Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
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Reading DICOM data into mitk::Images is a complicated business since DICOM and MITK have very different ideas of images.
DICOMITKSeriesGDCMReader (formerly: DicomSeriesReader) brings DICOM and MITK as close together as possible by offering methods to load DICOM CT and MR images into mitk::Images, optionally grouping slices to 3D+t images.
Since there are so many possible sources for mistakes with any change to this loading process, testing the many assumptions implemented in DICOMITKSeriesGDCMReader is worthwhile. This document describes what and how theses kind of tests are implemented.
The task of loading DICOM files into mitk::Images is a challenge because of major differences in the way that DICOM and MITK represent images:
Because image processing applications based on MITK still need a way to load DICOM images into mitk::Image objects, MITK needs a way to build image stacks and this needs to be well tested.
For more background information, see David Clunie's most valuable posts on comp.protocols.dicom, e.g.:
The general idea for DICOM loaing tests is to run a set of known DICOM files through DICOMITKSeriesGDCMReader's methods GetSeries() and LoadDicomSeries() to generate mitk::Images. These images are then compared to expected image properties, such as the number of individual mitk::Images, positions, orientations, spacings, etc.
Stored expectations look like this (should be self-explanatory):
-- Image 1 Pixeltype: s BitsPerPixel: 16 Dimension: 4 Dimensions: 64 64 6 1 Geometry: Matrix: 5.25 0 0 0 5.2468 0.139598 0 -0.183222 3.99757 Offset: -159.672 -309.974 -69.0122 Center: 0 0 0 Translation: -159.672 -309.974 -69.0122 Scale: 1 1 1 Origin: -159.672 -309.974 -69.0122 Spacing: 5.25 5.25 4 TimeBounds: 0 1 -- Image 2 Pixeltype: s BitsPerPixel: 16 Dimension: 4 Dimensions: 64 64 41 1 Geometry: Matrix: 5.25 0 0 0 5.25 0 0 0 4 Offset: -160.672 -311.672 -285 Center: 0 0 0 Translation: -160.672 -311.672 -285 Scale: 1 1 1 Origin: -160.672 -311.672 -285 Spacing: 5.25 5.25 4 TimeBounds: 0 1
Application DumpDICOMMitkImage
Takes a list of DICOM images, loads them using TestDICOMLoading, then dumps information about the resulting mitk::Images to standard output.
This application is helpful when defining reference data for tests.
Application VerifyDICOMMitkImageDump
Takes a list of DICOM images and loads them using TestDICOMLoading. Takes a dump file as generated by DumpDICOMMitkImage, parses it and compares it to actually generated mitk::Images.
This application is used to implement the majority of test cases. They all load images, then verify the expected result structure.
Class TestDICOMLoading
Individual test cases are stored in the MITK-Data repository and constructed by Core/Code/Testing/DICOMTesting/Testing/CMakeLists.txt
The CMake file parses given directories for subdirectories containing specific test cases. Each directory contains two files:
Each test case is translated into a CTest test which evaluates the return value of a call to VerifyDICOMMitkImageDump.
From test set TinyCTAbdomen (see description.txt in this directory for details on test images):
From test set TiltHead (see description.txt in this directory for details on test images):
This list is meant to provide an up-to-date list of all implemented DICOM loading tests. If you ever find this outdated, please update it or make the persons who invalidated the list update it.
mitkDICOMTestingSanityTest_* These tests implement basic testing of the implemented helper classes. The tests use DICOMITKSeriesGDCMReader to load a number of DICOM image. They verify: