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Sep 8 2020

goetzm added a comment to T27702: Create build-configuration for the MitkCLGlobalImageFeatures Miniapp (radiomics).

It really depends. I totally agree that it is not necessary for routine jobs, however it comes in really handy for controlling the data on remote locations were executing MITK is not possible/forbidden. That's why it had been build in.

Sep 8 2020, 9:31 AM · HiGHmed, Kaapana (internal), MITK
kislinsk claimed T27661: [Documentation] Update "How to create a new MITK Module".
Sep 8 2020, 9:25 AM · Cleared, MITK (v2021.02)
kislinsk claimed T27608: [MITKDoc] Documentation Refurbish - Developer Manual.
Sep 8 2020, 9:25 AM · MITK (v2024.06), Cleared
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

I think I fixed the OpenCV Ant issue by updating the volume snapshot for our Ubuntu 20.04 cloud instances to include the environment variable ANT_HOME=/usr/share/ant.

Sep 8 2020, 9:25 AM · CI, MITK (v2021.02), Restricted Project
kleina committed rOBSHYPPOPY2ffecdc1e877: If maximum iterations is reached, self.best contains Wrapped results. We now… (authored by kleina).
If maximum iterations is reached, self.best contains Wrapped results. We now…
Sep 8 2020, 4:29 AM

Sep 7 2020

kleina committed rOBSHYPPOPY1358b14d22f9: Merge branch 'T26755_mpi4hyppopy' of https://github.com/MIC-DKFZ/Hyppopy into… (authored by kleina).
Merge branch 'T26755_mpi4hyppopy' of https://github.com/MIC-DKFZ/Hyppopy into…
Sep 7 2020, 11:09 PM
kleina committed rOBSHYPPOPYea489f818b8b: Differentiate between "not implemented" and "not started via MPI". (authored by kleina).
Differentiate between "not implemented" and "not started via MPI".
Sep 7 2020, 11:09 PM
kleina committed rOBSHYPPOPY1b19f1049760: Handle errors if workers. If error occurs, we send np.nan to the master. (authored by kleina).
Handle errors if workers. If error occurs, we send np.nan to the master.
Sep 7 2020, 11:09 PM
kleina committed rOBSHYPPOPY7b1d6048c077: Code cleanup to improve readability. (authored by kleina).
Code cleanup to improve readability.
Sep 7 2020, 11:09 PM
floca added a revision to T27111: [MITKDoc] Revise Matchpoint Registration Visualizer Plugin Documentation: Unknown Object (Differential Revision).
Sep 7 2020, 10:08 PM · Cleared, MITK (v2021.02)
kleina removed a parent task for T26805: Make the MPI master work as well: Unknown Object (Maniphest Task).
Sep 7 2020, 9:52 PM · Hyppopy
wiesenfa moved T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise from Backlog to Done on the challengeR (v1.0) board.
Sep 7 2020, 7:06 PM · challengeR (v1.0)
wiesenfa added a comment to T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.

@eisenman I dont understand this task, could you give an example?

Sep 7 2020, 7:05 PM · challengeR (v1.0)
wiesenfa added a comment to T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise.

solved in T27338

Sep 7 2020, 7:03 PM · challengeR (v1.0)
wiesenfa created T27708: ggplot2 dendrogram .
Sep 7 2020, 7:01 PM · challengeR
wiesenfa added a comment to T27326: autolayout networks in multi task report ugly.

networks should be replaced by some ggplot2 implementation, see
https://journal.r-project.org/archive/2017/RJ-2017-023/RJ-2017-023.pdf

Sep 7 2020, 6:57 PM · challengeR
wiesenfa moved T27449: Consistent handling of plots created for multi-task data sets from In Progress to Done on the challengeR (v1.0) board.
Sep 7 2020, 6:55 PM · challengeR (v1.0)
wiesenfa added a comment to T27449: Consistent handling of plots created for multi-task data sets.

lists of ggplot objects can now be handled like single ggplot objects, e.g. boxbplot(...) + xlab(...) will apply xlab() to every ggplot object

Sep 7 2020, 6:54 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGERffd45a0c13bb: layouting of lists of ggplot objects (authored by wiesenfa).
layouting of lists of ggplot objects
Sep 7 2020, 6:49 PM
wiesenfa added a comment to T27447: significanceMap function raises warning about deprecated function call.

comes from significanceMap.data.frame

Sep 7 2020, 6:34 PM · challengeR (v1.0)
wiesenfa moved T27449: Consistent handling of plots created for multi-task data sets from Backlog to In Progress on the challengeR (v1.0) board.
Sep 7 2020, 6:21 PM · challengeR (v1.0)
wiesenfa added a comment to T27338: Report contains misleading information on missing values.

now as.challenge() as well as report contain extended information on missings and automatically inserted test cases.
@eisenman this changes the tests for as.challenge. Could you please 1. check whether the messages are well phrased and then 2. adapt tests, then 3. close task. Thanks!

Sep 7 2020, 2:40 PM · challengeR (v1.0)
wiesenfa moved T27338: Report contains misleading information on missing values from Backlog to In Progress on the challengeR (v1.0) board.
Sep 7 2020, 2:37 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGERc8b0952b6941: extend na.treat messages (authored by wiesenfa).
extend na.treat messages
Sep 7 2020, 2:37 PM
wiesenfa created T27707: na.treat obligatory for report .
Sep 7 2020, 2:24 PM · challengeR (v1.0)
floca committed rMITKe269e5930aef: T27113 - Revised documentation of MatchPoint Manipulator (authored by floca).
T27113 - Revised documentation of MatchPoint Manipulator
Sep 7 2020, 12:44 PM
floca committed rMITK921ed6752145: Revised documentation of MatchPoint Manipulator (authored by floca).
Revised documentation of MatchPoint Manipulator
Sep 7 2020, 12:44 PM
floca committed rMITK5c25fa6386a2: Fixed review comments (authored by floca).
Fixed review comments
Sep 7 2020, 12:44 PM
floca closed T27113: [MITKDoc] Revise Matchpoint Registration Manipulator Plugin Documentation as Resolved by committing rMITK921ed6752145: Revised documentation of MatchPoint Manipulator.
Sep 7 2020, 12:44 PM · Cleared, MITK (v2021.02)
floca claimed T27655: [statistics] Logic of DataGeneratorBase blocks the UI thread .

I have checked with a prototyp to just move also the core of the generator to an own thread. It helps to make the UI more responsive. BUT it is not enough because the UI (workbench) thread and all other threads must kept seperated, using Qt mechanisms, we need to use a lot of signal/slot and this seems to keep the UI thread (event loop) very bussy.

Sep 7 2020, 12:05 PM · MITK (v2024.06)
kislinsk committed rMITKac0bf7f5dce1: Merge branch 'bugfix/T25882-RewriteDashboardScript' into develop (authored by kislinsk).
Merge branch 'bugfix/T25882-RewriteDashboardScript' into develop
Sep 7 2020, 11:11 AM

Sep 5 2020

kislinsk committed rMITK94c50addf1ed: Merge branch 'bugfix/T25882-RewriteDashboardScript' into develop (authored by kislinsk).
Merge branch 'bugfix/T25882-RewriteDashboardScript' into develop
Sep 5 2020, 10:17 PM
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Pushed new branch bugfix/T25882-RewriteDashboardScript.

Sep 5 2020, 8:21 AM · CI, MITK (v2021.02), Restricted Project
kislinsk added a comment to T25882: Rewrite dashboard script for CDash 2.6.

Deleted branch bugfix/T25882-RewriteDashboardScript.

Sep 5 2020, 8:10 AM · CI, MITK (v2021.02), Restricted Project

Sep 4 2020

thomass committed rMITK0ec8c07ca152: T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems (authored by thomass).
T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems
Sep 4 2020, 8:58 PM
thomass closed T27691: [MITKDoc] Documentation links reference "The Phenotyping" subpages as Resolved by committing rMITK0ec8c07ca152: T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems.
Sep 4 2020, 8:58 PM · MITK (v2021.02)
floca added a comment to T27702: Create build-configuration for the MitkCLGlobalImageFeatures Miniapp (radiomics).

@goetzm Does the GIF mini app realy need the screenshot feature within the app (there is also a CLScreenshot app)?
Reason for the question is, that this feature is the only reason why Qt becomes dragged into the app and it bloats the container/deployment. Just wanted to now if we can the keep the configuration as slim as possible.

Sep 4 2020, 5:30 PM · HiGHmed, Kaapana (internal), MITK
floca added projects to T27702: Create build-configuration for the MitkCLGlobalImageFeatures Miniapp (radiomics): Kaapana (internal), HiGHmed.
Sep 4 2020, 5:25 PM · HiGHmed, Kaapana (internal), MITK
floca claimed T27702: Create build-configuration for the MitkCLGlobalImageFeatures Miniapp (radiomics).

@schererj Do you mean the XML result export?

Sep 4 2020, 5:24 PM · HiGHmed, Kaapana (internal), MITK
floca moved T27569: US DICOM images are displayed turquoise and LUT cannot be changed from Backlog to MITK Meeting on the Request for Discussion board.
Sep 4 2020, 4:25 PM · Restricted Project, MITK
kislinsk added a comment to T27571: Multilabel segmentation does not work with US DICOM images.

Yes, they are in the workspace of the Nightlies but I hesitate to provide them externally as they have a bunch of problems. Besides the DICOM-loading problem that we currently have with the installers in general, the macOS MITK Workbench from the installer is not executable by clicking on the MitkWorkbench.app. One have to use the terminal, cd into the package and execute the actual MitkWorkbench executable.

Sep 4 2020, 3:46 PM · MITK (v2021.10), Missing Info, Restricted Project
neher triaged T27706: Refactor kaapana radiomics workflow to output xml files as Normal priority.
Sep 4 2020, 3:21 PM · Kaapana (internal)
wiesenfa committed rCHALLENGER24782c58e8e3: fix column names (authored by wiesenfa).
fix column names
Sep 4 2020, 2:38 PM
wiesenfa added a comment to T27385: Variables holding the aggregated value are named differently for single- and multi-task challenges.

now
e.g. if FUN="mean" (i.e. a character) or if FUN=mean (i.e. a function)
the column name will be "value_mean"

Sep 4 2020, 2:32 PM · challengeR (v1.0)
wiesenfa moved T27385: Variables holding the aggregated value are named differently for single- and multi-task challenges from Backlog to In Progress on the challengeR (v1.0) board.
Sep 4 2020, 2:10 PM · challengeR (v1.0)
kompan committed rMITK99efaa26c3c8: Revise and update the concentration curve converter view documentation. (authored by kompan).
Revise and update the concentration curve converter view documentation.
Sep 4 2020, 2:01 PM
kompan committed rMITK4c8fc13639d6: Add section on T2-weighted conversion. (authored by kompan).
Add section on T2-weighted conversion.
Sep 4 2020, 2:00 PM
kompan committed rMITK4a0a481d9b94: Minor corrections in overview and T1-weighted conversion. (authored by kompan).
Minor corrections in overview and T1-weighted conversion.
Sep 4 2020, 2:00 PM
kompan committed rMITKe339686ff18f: Update name to DCE Concentration Curve Converter View. (authored by kompan).
Update name to DCE Concentration Curve Converter View.
Sep 4 2020, 2:00 PM
kompan committed rMITK232f5fe6efb7: Change page and view id name to org_mitk_views_pharmacokinetics_concentration_m… (authored by kompan).
Change page and view id name to org_mitk_views_pharmacokinetics_concentration_m…
Sep 4 2020, 2:00 PM
kompan committed rMITK43c24165bdac: Update Overview. (authored by kompan).
Update Overview.
Sep 4 2020, 2:00 PM
kompan committed rMITK5bfc7a8c7f5d: Add section "Conversion of T1-weighted MRI data". (authored by kompan).
Add section "Conversion of T1-weighted MRI data".
Sep 4 2020, 2:00 PM
kompan committed rMITK6b5d90116419: Update Contact information. (authored by kompan).
Update Contact information.
Sep 4 2020, 2:00 PM
floca added a comment to T27570: US DICOM images are read as 3D volume.

If looked a bit closer. The time information is encoded in Tags of the MultiFrame and the CINE module.

Sep 4 2020, 1:55 PM · Auto-closed, Missing Info, Restricted Project, MITK
floca added a comment to T27568: US 2D image cannot be read: invalid tilt information.

Remark regarding option 4:

Sep 4 2020, 12:56 PM · Restricted Project, MITK
floca added a project to T27569: US DICOM images are displayed turquoise and LUT cannot be changed: Request for Discussion.

@kleesiek thanks for the reminder after summer break.

Sep 4 2020, 12:53 PM · Restricted Project, MITK
floca added a comment to T27571: Multilabel segmentation does not work with US DICOM images.

@kislinsk can we currently produce MacOS Installer via CI? This would be the easiest way to provide a current installer for jens to test.

Sep 4 2020, 12:42 PM · MITK (v2021.10), Missing Info, Restricted Project
floca added a comment to T27570: US DICOM images are read as 3D volume.
  • data is taken as is (see also comment to T27568)
  • I'd say the probably correct description would be 2D-Realtime B-Mode where images are made at a constant frame rate (20 fps in the case of the Canon video). If you consider moving the transducer over the body it not necessarily results in a 3D image, more 2D+t - if you keep the transducer at a fixed spot and e.g. only tilt the tranducer, it is more 3D like.
  • I am not aware that there are sensors in the transducer that would give us its position and orientation in space

Yes you are right. I thought to much in the lines of CAMIs work.

Sep 4 2020, 12:34 PM · Auto-closed, Missing Info, Restricted Project, MITK
wiesenfa added a comment to T27252: Multiple cases per algorithm are not detected when missing data was added before.

@eisenman error message might have changed, please check tests

Sep 4 2020, 12:30 PM · challengeR (v1.0)
wiesenfa reassigned T27658: LaTeX Warning: There were undefined references from wiesenfa to eisenman.
Sep 4 2020, 12:22 PM · challengeR (v1.0)
wiesenfa added a comment to T27658: LaTeX Warning: There were undefined references.

@eisenman seems to come from "Blob plot similar to the one shown in Section \ref{blobByTask}" in visualizationAcrossTasks.Rmd. Could you please take care of it, you are more familiar with the restructured report

Sep 4 2020, 12:21 PM · challengeR (v1.0)
eisenman added a member for IMSY: wiesenfa.
Sep 4 2020, 12:10 PM
wiesenfa claimed T27658: LaTeX Warning: There were undefined references.
Sep 4 2020, 12:00 PM · challengeR (v1.0)
wiesenfa claimed T27385: Variables holding the aggregated value are named differently for single- and multi-task challenges.
Sep 4 2020, 12:00 PM · challengeR (v1.0)
kalali closed T27674: [Selection widgets] Enabling auto selection emits a signal that might not yet be connected as Resolved.

Closed with changes of D398 as discussed: Remark for developers.

Sep 4 2020, 11:15 AM · Cleared, MITK
kalali committed rMITKe33c81988106: Provide developer remark for auto selection mode (authored by kalali).
Provide developer remark for auto selection mode
Sep 4 2020, 11:14 AM
kalali committed rMITKccc798c6f898: Add remark on how to use the auto selection mode (authored by kalali).
Add remark on how to use the auto selection mode
Sep 4 2020, 11:14 AM
kalali committed rMITKba371719c114: Modify remark on how to use the auto selection mode (authored by kalali).
Modify remark on how to use the auto selection mode
Sep 4 2020, 11:14 AM
kalali added a comment to T27184: Clipping plane deformation tool doesn't show updates in 3d window.

I couldn't identify any differences between the latest develop branch and my installed MITK v2018.04.2.

Sep 4 2020, 11:10 AM · Next Milestone, MITK, Missing Info, Restricted Project
floca added a project to T27184: Clipping plane deformation tool doesn't show updates in 3d window: Missing Info.
Sep 4 2020, 10:53 AM · Next Milestone, MITK, Missing Info, Restricted Project
kalali added a comment to T27184: Clipping plane deformation tool doesn't show updates in 3d window.

Do you know when it worked the last time? What do you want to rewrite - I don't see any reference to the 3D window.

Sep 4 2020, 9:41 AM · Next Milestone, MITK, Missing Info, Restricted Project

Sep 3 2020

kislinsk added a comment to T27569: US DICOM images are displayed turquoise and LUT cannot be changed.

The Photometric Interpretation tag (0028,0004) of the Philips US image is set to YBR_FULL_422 and my first guess is that we do not take this tag fully into account, leading to a misinterpetation as RGB values while reading the data.

Sep 3 2020, 11:39 PM · Restricted Project, MITK
kislinsk added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

@kislinsk As a linux noob please pardon my question. Can we directly debug the nightly bild by the CI on e.g. Jonas system? I would like to see some of the parts of volume generation process running to see whats happening. My be it helps us getting a lead. At least we now a setup directly on site that makes the problems.

Sep 3 2020, 10:48 PM · Missing Info, DICOM, MITK
kalali awarded T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation a Cup of Joe token.
Sep 3 2020, 10:21 PM · MITK (v2021.10), Missing Info, Restricted Project
floca closed T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation as Resolved.

Closed as all sub tasks relevent for MITK2020 are checked and corrected.

Sep 3 2020, 9:20 PM · MITK (v2021.10), Missing Info, Restricted Project
floca committed rMITK22644d61abfd: Fixed T27641 - Refactored watershed tool for correct handling of dynamic… (authored by floca).
Fixed T27641 - Refactored watershed tool for correct handling of dynamic…
Sep 3 2020, 9:16 PM
floca committed rMITKd1cb157710f9: Workarround for T27703 to avoid problematic threshold values that (authored by floca).
Workarround for T27703 to avoid problematic threshold values that
Sep 3 2020, 9:16 PM
floca committed rMITK3250199d314b: Improve robustness of base class if derived classes cannot produce an ML… (authored by floca).
Improve robustness of base class if derived classes cannot produce an ML…
Sep 3 2020, 9:16 PM
floca committed rMITKf8f833cb5916: Changed default settings for Watershed tool (authored by floca).
Changed default settings for Watershed tool
Sep 3 2020, 9:16 PM
floca committed rMITK2e6b9c514b32: Reworked watershed tool. (authored by floca).
Reworked watershed tool.
Sep 3 2020, 9:16 PM
floca committed rMITK7a61414d4497: Improved UI sizes (authored by floca).
Improved UI sizes
Sep 3 2020, 9:16 PM
floca committed rMITK9df1d1b36b3a: Ensured that preview nodes cannot be selected as segmentation input. (authored by floca).
Ensured that preview nodes cannot be selected as segmentation input.
Sep 3 2020, 9:16 PM
floca committed rMITK4fb6097092e9: Refactor Otsu tool and GUI to use AutoMLSegmentationWithPreviewTool and… (authored by floca).
Refactor Otsu tool and GUI to use AutoMLSegmentationWithPreviewTool and…
Sep 3 2020, 9:16 PM
floca closed T27641: [Segmentation] Watershed does always generate a 3D static seg. Even if dynamic segmentation was generated. as Resolved by committing rMITK2e6b9c514b32: Reworked watershed tool..
Sep 3 2020, 9:16 PM · Cleared, MITK (v2021.02)
floca closed T27641: [Segmentation] Watershed does always generate a 3D static seg. Even if dynamic segmentation was generated., a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Resolved.
Sep 3 2020, 9:16 PM · MITK (v2021.10), Missing Info, Restricted Project
floca committed rMITK0793a56eac3d: Added SimpleLabelSetListWidget (authored by floca).
Added SimpleLabelSetListWidget
Sep 3 2020, 9:16 PM
floca committed rMITK490026873248: Added AutoMLSegmentationWithPreviewTool (authored by floca).
Added AutoMLSegmentationWithPreviewTool
Sep 3 2020, 9:16 PM
floca committed rMITKb22b6a152b41: Removed wrong tooltip hint (authored by floca).
Removed wrong tooltip hint
Sep 3 2020, 9:16 PM
floca created T27704: HyppopySolver: Setting default values unused #2.
Sep 3 2020, 8:55 PM · Hyppopy
floca added a comment to T27093: [MITKDoc] Revise Segmentation Plugin.

Another addition for the documentation:

Sep 3 2020, 6:24 PM · MITK (v2021.02)
floca lowered the priority of T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen from Normal to Low.

It is rooted in an known unfixed error in itk: https://discourse.itk.org/t/crash-in-watershedimagefilter/2428

Sep 3 2020, 6:01 PM · MITK
floca renamed T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen from [Segmentation] Watershed segmentation crashes on 4D images when high threshold is chosen to [Segmentation] Watershed segmentation crashes on images when high threshold is chosen.
Sep 3 2020, 5:22 PM · MITK
thomass updated the task description for T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen.
Sep 3 2020, 5:05 PM · MITK
thomass triaged T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen as Normal priority.
Sep 3 2020, 5:03 PM · MITK
kleesiek added a comment to T27569: US DICOM images are displayed turquoise and LUT cannot be changed.

Any update on this issue?

Sep 3 2020, 4:26 PM · Restricted Project, MITK
floca added a revision to T27113: [MITKDoc] Revise Matchpoint Registration Manipulator Plugin Documentation: Unknown Object (Differential Revision).
Sep 3 2020, 3:54 PM · Cleared, MITK (v2021.02)
thomass updated subscribers of T27184: Clipping plane deformation tool doesn't show updates in 3d window.

@kislinsk @kalali I have in mind that you recently had a look at the ClippingPlane. Since the clipping plane does not show the expected behavior, does it make sense to rewrite the documentation for it? I have in mind you even considered to declare it deprecated.

Sep 3 2020, 3:47 PM · Next Milestone, MITK, Missing Info, Restricted Project
gaoh closed T27683: Dockerized MITK ubuntu 18.04 on current Master rMITKf0e722f6a65d3aba98d674120683260564ce8db0 as Resolved.
Sep 3 2020, 2:09 PM · MITK
kalali added a revision to T27674: [Selection widgets] Enabling auto selection emits a signal that might not yet be connected: Restricted Differential Revision.
Sep 3 2020, 2:02 PM · Cleared, MITK
gaoh closed T27101: [MITKDoc] Revise Logging Plugin Documentation as Resolved.
Sep 3 2020, 12:48 PM · Cleared, MITK (v2021.02)