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Nov 9 2022

neher closed T26124: Add new systematic fiberfox tests as Wontfix.
Nov 9 2022, 11:36 AM · MITK Diffusion
neher closed T29262: Write / expand paragraph in methods section regarding nnU-Net and radiomics analysis as Resolved.
Nov 9 2022, 10:53 AM
neher closed T25501: Implement 3D visualization of parcellation images as Wontfix.
Nov 9 2022, 10:52 AM · MITK Diffusion
neher closed T27342: Implement gyral-shape fiber ending in fiberfox as Wontfix.
Nov 9 2022, 10:52 AM · MITK Diffusion
neher closed T25001: Add proton density maps as Wontfix.
Nov 9 2022, 10:52 AM · MITK Diffusion
neher closed T26061: Implement 3D sequences as Wontfix.
Nov 9 2022, 10:52 AM · MITK Diffusion
neher closed T26281: Simulation without fibers, only VFMs as Wontfix.
Nov 9 2022, 10:51 AM · MITK Diffusion
neher closed T26062: Implement parallel imaging as Wontfix.
Nov 9 2022, 10:51 AM · MITK Diffusion
neher closed T25567: Data quality analysis as Wontfix.
Nov 9 2022, 10:51 AM · MITK Diffusion
neher closed T26180: Implement readout gradient dephasing as Wontfix.
Nov 9 2022, 10:51 AM · MITK Diffusion
neher committed rMITKDIFF6075f50866a7: Merge branch 'T29323-FixWindows' (authored by neher).
Merge branch 'T29323-FixWindows'
Nov 9 2022, 10:36 AM
neher committed rMITKDIFFa5a33d3b857b: random_shuffle --> shuffle (authored by neher).
random_shuffle --> shuffle
Nov 9 2022, 10:35 AM
neher committed rMITKDIFF0123d5c4c45a: Merge branch 'T29323-FixWindows' (authored by neher).
Merge branch 'T29323-FixWindows'
Nov 9 2022, 10:19 AM
neher committed rMITKDIFFbac9fa937a24: Remve itk pointshell export macro (authored by neher).
Remve itk pointshell export macro
Nov 9 2022, 10:18 AM
kalali updated the task description for T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.
Nov 9 2022, 9:36 AM · Breaking Change, Noteworthy, MITK

Nov 8 2022

s434n removed a project from T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range?: Missing Info.

I just had another look at this. I was able to reproduce the bug this time. It seems that this problem only arises if the image holds floating point values, not when all values are integers.

Nov 8 2022, 6:05 PM · MITK (v2024.06), Restricted Project, Checklist
kalali claimed T28989: [Segmentation] CanHandle functions seem to be inconsistent.
Nov 8 2022, 5:56 PM · MITK, Request for Discussion
kalali added a comment to T28989: [Segmentation] CanHandle functions seem to be inconsistent.

mitk::Tool::CanHandle:

In T28989, @kalali wrote:

The basic mitk::Tool restricts the data that can be handled to reference-data - working-data pairs, where

  • the reference-data is valid

Why is it not required for the working-data to be valid? This is a requirement for all following CanHandle-functions (working data needs to be an mitk::LabelSetImage or an mitk::Image) that override the basic function, so why not put it in the basic class function?

Nov 8 2022, 5:56 PM · MITK, Request for Discussion
kalali added a revision to T28989: [Segmentation] CanHandle functions seem to be inconsistent: Unknown Object (Differential Revision).
Nov 8 2022, 5:56 PM · MITK, Request for Discussion
kalali updated the task description for T28989: [Segmentation] CanHandle functions seem to be inconsistent.
Nov 8 2022, 5:25 PM · MITK, Request for Discussion
kalali updated the task description for T28989: [Segmentation] CanHandle functions seem to be inconsistent.
Nov 8 2022, 5:21 PM · MITK, Request for Discussion
kalali updated the task description for T28989: [Segmentation] CanHandle functions seem to be inconsistent.
Nov 8 2022, 5:21 PM · MITK, Request for Discussion
kalali edited projects for T28989: [Segmentation] CanHandle functions seem to be inconsistent, added: MITK; removed MITK (v2022.10).
Nov 8 2022, 5:11 PM · MITK, Request for Discussion
kalali updated the task description for T28989: [Segmentation] CanHandle functions seem to be inconsistent.
Nov 8 2022, 5:11 PM · MITK, Request for Discussion
kislinsk committed rMITK51ababc09f67: Uninitialize slices interpolator when render window part is deactivated (authored by kislinsk).
Uninitialize slices interpolator when render window part is deactivated
Nov 8 2022, 5:04 PM
kislinsk committed rMITKb2928e2b2dc5: Uninitialize slices interpolator when render window part is deactivated (authored by kislinsk).
Uninitialize slices interpolator when render window part is deactivated
Nov 8 2022, 5:04 PM
kislinsk closed T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash as Resolved by committing rMITKb2928e2b2dc5: Uninitialize slices interpolator when render window part is deactivated.
Nov 8 2022, 5:04 PM · MITK
kalali updated subscribers of T27413: MITK Workflow Q&A.

@kompan and I created this guide some time ago. We can reuse it, extend it and put the content into the Phabricator wiki: https://hub.dkfz.de/f/7173768

Nov 8 2022, 4:42 PM · MITK, Request for Discussion
kalali updated the task description for T27413: MITK Workflow Q&A.
Nov 8 2022, 4:42 PM · MITK, Request for Discussion
kalali edited projects for T29140: [Selection widget] Optional selection can not be removed if a fitting node is always found, added: MITK, Next Milestone, Request for Discussion; removed MITK (v2022.10).
Nov 8 2022, 4:27 PM · MITK (v2024.06), Request for Discussion
kalali renamed T27413: MITK Workflow Q&A from MITK 2020 Workflow Q&A to MITK Workflow Q&A.
Nov 8 2022, 4:27 PM · MITK, Request for Discussion
kalali edited projects for T29313: Add a Test to check if the GrowCut algorithm produces a different output, added: MITK; removed MITK (v2022.10).
Nov 8 2022, 4:12 PM · MITK (v2024.06)
kalali added a revision to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations: Unknown Object (Differential Revision).
Nov 8 2022, 12:48 PM · Breaking Change, Noteworthy, MITK
kalali claimed T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.
Nov 8 2022, 12:48 PM · Breaking Change, Noteworthy, MITK
kalali added a comment to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.

It seems as if there is a mapping between the SliceNavigationController::ViewDirection and PlaneGeometry::PlaneOrientation, which makes it unnecessary to keep the direction / orientation in both classes.

Nov 8 2022, 12:47 PM · Breaking Change, Noteworthy, MITK
kislinsk added a revision to T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash: Unknown Object (Differential Revision).
Nov 8 2022, 5:27 AM · MITK
kislinsk added a comment to T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash.

Shortcut to reproduce the crash:

  • Start the Workbench
  • If not already opened, open the Segmentation View
  • Close the project or close the Standard Display
  • Load any segmentation
Nov 8 2022, 5:15 AM · MITK

Nov 7 2022

kalali edited projects for T26959: [Segmentation] Newly created LabelSet segmentation is not displayed as "outline binary", added: MITK, Next Milestone; removed MITK (v2022.10).
Nov 7 2022, 7:12 PM · MITK (v2024.06), Checklist, Request for Discussion
kalali edited projects for T29163: [XNAT] Opening XNAT session fails, added: MITK; removed MITK (v2022.10).
Nov 7 2022, 7:10 PM · MITK (v2024.06)
kalali edited projects for T25057: Check IContextMenuActions and extension points, added: MITK; removed MITK (v2022.10).
Nov 7 2022, 7:10 PM · MITK (v2024.06)
s434n added a revision to T29354: Double-clicking a label jumps to the label but not its centroid: Unknown Object (Differential Revision).
Nov 7 2022, 3:44 PM · MITK (v2023.04)
kalali closed T29220: StatusBar info is dependent on the pointer position, not on the crosshair / mouse click as Resolved.

All related tasks have been resolved so we can close this task as well. The "issue" still remains but we are exploiting it on purpose now using the changes made in {D686}, to show pixel information dynamically (position under the mouse cursor) in the status bar.
With the changes made in {D749} we now have the possibility to explicitly show image pixel information for the crosshair position in the newly introduced pixel value view.

Nov 7 2022, 3:06 PM · Request for Discussion, MITK
kalali triaged T29382: [Jenkins] Differential-clients do not clean old ui-files as Normal priority.
Nov 7 2022, 2:28 PM · CI, Next Milestone
kalali added a revision to T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module: Restricted Differential Revision.
Nov 7 2022, 2:01 PM · MITK (v2023.04)
kalali created T29381: Move Multilabel classes to Core module.
Nov 7 2022, 1:36 PM · MITK, Request for Discussion
kislinsk added a comment to T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash.

The interesting part here is that m_Time of mitk::BaseController is not supposed to be nullptr in particular as m_Slice is a valid stepper. My first guess is that a partly deconstructed controller is triggered here.

Nov 7 2022, 12:32 PM · MITK
kislinsk added a comment to T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash.

The crash happens in mitk::SliceNavigationController::GetSelectedTimeStep() as m_Time (mitk::Stepper::Pointer) is accessed while it is a nullptr. The events that lead to this situation are that the mitk::ToolManager notifies QmitkSlicesInterpolator via OnToolManagerWorkingDataModified(). This method calls SetCurrentContourListID() in turn, which executes the crashing line of code:

Nov 7 2022, 12:29 PM · MITK
kislinsk triaged T29380: [Segmentation] Loading a segmentation while the Segmentation View is open may lead to a crash as High priority.
Nov 7 2022, 12:08 PM · MITK
kalali added a comment to T29025: Preference service (access) based on cpp microservices.

I stumbled upon this while working on T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module. I would like to tackle this issue and already started looking into this. Do you already have an idea how to approach it or do we want to discuss it next week?

I already implemented most of it as core service a while ago but then was interrupted by something else. As far as I remember it is nearly complete except for the equivalent of BlueBerry's preference storage. I will look for the branch the upcoming week and push it. Never assigned the task, sorry.

Nov 7 2022, 11:38 AM · MITK (v2023.04), Breaking Change

Nov 6 2022

kislinsk claimed T29025: Preference service (access) based on cpp microservices.

I stumbled upon this while working on T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module. I would like to tackle this issue and already started looking into this. Do you already have an idea how to approach it or do we want to discuss it next week?

Nov 6 2022, 2:25 PM · MITK (v2023.04), Breaking Change

Nov 4 2022

kalali added a project to T29027: Move NodeSelectionWidgets to QtWidgets module: Next Milestone.
Nov 4 2022, 6:07 PM · MITK (v2023.04)
kalali added a comment to T29027: Move NodeSelectionWidgets to QtWidgets module.

Required for T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module / T27133: [Segmentation] Is QmitkDataSelectionWidget needed anymore?.

Nov 4 2022, 6:07 PM · MITK (v2023.04)
kalali added a comment to T29025: Preference service (access) based on cpp microservices.

I stumbled upon this while working on T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module. I would like to tackle this issue and already started looking into this. Do you already have an idea how to approach it or do we want to discuss it next week?

Nov 4 2022, 6:06 PM · MITK (v2023.04), Breaking Change

Nov 3 2022

a178n added a comment to T29239: Download models to new Results_Folder.

Deleted branch from rMITK MITK: feature/T29239-nnunet-download-without-resultsfolder.

Nov 3 2022, 5:39 PM · MITK (v2022.10)
a178n added a comment to T29238: Improve validation for Results_Folder structure.

Deleted branch from rMITK MITK: feature/T29238-nnunet-improve-validation.

Nov 3 2022, 5:38 PM · MITK (v2022.10)
a178n added a comment to T29227: Remove vestigial UI element "No. of extra Modalities" spinbox.

Deleted branch from rMITK MITK: feature/T29227-modify-modal-label.

Nov 3 2022, 5:36 PM · MITK (v2022.10)
s434n claimed T29354: Double-clicking a label jumps to the label but not its centroid.
Nov 3 2022, 4:41 PM · MITK (v2023.04)
s434n closed T29286: Rework segmentation checklist for new live wire and lasso tool as Resolved.
Nov 3 2022, 12:13 PM · MITK (v2022.10)

Nov 2 2022

kalali closed T29367: [Segmentation] New render window specific reinit warning is confusing as Resolved.

The warning was reverted for the StdMultiWidget. More changes (problems were already mentioned here in this task) will be further implemented using T29335: [Segmentation] Show interactive warning for uninitialized render window geometry.

Nov 2 2022, 12:08 PM · MITK (v2022.10)
s434n added a comment to T28578: [mxn multi widget] Optimization of the mxn multi widget.

Deleted branch from rMITK MITK: feature/T28578-MxN-development.

Nov 2 2022, 10:56 AM · MITK
s434n closed T29344: Image Rendering - No difference between "Jet" and "Jet Transparent" as Resolved.
Nov 2 2022, 10:32 AM · Cleared, Checklist, MITK (v2022.10)

Oct 31 2022

a178n added a comment to T29379: MONAI Label REST Response JSON issues, allegedly.
  1. The relevance of the labels list outside models? Perhaps, this entry can be used to describe all labels and their label ids used in the host app. And, models can then refer to label ids in their respective labels entries.
Oct 31 2022, 9:38 AM · MITK
a178n added a comment to T29379: MONAI Label REST Response JSON issues, allegedly.
  1. Lack of consistency in models->labels entries. For some models eg. deepedit there are label ids along with names, effectively assuming a Map datatype and for others, eg. deepgrow_2d it's a list. of label names. This creates unnecessary corner cases while parsing using strongly typed languages, like C++.
Oct 31 2022, 9:31 AM · MITK
a178n added a comment to T29379: MONAI Label REST Response JSON issues, allegedly.
  1. There is no indication in the JSON on which models are interactive click guided, scribble guided or automatic. Eg. Deepedit can be interactive click-guided or automatic, GMM+GraphCut is scribble guided, Segmentation Spleen is purely automatic. Hence, the JSON parameter type can be made more consistent for easy grouping.
Oct 31 2022, 9:26 AM · MITK
a178n updated the task description for T29379: MONAI Label REST Response JSON issues, allegedly.
Oct 31 2022, 9:25 AM · MITK
a178n triaged T29379: MONAI Label REST Response JSON issues, allegedly as Normal priority.
Oct 31 2022, 9:21 AM · MITK
r948e committed rMITKDIFF817f5c843f06: Bug in calcualting uncertainty samples fixed. (authored by r948e).
Bug in calcualting uncertainty samples fixed.
Oct 31 2022, 9:12 AM

Oct 29 2022

floca added a comment to MITK v2022.10.

👍

Oct 29 2022, 11:52 AM
kislinsk closed T29378: MITK v2022.10 as Resolved.
Oct 29 2022, 10:20 AM · MITK-ProjectTemplate, MITK (v2022.10)
kislinsk added a comment to T29378: MITK v2022.10.

Deleted branch from rMITK MITK: release/T29378-v2022.10.

Oct 29 2022, 10:19 AM · MITK-ProjectTemplate, MITK (v2022.10)
kislinsk committed rMITKa3784a36cec0: Bump version to v2022.10.99 (authored by kislinsk).
Bump version to v2022.10.99
Oct 29 2022, 10:18 AM
kislinsk committed rMITKf87d0d82930e: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Oct 29 2022, 10:18 AM
kislinsk committed rMITKef0a0e9df56a: Improve vector graphics (authored by kislinsk).
Improve vector graphics
Oct 29 2022, 10:15 AM
kislinsk committed rMITKbceb1c18270c: Bump version to v2022.10 (authored by kislinsk).
Bump version to v2022.10
Oct 29 2022, 10:15 AM
kislinsk committed rMITK9b7f10378dfe: v2022.10 (authored by kislinsk).
v2022.10
Oct 29 2022, 10:15 AM
kislinsk edited the content of Changelog.
Oct 29 2022, 10:14 AM · MITK
kislinsk edited the content of MITK v2022.10.
Oct 29 2022, 10:07 AM
kislinsk added a comment to T29138: MITK v2022.04.

Deleted branch from rMPT MITK-ProjectTemplate: release/T29138-v2022.10.

Oct 29 2022, 1:10 AM · MITK-ProjectTemplate, MITK (v2022.04)
kislinsk committed rMPT6f8e7eefb024: Update README (authored by kislinsk).
Update README
Oct 29 2022, 1:10 AM
kislinsk committed rMPT3af7a4dcb11d: Merge branch 'release/T29138-v2022.10' (authored by kislinsk).
Merge branch 'release/T29138-v2022.10'
Oct 29 2022, 1:10 AM
kislinsk edited the content of MITK v2022.10.
Oct 29 2022, 1:02 AM
kislinsk added a comment to T29138: MITK v2022.04.

Pushed new branch to rMPT MITK-ProjectTemplate: release/T29138-v2022.10.

Oct 29 2022, 12:46 AM · MITK-ProjectTemplate, MITK (v2022.04)
kislinsk added a comment to T29378: MITK v2022.10.

Pushed new branch to rMITK MITK: release/T29378-v2022.10.

Oct 29 2022, 12:45 AM · MITK-ProjectTemplate, MITK (v2022.10)
kislinsk edited the content of 2022 Week 43 (Late October).
Oct 29 2022, 12:41 AM
kislinsk created an object: MITK v2022.10.
Oct 29 2022, 12:41 AM
kislinsk triaged T29378: MITK v2022.10 as Normal priority.
Oct 29 2022, 12:23 AM · MITK-ProjectTemplate, MITK (v2022.10)
kislinsk renamed T29375: Cursor offset in 2D tools with Qt 5.15 on macOS from Cursor offset in 2D tools with Qt 5.12 on macOS to Cursor offset in 2D tools with Qt 5.15 on macOS.
Oct 29 2022, 12:21 AM · MITK (v2023.04)

Oct 28 2022

kislinsk closed T29377: 2022 Week 43 (Late October) as Resolved.
Oct 28 2022, 5:23 PM · MITK
kislinsk added a comment to T29377: 2022 Week 43 (Late October).

Deleted branch from rMITK MITK: release/T29377-2022-Week-43.

Oct 28 2022, 5:22 PM · MITK
kislinsk committed rMITKeeaec4da04df: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Oct 28 2022, 5:22 PM
kislinsk committed rMITK41af9e60c874: Adding voxel value view to replace status bar information (authored by s434n).
Adding voxel value view to replace status bar information
Oct 28 2022, 5:21 PM
kislinsk committed rMITK5efd14fb4be3: Merge branch 'develop' into arcpatch-D749 (authored by kislinsk).
Merge branch 'develop' into arcpatch-D749
Oct 28 2022, 5:21 PM
kislinsk committed rMITKd9bdff04d227: Improve Pixel Value plugin (authored by kislinsk).
Improve Pixel Value plugin
Oct 28 2022, 5:21 PM
kislinsk committed rMITK4687725cca01: Fix plugin metadata IID (authored by kislinsk).
Fix plugin metadata IID
Oct 28 2022, 5:21 PM
kislinsk committed rMITK60f9d724438d: Fix documentation warnings (authored by kislinsk).
Fix documentation warnings
Oct 28 2022, 5:21 PM
kislinsk committed rMITKe2a9d2db1788: Adding voxel value view to replace status bar information (authored by kislinsk).
Adding voxel value view to replace status bar information
Oct 28 2022, 5:21 PM
kislinsk committed rMITK4e833c5d9879: 2022 Week 43 (Late October) (authored by kislinsk).
2022 Week 43 (Late October)
Oct 28 2022, 5:21 PM
kislinsk edited the content of Changelog.
Oct 28 2022, 5:17 PM · MITK
kislinsk edited the content of 2022 Week 40 (Very Early October).
Oct 28 2022, 5:17 PM
kislinsk published a new version of 2022 Week 43 (Late October).
Oct 28 2022, 5:16 PM