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Recent Activity

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. 馃槈

Dec 22 2022, 12:17 PMNext 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 AMNext 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 AMMissing 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 PMMissing Info, MITK

Dec 13 2022

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 PMMissing Info, MITK

Nov 30 2022

floca moved T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types from In candidates to Segmentation on the MITK (v2023.04) board.
Nov 30 2022, 12:12 PMMissing Info, MITK (v2023.04)

Nov 25 2022

floca added a subtask for T27178: MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM : T25192: Enable DICOM SEG conversion for nrrd segmentations.
Nov 25 2022, 11:36 AMMissing Info, MITK
floca reopened T27178: MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM as "Open".
Nov 25 2022, 11:31 AMMissing Info, MITK

Nov 24 2022

floca moved T28785: Levelwindow UX proposals/comments from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:03 PMMITK (v2023.04), Checklist, Missing Info, Request for Discussion
neher added a comment to T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types.

Example data

Nov 24 2022, 11:57 AMMissing Info, MITK (v2023.04)

Nov 23 2022

floca moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 23 2022, 6:16 PMMITK (v2023.04), Missing Info
floca moved T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types from Backlog to In candidates on the MITK (v2023.04) board.
Nov 23 2022, 5:46 PMMissing Info, MITK (v2023.04)
floca edited projects for T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types, added: MITK (v2023.04), Missing Info; removed MITK.

Which data has been used to provoke the problem.

Nov 23 2022, 5:44 PMMissing Info, MITK (v2023.04)

Nov 9 2022

neher placed T26413: Nifti2 support up for grabs.
Nov 9 2022, 11:38 AMMissing Info, MITK
neher added a comment to T26413: Nifti2 support.

Unfortunately not solved. Same error.

Nov 9 2022, 11:37 AMMissing Info, MITK

Oct 25 2022

kislinsk placed T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations up for grabs.
Oct 25 2022, 10:53 AMMITK (v2023.04), Missing Info

Oct 21 2022

kalali reopened T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations as "Open".

I guess the second issue is not yet fixed and will be covered in T29369: [Segmentation Utilities] Handle / select different labels independently.

Oct 21 2022, 9:17 AMMITK (v2023.04), Missing Info
kislinsk closed T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations as Resolved by committing rMITK06e76d49de6b: Remove Multilabel Segmentation plugin.
Oct 21 2022, 6:00 AMMITK (v2023.04), Missing Info

Oct 19 2022

kalali renamed T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model" from [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smothed polygon model" to [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model".
Oct 19 2022, 2:34 PMCleared, MITK (v2022.10), Checklist
kalali added a revision to T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model": Restricted Differential Revision.
Oct 19 2022, 12:45 PMCleared, MITK (v2022.10), Checklist
kislinsk added a revision to T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations: Restricted Differential Revision.
Oct 19 2022, 12:20 PMMITK (v2023.04), Missing Info
kalali added a comment to T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model".

We discussed this and we decided to remove the options from the preferences completely. That means, that

  • the user cannot change the smoothing hint / value
  • the user cannot change the decimation rate
  • the checklists don't need to ask for changing these values
  • the smoothing will use the default values (set inside QmitkCreatePolygonModelAction::Run)
    • "smoothing hint" = true (will always use image spacing as hint)
    • "smoothing value" = 1.0
    • "decimation rate" = 0.5
    • "closing ratio" was not used at all
    • note that different default values are given in ShowSegmentationAsSurface::Initialize (and other functions of this class), but are overwritten / reset by the polygon action.
Oct 19 2022, 12:06 PMCleared, MITK (v2022.10), Checklist
kislinsk edited projects for T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers, added: Next Milestone; removed MITK (v2022.10).

I think it actually is an issue or at least unexpected. The level window seems to have trouble with color images in general.

Oct 19 2022, 10:27 AMNext Milestone, Missing Info, Checklist
kislinsk lowered the priority of T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers from Unbreak Now! to Normal.
Oct 19 2022, 10:26 AMNext Milestone, Missing Info, Checklist

Oct 18 2022

kalali moved T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model" from Segmentation to Cycle on the MITK (v2022.10) board.
Oct 18 2022, 5:45 PMCleared, MITK (v2022.10), Checklist
kalali claimed T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model".
Oct 18 2022, 5:45 PMCleared, MITK (v2022.10), Checklist
kalali added a comment to T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model".

I looked into this and can verify that there is no visible effect when changing the decimation rate. The property "Decimation rate" is correctly used inside ShowSegmentationAsSurface::ConvertBinaryImageToSurface as reductionRate. It is then used as an argument for ImageToSurfaceFilter::SetTargetReduction. The brief description of this parameter is:

Oct 18 2022, 5:45 PMCleared, MITK (v2022.10), Checklist

Oct 17 2022

s434n added a project to T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers: Request for Discussion.
Oct 17 2022, 4:43 PMNext Milestone, Missing Info, Checklist

Oct 14 2022

kislinsk closed T29345: Level Window Checklist - Default range of loaded image different for Ubuntu 22.04 and Windows 10. as Invalid.

Same for Windows 10, Ubuntu 20.04, and Ubuntu 22.04.

Oct 14 2022, 7:12 AMMissing Info, Checklist, MITK (v2022.10)

Oct 13 2022

a178n added a comment to T29345: Level Window Checklist - Default range of loaded image different for Ubuntu 22.04 and Windows 10..

On MacOS Monterey, the level window default values for the image are 83, 226.

Oct 13 2022, 12:10 PMMissing Info, Checklist, MITK (v2022.10)
s434n added a comment to T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers.

As far as I can tell, this is the expected behavior. Any voxel that has a (greyscale) value above the level-window range is shown completely white. The colors only extend this to multiple channels, but the behavior is still the same. So with very low level-window, the colors are expected to stay visible very strongly

Oct 13 2022, 10:51 AMNext Milestone, Missing Info, Checklist
floca added a project to T29337: Global Reinit HotKey functionality not there in Mac OSX: Missing Info.

We need information of the minimal setup to reproduce the problem.

Oct 13 2022, 10:39 AMMITK (v2023.04), Cleared, Checklist
floca raised the priority of T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers from Normal to Unbreak Now!.
Oct 13 2022, 10:37 AMNext Milestone, Missing Info, Checklist
kislinsk updated the task description for T29345: Level Window Checklist - Default range of loaded image different for Ubuntu 22.04 and Windows 10..
Oct 13 2022, 10:24 AMMissing Info, Checklist, MITK (v2022.10)
floca raised the priority of T29345: Level Window Checklist - Default range of loaded image different for Ubuntu 22.04 and Windows 10. from Normal to Unbreak Now!.

Needs more investigation, how and why the values are different. Naive assumption would be that they should be the same.

Oct 13 2022, 10:23 AMMissing Info, Checklist, MITK (v2022.10)
kislinsk added a project to T29344: Image Rendering - No difference between "Jet" and "Jet Transparent": Cleared.
Oct 13 2022, 10:19 AMCleared, Checklist, MITK (v2022.10)
floca added a project to T29347: Measurement Checklist - Possible inconsistent recentering behavior when clicking on geometry node in Data Manager.: Missing Info.

Verify if it is a code or a teaching problem

Oct 13 2022, 10:12 AMMITK (v2023.04), Cleared, Checklist
kislinsk added a comment to T29344: Image Rendering - No difference between "Jet" and "Jet Transparent".

We should double-check if there's really a bug as there's a good chance that it was just misunderstood how it works. Everything that's not covered by the level window is supposed to be transparent. We should probably improve the checklist to be more clear.

Oct 13 2022, 9:57 AMCleared, Checklist, MITK (v2022.10)
floca triaged T29344: Image Rendering - No difference between "Jet" and "Jet Transparent" as Normal priority.
Oct 13 2022, 9:57 AMCleared, Checklist, MITK (v2022.10)
floca added a project to T29344: Image Rendering - No difference between "Jet" and "Jet Transparent": Missing Info.

Please double check, if there is realy an error with Jet Transparent (or with the checklist). And on which systems.

Oct 13 2022, 9:55 AMCleared, Checklist, MITK (v2022.10)

Oct 10 2022

s349i updated the task description for T29341: Moving the LevelWindow slider too many times at extreme ranges makes MITK crash..
Oct 10 2022, 11:05 AMCleared, Checklist, MITK (v2022.10)
s349i updated the task description for T29340: Colored pixels remain unchanged, even when sliding the Level Window slider to low numbers.
Oct 10 2022, 11:04 AMNext Milestone, Missing Info, Checklist

Sep 28 2022

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

Thank you 馃檹

Sep 28 2022, 9:43 AMNext Milestone, MITK, Request for Discussion, Missing Info
kislinsk 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.

Sep 28 2022, 9:35 AMNext Milestone, MITK, Request for Discussion, Missing Info

Sep 27 2022

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

thank you for looking into that matter.

Sep 27 2022, 5:38 PMNext Milestone, MITK, Request for Discussion, Missing Info
floca edited projects for T24398: Dicom plugin: Retrieve does not work, added: MITK, Next Milestone; removed MITK (v2022.10).

I noticed that the whole plugin is a complete mess BTW and urgently needs at least some clean up to see all the potentials for improvements and bug fixes. :/

Our side or also the CTK part.

Sep 27 2022, 5:38 PMNext Milestone, MITK, Request for Discussion, Missing Info
kislinsk added a comment to T24398: Dicom plugin: Retrieve does not work.

I looked into the dicombrowser plugin and found out that the directory on Windows is something like %APPDATA%/../Local/Temp/TmpDicomFolder.************. However I didn't see pop up any files after retrieve.

Sep 27 2022, 10:56 AMNext Milestone, MITK, Request for Discussion, Missing Info

Sep 23 2022

kislinsk moved T24398: Dicom plugin: Retrieve does not work from Backlog to MITK Meeting on the Request for Discussion board.
Sep 23 2022, 9:50 AMNext Milestone, MITK, Request for Discussion, Missing Info
kislinsk added a project to T24398: Dicom plugin: Retrieve does not work: Request for Discussion.

I just tried to retrieve data from dicomserver.co.uk and I am able to query and kind of retrieve data. A repeated retrieve even tells me that existing files are overriden. At least that is what the console output tells me. But where are the retrieved images supposed to be stored? And shouldn't the retrieved images appear somewhere in the DICOM editor?

Sep 23 2022, 9:50 AMNext Milestone, MITK, Request for Discussion, Missing Info

Sep 21 2022

floca closed T28886: MITK Flowbench - Reopen created segmentation not working as Invalid.

To make our live a bit easier. I would say it is a data problem ;).

Sep 21 2022, 9:36 AMMITK (v2022.10), Missing Info, Kaapana (internal)