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May 16 2022

floca moved T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2024.06)
floca moved T28982: Weak Label Annotation Picking Tool from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10), Request for Discussion
floca moved T28991: [Segmentation] 3D tools overwrite / remove previous mask if reconfirmed from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29146: Union Mode for the picking tool from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29154: Show available Tasks for Download in the nnUnet GUI from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29157: NCT ISSO Annotation Support with MITK Segmentation Flow from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2024.06)
floca moved T29158: [Segmentation] Custom list for optional label names from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29159: [Segmentation] Flow bench worklist feature from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29160: [Segmentation] Worklist specification, data structure and io functions from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca moved T29161: [Segmentation] Extend flow bench control view to support worklists from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK (v2022.10)
floca added a revision to T29177: [Segmentation] TransferLabelToImage function should support to ignore locks: Restricted Differential Revision.
May 16 2022, 12:01 PM · MITK (v2022.10)
floca committed rMITKb3e02403b5db: Fixed T29139 - Fixed warnings when creating a 4D statistic with a 3D mask… (authored by floca).
Fixed T29139 - Fixed warnings when creating a 4D statistic with a 3D mask…
May 16 2022, 11:51 AM
floca committed rMITKfb1fc9101d2c: fixed gcc error and missed compile errors. (authored by floca).
fixed gcc error and missed compile errors.
May 16 2022, 11:51 AM
floca closed T29139: [Image statistics] Warning is shown for 4D image with 3D mask as Resolved by committing rMITKb3e02403b5db: Fixed T29139 - Fixed warnings when creating a 4D statistic with a 3D mask….
May 16 2022, 11:51 AM · Next Milestone, MITK
floca committed rMITK359dbcfcc6d6: fixed gcc errors (authored by floca).
fixed gcc errors
May 16 2022, 11:51 AM
floca committed rMITK89a7f0dc4b7f: BREAKING: MaskGenerators now return masks as const. (authored by floca).
BREAKING: MaskGenerators now return masks as const.
May 16 2022, 11:51 AM
wiesenfa added a comment to T29167: [dash] Bars and dots don't match in podium plot.

if the output is NULL, object[[by]] is not a factor, i.e. class(object[[by]]) is "character", in this case you need to use use unique() and probably your solution

May 16 2022, 10:21 AM · challengeR, webChallengeR
gaoh lowered the priority of T28884: MITK Flowbench -Save Seg not working, due to file naming issues from Normal to Low.

Yes, so I changed it already, and I am using the seriesUID as name for the images. Additionally, I had to add the layer property: Because by introducing the image name property, somehow the layer is also set (to a high number, probably). When I create a new SEG without setting the layer of the image to 0, the SEG is only put on top, when opening the data manager.

May 16 2022, 10:02 AM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca raised the priority of T29146: Union Mode for the picking tool from Wishlist to Normal.

It is explicitly wanted by the spectral imaging time... and almost done....

May 16 2022, 9:47 AM · MITK (v2022.10)
kislinsk triaged T29146: Union Mode for the picking tool as Wishlist priority.
May 16 2022, 9:34 AM · MITK (v2022.10)
aekavur added a comment to T29167: [dash] Bars and dots don't match in podium plot.

Hi again,

May 16 2022, 9:05 AM · challengeR, webChallengeR

May 13 2022

floca added a comment to T29139: [Image statistics] Warning is shown for 4D image with 3D mask.

In general yes, the behavior is correct if needed, but in this case it was caused by an incorrect/missing time point mapping between image and mask.

May 13 2022, 8:55 PM · Next Milestone, MITK
floca edited projects for T28989: [Segmentation] CanHandle functions seem to be inconsistent, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 7:35 PM · MITK, Request for Discussion
floca edited projects for T25445: MultiLabel segmentation mapper is very slow, added: Request for Discussion, MITK (v2022.10); removed MITK, Next Milestone.

is this still an issue?

May 13 2022, 7:35 PM · MITK (v2024.06), Request for Discussion
floca updated subscribers of T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

@s349i This should be also covered by your work, shouldn't it? If yes, please claim or merge with your working tasks.

May 13 2022, 7:34 PM · MITK (v2023.04)
floca edited projects for T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label , added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 7:33 PM · MITK (v2023.04)
floca edited projects for T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 7:29 PM · MITK (v2023.04), Restricted Project
floca moved T27613: Improve reinit behavior from Backlog to MITK Meeting on the Request for Discussion board.
May 13 2022, 7:29 PM · Request for Discussion, MITK (v2023.04)
floca added a project to T27613: Improve reinit behavior: Request for Discussion.

What is here still open?

May 13 2022, 7:28 PM · Request for Discussion, MITK (v2023.04)
floca edited projects for T27872: [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 7:27 PM · MITK (v2022.10), Cleared
floca edited projects for T27913: [Segmentation] Warnings in utilities view are inconsistent, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 7:27 PM · MITK (v2024.06)
floca edited projects for T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 7:04 PM · MITK (v2023.04)
floca updated the task description for T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage.
May 13 2022, 7:03 PM · MITK (v2023.12), Request for Discussion
floca edited projects for T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 7:00 PM · MITK (v2023.12), Request for Discussion
floca edited projects for T28297: Add Stitching MiniApp to installer, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 6:58 PM · MITK (v2022.10), Restricted Project, Cleared
floca edited projects for T28557: Cannot load segmentations from KITS challenge due to unknown pixel type, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 6:57 PM · MITK, Request for Discussion
floca edited projects for T28675: Boolean Operations in Segmentation utilities are slow, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 6:08 PM · MITK (v2024.06), Request for Discussion
floca moved T28691: AutoSegmentationWithPreviewTool tool manager won't support multithreading from Backlog to MITK Meeting on the Request for Discussion board.
May 13 2022, 5:23 PM · MITK
floca edited projects for T28691: AutoSegmentationWithPreviewTool tool manager won't support multithreading, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 5:23 PM · MITK
floca edited projects for T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 5:21 PM · MITK (v2023.04)
floca edited projects for T28763: [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 5:20 PM · MITK (v2022.10), Request for Discussion
kalali committed rMITK01b95b178454: Merge branch 'T25991-Update-semantic-relations-test' into develop (authored by kalali).
Merge branch 'T25991-Update-semantic-relations-test' into develop
May 13 2022, 4:41 PM
kalali added a comment to T29163: [XNAT] Opening XNAT session fails.

One difference that I saw: Two openssl-related files were added to the MITK-directory of the working version:

  • libcrypto-1_1-x64.dll
  • libssl-1_1-x64.dll
May 13 2022, 3:41 PM · MITK (v2024.06)
kalali added a comment to T29163: [XNAT] Opening XNAT session fails.

I met with Nikolas Stanczyk today and he showed me his working version of MITK, connecting to XNAT via the provided plugin. I also used my credentials and I was able to successfully login.
I copied his version to my laptop and here he was also able to login.
I just tested my credentials with this copy on my laptop and I was able to successfully login:

image.png (706×897 px, 35 KB)

May 13 2022, 3:22 PM · MITK (v2024.06)
wiesenfa added a comment to T29167: [dash] Bars and dots don't match in podium plot.

Thanks Emre!
Thats a weird change. I didn't find any mention in R changelog.
probably instead of

algorithms=factor(unique(object[[by]]))

it will be preferred

May 13 2022, 2:45 PM · challengeR, webChallengeR
floca edited projects for T28884: MITK Flowbench -Save Seg not working, due to file naming issues, added: MITK (v2022.10), Request for Discussion; removed MITK, Next Milestone.

@gaoh could you join the discussion?
Also may be the worklist feature T29159 would be an additional way to circumvent it.?!?

May 13 2022, 2:39 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca edited projects for T28886: MITK Flowbench - Reopen created segmentation not working, added: MITK (v2022.10); removed MITK, Next Milestone.

@gaoh Would you be so kind and verify that the problem still exists? Thanks.

May 13 2022, 2:35 PM · MITK (v2022.10), Missing Info, Kaapana (internal)
floca claimed T28991: [Segmentation] 3D tools overwrite / remove previous mask if reconfirmed.
May 13 2022, 2:13 PM · MITK (v2022.10)
floca edited projects for T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All", added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 2:12 PM · MITK (v2024.06)
floca edited projects for T29067: Introduce option to save the segmentation in the nnUNet tool GUI itself., added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 2:11 PM · MITK
floca moved T29154: Show available Tasks for Download in the nnUnet GUI from Backlog to MITK Meeting on the Request for Discussion board.
May 13 2022, 2:05 PM · MITK (v2022.10)
floca edited projects for T29154: Show available Tasks for Download in the nnUnet GUI, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 2:05 PM · MITK (v2022.10)
floca edited projects for T29158: [Segmentation] Custom list for optional label names, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 2:04 PM · MITK (v2022.10)
floca edited projects for T29159: [Segmentation] Flow bench worklist feature , added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 2:04 PM · MITK (v2022.10)
floca edited projects for T29160: [Segmentation] Worklist specification, data structure and io functions, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 2:03 PM · MITK (v2022.10)
floca added a project to T29146: Union Mode for the picking tool: MITK (v2022.10).
May 13 2022, 2:03 PM · MITK (v2022.10)
floca claimed T29146: Union Mode for the picking tool.
May 13 2022, 2:02 PM · MITK (v2022.10)
floca claimed T28982: Weak Label Annotation Picking Tool.
May 13 2022, 2:02 PM · MITK (v2022.10), Request for Discussion
floca edited projects for T28982: Weak Label Annotation Picking Tool, added: MITK (v2022.10); removed MITK.
May 13 2022, 2:01 PM · MITK (v2022.10), Request for Discussion
floca edited projects for T29157: NCT ISSO Annotation Support with MITK Segmentation Flow, added: MITK (v2022.10); removed MITK.
May 13 2022, 2:01 PM · MITK (v2024.06)
floca edited projects for T29161: [Segmentation] Extend flow bench control view to support worklists, added: MITK (v2022.10); removed Next Milestone, MITK.
May 13 2022, 2:00 PM · MITK (v2022.10)
floca edited projects for T27413: MITK Workflow Q&A, added: MITK (v2022.10); removed MITK, Next Milestone.
May 13 2022, 2:00 PM · MITK, Request for Discussion
scholzpa added a comment to T29167: [dash] Bars and dots don't match in podium plot.

Congrats for tracing this down!

May 13 2022, 1:46 PM · challengeR, webChallengeR
aekavur added a comment to T29167: [dash] Bars and dots don't match in podium plot.

Finally, I could find the source of the bug. 😊 It is caused by changed output type of unique() function in R:Base from R-3 to R-4.

May 13 2022, 1:40 PM · challengeR, webChallengeR
aekavur added a project to T29167: [dash] Bars and dots don't match in podium plot: challengeR.
May 13 2022, 1:14 PM · challengeR, webChallengeR
kalali moved T29141: [Segmentation] Color change not immediately applied from Tests/Checklists to Cycle on the MITK (v2022.10) board.
May 13 2022, 11:46 AM · MITK (v2022.10), Checklist
kalali claimed T29141: [Segmentation] Color change not immediately applied.

Is this the same (T29110, see description point 3) and specifically T29110#235991?
If so, I have a fix for the > layer 0 problem which can be tested and reviewed in D632.

May 13 2022, 11:46 AM · MITK (v2022.10), Checklist
kalali closed T28138: [MultiLabel Segmentation] Add tests for the LabelSetImage as Resolved.
May 13 2022, 11:16 AM · MITK (v2022.10)
kalali committed rMITK71841b57eb56: Add tests for labelsetimage (authored by kalali).
Add tests for labelsetimage
May 13 2022, 11:16 AM
kalali committed rMITKa77d9ee456f2: Modify function to test label merging (authored by kalali).
Modify function to test label merging
May 13 2022, 11:16 AM
kalali committed rMITK0090ef8cb18c: Add and test function for single label removal (authored by kalali).
Add and test function for single label removal
May 13 2022, 11:16 AM
kalali committed rMITK1449f510c236: Add function to test label erasure (authored by kalali).
Add function to test label erasure
May 13 2022, 11:15 AM
kalali committed rMITK7138f033c397: Add function to test label mask creation (authored by kalali).
Add function to test label mask creation
May 13 2022, 11:15 AM
kalali committed rMITK8d86c898beb5: Fix wrong error output; reset labelsetimage (authored by kalali).
Fix wrong error output; reset labelsetimage
May 13 2022, 11:15 AM
kalali updated the task description for T29145: [Segmentation] Unused classes can be removed.
May 13 2022, 10:27 AM · Breaking Change, MITK (v2022.10)
floca moved T28464: [Segmentation] New Add/Remove tool from Backlog to Segmentation on the MITK (v2022.10) board.
May 13 2022, 10:25 AM · MITK (v2022.10)
floca raised the priority of T28464: [Segmentation] New Add/Remove tool from Normal to High.

What is the status here?

May 13 2022, 10:24 AM · MITK (v2022.10)
a178n added a comment to T28808: [Properties] Some Pointset 2D shape selection not shown in the image views.

I expect a circle in the cross-hairs, akin to Shape: cross or vertex. But there is None. Is this expected behaviour?
@s434n is right. Vertex is almost invisible although exists.

May 13 2022, 10:15 AM · MITK (v2022.10)
floca moved T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view from Backlog to Segmentation on the MITK (v2022.10) board.
May 13 2022, 10:14 AM · MITK (v2022.10), Cleared, Restricted Project
floca moved T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation from Backlog to Segmentation on the MITK (v2022.10) board.
May 13 2022, 10:14 AM · MITK (v2022.10), Breaking Change

May 12 2022

floca closed T23721: Project "Astonishing Angelfish" as Resolved.
May 12 2022, 5:50 PM · Request for Discussion, MITK (v2022.10)
floca added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG).
May 12 2022, 5:50 PM · MITK (v2024.06)
floca added a parent task for T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG): T27807: [MultiLabel Segmentation] Inspection of module and plugin.
May 12 2022, 5:50 PM · MITK (v2024.06)
floca added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object.
May 12 2022, 5:50 PM · MITK (v2024.06)
floca added a parent task for T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
May 12 2022, 5:50 PM · MITK (v2024.06)
floca added a parent task for T23748: Image should have a valid DICOM.0008.0018 proprety: T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes).
May 12 2022, 5:46 PM · MITK
floca added a subtask for T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes): T23748: Image should have a valid DICOM.0008.0018 proprety.
May 12 2022, 5:46 PM · MITK
floca closed T23746: MITK and DICOM (realization), a subtask of T23721: Project "Astonishing Angelfish", as Resolved.
May 12 2022, 5:45 PM · Request for Discussion, MITK (v2022.10)
floca closed T23746: MITK and DICOM (realization) as Resolved.
May 12 2022, 5:45 PM · MITK
floca added a subtask for T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes): T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG).
May 12 2022, 5:43 PM · MITK
floca added a parent task for T26952: Implement helper to correct (DICOM conformal) set the properties of a segmentation (DICOM SEG): T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes).
May 12 2022, 5:43 PM · MITK (v2024.06)
floca closed T23754: DataStorage/Relationship clean up/refactoring, a subtask of T23721: Project "Astonishing Angelfish", as Resolved.
May 12 2022, 5:40 PM · Request for Discussion, MITK (v2022.10)
floca closed T23754: DataStorage/Relationship clean up/refactoring as Resolved.
May 12 2022, 5:40 PM · MITK
floca closed T23742: Implement proof of concept for new segmentation data type, a subtask of T23721: Project "Astonishing Angelfish", as Resolved.
May 12 2022, 5:39 PM · Request for Discussion, MITK (v2022.10)
floca closed T23742: Implement proof of concept for new segmentation data type, a subtask of T28524: Refactor LabelSetImage and associated classes., as Resolved.
May 12 2022, 5:39 PM · Next Milestone
floca closed T23742: Implement proof of concept for new segmentation data type as Resolved.

Close this task. The successor for our current planned implementation is T28524.

May 12 2022, 5:39 PM · MITK
floca added a subtask for T28524: Refactor LabelSetImage and associated classes.: T23742: Implement proof of concept for new segmentation data type.
May 12 2022, 5:37 PM · Next Milestone
floca added a parent task for T23742: Implement proof of concept for new segmentation data type: T28524: Refactor LabelSetImage and associated classes..
May 12 2022, 5:37 PM · MITK
floca edited projects for T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation, added: MITK (v2022.10); removed MITK, Next Milestone.
May 12 2022, 5:34 PM · MITK (v2022.10), Breaking Change
floca moved T24398: Dicom plugin: Retrieve does not work from Backlog to Tests/Checklists on the MITK (v2022.10) board.
May 12 2022, 5:33 PM · MITK (v2024.06)