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Sep 30 2020

aguilera moved T27788: [shiny] Several blocks for configuration of data structure appear when switching from options "head" and "all" from Backlog to Done on the webChallengeR board.
Sep 30 2020, 6:07 PM · webChallengeR
eisenman added a comment to T27494: Check which files are still relevant.

In my opinion, the functionality that we want to keep should also have unit tests to (1) indicate that it is maintained and (2) to demonstrate how to use it.

Sep 30 2020, 4:49 PM · challengeR
eisenman claimed T27450: Consistent use of attribute indicating whether small metric values lead to a better rank.
Sep 30 2020, 4:39 PM · challengeR (v1.0)
eisenman moved T27686: tutorial can be added as vignette to embed it in the package from In Progress to Done on the challengeR (v1.0) board.
Sep 30 2020, 3:20 PM · challengeR (v1.0)
eisenman committed rCHALLENGER65aafab4f19f: Merge branch 'feature/T27686-EnableVignettes' into develop (authored by eisenman).
Merge branch 'feature/T27686-EnableVignettes' into develop
Sep 30 2020, 3:20 PM
eisenman committed rCHALLENGERcae4c2246723: Fix typos (authored by eisenman).
Fix typos
Sep 30 2020, 3:18 PM
eisenman committed rCHALLENGER57df2806e9e3: Add metadata for usage of vignettes (authored by eisenman).
Add metadata for usage of vignettes
Sep 30 2020, 3:18 PM
kalali claimed T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.
Sep 30 2020, 2:05 PM · MITK (v2021.02)
eisenman committed rCHALLENGERe70a83c00a2c: Rename directory (authored by eisenman).
Rename directory
Sep 30 2020, 1:56 PM
eisenman claimed T27686: tutorial can be added as vignette to embed it in the package .
Sep 30 2020, 1:36 PM · challengeR (v1.0)
kalali moved T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation from Backlog to MITK Meeting on the Request for Discussion board.
Sep 30 2020, 1:35 PM · MITK (v2021.02)
kalali moved T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation from Backlog to MITK Meeting on the Request for Discussion board.
Sep 30 2020, 1:35 PM · MITK (v2021.02)
kalali added a project to T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation: Request for Discussion.

I found a way to solve this, similar to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation: By transforming the time step from the reference image to the working image with

TimePointType referenceImageTimePoint = referenceImage->GetTimeGeometry()->TimeStepToTimePoint(t);
TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(referenceImageTimePoint);

in mitk::LiveWireTool2D::ConfirmSegmentation().
However, inside mitk::LiveWireTool2D there are a lot of uses of positionEvent->GetSender()->GetTimeStep() which all lead to a wrong timestep (e.g t = 2, although a static segmentation only has 1 timestep = 0).
That means:

  1. I'm not sure about any negative side-effects which I don't see with my manual testing right now
  2. There is a basic flaw in the design which should be discussed instead of just fixing the symptoms with the suggested fix
Sep 30 2020, 1:34 PM · MITK (v2021.02)
aguilera moved T27761: [shiny] Prevent generation of report if field "name" is empty from In Progress to Done on the webChallengeR board.
Sep 30 2020, 1:32 PM · webChallengeR
kalali added a revision to T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation: Unknown Object (Differential Revision).
Sep 30 2020, 1:29 PM · MITK (v2021.02)
eisenman merged task T27288: separate readme.md and readme.Rmd into T27241: Readme improvements.
Sep 30 2020, 1:23 PM · challengeR (v1.0)
eisenman merged T27288: separate readme.md and readme.Rmd into T27241: Readme improvements.
Sep 30 2020, 1:23 PM · challengeR (v1.0)
eisenman moved T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test from In Progress to Done on the challengeR (v1.0) board.
Sep 30 2020, 1:21 PM · challengeR (v1.0)
kalali added a revision to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation: Unknown Object (Differential Revision).
Sep 30 2020, 1:21 PM · MITK (v2021.02)
eisenman added a comment to T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.

The idea is to raise an error if the user tries to extract a task that is not contained in the set of tasks.

Sep 30 2020, 1:19 PM · challengeR (v1.0)
kalali moved T18014: write tool interaction tests for segmentation from Backlog to Segmentation on the MITK (v2021.02) board.
Sep 30 2020, 1:18 PM · MITK (v2024.12), Bugzilla
kalali edited projects for T18014: write tool interaction tests for segmentation, added: MITK (v2021.02); removed MITK.

mitkToolInteractionTestSuite in mitkToolInteractionTest.cpp does not contain any tests (all disabled)

Sep 30 2020, 1:18 PM · MITK (v2024.12), Bugzilla
eisenman committed rCHALLENGERa9f26cb623be: Merge branch 'feature/T27282-AddTestsForTestThenRank' into develop (authored by eisenman).
Merge branch 'feature/T27282-AddTestsForTestThenRank' into develop
Sep 30 2020, 12:57 PM
eisenman committed rCHALLENGER4ba8b0ba84a7: Adapt column heading (authored by eisenman).
Adapt column heading
Sep 30 2020, 12:55 PM
eisenman committed rCHALLENGERb22ed4b2ebc8: Clean up (authored by eisenman).
Clean up
Sep 30 2020, 12:55 PM
eisenman added a comment to T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.

The function testThenRank has an argument FUN that is set to "significance" internally. The value that is actually passed is not used.
@wiesenfa Should "significance" be the default value in the signature already or should the argument be removed?

Sep 30 2020, 12:51 PM · challengeR (v1.0)
eisenman triaged T27802: Revise signature of function testThenRank as High priority.
Sep 30 2020, 12:50 PM · challengeR (v1.0)
kalali moved T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation from Backlog to Segmentation on the MITK (v2021.02) board.
Sep 30 2020, 10:51 AM · MITK (v2021.02)
kalali added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.

The same problem exists in T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation: Here, mitk::SegTool2D::GetAffectedImageSliceAs2DImageis called with a reference image (the segmentation) inside mitk::LiveWireTool2D::ConfirmSegmentation() with t != 0.

Sep 30 2020, 10:47 AM · MITK (v2021.02)
kalali triaged T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation as High priority.
Sep 30 2020, 10:45 AM · MITK (v2021.02)
kalali added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.

I just found out that the same code (mitk::SegTool2D::GetAffectedImageSliceAs2DImage) is used when using e.g. the simple add-tool. However, here unsigned int timeStep = positionEvent->GetSender()->GetTimeStep(image); returns 0 as timestep, although the timestep was set to something != 0 in the image navigator. This works, because mitk::BaseRenderer::GetTimeStep already transforms the current timepoint with data->GetTimeGeometry()->TimePointToTimeStep(GetTime());.

Sep 30 2020, 9:48 AM · MITK (v2021.02)

Sep 29 2020

kalali added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.

Maybe it's possible to change

Sep 29 2020, 10:25 PM · MITK (v2021.02)
kalali added a project to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation: Request for Discussion.

I tried to find a solution. The problem is the same problem we had with other segmentation operations:
mitk::SegTool2D::GetAffectedImageSliceAs2DImage is called with a reference image (the segmentation) and a timestep although the segmentation is static and the timestep != 0 does not exist.
So obviously one would need to translate a timepoint into the timestep of the static segmentation. But I don't see a way to access the current timepoint and also the whole 2D fast marching is totally unclear to me.
mitk::FastMarchingTool already holds the current timestep, which is changed by listening to the image navigator. But the timestep does not help us here.

Sep 29 2020, 10:07 PM · MITK (v2021.02)
kalali added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

I can partly confirm it.

  1. The segmentation is performed on the current selected timestep (if you switch to timestep 2 --> segmentation occurs on timestep 2 = CORRECT; maybe fixed with the task!?)
Sep 29 2020, 9:41 PM · Missing Info, MITK (v2021.02)
kalali updated the task description for T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.
Sep 29 2020, 8:40 PM · MITK (v2021.02)
kalali moved T25804: [Selection concept] Set 'selected' property when using the new selection concept from MITK Meeting to Backlog on the Request for Discussion board.
Sep 29 2020, 8:20 PM · MITK (v2024.12), Request for Discussion
kalali updated the task description for T25804: [Selection concept] Set 'selected' property when using the new selection concept.
Sep 29 2020, 8:19 PM · MITK (v2024.12), Request for Discussion
eisenman committed rCHALLENGER0d18d9a64990: Test that test-then-rank raises warning for one algorithm (authored by eisenman).
Test that test-then-rank raises warning for one algorithm
Sep 29 2020, 5:37 PM
floca added a comment to T27096: [MITKDoc] Revise MultiLabel Segmentation Utilities Plugin Documentation.

I will land the current documentation onto develop now. Open questions still remain but for me the whole plugin is chaotic and therefore I don't want to dive deeper into it before discussing the current status.
The "Labels" tab does not even show the widgets it's supposed to show. Lots of functions are not implemented, functionality is not consistent :|

Sep 29 2020, 4:24 PM · MITK (v2021.02)
eisenman committed rCHALLENGER16fec9a23aa9: Test that NAs are replaced by numeric value in multi-task data set (authored by eisenman).
Test that NAs are replaced by numeric value in multi-task data set
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGER186cda66338e: Test that test-then-rank raises error when no NA treatment specified but NAs… (authored by eisenman).
Test that test-then-rank raises error when no NA treatment specified but NAs…
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGERdf8b11ee1286: Test that test-then-rank works for multi-task data set with no missing data (authored by eisenman).
Test that test-then-rank works for multi-task data set with no missing data
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGERa0fadafa4197: Test options for handling of NAs (authored by eisenman).
Test options for handling of NAs
Sep 29 2020, 3:38 PM
eisenman committed rCHALLENGERf948633a42b8: Test that test-then-rank raises error for invalid ties method even when no ties… (authored by eisenman).
Test that test-then-rank raises error for invalid ties method even when no ties…
Sep 29 2020, 3:17 PM
eisenman committed rCHALLENGERe281136cf0a9: Test that test-then-rank works for ties method 'max' (authored by eisenman).
Test that test-then-rank works for ties method 'max'
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGER4d962dc2db24: Test that test-then-rank raises error for invalid ties method (authored by eisenman).
Test that test-then-rank raises error for invalid ties method
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERb680f023acdc: Test that test-then-rank raises warning for one case (authored by eisenman).
Test that test-then-rank raises warning for one case
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERa9b5e6e1c840: Test that test-then-rank works with two algorithms (authored by eisenman).
Test that test-then-rank works with two algorithms
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERc1e510e404ba: Clean up (authored by eisenman).
Clean up
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGER3ac8798d0c48: Fix typos (authored by eisenman).
Fix typos
Sep 29 2020, 3:12 PM
kalali raised the priority of T27100: [MITKDoc] Revise DataManager Plugin Documentation from Normal to Unbreak Now!.

I'm was able to land the differential. I simply merged the branch, after I updated D255 with it. Everything seems fine but I'm not sure if old changes of the documentation have also been re-added. Please check (hint could be the removed "The" in front of the documentation page names).

Sep 29 2020, 1:19 PM · Cleared, MITK (v2021.02)
kalali committed rMITKae21cdc44627: Merge branch 'T27100-Develop-integration' into develop (authored by kalali).
Merge branch 'T27100-Develop-integration' into develop
Sep 29 2020, 1:16 PM
eisenman added a comment to T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.

The function testThenRank has an argument FUN that is set to "significance" internally. The value that is actually passed is not used.
@wiesenfa Should "significance" be the default value in the signature already or should the argument be removed?

Sep 29 2020, 1:00 PM · challengeR (v1.0)
kalali closed T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets as Resolved.
Sep 29 2020, 11:50 AM · MITK (v2021.02)
kalali moved T27792: [Segmentation] Utilities view shows gaps between multiple selection widgets from Backlog to Segmentation on the MITK (v2021.02) board.
Sep 29 2020, 11:50 AM · MITK (v2021.02)
kalali committed rMITK33b490954a78: MultiLabel Segmentation Utilities view shows gaps between multiple selection… (authored by kalali).
MultiLabel Segmentation Utilities view shows gaps between multiple selection…
Sep 29 2020, 11:48 AM
kalali committed rMITKd6a7af6ae1af: Fix stretch policy to minimize the gap between multiple selection widgets (authored by kalali).
Fix stretch policy to minimize the gap between multiple selection widgets
Sep 29 2020, 11:48 AM
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Found the bug in CDash. In app/Model/AuthToken.php:51 the "special value" 9999-12-31 23:59:59 is inserted into the database whereas the maximum value for TIMESTAMP is 2038-01-19 03:14:07. Hence the "special value" appears as 0000-00-00 00:00:00 in the database which will trigger the deletion when it is compared with the current date.

Sep 29 2020, 11:32 AM · CI, MITK (v2021.02), Restricted Project
kalali edited projects for T27096: [MITKDoc] Revise MultiLabel Segmentation Utilities Plugin Documentation, added: Missing Info, Request for Discussion; removed Cleared.

I will land the current documentation onto develop now. Open questions still remain but for me the whole plugin is chaotic and therefore I don't want to dive deeper into it before discussing the current status.

Sep 29 2020, 10:59 AM · MITK (v2021.02)
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Sigh. Just one time I'd like not to stumble over bugs when dealing with CDash. I implemented the authorization, double-checked that the proxy does not throw away the authorization HTTP header, watched the cdash database, and figured out that as soon as CDash is comparing a valid token... it deletes it from the database.

Sep 29 2020, 10:36 AM · CI, MITK (v2021.02), Restricted Project
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Deleted branch feature/T25882-CDashAuthorization.

Sep 29 2020, 10:32 AM · CI, MITK (v2021.02), Restricted Project
aguilera moved T27779: [shiny] Clarifications on page "Configure ranking" from Backlog to In Progress on the webChallengeR board.
Sep 29 2020, 10:25 AM · webChallengeR
aguilera added a comment to T27779: [shiny] Clarifications on page "Configure ranking".

Consensus explanations to be updated after input request.

Sep 29 2020, 10:25 AM · webChallengeR
kislinsk committed rMITKebe44be1fd0d: Merge branch 'feature/T25882-CDashAuthorization' into develop (authored by kislinsk).
Merge branch 'feature/T25882-CDashAuthorization' into develop
Sep 29 2020, 9:28 AM
aguilera moved T27757: [shiny] Contradicting instruction on page "Uncertainty analysis" from Backlog to Done on the webChallengeR board.
Sep 29 2020, 9:23 AM · webChallengeR
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Pushed new branch feature/T25882-CDashAuthorization.

Sep 29 2020, 9:18 AM · CI, MITK (v2021.02), Restricted Project

Sep 28 2020

kalali added a revision to T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets: Unknown Object (Differential Revision).
Sep 28 2020, 11:06 PM · MITK (v2021.02)
kalali closed T27792: [Segmentation] Utilities view shows gaps between multiple selection widgets as Resolved.
Sep 28 2020, 10:45 PM · MITK (v2021.02)
kalali committed rMITK444716c43250: Segmentation Utilities view shows gaps between multiple selection widgets (authored by kalali).
Segmentation Utilities view shows gaps between multiple selection widgets
Sep 28 2020, 10:43 PM
kalali committed rMITK4aa4dc21925c: Fix stretch policy to minimize the gap between multiple selection widgets (authored by kalali).
Fix stretch policy to minimize the gap between multiple selection widgets
Sep 28 2020, 10:43 PM
kalali edited projects for T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets, added: MITK (v2021.02); removed MITK.
Sep 28 2020, 10:32 PM · MITK (v2021.02)
kalali updated the task description for T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets.
Sep 28 2020, 10:32 PM · MITK (v2021.02)
kalali updated the task description for T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets.
Sep 28 2020, 10:32 PM · MITK (v2021.02)
kalali triaged T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets as Normal priority.
Sep 28 2020, 10:31 PM · MITK (v2021.02)
kalali created T27795: [MultiLabel Segmentation] Utilities view shows gaps between multiple selection widgets.
Sep 28 2020, 10:31 PM · MITK (v2021.02)
eisenman updated the task description for T27794: Stacked frequency plots should switch to single page layout.
Sep 28 2020, 6:27 PM · challengeR (v1.0)
eisenman created T27794: Stacked frequency plots should switch to single page layout.
Sep 28 2020, 4:44 PM · challengeR (v1.0)
eisenman triaged T27793: Plot titles are missing in some line plots as High priority.
Sep 28 2020, 4:32 PM · challengeR (v1.0)
aguilera moved T27783: [shiny] Typo in waiting pop-up from Backlog to Done on the webChallengeR board.
Sep 28 2020, 4:23 PM · webChallengeR
aguilera moved T27761: [shiny] Prevent generation of report if field "name" is empty from Backlog to In Progress on the webChallengeR board.
Sep 28 2020, 4:22 PM · webChallengeR
eisenman claimed T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.
Sep 28 2020, 3:48 PM · challengeR (v1.0)
kompan committed rMITK61c29856fd9a: The concentration curve converter view is updated to have all the… (authored by kompan).
The concentration curve converter view is updated to have all the…
Sep 28 2020, 3:28 PM
kompan committed rMITK6d502dec2546: Set Convert to concentration button enabled after data and settings are checked. (authored by kompan).
Set Convert to concentration button enabled after data and settings are checked.
Sep 28 2020, 3:28 PM
kompan committed rMITK3362eb74daeb: remove redundant code. (authored by kompan).
remove redundant code.
Sep 28 2020, 3:28 PM
kompan committed rMITK5b7299ab3774: Better handling of numeric number division. (authored by kompan).
Better handling of numeric number division.
Sep 28 2020, 3:28 PM
kompan committed rMITKf291594557c3: Rename qmitkSingleNodeSelectionWidget.h to QmitkSingleNodeSelectionWidget.h (authored by kompan).
Rename qmitkSingleNodeSelectionWidget.h to QmitkSingleNodeSelectionWidget.h
Sep 28 2020, 3:28 PM
kompan committed rMITK83863702a41e: Change OnSelectionChanged to OnNodeSelectionChanged. (authored by kompan).
Change OnSelectionChanged to OnNodeSelectionChanged.
Sep 28 2020, 3:28 PM
kompan committed rMITK0886d961c240: Only enable T2 conversion button, when baseline selection settings are ok. (authored by kompan).
Only enable T2 conversion button, when baseline selection settings are ok.
Sep 28 2020, 3:28 PM
kompan committed rMITKa0fe6d907db9: Change size policy of groupBox_T2 to improve UI appearance. (authored by kompan).
Change size policy of groupBox_T2 to improve UI appearance.
Sep 28 2020, 3:28 PM
kompan committed rMITK5b44478aba39: Add unit ms to echo time TE label. (authored by kompan).
Add unit ms to echo time TE label.
Sep 28 2020, 3:28 PM
kompan committed rMITK4097514c35b7: Correct typo. (authored by kompan).
Correct typo.
Sep 28 2020, 3:28 PM
kompan committed rMITK65fd44ec4653: Use modelFitResultRelationRules to define isNoModelFitNodePredicate. (authored by kompan).
Use modelFitResultRelationRules to define isNoModelFitNodePredicate.
Sep 28 2020, 3:28 PM
kompan committed rMITK5359d830fc78: Remove commented out/unnecessary code. (authored by kompan).
Remove commented out/unnecessary code.
Sep 28 2020, 3:28 PM
kompan committed rMITKb75f19da4716: Add baseline averaging functionality to T2 conversion. (authored by kompan).
Add baseline averaging functionality to T2 conversion.
Sep 28 2020, 3:28 PM
kompan committed rMITK3828d7b1a66c: Correct T2 conversion conversion formula. (authored by kompan).
Correct T2 conversion conversion formula.
Sep 28 2020, 3:28 PM
kompan committed rMITK277fc5810f72: Remove autoselect, otherwise images get chosen before settings are set. (authored by kompan).
Remove autoselect, otherwise images get chosen before settings are set.
Sep 28 2020, 3:28 PM
kompan committed rMITK6a5ad72f8ac9: Correct T2-conversion formula as described in T27667. (authored by kompan).
Correct T2-conversion formula as described in T27667.
Sep 28 2020, 3:28 PM
kompan committed rMITKc8f42d8a4504: Use new selection widget concept for T2-weightes times series. (authored by kompan).
Use new selection widget concept for T2-weightes times series.
Sep 28 2020, 3:28 PM
kompan committed rMITK468cb880fd39: New selection widget for time series, 3D image and baseline image selection. (authored by kompan).
New selection widget for time series, 3D image and baseline image selection.
Sep 28 2020, 3:28 PM
kompan committed rMITKa0b8b52201fb: Ass missing BaselineStartTime/EndTimeStep input. (authored by kompan).
Ass missing BaselineStartTime/EndTimeStep input.
Sep 28 2020, 3:28 PM