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Nov 27 2020

kislinsk committed rMITK665a1d1281a6: Improve ITK package depends file (authored by kislinsk).
Improve ITK package depends file
Nov 27 2020, 9:59 AM
kislinsk committed rMITK6ea1fd8356da: Add Boost dependencies (authored by kislinsk).
Add Boost dependencies
Nov 27 2020, 9:59 AM
kislinsk committed rMITKc670e289d6e7: Merge branch 'bugfix/T28002-ImprovePackageDependsFiles' into develop (authored by kislinsk).
Merge branch 'bugfix/T28002-ImprovePackageDependsFiles' into develop
Nov 27 2020, 9:59 AM
nolden committed rMITK6eaeaca7975f: Fix uninitialized reference warning/error (authored by nolden).
Fix uninitialized reference warning/error
Nov 27 2020, 9:21 AM
nolden committed rMITK857976ed83c8: Fix uninitialized reference warning/error (authored by nolden).
Fix uninitialized reference warning/error
Nov 27 2020, 9:20 AM

Nov 26 2020

eisenman moved T27420: report text from In Progress to Done on the challengeR (v1.0) board.

Compensated for 2. Text was revised in T27677.

Nov 26 2020, 10:35 PM · challengeR (v1.0)
eisenman committed rCHALLENGEReffec2e25455: Merge branch 'feature/T27770-ImproveReportFormat' into develop (authored by eisenman).
Merge branch 'feature/T27770-ImproveReportFormat' into develop
Nov 26 2020, 10:33 PM
eisenman committed rCHALLENGER0f1d4a7a652a: Add page breaks such that descriptions appear along with the plot (authored by eisenman).
Add page breaks such that descriptions appear along with the plot
Nov 26 2020, 10:32 PM
nolden added a comment to T28006: MatchPointRegistration module compilation fails with Clang 11.

https://phabricator.mitk.org/D443

Nov 26 2020, 4:20 PM · MITK
nolden added a comment to T28006: MatchPointRegistration module compilation fails with Clang 11.

I can confirm this fixes the issue, I can merge it tomorrow

Nov 26 2020, 4:18 PM · MITK
eisenman moved T27420: report text from Backlog to In Progress on the challengeR (v1.0) board.
Nov 26 2020, 3:38 PM · challengeR (v1.0)
neher committed rMITKDIFF7377ebb4907d: Merge branch 'T28017-VTK9' (authored by neher).
Merge branch 'T28017-VTK9'
Nov 26 2020, 3:09 PM
neher committed rMITKDIFFf6421a87b933: cell array nextcell (authored by neher).
cell array nextcell
Nov 26 2020, 3:09 PM
neher committed rMITKDIFF96cc00455433: update vtk connectomics (authored by neher).
update vtk connectomics
Nov 26 2020, 3:09 PM
neher committed rMITKDIFFeef11174f790: Merge branch 'T28017-VTK9' (authored by neher).
Merge branch 'T28017-VTK9'
Nov 26 2020, 3:09 PM
holzwart closed T28005: General Code Review as Resolved.
Nov 26 2020, 1:21 PM
schererj updated subscribers of T27968: CTP gets stuck on large import.

I would consider three different variants:

  1. Keep CTP as receiver -> move the dcmsend from ctp-pipeline to airflow (unknown end of transfer issue)
  2. Keep CTP as receiver and change the DICOMweb send pipline-step to the old DIMSE step (possible issue with missing slices <-> really fast)
  3. Don't use CTP at all -> Start a DICOM receiver in Airflow as a sensor and trigger DAGs at arrival (performance unknown)
Nov 26 2020, 1:03 PM · Kaapana (internal)
schererj moved T28018: Firecracker-AWS Isolated container from Discussion to Resolved on the Kaapana (internal) board.
Nov 26 2020, 12:56 PM · Request for Discussion, Kaapana (internal)
schererj closed T28018: Firecracker-AWS Isolated container as Resolved.
Nov 26 2020, 12:56 PM · Request for Discussion, Kaapana (internal)
neher added a comment to T28017: Update to vtk 9.

Pushed new branch T28017-VTK9-CodeIssues.

Nov 26 2020, 12:51 PM · MITK Diffusion
gaoh added a comment to T27968: CTP gets stuck on large import.

In T27573 we discussed the problem of data transfer from CTP to DCM4CHE.
So basically it is a kind of similar problem: A datatransfer between CTP and DCM4CHE fails.
The problem is then, CTP just keeps the data in the queue (here) or inserts in the quarantine folder (T27573).
Anyway, we do not get notified, that there is a problem.

Nov 26 2020, 12:09 PM · Kaapana (internal)
eisenman added a comment to T28016: embed web app in package.

It sounds nice, but I also think that we can run into cumbersome situations w.r.t. package management and version control with this approach: If the web app is located within the package, for each change to the package itself, it has to be investigated how the change affects the web app. The developer also has to adapt and test the web app then. This also means that for each package release, a corresponding web app has to be provided. In my opinion it makes more sense to focus either on the package or the web app during the development. Probably, we want to improve the web app that is based on a fixed package version x most frequently. This use case is then hampered by this approach as the package itself also evolves.

Nov 26 2020, 12:07 PM · challengeR (v1.0)
schererj archived Kaapana (internal) (Open Source Rocketplant).
Nov 26 2020, 10:56 AM
s669m raised the priority of T28018: Firecracker-AWS Isolated container from Normal to Unbreak Now!.
Nov 26 2020, 10:51 AM · Request for Discussion, Kaapana (internal)
s669m triaged T28018: Firecracker-AWS Isolated container as Normal priority.
Nov 26 2020, 10:13 AM · Request for Discussion, Kaapana (internal)
neher committed rMITKDIFF72706e00fe52: vtk changes (authored by neher).
vtk changes
Nov 26 2020, 9:09 AM
neher added a comment to T28017: Update to vtk 9.

Pushed new branch T28017-VTK9.

Nov 26 2020, 9:09 AM · MITK Diffusion
neher claimed T28017: Update to vtk 9.
Nov 26 2020, 9:08 AM · MITK Diffusion
neher triaged T28017: Update to vtk 9 as Normal priority.
Nov 26 2020, 9:08 AM · MITK Diffusion
wiesenfa created T28016: embed web app in package.
Nov 26 2020, 8:48 AM · challengeR (v1.0)

Nov 25 2020

kislinsk triaged T28006: MatchPointRegistration module compilation fails with Clang 11 as Normal priority.
Nov 25 2020, 11:47 PM · MITK
kislinsk added a comment to T28006: MatchPointRegistration module compilation fails with Clang 11.

After reading the itk::NumericTraits documentation and looking into the actual definitions of ZeroValue() I guess the fix could be:

Nov 25 2020, 11:46 PM · MITK
kislinsk added a comment to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies.

TARGET_DEPENDS parameters are directly passed to target_link_libraries() and bypass the PACKAGE_DEPENDS mechanism.

Nov 25 2020, 11:34 PM · Noteworthy, MITK (v2021.02)
kislinsk added a project to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies: Noteworthy.

Public API change: Depending on VTK does not add a transitive dependency to Qt5 Widgets anymore, except, when the required VTK components have a public dependency to Qt5 Widgets of course.

Nov 25 2020, 9:05 PM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies.

Fixed VTK and TinyXML-2 so far.

Nov 25 2020, 8:49 PM · Noteworthy, MITK (v2021.02)
kislinsk committed rMITKfc9c00185dfe: Move VTK-specific code to dedicated package depends file (authored by kislinsk).
Move VTK-specific code to dedicated package depends file
Nov 25 2020, 8:46 PM
kislinsk committed rMITK64ae7f4ccf69: Use package depends file for TinyXML-2 (authored by kislinsk).
Use package depends file for TinyXML-2
Nov 25 2020, 8:46 PM
kislinsk committed rMITK68f5331438a2: Merge branch 'bugfix/T28002-ImprovePackageDependsFiles' into develop (authored by kislinsk).
Merge branch 'bugfix/T28002-ImprovePackageDependsFiles' into develop
Nov 25 2020, 8:46 PM
kislinsk added a comment to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies.

Pushed new branch bugfix/T28002-ImprovePackageDependsFiles.

Nov 25 2020, 8:46 PM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies.

Holy moly, I just learned that the package depends files work completely different than I thought/was told the past 9 years. Instead of fixing the mitk_use_modules() function we just need to use the package depends files correctly.

Nov 25 2020, 8:22 PM · Noteworthy, MITK (v2021.02)
gaoh placed T24398: Dicom plugin: Retrieve does not work up for grabs.

So for the current develop:
With or without CGET activated. When trying to Retrieve a dataset after Query, I get an Exception:

Nov 25 2020, 3:36 PM · MITK (v2024.12)
m113r created T28014: Augmentation Refinement.
Nov 25 2020, 12:53 PM · m113r
kalali added a member for MITK: a178n.
Nov 25 2020, 11:35 AM
kislinsk changed the edit policy for MITK.
Nov 25 2020, 11:26 AM
kislinsk archived mitk.org.
Nov 25 2020, 11:25 AM
kislinsk archived SIDT.
Nov 25 2020, 11:24 AM
gaoh closed Restricted Maniphest Task, a subtask of T27196: Rewrite packaging of MITK, as Invalid.
Nov 25 2020, 10:57 AM · Moved to git.dkfz.de, MITK, Cleared
thomass closed T27696: Dicom loading does not work for some 4D data with the latest installer as Resolved.
Nov 25 2020, 8:25 AM · DICOM, Missing Info, MITK
kislinsk added a comment to T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies.
  • mitk_create_module() passes PACKAGE_DEPENDS to _mitk_parse_package_args()
    • The PACKAGE[|COMPONENT1[+COMPONENT2]...] syntax is processed and the following variables are set in parent scope:
      • <PUBLIC|PRIVATE|INTERFACE>_PACKAGE_NAMES: Lists of package names for different visibilities
      • PACKAGE_NAMES: Joined lists from above (may contain duplicates!)
      • <PUBLIC|PRIVATE|INTERFACE>_<PACKAGE>_REQUIRED_COMPONENTS: Lists of components for different visibilities and packages
  • mitk_create_module() passes PACKAGE_NAMES to mitk_check_module_dependencies()
    • mitk_check_module_dependencies() passes PACKAGE_NAMES to _mitk_parse_package_args()
      • Notice that PACKAGE_NAMES does not contain visibilities anymore, so everything is put into PRIVATE_PACKAGE_NAMES by default
    • Nevertheless, all visibility lists are joined into package_names and duplicates are removed (why not just use PACKAGE_NAMES in the first place and remove duplicates?)
    • For each package, check if MITK_USE_<package> is not set and add package to _MISSING_DEP in parent scope together with missing modules
  • Also: Duplicates in PACKAGE_NAMES were removed by mitk_check_module_dependencies()
  • The module is disabled if there are any missing dependencies
  • PACKAGE_DEPENDS is passed to mitk_use_modules() as PACKAGES parameter
Nov 25 2020, 8:02 AM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T26451: DICOM plugin cannot parse DICOM directories in macOS installer.

@jsolislemus There's a workaround if you can't wait for the next release which would also verify if your issue is fixed:

Nov 25 2020, 7:15 AM · MITK

Nov 24 2020

kislinsk added a comment to T27985: Migrate from TinyXML to TinyXML-2.
WARNING: While the APIs of TinyXML and TinyXML-2 are similar enough for a straight forward migration except for a few edge cases, it usually affects critical code. If not done thoroughly, migration may result in silently writing valid XML yet corrupt file formats (for example unexpected values). Beware of the few pitfalls! ⚠️
Nov 24 2020, 9:55 PM · Noteworthy, MITK (v2021.02)
floca updated the task description for T27992: Release of MITK CLIs.
Nov 24 2020, 9:22 PM · MITK (v2021.02), Request for Discussion
gaoh claimed T24398: Dicom plugin: Retrieve does not work.
Nov 24 2020, 5:21 PM · MITK (v2024.12)
floca added a comment to T27696: Dicom loading does not work for some 4D data with the latest installer.

@thomass could you check if the problem was realy just cuased by slow network drive and is solved. If this is the case, could you close the task? If the problem still exists, may be the issue solved by Stefan is a solution.

Nov 24 2020, 5:17 PM · DICOM, Missing Info, MITK
floca added a comment to T24398: Dicom plugin: Retrieve does not work.

@gaoh could you check if the problem is solved either with the branch or as soon as it is in develop?

Nov 24 2020, 5:15 PM · MITK (v2024.12)
floca added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

I would see it positiv. No sense crying over spilt milk. Thanks for solving that problem!

Nov 24 2020, 5:12 PM · Cleared, MITK (v2021.02)
thomass added a project to T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range : Request for Discussion.

apparently a vtkLoopUpTable is set automatically so the property as such cannot be used to handle custom vtkLookUpTables

Nov 24 2020, 4:07 PM · Request for Discussion, MITK
thomass triaged T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range as Normal priority.
Nov 24 2020, 2:25 PM · Request for Discussion, MITK
jsolislemus added a comment to T26451: DICOM plugin cannot parse DICOM directories in macOS installer.

Hi, from what I've been reading, it seems this issue might be fixed? I read on T26264 that it might be fixed with a CMake variables related to the DCMTK dictionaries; although I'm not sure how could I implement it myself, while waiting for the next release (we're still developing on top of 2018.04.2). Thanks a lot for the effort, this error seemed very difficult to pinpoint.

Nov 24 2020, 2:19 PM · MITK
jaegerp added a member for MIC: d587s.
Nov 24 2020, 1:09 PM
kislinsk removed a member for OP 4.1: kislinsk.
Nov 24 2020, 10:14 AM
kislinsk added members for MIC: reicht, gaoh, kraeuter, d485r, rasheed, steint, graf, c082x, j762e, m097t, e249r, s669m, m139l.
Nov 24 2020, 10:13 AM
kislinsk added members for MIC: kalali, a178n, kompan, floca, thomass.
Nov 24 2020, 10:10 AM
kislinsk closed T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers, a subtask of T24398: Dicom plugin: Retrieve does not work, as Resolved.
Nov 24 2020, 9:53 AM · MITK (v2024.12)
kislinsk closed T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers, a subtask of T26451: DICOM plugin cannot parse DICOM directories in macOS installer, as Resolved.
Nov 24 2020, 9:53 AM · MITK
kislinsk closed T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers, a subtask of T27669: Dicom import issue with MITK binaries (package) and Ubuntu, as Resolved.
Nov 24 2020, 9:53 AM · Missing Info, DICOM, MITK
kislinsk closed T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers as Resolved.
Nov 24 2020, 9:53 AM · Cleared, MITK (v2021.02)
kislinsk closed T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers, a subtask of T27696: Dicom loading does not work for some 4D data with the latest installer, as Resolved.
Nov 24 2020, 9:53 AM · DICOM, Missing Info, MITK
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Mixed feelings here: On one hand I'm happy that we, with a single trivial line of CMake code, finally fixed a decade old severe issue we had in MITK without really noticing it causing quite some inconvenience for our users and we were not able to reproduce it over the years. Maybe we even lost some users right before they actually used MITK because "it cannot open my DICOM files". On the other hand, we fixed a decade old severe issue with a single line of CMake code.

Nov 24 2020, 9:53 AM · Cleared, MITK (v2021.02)
reinkea added a member for IMSY: t470h.
Nov 24 2020, 9:51 AM
kislinsk added a member for MIC: s280a.
Nov 24 2020, 9:43 AM
kislinsk removed a member for MIC: Unknown Object (User).
Nov 24 2020, 9:38 AM
nolden created T28006: MatchPointRegistration module compilation fails with Clang 11.
Nov 24 2020, 9:25 AM · MITK
kislinsk added a member for MIC: Unknown Object (User).
Nov 24 2020, 9:19 AM
holzwart updated the task description for T28005: General Code Review.
Nov 24 2020, 8:24 AM
holzwart raised the priority of T28005: General Code Review from Wishlist to Normal.
Nov 24 2020, 8:23 AM
holzwart triaged T28005: General Code Review as Wishlist priority.
Nov 24 2020, 8:23 AM

Nov 23 2020

kislinsk added a comment to T27992: Release of MITK CLIs.

I think the only reason that they are not part of the release installers is simply that they are not enabled in the WorkbenchRelease build configuration. The actual todo is to specify what CLI apps we want to include I guess.

Nov 23 2020, 11:42 PM · MITK (v2021.02), Request for Discussion
kislinsk triaged T28002: MITK cannot handle CMake target namespaces in module and plugin package dependencies as Unbreak Now! priority.
Nov 23 2020, 11:35 PM · Noteworthy, MITK (v2021.02)
floca added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

🤞

Nov 23 2020, 11:24 PM · Cleared, MITK (v2021.02)
kislinsk added a comment to T27985: Migrate from TinyXML to TinyXML-2.

Changes in header files: git diff -U0 ff0027ee 8e328dab *.h > output.txt

Nov 23 2020, 11:15 PM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Let's see if the Nightly installers tomorrow morning are able to load Sarah's DICOM files. 🤞

Nov 23 2020, 11:03 PM · Cleared, MITK (v2021.02)
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Deleted branch bugfix/T26164-AlwaysUseDCMTKBuiltInDICOMDictionaries.

Nov 23 2020, 11:01 PM · Cleared, MITK (v2021.02)
kislinsk committed rMITK5e254ee7298e: Always use built-in DICOM dictionaries (authored by kislinsk).
Always use built-in DICOM dictionaries
Nov 23 2020, 11:00 PM
kislinsk committed rMITKfa2b431b38e4: Merge branch 'bugfix/T26164-AlwaysUseDCMTKBuiltInDICOMDictionaries' into develop (authored by kislinsk).
Merge branch 'bugfix/T26164-AlwaysUseDCMTKBuiltInDICOMDictionaries' into develop
Nov 23 2020, 11:00 PM
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Pushed new branch bugfix/T26164-AlwaysUseDCMTKBuiltInDICOMDictionaries.

Nov 23 2020, 10:59 PM · Cleared, MITK (v2021.02)
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Everything you need to know about the DICOM dictionaries and how DCMTK is handling them is described here: https://github.com/InsightSoftwareConsortium/DCMTK/blob/master/dcmdata/docs/datadict.txt

Nov 23 2020, 10:55 PM · Cleared, MITK (v2021.02)
kislinsk added a comment to T26164: DICOM Query/Retrieve doesn't work at least in Ubuntu release installers.

Verified on macOS. I downloaded the dictionary and exported DCMDICTPATH. The MITK Workbench was able to load the DICOM files correctly afterwards. 🎉

Nov 23 2020, 10:40 PM · Cleared, MITK (v2021.02)
kislinsk closed T28001: Fix mitkRESTClientTest as Resolved.

I made the variable thread-safe by making it an atomic.

Nov 23 2020, 10:31 PM · MITK
kislinsk added a comment to T28001: Fix mitkRESTClientTest.

Deleted branch bugfix/T28001-FixRESTClientTest.

Nov 23 2020, 10:30 PM · MITK
kislinsk committed rMITK236c4a1ee0a4: Make counter variable thread-safe (authored by kislinsk).
Make counter variable thread-safe
Nov 23 2020, 10:30 PM
kislinsk committed rMITK13c4a5937ef9: Merge branch 'bugfix/T28001-FixRESTClientTest' into develop (authored by kislinsk).
Merge branch 'bugfix/T28001-FixRESTClientTest' into develop
Nov 23 2020, 10:30 PM
kislinsk added a comment to T28001: Fix mitkRESTClientTest.

Pushed new branch bugfix/T28001-FixRESTClientTest.

Nov 23 2020, 10:30 PM · MITK
kislinsk triaged T28001: Fix mitkRESTClientTest as Normal priority.
Nov 23 2020, 10:28 PM · MITK
kislinsk added a project to T27999: Remove Biophotonics and Photo Acoustics from MITK: Noteworthy.
Nov 23 2020, 9:36 PM · Noteworthy, MITK
kislinsk closed T27999: Remove Biophotonics and Photo Acoustics from MITK as Resolved.
Nov 23 2020, 9:32 PM · Noteworthy, MITK
kislinsk added a comment to T27999: Remove Biophotonics and Photo Acoustics from MITK.

Deleted branch bugfix/T27999-RemovePhotoacoustics.

Nov 23 2020, 9:32 PM · Noteworthy, MITK
kislinsk committed rMITKcb17cca5ef28: Remove Biophotonics and Photoacoustics (authored by kislinsk).
Remove Biophotonics and Photoacoustics
Nov 23 2020, 9:31 PM
kislinsk committed rMITKfc048ef737a2: Merge branch 'bugfix/T27999-RemovePhotoacoustics' into develop (authored by kislinsk).
Merge branch 'bugfix/T27999-RemovePhotoacoustics' into develop
Nov 23 2020, 9:31 PM
kislinsk added a comment to T27999: Remove Biophotonics and Photo Acoustics from MITK.

Pushed new branch bugfix/T27999-RemovePhotoacoustics.

Nov 23 2020, 9:30 PM · Noteworthy, MITK