Page MenuHomePhabricator

kleina (André Klein)
Bone guy

Projects (9)

User Details

User Since
Aug 1 2016, 12:10 PM (286 w, 1 d)

Recent Activity

Dec 20 2021

kleina placed T28332: Support cascaded MPI processing up for grabs.

We did the draft together, but it was not implemented into Hyppopy yet.

Dec 20 2021, 3:00 PM · Hyppopy

Dec 16 2021

kleina updated subscribers of T28913: Myeloma worklow on kaapana.
Dec 16 2021, 2:53 PM · Kaapana (internal)
kleina closed T28913: Myeloma worklow on kaapana as Resolved.

https://phabricator.mitk.org/source/kaapana/history/feature%252FT28913-myeloma-kaapana/

Dec 16 2021, 9:53 AM · Kaapana (internal)
kleina committed rKAAPANA4d92c5e8eca9: Added myeloma workflows. (authored by kleina).
Added myeloma workflows.
Dec 16 2021, 9:52 AM
kleina updated subscribers of T28913: Myeloma worklow on kaapana.

@gaoh @floca I subscribed you so that you known where to find it, if the question comes up. At the moment there is no open todo on this front.

Dec 16 2021, 9:49 AM · Kaapana (internal)
kleina triaged T28913: Myeloma worklow on kaapana as Normal priority.
Dec 16 2021, 9:48 AM · Kaapana (internal)

Dec 15 2021

kleina placed T28544: Difference of loading RT data DicomBrowser vs. "Standard loading" up for grabs.

I am removing myself as an assignee. I just reported this.

Dec 15 2021, 5:31 PM · MITK (v2022.04), Request for Discussion
kleina placed T28557: Cannot load segmentations from KITS challenge due to unknown pixel type up for grabs.

This task is still open and still on the workboard. I am removing myself as an assignee, what I did was basically reporting and a bit of investigation as written above.

Dec 15 2021, 5:29 PM · MITK (v2022.04), Request for Discussion
kleina reassigned T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior from kleina to kahl.

@kahl I assigned you. If I understand correctly, this is what you did for the new add tool and the new base class.

Dec 15 2021, 5:22 PM · MITK
kleina reassigned T28607: [Segmentation] LiveWire tool issues and improvements from kleina to kahl.

@kahl Again, I assigned you, this is in the context of the new add tool.

Dec 15 2021, 5:19 PM · MITK (v2022.04)
kleina closed T28671: XNAT plugin does not work with XNAT version 1.8.2 as Resolved.

There is already a pull request for CTK that fixes this issue. I commented on it. Nothing to do from our side I guess.

Dec 15 2021, 5:18 PM · MITK
kleina reassigned T28464: [Segmentation] New Add/Remove tool from kleina to kahl.

@kahl I hope it is ok, that I assigned you, since you are working on this anyways.

Dec 15 2021, 5:17 PM · MITK (v2022.04), Cleared

Dec 2 2021

kleina committed rKAAPANA2d39bc3c0298: Changed avid_session.actionTools to Linux compatible call to run inside the… (authored by kleina).
Changed avid_session.actionTools to Linux compatible call to run inside the…
Dec 2 2021, 3:43 PM
kleina committed rKAAPANAc73fdac74b6e: Added shebang for Linux execution and added needed parameters to… (authored by kleina).
Added shebang for Linux execution and added needed parameters to…
Dec 2 2021, 3:40 PM

Nov 3 2021

kleina triaged T28829: [Segmentation][Interpolation] Interpolation area is still enabled, when segmentation node is hidden. as Low priority.
Nov 3 2021, 10:24 AM · Checklist, MITK
kleina triaged T28827: [Segmentation][Interpolation] Color of 3D interpolated segmentations is red, not green as Low priority.
Nov 3 2021, 10:22 AM · Checklist, MITK
kleina triaged T28826: [Segmentation][Interpolation] Color of 2D interpolated slice is not yellow but segmentation color as Low priority.
Nov 3 2021, 10:20 AM · Checklist, MITK
kleina triaged T28825: [Segmentation] Thresholding overwrites existing label without warning as Wishlist priority.
Nov 3 2021, 10:00 AM · MITK
kleina triaged T28824: [Segmentation] UL Threshold range changes when draged towards borders of scale. as Low priority.
Nov 3 2021, 9:55 AM · Checklist, MITK

Nov 2 2021

kleina triaged T28816: [Segmentation] "New Segmentation" dialog to small as Low priority.
Nov 2 2021, 2:48 PM · Checklist, MITK
kleina triaged T28815: [Segmentation] Segmentation is still rendered after "clear" was clicked as Low priority.
Nov 2 2021, 2:27 PM · Checklist, MITK
kleina triaged T28814: [Segmentation] Theshold segmentation is updated after each digit entered in spinbox as Low priority.
Nov 2 2021, 2:26 PM · Checklist, MITK

Oct 29 2021

kleina triaged T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smothed polygon model" as Normal priority.
Oct 29 2021, 2:20 PM · Checklist, MITK
kleina triaged T28792: [Segmentation][Multilabel][Options] "Smoothed surface creation" is unclear or does not work. as Normal priority.
Oct 29 2021, 2:19 PM · Checklist, MITK
kleina triaged T28791: [Segmentation][Multilabel][Options]"Create polygon model" issues for large images as Normal priority.
Oct 29 2021, 2:17 PM · Checklist, MITK
kleina triaged T28790: [Segmentation][Multilabel] Changing of 2D display mode (transparent/outline) does not work es expected. as Normal priority.
Oct 29 2021, 2:14 PM · Checklist, MITK
kleina triaged T28789: [Segmentation][Multilabel][Options] Auto-selection mode is unclear in checklist or broken as Normal priority.
Oct 29 2021, 2:14 PM · Checklist, MITK

Oct 18 2021

kleina committed rMITK70c956ac9b1f: Add segment that visually connects the current mouse position with the contour… (authored by kleina).
Add segment that visually connects the current mouse position with the contour…
Oct 18 2021, 9:48 AM
kleina committed rMITKf00e1392bc00: Increase "hit box" for contour points. (authored by kleina).
Increase "hit box" for contour points.
Oct 18 2021, 9:48 AM
kleina committed rMITKc0e8a4f6930d: Always close the contour on double click , not just if start point is clicked. (authored by kleina).
Always close the contour on double click , not just if start point is clicked.
Oct 18 2021, 9:48 AM
kleina committed rMITKf5e005e0f53b: renamed contour (authored by kleina).
renamed contour
Oct 18 2021, 9:48 AM
kleina committed rMITK2961a363ab60: Add constant for vertex eps. (authored by kleina).
Add constant for vertex eps.
Oct 18 2021, 9:48 AM
kleina committed rMITK6da0cebf157f: Check plane geometry during drawing of contours to make sure (authored by kleina).
Check plane geometry during drawing of contours to make sure
Oct 18 2021, 9:48 AM
kleina added a comment to T28748: [Segmentation] New Add tool: Behavior for modifying painted regions.

I guess in GIMP the behavior is somewhat similar to your second suggestion. As you are not able to set additional points, it is a "restricted region". You can still modify existing points. This is what the tool looks like in GIMP if you move one of the existing points.

Oct 18 2021, 9:40 AM · MITK
kleina added a comment to T28748: [Segmentation] New Add tool: Behavior for modifying painted regions.

One comment to this: The tool was inspired by the behavior of a similar tool in GIMP. In GIMP it is not possible to add additional points after finishing the contour. So they don't have that problem.

Oct 18 2021, 9:35 AM · MITK

Oct 15 2021

kleina added a comment to T28726: [Segmentation] Temporal interpolation.

The users have 2D+t data. The current workaround is to convert the 2D+t data to a 3D volume, where one slice is one timepoint and interpolate like this. This is not a perfect solution, as the 3D interpolation tries to interpolate to something like a "round" or "organ shaped" object, which does not make sense in this case.

Oct 15 2021, 3:31 PM · MITK

Oct 11 2021

kleina created T28728: [Registration] Translation vector changes when saving a project and loading it again.
Oct 11 2021, 2:08 PM · MITK
kleina triaged T28726: [Segmentation] Temporal interpolation as Normal priority.
Oct 11 2021, 1:19 PM · MITK
kleina moved T28725: VTP files cannot be opened from paths with "special" characters from Backlog to MITK Meeting on the Request for Discussion board.
Oct 11 2021, 12:11 PM · MITK (v2022.04)
kleina triaged T28725: VTP files cannot be opened from paths with "special" characters as High priority.
Oct 11 2021, 12:11 PM · MITK (v2022.04)
kleina created T28725: VTP files cannot be opened from paths with "special" characters.
Oct 11 2021, 12:10 PM · MITK (v2022.04)

Oct 6 2021

kleina updated subscribers of T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.
Oct 6 2021, 2:18 PM · MITK
kleina updated subscribers of T28464: [Segmentation] New Add/Remove tool.
Oct 6 2021, 2:18 PM · MITK (v2022.04), Cleared

Sep 15 2021

kleina added a comment to T28489: int64 not supported.

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

Sep 15 2021, 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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion

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 · MITK (v2022.04), Request for Discussion

Jul 29 2021

kleina updated subscribers of T28607: [Segmentation] LiveWire tool issues and improvements.
Jul 29 2021, 3:45 PM · MITK (v2022.04)
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 (v2022.04)

Jul 28 2021

kleina claimed T28464: [Segmentation] New Add/Remove tool.
Jul 28 2021, 10:24 AM · MITK (v2022.04), Cleared

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 (v2022.04)

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 (v2022.04)
kleina raised the priority of T28607: [Segmentation] LiveWire tool issues and improvements from Low to Normal.
Jul 7 2021, 4:14 PM · MITK (v2022.04)
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 (v2022.04)
kleina claimed T28607: [Segmentation] LiveWire tool issues and improvements.
Jul 7 2021, 11:45 AM · MITK (v2022.04)
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 (v2022.04)
kleina triaged T28607: [Segmentation] LiveWire tool issues and improvements as Low priority.
Jul 6 2021, 1:31 PM · MITK (v2022.04)
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 (v2022.04)
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 (v2022.04)
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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion
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 · MITK (v2022.04), Request for Discussion
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)