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Mar 27 2018

goch added a comment to T24439: Add category to plugins.

Pushed new branch T24439-categorical-imperative.

Mar 27 2018, 11:51 AM · MITK (2018-04)
goch claimed T24439: Add category to plugins.
Mar 27 2018, 11:20 AM · MITK (2018-04)
goch closed T24351: MITK tutorial StartVS_release.bat no longer exists as Resolved.

Did a quick grep for StartVS and replaced any reference by telling the reader to open the solution file instead.

Mar 27 2018, 11:17 AM · MITK (2018-04)
goch committed rMITKe5b4379c0d65: Merge branch 'T24351-remove-reference-to-bat' (authored by goch).
Merge branch 'T24351-remove-reference-to-bat'
Mar 27 2018, 11:16 AM
goch committed rMITKcff6f2d9f5a4: Remove references to batch files (authored by goch).
Remove references to batch files
Mar 27 2018, 11:16 AM
goch added a comment to T24351: MITK tutorial StartVS_release.bat no longer exists.

Pushed new branch T24351-remove-reference-to-bat.

Mar 27 2018, 11:16 AM · MITK (2018-04)
goch claimed T24351: MITK tutorial StartVS_release.bat no longer exists.
Mar 27 2018, 10:52 AM · MITK (2018-04)
goch added a comment to T24519: Speed up CMake fixup bundle.

Basically what you said. We have a number of executables in the /bin/ folder (however many BlueBerryApps and command line applications have been switched on). As we might have either one, several or none of each we need to trigger prerequisite collection for each of them. However for many applications (such as the twenty-odd diffusion command line app activated by a single CMake switch) that resulted in unbearably slow installer builds.
This has been an issue for example in T22794 where the solution for now was to just not add the prerequisite trigger for command line apps.

Mar 27 2018, 10:01 AM · MITK (2018-04)

Mar 26 2018

goch added a comment to T24519: Speed up CMake fixup bundle.

The provided files significantly speed up the analysis for each individual executable. However, they do need some adaption to our use case, as previously we started a new analysis for each executable and they automatically do the analysis for each executable found in the same folder. No using this automatic feature still results in a long (if now somewhat shorter) package build.

Mar 26 2018, 5:25 PM · MITK (2018-04)
goch triaged T24519: Speed up CMake fixup bundle as Wishlist priority.
Mar 26 2018, 2:55 PM · MITK (2018-04)
goch added a comment to T24259: OpenMP not working on OSX.

Is there some kind of intended replacement for clang? What is the go-to way for other tools?

Mar 26 2018, 1:34 PM · Auto-closed, MITK
goch added a comment to T23104: Deprecate QmitkPlotWidget.

@hentsch at least for CEST showing error bars was one of the requirements. So no.

Mar 26 2018, 1:32 PM · Restricted Project, MITK

Mar 5 2018

goch added a comment to T24316: Design Decision: Interface of MITK Python Wrapping.

Sorry to be a nitpicker, but regarding 3 (and as I can find no reference to SlicedImage anywhere in the code or phabricator, apart from this task):

Mar 5 2018, 10:38 AM · Request for Discussion, MITK

Mar 2 2018

goch moved T24333: Noteworthy new features since MITK 2016.11 from Backlog to Release management on the MITK (2018-04) board.
Mar 2 2018, 10:05 AM · MITK (2018-04)
goch triaged T24332: Limit MITK to python 3 as High priority.
Mar 2 2018, 9:32 AM · MITK (2018-04)
goch edited projects for T24270: Update CTK and PythonQt, added: MITK (2018-04); removed MITK.
Mar 2 2018, 9:28 AM · MITK (2018-04)

Mar 1 2018

goch added a member for MITK: wieset.
Mar 1 2018, 10:39 AM

Feb 28 2018

goch added a comment to T24315: Design Decision: Create a ConvertTo Method for MITK Objects.

I do not really mind either way. Implementation should be pretty straightforward, it does not really save any lines of code. Instead of

mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
if(image.IsNull())
{
  //Error handling here
}
Feb 28 2018, 10:45 AM · Request for Discussion, MITK
goch added a comment to T24316: Design Decision: Interface of MITK Python Wrapping.
  1. How maintenance intensive is the wrapping going to be? The more custom the solution and the more hand-written code it contains the more of a nightmare I assume it to be if the inevitable interface change of some central class arrives.
  2. Is there a way to automatically test this via a python dart client? Do you already have something like that?
  3. If I understand correctly we "only" have to wrap parent classes of the classes we want to use in python?
Feb 28 2018, 10:20 AM · Request for Discussion, MITK

Feb 20 2018

goch closed T24293: Verify LocaleSwitch usage in MITK CEST as Resolved.
Feb 20 2018, 2:05 PM · MITK
goch committed rMITK0f31f37c8d8f: Merge branch 'T24293-locale-switch-in-CEST-2' (authored by goch).
Merge branch 'T24293-locale-switch-in-CEST-2'
Feb 20 2018, 12:29 PM
goch committed rMITK0e5eaafed259: Use C locale for normalizing (authored by goch).
Use C locale for normalizing
Feb 20 2018, 12:29 PM
goch added a comment to T24293: Verify LocaleSwitch usage in MITK CEST.

Pushed new branch T24293-locale-switch-in-CEST-2.

Feb 20 2018, 12:28 PM · MITK
goch committed rMITKca8b9fd1a552: Use C locale for normalizing (authored by goch).
Use C locale for normalizing
Feb 20 2018, 11:54 AM
goch added a comment to T24293: Verify LocaleSwitch usage in MITK CEST.

Pushed new branch T24293-locale-switch-in-CEST.

Feb 20 2018, 11:54 AM · MITK
goch triaged T24293: Verify LocaleSwitch usage in MITK CEST as High priority.
Feb 20 2018, 11:51 AM · MITK

Feb 19 2018

goch added a member for Deep Learning: beuckelm.
Feb 19 2018, 12:40 PM
goch added a member for MIC: beuckelm.
Feb 19 2018, 12:39 PM
goch triaged T24285: Add CEST data reading test and test data as Normal priority.
Feb 19 2018, 11:00 AM · Restricted Project, MITK

Feb 15 2018

goch added a member for MICO: huberma.
Feb 15 2018, 2:45 PM
goch added a member for MITK: huberma.
Feb 15 2018, 2:45 PM
goch triaged T24270: Update CTK and PythonQt as Wishlist priority.
Feb 15 2018, 12:22 PM · MITK (2018-04)
goch added a comment to T24259: OpenMP not working on OSX.

@wasserth Could you provide the error logs?

Feb 15 2018, 9:42 AM · Auto-closed, MITK

Feb 9 2018

goch added a comment to T24085: MITK make PACKAGE does not work on windows if Python is enabled.

The change to the python use, sytem instead of setup, might require us adding a redistributable/installer to the MITK installer.

Feb 9 2018, 1:39 PM · MITK
goch added a comment to T24230: Linux make package with python fails.

See also T24085: MITK make PACKAGE does not work on windows if Python is enabled for windows package errors.

Feb 9 2018, 1:24 PM · MITK
goch added a comment to T24085: MITK make PACKAGE does not work on windows if Python is enabled.

A pull request has been opened with CTK to include the changes necessary to support our switch to python3

Feb 9 2018, 12:52 PM · MITK

Feb 8 2018

goch added a comment to T24085: MITK make PACKAGE does not work on windows if Python is enabled.

Got the build working on windows up to and including the MITK build. There is a CTK change that I will contribute once I have verified Python works fine with MITK and python 3 and CTK still builds with python 2.

Feb 8 2018, 1:07 PM · MITK
goch added a member for MITK: jungsi.
Feb 8 2018, 11:44 AM

Feb 6 2018

goch closed T23756: Investigate use of precompiled headers as Wontfix.

I did not manage to get a running windows build with cotire.

Feb 6 2018, 12:05 PM · MITK
goch closed T23756: Investigate use of precompiled headers, a subtask of T23721: Project "Astonishing Angelfish", as Wontfix.
Feb 6 2018, 12:05 PM · Request for Discussion, MITK (v2022.10)

Feb 5 2018

goch added a comment to T24167: MITK Extension mechanism and naming prefix of modules.

I was just pointing out that it goes beyond convenience.

Feb 5 2018, 1:16 PM · MITK
goch added a comment to T24149: MITK Extension mechanism should allow custom plugin naming schemes.

I would prefer offering the option to ensure naming. Partly because a lot of the first extensions will be maintained by us anyway and we currently have a naming convention.

Feb 5 2018, 1:08 PM · MITK
goch added a comment to T24167: MITK Extension mechanism and naming prefix of modules.

To clarify:
There are three external directories,

A/Modules/Potato
B/Modules/Tomato
C/Modules/Banana
Feb 5 2018, 1:00 PM · MITK
goch added a comment to T24167: MITK Extension mechanism and naming prefix of modules.

Even more important than having a default would be consistency. Whether you DEPEND on MITKSegmentation or AwesomeSegmentation should not be determined by the order of external modules.

Feb 5 2018, 10:20 AM · MITK
goch added a comment to T24149: MITK Extension mechanism should allow custom plugin naming schemes.

My suggestion could only enforce org.* if you set the extension names explicitly to "". Would this still be to restrictive for you?

Feb 5 2018, 10:04 AM · MITK
goch added a comment to T24167: MITK Extension mechanism and naming prefix of modules.

I seem to remember that not working. At least this should make sure there is always a ModulePrefix.
Didn't you have to switch MITK_MODULE_NAME_PREFIX to ""?

Feb 5 2018, 9:57 AM · MITK

Feb 2 2018

goch committed rMITK732d90ffcbc3: Make our FindNumpy.cmake python3 compatible (authored by goch).
Make our FindNumpy.cmake python3 compatible
Feb 2 2018, 5:22 PM
goch added a member for MITK: sridhara.
Feb 2 2018, 3:09 PM
goch added a member for Kaapana (internal): thomass.
Feb 2 2018, 9:13 AM

Feb 1 2018

goch triaged T24125: Missing figures in tutorial slides as High priority.

This would be a good community day candidate.

Feb 1 2018, 2:52 PM · MITK (2018-04), Restricted Project
goch triaged T24167: MITK Extension mechanism and naming prefix of modules as Wishlist priority.

So far we have solved this by setting the MITK_MODULE_NAME_PREFIX correspondingly as it will be used to determine what, if anythingm should be used as a prefix.

Feb 1 2018, 2:50 PM · MITK
goch triaged T24131: Voxel value indicator in workbench is broken as Normal priority.
Feb 1 2018, 2:43 PM · Restricted Project, MITK
goch closed T24126: Dead data download link on tutorials website as Resolved.

Links have been removed, the data section had been removed previously. Presumably because the TCGA no longer offers the data itself. instead it can be gotten via https://portal.gdc.cancer.gov/legacy-archive/ . However that tool seems to be inconvenient enough to be not much help.

Feb 1 2018, 2:42 PM · MITK
goch merged T24127: Dead data download link on tutorials website into T24126: Dead data download link on tutorials website.
Feb 1 2018, 2:31 PM · MITK
goch merged task T24127: Dead data download link on tutorials website into T24126: Dead data download link on tutorials website.
Feb 1 2018, 2:31 PM · MITK
goch triaged T24149: MITK Extension mechanism should allow custom plugin naming schemes as Wishlist priority.
Feb 1 2018, 2:30 PM · MITK
goch added a comment to T24149: MITK Extension mechanism should allow custom plugin naming schemes.

I would suggest a best practice of one naming scheme per extension directory and adding it to the PluginList.cmake

list(APPEND extensionNames exProject)
# Plug-ins must be ordered according to their dependencies
set(MITK_PLUGINS
  org.exProject.gui.qt.testplugin:ON
)
Feb 1 2018, 11:23 AM · MITK
goch added a comment to T24149: MITK Extension mechanism should allow custom plugin naming schemes.

I think that is governed by this code, which is then used by CTK

#!
#! Extract all library names which are build within this project
#!
#! \ingroup CMakeUtilities
macro(ctkMacroGetAllProjectTargetLibraries all_target_libraries varname)
  # Allow external projects to override the set of internal targets
  if(COMMAND GetMyTargetLibraries)
    GetMyTargetLibraries("${all_target_libraries}" ${varname})
  else()
    set(re_ctklib "^(c|C)(t|T)(k|K)[a-zA-Z0-9]+$")
    set(re_ctkplugin "^org_commontk_[a-zA-Z0-9_]+$")
    set(_tmp_list)
    list(APPEND _tmp_list ${all_target_libraries})
    #message("calling ctkMacroListFilter with varname:${varname}")
    ctkMacroListFilter(_tmp_list re_ctklib re_ctkplugin OUTPUT_VARIABLE ${varname})
    #message(STATUS "getallctklibs from ${all_target_libraries}")
    #message(STATUS varname:${varname}:${${varname}})
  endif()
endmacro()
Feb 1 2018, 10:21 AM · MITK

Jan 31 2018

goch added a comment to T24131: Voxel value indicator in workbench is broken.

As far as I am aware prior behaviour was showing the value of the topmost visible image at a given point. So if you have multiple images at different locations in the world geometry you would not get "No image information at this position" if you happen to set the crosshair at a location which is out of bounds for the topmost image.

Jan 31 2018, 10:00 AM · Restricted Project, MITK

Jan 29 2018

goch added a member for MIC: zhangs.
Jan 29 2018, 11:48 AM

Jan 25 2018

goch committed rMITK81df3fc72078: SimpleITK builds on Windows (authored by goch).
SimpleITK builds on Windows
Jan 25 2018, 2:25 PM
goch committed rMITK2deb3f6459df: Update ITK and SimpleITK (authored by goch).
Update ITK and SimpleITK
Jan 25 2018, 2:25 PM
goch added a comment to T24085: MITK make PACKAGE does not work on windows if Python is enabled.

Pushed new branch T24085-mitk-python-installer-fix.

Jan 25 2018, 2:25 PM · MITK

Jan 24 2018

goch added a member for MITK: aguilera.
Jan 24 2018, 12:17 PM

Jan 19 2018

goch triaged T24085: MITK make PACKAGE does not work on windows if Python is enabled as Normal priority.
Jan 19 2018, 11:17 AM · MITK
goch added a comment to T24011: ImageStatisticsView crashes after calculating image statistics.

Just to clarify, two versions of the plugin means just two different histogram widgets in the statistics view.

Jan 19 2018, 10:55 AM · Restricted Project, MITK

Jan 18 2018

goch closed T24043: [Dashboard] Fix Photoacoustics build errors as Resolved.
Jan 18 2018, 2:25 PM · MITK
goch closed T23798: MITK has new memory leaks breaking unit tests as Resolved.

Has been fixed.

Jan 18 2018, 2:25 PM · MITK
goch changed the status of T23800: Fix mitkSegmentationInterpolationTest from Duplicate to Resolved by committing rMITK3d69740b7215: Fixes T24021 and fixes T23800.
Jan 18 2018, 2:22 PM · Restricted Project, MITK
goch committed rMITKcb312717ee6e: Merge branch 'T24021-fix-segmentationinterpolationtest' (authored by goch).
Merge branch 'T24021-fix-segmentationinterpolationtest'
Jan 18 2018, 2:22 PM
goch closed T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail as Resolved by committing rMITK3d69740b7215: Fixes T24021 and fixes T23800.
Jan 18 2018, 2:22 PM · MITK
goch committed rMITK3d69740b7215: Fixes T24021 and fixes T23800 (authored by goch).
Fixes T24021 and fixes T23800
Jan 18 2018, 2:21 PM
goch added a comment to T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail.

Pushed new branch T24021-fix-segmentationinterpolationtest.

Jan 18 2018, 2:21 PM · MITK
goch added a comment to T23800: Fix mitkSegmentationInterpolationTest.

That seems to be it, my regular build still uses a ITK 4.11 template header instead of the ITK 4.12.2 one.

Jan 18 2018, 2:13 PM · Restricted Project, MITK
goch added a comment to T23800: Fix mitkSegmentationInterpolationTest.

The cause of the error seems to be in

Modules\Segmentation\Algorithms\mitkShapeBasedInterpolationAlgorithm.cpp

in the following lines (std::cout added for debugging purposes)

isoContourFilter->SetInput(binaryImage);
isoContourFilter->SetFarValue(maximumDistance + 1);
isoContourFilter->SetLevelSetValue(0.5);
std::cout << "LevelSetValue: " << isoContourFilter->GetLevelSetValue() <<std::endl;
// Prints
//   LevelSetValue: 0    - for my regular build
//   LevelSetValue: 0.50 - for the dart client
Jan 18 2018, 1:44 PM · Restricted Project, MITK
goch added a comment to T23800: Fix mitkSegmentationInterpolationTest.

See also T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail

Jan 18 2018, 11:30 AM · Restricted Project, MITK

Jan 15 2018

goch committed rMITKb12a23090b25: Merge branch 'T24021-fix-logo-annotation-test' (authored by goch).
Merge branch 'T24021-fix-logo-annotation-test'
Jan 15 2018, 11:07 AM
goch committed rMITK3f6294d1831d: Update test data hash (authored by goch).
Update test data hash
Jan 15 2018, 11:05 AM
goch committed rMD6001ab9cd6c6: Add new alternatives for rendering tests (authored by goch).
Add new alternatives for rendering tests
Jan 15 2018, 11:00 AM

Jan 12 2018

goch committed rMITKf781f9c1b1cc: Add capability to actually load logos from disk (authored by goch).
Add capability to actually load logos from disk
Jan 12 2018, 5:57 PM
goch added a comment to T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail.

Pushed new branch T24021-fix-logo-annotation-test.

Jan 12 2018, 5:57 PM · MITK
goch committed rMDfb03141ee609: Use new logo in reference screenshot (authored by goch).
Use new logo in reference screenshot
Jan 12 2018, 5:49 PM
goch renamed T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail from [Dashboard] mitkImageStatisticsCalculatorTest and mitkSegmentationInterpolationTest fail to [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail.
Jan 12 2018, 5:43 PM · MITK
goch committed rMITKdd46eee88a3f: Merge branch 'T24021-fix-debug-leaks' (authored by goch).
Merge branch 'T24021-fix-debug-leaks'
Jan 12 2018, 11:18 AM
goch committed rMITK722518ed42c9: Fix debug leaks (authored by goch).
Fix debug leaks
Jan 12 2018, 11:17 AM
goch added a comment to T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail.

Pushed new branch T24021-fix-debug-leaks.

Jan 12 2018, 11:17 AM · MITK

Jan 11 2018

goch committed rMITK3cba4ed2bea7: Merge branch 'T24043-fix-dashboard-errors' (authored by goch).
Merge branch 'T24043-fix-dashboard-errors'
Jan 11 2018, 12:54 PM
goch committed rMITKf716b5ca56f4: Do not build files that require OpenCL if no OpenCL (authored by goch).
Do not build files that require OpenCL if no OpenCL
Jan 11 2018, 12:54 PM
goch added a comment to T24043: [Dashboard] Fix Photoacoustics build errors.

Pushed new branch T24043-fix-dashboard-errors.

Jan 11 2018, 12:53 PM · MITK
goch triaged T24043: [Dashboard] Fix Photoacoustics build errors as Unbreak Now! priority.
Jan 11 2018, 12:53 PM · MITK
goch awarded T24041: VolumeMapperVtkSmart3D illegaly changes spacing of every mitk::Image's vtkImageData to (1, 1, 1) a Manufacturing Defect? token.
Jan 11 2018, 11:06 AM · MITK

Jan 10 2018

goch moved T23988: Handle CEST normalization for M0 voxels that are zero from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Jan 10 2018, 10:11 AM · Restricted Project, MITK
goch added a project to T23988: Handle CEST normalization for M0 voxels that are zero: Restricted Project.
Jan 10 2018, 10:11 AM · Restricted Project, MITK

Jan 9 2018

goch committed rMITK41b44de83ee6: Merge branch 'T24021-fix-test' (authored by goch).
Merge branch 'T24021-fix-test'
Jan 9 2018, 1:50 PM
goch committed rMITK97c3db136aa1: Use 4D accessor for 4D images (authored by goch).
Use 4D accessor for 4D images
Jan 9 2018, 1:50 PM
goch added a comment to T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail.

Pushed new branch T24021-fix-test.

Jan 9 2018, 1:49 PM · MITK
goch triaged T24021: [Dashboard] mitkImageStatisticsCalculatorTest, mitkSegmentationInterpolationTest and more fail as High priority.
Jan 9 2018, 10:27 AM · MITK
goch closed T8235: ENH: Create Modules ImageStatistics and ImageExtraction as Resolved.

I believe this has happened at some point.

Jan 9 2018, 10:26 AM · Bugzilla, MITK
goch added a comment to T23741: Specify default UID generation method.

Tests no longer fail as there is no longer a uid property.

Jan 9 2018, 10:18 AM · MITK (v2021.02), Noteworthy

Jan 8 2018

goch committed rMITKb8ba5eacc37f: Fixes T23988 - set to zero instead of dividing by it (authored by goch).
Fixes T23988 - set to zero instead of dividing by it
Jan 8 2018, 4:35 PM