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Jul 5 2019

kislinsk committed rMITK2a918091f567: Merge branch 'T26107-MoveMITKDiffusionToSeparateRepo' (authored by kislinsk).
Merge branch 'T26107-MoveMITKDiffusionToSeparateRepo'
Jul 5 2019, 12:46 PM
kislinsk committed rMITKDIFF7a7182482bee: Clarify licensing (authored by kislinsk).
Clarify licensing
Jul 5 2019, 12:15 PM
kislinsk committed rMITKDIFF03fd22d4c461: Move BetData to separate repository (authored by kislinsk).
Move BetData to separate repository
Jul 5 2019, 11:53 AM
kislinsk committed rMITK485aee32c46b: Move BetData to MITK Diffusion repository (authored by kislinsk).
Move BetData to MITK Diffusion repository
Jul 5 2019, 11:51 AM
kislinsk committed rMITKDIFF6b86b864edf4: Move MITK Diffusion to separate repository (authored by kislinsk).
Move MITK Diffusion to separate repository
Jul 5 2019, 10:59 AM
kislinsk committed rMITK427fb8a68c7d: Move MITK Diffusion to separate repository (authored by kislinsk).
Move MITK Diffusion to separate repository
Jul 5 2019, 10:55 AM
kislinsk added a comment to T26107: Move MITK Diffusion to external repository.

Pushed new branch T26107-MoveMITKDiffusionToSeparateRepo.

Jul 5 2019, 10:55 AM · MITK
kislinsk deleted Guide for DKFZ-internal setup of Git and Phabricator (obsolete, see Onboarding guide).
Jul 5 2019, 10:28 AM
jungsi moved T23742: Implement proof of concept for new segmentation data type from Backlog to MITK Meeting on the Request for Discussion board.
Jul 5 2019, 10:16 AM · MITK
jungsi added a project to T23742: Implement proof of concept for new segmentation data type: Request for Discussion.

Regarding the segmentation data type the PolySeg project should be kept in mind as it offers flexibility in the representation of the segments.
They also define a segmentation and a segment class although neither of them directy "is" the data. A segment keeps a list of representations (i.e. vtkDataObjects in their case) that actually hold the image / surface / contour data.
Making the segment directy inherit from Image creates a strong bond to the representation as labelmask (binary or fractional) but leaves out representation of contours and surfaces for example.
In this regard one proposal would roughly follow this class layout:

SegmentationModuleDraft.png (2×4 px, 605 KB)

Here one segment could be represented as one label (or as contours, a surface, etc.).
In the case of a labelmap it would make sense to hold a binary image or as Stefan mentioned uint16 or unsigned short for fractional labels.

Jul 5 2019, 10:16 AM · MITK
neher added a parent task for T26456: Update ITK to v5: T26413: Nifti2 support.
Jul 5 2019, 9:52 AM · MITK
neher added a subtask for T26413: Nifti2 support: T26456: Update ITK to v5.
Jul 5 2019, 9:52 AM · Auto-closed, Missing Info, MITK
neher triaged T26456: Update ITK to v5 as Wishlist priority.
Jul 5 2019, 9:50 AM · MITK
neher committed rMITKd564020d71f0: Merge branch 'T26413-Nifti2-Diffusion' (authored by neher).
Merge branch 'T26413-Nifti2-Diffusion'
Jul 5 2019, 9:37 AM
neher committed rMITKd7a8439bf9f8: Nifti2-support for diffusion-weighted images (authored by neher).
Nifti2-support for diffusion-weighted images
Jul 5 2019, 9:18 AM
neher added a comment to T26413: Nifti2 support.

Pushed new branch T26413-Nifti2-Diffusion.

Jul 5 2019, 9:17 AM · Auto-closed, Missing Info, MITK
neher closed T25424: Since cmake 3.12 FindPythonLibs is deprecated as Resolved.
Jul 5 2019, 8:29 AM · MITK

Jul 4 2019

kalali committed rMITK8761d5db7396: Fix wrong comparison detected by updated tests (authored by kalali).
Fix wrong comparison detected by updated tests
Jul 4 2019, 3:49 PM
kalali committed rMITK9390484ec16d: Update semantic relations tests (authored by kalali).
Update semantic relations tests
Jul 4 2019, 3:49 PM
kislinsk updated the task description for T26451: DICOM plugin cannot parse DICOM directories in macOS installer.
Jul 4 2019, 12:23 PM · MITK
k656s updated the task description for T26445: Think about more similarity measures based on the data.
Jul 4 2019, 11:10 AM · NLP
neher committed rMITKdb2f41beadc2: Switch to new FindPython3 cmake command (authored by neher).
Switch to new FindPython3 cmake command
Jul 4 2019, 10:58 AM
neher committed rMITKbecf6c7ab7d3: Only quote non-lists (authored by neher).
Only quote non-lists
Jul 4 2019, 10:53 AM
neher committed rMITK86626082b70e: More refactoring (authored by neher).
More refactoring
Jul 4 2019, 10:53 AM
neher committed rMITK51f5c76945d2: Refactoring (authored by neher).
Refactoring
Jul 4 2019, 10:53 AM
zimmerer committed rVAEd270345f3d05: Remve ignored stuff (authored by zimmerer).
Remve ignored stuff
Jul 4 2019, 10:30 AM
zimmerer committed rVAEedab5413a1eb: Add license and gitignore (authored by zimmerer).
Add license and gitignore
Jul 4 2019, 10:29 AM
zimmerer committed rVAE568642a520a2: Inital commit (authored by zimmerer).
Inital commit
Jul 4 2019, 10:24 AM
kislinsk committed rMITK0bd410d13c51: Prevent Arcanist from squashing commits (authored by kislinsk).
Prevent Arcanist from squashing commits
Jul 4 2019, 10:02 AM
kislinsk committed rMITKb66d51c77fee: Merge branch 'T26453-CMakeGeneratorPlatform' (authored by kislinsk).
Merge branch 'T26453-CMakeGeneratorPlatform'
Jul 4 2019, 9:19 AM
kislinsk closed T26453: Pass generator platform to CMake in CTest script as Resolved.
Jul 4 2019, 9:19 AM · MITK
kislinsk committed rMITKc99e60d33ba4: Utilize CTEST_CMAKE_GENERATOR_PLATFORM (authored by kislinsk).
Utilize CTEST_CMAKE_GENERATOR_PLATFORM
Jul 4 2019, 9:18 AM
kislinsk added a comment to T26453: Pass generator platform to CMake in CTest script.

Pushed new branch T26453-CMakeGeneratorPlatform.

Jul 4 2019, 9:18 AM · MITK
kislinsk triaged T26453: Pass generator platform to CMake in CTest script as High priority.
Jul 4 2019, 9:17 AM · MITK
kalali added a comment to T26452: Do not squash commits on arc land.

If we think about establishing a new Git Workflow, we might rethink this. It might be useful to have some mainline that only consists of squashed commits so each feature is represented by a single entry. However, the current scenario does neither force one or the other way to do it so we have both merge- and squash commits which makes it a bit arbitrary, in my opinion.

Jul 4 2019, 9:12 AM · MITK
kislinsk closed T26452: Do not squash commits on arc land as Resolved.

merge --no-ff is now the default of arc land. It's equal to using arc land --merge.

Jul 4 2019, 9:12 AM · MITK
kislinsk committed rMITK5251def0b26b: Merge branch 'T26452-DoNotSquash' (authored by kislinsk).
Merge branch 'T26452-DoNotSquash'
Jul 4 2019, 9:11 AM
kislinsk committed rMITK1252396c77cf: Prevent Arcanist from squashing commits (authored by kislinsk).
Prevent Arcanist from squashing commits
Jul 4 2019, 9:10 AM
kislinsk added a comment to T26452: Do not squash commits on arc land.

Pushed new branch T26452-DoNotSquash.

Jul 4 2019, 9:10 AM · MITK
kislinsk triaged T26452: Do not squash commits on arc land as Wishlist priority.
Jul 4 2019, 9:09 AM · MITK
kislinsk added a comment to T26427: Support software rendering.

Built Mesa. Same result. Mesa keeps reporting OpenGL 3.1 with GLSL 1.40. If we figure out how to squeeze the correct OpenGL context out of Mesa, it could be the breakthough.

Jul 4 2019, 8:58 AM · Auto-closed, MITK
kislinsk triaged T26451: DICOM plugin cannot parse DICOM directories in macOS installer as High priority.
Jul 4 2019, 8:55 AM · MITK
neher added a revision to T25424: Since cmake 3.12 FindPythonLibs is deprecated: Unknown Object (Differential Revision).
Jul 4 2019, 7:25 AM · MITK

Jul 3 2019

kalali committed rMITK73ab74b2fe4a: Merge branch 'T22946-Integration-beta' (authored by kalali).
Merge branch 'T22946-Integration-beta'
Jul 3 2019, 6:19 PM
kalali committed rMITK7b8a070d83ed: retrieve all lesions / lesion classes in lesion manager (authored by kalali).
retrieve all lesions / lesion classes in lesion manager
Jul 3 2019, 6:18 PM
kalali committed rMITK7c18fa5700fa: Fix gcc error (authored by kalali).
Fix gcc error
Jul 3 2019, 6:18 PM
kalali committed rMITKcc5df6670268: Merge branch 'T22946-Integration-beta' (authored by kalali).
Merge branch 'T22946-Integration-beta'
Jul 3 2019, 3:22 PM
kalali committed rMITKc232939c3988: Fixed unused for-loop (authored by kalali).
Fixed unused for-loop
Jul 3 2019, 3:20 PM
kleina closed T26449: XNAT connection failes due to missing OpenSSL connections as Resolved.

Here are the DLLs we used for the BlackSwan demo.

Jul 3 2019, 3:10 PM · Noteworthy, MITK (v2021.02)
kleina added a comment to T26449: XNAT connection failes due to missing OpenSSL connections.

This issue can be solved by copying the following DLLs to the exe path of the workbench:

Jul 3 2019, 3:08 PM · Noteworthy, MITK (v2021.02)
kleina triaged T26449: XNAT connection failes due to missing OpenSSL connections as Normal priority.
Jul 3 2019, 3:06 PM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T26427: Support software rendering.

According to https://mesamatrix.net/, Mesa (llvmpipe) should be able to 100% support OpenGL 3.3 with GLSL 3.30 and hence OpenGL 3.2 with GLSL 1.50. Next test: build Mesa by myself.

Jul 3 2019, 10:49 AM · Auto-closed, MITK
kislinsk added a comment to T26427: Support software rendering.

I did the same for the Qt contextinfo example. When creating a 2.1 context Mesa is reporting:

Jul 3 2019, 10:45 AM · Auto-closed, MITK
kislinsk added a comment to T26427: Support software rendering.

Wrote my own minimal Qt application with QVTKOpenGLNativeWidget and it basially has the same problems.

Jul 3 2019, 10:34 AM · Auto-closed, MITK
kalali committed rMITKe5f32e0218b2: Merge branch 'T22946-Integration-beta' (authored by kalali).
Merge branch 'T22946-Integration-beta'
Jul 3 2019, 10:05 AM
kalali committed rMITKe4798362440a: Fix unused parameter (authored by kalali).
Fix unused parameter
Jul 3 2019, 10:03 AM
neher committed rMITKa91697ff6450: replace backslash by slash (authored by neher).
replace backslash by slash
Jul 3 2019, 8:45 AM

Jul 2 2019

kalali committed rMITK82f6c4117fbd: Merge branch 'T22946-Integration-beta' (authored by kalali).
Merge branch 'T22946-Integration-beta'
Jul 2 2019, 3:49 PM
thomass added a project to T26388: Colorcoding for surfaces does not work correctly: Restricted Project.
Jul 2 2019, 2:24 PM · Restricted Project, MITK
nolden added a comment to T25535: DCMTK won't build if Anaconda is installed.

Sorry for jumping in late. I'm afraid currently we are anyway not testing any encoding stuff sufficiently.

Jul 2 2019, 2:24 PM · Auto-closed, MITK
kalali moved T26381: QmitkDataStorageComboBox does not react on DICOM node changes from Backlog to MITK Meeting on the Request for Discussion board.
Jul 2 2019, 2:23 PM · Restricted Project, MITK
thomass moved T26388: Colorcoding for surfaces does not work correctly from Backlog to MITK Meeting on the Request for Discussion board.
Jul 2 2019, 2:22 PM · Restricted Project, MITK
nolden committed rMITK5ad6bccb0282: Use a more recent version of ITK for GCC 9 compatibility (authored by nolden).
Use a more recent version of ITK for GCC 9 compatibility
Jul 2 2019, 2:03 PM
kalali closed T25176: Using "Show only selected nodes" from the data manager context menu hides helper nodes, a subtask of T25056: Refactor data manager context menu, as Resolved.
Jul 2 2019, 12:01 PM · Moved to git.dkfz.de, MITK (v2024.12), Noteworthy
kalali closed T25176: Using "Show only selected nodes" from the data manager context menu hides helper nodes as Resolved.

Was resolved with T19683.

Jul 2 2019, 12:01 PM · Restricted Project, MITK
kalali updated subscribers of T26438: DCMTK disable ICU.

Please check this: T25535
@kislinsk: What changed your mind?

Jul 2 2019, 11:55 AM · MITK
neher committed rMITK61477b30242e: Switch to new FindPython3 cmake command (authored by neher).
Switch to new FindPython3 cmake command
Jul 2 2019, 11:32 AM
neher added a comment to T25424: Since cmake 3.12 FindPythonLibs is deprecated.

Pushed new branch T25424-FindPython3New.

Jul 2 2019, 11:31 AM · MITK
neher closed T26438: DCMTK disable ICU as Resolved.
Jul 2 2019, 11:19 AM · MITK
k656s triaged T26447: Create pipeline for experiment execution form json file as Normal priority.
Jul 2 2019, 10:56 AM · NLP
k656s triaged T26446: Implement training and fine-tuning of different embeddings as Normal priority.
Jul 2 2019, 10:55 AM · NLP
k656s triaged T26445: Think about more similarity measures based on the data as Normal priority.
Jul 2 2019, 10:54 AM · NLP
k656s triaged T26444: Implement more similarity measures as Normal priority.
Jul 2 2019, 10:54 AM · NLP
k656s created T26442: Implement preprocessing methods.
Jul 2 2019, 10:53 AM · NLP
k656s moved T26441: Detailed evaluation log of experiment from Backlog to In Progress on the NLP board.
Jul 2 2019, 10:52 AM · NLP
k656s created T26441: Detailed evaluation log of experiment.
Jul 2 2019, 10:52 AM · NLP
k656s triaged T26439: Extending embeddings.py with gensen and skipthought as Low priority.
Jul 2 2019, 10:51 AM · NLP
k656s triaged T26440: Including medical dictionaries in preprocessing as Normal priority.
Jul 2 2019, 10:51 AM · NLP
k656s created T26439: Extending embeddings.py with gensen and skipthought.
Jul 2 2019, 10:50 AM · NLP
kislinsk reopened T26431: Fix gcc 9 and clang 8 compilation as "Open".
Jul 2 2019, 9:07 AM · MITK

Jul 1 2019

nolden added a revision to T26431: Fix gcc 9 and clang 8 compilation: Unknown Object (Differential Revision).
Jul 1 2019, 5:26 PM · MITK
neher closed T25033: Python console colors do not work with dark theme as Resolved.
Jul 1 2019, 2:40 PM · Restricted Project, MITK
neher committed rMITKc69e992d6fa2: Disabling ICU (authored by neher).
Disabling ICU
Jul 1 2019, 2:35 PM
neher added a revision to T26438: DCMTK disable ICU: Unknown Object (Differential Revision).
Jul 1 2019, 2:20 PM · MITK
neher committed rMITKde9ca312c5b8: Disabling ICU (authored by neher).
Disabling ICU
Jul 1 2019, 2:18 PM
neher added a comment to T26438: DCMTK disable ICU.

Pushed new branch T26438-DisableIcu.

Jul 1 2019, 2:18 PM · MITK
neher triaged T26438: DCMTK disable ICU as High priority.
Jul 1 2019, 2:16 PM · MITK
kislinsk closed T26437: Increase minimum required version of CMake to 3.14 as Resolved.
Jul 1 2019, 2:03 PM · MITK
kislinsk committed rMITKe00069aecd44: Merge branch 'T26437-CMake-3.14' (authored by kislinsk).
Merge branch 'T26437-CMake-3.14'
Jul 1 2019, 12:50 PM
kislinsk committed rMITK2a1a4685922c: Remove CTEST_CMAKE_GENERATOR_PLATFORM (authored by kislinsk).
Remove CTEST_CMAKE_GENERATOR_PLATFORM
Jul 1 2019, 12:50 PM
kislinsk committed rMITK7172da308e72: Merge branch 'T26437-CMake-3.14' (authored by kislinsk).
Merge branch 'T26437-CMake-3.14'
Jul 1 2019, 12:41 PM
kislinsk committed rMITK0f8ef678c1b9: Merge remote-tracking branch 'origin/releases/2018-04' into T26437-CMake-3.14 (authored by kislinsk).
Merge remote-tracking branch 'origin/releases/2018-04' into T26437-CMake-3.14
Jul 1 2019, 12:39 PM
kislinsk committed rMITKced2c8feeffd: Set minimum required version of CMake to 3.14.5 (authored by kislinsk).
Set minimum required version of CMake to 3.14.5
Jul 1 2019, 12:39 PM
kislinsk added a comment to T26437: Increase minimum required version of CMake to 3.14.

Pushed new branch T26437-CMake-3.14.

Jul 1 2019, 12:39 PM · MITK
kislinsk triaged T26437: Increase minimum required version of CMake to 3.14 as Normal priority.
Jul 1 2019, 12:18 PM · MITK
kislinsk closed T25491: OpenGL warning in Cmake as Resolved.
Jul 1 2019, 12:16 PM · MITK
kislinsk closed T26431: Fix gcc 9 and clang 8 compilation as Resolved.

Cherry-picked into releases/2018-04. Peter's fixes do not affect code available there.

Jul 1 2019, 9:59 AM · MITK
kislinsk committed rMITKf7bd07a6c604: Fixed some exception handling code to be more correct (authored by nolden).
Fixed some exception handling code to be more correct
Jul 1 2019, 9:51 AM
kislinsk committed rMITKc783c512ba1c: Don't fail on gcc 9 warnings about copy ctors (authored by nolden).
Don't fail on gcc 9 warnings about copy ctors
Jul 1 2019, 9:51 AM
kislinsk committed rMITK53eacaea95bb: Fixes for clang compilation (authored by nolden).
Fixes for clang compilation
Jul 1 2019, 9:51 AM