MITK ReleaseNotes 2014.10

MITK ReleaseNotes 2014.10

This is the 2014.10 release of the MITK release cycle. The complete list of new features, bug fixes and known issues is down on this page.

What's included?

Binary installers for Windows, Mac OS X and Linux are provided, which contain the MITK Workbench application. In addition to image loading/saving and level windowing, the following plugins are included:

• Volume Visualization
• Measurement
• Interactive Segmentation
• Logging View
• experimental DICOM Query/Retrieve (based on components from the Common Toolkit CTK)

The following plugins have been newly added in this version:

• Remeshing:

Optimize and resample your surface meshes

• Pointset Interaction:

Place seedpoints, correspondences, or landmarks

• Image Cropper:

VOI selection based on various shapes

• View Navigator:

Easily access views and perspectives & create new perspectives

• Screenshot Maker:

Create high resolution screenshots of your data

• experimental Movie Maker:

Create videos of your data using timeline based animations

• experimental Point-based, rigid and manual registration

Please note that the installers do not contain the source code or header files for the precompiled libraries. To develop applications or plugins with MITK please get the source code.

How to get it?

Please have a look at the download page.

Highlights of 2014.10 release

Build system

• Support for CMake 3.0
• Recommended Doxygen version is now 1.8.7
• Mac OS X
  • MITK Workbench Installers for Mac OS X 10.7+
  • Full support for MITK development on Mac OS X 10.9
  • Full support for clang 6.0 compiler
  • Dropped support for gcc compiler

Core modules

The MitkCore module gained the following new features:

• New I/O concept based on new new IFileReader and IFileWriter interfaces
• Vector image support has been added to mitk::Image and the ITK access macros
• Image read and write accessors together with ITK macros now handle const and non-const mitk::Image instances correctly
• Ongoing refactoring of the geometry classes:
  • New abstract BaseGeometry class
  • New inheritance of geometry classes
  • Geometry2D replaced by existing PlaneGeometry
  • All variables are private now
  • More information here

The CppMicroServices library now features:

• Usage of arbitray classes as service interfaces without the need to decorate the class with a US_DECLARE_SERVICE_INTERFACE macro.
• Improved static library handling.
• Improved resources system based on embedded zip files.

Modules

The following modules were newly added or factored out from existing modules:

• DICOMReader and DICOMTesting for advanced reading of DICOM files
• DicomRT for handling Radio-Therapy dose images and RT structure sets
• LegacyIO containing the deprecated I/O system (this module will be removed again in the future)
• QtOverlays containing Qt-based overlays (factored out from the Overlays module)
• XNAT (experimental) for accessing XNAT session objects as service objects

Python

• Reworked Python-Wrapping: More information here.

Segmentation

The 3D interpolation has been improved in many areas:

• Speed-up of interpolation time
• Undo/Redo working
• Live Wire tool is now also working in combination with the 3D interpolation
• Save 3D interpolation as a MITK scene file and reinit interpolation across application restart

MITK Workbench

• New icon theme

IGT

• New persistence framework to store GUI parameters until next start of the application
• New design of the navigation data player

Third-Party Toolkits

The following toolkits were updated:

• Boost (1.56)
• CTK (65420ed0)
• Qxt (3e7424f842d4)
• VTK (6.1.0+74f4888)

The following third-party toolkits were added to the MITK superbuild:

• Numpy
• Eigen
• PCRE
• Python
• SimpleITK
• Swig
• ZLIB

Deprecated Functionality

The documentation contains a detailed list of deprecated functionality. Please find a summary below:

• The previous I/O system has been deprecated and will be removed in the future.
• Some MITK macros for C++ unit testing have been deprecated.
• The Qxt library will not be included anymore starting with the next release
• Early announcement: The next release will be based on Qt5. Qt4 support might be declared deprecated in the next release and dropped in the release after next.

Breaking Changes

Breaking changes related to CTK:

• The syntax for specifying library versions when pre-loading them using berry::Platform::ARG_PRELOAD_LIBRARY changed from *libMyLibrary:1.0* to *libMyLibrary$1.0* (fixing a bug when using absolute library paths on Windows).

Breaking changes related to CppMicroServices:

• The signature of the usFunctionEmbedResources CMake macro changed.
• If a service interface was used in qobject_cast calls (e.g. in the CTK Plugin Framework context) and that service interface does not inherit from QObject and does not provide its own Q_DECLARE_INTERFACE macro, the newly introduced MITK_DECLARE_SERVICE_INTERFACE macro must be used (instead of the US_DECLARE_SERVICE_INTERFACE macro). See this code for an example.

Bugfixes

In the 8 months since the last release more than 400 bugs were fixed.

Not everything could be fixed in time, so here are the most important known issues

New feature list

Complete list of new features since MITK 2014.10:

ID	Comp	Summary
16117	BlueBerry	Add print(er) support
16272	Build system	Build system support for Qt5 + QML demo application
16865	Build system
18035	Build system	CDash clients should display pretty distribution names in their build name
18160	Build system	Implement possibility to switch between different icon sets
18323	Build system	Define MITK Diffusion specific MITK_BUILD_CONFIGURATION
17832	Build system	Update CTK for improved XNAT support
15749	Core	Compression should be configurable in mitkImageWriter
17738	Core	Alternative projections for thick slice mode
17196	Core	DisplayInteractor should support more configuration
15852	Core	platformproject: enable easy conversion of datatypes Point/Vector/Matrix from and to MITK
17934	Core	ImageWriteAccessor should ignore ReadAccessors with IgnoreLock option
17931	Core	ImageToItk should lock input image for reading if output image is const
17986	Core	Enable mitk::Image to contain itk::VectorImage
15821	Core	Add possibility to accessByItk using ReadAccessor
17960	Core	Image loaded from DICOM should have property containing the modality
16862	Core	Disable repositioning region on window resize
17727	Core	Add support for renderer specific property predicate
17035	Core	Introduce new Geometry concept: BaseGeometry class, less inheritance, etc (Platform project)
16744	Core	Refactoring of DicomSeriesReader
17918	Core	Introduce hidden objects in the data storage
17441	Diffusion	Setup NonLocalMeansDenoisingTest
17592	Diffusion	Fiberfox: image input to determine non-fiber volume fractions
15770	Diffusion	Multishell Signal Processing
17757	Diffusion	DICOM export from CL (MiniApp)
17760	Diffusion	Include Resampling to fixed spacing into BatchedRegistration
17626	Diffusion	refactor PreprocessingView Layout
17820	Diffusion	Enhance BatchedFolderRegistration
17961	Diffusion	Resampling MiniApp for regular Images and DW Images
17811	Diffusion	Improve Connectomics mini apps functionality
17968	Diffusion	Implement mit diffusion navigator view
17994	Diffusion	Create random parcellation view
8870	Diffusion	Highlight selected ROI if Fiber Bundle Operations View is active
17973	Diffusion	XML support for diffusion miniapps
18234	Diffusion	segmentation view should be included in fiber processing perspective
15630	Documentation	Refer to image documentation in doxygen class description
14420	Documentation	Fix up documentation to be pdf ready
18146	Documentation	Improve Viewnavigator documentation
17718	IGT	Workerthreads for tracking plugins
17735	IGT	Make tool landmarks editable in the navigation tool manager
17922	IGT	Change tool color if navigation tool is invalid
17771	IGT	Add method to get raw displacement navigation data from mitk::NodeDisplacementFilter
17690	Measurement	Refactor intensity profile computation
18094	Measurement	Implement intensity profile computation
17824	Modules	QmitkUSNewVideoDeviceWidget does not offer a file open dialog for video files
17840	Modules	USDevice should notify about property changes.
17859	Modules	Method for getting if at least one calibration for a Combined Modality was loaded.
17861	Modules	Documentation of the ultrasound module should be updated to reflect the current status of the module
16625	Modules	PlanarCircle should be editable with each point on the circle
16623	Modules	Make OpenCV GrabCut algorithm available in MITK
18116	Modules	Integrate personal simulation branch
15104	Modules	Create Overlay framework for managing different types of graphic items in the renderwindows
17911	Modules	US Telemed devices: get image geometry from device
17846	Modules	RT structureset reader refactoring
17847	Modules	RT dose-image reader refactoring
16643	Modules	Persistence framework for MITK
17987	Other	Enable / disable mbilog output
15803	Other	Eliminate compiler warnings
17689	QtWidget	Implement plot widget based on gnuplot
17536	QtWidget	Clean up QtWidgetsExt
15912	QtWidget	QmitkTransferFunctionWidget lacks renderer-specific transfer function ability
14386	Rendering	Colormaps and look-up tables
18136	Rendering	Use existing scalar lookup table from vtkPolyData in SurfaceGLMapper2D
17567	Segmentation	Otsu 3D Tool: selection of multiple classes
16095	Segmentation	When creating a polygon the resulting data nodes should clear naming
15851	Segmentation	Create user manual for clipping plane view
12304	Segmentation	Intersection contour detection should cover more cases
18007	Segmentation	Re-initialization of the 3D interpolation after application restart
17803	Segmentation	Implement ImageToContourModelFilter
17124	ToF	Kinect V2 texture mapping
12047	Workbench	Segmentation perspective missing in ext app installer
17525	Workbench	Number of bins of the histogram in the statistics view is fix defined
17866	Workbench	Ultrasound plugin should automatically select first entry on the device lists
16294	Workbench	XNAT Browsing Editor for MITK
18157	Workbench	Set default focus of view navigator to search bar
17923	Workbench	Persistence for Ultrasound plugin