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Nov 10 2021

kislinsk created Checklist.
Nov 10 2021, 4:26 PM
kislinsk created MITK (v2022.04).
Nov 10 2021, 4:24 PM
kislinsk renamed T28833: Label masks have wrong geometry from Create polygon model from segmentation with spacing != 1 results in scaled surface to Label masks have wrong geometry.
Nov 10 2021, 7:28 AM · MITK
kislinsk committed rMITK43fa75fab5bf: Fix geometry of label masks (authored by kislinsk).
Fix geometry of label masks
Nov 10 2021, 7:26 AM
kislinsk closed T28833: Label masks have wrong geometry as Resolved.
Nov 10 2021, 7:26 AM · MITK
kislinsk committed rMITKf98f284f26c9: Merge branch 'bugfix/T28833-FixGeometryOfLabelMaskImages' into develop (authored by kislinsk).
Merge branch 'bugfix/T28833-FixGeometryOfLabelMaskImages' into develop
Nov 10 2021, 7:26 AM
kislinsk added a comment to T28833: Label masks have wrong geometry.

Pushed new branch to rMITK MITK: bugfix/T28833-FixGeometryOfLabelMaskImages.

Nov 10 2021, 7:25 AM · MITK
kislinsk claimed T28833: Label masks have wrong geometry.

Oh no, this bug sneaked in with the fix of T28806: Crash in "Create smooth polygon model" for 2-d images. The initialization of the mask images for labels was changed to have the correct dimensions for 2-d images. However, the original transform of the label set image is not lost and has to be set explicitly.

Nov 10 2021, 7:09 AM · MITK

Nov 9 2021

kislinsk closed T28841: MITK v2021.10 as Resolved.
Nov 9 2021, 9:24 AM · MITK-ProjectTemplate, MITK
kislinsk added a comment to T28841: MITK v2021.10.

Deleted branch from rMPT MITK-ProjectTemplate: release/T28841-MITK-v2021.10.

Nov 9 2021, 9:23 AM · MITK-ProjectTemplate, MITK
kislinsk committed rMPT300f4a651346: Update README (authored by kislinsk).
Update README
Nov 9 2021, 9:23 AM
kislinsk committed rMPTb09c4706ddf4: Merge branch 'release/T28841-MITK-v2021.10' (authored by kislinsk).
Merge branch 'release/T28841-MITK-v2021.10'
Nov 9 2021, 9:23 AM
kislinsk added a comment to T28841: MITK v2021.10.

Deleted branch from rMITK MITK: release/T28841-MITK-v2021.10.

Nov 9 2021, 9:16 AM · MITK-ProjectTemplate, MITK
kislinsk added a reverting change for rMITKaa27aca85882: Change nightly documentation URIs to release-specific URIs: rMITK1ba2a7085c84: Revert "Change nightly documentation URIs to release-specific URIs".
Nov 9 2021, 9:16 AM
kislinsk committed rMITK1ba2a7085c84: Revert "Change nightly documentation URIs to release-specific URIs" (authored by kislinsk).
Revert "Change nightly documentation URIs to release-specific URIs"
Nov 9 2021, 9:16 AM
kislinsk committed rMITKadbd98c20761: Bump MITK development version (authored by kislinsk).
Bump MITK development version
Nov 9 2021, 9:16 AM
kislinsk committed rMITK4c6efc27294a: Revert "Disable Multilabel Segmentation Utilities" (authored by kislinsk).
Revert "Disable Multilabel Segmentation Utilities"
Nov 9 2021, 9:16 AM
kislinsk added a reverting change for rMITK9f2da2ef311b: Disable Multilabel Segmentation Utilities: rMITK4c6efc27294a: Revert "Disable Multilabel Segmentation Utilities".
Nov 9 2021, 9:16 AM
kislinsk committed rMITK1d891123341a: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Nov 9 2021, 9:16 AM
kislinsk committed rMITK9f2da2ef311b: Disable Multilabel Segmentation Utilities (authored by kislinsk).
Disable Multilabel Segmentation Utilities
Nov 9 2021, 9:11 AM
kislinsk committed rMITK54eaa4de3ffd: Bump MITK version (authored by kislinsk).
Bump MITK version
Nov 9 2021, 9:11 AM
kislinsk committed rMITKaa27aca85882: Change nightly documentation URIs to release-specific URIs (authored by kislinsk).
Change nightly documentation URIs to release-specific URIs
Nov 9 2021, 9:11 AM
kislinsk committed rMITK4545383c0841: v2021.10 (authored by kislinsk).
v2021.10
Nov 9 2021, 9:11 AM
kislinsk edited the content of Changelog.
Nov 9 2021, 7:59 AM · MITK
kislinsk edited the content of MITK v2021.10.
Nov 9 2021, 7:56 AM
kislinsk edited the content of MITK v2021.10.
Nov 9 2021, 7:56 AM
kislinsk published a new version of MITK v2021.10.
Nov 9 2021, 7:55 AM
kislinsk added a comment to T28841: MITK v2021.10.

Pushed new branch to rMPT MITK-ProjectTemplate: release/T28841-MITK-v2021.10.

Nov 9 2021, 5:58 AM · MITK-ProjectTemplate, MITK
kislinsk added a project to T28841: MITK v2021.10: MITK-ProjectTemplate.
Nov 9 2021, 5:57 AM · MITK-ProjectTemplate, MITK
kislinsk added a comment to T28841: MITK v2021.10.

Pushed new branch to rMITK MITK: release/T28841-MITK-v2021.10.

Nov 9 2021, 5:52 AM · MITK-ProjectTemplate, MITK
kislinsk triaged T28841: MITK v2021.10 as Normal priority.
Nov 9 2021, 5:50 AM · MITK-ProjectTemplate, MITK
kislinsk added a comment to T28802: 2021 Week 45 (Early November).

Deleted branch from rMITK MITK: release/T28802-MITK-v2021.10.

Nov 9 2021, 5:47 AM · MITK (v2021.10)
kislinsk closed T28802: 2021 Week 45 (Early November) as Resolved.
Nov 9 2021, 5:46 AM · MITK (v2021.10)
kislinsk edited the content of Changelog.
Nov 9 2021, 5:38 AM · MITK
kislinsk added a comment to T28802: 2021 Week 45 (Early November).

Deleted branch from rMITK MITK: release/T28802-2021-Week-45.

Nov 9 2021, 5:37 AM · MITK (v2021.10)
kislinsk committed rMITK23583c92aafc: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Nov 9 2021, 5:37 AM
kislinsk committed rMITK59b812a61b86: Prevent error output on terminal if there is nothing to smooth (authored by kislinsk).
Prevent error output on terminal if there is nothing to smooth
Nov 9 2021, 5:37 AM
kislinsk committed rMITKe1257e98f775: Pad single-sliced images with empty slice to make them 3-d for VTK (authored by kislinsk).
Pad single-sliced images with empty slice to make them 3-d for VTK
Nov 9 2021, 5:37 AM
kislinsk committed rMITKa1ff2b922b83: Ensure equal dimensionality between label set images and label masks (authored by kislinsk).
Ensure equal dimensionality between label set images and label masks
Nov 9 2021, 5:37 AM
kislinsk committed rMITK922557c2ab9d: Only add surface nodes if they actually contain data (authored by kislinsk).
Only add surface nodes if they actually contain data
Nov 9 2021, 5:37 AM
kislinsk committed rMITK0302f599f52e: T28799 Multilable 3D tools crash when multiple layers/labels are generated. (authored by floca).
T28799 Multilable 3D tools crash when multiple layers/labels are generated.
Nov 9 2021, 5:37 AM
kislinsk committed rMITKeb848d840bf7: Always expand all tree nodes (authored by kislinsk).
Always expand all tree nodes
Nov 9 2021, 5:37 AM
kislinsk committed rMITKc3e2b79d91b9: Fix initial selection and auto-selection of invisible nodes (authored by kislinsk).
Fix initial selection and auto-selection of invisible nodes
Nov 9 2021, 5:37 AM
kislinsk committed rMITK8562c6636ed4: T28799 Multilable 3D tools crash when multiple layers/labels are generated. (authored by floca).
T28799 Multilable 3D tools crash when multiple layers/labels are generated.
Nov 9 2021, 5:36 AM
kislinsk closed T28799: [Segmentation] Multilable 3D tools crash when multiple layers/labels are generated. as Resolved by committing rMITK8562c6636ed4: T28799 Multilable 3D tools crash when multiple layers/labels are generated..
Nov 9 2021, 5:36 AM · MITK (v2021.10)
kislinsk committed rMITKbf2f49835837: Apply levelwindow preset regardless of current scale range (authored by s434n).
Apply levelwindow preset regardless of current scale range
Nov 9 2021, 5:36 AM
kislinsk committed rMITKb52535d09e68: Apply levelwindow preset regardless of current scale range (authored by s434n).
Apply levelwindow preset regardless of current scale range
Nov 9 2021, 5:36 AM
kislinsk committed rMITK0175a97810d0: fix image masking issues for images with multiple timesteps (authored by kislinsk).
fix image masking issues for images with multiple timesteps
Nov 9 2021, 5:36 AM
kislinsk committed rMITKb4acd382aa0d: fix image masking issues for images with multiple timesteps (authored by kislinsk).
fix image masking issues for images with multiple timesteps
Nov 9 2021, 5:36 AM
kislinsk closed T28795: [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality as Resolved by committing rMITKb4acd382aa0d: fix image masking issues for images with multiple timesteps.
Nov 9 2021, 5:36 AM · MITK
kislinsk committed rMITK489ca48b85b8: 2021 Week 45 (Early November) (authored by kislinsk).
2021 Week 45 (Early November)
Nov 9 2021, 5:36 AM
kislinsk edited the content of 2021 Week 45 (Early November).
Nov 9 2021, 5:30 AM
kislinsk edited the content of 2021 Week 42 (Late October).
Nov 9 2021, 5:01 AM
kislinsk created an object: 2021 Week 45 (Early November).
Nov 9 2021, 5:00 AM
kislinsk updated the task description for T28802: 2021 Week 45 (Early November).
Nov 9 2021, 4:59 AM · MITK (v2021.10)
kislinsk renamed T28802: 2021 Week 45 (Early November) from MITK v2021.10 to 2021 Week 45 (Early November).
Nov 9 2021, 4:59 AM · MITK (v2021.10)
kislinsk added a comment to T28802: 2021 Week 45 (Early November).

Pushed new branch to rMITK MITK: release/T28802-2021-Week-45.

Nov 9 2021, 4:55 AM · MITK (v2021.10)
kislinsk added a comment to T28802: 2021 Week 45 (Early November).
Nov 9 2021, 4:52 AM · MITK (v2021.10)

Nov 4 2021

kislinsk renamed T28795: [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality from [Segmentation][Utilities] Using custom background pixels for "Image Masking" fails to [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality.
Nov 4 2021, 7:52 AM · MITK
kislinsk claimed T28795: [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality.
Nov 4 2021, 7:51 AM · MITK
kislinsk added a comment to T28795: [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality.

Works with Zero and Minimum background value options, only "custom" results in an uncaught "dimension (4) is not in (2)(3)" exception + crash.

Nov 4 2021, 7:50 AM · MITK
kislinsk updated the task description for T28795: [Segmentation][Utilities] "Image Masking" has several issues regarding image dimensionality.
Nov 4 2021, 7:40 AM · MITK
kislinsk triaged T28833: Label masks have wrong geometry as Normal priority.
Nov 4 2021, 7:39 AM · MITK

Nov 3 2021

kislinsk closed T28807: [Properties] Changing any tree view element makes the tree view collapse as Resolved.

Sadly, a few years ago I was overruled by the decision that modifications of a single property should also modify the property list it is part of with the standard Modified() event. This bits back in cases like the Properties View and there is no feasible solution for it under these circumstances. The issue is that modifying a property value in the tree view itself now indirectly modifies the whole property list which must trigger a model reset. A workaround is to always expand everything instead of collapse everything, as it won't fight against most of the users intents regarding nested items. The displayed property list is typically longer now by default but there's a filter widget for that anyway.

Nov 3 2021, 11:30 PM · Request for Discussion, MITK
kislinsk lowered the priority of T28817: MITK crashes with Fast Marching 3d and watershed tool on old laptop with Ubuntu 20.04 from High to Normal.

Lowering the priority since it is hard to reproduce without any more information and terminal/console output. I am sure that somehow these obscure tools can be forced to crash independent of the hardware. An unsolved question from last release is still: do we want to keep these tools anyway since they are basically unusable for any user and even developer with code insight.

Nov 3 2021, 8:38 PM · Checklist, Request for Discussion, Missing Info, MITK
kislinsk lowered the priority of T28801: [MultiLabel Segmentation][Utilities] Exception thrown when converting to MultiLabel from High to Normal.

I lower the priority since the exception is caught and it results in an error message instead of a crash. It's also an academic edge case, since it hardly makes any sense in a real world scenario to convert an actual image with more than 65000 different pixel values into a segmentation. Converting binary images or segmentation-like images works as expected.

Nov 3 2021, 8:11 PM · MITK (v2022.10), Checklist
kislinsk closed T28806: Crash in "Create smooth polygon model" for 2-d images as Resolved.
Nov 3 2021, 12:25 AM · MITK
kislinsk claimed T28806: Crash in "Create smooth polygon model" for 2-d images.
Nov 3 2021, 12:19 AM · MITK
kislinsk added a comment to T28806: Crash in "Create smooth polygon model" for 2-d images.

Turns out that VTK has the same issue as MITK in a few filters regarding recognizing a 3-d image as such when it has only a single slice. To fix it, I also added a check in the corresponding MITK filter that adds an empty pad slice to an intermediate pipeline image output for single-sliced images. Also, the result of the filter pipeline is now checked more thoroughly whether it is containing actual surface data or not. If there is no surface data, no surface node is created but instead a warning is printed for all affected labels and a hint is given to try again without smoothing (smoothing does always smooth out single slices completely).

Nov 3 2021, 12:19 AM · MITK

Nov 2 2021

kislinsk added a comment to T28806: Crash in "Create smooth polygon model" for 2-d images.

Thanks for the first look. I come to a slightly different but related conclusion. Segmentations are always created with 3 or more dimensions by design choice. So, for the 2-d image, a 3-d segmentation with the third dimension set to 1 is created. Checking the dimension of that segmentation image returns 3 as expected.

Nov 2 2021, 9:51 PM · MITK
kislinsk triaged T28822: [Segmentation Interpolation] Intepolation contour shown even after segmentation node is invisible as Wishlist priority.

I changed the priority to Wishlist because the behavior is as expected. We can discuss if we want another preference to change the behavior so that visibility changes of parent nodes also affect child nodes.

Nov 2 2021, 8:37 PM · Auto-closed, MITK
kislinsk triaged T28821: [Segmentation] Create (Smooth) Polygon Model hardly works for large images. as Low priority.
Nov 2 2021, 8:35 PM · Checklist, MITK
kislinsk triaged T28820: [Segmentation] Auto-Selection Mode Not responsive as Low priority.
Nov 2 2021, 8:34 PM · Checklist, MITK
kislinsk triaged T28819: [View Navigator] View Names don't become bold when opened as Low priority.
Nov 2 2021, 8:33 PM · MITK (v2022.04), Checklist
kislinsk merged task T18866: Highlighting in View Navigator is not updated into T28819: [View Navigator] View Names don't become bold when opened.
Nov 2 2021, 8:33 PM · MITK (v2021.10), Restricted Project, Bugzilla
kislinsk merged T18866: Highlighting in View Navigator is not updated into T28819: [View Navigator] View Names don't become bold when opened.
Nov 2 2021, 8:33 PM · MITK (v2022.04), Checklist
kislinsk closed T28818: [View Navigator] Text Search Filter bug as Invalid.

I guess it is because the Description of the plugin is "View, Set, and Change properties of DataNodes". There are also keywords for plugins (see the plugin.xml of the Properties plugin for example). It is expected behavior.

Nov 2 2021, 8:32 PM · MITK
kislinsk added a project to T28817: MITK crashes with Fast Marching 3d and watershed tool on old laptop with Ubuntu 20.04: Missing Info.
Nov 2 2021, 8:28 PM · Checklist, Request for Discussion, Missing Info, MITK
kislinsk triaged T28817: MITK crashes with Fast Marching 3d and watershed tool on old laptop with Ubuntu 20.04 as High priority.

@floca What is the current status of these two tools?

Nov 2 2021, 8:28 PM · Checklist, Request for Discussion, Missing Info, MITK
kislinsk triaged T28823: [Volume Visualization] Auto-selection is not handled in view initialization as Normal priority.
Nov 2 2021, 8:27 PM · Cleared, MITK
kislinsk triaged T28811: [Volume Visualization] [UX] Missing labels for dropdowns as Low priority.
Nov 2 2021, 8:22 PM · Breaking Change, MITK (v2022.04), Checklist
kislinsk renamed T28811: [Volume Visualization] [UX] Missing labels for dropdowns from [Volume Visualization] Missing labels for dropdowns to [Volume Visualization] [UX] Missing labels for dropdowns.
Nov 2 2021, 8:22 PM · Breaking Change, MITK (v2022.04), Checklist
kislinsk closed T28810: Surface image Point Representation too small as Invalid.

The thing is, most surfaces that are generated within MITK have a very high vertex count and changing the default point size could lead to a lot of visual clutter. You found already a way to change the point size. BTW, be aware, that in general the Properties view is meant as a Power User / Developer view. Changing properties here should be a last resort for typical users in case there isn't any dedicated widget for the same setting in any other view.

Nov 2 2021, 8:18 PM · Request for Discussion, MITK
kislinsk triaged T28808: [Properties] Some Pointset 2D shape selection not shown in the image views as Normal priority.

I cannot reproduce it with the latest Windows snapshot installer. I used Pic3D.nrrd + RenderingTestData/PointSetForPicD.mps.

Nov 2 2021, 8:13 PM · MITK (v2022.10)
kislinsk renamed T28807: [Properties] Changing any tree view element makes the tree view collapse from [Properties] Pointset Submenu auto collapse after 2D shape property changed to [Properties] Changing any tree view element makes the tree view collapse.
Nov 2 2021, 8:08 PM · Request for Discussion, MITK
kislinsk merged T28809: [Properties] Surface Submenu auto collapse after 2D->Normals properties changed into T28807: [Properties] Changing any tree view element makes the tree view collapse.
Nov 2 2021, 8:06 PM · Request for Discussion, MITK
kislinsk merged task T28809: [Properties] Surface Submenu auto collapse after 2D->Normals properties changed into T28807: [Properties] Changing any tree view element makes the tree view collapse.
Nov 2 2021, 8:06 PM · MITK

Oct 30 2021

kislinsk added a comment to T28801: [MultiLabel Segmentation][Utilities] Exception thrown when converting to MultiLabel.

The description of the actual but swallowed exception is "Prohibited image access: the requested image part is already in use and cannot be requested recursively!" thrown indirectly from line 315 in mitkLabelSetImage.cpp: AccessFixedDimensionByItk_n(), which eventually calls ImageToItkImage() in mitkImageToItk.h:132. There, the Update() call of the ImageToItk class throws the exception mentioned above,

Oct 30 2021, 12:32 AM · MITK (v2022.10), Checklist

Oct 29 2021

kislinsk raised the priority of T28806: Crash in "Create smooth polygon model" for 2-d images from Normal to High.
Oct 29 2021, 8:43 PM · MITK
kislinsk triaged T28806: Crash in "Create smooth polygon model" for 2-d images as Normal priority.
Oct 29 2021, 8:43 PM · MITK
kislinsk triaged T28805: [Preferences] Check Qt size policies for Multilabel Segmentation preferences as Low priority.
Oct 29 2021, 8:39 PM · Checklist, MITK
kislinsk triaged T28804: [Help] Hard to read color scheme (blue on dark background) as Normal priority.
Oct 29 2021, 8:35 PM · MITK (v2022.04), Checklist
kislinsk triaged T28767: 2D (multi-label) segmentation tools -> paint/wipe unusable for larger images as Normal priority.
Oct 29 2021, 8:31 PM · Request for Discussion, MITK (v2022.10), Checklist
kislinsk triaged T28768: Region Growing in its current state is unintuitive as Normal priority.

100% agree. Also, the fact that the level window has an impact should be made clear by a widget. Maybe even a checkbox to decide if the region growing should depend on true image values or displayed image values.

Oct 29 2021, 8:30 PM · MITK (v2022.04), Checklist
kislinsk triaged T28783: Levelwindow presets are not always applied correctly as Normal priority.

I also think that if you realy select a preset it should be aplied, even if it is (partially) out of range. Everything else would have an impact on the visualization and would for example lead to the fact that a certain preset has for the same value different appearances in different images.

Oct 29 2021, 8:28 PM · MITK
kislinsk closed T28784: Levelwindow context menu - selected elements have no checkmark on Mac as Invalid.

Is it realy a check box element or just an action to apply?

Oct 29 2021, 8:26 PM · MITK
kislinsk triaged T28785: Levelwindow UX proposals/comments as Normal priority.

The level window widget really is too cryptic and has too many hidden features and behaviors. At least we need to clarify how it is working / applied currently and what we would expect. With multiple data sets there won't be an optimal solution that pleases everyone as us is dependent on taste/workflow.

Oct 29 2021, 8:25 PM · Moved to git.dkfz.de, MITK (v2024.12), Checklist, Missing Info, Request for Discussion
kislinsk triaged T28786: Measurement - “Fixed sized circle/double ellipse” checkbox is not greyed out as Low priority.
Oct 29 2021, 8:22 PM · Checklist, MITK
kislinsk renamed T28803: [Properties] Fine-tune selection widget from Point Set Rendering Properties: Selected Node shows other planes too to [Properties] Fine-tune selection widget.
Oct 29 2021, 8:22 PM · Moved to git.dkfz.de, MITK, Checklist
kislinsk added a comment to T28802: 2021 Week 45 (Early November).
Oct 29 2021, 4:15 PM · MITK (v2021.10)