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schererj triaged T27669: Dicom import issue with MITK binaries (package) and Ubuntu as Low priority.
Wed, Aug 12, 5:30 PM · DICOM, MITK
floca added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

How do we proceed with (ML)Segmentation

Segmentation already uses AutoSelection as default (can be configured via preferences, default is true)

Wed, Aug 12, 3:21 PM · Restricted Project, MITK (2020)
kislinsk added a revision to T27668: Fix Visual Studio 2017 warnings/errors: Unknown Object (Differential Revision).
Wed, Aug 12, 1:54 PM · MITK (2020)
kislinsk triaged T27668: Fix Visual Studio 2017 warnings/errors as Normal priority.
Wed, Aug 12, 1:46 PM · MITK (2020)
kalali added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

I started fixing some plugins. How do we proceed with (ML)Segmentation and MatchPoint?

Wed, Aug 12, 12:34 PM · Restricted Project, MITK (2020)
kalali claimed T27659: Refactor BasicImageProcessing plugin to use the new node selection widgets.
Wed, Aug 12, 12:32 PM · MITK, Cleared
kompan moved T27667: Concentration curve converter view- errors in formula for T2-weighted signal conversion from Backlog to Perfusion on the MITK (2020) board.
Wed, Aug 12, 12:07 PM · Cleared, MITK (2020)
kompan triaged T27667: Concentration curve converter view- errors in formula for T2-weighted signal conversion as Normal priority.
Wed, Aug 12, 12:06 PM · Cleared, MITK (2020)
kompan moved T27666: Concentration curve converter view- missing echo time unit from Backlog to Perfusion on the MITK (2020) board.
Wed, Aug 12, 11:49 AM · Cleared, MITK (2020)
kompan triaged T27666: Concentration curve converter view- missing echo time unit as Normal priority.
Wed, Aug 12, 11:49 AM · Cleared, MITK (2020)
kalali added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

Pushed new branch T27498-Set-selection-mode-to-auto-selection.

Wed, Aug 12, 11:24 AM · Restricted Project, MITK (2020)
kalali renamed T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper from PlanarFigure tests faile due to DICOMTagsOfInterestAddHelper to PlanarFigure tests show error with DICOMTagsOfInterestAddHelper.
Wed, Aug 12, 9:34 AM · MITK
kalali triaged T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper as Normal priority.
Wed, Aug 12, 9:33 AM · MITK
kalali closed T27061: Planar figures crash if drawn with empty data storage, a subtask of T27049: Refactor Measurement plugin to use the new node selection widgets, as Resolved.
Wed, Aug 12, 8:19 AM · MITK
kalali closed T27061: Planar figures crash if drawn with empty data storage as Resolved.
Wed, Aug 12, 8:19 AM · Restricted Project, MITK
kalali committed rMITK67d34b5de004: Introduce nullptr checks in PlanarFigureInteractor to avoid nullptr exception (authored by kalali).
Introduce nullptr checks in PlanarFigureInteractor to avoid nullptr exception
Wed, Aug 12, 8:18 AM
kalali committed rMITK5b5d523a5c51: Add nullptr checks to prevent crashes (authored by kalali).
Add nullptr checks to prevent crashes
Wed, Aug 12, 8:18 AM
kalali committed rMITK780e8d84937f: Clean class (authored by kalali).
Clean class
Wed, Aug 12, 8:18 AM

Tue, Aug 11

kalali added a revision to T27061: Planar figures crash if drawn with empty data storage: Unknown Object (Differential Revision).
Tue, Aug 11, 4:51 PM · Restricted Project, MITK
kalali added a revision to T27101: [MITKDoc] Revise Logging Plugin Documentation: Unknown Object (Differential Revision).
Tue, Aug 11, 1:58 PM · Cleared, MITK (2020)
kompan moved T27664: Check conversion from signal to concentration for a turboFLASH sequence from Backlog to Perfusion on the MITK (2020) board.
Tue, Aug 11, 11:16 AM · Cleared, MITK (2020)
kompan triaged T27664: Check conversion from signal to concentration for a turboFLASH sequence as Normal priority.
Tue, Aug 11, 11:15 AM · Cleared, MITK (2020)
kompan committed rMITKa28b433c2303: Update Contact information. (authored by kompan).
Update Contact information.
Tue, Aug 11, 9:56 AM
kompan committed rMITKe9c455a256e8: Explain how to change type in the start parameter section. (authored by kompan).
Explain how to change type in the start parameter section.
Tue, Aug 11, 9:56 AM
kompan committed rMITK8eec47c8e7d2: Reword model specific setting, such that is is clear that selection widgets are… (authored by kompan).
Reword model specific setting, such that is is clear that selection widgets are…
Tue, Aug 11, 9:56 AM
kompan committed rMITKe5650ba95249: Partially remove contact information. (authored by kompan).
Partially remove contact information.
Tue, Aug 11, 9:56 AM
kompan committed rMITK96d9cdca44a6: Reword mask selection section. (authored by kompan).
Reword mask selection section.
Tue, Aug 11, 9:56 AM
kompan committed rMITK2276f918f29c: Change view id and page name to org.mitk.views.pharmacokinetics.mri (authored by kompan).
Change view id and page name to org.mitk.views.pharmacokinetics.mri
Tue, Aug 11, 9:56 AM
kompan committed rMITKd806025ef630: Minor corrections. (authored by kompan).
Minor corrections.
Tue, Aug 11, 9:56 AM
kompan committed rMITK70d9572ad8c2: Update Executing a Fit (authored by kompan).
Update Executing a Fit
Tue, Aug 11, 9:56 AM
kompan committed rMITK5897a9cc646a: Update Signal to concentration conversion settings (authored by kompan).
Update Signal to concentration conversion settings
Tue, Aug 11, 9:56 AM
kompan committed rMITKd27194deebe7: Update model settings, model specific setting and start parameter (authored by kompan).
Update model settings, model specific setting and start parameter
Tue, Aug 11, 9:56 AM
kompan committed rMITKf73f1ed9c381: Update contraints settings (authored by kompan).
Update contraints settings
Tue, Aug 11, 9:56 AM
kompan committed rMITKa68895f7828f: Model settings update. (authored by kompan).
Model settings update.
Tue, Aug 11, 9:56 AM
kompan committed rMITK599971240e0f: Update Cite information and Data/Roi Secetion. (authored by kompan).
Update Cite information and Data/Roi Secetion.
Tue, Aug 11, 9:56 AM
kompan committed rMITKb15d9f0912fe: Update General information (authored by kompan).
Update General information
Tue, Aug 11, 9:56 AM
kompan committed rMITK876db5449175: Update introduction. (authored by kompan).
Update introduction.
Tue, Aug 11, 9:55 AM
kompan committed rMITK862290209a6d: Update citation information. (authored by kompan).
Update citation information.
Tue, Aug 11, 9:55 AM
kompan committed rMITK63744d90fa28: Update Contact information. (authored by kompan).
Update Contact information.
Tue, Aug 11, 9:55 AM

Mon, Aug 10

amancino90 created T27663: Crosshair navigation not disabled in QmitkMeasurementView .
Mon, Aug 10, 10:49 PM · MITK
kahl added a comment to T27564: [Segmentation] Integrate deep learning methods for Segmentation in MITK.

Pushed new branch feature/T27564-integrate-deeplearning-segmentation-evaluation.

Mon, Aug 10, 5:36 PM · MITK
kislinsk added a project to T27661: [Documentation] Update "How to create a new MITK Module": Cleared.
Mon, Aug 10, 12:41 PM · Cleared, MITK (2020)
kislinsk added a comment to T27661: [Documentation] Update "How to create a new MITK Module".

Thanks for the report. I renamed the task to an actual task as the documentation you are referring to seems not up-to-date regarding ModuleList.cmake. For questions, though, please use the #help-mitk Slack channel or the mitk-users mailing list (public).

Mon, Aug 10, 12:41 PM · Cleared, MITK (2020)
kislinsk moved T27661: [Documentation] Update "How to create a new MITK Module" from Backlog to Documentation on the MITK (2020) board.
Mon, Aug 10, 12:29 PM · Cleared, MITK (2020)
kislinsk renamed T27661: [Documentation] Update "How to create a new MITK Module" from How to create a new MITK Module to [Documentation] Update "How to create a new MITK Module".
Mon, Aug 10, 12:29 PM · Cleared, MITK (2020)
e249r created T27661: [Documentation] Update "How to create a new MITK Module".
Mon, Aug 10, 12:14 PM · Cleared, MITK (2020)
thomass committed rMITK18ddd2ed4fc8: rewrote some sections and enabled auto select (authored by thomass).
rewrote some sections and enabled auto select
Mon, Aug 10, 10:06 AM
thomass closed T27098: [MITKDoc] Revise Image Cropper Plugin Documentation as Resolved by committing rMITK18ddd2ed4fc8: rewrote some sections and enabled auto select.
Mon, Aug 10, 10:06 AM · Cleared, MITK (2020)

Sun, Aug 9

floca added a comment to T27605: Stitching functionality.

Pushed new branch feature/T27605-Stitching_filter.

Sun, Aug 9, 4:44 PM · MITK

Sat, Aug 8

kalali added a revision to T27659: Refactor BasicImageProcessing plugin to use the new node selection widgets: Restricted Differential Revision.
Sat, Aug 8, 5:34 PM · MITK, Cleared
kalali triaged T27659: Refactor BasicImageProcessing plugin to use the new node selection widgets as Normal priority.
Sat, Aug 8, 5:01 PM · MITK, Cleared
floca added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

Just a comment: Image Statistcs uses the MultiNodeSelectionWidget which offers no AutoSelect feature (on purpose, because it could be a lot selections at once...).

Sat, Aug 8, 11:56 AM · Restricted Project, MITK (2020)
kalali added a comment to T27498: [Selection widgets] Define default for auto selection / listening mechanism.

Plugins from {24775} that do not follow the discussion result and need to be refactored (SetAutoSelectNewNodes(true)):
No auto selection

  • Dicom Inspector
  • Segmentation (although it is working if the segmentation plugin is opened after a node has been loadad - but not the other way around)
  • Segmentation Utilities (QmitkDataSelectionWidget)
  • MultiLabel Segmentation Utilities (QmitkDataSelectionWidget)
  • Image Cropper (will be fixed in D375)
  • Image Statistics
  • Measurement (will be fixed in D372)
  • MatchPoint
  • Properties
  • Point Set Interaction
  • Semantic Relations
  • Semantic Relations Statistics
  • Volume Visualization
Sat, Aug 8, 10:00 AM · Restricted Project, MITK (2020)

Fri, Aug 7

amancino90 added a comment to T27652: CMake/mitkInstallRules.cmake set invalid install directory for QtWebEngine resources and translations in Linux.

I found a similar error using Qt version 5.12.6 and the pluginGenerator.
The linker's path to Qt5WebEngine is wrongly parsed as "-lQt5::WebEngine" in "MyProject/Apps/MyApp/CMakeFiles/MyApp.dir/link.txt".

Fri, Aug 7, 10:41 PM · MITK
floca added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Oh I didn’t look into the Differential yet, only tried it with the current develop. The crash I observed in with FastMarching3D

Fri, Aug 7, 8:51 PM · MITK (2020), Bugzilla
thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Oh I didn’t look into the Differential yet, only tried it with the current develop. The crash I observed in with FastMarching3D

Fri, Aug 7, 8:49 PM · MITK (2020), Bugzilla
floca added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Did you experience the error based on the Differential? Did you open FastMarching for 2D or 3D?

Fri, Aug 7, 8:43 PM · MITK (2020), Bugzilla
wiesenfa reassigned T27252: Multiple cases per algorithm are not detected when missing data was added before from wiesenfa to eisenman.
Fri, Aug 7, 2:49 PM · challengeR (v1.0)
wiesenfa added a comment to T27252: Multiple cases per algorithm are not detected when missing data was added before.

should work now, tests successful.
However warning is

Performance of not all algorithms is observed for all cases in task 'dummyTask'

despite being single task challenge. see also separate task

Fri, Aug 7, 2:47 PM · challengeR (v1.0)
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

So I have a fix for the contour problem but what is missing is that the pointset is still drawn on timestep 0 instead of the current timestep and I have to figure out why.

Fri, Aug 7, 2:46 PM · Missing Info, MITK (2020)
wiesenfa committed rCHALLENGER4a2a4d181421: always check both for missings and duplicates (authored by wiesenfa).
always check both for missings and duplicates
Fri, Aug 7, 2:41 PM
thomass committed rMITK36d69b77aeaf: rewrote some sections and added new image (authored by thomass).
rewrote some sections and added new image
Fri, Aug 7, 2:31 PM
thomass closed T27107: [MITKDoc] Revise Screenshot Maker Plugin Documentation as Resolved by committing rMITK36d69b77aeaf: rewrote some sections and added new image.
Fri, Aug 7, 2:31 PM · Cleared, MITK (2020)
wiesenfa created T27658: LaTeX Warning: There were undefined references.
Fri, Aug 7, 2:31 PM · challengeR (v1.0)
wiesenfa moved T27252: Multiple cases per algorithm are not detected when missing data was added before from Backlog to In Progress on the challengeR (v1.0) board.
Fri, Aug 7, 2:10 PM · challengeR (v1.0)
wiesenfa created T27657: single task challenge treated as multi task in sanity checks gives unuseful warnings.
Fri, Aug 7, 2:10 PM · challengeR (v1.0)
thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

I also experience a crash in the tool:

Fri, Aug 7, 1:12 PM · MITK (2020), Bugzilla
wiesenfa moved T27453: Create complete network plot in its function from Backlog to In Progress on the challengeR (v1.0) board.
Fri, Aug 7, 1:05 PM · challengeR (v1.0)
wiesenfa moved T27494: Check which files are still relevant from Backlog to In Progress on the challengeR (v1.0) board.
Fri, Aug 7, 1:03 PM · challengeR (v1.0)
wiesenfa moved T27407: Warnings are shown in multi-task challenge report for violin plot from Backlog to Done on the challengeR (v1.0) board.
Fri, Aug 7, 12:59 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER48b7e35505c6: handle warnings in violin (authored by wiesenfa).
handle warnings in violin
Fri, Aug 7, 12:57 PM
wiesenfa added a comment to T27494: Check which files are still relevant.
  • compareRanks() allows to compare 2 ranking lists and compute Kendall's tau, would leave it in package
  • benchmarkUtils allows to link with benchmark package (CRAN archived) which has some more features, but is not maintained anymore. might be dropped
Fri, Aug 7, 12:36 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER4520859fe0f3: ensure that challenge object is data.frame (authored by wiesenfa).
ensure that challenge object is data.frame
Fri, Aug 7, 12:10 PM
wiesenfa moved T27656: make sure data set is data.frame from In Progress to Done on the challengeR (v1.0) board.
Fri, Aug 7, 12:00 PM · challengeR (v1.0)
wiesenfa moved T27656: make sure data set is data.frame from Backlog to In Progress on the challengeR (v1.0) board.
Fri, Aug 7, 12:00 PM · challengeR (v1.0)
wiesenfa created T27656: make sure data set is data.frame.
Fri, Aug 7, 11:48 AM · challengeR (v1.0)
thomass updated subscribers of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Fri, Aug 7, 8:46 AM · Missing Info, Restricted Project, MITK (2020)
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

File is FastMarchingTool.cpp

Fri, Aug 7, 8:42 AM · Missing Info, MITK (2020)
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

I can partly confirm it.

Fri, Aug 7, 8:07 AM · Missing Info, MITK (2020)

Thu, Aug 6

floca triaged T27655: [statistics] Logic of DataGeneratorBase blocks the UI thread as High priority.
Thu, Aug 6, 11:48 PM · MITK (2020)
floca created T27655: [statistics] Logic of DataGeneratorBase blocks the UI thread .
Thu, Aug 6, 11:47 PM · MITK (2020)
floca updated subscribers of T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

@thomass Can you confirm the problem in your todays check or is it fixed by the tasks mentioned above?

Thu, Aug 6, 11:32 PM · Missing Info, MITK (2020)
floca closed T26967: [Segmentation] Pressing the X button on threshold confirm dialogs does not stop the execution as Resolved.

Fixed by/with T27621/T27622

Thu, Aug 6, 11:29 PM · Restricted Project, Cleared, MITK (2020)
floca closed T27509: [Segmentation] How to handle 3D and 4D Segmentations on 4D images as Resolved.

Covered by the clarification for T27507

Thu, Aug 6, 11:27 PM · MITK (2020), Request for Discussion
floca added a revision to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images: Unknown Object (Differential Revision).
Thu, Aug 6, 9:08 PM · MITK (2020), Bugzilla
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

2D Segmentation tools:

Thu, Aug 6, 3:45 PM · Missing Info, Restricted Project, MITK (2020)
wiesenfa added a comment to T27453: Create complete network plot in its function.

can be closed?

Thu, Aug 6, 12:29 PM · challengeR (v1.0)
wiesenfa added a comment to T27453: Create complete network plot in its function.

the complication arises to handle the automatic sizing of the plot, which is why in the first chunk it reads out the width without plotting and in the second chunk the figure width is adapted

Thu, Aug 6, 12:28 PM · challengeR (v1.0)
gaoh claimed T27101: [MITKDoc] Revise Logging Plugin Documentation.
Thu, Aug 6, 11:49 AM · Cleared, MITK (2020)
kompan moved T27654: Refactor concentration curve converter view to use new selection concept from Backlog to Perfusion on the MITK (2020) board.
Thu, Aug 6, 11:27 AM · Cleared, MITK (2020)
kompan triaged T27654: Refactor concentration curve converter view to use new selection concept as Normal priority.
Thu, Aug 6, 11:27 AM · Cleared, MITK (2020)
floca claimed T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice.
Thu, Aug 6, 11:09 AM · MITK (2020)
wiesenfa added a comment to T27453: Create complete network plot in its function.

the function is network() and is already in the report

Thu, Aug 6, 10:09 AM · challengeR (v1.0)

Wed, Aug 5

kislinsk added a parent task for T27652: CMake/mitkInstallRules.cmake set invalid install directory for QtWebEngine resources and translations in Linux: T27196: Rewrite packaging of MITK.
Wed, Aug 5, 8:52 PM · MITK
kislinsk added a subtask for T27196: Rewrite packaging of MITK: T27652: CMake/mitkInstallRules.cmake set invalid install directory for QtWebEngine resources and translations in Linux.
Wed, Aug 5, 8:52 PM · Cleared, MITK (2020)
kislinsk triaged T27652: CMake/mitkInstallRules.cmake set invalid install directory for QtWebEngine resources and translations in Linux as Low priority.

Thanks for the report. The complete packaging will be rewritten soon. Until then we strongly recommend to not use system Qt but to install Qt (version 5.12.9 is a good choice) with the official qt installer and to use Qt5_DIR to hint our CMake scripts to the lib/cmake/Qt5 directory. Don't forget to install the optional packages Qt Web Engine and Qt Script.

Wed, Aug 5, 8:51 PM · MITK
jmcuadra created T27652: CMake/mitkInstallRules.cmake set invalid install directory for QtWebEngine resources and translations in Linux.
Wed, Aug 5, 2:31 PM · MITK
kislinsk archived MICO.
Wed, Aug 5, 2:21 PM
kislinsk renamed MIC from MIA to MIC.
Wed, Aug 5, 2:21 PM
floca closed T27649: [Segmentation] How should tools listen to time changes as Resolved.
Wed, Aug 5, 11:57 AM · MITK (2020)