitelist contains the enabled plugins, and if it's not empty, then all plugins not in the list are disabled.
- Blacklist contains the disabled plugins; all other plugins are enabled. By default both lists are empty, meaning that all plugins are enabled.

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@27583 3bd1e089-480b-0410-8dfb-8563597acbee

slicerbot pushed a commit to Slicer/Slicer that referenced this issue Nov 30, 2018

cpinter
ENH: Add opacity plugin to subject hierarchy
The opacity plugin adds an Opacity action in the visibility context menu with a sub-menu that contains a slider showing the opacity and which can be used to change the opacity of the item.

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@27585 3bd1e089-480b-0410-8dfb-8563597acbee
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cpinter commented Nov 30, 2018

@lassoan I finished all items in this ticket. I think we are now ready to replace the model hierarchy to subject hierarchy in the Models module.

slicerbot pushed a commit to Slicer/Slicer that referenced this issue Dec 4, 2018

cpinter
ENH: Allow folder to override branch color
An important step towards making subject hierarchy usable as model hierarchy. Model hierarchy nodes have been represented as folders in subject hierarchy already, so it makes sense to use the folders for the same purpose.
- Folders now can have color associated to them. If it's a mirrored model hierarchy node, then it uses the display node of the MH node, otherwise it creates a model display node associated to the folder item
- A visibility context menu action called 'Apply color to branch' allows overriding the color of the model nodes in the folder, the same way the checkbox does in the model hierarchy (the two functions are reflected in the two types of hierarchies so there is no confusion if used together)
- Right-clicking the color column now shows the visibility context menu as color is related to visibility

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@27592 3bd1e089-480b-0410-8dfb-8563597acbee
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cpinter commented Dec 12, 2018

Pull request for replacing model hierarchy with subject hierarchy in the Models module:
Slicer/Slicer#1054

This PR enables managing atlases in Slicer accoridng to the needs defined by the OpenAnatomy project. Expected integration is after the release of Slicer 4.10.1.

jcfr added a commit to Slicer/Slicer that referenced this issue Jan 16, 2019

ENH: Add color column and improve transform column in subject hierarchy
- Add new column for color between visibility and transform columns. It shows the color for segments, models, and markup fiducials (selected color)
- Double-clicking the color brings up terminology selector where terminology and color can be selected. Terminology information is stored in segments as before (segment attributes), and for models and markups it is stored in MRML node attributes. When selecting a terminology type, color is overwritten but name is not by default
Re PerkLab/SlicerOpenAnatomy#4

- Transform column now shows icon instead of the first few letters of the transform name. There is a separate icon for linear and deformable transforms
- Double-clicking the icon brings up a menu instead of a node selector that had to be clicked again
- Subject hierarchy reference highlights are now updated immediately after selecting a transforms, so the highlighted transform node is always correct
Re https://issues.slicer.org/view.php?id=4401

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-10@27784 3bd1e089-480b-0410-8dfb-8563597acbee

jcfr added a commit to Slicer/Slicer that referenced this issue Jan 16, 2019

ENH: Implement whitelist and blacklist for SH plugins
It is now possible to determine a subset of enabled subject hierarchy plugins for each subject hierarchy tree and combobox.
- Whitelist contains the enabled plugins, and if it's not empty, then all plugins not in the list are disabled.
- Blacklist contains the disabled plugins; all other plugins are enabled. By default both lists are empty, meaning that all plugins are enabled.

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-10@27796 3bd1e089-480b-0410-8dfb-8563597acbee

jcfr added a commit to Slicer/Slicer that referenced this issue Jan 16, 2019

ENH: Add opacity plugin to subject hierarchy
The opacity plugin adds an Opacity action in the visibility context menu with a sub-menu that contains a slider showing the opacity and which can be used to change the opacity of the item.

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-10@27798 3bd1e089-480b-0410-8dfb-8563597acbee

jcfr added a commit to Slicer/Slicer that referenced this issue Jan 16, 2019

ENH: Allow folder to override branch color
An important step towards making subject hierarchy usable as model hierarchy. Model hierarchy nodes have been represented as folders in subject hierarchy already, so it makes sense to use the folders for the same purpose.
- Folders now can have color associated to them. If it's a mirrored model hierarchy node, then it uses the display node of the MH node, otherwise it creates a model display node associated to the folder item
- A visibility context menu action called 'Apply color to branch' allows overriding the color of the model nodes in the folder, the same way the checkbox does in the model hierarchy (the two functions are reflected in the two types of hierarchies so there is no confusion if used together)
- Right-clicking the color column now shows the visibility context menu as color is related to visibility

Re PerkLab/SlicerOpenAnatomy#4

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-10@27805 3bd1e089-480b-0410-8dfb-8563597acbee
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