Using qMRMLNodeAttributeTableWidget with qMRMLSegmentEditorWidget

NguyenVuHoaBinh · September 26, 2023, 4:18am

Hello everyone! I am new to 3D Slicer.
I am currently creating a sample extension that allow user add additional information about the segmentation when using segment editor, but i got stuck. I dont know how to mapping the qMRMLNodeAttributeTableWidget with qMRMLSegmentEditorWidget. I will really appreaciate any help.

Sorry if my bad English make you confuse to understand. Have a nice day!

Operating system: Window 11
Slicer version: 5.2.2
Expected behavior: Can perform add/remove attribute name and value for the selected segmentation node from segment editor widget
Actual behavior: Failed to instantiate module

cpinter · September 26, 2023, 11:24am

What you describe that you want to do seems quite unusual. To my understanding you want to change node attributes visually for the segment editor node. However, that’s kind of halfway between UI and programming, and would be very error-prone and would require continual lookup of attributes in the source code etc.

Can you please describe what you actually want to achieve from the user’s perspective?

NguyenVuHoaBinh · September 26, 2023, 1:04pm

Thank you for your support. I will provide detail what i want to achieve.
Assume that i am a radiologist using 3D slicer to annotate multiple segmentations like this.

However, i want to make more comment for each segmentation label i made by using the [qMRMLNodeAttributeTableWidget], giving some fixed attribute and add the value for them so whenever i re-open the file, i can review it or modify the attribute value i created before. Here is the [qMRMLNodeAttributeTableWidget]

My desired output is like this

Hope you will understand what i am trying to achieve.
Thank you.

cpinter · September 26, 2023, 1:56pm

Segments are not nodes, so this idea won’t work for individual segments. See this part of the documentation:
https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html

The segments do not have attributes, but they have “tags” that can be used for this purpose, see

github.com

Slicer/Slicer/blob/d9485819db2e8e71a4cf0e4d914946f704bbcb39/Libs/vtkSegmentationCore/vtkSegment.h#L94-L110


      
          /// Set/add tag
          void SetTag(std::string tag, std::string value);
          /// Set/add integer tag
          void SetTag(std::string tag, int value);
          
          /// Remove tag
          void RemoveTag(std::string tag);
          
          /// Get tag
          /// \param tag Name of requested tag
          /// \param value Output argument for the value of the tag if found
          /// \return True if tag is found, false otherwise
          bool GetTag(std::string tag, std::string &value);
          /// Determine if a tag is present
          bool HasTag(std::string tag);
          /// Get tags
          void GetTags(std::map<std::string,std::string> &tags);

But there is no table for the tags. Maybe you can look at this class as inspiration:

github.com

Slicer/Slicer/blob/main/Modules/Loadable/Segmentations/Widgets/qMRMLSegmentationConversionParametersWidget.h

/*==============================================================================

  Program: 3D Slicer

  Copyright (c) Laboratory for Percutaneous Surgery (PerkLab)
  Queen's University, Kingston, ON, Canada. All Rights Reserved.

  See COPYRIGHT.txt
  or http://www.slicer.org/copyright/copyright.txt for details.

  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.

  This file was originally developed by Csaba Pinter, PerkLab, Queen's University
  and was supported through the Applied Cancer Research Unit program of Cancer Care
  Ontario with funds provided by the Ontario Ministry of Health and Long-Term Care

This file has been truncated. show original

NguyenVuHoaBinh · September 26, 2023, 3:08pm

Wonderful! I will check that out. By the way, is it possible to create separate tables like that for each segmentation label map like the sample image below?
P/s: The image is a sample and does not contain any confidential information.

cpinter · September 26, 2023, 8:27pm

I think you should use split islands and separate these into a segment each. In the default terminology you can specify the same type with left/right modifiers, so you can uniquely identify the structures.

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Using qMRMLNodeAttributeTableWidget with qMRMLSegmentEditorWidget

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