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Maniphest T29390

How to ease the handling of external generated segmentations
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Description

Currently the workbench does not support simple binary segs any more directly (only DICOM Seg and our own multi label nrrds are supported). They have to be converted manually. This could be tedious.

How to make it easier?

Ideas:

  • Command line tool to convert data into multi label seg format
  • python support module
  • offer a reader in case of binary itk images to load as seg
    • as a new reader: convinient, but slows the loading even more as the image has to be interpreted and completly processed on mime type level to decide if the reader should be applied
    • as a new mime type: faster, but not so convinient would enforce a pop up for all supported data formates in order to choose if it should be loaded as image or as segmentation)
  • introduce a hook (at application level (here it could be more general ?!? or seg view level) that monitors the data storage and proposes conversion (or does auto convert as soon as a legacy segmentation is loaded).

Revisions and Commits

Restricted Differential Revision

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Event Timeline

floca created this task.Nov 15 2022, 8:12 PM
floca updated the task description. (Show Details)Nov 15 2022, 8:26 PM
floca moved this task from Backlog to MITK Meeting on the Request for Discussion board.Nov 16 2022, 10:59 AM
floca added a comment.Nov 25 2022, 11:14 AM

this is also partially covered/related with T29392: [SEG] Add dedicated writer to store multi-label images in nifti

floca edited projects, added MITK (v2023.04); removed MITK.Nov 25 2022, 11:14 AM
floca moved this task from Backlog to In candidates on the MITK (v2023.04) board.
floca added a subtask: T29389: Python utility module.Nov 25 2022, 11:17 AM
floca renamed this task from How to easy the handling of external generated segmentations to How to ease the handling of external generated segmentations.Nov 30 2022, 11:14 AM
floca triaged this task as Normal priority.Nov 30 2022, 11:17 AM
floca moved this task from In candidates to Segmentation on the MITK (v2023.04) board.
kislinsk removed a project: Request for Discussion.Mar 22 2023, 10:15 AM
kislinsk added a subscriber: kislinsk.

Request for Discussion Discussion result:

  • Remove special "binary" flag since we do not support legacy binary images anymore anyways (icon, property, mapper)
  • Somehow make it more convenient to open plain images as segmentations compared to "Convert to Segmentation"
kislinsk added a comment.EditedMar 23 2023, 11:23 AM

Turned out it is not straight forward to remove the "binary" feature since it is still used in quite a few crucial places like the segmentation paintbrush tool preview.

floca added a comment.Mar 23 2023, 12:30 PM

Is it realy used or just still supported?

kislinsk added a comment.Mar 23 2023, 2:25 PM

Really used.

floca added a project: Request for Discussion.Mar 24 2023, 8:26 PM

is the discussion realy over now? I think this is also more an meta task, concrete actions like removing binary tag and such should be sub tasks.
@kislinsk Could you make sub tasks out of your discussion points. Thanks.

kislinsk edited projects, added MITK (v2023.12); removed MITK (v2023.04).May 17 2023, 2:55 PM
kislinsk moved this task from Backlog to Segmentation on the MITK (v2023.12) board.May 17 2023, 3:08 PM
kislinsk edited projects, added MITK (v2024.06); removed MITK (v2023.12).Dec 5 2023, 10:39 AM
kislinsk moved this task from Backlog to Segmentation on the MITK (v2024.06) board.
s434n removed a project: Request for Discussion.Feb 7 2024, 11:52 AM
s434n added a subscriber: s434n.

Conclusion: still needs subtasks

  • can the binary tag be removed?
  • convert binary images easier into segmentations
  • offer python utility package as a way to convert -> T29389
s434n assigned this task to kislinsk.Feb 7 2024, 11:52 AM
kislinsk removed kislinsk as the assignee of this task.Mar 7 2024, 8:23 PM

Instead of creating another subtask, this task, as the title already hints, is about improving conversion between binary images/masks and multi-label segmentations. Removal of the binary flag is not yet worth again for evaluation but might be a future task if driven by demand.

floca claimed this task.Mar 19 2024, 9:53 AM
floca moved this task from Segmentation to Cycle on the MITK (v2024.06) board.
floca mentioned this in rMITK7261d84c48c0: T29390 Improve_conversion_for_multilabel.Wed, Apr 10, 3:11 PM
kislinsk mentioned this in rMITK7efda63428f8: T29390 Improve_conversion_for_multilabel.Wed, Apr 10, 8:54 PM
kislinsk mentioned this in rMITK561a06dc3c79: T29390 Improve_conversion_for_multilabel.
kislinsk added a revision: Restricted Differential Revision.Wed, Apr 10, 8:57 PM
kislinsk added a comment.Wed, Apr 10, 9:01 PM

Pushed new branch to rMITK MITK: bugfix/T29390-FixLandingOfD910.

kislinsk added a comment.Wed, Apr 10, 9:08 PM

Deleted branch from rMITK MITK: bugfix/T29390-FixLandingOfD910.

floca added a comment.Thu, Apr 11, 8:35 AM

Pushed new branch to rMITK MITK: feature/T29390-Improve_conversion_for_multilabel.

floca mentioned this in rMITKccb469becb9f: Merge branch 'feature/T29390-Improve_conversion_for_multilabel' into develop.Thu, Apr 11, 9:37 AM
floca mentioned this in rMITK7c1b545dfcba: Merge branch 'feature/T29390-Improve_conversion_for_multilabel' of ssh….
floca closed this task as Resolved.Thu, Apr 18, 4:36 PM
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