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Thu, Jul 11

isensee added members for Deep Learning: a332l, o340n.
Thu, Jul 11, 10:54 AM

Wed, Jul 10

floca added a comment to T30359: MITK MiniApps in Kaapana.
In T30359#260125, @gaoh wrote:

What is with MitkCLGlobalImageFeatures, it is not expected to be part of MITK anymore? Or is it still part of it?

Wed, Jul 10, 3:32 PM · MITK
gaoh added a comment to T30359: MITK MiniApps in Kaapana.

What is with MitkCLGlobalImageFeatures, it is not expected to be part of MITK anymore? Or is it still part of it?

Wed, Jul 10, 3:30 PM · MITK
s434n removed a project from T29024: [Core] Crash-inducing racing condition in TimeGeometry: Request for Discussion.
Wed, Jul 10, 11:46 AM · MITK
s434n added a comment to T29024: [Core] Crash-inducing racing condition in TimeGeometry.

Discussion result: we'll keep the task open. When eMITK builds again for the current state, try to reproduce the crash by going through the Geldosimetry workflow.
If it can't be reproduced, close the task.
If it can be reproduced, depending on the way the error expresses itself, either fix or accept as is.

Wed, Jul 10, 11:46 AM · MITK
a178n triaged T30487: Setup unit testing script for pyMITK as Normal priority.
Wed, Jul 10, 10:25 AM · MITK

Tue, Jul 9

kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

Deleted branch from rMITK MITK: bugfix/T30485-HandleNaNImages.

Tue, Jul 9, 9:14 PM · MITK
kislinsk committed rMITKf77bc512c1f3: Check if an image contains any valid pixel value at all (authored by kislinsk).
Check if an image contains any valid pixel value at all
Tue, Jul 9, 9:13 PM
kislinsk committed rMITK1de260a7c1a9: Remove unused typedef (authored by kislinsk).
Remove unused typedef
Tue, Jul 9, 9:13 PM
kislinsk committed rMITK00ef843ff8d9: Extend the search for appropriate level window values to other time steps (authored by kislinsk).
Extend the search for appropriate level window values to other time steps
Tue, Jul 9, 9:13 PM
kislinsk committed rMITK570c0df8de3a: Improve variable name (authored by kislinsk).
Improve variable name
Tue, Jul 9, 9:13 PM
kislinsk committed rMITKb226db94d9e8: Improve readability (authored by kislinsk).
Improve readability
Tue, Jul 9, 9:13 PM
kislinsk closed T30485: MITK Workbench freezes on 4-d images with empty time steps as Resolved by committing rMITK31d3c0df98b6: Fix handling of images with NaN pixel values.
Tue, Jul 9, 9:13 PM · MITK
kislinsk committed rMITK31d3c0df98b6: Fix handling of images with NaN pixel values (authored by kislinsk).
Fix handling of images with NaN pixel values
Tue, Jul 9, 9:13 PM
floca added a comment to T30476: Expose information of the DICOM reader why blocks where splitted.

Pushed new branch to rMITK MITK: feature/T30476-Expose_DCM_block_split_reason.

Tue, Jul 9, 10:58 AM · MITK (v2024.12)
floca triaged T30486: [DCM] Directory loading feature does not work sometimes as Normal priority.
Tue, Jul 9, 10:50 AM · MITK (v2024.12)

Mon, Jul 8

kislinsk added a comment to T30454: IO Support for Blosc2.

If I would be them, I also wouldn't like to have another metalayer under my belt. I think we can directly go with our own publishing. We may consider to suggest something like a registry, though, for third-party metalayers. :)

Mon, Jul 8, 10:23 PM · MITK (v2024.12)
isensee added a comment to T30454: IO Support for Blosc2.

I am not knowledgeable enough to have a well informed opinion. Some thoughts to consider:

Mon, Jul 8, 4:42 PM · MITK (v2024.12)
kislinsk closed T30484: MITK fails to start workbench as Resolved.

A few people reported trouble starting any MITK application with v2024.06.2. The culprit turned out to be Qt v6.7.1. I refreshed all Windows installers and packages with Qt v6.7.2.

Mon, Jul 8, 3:40 PM · MITK
floca added a comment to T30454: IO Support for Blosc2.

I think you proposal is worth trying! Great idea.

Mon, Jul 8, 9:35 AM · MITK (v2024.12)
kislinsk added a comment to T30454: IO Support for Blosc2.

Is there a defined anatomic coordinate system for blosc or the code that wrote the blosc images? Like LPS or RSA (https://www.slicer.org/wiki/Coordinate_systems) may be it differs form the assumption we have in MITK and therefore the memory layout of the pixels is different.

Mon, Jul 8, 8:56 AM · MITK (v2024.12)

Sat, Jul 6

floca added a comment to T30454: IO Support for Blosc2.

Is there a defined anatomic coordinate system for blosc or the code that wrote the blosc images? Like LPS or RSA (https://www.slicer.org/wiki/Coordinate_systems) may be it differs form the assumption we have in MITK and therefore the memory layout of the pixels is different.

Sat, Jul 6, 11:46 AM · MITK (v2024.12)

Fri, Jul 5

kislinsk changed the visibility for F5241891: Screenshot 2024-07-05 224840.png.
Fri, Jul 5, 11:17 PM
kislinsk added a comment to T30454: IO Support for Blosc2.

First breakthrough: I was able to load and display the n2nd example image from @isensee. The orientation is unexpected, though. Probably rotated 180° (not mirrored?) around the axial axis. Trying to figure out the culprit. I use a the b2nd_to_cbuffer() function to copy the pixel data into the MITK image memory. If this orientation mismatch is systematic, we may be able to solve it by creating a geometry accordingly. At the moment the MITK image is just initialized via pixel type and image dimensions. As far as I am aware, the Blosc2 image does not contain any orientation meta data, right?

Fri, Jul 5, 11:17 PM · MITK (v2024.12)
menjivar added a comment to T30454: IO Support for Blosc2.

If you need additional files to test, I could give you one :)

Fri, Jul 5, 12:03 PM · MITK (v2024.12)
kislinsk updated subscribers of T30454: IO Support for Blosc2.

c-blosc2 basically has 3 dependencies. We already fulfill an can/should use 2 of them: zlib (resp. zlib-ng) and lz4. The third one is zstd which is no issue, since c-blosc2 comes with an internal version of it if not provided externally.

Fri, Jul 5, 11:50 AM · MITK (v2024.12)
kislinsk added a comment to T30454: IO Support for Blosc2.

Pushed new branch to rMITK MITK: feature/T30454-Blosc2.

Fri, Jul 5, 11:41 AM · MITK (v2024.12)
kislinsk claimed T30454: IO Support for Blosc2.
Fri, Jul 5, 10:14 AM · MITK (v2024.12)

Thu, Jul 4

kislinsk added a revision to T30485: MITK Workbench freezes on 4-d images with empty time steps: Unknown Object (Differential Revision).
Thu, Jul 4, 10:40 AM · MITK
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

Pushed new branch to rMITK MITK: bugfix/T30485-HandleNaNImages.

Thu, Jul 4, 10:36 AM · MITK
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

I think I found a adequate solution:

Thu, Jul 4, 10:32 AM · MITK
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

The origin of the huge level window range is the calculation of the image statistics in mitkImageStatisticsHolder.cpp:100. The function template mitk::_ComputeExtremaInItkImage() is supposed to calculate the extrema and 2nd largest/smallest extrema as well as their counts. However, it does not check for NaN and compares it against the default values (itk::NumericTraits<>::max() resp. NonpositiveMin()). Hence, these extrema stay at their initial default values.

Thu, Jul 4, 9:40 AM · MITK

Wed, Jul 3

kislinsk changed the visibility for F5235634: NoNaN.nrrd.
Wed, Jul 3, 1:35 PM
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

"Empty time steps" turn out be be represented by frames filled with NaN (double). And I think this is the issue. Here's the file were I replaced all NaNs with 0s:

Wed, Jul 3, 1:35 PM · MITK
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

Sounds like a default value initialized with max possible value and the assumption that it would always be set to the actual value later on? How did you step into QmitkSliderLevelWindowWidget::paintEvent()? I always get stuck right before in Qt6Widgets.

Wed, Jul 3, 1:01 PM · MITK
floca added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

The problem is in QmitkSliderLevelWindowWidget::paintEvent.
The example data lead to a level window range that 2*10^300 and that is why the painting takes for ages because it iterates exhaustively and it does not make realy sense.

Wed, Jul 3, 12:00 PM · MITK
kislinsk added a comment to T30485: MITK Workbench freezes on 4-d images with empty time steps.

The freeze happens at the end of QmitkSliderLevelWindowWidget::resizeEvent() but we need to install the debug files of Qt (Qt6Widgetsd.pdb) for further investigation.

Wed, Jul 3, 11:36 AM · MITK
kislinsk changed the visibility for F5235069: Scan_33.PA.bf.frame.0000047.nrrd.
Wed, Jul 3, 9:42 AM
kislinsk triaged T30485: MITK Workbench freezes on 4-d images with empty time steps as High priority.
Wed, Jul 3, 9:42 AM · MITK

Tue, Jul 2

a178n claimed T30335: [Py] UC2.2 - Load images and manipulate with a sitk filter.
Tue, Jul 2, 6:10 PM · MITK
a178n claimed T30363: [Py] UC2.4 - Load image and clone it.
Tue, Jul 2, 6:10 PM · MITK
kislinsk added a comment to T30484: MITK fails to start workbench.

Okay, maybe it is really simple and obvious: I noticed the path in video implies that the Workbench was installed in a OneDrive directory that is synced between multiple PCs. What if it really is just the DLLs missing locally since they are not synced? For example, does C:\Users\adiazpinto\OneDrive - NVIDIA Corporation\Documents\MITK v2024.06.2\bin\MitkCore\MitkModelFitIOServices.dll really exist locally?

Tue, Jul 2, 11:13 AM · MITK
kislinsk added a comment to T30484: MITK fails to start workbench.

I was finally able to play the video from the link above. This looks more like a common system DLL or something similar is missing since basically every DLL is unable to load. We can't really figure out anything without access to an affected system. In that case I would run Dependencies on the Workbench executable after making sure to set the same path as in the start batch file.

Tue, Jul 2, 11:05 AM · MITK
kislinsk added a comment to T30484: MITK fails to start workbench.

Here's the other report: T30448: MITK snapshots/2024-05-02 Workbench not restarting

Tue, Jul 2, 9:54 AM · MITK

Mon, Jul 1

kislinsk added a comment to T30484: MITK fails to start workbench.

I use it on Windows 11 just fine. We recently had a similar report from someone using Windows 10. I throw anti-virus / defender as culprint into the ring.

Mon, Jul 1, 6:50 PM · MITK
a178n added a comment to T30484: MITK fails to start workbench.

I tried installing MITK but I cannot replicate the error on Windows 10.

Mon, Jul 1, 6:23 PM · MITK
a178n triaged T30484: MITK fails to start workbench as Unbreak Now! priority.
Mon, Jul 1, 6:15 PM · MITK

Sat, Jun 29

floca closed T30481: [DICOM] Handle multiple images with no position information correctly as Resolved.
Sat, Jun 29, 6:17 PM · MITK (v2024.12), Request for Discussion

Fri, Jun 28

floca committed rMITKb43651fc8666: T30475 Added app for splitting dynamic images (authored by floca).
T30475 Added app for splitting dynamic images
Fri, Jun 28, 12:07 PM
floca committed rMITK9de556569670: Fixed review comments (authored by floca).
Fixed review comments
Fri, Jun 28, 12:07 PM
floca closed T30475: Add app for Splitting dynamic data sets as Resolved by committing rMITK3f730792e113: Added app for splitting dynamic images.
Fri, Jun 28, 12:07 PM · MITK
floca committed rMITK3f730792e113: Added app for splitting dynamic images (authored by floca).
Added app for splitting dynamic images
Fri, Jun 28, 12:07 PM
floca committed rMITKcaba07b2e50a: BREAKING removed MiniApp suffix from model fit apps (authored by floca).
BREAKING removed MiniApp suffix from model fit apps
Fri, Jun 28, 12:07 PM
floca closed T30477: Remove MiniApp suffix from ModelFit cmdapps as Resolved by committing rMITKcaba07b2e50a: BREAKING removed MiniApp suffix from model fit apps.
Fri, Jun 28, 12:07 PM · Breaking Change, MITK (v2024.12)
floca committed rMITK7f6f75613914: Added extraction helper to TemporoSatialStringProperty (authored by floca).
Added extraction helper to TemporoSatialStringProperty
Fri, Jun 28, 12:07 PM
floca committed rMITKc07e7ef1cdb4: T30481 DICOM handling multiple images with no position (authored by floca).
T30481 DICOM handling multiple images with no position
Fri, Jun 28, 11:43 AM
floca committed rMITK946a07dd286f: fixed review remarks (authored by floca).
fixed review remarks
Fri, Jun 28, 11:43 AM
floca committed rMITK5f9aed9c3865: Introduced a delimiter to make the UID more robust. (authored by floca).
Introduced a delimiter to make the UID more robust.
Fri, Jun 28, 11:43 AM
floca committed rMITKa2a1fca0dcc4: BREAKING (authored by floca).
BREAKING
Fri, Jun 28, 11:43 AM
floca committed rMITKf9785e2e6b8c: BREAKING: DICOMGDCMImageFrameInfo does not return a (authored by floca).
BREAKING: DICOMGDCMImageFrameInfo does not return a
Fri, Jun 28, 11:43 AM
kislinsk closed T29421: Finding CppRestSDK library alternative as Resolved.
Fri, Jun 28, 8:51 AM · MITK (v2024.12)
kislinsk added a comment to T29421: Finding CppRestSDK library alternative.

Deleted branch from rMITK MITK: bugfix/T29421-RemoveCPPRestSDK.

Fri, Jun 28, 8:51 AM · MITK (v2024.12)
kislinsk committed rMITKf3f41401d040: Remove C++ REST SDK dependency (authored by kislinsk).
Remove C++ REST SDK dependency
Fri, Jun 28, 8:50 AM
kislinsk committed rMITK846e41531a9c: Merge branch 'bugfix/T29421-RemoveCPPRestSDK' into develop (authored by kislinsk).
Merge branch 'bugfix/T29421-RemoveCPPRestSDK' into develop
Fri, Jun 28, 8:50 AM

Thu, Jun 27

a178n added a comment to T30361: [Py] pyMITK package to use MITK in a python environement.

Pushed new branch to rMITK MITK: feature/T30361-pyMITK-wrapping.

Thu, Jun 27, 2:25 PM · MITK
kislinsk closed T30482: MITK v2024.06.2 as Resolved.
Thu, Jun 27, 8:22 AM · MITK
kislinsk edited the content of Changelog.
Thu, Jun 27, 8:22 AM · MITK
kislinsk edited the content of MITK v2024.06.2.
Thu, Jun 27, 8:21 AM
kislinsk edited the content of MITK v2024.06.
Thu, Jun 27, 8:20 AM
kislinsk edited the content of MITK v2024.06.
Thu, Jun 27, 8:19 AM
kislinsk closed T30483: Fix typos in Segmentation Utilities as Resolved.
Thu, Jun 27, 8:17 AM · MITK
kislinsk added a comment to T30482: MITK v2024.06.2.

Pushed new branch to rMITK MITK: hotfix/T30482-v2024.06.2.

Thu, Jun 27, 8:08 AM · MITK
kislinsk added a comment to T30483: Fix typos in Segmentation Utilities.

Deleted branch from rMITK MITK: bugfix/T30483-FixTyposInSegmentationUtilities.

Thu, Jun 27, 8:07 AM · MITK
kislinsk committed rMITKb1cb1e823bde: Fix typos (authored by kislinsk).
Fix typos
Thu, Jun 27, 8:06 AM
kislinsk committed rMITKdfee4f84afad: Merge branch 'bugfix/T30483-FixTyposInSegmentationUtilities' into develop (authored by kislinsk).
Merge branch 'bugfix/T30483-FixTyposInSegmentationUtilities' into develop
Thu, Jun 27, 8:06 AM
kislinsk added a comment to T30483: Fix typos in Segmentation Utilities.

Pushed new branch to rMITK MITK: bugfix/T30483-FixTyposInSegmentationUtilities.

Thu, Jun 27, 8:06 AM · MITK
kislinsk triaged T30483: Fix typos in Segmentation Utilities as Normal priority.
Thu, Jun 27, 8:03 AM · MITK
kislinsk triaged T30482: MITK v2024.06.2 as Normal priority.
Thu, Jun 27, 7:58 AM · MITK
kislinsk edited the content of MITK v2024.06.2.
Thu, Jun 27, 7:57 AM
kislinsk created an object: MITK v2024.06.2.
Thu, Jun 27, 7:56 AM
kislinsk deleted MITK v2024.04.2.
Thu, Jun 27, 7:56 AM
kislinsk created an object: MITK v2024.04.2.
Thu, Jun 27, 7:55 AM

Wed, Jun 26

kislinsk added a revision to T30481: [DICOM] Handle multiple images with no position information correctly: Unknown Object (Differential Revision).
Wed, Jun 26, 11:53 PM · MITK (v2024.12), Request for Discussion
floca triaged T30481: [DICOM] Handle multiple images with no position information correctly as High priority.
Wed, Jun 26, 1:41 PM · MITK (v2024.12), Request for Discussion
a178n committed rMITK59ed6846f4f1: Totalsegmentator dependency fix non-version specific package listing (authored by a178n).
Totalsegmentator dependency fix non-version specific package listing
Wed, Jun 26, 1:22 PM
a178n committed rMITK908ee3e33fd8: Totalsegmentator dependency fix (authored by a178n).
Totalsegmentator dependency fix
Wed, Jun 26, 1:22 PM
a178n added a subtask for T30479: [Seg] Totalseg and SAM/MedSAM tool fails: T30480: Installation 'agent' for Totalsegmentator.
Wed, Jun 26, 8:26 AM · MITK
a178n added a parent task for T30480: Installation 'agent' for Totalsegmentator: T30479: [Seg] Totalseg and SAM/MedSAM tool fails.
Wed, Jun 26, 8:26 AM · Request for Discussion, MITK
a178n triaged T30480: Installation 'agent' for Totalsegmentator as Normal priority.
Wed, Jun 26, 8:26 AM · Request for Discussion, MITK

Tue, Jun 25

a178n added a comment to T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

Numpy dependency updated for SegmentAnything & MedSAM installation in https://github.com/MIC-DKFZ/agent-sam.git
Now the both tools should work.

Tue, Jun 25, 4:45 PM · MITK
a178n added a revision to T30479: [Seg] Totalseg and SAM/MedSAM tool fails: Unknown Object (Differential Revision).
Tue, Jun 25, 4:42 PM · MITK
a178n added a comment to T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

Pushed new branch to rMITK MITK: bugfix/T30479-totalseg-dependency-update.

Tue, Jun 25, 1:02 PM · MITK
a178n added a comment to T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

As far as SAM/MedSAM is concerned, we can add numpy<2 in our agent-sam repo and fix the issue without code changes to MITK.
Perhaps we should think about creating Totalsegmentator "agents" scripts to deal with such production issues.

Tue, Jun 25, 12:07 PM · MITK
a178n added a comment to T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

The numpy version upgrade seems disruptive. The current latest torch version 2.3.1 is incompatible with numpy v2 while running torch.from_numpy conversions
Since numpy v2 release, Totalsegmentator dev has updated its dependency specification. See: https://github.com/wasserth/TotalSegmentator/commit/e648b08445434585511a8a7c8118e34f5309ce05
However, new a release hasn't occurred since on pypi.

Tue, Jun 25, 12:01 PM · MITK
a178n updated the task description for T30479: [Seg] Totalseg and SAM/MedSAM tool fails.
Tue, Jun 25, 11:28 AM · MITK
a178n triaged T30479: [Seg] Totalseg and SAM/MedSAM tool fails as High priority.
Tue, Jun 25, 11:27 AM · MITK
floca closed T30478: MITKFileConverter multiple output index before last extension as Invalid.

damn. you are right. Than i will revert it and change AVID to add in front of the first '.'.

Tue, Jun 25, 11:02 AM · MITK (v2024.12), Request for Discussion, Breaking Change
kislinsk added a comment to T30478: MITKFileConverter multiple output index before last extension.

Wouldn't that break support of compressed files like foo.nii.gz for example?

Tue, Jun 25, 9:57 AM · MITK (v2024.12), Request for Discussion, Breaking Change
floca moved T30478: MITKFileConverter multiple output index before last extension from Backlog to MITK Meeting on the Request for Discussion board.
Tue, Jun 25, 9:17 AM · MITK (v2024.12), Request for Discussion, Breaking Change
floca triaged T30478: MITKFileConverter multiple output index before last extension as Normal priority.
Tue, Jun 25, 9:17 AM · MITK (v2024.12), Request for Discussion, Breaking Change