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Wed, Jan 11

franza added a comment to T29435: MITK example for usage of the ICP algorithm.

Created an example in this pull request: https://github.com/MITK/MITK/pull/271

Wed, Jan 11, 10:40 AM · Pull Request, MITK (v2023.04)
kislinsk added a comment to T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.

We talked about this task in our meeting today and concluded that we will migrate the DataStorageComboBox in our code to the SingleSelectionWidget and even deprecate the DataStorageComboBox.

Wed, Jan 11, 10:15 AM · MITK (v2023.04)

Tue, Jan 10

kalali added a comment to T29297: [mxn multi widget] Optimize data accessibility inside render windows.

Pushed new branch to rMITK MITK: feature/T29297-Use-selection-widgets-in-render-window-utility.

Tue, Jan 10, 3:15 PM · MITK (v2023.04)
kalali closed T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module, a subtask of T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation, as Resolved.
Tue, Jan 10, 2:57 PM · MITK (v2022.10), Breaking Change
kalali closed T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module as Resolved.
Tue, Jan 10, 2:57 PM · MITK (v2023.04)
kalali committed rMITK12e940a97f08: Move utilities widgets to module (authored by kalali).
Move utilities widgets to module
Tue, Jan 10, 2:56 PM
kalali committed rMITKedc932665302: Fix wrong icon reference after moving the selection widgets (authored by kalali).
Fix wrong icon reference after moving the selection widgets
Tue, Jan 10, 2:56 PM
kalali committed rMITK3274299dbde3: Provide getter/setter for data storage and add contructor parameter (authored by kalali).
Provide getter/setter for data storage and add contructor parameter
Tue, Jan 10, 2:56 PM
kalali committed rMITK162230469962: Move controls include to .cpp-file (authored by kalali).
Move controls include to .cpp-file
Tue, Jan 10, 2:56 PM
kalali committed rMITKfc363dd5f9e2: Fix includes for ui-files (authored by kalali).
Fix includes for ui-files
Tue, Jan 10, 2:56 PM
kalali committed rMITKf0a3da3acbe2: Move DataSelectionWidget to the SegmentationUI module (authored by kalali).
Move DataSelectionWidget to the SegmentationUI module
Tue, Jan 10, 2:56 PM
kalali committed rMITK49949baef127: Remove the "SegmentationUtilities" subdirectory (authored by kalali).
Remove the "SegmentationUtilities" subdirectory
Tue, Jan 10, 2:56 PM
kalali committed rMITK195b495c9533: Add utility tools to the segmentation ui module (authored by kalali).
Add utility tools to the segmentation ui module
Tue, Jan 10, 2:56 PM
kalali committed rMITK63c5bab4c89e: Remove utility tools from the segmentation plugin (authored by kalali).
Remove utility tools from the segmentation plugin
Tue, Jan 10, 2:56 PM
kausch added a member for MIC: a564y.
Tue, Jan 10, 11:36 AM
isensee added a member for Deep Learning: kahl.
Tue, Jan 10, 8:07 AM

Mon, Jan 9

kalali closed T29027: Move NodeSelectionWidgets to QtWidgets module, a subtask of T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI, as Resolved.
Mon, Jan 9, 1:32 PM · MITK (v2023.04)
kalali closed T29027: Move NodeSelectionWidgets to QtWidgets module as Resolved.
Mon, Jan 9, 1:32 PM · MITK (v2023.04)
kalali committed rMITK3991d268266b: Move selection widgets to module (authored by kalali).
Move selection widgets to module
Mon, Jan 9, 12:48 PM
kalali committed rMITKa69ec5fd4f4e: Move selection widget and related classes to module (authored by kalali).
Move selection widget and related classes to module
Mon, Jan 9, 12:48 PM
kalali committed rMITK050d60110c49: Remove selection widget and related classes from plugin (authored by kalali).
Remove selection widget and related classes from plugin
Mon, Jan 9, 12:48 PM

Fri, Jan 6

kalali closed T29438: org.mitk.gui.common plugin is not initializing the CppMicroService as Resolved.
Fri, Jan 6, 9:15 AM · MITK
kalali committed rMITKc82c8ebf64bd: Initialize CppMicroService in gui.common plugin (authored by kalali).
Initialize CppMicroService in gui.common plugin
Fri, Jan 6, 9:14 AM
kalali committed rMITK58ccd21018c6: Clean up the gui.qt.application plugin (authored by kalali).
Clean up the gui.qt.application plugin
Fri, Jan 6, 9:14 AM
kalali committed rMITKf7e8412f739f: Initialize CppMicroService inside the plugin activator class (authored by kalali).
Initialize CppMicroService inside the plugin activator class
Fri, Jan 6, 9:14 AM

Jan 5 2023

kalali added a revision to T29438: org.mitk.gui.common plugin is not initializing the CppMicroService: Unknown Object (Differential Revision).
Jan 5 2023, 1:34 PM · MITK
kalali renamed T29438: org.mitk.gui.common plugin is not initializing the CppMicroService from org.mitk.gui.common plugin is not initializing the the CppMicroService to org.mitk.gui.common plugin is not initializing the CppMicroService.
Jan 5 2023, 12:47 PM · MITK
kalali created T29438: org.mitk.gui.common plugin is not initializing the CppMicroService.
Jan 5 2023, 12:45 PM · MITK
kalali edited parent tasks for T24216: Synchronization of individual render windows: camera position, added: T29393: [mxn multi widget] Concept for individual render window synchronization; removed: T23758: Introduction of custom multi widget editor.
Jan 5 2023, 9:37 AM · MITK (v2023.04)
kalali removed a subtask for T23758: Introduction of custom multi widget editor: T24216: Synchronization of individual render windows: camera position.
Jan 5 2023, 9:37 AM · Restricted Project, MITK
kalali added a subtask for T29393: [mxn multi widget] Concept for individual render window synchronization: T24216: Synchronization of individual render windows: camera position.
Jan 5 2023, 9:37 AM · MITK
kalali added a comment to T29393: [mxn multi widget] Concept for individual render window synchronization.

Somehow related:

Jan 5 2023, 9:37 AM · MITK
kalali moved T24216: Synchronization of individual render windows: camera position from Backlog to mxn MultiWidget on the MITK (v2023.04) board.
Jan 5 2023, 9:37 AM · MITK (v2023.04)
kalali reopened T24216: Synchronization of individual render windows: camera position, a subtask of T23758: Introduction of custom multi widget editor, as Open.
Jan 5 2023, 9:37 AM · Restricted Project, MITK
kalali reopened T24216: Synchronization of individual render windows: camera position as "Open".
Jan 5 2023, 9:37 AM · MITK (v2023.04)
kalali moved T29297: [mxn multi widget] Optimize data accessibility inside render windows from mxn MultiWidget to Cycle on the MITK (v2023.04) board.
Jan 5 2023, 9:29 AM · MITK (v2023.04)
kalali claimed T29297: [mxn multi widget] Optimize data accessibility inside render windows.
Jan 5 2023, 9:29 AM · MITK (v2023.04)
kalali added a comment to T27320: No LocalStorage for PlaneGeometryDataVtkMapper3D.

Related: T13465: Two 3D RenderWindows at the same time interfere with each other.

Jan 5 2023, 9:26 AM · MITK, Pull Request

Jan 4 2023

kalali claimed T29027: Move NodeSelectionWidgets to QtWidgets module.
Jan 4 2023, 10:03 AM · MITK (v2023.04)
kalali claimed T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module.
Jan 4 2023, 10:03 AM · MITK (v2023.04)
kalali moved T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module from Segmentation to Cycle on the MITK (v2023.04) board.
Jan 4 2023, 10:02 AM · MITK (v2023.04)
kalali moved T29027: Move NodeSelectionWidgets to QtWidgets module from Backlog to Cycle on the MITK (v2023.04) board.
Jan 4 2023, 10:02 AM · MITK (v2023.04)

Jan 3 2023

kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

I may have found the problem but unfortunately for me that looks like it cannot be easily fixed:
During PlaneGeometryDataVtkMapper3D::ProcessNode, when the plane node to be rendered is processed (called from PlaneGeometryDataVtkMapper3D::GenerateDataForRenderer), imageMapper->Update(planeRenderer) is called. Here the imageMapper is the 2D mapper from the plane node.
Inside ImageVtkMapper2D::Update the mapper is updated by calling ImageVtkMapper2D::GenerateDataForRenderer. This in turn leads to the following line: const PlaneGeometry *worldGeometry = renderer->GetCurrentWorldPlaneGeometry(). I think this is problematic since here the current world plane geometry is used, which is the sliced geometry from the base renderer. However, for the 3D render window the sliced geometry is still either the axial, sagittal or coronal plane. It doesn't matter if we created three different planes from the world time geometry for the base renderer, the world plane geomertry will always be a specific sliced geometry.
Since these steps are performed for all three plane nodes to be rendered, all three plane nodes render the same world plane geometry.

Jan 3 2023, 9:11 PM · MITK (v2023.04)
kalali claimed T29415: [mxn multi widget] Allow mxn windows to show 3D view.
Jan 3 2023, 3:41 PM · MITK (v2023.04)
kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

It seems as if there is a general problem with the current crosshair: The crosshair manager provides three planes / plane geometries for each render window such that changing the view direction / anatomical plane will just switch to the corresponding geometry and render the information based on that geometry.
Having done some test with the visiblity of the planes, rendering inside the StdMultiWidget shows that all three planes (axial, sagittal, coronal) of a render window show the same image information / anatomical plane. Changing the view diretion inside the render window will change the anatomical plane, but then all three planes show the same image information of the newly selected anatomical plane.

Jan 3 2023, 3:39 PM · MITK (v2023.04)
kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

I managed to fix the rendering of the 3D data even more and now the image information / pixel are shown.
But now the data seems to be inverted on some planes such that the three 2D planes do not match and form a 3D object.

Jan 3 2023, 10:19 AM · MITK (v2023.04)

Jan 2 2023

kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

So I fixed part of it by setting a PlaneGeometryDataVtkMapper3D explicitly as done in {D759} for the 2D mapper. Then I was able to immediately set a valid data storage and the crash is fixed.
The three planes are rendered inside the 3D render window but only the frame is visible - no image information / pixel is shown.

Jan 2 2023, 4:43 PM · MITK (v2023.04)
kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

So it seems as if the PlaneGeometryDataVtkMapper3D is newly created (automatically) when a render window is changed to a 3D render window (mapper changed to Standard3D).
In that case, the m_DataStorage is empty and the following functions crash (e.g. mitk::DataStorage::SetOfObjects::ConstPointer all = m_DataStorage.Lock()->GetSubset(predicateAllImages);) inside PlaneGeometryDataVtkMapper3D::GenerateDataForRenderer.

Jan 2 2023, 11:41 AM · MITK (v2023.04)
kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

I found out that the 3D render window of the StdMultiWidget does not render the data if the widget-plane helper-nodes are removed from the data storage.
If the widget-plane helper-nodes are available but hidden only from the 3D render window (set visibility for that render window to false using properties), the 3D render window does not render the data.
If e.g. one widget-plane helper-node is visible that 2D plane allows to render the data inside the 3D render window, but only the specific 2D plane is visible and not all three view directions.

Jan 2 2023, 10:36 AM · MITK (v2023.04)
kalali added a comment to T29415: [mxn multi widget] Allow mxn windows to show 3D view.

We discovered that it is currently not possible to use RenderWindowViewDirectionController::SetViewDirectionOfRenderer to change the view direction / rendering of a render window to 3D.
@s434n found out that in order to show the 3D rendering other render windows need to provide the three 2D views for the object in order to have data available to render.

Jan 2 2023, 8:48 AM · MITK (v2023.04)

Dec 22 2022

kislinsk added a comment to T24398: Dicom plugin: Retrieve does not work.

Have you pushed your clean ups? Not that your efforts get lost. 😉

Dec 22 2022, 12:17 PM · Next Milestone, MITK, Request for Discussion, Missing Info

Dec 19 2022

floca added a comment to T24398: Dicom plugin: Retrieve does not work.

Our side or also the CTK part.

Hm, lets put it as known issue and discuss its priority when we plan the spring release.

Only looked into our side so far. I'll create a separate task and push my clean-up that I already did so far.

Dec 19 2022, 10:43 AM · Next Milestone, MITK, Request for Discussion, Missing Info

Dec 16 2022

kislinsk added a comment to T29433: MITK Workbench Persistent Crash.

Without a data sample we are not able to reproduce this issue. Can you upload one of these nrrd files? Please make sure that the data does not contain any personal information. You can also restrict access to uploaded files to certain users like me.

Dec 16 2022, 11:05 AM · Missing Info, MITK

Dec 14 2022

sonoaswartz added a comment to T29433: MITK Workbench Persistent Crash.

Unfortunately, it is all nrrd files. I updated my nvidia drivers and it seems to have improved slightly in that it doesn't crash within moments of loading a base nrrd file, but after I create, save and remove a segmentation nrrd, MITK Workbench crashes when I try to reload (open) the segmentation nrrd.

Dec 14 2022, 12:38 PM · Missing Info, MITK
floca moved T29294: Extend &/or Test nnUnet(v2) on Windows from Backlog to MITK Meeting on the Request for Discussion board.
Dec 14 2022, 11:43 AM · MITK (v2023.04), Request for Discussion
a178n placed T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" up for grabs.
Dec 14 2022, 11:39 AM · MITK (v2023.04)
a178n edited projects for T29379: MONAI Label REST Response JSON issues, allegedly, added: MITK; removed MITK (v2023.04).
Dec 14 2022, 11:37 AM · MITK
isensee added a member for Deep Learning: j115e.
Dec 14 2022, 10:35 AM
a178n added a comment to T29295: MONAI Label App as auto-segmentation tool in MITK.

Pushed new branch to rMITK MITK: feature/T29295-monai-tool-httplib.

Dec 14 2022, 9:06 AM · MITK (v2023.04)
floca moved T29437: [SEG] Add TotalSegmentator from Backlog to Segmentation on the MITK (v2023.04) board.
Dec 14 2022, 8:26 AM · MITK (v2023.04)
floca moved T29437: [SEG] Add TotalSegmentator from Backlog to MITK Meeting on the Request for Discussion board.
Dec 14 2022, 8:26 AM · MITK (v2023.04)
floca renamed T29437: [SEG] Add TotalSegmentator from [SEG] Add Totel to [SEG] Add TotalSegmentator.
Dec 14 2022, 8:25 AM · MITK (v2023.04)
floca created T29437: [SEG] Add TotalSegmentator.
Dec 14 2022, 8:25 AM · MITK (v2023.04)

Dec 13 2022

floca triaged T29436: CLGlobalImageFeature is to pedantic on its geometry checks. as Normal priority.
Dec 13 2022, 10:01 PM · MITK (v2023.04)
kislinsk moved T29432: [worklist] mitk-flow preload first task from Backlog to MITK Meeting on the Request for Discussion board.
Dec 13 2022, 8:55 PM · Request for Discussion, MITK
kislinsk added a project to T29432: [worklist] mitk-flow preload first task: Request for Discussion.
Dec 13 2022, 8:54 PM · Request for Discussion, MITK
kislinsk added a comment to T29432: [worklist] mitk-flow preload first task.

Without any extra preferences, it's as easy as adding the line this->LoadNextUnfinishedTask(); at the end of the OnTaskListChanged() method.

Dec 13 2022, 8:54 PM · Request for Discussion, MITK
kislinsk closed T29434: Clean up preference pointer anti pattern as Resolved.
Dec 13 2022, 2:46 PM · MITK
kislinsk added a comment to T29434: Clean up preference pointer anti pattern.

Deleted branch from rMITK MITK: bugfix/T29434-CleanUpPrefPtrAntiPattern.

Dec 13 2022, 2:46 PM · MITK
kislinsk committed rMITKcbf2e888a72c: Clean up preferences pointer anti pattern (authored by kislinsk).
Clean up preferences pointer anti pattern
Dec 13 2022, 2:45 PM
kislinsk committed rMITKe3f615b43c0b: Remove old preferences pointer from ctor init list (authored by kislinsk).
Remove old preferences pointer from ctor init list
Dec 13 2022, 2:45 PM
kislinsk committed rMITKc2904532ff3f: Merge branch 'bugfix/T29434-CleanUpPrefPtrAntiPattern' into develop (authored by kislinsk).
Merge branch 'bugfix/T29434-CleanUpPrefPtrAntiPattern' into develop
Dec 13 2022, 2:45 PM
kislinsk triaged T29433: MITK Workbench Persistent Crash as Normal priority.

Thanks for reporting. We are not aware of any crash like this with valid nrrd files. Since ITK snap crashes as well it could be a strong indicator that the crash is happening in the ITK reader that we use as well. It could be probably related to a corrupt nrrd file, or, in case it is a huge file, it could be simply related to running out of memory. Anyway, without the data we are not able to reproduce this issue.

Dec 13 2022, 1:19 PM · Missing Info, MITK
kislinsk added a revision to T29434: Clean up preference pointer anti pattern: Restricted Differential Revision.
Dec 13 2022, 12:30 PM · MITK
kislinsk added a comment to T29434: Clean up preference pointer anti pattern.

Pushed new branch to rMITK MITK: bugfix/T29434-CleanUpPrefPtrAntiPattern.

Dec 13 2022, 12:23 PM · MITK
isensee added a member for Deep Learning: m574s.
Dec 13 2022, 10:46 AM
franza triaged T29435: MITK example for usage of the ICP algorithm as Wishlist priority.
Dec 13 2022, 10:42 AM · Pull Request, MITK (v2023.04)
kislinsk added a comment to T29025: Preference service (access) based on cpp microservices.

Deleted branch from rMITK MITK: feature/T29025-PreferencesCoreService.

Dec 13 2022, 10:32 AM · MITK (v2023.04), Breaking Change
kislinsk triaged T29434: Clean up preference pointer anti pattern as Normal priority.
Dec 13 2022, 10:31 AM · MITK
kislinsk committed rMITK207ecdb75531: Move BlueBerry preferences to MITK Core services (authored by kislinsk).
Move BlueBerry preferences to MITK Core services
Dec 13 2022, 10:22 AM
kislinsk committed rMITK952b9648480a: Move BlueBerry preferences to MITK Core services (authored by kislinsk).
Move BlueBerry preferences to MITK Core services
Dec 13 2022, 10:22 AM
kislinsk closed T29025: Preference service (access) based on cpp microservices as Resolved by committing rMITK952b9648480a: Move BlueBerry preferences to MITK Core services.
Dec 13 2022, 10:22 AM · MITK (v2023.04), Breaking Change
kislinsk closed T29025: Preference service (access) based on cpp microservices, a subtask of T29027: Move NodeSelectionWidgets to QtWidgets module, as Resolved.
Dec 13 2022, 10:22 AM · MITK (v2023.04)
sonoaswartz renamed T29433: MITK Workbench Persistent Crash from Please enter a meaningful title to MITK Workbench Persistent Crash.
Dec 13 2022, 12:11 AM · Missing Info, MITK
sonoaswartz created T29433: MITK Workbench Persistent Crash.
Dec 13 2022, 12:10 AM · Missing Info, MITK

Dec 12 2022

kislinsk triaged T29381: Move Multilabel classes to Core module as Low priority.

The hash above doesn't seem to be auto-linked. So here it is: rMITKa73e482c0387: moved labelset-related classes out from core

Dec 12 2022, 11:27 AM · MITK, Request for Discussion
kislinsk triaged T29389: Python utility module as Normal priority.

I big leap into the Python direction would be to finally resolve T27923: Integrate possibility to execute Python Code in MITK , which is complete for a while now but we weren't able to figure out why it fails on Ubuntu build clients. Since the ITK v5 upgrade, we also need to adjust a little more I guess.

Dec 12 2022, 11:25 AM · Next Milestone, Request for Discussion, MITK
kislinsk updated subscribers of T29431: [worklist] mitk-flow: save changed dicom segmentation not possible.

Task lists don't do anything special regarding saving/loading data. So in theory, this bug should be reproducible by regular loading and saving via the menu in the Workbench?
However, task lists are prone to expose existing bugs related to repeated saving/loading of data. We indeed noticed another bug in this direction with .nrrd files, which were erroneous when loaded a second time in certain situations. The reason was faulty handling of properties: T29274: Label Loss on repeatedly loaded and saved segmentations.

Dec 12 2022, 11:21 AM · MITK
gaoh triaged T29432: [worklist] mitk-flow preload first task as Wishlist priority.
Dec 12 2022, 10:52 AM · Request for Discussion, MITK
gaoh triaged T29431: [worklist] mitk-flow: save changed dicom segmentation not possible as Normal priority.
Dec 12 2022, 10:46 AM · MITK

Dec 9 2022

k688h triaged T28387: Testing Gvisor with Kube8s as High priority.
Dec 9 2022, 12:08 PM · Restricted Project
k688h moved T28387: Testing Gvisor with Kube8s from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28351: Trial Run with Kata Isolated Container from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28165: TFDA Repo Creation from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28350: Trial Run with Isolated Sandbox Container gVisor from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28357: Running Isolated container in Kaapana ( Instead of Default Docker) from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project, Kaapana (internal)
k688h moved T28043: TFDA MVP1-Tasks:Tools and Technologies from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project, Kaapana (internal)
k688h moved T28382: Testing Kata and Gvisor on Local from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28567: Microk8s Integration of Kata and Testing from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:07 PM · Restricted Project
k688h moved T28575: Test Kata with Sample workloads in a Kaapana env from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Dec 9 2022, 12:06 PM · Restricted Project