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Diffusion MITK 88aa43536c8c

2020 Week 31 (Very Late July)

Authored by kislinsk on Sat, Aug 1, 1:22 AM.

Description

2020 Week 31 (Very Late July)

The following - possibly updated - changelog can be viewed as formatted
article at https://phabricator.mitk.org/w/mitk/changelog/2020.31/.

🛠 Third-party dependency changes

  • Patched VTK 8.1 to work with GCC 10

✨ New features

  • Removed Ubuntu 16.04 from the tier 1 supported platforms in favor of Ubuntu 20.04
  • Added auto-crop feature for multi-label segmentation images to the context menu of the Data Manager view
  • Migrated more plugins/views to new selection concept introduced in 2020 Week 25 (Late June)
    • DCE MR Perfusion Datafit View
    • Remeshing
    • Volume Visualization
  • Added new DICOM reader MITK DICOM Reader v2 (manual) to manually select the reader configuration instead of automatically choosing the configuration based on the least number of image volumes that would be generated from the input files
  • Improved and restructured MITK documentation (ongoing effort)
  • Refactored MITK Workbench intro part into separate org.mitk.gui.qt.mitkworkbench.intro plugin to enable easy replacement with custom intro parts by other MITK applications
  • Introduced ModelFitResultRelationRule to reference between input images and produced parameter maps
  • Matched naming convention of DICOM-related modules (see API-breaking changes below)

🐛 Bugfixes

  • Fixed a crash when multiple dynamic/3d+t images are loaded
  • Fixed a crash when a data node is drag'n'dropped to a different parent data node in the Data Manager view
  • Segmentation tools
    • Region Growing: fixed thresholding for images with unsigned pixel types
    • Region Growing 3D: seed points can now be set in dynamic/3d+t images
  • Welcome page is shown on top of editors again at first application start
  • Improved geometry comparison by choosing less strict epsilon values for directions and other spatial aspects
  • Fixed IsSubGeometry() for oblique geometries
  • Fixed build errors with Clang 10

🔥 API-breaking changes

  • Several DICOM-related modules were renamed. We strongly recommend to clean the build directory and rebuild MITK as some old auto-load modules will linger on otherwise.
    • DICOMReader DICOM
    • DICOMReaderService DICOMImageIO (now auto-load dependency of DICOM module)
    • DicomRT RT
    • DicomRTIO DICOMRTIO
  • Other API-breaking changes are located only in experimental or deprecated parts of MITK

Rework of the Global Image Feature classes and command-line apps

The main purpose of the rework was (1) to decouple the features from the legacy ID to allow more flexible output formats and (2) to offer a well-defined XML output of GIF analysis that stores a lot of useful and necessary meta and provenience information.

Amongst others, the following things have been done:

  • Introduced FeatureID to reference features in the result sets of GIF classes instead of plain strings
  • Reworked AbstractGlobalImageFeature class and derived classes
    • Ensured that there is no difference between the explicit setting of feature parameters via specific class setters or the generic parameter setter. CalculateFeaturesUsingParameters and CalculateFeaturesSliceWiseUsingParameters are not necessary anymore and misleading
    • Improved const correctness
  • Added CalculateAndAppendFeaturesSliceWise and CalculateAndAppendFeatures for adding features to a given feature list
  • Added new result format (writer) that stores the feature list in a structured XML file, containing the feature results and details parameter settings, data loading meta information and provenience information
  • GIF command-line apps now regard DICOM meta information of the input data for provenience if available.
  • Fixed several minor bugs and glitches

Details

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.
CommitAuthorDetailsCommitted
582aadc6da8dthomass
Update text and pngs of the point set interaction documentation 
Jul 31
c5e3da10dab6floca
T27692 Fixed mitk::IsSubGeometry for oblique geometries. 
Jul 30
c72fa5e21c97floca
T25805 Cleaned up naming of DICOM related modules 
Jul 29
99e147b96882kislinsk
Keep region grower thresholds within the pixel type extrema of the reference… 
Jul 29
af6ba9b47f82kislinsk
Keep region grower thresholds within the pixel type extrema of the reference… 
Jul 29
ec3a2c5a9588floca
Merge branch 'develop' into feature/T25805-merged 
Jul 29
b0e2beec1246floca
T27581 Fixed PerfusionMiniApp to also support 2 step linear model 
Jul 29
dac974bc335dfloca
Fixed mitk::IsSubGeometry for oblique geometries. 
Jul 29
64c4c822e255nolden
Fix ImageCropper startup crash 
Jul 29
be8970e7a285nolden
Fix ImageCropper startup crash 
Jul 29
24158ffb55c1kompan
Use mitkSingleNodeSelectionWidget instead of QmitkDataStorageComboBox. 
Jul 29
978e3fbf6328floca
Introduced ModelFitResultRelationRule 
Jul 29
1b30808db9e5kislinsk
Revise Movie Maker documentation 
Jul 28
6d34627b39d0kislinsk
Add documentation to Properties View 
Jul 28
3d31d74f9e36nolden
Patch VTK to properly detect gcc 10 
Jul 28
9b8c2ef3cbc2floca
Fixed missed case sensitive naming change 
Jul 28
bc8bf3835b5enolden
Patch VTK to properly detect gcc 10 
Jul 28
738dae120e75floca
Fixed review remarks 
Jul 28
3340d7805c11floca
Fixed broken tests for T27583 
Jul 28
467d01b492e2nolden
Fix some clang triggered issues 
Jul 28
01fc3468ed94kislinsk
Add documentation to Properties View 
Jul 28
1153771459b8floca
Fixed broken tests for T27583 
Jul 28
c6c5256a8dd7kislinsk
Fix QWebEngine warning about unregistered qthelp scheme 
Jul 28
4d0d5b8358b6kislinsk
Remove references to libav from code and documentation 
Jul 28
3117a4d3c970floca
T27582 BaseGeometry equality checks (in ImageStatistics) should be less… 
Jul 28
3575c71b077afloca
Fixed review remarks. 
Jul 27
71718abcc2b2kislinsk
Migrate .arcconfig to mid 2020 changes of "arc land" 
Jul 27
51b7a790230akislinsk
Migrate .arcconfig to mid 2020 changes of "arc land" 
Jul 27
efc061e82760nolden
Use std::string instead of const char* in file extension handling 
Jul 27
b73371b41722nolden
Silence clang on float int conversion in uServices 
Jul 27
87e3bb7e499bnolden
Git ignore .clangd 
Jul 27
f2d1b2910f34nolden
Fixed some range-based loops 
Jul 27
1511e63fc5bathomass
Rename documentation manual page names with leading the 
Jul 27
db8bf5c52f67thomass
Rename documentation manual page names with leading the 
Jul 27
cb4b1a8e3f65kislinsk
Merge branch 'bugfix/T27607-chartExample-UserManual' into develop 
Jul 27
2e04dd35ba46kislinsk
Remove dummy documentation of chartExample plugin 
Jul 27
0e7a0a80bd97kislinsk
Merge branch 'bugfix/T27607-chartExample-UserManual' into develop 
Jul 27
0004178ffad0kislinsk
Reinsert table of contents but fix page id 
Jul 27
5c239b6d51fbkislinsk
Merge branch 'bugfix/T27607-chartExample-UserManual' into develop 
Jul 27
31775ce54d69kislinsk
Remove table of contents instead of imageMacro 
Jul 27
67f46b71eabfkislinsk
Merge branch 'bugfix/T27607-chartExample-UserManual' into develop 
Jul 27
4aac1ab54990kislinsk
Temporarily remove imageMacro 
Jul 27
31d634d52d40kislinsk
Merge branch 'bugfix/T27607-chartExample-UserManual' into develop 
Jul 27
d724ea792c4bkislinsk
Move table of contents above any imageMacros 
Jul 27
c2b11310095fthomass/kislinsk
Task T26840-MitkHomepageReorganization-TopLevel-integrationBranch 
Jul 27
a7752cd49b46thomass/kislinsk
Task T26840-MitkHomepageReorganization-TopLevel-integrationBranch 
Jul 27
61b852be152cfloca
Commit missed changes of one renamed directory 
Jul 25
fb6195ff763afloca
Cleaned up naming of DICOM related modules 
Jul 25
e72944cdcf37floca
Renamed plugin org.mitk.gui.qt.dicom into org.mitk.gui.qt.dicombrowser 
Jul 24
b9af16068179floca
Fixed review remarks 
Jul 24