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Aug 31 2020

wiesenfa claimed T27337: Report contains wrong ranking method when rank-then-aggregate is used.
Aug 31 2020, 2:50 PM · challengeR (v1.0)
wiesenfa added a comment to T27447: significanceMap function raises warning about deprecated function call.

@eisenman I don't get this warning. Could you give more details/ an example? or is this already solved/not relevant anymore?

Aug 31 2020, 2:48 PM · challengeR (v1.0)
wiesenfa lowered the priority of T27450: Consistent use of attribute indicating whether small metric values lead to a better rank from Normal to Low.
Aug 31 2020, 2:45 PM · challengeR (v1.0)
wiesenfa added a comment to T27450: Consistent use of attribute indicating whether small metric values lead to a better rank.

yes this has historical reasons (largeBetter had been "inverseOrder" in the beginning which was horrible;-))
smallBetter would have the advantage that the user interface would not change, modifying as.challenge with largeBetter would mean that existing scripts lead to wrong results which is problematic.
could someone of you please take care of this one?

Aug 31 2020, 2:43 PM · challengeR (v1.0)
wiesenfa lowered the priority of T27327: warning in docx report from Normal to Low.
Aug 31 2020, 2:39 PM · challengeR (v1.0)
wiesenfa added a comment to T27288: separate readme.md and readme.Rmd.

see comment in T27241

Aug 31 2020, 2:37 PM · challengeR (v1.0)
wiesenfa added a comment to T27288: separate readme.md and readme.Rmd.
Aug 31 2020, 2:32 PM · challengeR (v1.0)
wiesenfa added a comment to T27241: Readme improvements.

@aguilera
regarding issue 1: Rmd should be changed if we want to keep that the current package version at the beginning is automatically inserted. otherwise we could only work with the md file and drop the Rmd file. the readme.md file has to stay in the root directory such that GitHub finds it. If .Rmd file is also in root the easiest thing is to compile it such that it will be in the same directory. I don't remember, why do we need to change this?

Aug 31 2020, 2:22 PM · challengeR (v1.0)
gaoh added a comment to T27110: [MITKDoc] Revise Command Line Tool/ Automatisation Plugin Documentation.

Is this the correct module? https://docs.mitk.org/2018.04/org_mitk_views_cmdlinemodules.html ? Or is there another command line tool?

Aug 31 2020, 2:17 PM · Cleared, MITK (v2021.02)
thomass added a comment to T27094: [MITKDoc] Revise Segmentation Utilities Plugin Documentation.
  1. To my knowledge it should generate a mask out of a Surface and in MITKData there should be some...I will have a look
  2. That is rather a bug, because in Phenotyping there is a reference that shouldn't be there, maybe we can remove that.
Aug 31 2020, 2:16 PM · Cleared, MITK (v2021.02)
reinkea added a comment to T27474: Legend of line plot has missing legend title and algorithm.

@eisenman Yes, I have a dataset with ~200 Algorithms, will send it to you!

Aug 31 2020, 2:15 PM · challengeR (v1.0)
eisenman added a comment to T27474: Legend of line plot has missing legend title and algorithm.

@reinkea Do you have a dataset containing more algorithms?

Aug 31 2020, 2:11 PM · challengeR (v1.0)
wiesenfa added a comment to T27474: Legend of line plot has missing legend title and algorithm.

@eisenman can larger number of algorithms be checked? what's your opinion? please close otherwise.

Aug 31 2020, 2:05 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER1b5c2b17a680: adapt figure heights to avoid crop (authored by wiesenfa).
adapt figure heights to avoid crop
Aug 31 2020, 1:58 PM
wiesenfa added a comment to T27475: Legend of blob plot has missing legend title and algorithms.

solved (at least for 19 tasks) in merge for T27474

Aug 31 2020, 1:56 PM · challengeR (v1.0)
wiesenfa added a comment to T27420: report text.

items 3 and 4 solved (see separate tasks).
solved at least for 19 algorithms.

Aug 31 2020, 1:55 PM · challengeR (v1.0)
wiesenfa moved T27474: Legend of line plot has missing legend title and algorithm from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 1:53 PM · challengeR (v1.0)
wiesenfa moved T27475: Legend of blob plot has missing legend title and algorithms from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 1:53 PM · challengeR (v1.0)
wiesenfa added a comment to T27474: Legend of line plot has missing legend title and algorithm.

solved at least for 19 algorithms (MSD data).

Aug 31 2020, 1:52 PM · challengeR (v1.0)
gaoh claimed T27110: [MITKDoc] Revise Command Line Tool/ Automatisation Plugin Documentation.
Aug 31 2020, 1:28 PM · Cleared, MITK (v2021.02)
gaoh added a revision to T27097: [MITKDoc] Revise Statistics Plugin Documentation: Unknown Object (Differential Revision).
Aug 31 2020, 1:28 PM · Cleared, MITK (v2021.02)
gaoh claimed T27097: [MITKDoc] Revise Statistics Plugin Documentation.
Aug 31 2020, 1:20 PM · Cleared, MITK (v2021.02)
neher triaged T27690: Make FAST_DATA_DIR and SLOW_DATA_DIR configurable as Wishlist priority.
Aug 31 2020, 12:02 PM · Kaapana (internal)
thomass triaged T27689: RTDose image can not be serialized and workbench crashes upon loading as High priority.
Aug 31 2020, 11:19 AM · Request for Discussion, MITK
wiesenfa added a comment to T27449: Consistent handling of plots created for multi-task data sets.

maybe introduce some utility function that takes care of it

Aug 31 2020, 10:02 AM · challengeR (v1.0)
wiesenfa lowered the priority of T27286: interactive plots from Normal to Wishlist.
Aug 31 2020, 9:54 AM · challengeR

Aug 30 2020

floca added a revision to T27641: [Segmentation] Watershed does always generate a 3D static seg. Even if dynamic segmentation was generated.: Unknown Object (Differential Revision).
Aug 30 2020, 8:48 PM · Cleared, MITK (v2021.02)

Aug 28 2020

kalali added a comment to T27094: [MITKDoc] Revise Segmentation Utilities Plugin Documentation.

I started with the modifications but I have two questions (@thomass):

Aug 28 2020, 4:58 PM · Cleared, MITK (v2021.02)
floca removed a project from T27568: US 2D image cannot be read: invalid tilt information: Request for Discussion.

Discussion result:
For a fast mitigation one should choose option 2 or 3 (see description) or ensure that the dicom tag values stay distinctive (see reason 1).

Aug 28 2020, 12:19 PM · Moved to git.dkfz.de, Restricted Project, MITK
floca closed T24710: Check failing dicom data in MITK-Data as Resolved.
Aug 28 2020, 12:08 PM · DICOM, Restricted Project, MITK
floca removed projects from T24710: Check failing dicom data in MITK-Data: Request for Discussion, Missing Info.

Discussion result: We close this task. All known issues still open are covered by T27568: US 2D image cannot be read: invalid tilt information. If needed we can open the task again.

Aug 28 2020, 12:08 PM · DICOM, Restricted Project, MITK
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

Region growing task can be found here T27684

Aug 28 2020, 12:05 PM · MITK (v2021.10), Missing Info, Restricted Project
thomass added a revision to T27672: [Measurement] Planar figures are disabled when the image is already loaded: Unknown Object (Differential Revision).
Aug 28 2020, 11:55 AM · MITK (v2021.02)
kalali moved T27674: [Selection widgets] Enabling auto selection emits a signal that might not yet be connected from Backlog to MITK Meeting on the Request for Discussion board.
Aug 28 2020, 11:32 AM · Cleared, MITK
thomass added a revision to T27106: [MITKDoc] Revise Volume Visualization Plugin Documentation: Unknown Object (Differential Revision).
Aug 28 2020, 11:29 AM · Cleared, MITK (v2021.02)

Aug 27 2020

thomass claimed T27095: [MITKDoc] Revise MultiLabel Segmentation Plugin Documentation.
Aug 27 2020, 11:23 AM · MITK (v2021.02)
thomass claimed T27099: [MITKDoc] Revise Clipping Plane Plugin Documentation.
Aug 27 2020, 11:20 AM · Moved to git.dkfz.de, MITK (v2024.12), Cleared
wiesenfa updated subscribers of T27686: tutorial can be added as vignette to embed it in the package .
Aug 27 2020, 10:54 AM · challengeR (v1.0)
wiesenfa created T27686: tutorial can be added as vignette to embed it in the package .
Aug 27 2020, 10:53 AM · challengeR (v1.0)
wiesenfa created T27685: changes in subset().
Aug 27 2020, 10:44 AM · challengeR (v1.0)
floca added a parent task for T27661: [Documentation] Update "How to create a new MITK Module": Unknown Object (Maniphest Task).
Aug 27 2020, 9:53 AM · Cleared, MITK (v2021.02)
floca added a parent task for T27670: [Documentation] invalid link in MITK Style Guide: Unknown Object (Maniphest Task).
Aug 27 2020, 9:53 AM · MITK (v2021.02)
thomass triaged T27684: [Segmentation] Improve Region Growing 2D algorithm and interaction as High priority.
Aug 27 2020, 8:28 AM · Moved to git.dkfz.de, MITK (v2024.12)

Aug 26 2020

floca triaged T27670: [Documentation] invalid link in MITK Style Guide as Normal priority.
Aug 26 2020, 11:37 AM · MITK (v2021.02)
floca moved T27670: [Documentation] invalid link in MITK Style Guide from Backlog to Documentation on the MITK (v2021.02) board.
Aug 26 2020, 11:37 AM · MITK (v2021.02)
floca added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

2D Segmentation tools:

  • Add
  • Substract
  • Correction
  • Paint
  • Wipe
  • Region Growing
  • Fill
  • Erase
  • Live Wire
  • 2D Fast Marching

--> First test Looks suprisingly good, even 2D Fast Marching tool works as expected on US4DCyl.nrrd for dynamic and static Segmentation
--> Region Growing works correctly in terms of timesteps but shows odd behavior (the mouse cursor is released but still more foreground pixels are added --> this often causes an oversegmentation on US4DCyl @kislinsk is this something potentially caused by your recent change?

wip

Aug 26 2020, 11:35 AM · MITK (v2021.10), Missing Info, Restricted Project
floca claimed T27641: [Segmentation] Watershed does always generate a 3D static seg. Even if dynamic segmentation was generated..
Aug 26 2020, 11:34 AM · Cleared, MITK (v2021.02)
floca added a project to T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice: Breaking Change.

With D380 2 breaking changes where introduced. See commit messages.

Aug 26 2020, 11:33 AM · Breaking Change, MITK (v2021.02)
floca added a comment to T27543: [Segmentation] Crash on FastMarching3D tool when loading 4D data .

By D380

Aug 26 2020, 11:25 AM · MITK (v2021.02)
floca closed T27543: [Segmentation] Crash on FastMarching3D tool when loading 4D data as Resolved.
Aug 26 2020, 11:25 AM · MITK (v2021.02)
floca closed T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice, a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Resolved.
Aug 26 2020, 11:24 AM · MITK (v2021.10), Missing Info, Restricted Project
floca closed T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice as Resolved.
Aug 26 2020, 11:24 AM · Breaking Change, MITK (v2021.02)
floca committed rMITK01ec63137fc5: Refactoring of segmentation tools (authored by floca).
Refactoring of segmentation tools
Aug 26 2020, 11:23 AM
floca committed rMITKe7f10292bd56: BEAKING CHANGE: renamed mitk::AutoSegmentationTool::Get3DImage() -> mitk… (authored by floca).
BEAKING CHANGE: renamed mitk::AutoSegmentationTool::Get3DImage() -> mitk…
Aug 26 2020, 11:23 AM
floca committed rMITK5ba8241108f8: Corrected and refactored Otsu. (authored by floca).
Corrected and refactored Otsu.
Aug 26 2020, 11:23 AM
floca committed rMITKc8d3d2fcbf5f: fixed gcc error (authored by floca).
fixed gcc error
Aug 26 2020, 11:23 AM
floca committed rMITK290e64ed3d0a: Corrected and refactored FastMarching3DTool. (authored by floca).
Corrected and refactored FastMarching3DTool.
Aug 26 2020, 11:23 AM
floca committed rMITKc245edfec492: Refactore BinaryThresholdBaseTool to use new AutoSegmentationWithPreviewTool (authored by floca).
Refactore BinaryThresholdBaseTool to use new AutoSegmentationWithPreviewTool
Aug 26 2020, 11:23 AM
floca committed rMITKd4a8d54db37e: BREAKING CHANGE: CanHandle signature changed to also check for the workingdata. (authored by floca).
BREAKING CHANGE: CanHandle signature changed to also check for the workingdata.
Aug 26 2020, 11:23 AM
floca closed T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images as Resolved by committing rMITK290e64ed3d0a: Corrected and refactored FastMarching3DTool..
Aug 26 2020, 11:23 AM · MITK (v2021.02), Bugzilla
floca closed T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images, a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Resolved.
Aug 26 2020, 11:23 AM · MITK (v2021.10), Missing Info, Restricted Project
floca committed rMITK59f4be0819b6: Added a AutoSegmentationWithPreviewTool base class to resolve redundancy in… (authored by floca).
Added a AutoSegmentationWithPreviewTool base class to resolve redundancy in…
Aug 26 2020, 11:23 AM
floca committed rMITK3a866b5069ef: Improved documentation and constness. (authored by floca).
Improved documentation and constness.
Aug 26 2020, 11:23 AM
kalali added a comment to T16026: Distinct tool names for 2d and 3d segmentation tools.

Is this still a topic?

Aug 26 2020, 10:01 AM · Auto-closed, MITK, Bugzilla

Aug 25 2020

gaoh created T27683: Dockerized MITK ubuntu 18.04 on current Master rMITKf0e722f6a65d3aba98d674120683260564ce8db0.
Aug 25 2020, 3:41 PM · MITK

Aug 24 2020

floca added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

Checked on windows (develop branch 10.8.; binaries and build tree): DICOM Reader v2 (auto select) works correctly. Have to look into it on Ubuntu.

Aug 24 2020, 1:31 PM · Missing Info, DICOM, MITK
kalali renamed T27681: Image cropper image selection widget accepts bounding box from Image cropper image selection widgets accepts bounding box to Image cropper image selection widget accepts bounding box.
Aug 24 2020, 1:21 PM · Auto-closed, MITK
kalali triaged T27681: Image cropper image selection widget accepts bounding box as Normal priority.
Aug 24 2020, 12:45 PM · Auto-closed, MITK

Aug 22 2020

mahesh_s added a comment to T27670: [Documentation] invalid link in MITK Style Guide.

Aug 22 2020, 4:44 PM · MITK (v2021.02)
mahesh_s claimed T27670: [Documentation] invalid link in MITK Style Guide.
Aug 22 2020, 3:24 PM · MITK (v2021.02)

Aug 21 2020

thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Crash fixed by D380 :)

Aug 21 2020, 2:17 PM · MITK (v2021.02), Bugzilla

Aug 19 2020

kleina updated kleina.
Aug 19 2020, 10:59 AM
neher closed T27676: crate command line only build config for diffusion as Resolved.
Aug 19 2020, 10:58 AM · MITK Diffusion
neher committed rMITKDIFF663c55f14d73: Merge branch 'T27676-CmdOnly' (authored by neher).
Merge branch 'T27676-CmdOnly'
Aug 19 2020, 10:08 AM
neher committed rMITKDIFF70734f7bacb7: Update revision names (authored by neher).
Update revision names
Aug 19 2020, 10:08 AM
reinkea updated the task description for T27677: Update text in reports (feedback from Lena).
Aug 19 2020, 8:19 AM · challengeR (v1.0)
reinkea created T27677: Update text in reports (feedback from Lena).
Aug 19 2020, 8:19 AM · challengeR (v1.0)

Aug 18 2020

neher committed rMITKDIFF5f6d4ad46f6d: Merge branch 'T27676-CmdOnly' (authored by neher).
Merge branch 'T27676-CmdOnly'
Aug 18 2020, 3:20 PM
neher committed rMITKDIFF64c2fb2b3ed7: Disabling qt help (authored by neher).
Disabling qt help
Aug 18 2020, 3:18 PM
neher committed rMITKDIFFbdc1268c179d: Added config (authored by neher).
Added config
Aug 18 2020, 2:54 PM
neher added a comment to T27676: crate command line only build config for diffusion.

Pushed new branch T27676-CmdOnly.

Aug 18 2020, 2:53 PM · MITK Diffusion
neher triaged T27676: crate command line only build config for diffusion as Wishlist priority.
Aug 18 2020, 2:39 PM · MITK Diffusion

Aug 17 2020

kalali added a comment to T27524: Should RenderingManager be used without singleton?.

I cannot see any declaration of GetRenderingManager() in BaseRenderer

Aug 17 2020, 11:38 AM · Request for Discussion, MITK
zimmerer added a member for Deep Learning: clueth.
Aug 17 2020, 11:29 AM
zimmerer added a member for MIC: clueth.
Aug 17 2020, 11:29 AM
kalali added a comment to T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.

You're right, I was mistakenly reading the dialog that shows up when you create a new layer for a layer name dialog.

Aug 17 2020, 10:35 AM · MITK (v2022.04), Cleared

Aug 14 2020

kislinsk closed T27668: Fix Visual Studio 2017 warnings/errors as Resolved.
Aug 14 2020, 9:20 PM · MITK (v2021.02)
kislinsk committed rMITKdcb22cd781bb: Fix Visual Studio 2017 warnings (errors) in RegionGrowingTool (authored by kislinsk).
Fix Visual Studio 2017 warnings (errors) in RegionGrowingTool
Aug 14 2020, 9:19 PM
kislinsk committed rMITKaad6f78d84ee: Fix Visual Studio 2017 warnings (errors) in RegionGrowingTool (authored by kislinsk).
Fix Visual Studio 2017 warnings (errors) in RegionGrowingTool
Aug 14 2020, 9:19 PM
kislinsk added a comment to T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.

Layers don't have names. The plugin is only asking for label names which are important of course. For a new segmentation there are two dialogs: for the segmentation name, and for the fist label name + color. I think it evolved from the UI pattern of the old segmentation plugin and I agree that the label dialog should be omitted. A "New label <i>" could be added to the label widget instead and we should probably improve this widget so a double click on the name opens an in-place editor for the name string instead of requiring the user to right click -> Rename... -> Dialog. Color editor already works this way.

Aug 14 2020, 9:15 PM · MITK (v2022.04), Cleared
kislinsk lowered the priority of T27646: [Data manager] Option to change color of segmentation disappeared in data manager from Normal to Wishlist.
Aug 14 2020, 9:04 PM · Auto-closed, Request for Discussion, MITK
kislinsk added a comment to T27524: Should RenderingManager be used without singleton?.

I cannot see any declaration of GetRenderingManager() in BaseRenderer (even before rMITK5e0e87c3)? In the second example I even cannot see anything related to RenderingManager? :-)

Aug 14 2020, 9:03 PM · Request for Discussion, MITK
kalali updated the task description for T27524: Should RenderingManager be used without singleton?.
Aug 14 2020, 5:58 PM · Request for Discussion, MITK
kalali added a comment to T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.

+1 and I'm also not sure why a Layer needs to have a name. I can't see it anywhere and if the name is used somewhere, the same discussion as for the labels might be needed for layers.

Aug 14 2020, 5:57 PM · MITK (v2022.04), Cleared
kalali added a project to T27674: [Selection widgets] Enabling auto selection emits a signal that might not yet be connected: Request for Discussion.
Aug 14 2020, 5:52 PM · Cleared, MITK
kalali triaged T27674: [Selection widgets] Enabling auto selection emits a signal that might not yet be connected as Normal priority.
Aug 14 2020, 5:51 PM · Cleared, MITK
kalali added a revision to T27105: [MITKDoc] Revise Measurement Plugin Documentation: Unknown Object (Differential Revision).
Aug 14 2020, 5:30 PM · Cleared, MITK (v2021.02)
thomass committed rMITK92d4566b0ea0: T27105 correct renaming of measurement documentation image (authored by thomass).
T27105 correct renaming of measurement documentation image
Aug 14 2020, 3:46 PM
kalali added a comment to T27672: [Measurement] Planar figures are disabled when the image is already loaded.

Proposed a fix in D388, maybe there is a more elegant way but it works now

Aug 14 2020, 3:10 PM · MITK (v2021.02)
thomass added a comment to T27672: [Measurement] Planar figures are disabled when the image is already loaded.

Proposed a fix in D388, maybe there is a more elegant way but it works now

Aug 14 2020, 2:04 PM · MITK (v2021.02)