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kleina (André Klein)
Bone guy

Projects (9)

User Details

User Since
Aug 1 2016, 12:10 PM (269 w, 15 h)

Recent Activity

Wed, Sep 15

kleina added a comment to T28489: int64 not supported.

True, I tried this. There is even a task for it: T28557

Wed, Sep 15, 12:20 PM · MITK

Aug 16 2021

kleina updated subscribers of T28671: XNAT plugin does not work with XNAT version 1.8.2.

Seems to work. I am now able to connect to XNAT 1.6.4 and XNAT 1.8.2. Idk if there are more versions with different calls, these are the only two that I have available to test.

Aug 16 2021, 12:34 PM · MITK
kleina added a comment to T28671: XNAT plugin does not work with XNAT version 1.8.2.

I looked into this together with @kislinsk. It looks like CTK cannot handle newer versions of XNAT. THey try to retrieve the XNAT version via

QUuid uuid = QUuid uuid = xnat->get("/data/version");  //ctkXnatSession.cpp:192
Aug 16 2021, 11:49 AM · MITK
kleina triaged T28671: XNAT plugin does not work with XNAT version 1.8.2 as Normal priority.
Aug 16 2021, 11:46 AM · MITK

Aug 2 2021

kleina added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

That is what I assumed... the labels created by multi-label plugin always contain only two values, if I am not mistaken: 0 and x with x e [1,2,3,...]. One could check for the label values and if there is only two different ones, use these two. This does not include the case when a label was created externally,e.g., by U-Net and contains several values in a single image.

Aug 2 2021, 4:35 PM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

Tested it on Windows. I can confirm what @kalali said in 2018.04.0. In 2018.04.2 it seems to work on single segmentations.
For multi-label segmentations it interpolates always for the first label (label value=1). So the bug described can be confirmed.

Aug 2 2021, 11:54 AM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

Ah ok, thx. I will try later.

Aug 2 2021, 9:16 AM · Request for Discussion, MITK (v2021.10)

Jul 30 2021

kleina added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

Ehm... I cannot do Interpolation in MultiLabelSegmentation I think. Shouldn't there be a drop down?

image.png (431×495 px, 15 KB)

Jul 30 2021, 4:26 PM · Request for Discussion, MITK (v2021.10)

Jul 29 2021

kleina updated subscribers of T28607: [Segmentation] LiveWire tool issues and improvements.
Jul 29 2021, 3:45 PM · MITK (v2021.10)
kleina added a comment to T28607: [Segmentation] LiveWire tool issues and improvements.

The listed changes have been implemented. I realized that there is an issue with the automatically created "last segment". If I click there to create a new control point and move it, I get the behavior shown in the image (sorry, I tried to explain it in words but failed).

image.png (649×696 px, 206 KB)

Jul 29 2021, 3:45 PM · MITK (v2021.10)

Jul 28 2021

kleina claimed T28464: [Segmentation] New Add/Remove tool.
Jul 28 2021, 10:24 AM · Cleared, MITK (v2021.10)

Jul 9 2021

kleina added a comment to T28607: [Segmentation] LiveWire tool issues and improvements.

Pushed new branch to rMITK MITK: feature/T28607-live-wire-improvements.

Jul 9 2021, 3:38 PM · MITK (v2021.10)

Jul 7 2021

kleina added a comment to T28607: [Segmentation] LiveWire tool issues and improvements.

LiveWire tool now always connects the current mouse position with the starting point (here displayed in red for demonstration purposes). The mouse cursor is not visible here due to me taking a screenshot via noMachine. The position is where green and red meet. If double-clicked, the green and red line turn into yellow segments.

image.png (417×538 px, 341 KB)

Jul 7 2021, 4:15 PM · MITK (v2021.10)
kleina raised the priority of T28607: [Segmentation] LiveWire tool issues and improvements from Low to Normal.
Jul 7 2021, 4:14 PM · MITK (v2021.10)
kleina moved T28607: [Segmentation] LiveWire tool issues and improvements from Segmentation to Cycle on the MITK (v2021.10) board.
Jul 7 2021, 11:45 AM · MITK (v2021.10)
kleina claimed T28607: [Segmentation] LiveWire tool issues and improvements.
Jul 7 2021, 11:45 AM · MITK (v2021.10)
kleina placed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation up for grabs.
Jul 7 2021, 11:44 AM · Cleared, MITK (v2021.10)
kleina added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Oh, ok. Did not know that. I will postpone it then.

Jul 7 2021, 11:43 AM · Cleared, MITK (v2021.10)
kleina claimed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.
Jul 7 2021, 10:55 AM · Cleared, MITK (v2021.10)

Jul 6 2021

kleina renamed T28607: [Segmentation] LiveWire tool issues and improvements from LiveWire tool issues and improvements to [Segmentation] LiveWire tool issues and improvements.
Jul 6 2021, 1:32 PM · MITK (v2021.10)
kleina triaged T28607: [Segmentation] LiveWire tool issues and improvements as Low priority.
Jul 6 2021, 1:31 PM · MITK (v2021.10)
kleina added a comment to T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.

This is related to T28464.

Jul 6 2021, 1:16 PM · MITK
kleina placed T27713: [Segmentation] Disable "New" button when no image is selected up for grabs.
Jul 6 2021, 1:13 PM · MITK (v2021.10), Request for Discussion
kleina moved T27713: [Segmentation] Disable "New" button when no image is selected from Cycle to Segmentation on the MITK (v2021.10) board.
Jul 6 2021, 1:13 PM · MITK (v2021.10), Request for Discussion
kleina added a comment to T27713: [Segmentation] Disable "New" button when no image is selected.

I looked into this (to be honest, I did not read Amirs last comment): I totally agree. I fixed the issue, which was not to complicated, but there is a lot of spaghetti code involved. I agree with Amirs suggestion to not fix it this way.

Jul 6 2021, 1:12 PM · MITK (v2021.10), Request for Discussion
kleina closed T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change, a subtask of T28176: [Segmentation] Inspection of module and plugin, as Resolved.
Jul 6 2021, 12:58 PM · MITK (v2021.10)
kleina closed T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change as Resolved.

I tested it again with feedback from @kalali and @s434n. The behavior that the tool has is ok for now. I adapted the checklist accordingly. We found some minor issues, that we propose to fix on the near future:

Jul 6 2021, 12:58 PM · Request for Discussion, MITK (v2021.10)

Jun 28 2021

kleina added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

Additionally, I would not auto-confirm as a default. As a user I would first finish the outline and then correct it if needed. I would be really frustrated, if that is then not possible anymore.

Jun 28 2021, 4:57 PM · Request for Discussion, MITK (v2021.10)
kleina claimed T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Jun 28 2021, 4:47 PM · Request for Discussion, MITK (v2021.10)
kleina added a project to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change: Request for Discussion.
Jun 28 2021, 4:43 PM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

I haven't made up my mind about the best way to go, I'm open for suggestions. I just wanted to state that even the checklists state something different. So to align the tests with what the workbench actually does, we should clarify, how the tools actually behave or should behave.

  • If the tool is deactivated (explicitly, by selecting another tool, by closing the view) all unconfirmed contours will be removed.

And this is not the case right now. Currently, a mask will be generated and drawn into the image.

Oops, you are right. On second thought, I would keep it like this for now and make the checklist accordingly. I think would get more frustrated users if the contour just vanishes if the close the segmentation or tool. If we introduce a option for auto confirm we could think of adapting the behavior.

Jun 28 2021, 4:42 PM · Request for Discussion, MITK (v2021.10)

Jun 22 2021

kleina closed T27711: Rename segmentation image selection label, a subtask of T28176: [Segmentation] Inspection of module and plugin, as Resolved.
Jun 22 2021, 9:44 AM · MITK (v2021.10)
kleina closed T27711: Rename segmentation image selection label as Resolved.
Jun 22 2021, 9:44 AM · MITK (v2021.10)
kleina committed rMITK752ead6f5e3d: Renamed "Patient Image" to "Selected Image" in segmentation and multilabel… (authored by kleina).
Renamed "Patient Image" to "Selected Image" in segmentation and multilabel…
Jun 22 2021, 9:43 AM
kleina committed rMITK29e507328f2d: Added label "Selected Image" to measurement view. (authored by kleina).
Added label "Selected Image" to measurement view.
Jun 22 2021, 9:43 AM
kleina committed rMITK79b8ddcbb77a: Summary: Renamed "Patient Image" to "Selected Image" in segmentation and… (authored by kleina).
Summary: Renamed "Patient Image" to "Selected Image" in segmentation and…
Jun 22 2021, 9:43 AM

Jun 21 2021

kleina claimed T27711: Rename segmentation image selection label.
Jun 21 2021, 4:18 PM · MITK (v2021.10)
kleina moved T27711: Rename segmentation image selection label from Segmentation to Cycle on the MITK (v2021.10) board.
Jun 21 2021, 4:18 PM · MITK (v2021.10)
kleina moved T27713: [Segmentation] Disable "New" button when no image is selected from Segmentation to Cycle on the MITK (v2021.10) board.
Jun 21 2021, 4:17 PM · MITK (v2021.10), Request for Discussion
kleina claimed T27713: [Segmentation] Disable "New" button when no image is selected.
Jun 21 2021, 4:17 PM · MITK (v2021.10), Request for Discussion
kleina closed T28455: RT struct 3D visibility is not working correctly as Resolved.
Jun 21 2021, 4:16 PM · MITK (v2021.10)
kleina committed rMITK67dbb16a81a2: Removed special visibility for 3D render window. It was permanently set to true. (authored by kleina).
Removed special visibility for 3D render window. It was permanently set to true.
Jun 21 2021, 4:15 PM
kleina committed rMITK44e20fed9e54: Removed all special visibility rules for RT struct. Now it behaves the same no… (authored by kleina).
Removed all special visibility rules for RT struct. Now it behaves the same no…
Jun 21 2021, 4:15 PM
kleina committed rMITKf0b8f189c530: Summary: Removed special visibility for 3D render window. It was permanently… (authored by kleina).
Summary: Removed special visibility for 3D render window. It was permanently…
Jun 21 2021, 4:15 PM
kleina committed rMITK1312ed6fdc85: Merge remote-tracking branch 'origin/develop' into bugfix/T28455-rt-struct-3d… (authored by kleina).
Merge remote-tracking branch 'origin/develop' into bugfix/T28455-rt-struct-3d…
Jun 21 2021, 4:15 PM
kleina added a comment to T27711: Rename segmentation image selection label.

Pushed new branch to rMITK MITK: bugfix/T27711-rename-image-selection-label.

Jun 21 2021, 4:07 PM · MITK (v2021.10)

Jun 17 2021

kleina added a project to T28557: Cannot load segmentations from KITS challenge due to unknown pixel type: Request for Discussion.
Jun 17 2021, 3:55 PM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T28557: Cannot load segmentations from KITS challenge due to unknown pixel type.

I tried to add

long long

to the list. That caused my superbuild to crash. Then I added

int64_t

The superbuild worked, but now the workbench crashes during the load attempt with:

Jun 17 2021, 3:55 PM · Request for Discussion, MITK (v2021.10)
kleina added a project to T28544: Difference of loading RT data DicomBrowser vs. "Standard loading": Request for Discussion.

There was a discrepancy regarding how the RtStruts are displayed. When loading via DICOMBrowser, they were now visible on stdmulti.widget2 and 3. Is this the desired behavior? On there planes, one can only see "dots". We should discuss this.

Jun 17 2021, 2:30 PM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T27711: Rename segmentation image selection label.

Same goes for MultiLabel Segmentation.

Jun 17 2021, 2:05 PM · MITK (v2021.10)
kleina added a comment to T27711: Rename segmentation image selection label.

While we are doing that: The measurement Plugin does not have a label at all. I would suggest having this consistent.

Jun 17 2021, 2:04 PM · MITK (v2021.10)
kleina added a comment to T28523: Evaluate MITK segmentation survey.

What is the status here? This is on "unbreak now", but no assignee. Is there something to evaluate yet?

Jun 17 2021, 1:59 PM · MITK (v2021.10)
kleina triaged T28557: Cannot load segmentations from KITS challenge due to unknown pixel type as Normal priority.
Jun 17 2021, 10:44 AM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T28544: Difference of loading RT data DicomBrowser vs. "Standard loading".

Pushed new branch to rMITK MITK: bugfix/T28544-difference-RT-data-loading.

Jun 17 2021, 10:03 AM · Request for Discussion, MITK (v2021.10)
kleina triaged T28556: I/O handling of folder/subfolder structures and automatic scene creation as Low priority.
Jun 17 2021, 9:52 AM · Missing Info, MITK
kleina triaged T28555: Simplified version of segmentation with only desired tools as Low priority.
Jun 17 2021, 9:47 AM · MITK, Missing Info

Jun 15 2021

kleina added a comment to T28358: Data Manager context menu items added multiple times for multi-selections.

I could not reproduce this.

image.png (315×416 px, 36 KB)

Jun 15 2021, 11:07 AM · MITK (v2021.10)
kleina updated the task description for T28550: MitkResampleImage and MitkResampleMask CL tools produce result with different dimensions.
Jun 15 2021, 10:03 AM · Request for Discussion, MITK
kleina triaged T28550: MitkResampleImage and MitkResampleMask CL tools produce result with different dimensions as Low priority.
Jun 15 2021, 10:03 AM · Request for Discussion, MITK

Jun 14 2021

kleina triaged T28548: Allow Zooming during creation of Segmentation. as Normal priority.
Jun 14 2021, 4:51 PM · Request for Discussion, MITK (v2021.10)

Jun 10 2021

kleina added a comment to T28544: Difference of loading RT data DicomBrowser vs. "Standard loading".

We commented out the entire if-else clause for the RT data and it seems to do what it is supposed to do, even without the special conditions. Need to check that in more detail.

Jun 10 2021, 4:35 PM · Request for Discussion, MITK (v2021.10)
kleina removed a project from T28455: RT struct 3D visibility is not working correctly: Request for Discussion.
Jun 10 2021, 3:36 PM · MITK (v2021.10)
kleina triaged T28544: Difference of loading RT data DicomBrowser vs. "Standard loading" as Normal priority.
Jun 10 2021, 2:45 PM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

Pushed new branch to rMITK MITK: bugfix/T28455-rt-struct-3d-visibility.

Jun 10 2021, 2:32 PM · MITK (v2021.10)

Jun 8 2021

kleina committed rOBSHYPPOPYd59c6efb638f: Usage of default value for new member. (authored by kleina).
Usage of default value for new member.
Jun 8 2021, 9:48 AM

Jun 7 2021

kleina committed rOBSHYPPOPYb8dfe382dd47: Added .arcconfig for Hyppopy (authored by kleina).
Added .arcconfig for Hyppopy
Jun 7 2021, 4:22 PM
kleina committed rOBSHYPPOPY4de04affc17e: Added test for setting of default value for _add_member (authored by kleina).
Added test for setting of default value for _add_member
Jun 7 2021, 4:22 PM
kleina committed rOBSHYPPOPY019b7655537b: If the passed value for a new member equals 'None', (authored by kleina).
If the passed value for a new member equals 'None',
Jun 7 2021, 4:22 PM
kleina moved T28300: [MPI] MPI as a general dependency might be problematic from In Progress to Bugfixes on the Hyppopy board.
Jun 7 2021, 3:08 PM · Request for Discussion, Hyppopy

Jun 4 2021

kleina updated subscribers of T28520: XNAT on e230-xnat.
Jun 4 2021, 12:21 PM · Restricted Project
kleina updated the task description for T28520: XNAT on e230-xnat.
Jun 4 2021, 12:21 PM · Restricted Project
kleina triaged T28520: XNAT on e230-xnat as Normal priority.
Jun 4 2021, 12:06 PM · Restricted Project

Jun 2 2021

kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

Discussed it in the MITK meeting:

Jun 2 2021, 11:39 AM · MITK (v2021.10)
kleina moved T28455: RT struct 3D visibility is not working correctly from Backlog to MITK Meeting on the Request for Discussion board.
Jun 2 2021, 11:14 AM · MITK (v2021.10)

May 10 2021

kleina added a project to T28455: RT struct 3D visibility is not working correctly: Request for Discussion.
May 10 2021, 3:12 PM · MITK (v2021.10)
kleina updated subscribers of T28455: RT struct 3D visibility is not working correctly.

I narrowed it down.

May 10 2021, 3:11 PM · MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

If you load a RTStruct via DICOMBrwoser, the node has a special "visible" property for stdmulti.widget3 (the 3D view). You can enable/disbale it via the Properties plugin. #Workaround :-P

May 10 2021, 11:51 AM · MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

Ok, we tested it on several machines and it is as described above: After loading via DICOM Browser we can confirm the issue.

May 10 2021, 11:32 AM · MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

@s434n and I tried this on Windows and Linux. It looks like, if you load the data via "classical drag'n'drop", it works as expected. If we use the DICOM browser to load the exact same dataset, we can reproduce @nolden's issue.

May 10 2021, 10:43 AM · MITK (v2021.10)
kleina added a comment to T28332: Support cascaded MPI processing.

Sure, here it is:
https://phabricator.mitk.org/rOBSHYPPOPYa340b927d14acdef69cea4e64b92524270066920

May 10 2021, 9:32 AM · Hyppopy

Apr 22 2021

kleina committed rOBSHYPPOPY04b807b9d85f: Added .arcconfig (authored by kleina).
Added .arcconfig
Apr 22 2021, 10:26 AM
kleina closed T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as Resolved by committing rOBSHYPPOPYace9c97f5ba3: Fixed MPISolverWrapper's direct call of blackbox internal.
Apr 22 2021, 10:08 AM · Hyppopy
kleina committed rOBSHYPPOPYace9c97f5ba3: Fixed MPISolverWrapper's direct call of blackbox internal (authored by kleina).
Fixed MPISolverWrapper's direct call of blackbox internal
Apr 22 2021, 10:08 AM

Apr 21 2021

kleina reopened T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as "Open".
Apr 21 2021, 4:12 PM · Hyppopy
kleina committed rOBSHYPPOPY727320895a4e: Removed deprecated loss_function_batch_call (authored by kleina).
Removed deprecated loss_function_batch_call
Apr 21 2021, 3:57 PM
kleina committed rOBSHYPPOPY543bba87253a: Make sure fallback only gets executed when batch_call fails. (authored by kleina).
Make sure fallback only gets executed when batch_call fails.
Apr 21 2021, 3:33 PM
kleina closed T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as Resolved by committing rOBSHYPPOPYa2cfa7ce75ac: Fixed MPISolverWrapper's direct call of blackbox internal.
Apr 21 2021, 3:33 PM · Hyppopy
kleina committed rOBSHYPPOPYa2cfa7ce75ac: Fixed MPISolverWrapper's direct call of blackbox internal (authored by kleina).
Fixed MPISolverWrapper's direct call of blackbox internal
Apr 21 2021, 3:32 PM
kleina added a project to T28300: [MPI] MPI as a general dependency might be problematic: Request for Discussion.
Apr 21 2021, 3:27 PM · Request for Discussion, Hyppopy
kleina moved T28376: Blackbox class - reorder the loss function call try from In Progress to Done on the Hyppopy board.
Apr 21 2021, 3:25 PM · Hyppopy
kleina moved T28298: Check for all print outputs in code base and convert them to log messages from In Progress to Done on the Hyppopy board.
Apr 21 2021, 3:25 PM · Hyppopy
kleina closed T28376: Blackbox class - reorder the loss function call try as Resolved by committing rOBSHYPPOPY5f8b57e426c0: Reordered the loss function call try..
Apr 21 2021, 3:25 PM · Hyppopy
kleina committed rOBSHYPPOPY5f8b57e426c0: Reordered the loss function call try. (authored by kleina).
Reordered the loss function call try.
Apr 21 2021, 3:25 PM
kleina added a revision to T28376: Blackbox class - reorder the loss function call try: Unknown Object (Differential Revision).
Apr 21 2021, 1:21 PM · Hyppopy
kleina committed rOBSHYPPOPYe704bebf3217: Reordered the loss function call try. (authored by kleina).
Reordered the loss function call try.
Apr 21 2021, 1:16 PM
kleina removed a project from T28376: Blackbox class - reorder the loss function call try: Request for Discussion.
Apr 21 2021, 1:13 PM · Hyppopy
kleina moved T28410: MPISolverWrapper's direct call of blackbox internal seems wrong from In Progress to Done on the Hyppopy board.
Apr 21 2021, 1:12 PM · Hyppopy
kleina added a revision to T28410: MPISolverWrapper's direct call of blackbox internal seems wrong: Unknown Object (Differential Revision).
Apr 21 2021, 1:10 PM · Hyppopy
kleina committed rOBSHYPPOPY19e487728222: Converted "print" outputs to "log" outputs. (authored by kleina).
Converted "print" outputs to "log" outputs.
Apr 21 2021, 1:01 PM
kleina moved T28410: MPISolverWrapper's direct call of blackbox internal seems wrong from Done to In Progress on the Hyppopy board.
Apr 21 2021, 12:18 PM · Hyppopy