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Maniphest T27807

[MultiLabel Segmentation] Inspection of module and plugin
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Description

Several flaws of the multi label functionality regularly pop up. This meta task will gather the known problems and offer a room for discussion on how to continue with the multi label segmentation plugin.

A substantial amount of work, which can be used for the discussion about the future of the (multi label) segmentation, was already done in {T23602} and {T26506}.
The child tasks of this meta task focus more on the open bugs in the already existing implementation.

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StatusAssignedTask
ResolvedflocaT29132 [MultiLabel Segmentation] Define desired behavior of fill / erase tool
ResolvedflocaT28145 SetRegionTool does not work as expected (flood fill like) with concentric structures.
Restricted Maniphest Task
WontfixNoneT27178 MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM
ResolvedkislinskT26953 DICOM SEG - Cannot rewrite segmentations as DICOM SEG
OpenNoneT25192 Enable DICOM SEG conversion for nrrd segmentations
ResolvedkislinskT30182 [SEG] Storing segmentation as DICOM Seg failes if reference image is not a valid DICOM
ResolvedkislinskT27807 [MultiLabel Segmentation] Inspection of module and plugin
WontfixNoneT22593 Update the MitkMultilabelTestDriver
Restricted Maniphest Task
Restricted Maniphest Task
ResolvedkalaliT25754 Cannot use tools in multilabel segmentation view without restart
WontfixNoneT22458 Merging a label in the MultiLabel segmentation plugin leaves one label without a segmentation
InvalidNoneT20110 [Multilabel Segmentation] Contour broken for 3D and 2D interpolation
OpenNoneT26397 Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK
ResolvedflocaT23981 Multilabel color map should disable interpolation
ResolvedkislinskT25445 MultiLabel segmentation mapper is very slow
InvalidNoneT27571 Multilabel segmentation does not work with US DICOM images
ResolvedkalaliT27817 [Multilabel] Live Wire tool always assigns first label when being used with multiple labels
ResolvedkalaliT28051 [Multilabel Segmentation] Fill / Erase tool does not respect multiple layers
ResolvedkalaliT28076 [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers
ResolvedkalaliT28131 [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers
ResolvedflocaT28526 [Segmentation] Check tools (especially 3D tools) to correctly handle updating of LabelSetImage
OpenflocaT28524 Refactor LabelSetImage and associated classes.
ResolvedflocaT28525 Design refactoring of LabelSetImage and associated classes
ResolvedflocaT28140 [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems
ResolvedflocaT28139 [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage
DuplicateNoneT16153 [Segmentation] Jump to center of mass of segmentation on click
ResolvedflocaT28549 Remove deprecated functions from classes involved in the LabelSetImage refactoring
ResolvedkislinskT28561 Refactor/Fix mitk::SegmentationInteractor::ChangeActiveLabel
ResolvedflocaT23742 Implement proof of concept for new segmentation data type
WontfixNoneT23772 Implement adaptor between new segmentation data type and current segmentation data type
ResolvedkislinskT23867 Improve mitk::WeakPointer
ResolvedkislinskT23971 Implement robust, easy-to-use ExtractSliceFilter
WontfixNoneT24303 A segmentation should generate all DICOM relevant IDs as soon as it can be referenced.
ResolvedflocaT29204 [SEG] Rework properties of Label class + add instance information
ResolvedflocaT29474 [SEG] Remove exterior label
OpenflocaT30194 [SEG] Refactor LabelSetImage to MultiLabelSegmentation class
ResolvedflocaT30294 {SEG] Remove label set structure
ResolvedflocaT28763 [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels
ResolvedkislinskT28493 Multilabel color map colors are not very nice
ResolvedkislinskT26951 DICOM SEG - DicomSegIO should just use properties of the passed segmentation object
ResolvedkislinskT26952 Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG)
ResolvedkislinskT26950 Add rule class for DICOM Seg relations to source image
ResolvedflocaT26843 Rethink/CleanUp PropertyRelation connection levels and RII properties used in SourceImageRelationRule

Event Timeline

kalali triaged this task as Normal priority.Oct 1 2020, 2:37 PM
kalali created this task.
kalali added a subtask: T22593: Update the MitkMultilabelTestDriver.
kalali added a subtask: Restricted Maniphest Task.
kalali added a subtask: T25754: Cannot use tools in multilabel segmentation view without restart.
kalali added a subtask: T22458: Merging a label in the MultiLabel segmentation plugin leaves one label without a segmentation.
kalali updated the task description. (Show Details)Oct 1 2020, 2:43 PM
kalali added a subtask: T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.Oct 1 2020, 2:49 PM
kalali added a subtask: T20110: [Multilabel Segmentation] Contour broken for 3D and 2D interpolation.
kalali added a subtask: T26397: Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK.
kalali added a subtask: T25445: MultiLabel segmentation mapper is very slow.
kalali added a subtask: T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.
kalali added a subtask: T23981: Multilabel color map should disable interpolation.Oct 1 2020, 2:54 PM
kalali added a subtask: T27571: Multilabel segmentation does not work with US DICOM images.
kalali mentioned this in T27096: [MITKDoc] Revise MultiLabel Segmentation Utilities Plugin Documentation.Oct 8 2020, 3:47 PM
kalali added a subtask: T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.Oct 9 2020, 10:02 AM
kalali closed subtask T28051: [Multilabel Segmentation] Fill / Erase tool does not respect multiple layers as Resolved.Dec 7 2020, 1:10 PM
kalali closed subtask T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels as Resolved.Dec 14 2020, 2:15 PM
kalali added a subtask: T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers.Dec 14 2020, 2:20 PM
kalali mentioned this in T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation.Jan 4 2021, 12:29 PM
kislinsk closed subtask T20110: [Multilabel Segmentation] Contour broken for 3D and 2D interpolation as Invalid.Jan 31 2021, 9:13 AM
kalali edited projects, added MITK (v2021.10); removed Next Milestone, MITK.Apr 7 2021, 12:29 PM
kalali moved this task from Backlog to Segmentation on the MITK (v2021.10) board.
kalali mentioned this in T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms.May 6 2021, 10:48 AM
floca closed subtask T27571: Multilabel segmentation does not work with US DICOM images as Invalid.Jul 27 2021, 9:59 AM
kalali added a subtask: T28763: [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels.Oct 21 2021, 5:18 PM
kislinsk edited projects, added MITK (v2022.04); removed MITK (v2021.10).Nov 10 2021, 4:32 PM
floca moved this task from Backlog to Segmentation on the MITK (v2022.04) board.Nov 17 2021, 11:59 AM
kalali removed a subtask: T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations.Jan 20 2022, 10:58 AM
kalali removed a subtask: T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries / dimensions in Utilities View.Jan 20 2022, 11:04 AM
kalali removed a subtask: T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view.Jan 20 2022, 11:10 AM
kalali removed a subtask: T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty.
kalali removed a subtask: T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.Jan 20 2022, 1:58 PM
kalali added a subtask: T28493: Multilabel color map colors are not very nice.Feb 8 2022, 3:16 PM
kalali added a subtask: T26396: [Segmentation] Refactor functions to create new (empty) segmentations.Feb 8 2022, 3:21 PM
kalali removed a subtask: T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.Feb 9 2022, 11:26 AM
kalali removed a subtask: T26396: [Segmentation] Refactor functions to create new (empty) segmentations.Feb 16 2022, 9:59 AM
kalali closed subtask T28131: [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers as Resolved.Feb 24 2022, 10:01 AM
kislinsk closed subtask T28493: Multilabel color map colors are not very nice as Resolved.Mar 30 2022, 11:35 AM
kalali closed subtask T25754: Cannot use tools in multilabel segmentation view without restart as Resolved.Apr 21 2022, 11:13 AM
kislinsk edited projects, added Next Milestone, MITK; removed MITK (v2022.04).Apr 29 2022, 1:38 PM
floca added a subtask: T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object.May 12 2022, 5:50 PM
floca added a subtask: T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG).
floca closed subtask T28763: [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels as Resolved.Oct 4 2022, 4:38 PM
kislinsk edited projects, added MITK (v2023.12); removed MITK, Next Milestone.May 17 2023, 2:57 PM
kislinsk edited projects, added MITK (v2024.06); removed MITK (v2023.12).Dec 5 2023, 10:38 AM
floca closed subtask T23981: Multilabel color map should disable interpolation as Resolved.Feb 11 2024, 11:12 PM
floca closed subtask T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems as Resolved.Feb 22 2024, 5:26 PM
kislinsk edited projects, added MITK (v2024.12); removed MITK (v2024.06).Jun 17 2024, 2:33 PM
kislinsk closed subtask T22458: Merging a label in the MultiLabel segmentation plugin leaves one label without a segmentation as Wontfix.Jun 17 2024, 2:36 PM
kislinsk closed subtask T22593: Update the MitkMultilabelTestDriver as Wontfix.
kislinsk closed this task as Resolved.Sep 16 2024, 1:49 PM
kislinsk claimed this task.
kislinsk added a project: Moved to git.dkfz.de.
kislinsk added a subscriber: kislinsk.

This task was closed here on Phabricator since it was migrated to GitLab. Please continue on GitLab.

kislinsk closed subtask T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG) as Resolved.Sep 16 2024, 1:49 PM
kislinsk closed subtask T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object as Resolved.
kislinsk closed subtask T25445: MultiLabel segmentation mapper is very slow as Resolved.
MITK · MIC · IMSY · DKFZ