Page MenuHomePhabricator

MITKProject
ActivePublic

Recent Activity

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 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

Mon, Jul 8

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

Thu, Jul 4

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

Fri, Jun 28

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

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 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 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

Wed, Jun 26

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: Restricted 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

Mon, Jun 24

floca updated subscribers of T30475: Add app for Splitting dynamic data sets.

FYI

Mon, Jun 24, 11:39 AM · MITK
floca added a revision to T30475: Add app for Splitting dynamic data sets: Restricted Differential Revision.
Mon, Jun 24, 11:38 AM · MITK
floca triaged T30475: Add app for Splitting dynamic data sets as High priority.
Mon, Jun 24, 9:44 AM · MITK

Wed, Jun 19

kislinsk added a comment to T28487: MitkMRSignal2Concentration MiniApp does not correctly handles exceptions in app configuration step.

Deleted branch from rMITK MITK: bugfix/T28487-MitkMRSignal2Concentration_handle_exceptions.

Wed, Jun 19, 11:33 AM · MITK
kislinsk added a comment to T27196: Rewrite packaging of MITK.

Deleted branch from rMITK MITK: bugfix/T27196-RewritePackaging.

Wed, Jun 19, 11:31 AM · MITK, Cleared