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Wed, Apr 28

kahl committed rMITKf0703a7a08e9: modify region growing 3D to work with low seed point value (authored by kahl).
modify region growing 3D to work with low seed point value
Wed, Apr 28, 12:06 PM
kahl committed rMITK068b2c265ba8: avoid underflows (authored by kahl).
avoid underflows
Wed, Apr 28, 12:06 PM
kahl committed rMITKa3ee5afa1b98: modify region growing 3D to work with low seed point value (authored by kahl).
modify region growing 3D to work with low seed point value
Wed, Apr 28, 12:06 PM
kahl closed T28437: 3D region growing may have issues when the seed point is on a pixel with value 0 as Resolved by committing rMITKa3ee5afa1b98: modify region growing 3D to work with low seed point value.
Wed, Apr 28, 12:06 PM · MITK (v2021.10)
schererj committed rKAAPANA15cac706b3a7: prediction without dataset.json fix (authored by schererj).
prediction without dataset.json fix
Wed, Apr 28, 11:33 AM
schererj committed rKAAPANA7cca4c336dfd: set use_nifti_encoding to false per default + mini improvements (authored by schererj).
set use_nifti_encoding to false per default + mini improvements
Wed, Apr 28, 10:49 AM
schererj committed rKAAPANAa888486cbdef: dice evaluation single plot export + DCMQI seg-filter bugfix (authored by schererj).
dice evaluation single plot export + DCMQI seg-filter bugfix
Wed, Apr 28, 10:37 AM

Tue, Apr 27

schererj committed rKAAPANA120c2d59b3fb: nnunet prediction label adaptions (authored by schererj).
nnunet prediction label adaptions
Tue, Apr 27, 10:21 PM
k656s committed rKAAPANAa3c108e27ce6: fixed color coding for OHIF viewer (authored by k656s).
fixed color coding for OHIF viewer
Tue, Apr 27, 4:36 PM
thomass closed T27067: ImageCropper cannot crop some images (4d?) as Resolved.

The task as such is resolved. Another task with open questions from D279 is created with T28466

Tue, Apr 27, 4:34 PM · MITK
thomass triaged T28466: [Image Cropper] Bounding shape cropper behavior not clear as Normal priority.
Tue, Apr 27, 4:32 PM · MITK
m564f committed rKAAPANA9856b0394e59: added fed chest-xray experiment (authored by m564f).
added fed chest-xray experiment
Tue, Apr 27, 4:03 PM
m564f committed rKAAPANA34ac713f9971: added general operators for fed learning (authored by m564f).
added general operators for fed learning
Tue, Apr 27, 4:03 PM
m564f committed rKAAPANA5c6d036a0576: removed depreciated operators (authored by m564f).
removed depreciated operators
Tue, Apr 27, 4:03 PM
schererj committed rKAAPANA76b72b904f0e: push (authored by schererj).
push
Tue, Apr 27, 4:02 PM
schererj committed rKAAPANA687a8dd7d7c5: bug-fixes train_network -> model (authored by schererj).
bug-fixes train_network -> model
Tue, Apr 27, 4:02 PM
schererj committed rKAAPANA547b94c5fcf1: before testing (authored by schererj).
before testing
Tue, Apr 27, 4:02 PM
schererj committed rKAAPANA4278e55343ad: progress (authored by schererj).
progress
Tue, Apr 27, 4:02 PM
m564f committed rKAAPANA9847c64da5e9: minor things & typos fixed (authored by m564f).
minor things & typos fixed
Tue, Apr 27, 3:31 PM
m564f committed rKAAPANAc528b7438f11: mnist exp added - major changes on dag, new process (authored by m564f).
mnist exp added - major changes on dag, new process
Tue, Apr 27, 3:31 PM
m564f committed rKAAPANAc6ecae067073: dag update to enable log-sharing with scheduler (authored by m564f).
dag update to enable log-sharing with scheduler
Tue, Apr 27, 10:00 AM
m564f committed rKAAPANA87c6b18d82d1: removed env-default from container script (authored by m564f).
removed env-default from container script
Tue, Apr 27, 10:00 AM
m564f committed rKAAPANA2cc5aeb8a6f3: added tb logging to training step (authored by m564f).
added tb logging to training step
Tue, Apr 27, 10:00 AM
m564f committed rKAAPANA3123cce577c7: print number of epochs (authored by m564f).
print number of epochs
Tue, Apr 27, 10:00 AM
m564f committed rKAAPANA48976cb1af94: minor fixes | parameter (i.e. epochs) via envs added (authored by m564f).
minor fixes | parameter (i.e. epochs) via envs added
Tue, Apr 27, 10:00 AM

Mon, Apr 26

eisenman moved T28465: Wrong numer of algorithms shown in report summary from In Progress to Done on the challengeR board.
Mon, Apr 26, 12:07 PM · challengeR
eisenman committed rCHALLENGERa60677ce9cb2: Merge branch 'feature/T28465-FixNumberOfAlgorithms' into develop (authored by eisenman).
Merge branch 'feature/T28465-FixNumberOfAlgorithms' into develop
Mon, Apr 26, 12:05 PM
eisenman committed rCHALLENGERd972cd37263d: Fix typo (authored by eisenman).
Fix typo
Mon, Apr 26, 12:01 PM
eisenman committed rCHALLENGERe03b3780a56c: Fix extraction of algorithm count (authored by eisenman).
Fix extraction of algorithm count
Mon, Apr 26, 12:01 PM
eisenman moved T28465: Wrong numer of algorithms shown in report summary from Backlog to In Progress on the challengeR board.
Mon, Apr 26, 11:50 AM · challengeR
eisenman triaged T28465: Wrong numer of algorithms shown in report summary as High priority.
Mon, Apr 26, 11:50 AM · challengeR
al-sabr added a comment to T27437: Migrate MITK to use ITK 5.x .

Fixed the task policy :D

Mon, Apr 26, 10:32 AM · MITK (v2021.10)
kislinsk edited the content of MITK v2021.02.
Mon, Apr 26, 9:52 AM
wiesenfa added a comment to T28453: [external] Error when all metric values are the same.

@eisenman the change in develop branch has not been uploaded to GitHub, is this not automatically synchronized?. So the user who reported the bug still has the same problem. It would be good to merge into master as well

Mon, Apr 26, 9:32 AM · challengeR
wiesenfa moved T28453: [external] Error when all metric values are the same from Done to In Progress on the challengeR board.
Mon, Apr 26, 9:29 AM · challengeR
kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Can this also be matched with this other task I created?

https://phabricator.mitk.org/T28454

I only need help in one place if that part is cleared then I already refactored the Core to reflect the changes suitable for version 3.6.0 of CppMicroServices.

Mon, Apr 26, 9:18 AM · MITK (v2021.10)

Sun, Apr 25

floca triaged T28464: [Segmentation] New Add/Remove tool as Normal priority.
Sun, Apr 25, 9:59 PM · Request for Discussion, MITK (v2021.10)

Fri, Apr 23

kalali moved T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe from Doing to Backlog on the MatchPoint board.
Fri, Apr 23, 2:50 PM · MatchPoint, Restricted Project
kalali moved T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Fri, Apr 23, 2:50 PM · MatchPoint, Restricted Project
kalali placed T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe up for grabs.

I will put this up for graps as it does not make sense to start a new project now. Personally I will investigate further after the Conan evaluation report has been written.

Fri, Apr 23, 2:50 PM · MatchPoint, Restricted Project
kalali added a comment to T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe.

One long term solution would also be to create an own Litmus Conan recipe and use this external Litmus package inside MatchPoint.

Fri, Apr 23, 1:24 PM · MatchPoint, Restricted Project
kalali added a comment to T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe.

I was trying to test if I can forward the ITK_USE_FILE variable inside the ExternalProject call to Litmus, as we did in the change for the CMAKE_PREFIX_PATH. I realized that neither the CMAKE_PREFIX_PATH nor the ITK_USE_FILE is correctly forwarded and accessible inside Litmus CMake configuration. I don't know what's going on here, I will investigate further.

Fri, Apr 23, 1:13 PM · MatchPoint, Restricted Project
wiesenfa added a comment to T28453: [external] Error when all metric values are the same.

now test case in test-report.R

Fri, Apr 23, 1:01 PM · challengeR
wiesenfa committed rCHALLENGER00085cd910f5: T28453 (authored by wiesenfa).
T28453
Fri, Apr 23, 1:00 PM
kalali moved T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe from Backlog to Doing on the MatchPoint board.
Fri, Apr 23, 12:08 PM · MatchPoint, Restricted Project
kalali moved T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Fri, Apr 23, 12:07 PM · MatchPoint, Restricted Project
kalali added a comment to T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe.

I started looking into this and some changes need to be made in order to get some errors out of the way:

  • Conan-center recipes are built without CMake find / config files, as mentioned here: In short: Conan creates own find / config files so they are removed from the original package.
Fri, Apr 23, 12:07 PM · MatchPoint, Restricted Project
eisenman added a comment to T28453: [external] Error when all metric values are the same.

Do you have a minimum example to reproduce this? Would be great to have that in the test checklists as well.

Fri, Apr 23, 11:40 AM · challengeR
kahl added a revision to T28437: 3D region growing may have issues when the seed point is on a pixel with value 0: Unknown Object (Differential Revision).
Fri, Apr 23, 10:26 AM · MITK (v2021.10)
kalali triaged T28462: [Conan] Build MatchPoint with ITK 5.1.0 recipe as Normal priority.
Fri, Apr 23, 10:20 AM · MatchPoint, Restricted Project
kahl added a comment to T28437: 3D region growing may have issues when the seed point is on a pixel with value 0.

Pushed new branch to rMITK MITK: bugfix/T28437-RegionGrowing3DSeedPoint0.

Fri, Apr 23, 10:02 AM · MITK (v2021.10)

Thu, Apr 22

wiesenfa added a comment to T28453: [external] Error when all metric values are the same.

very simple fix in rankingHeatmap.challenge
@eisenman can this be merged into master branch?

Thu, Apr 22, 10:30 PM · challengeR
wiesenfa moved T28453: [external] Error when all metric values are the same from In Progress to Done on the challengeR board.
Thu, Apr 22, 10:28 PM · challengeR
wiesenfa moved T28453: [external] Error when all metric values are the same from Backlog to In Progress on the challengeR board.
Thu, Apr 22, 10:27 PM · challengeR
wiesenfa committed rCHALLENGER6ceb955c61a3: Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into… (authored by wiesenfa).
Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into…
Thu, Apr 22, 10:27 PM
wiesenfa committed rCHALLENGER3f5ea60c7f28: hotfix T28453 (authored by wiesenfa).
hotfix T28453
Thu, Apr 22, 10:27 PM
floca added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

could you make an arc diff. Then it is easier to review and comment in code. Thanks.

Thu, Apr 22, 2:17 PM · Next Milestone, MITK (v2021.10)
thomass closed T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range as Resolved.

Could be solved by @kislinsk suggestion to change rendering mode to LOOKUPTABLE_COLOR to not envoke the levelwindow to overwrite the range

Thu, Apr 22, 1:30 PM · Request for Discussion, MITK
kalali moved T26989: [Checklist] GUI test data originates from different sources from Tests/Checklists to Cycle on the MITK (v2021.10) board.
Thu, Apr 22, 12:18 PM · MITK (v2021.10), Restricted Project
kalali raised the priority of T26989: [Checklist] GUI test data originates from different sources from Normal to High.

I set the priority to high because we defined that having appropriate data at a reachable location is one of the most pressing issues when it comes to manual GUI tests.

Thu, Apr 22, 12:11 PM · MITK (v2021.10), Restricted Project
kalali added a parent task for T26989: [Checklist] GUI test data originates from different sources: T26754: Review checklists.
Thu, Apr 22, 12:06 PM · MITK (v2021.10), Restricted Project
kalali added a subtask for T26754: Review checklists: T26989: [Checklist] GUI test data originates from different sources.
Thu, Apr 22, 12:06 PM · MITK (v2021.10), Restricted Project
kalali moved T26989: [Checklist] GUI test data originates from different sources from Backlog to Tests/Checklists on the MITK (v2021.10) board.
Thu, Apr 22, 12:06 PM · MITK (v2021.10), Restricted Project
kalali edited projects for T26989: [Checklist] GUI test data originates from different sources, added: MITK (v2021.10); removed Request for Discussion, MITK.
Thu, Apr 22, 12:06 PM · MITK (v2021.10), Restricted Project
kalali moved T26754: Review checklists from Backlog to Tests/Checklists on the MITK (v2021.10) board.
Thu, Apr 22, 12:05 PM · MITK (v2021.10), Restricted Project
kalali edited projects for T26754: Review checklists, added: MITK (v2021.10); removed Next Milestone.
Thu, Apr 22, 12:05 PM · MITK (v2021.10), Restricted Project
schererj committed rKAAPANA25d55af6dd00: dicom port fix for dicom-node-port change (authored by schererj).
dicom port fix for dicom-node-port change
Thu, Apr 22, 10:55 AM
thomass committed rRTTBed98724bd7ae: Added tests for value comparison (authored by thomass).
Added tests for value comparison
Thu, Apr 22, 10:52 AM
al-sabr added a comment to T27437: Migrate MITK to use ITK 5.x .

Can this also be matched with this other task I created?

Thu, Apr 22, 10:33 AM · MITK (v2021.10)
kleina committed rOBSHYPPOPY04b807b9d85f: Added .arcconfig (authored by kleina).
Added .arcconfig
Thu, Apr 22, 10:26 AM
kleina closed T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as Resolved by committing rOBSHYPPOPYace9c97f5ba3: Fixed MPISolverWrapper's direct call of blackbox internal.
Thu, Apr 22, 10:08 AM · Hyppopy
kleina committed rOBSHYPPOPYace9c97f5ba3: Fixed MPISolverWrapper's direct call of blackbox internal (authored by kleina).
Fixed MPISolverWrapper's direct call of blackbox internal
Thu, Apr 22, 10:08 AM
schererj reopened T28458: Airflow-App as "Open".
Thu, Apr 22, 9:33 AM · Kaapana (internal)
a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

Changes are pushed into the new branch T28353-cmake_faq branch.

Thu, Apr 22, 7:25 AM · Next Milestone, MITK (v2021.10)
a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

Pushed new branch to rMITK MITK: feature/T28354-cmake_faq.

Thu, Apr 22, 7:17 AM · Next Milestone, MITK (v2021.10)
schererj committed rKAAPANA53ac32b5d88e: sort labels (authored by schererj).
sort labels
Thu, Apr 22, 12:09 AM

Wed, Apr 21

kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Is this task finished or if not when is it planned?

Wed, Apr 21, 10:19 PM · MITK (v2021.10)
kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Pushed new branch to rMITK MITK: feature/T27437-ITK-v5.1.

Wed, Apr 21, 10:16 PM · MITK (v2021.10)
m139l closed T28458: Airflow-App as Resolved.
Wed, Apr 21, 7:53 PM · Kaapana (internal)
schererj committed rKAAPANA57931f14d590: DICOM port workaround (authored by schererj).
DICOM port workaround
Wed, Apr 21, 7:50 PM
floca moved T27189: REST API for data storage from Backlog to MaaS on the MITK (v2021.10) board.
Wed, Apr 21, 6:56 PM · MITK (v2021.10), Restricted Project, Request for Discussion
floca edited projects for T27189: REST API for data storage, added: MITK (v2021.10); removed MITK.
Wed, Apr 21, 6:56 PM · MITK (v2021.10), Restricted Project, Request for Discussion
kleina reopened T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as "Open".
Wed, Apr 21, 4:12 PM · Hyppopy
kleina committed rOBSHYPPOPY727320895a4e: Removed deprecated loss_function_batch_call (authored by kleina).
Removed deprecated loss_function_batch_call
Wed, Apr 21, 3:57 PM
kleina committed rOBSHYPPOPY543bba87253a: Make sure fallback only gets executed when batch_call fails. (authored by kleina).
Make sure fallback only gets executed when batch_call fails.
Wed, Apr 21, 3:33 PM
kleina closed T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as Resolved by committing rOBSHYPPOPYa2cfa7ce75ac: Fixed MPISolverWrapper's direct call of blackbox internal.
Wed, Apr 21, 3:33 PM · Hyppopy
kleina committed rOBSHYPPOPYa2cfa7ce75ac: Fixed MPISolverWrapper's direct call of blackbox internal (authored by kleina).
Fixed MPISolverWrapper's direct call of blackbox internal
Wed, Apr 21, 3:32 PM
kleina added a project to T28300: [MPI] MPI as a general dependency might be problematic: Request for Discussion.
Wed, Apr 21, 3:27 PM · Request for Discussion, Hyppopy
kleina moved T28376: Blackbox class - reorder the loss function call try from In Progress to Done on the Hyppopy board.
Wed, Apr 21, 3:25 PM · Hyppopy
kleina moved T28298: Check for all print outputs in code base and convert them to log messages from In Progress to Done on the Hyppopy board.
Wed, Apr 21, 3:25 PM · Hyppopy
kleina closed T28376: Blackbox class - reorder the loss function call try as Resolved by committing rOBSHYPPOPY5f8b57e426c0: Reordered the loss function call try..
Wed, Apr 21, 3:25 PM · Hyppopy
kleina committed rOBSHYPPOPY5f8b57e426c0: Reordered the loss function call try. (authored by kleina).
Reordered the loss function call try.
Wed, Apr 21, 3:25 PM
kleina added a revision to T28376: Blackbox class - reorder the loss function call try: Unknown Object (Differential Revision).
Wed, Apr 21, 1:21 PM · Hyppopy
kleina committed rOBSHYPPOPYe704bebf3217: Reordered the loss function call try. (authored by kleina).
Reordered the loss function call try.
Wed, Apr 21, 1:16 PM
kleina removed a project from T28376: Blackbox class - reorder the loss function call try: Request for Discussion.
Wed, Apr 21, 1:13 PM · Hyppopy
kleina moved T28410: MPISolverWrapper's direct call of blackbox internal seems wrong from In Progress to Done on the Hyppopy board.
Wed, Apr 21, 1:12 PM · Hyppopy
kleina added a revision to T28410: MPISolverWrapper's direct call of blackbox internal seems wrong: Unknown Object (Differential Revision).
Wed, Apr 21, 1:10 PM · Hyppopy
kleina committed rOBSHYPPOPY19e487728222: Converted "print" outputs to "log" outputs. (authored by kleina).
Converted "print" outputs to "log" outputs.
Wed, Apr 21, 1:01 PM
floca added a comment to T28376: Blackbox class - reorder the loss function call try.

Thanks

Wed, Apr 21, 12:19 PM · Hyppopy
kleina moved T28410: MPISolverWrapper's direct call of blackbox internal seems wrong from Done to In Progress on the Hyppopy board.
Wed, Apr 21, 12:18 PM · Hyppopy