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Jan 2 2021

kalali triaged T28137: Extension point for org.mitk.gui.qt.datamanager.contextMenuActions does not work anymore as High priority.
Jan 2 2021, 4:00 PM · MITK (v2021.02)
kalali added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.
Jan 2 2021, 2:08 PM · Restricted Project, MITK (v2021.02)
kalali added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

I just realized that the auto-selection mode of the Data node selection mode in the preferences pages of the Segmentation and MultiLabel Segmentation does not work anymore. I did not look into it but it might be related to the new selection concept.

Jan 2 2021, 2:08 PM · Restricted Project, MITK (v2021.02)
kalali moved T19522: Segmentation not displayed in 3d-render window from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 2 2021, 2:03 PM · MITK, Bugzilla
kalali edited projects for T19522: Segmentation not displayed in 3d-render window, added: MITK (v2021.02); removed MITK.
Jan 2 2021, 2:03 PM · MITK, Bugzilla
kalali updated the task description for T28136: Extend "Checkliste MultiLabel Segmentierung – Optionen".
Jan 2 2021, 1:49 PM · MITK (v2022.04)
kalali updated the task description for T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities".
Jan 2 2021, 1:48 PM · MITK (v2022.04)
kalali updated the task description for T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung".
Jan 2 2021, 1:48 PM · MITK (v2022.04)
kalali updated the task description for T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung".
Jan 2 2021, 1:48 PM · MITK (v2022.04)
kalali updated the task description for T27906: Extend "Checkliste Segmentierung – Utilities".
Jan 2 2021, 1:47 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27873: Extend "Checkliste Segmentierung – Interpolation".
Jan 2 2021, 1:47 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27850: Extend "Checkliste Segmentierung – 3D Segmentierung".
Jan 2 2021, 1:47 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27737: Extend "Checkliste Segmentierung – Optionen".
Jan 2 2021, 1:47 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".
Jan 2 2021, 1:47 PM · MITK (v2022.04), Cleared
kalali removed a project from T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries / dimensions in Utilities View: Restricted Project.
Jan 2 2021, 1:38 PM · MITK (v2022.10), Cleared

Jan 1 2021

kalali placed T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities" up for grabs.
Jan 1 2021, 3:01 PM · MITK (v2022.04)
kalali moved T28132: Extend "Checkliste MultiLabel Segmentierung – Interpolation" from Backlog to Test/Checklists on the MITK (v2021.02) board.
Jan 1 2021, 3:00 PM · MITK (v2022.04)
kalali moved T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities" from Backlog to Test/Checklists on the MITK (v2021.02) board.
Jan 1 2021, 3:00 PM · MITK (v2022.04)
kalali moved T28136: Extend "Checkliste MultiLabel Segmentierung – Optionen" from Backlog to Test/Checklists on the MITK (v2021.02) board.
Jan 1 2021, 3:00 PM · MITK (v2022.04)
kalali triaged T28136: Extend "Checkliste MultiLabel Segmentierung – Optionen" as High priority.
Jan 1 2021, 3:00 PM · MITK (v2022.04)
kalali added a comment to T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities".

There are some major issues / open questions regarding the MultiLabel Segmentation View, which make it difficult to define tests and create checklists. These issues / questions should be addresses first to understand the utilities view better: T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty, T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view, T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries / dimensions in Utilities View, T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations.

Jan 1 2021, 2:56 PM · MITK (v2022.04)
kalali triaged T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations as Normal priority.
Jan 1 2021, 2:37 PM · MITK (v2023.04)
kalali triaged T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries / dimensions in Utilities View as Normal priority.
Jan 1 2021, 1:59 PM · MITK (v2022.10), Cleared
kalali renamed T27571: Multilabel segmentation does not work with US DICOM images from Multilable segmentation does not work with US DICOM images to Multilabel segmentation does not work with US DICOM images.
Jan 1 2021, 1:56 PM · MITK (v2021.10), Missing Info, Restricted Project
kalali triaged T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities" as High priority.
Jan 1 2021, 1:33 PM · MITK (v2022.04)
kalali updated the task description for T28132: Extend "Checkliste MultiLabel Segmentierung – Interpolation".
Jan 1 2021, 1:17 PM · MITK (v2022.04)
kalali triaged T28132: Extend "Checkliste MultiLabel Segmentierung – Interpolation" as High priority.
Jan 1 2021, 12:51 PM · MITK (v2022.04)
kalali updated the task description for T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung".
Jan 1 2021, 12:49 PM · MITK (v2022.04)

Dec 23 2020

kleina added a member for Deep Learning: j902n.
Dec 23 2020, 12:44 PM
kleina added a member for MIC: j902n.
Dec 23 2020, 12:43 PM

Dec 22 2020

kalali added a comment to T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung".

Similar to T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" I updated the document and added content to explicitly tests different image types / segmentation types, labels and layers.
I copied the modified document to E130-Daten\Release\Checklisten\MITK Workbench Release and named it Checkliste MultiLabel Segmentierung – 3D Segmentierung.

Dec 22 2020, 12:57 PM · MITK (v2022.04)
kalali triaged T28131: [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers as Normal priority.
Dec 22 2020, 12:53 PM · Request for Discussion, MITK (v2022.04)
kalali added a comment to T28118: Refactoring of SegTool2D.

Looking through the checklists I found that the 2D tools of the segmentation view are different than the 2D tools of the Multilabel segmentation (one more: Fast Marching is missing). The 3D tools of the multi label segmentation even contain only the Threshold tool.
Thinking about the idea of the MultiLabel segmentation (and that our normal segmentation view also generates labelset images) it should actually not make any difference and thus the tools should be the same (2D and 3D are of course different).
Also, there seems to be a lot of redundancy UI-wise so even having multiple segmentation views and the 2D / 3D tool view for both views seems unnecessary. I would keep that in mind while refactoring the tools. But I am open for discussion on this topic.

Dec 22 2020, 11:55 AM · MITK (v2021.02)
floca 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.

Dec 22 2020, 11:21 AM · Request for Discussion, MITK (v2021.10)
kalali moved T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung" from Backlog to Test/Checklists on the MITK (v2021.02) board.
Dec 22 2020, 11:21 AM · MITK (v2022.04)
kalali triaged T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung" as High priority.
Dec 22 2020, 11:20 AM · MITK (v2022.04)
kalali 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.

Dec 22 2020, 11:07 AM · Request for Discussion, MITK (v2021.10)
floca added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

Regarding the issue itself: I think it is a fundamental question of the capability of the tool. Auto confirm when closing the contour would
Pro: be a faster UX
Contra: won't allow to alter live wires before confirmation.

Dec 22 2020, 10:47 AM · Request for Discussion, MITK (v2021.10)
floca added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

I just found out that the Checklists also states the following:

Deaktiveren des Live Wire Tools
  Tool Icon verschwindet vom Mouse Cursor
  Die gelben Konturen werden weiterhin angezeigt, können aber nicht mehr bearbeitet werden

So even the experienced behavior does not fit the checklist test. We should clarify which workflow we want to provide.

Dec 22 2020, 10:44 AM · Request for Discussion, MITK (v2021.10)
floca triaged T28129: Contour interactor do not handle time steps > 0 correctly and do not support time geometries correctly as Normal priority.
Dec 22 2020, 10:13 AM · MITK
floca triaged T28128: ContourModels are not correctly rendered on time steps > 0 as Normal priority.
Dec 22 2020, 10:09 AM · MITK
floca claimed T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation.

Will be fixed (is fixed already) by the rework done in T28118.

Dec 22 2020, 9:35 AM · MITK (v2021.02)
kalali accepted rMITKfd4af29ccbb8: Add mitkImageStatisticsContainerTest.cpp.
Dec 22 2020, 9:11 AM
kalali accepted rMITK318208495e06: Adapt printTest to just check if no exception is thrown.
Dec 22 2020, 9:08 AM
kalali accepted rMITKda6b13dcd728: Add a test to check if empty container trigger an exception if….
Dec 22 2020, 9:07 AM
kalali accepted rMITK9564428ee562: Correct AllStatisticNamesForContainer() Test.
Dec 22 2020, 9:04 AM

Dec 21 2020

kalali added a subtask for T28108: [Release Checklists] Prepare release checklists: T28110: Extend checklists for multilabel segmentation view.
Dec 21 2020, 2:59 PM · MITK
kalali added a parent task for T28110: Extend checklists for multilabel segmentation view: T28108: [Release Checklists] Prepare release checklists.
Dec 21 2020, 2:59 PM · MITK (v2022.04)
kalali updated the task description for T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung".
Dec 21 2020, 2:58 PM · MITK (v2022.04)
kalali added a comment to T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung".

I created the document and added content to explicitly test

  • segmentation on a 3D image
  • 3D segmentation (static) on a 4D image
  • 4D segmentation (dynamic) on a 4D image
  • segmenting with different labels / on different layers
Dec 21 2020, 2:58 PM · MITK (v2022.04)
kalali reopened T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation as "Open".

Reopened this because this error still occurs / occurs again. This should be investigated with the work of T28118: Refactoring of SegTool2D.

Dec 21 2020, 1:57 PM · MITK (v2021.02)
kalali reopened T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation, a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Open.
Dec 21 2020, 1:57 PM · MITK (v2021.10), Missing Info, Restricted Project
kalali added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

I just found out that the Checklists also states the following:

Deaktiveren des Live Wire Tools
  Tool Icon verschwindet vom Mouse Cursor
  Die gelben Konturen werden weiterhin angezeigt, können aber nicht mehr bearbeitet werden
Dec 21 2020, 12:52 PM · Request for Discussion, MITK (v2021.10)
gaoh triaged T28127: Reopen segmentation in MITK as High priority.
Dec 21 2020, 9:57 AM · MITK (v2021.02), Restricted Project, Kaapana (internal)
kalali added a comment to T28110: Extend checklists for multilabel segmentation view.

Btw: I never found any multilabel segmentation checklists. Did I miss something? For this meta-task and its sub-tasks I will create all the required checklists.

Dec 21 2020, 8:57 AM · MITK (v2022.04)
kislinsk closed T28126: 2020 Week 52 (Late December) as Resolved.
Dec 21 2020, 6:52 AM · MITK
kislinsk edited the content of Changelog.
Dec 21 2020, 6:52 AM · MITK
kislinsk added a comment to T28126: 2020 Week 52 (Late December).

Deleted branch release/T28126-2020-Week-52.

Dec 21 2020, 6:51 AM · MITK
kislinsk committed rMITK5dc9bf8b39f9: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Dec 21 2020, 6:51 AM
kislinsk committed rMITKbd9ce02f928c: 2020 Week 52 (Late December) (authored by kislinsk).
2020 Week 52 (Late December)
Dec 21 2020, 6:50 AM
kislinsk edited the content of 2020 Week 52 (Late December).
Dec 21 2020, 6:44 AM
kislinsk added a comment to T28126: 2020 Week 52 (Late December).

Pushed new branch release/T28126-2020-Week-52.

Dec 21 2020, 5:16 AM · MITK
kislinsk triaged T28126: 2020 Week 52 (Late December) as Normal priority.
Dec 21 2020, 5:14 AM · MITK
kislinsk created an object: 2020 Week 52 (Late December).
Dec 21 2020, 5:13 AM

Dec 20 2020

eisenman closed T28125: challangeR Release v1.0.0 as Resolved.
Dec 20 2020, 9:34 PM · challengeR (v1.0)
eisenman moved T28125: challangeR Release v1.0.0 from In Progress to Done on the challengeR (v1.0) board.
Dec 20 2020, 9:34 PM · challengeR (v1.0)
eisenman closed T27396: Represent single-task challenge as multi-task challenge with one task as Resolved.
Dec 20 2020, 9:34 PM · challengeR (v1.0)
eisenman closed T27325: Plot titles in rankingHeatmap missing in multi task report as Resolved.
Dec 20 2020, 9:34 PM · challengeR (v1.0)
eisenman closed T27404: Fix the 2.1 section title format of the report as Resolved.
Dec 20 2020, 9:34 PM · challengeR (v1.0)
eisenman closed T27408: Description of cluster analysis contains unnecessary symbol as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27410: Correct description of variability of achieved rankings across tasks as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27281: Implement tests for ranking method "rank-then-aggregate" as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27412: Description of variability of achieved rankings across tasks is missing in short report as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27316: Aggregate-than-rank does not throw an error when an invalid NA treatment option is specified as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27302: Add sections to the readme as Resolved.
Dec 20 2020, 9:33 PM · challengeR (v1.0)
eisenman closed T27237: Implement tests for ranking method "aggregate-then-rank" as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27301: Add on boarding tutorial as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27244: Implement tests for the "challenge" class as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27236: Set up test infrastructure as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27407: Warnings are shown in multi-task challenge report for violin plot as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27656: make sure data set is data.frame as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27411: Improve labels in cluster dendrogram as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27327: warning in docx report as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27449: Consistent handling of plots created for multi-task data sets as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27694: Fix failing unit tests as Resolved.
Dec 20 2020, 9:32 PM · challengeR (v1.0)
eisenman closed T27253: Notify user when multi-task data set is interpreted as single-task data set as Resolved.
Dec 20 2020, 9:31 PM · challengeR (v1.0)
eisenman closed T27385: Variables holding the aggregated value are named differently for single- and multi-task challenges as Resolved.
Dec 20 2020, 9:31 PM · challengeR (v1.0)
eisenman closed T27657: When missing algorithm performances are added as NAs, task is also NA as Resolved.
Dec 20 2020, 9:31 PM · challengeR (v1.0)
eisenman closed T27715: Specify minimum required versions of dependencies as Resolved.
Dec 20 2020, 9:31 PM · challengeR (v1.0)
eisenman closed T27252: Multiple cases per algorithm are not detected when missing data was added before as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27740: Add missing imports as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27658: LaTeX Warning: There were undefined references as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27475: Legend of blob plot has missing legend title and algorithms as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27474: Legend of line plot has missing legend title and algorithm as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27677: Update text in reports (feedback from Lena) as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27769: Top x performing algorithms are not mentioned in the reports anymore as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27338: Report contains misleading information on missing values as Resolved.
Dec 20 2020, 9:30 PM · challengeR (v1.0)
eisenman closed T27773: package dependencies as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27294: add multiple figure output formats in report with option clean=TRUE as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)