ITK/Release 4/DICOM

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Improving DICOM Support

Goals

Improve the support for DICOM in ITK

  1. DICOM communication layer (a.k.a. PACS support, DICOM Protocol)
  2. Streaming of DICOM Objects
  3. Read and write RTStruct
  4. Type checking
  5. Minimum DICOM skeleton generation

Other requests from the ITK community

  • handling of higher order manifold as described in DICOM standard
  • handling of DICOMDIR format disk archives (navneeth)
    • Unlike a standard dicom series (located in a single directory) the DICOMDIR format spreads files across directories
    • A reader that reads the DICOMDIR file and parses appropriate files & directories is desirable

Development process

The idea is to simplify the maintenance in the future:

  • update included version of gdcm
  • synchronise included version and gdcm proper
  • send the patches upstream

To do this, we forked a version of gdcm in github to use for integration and maintenance in iTK v4 (https://github.com/ComplexSystemsModeling/GDCM). This fork will get all the modifications and patches from ITK, and will let us easily send them upstream. Builds for ITK using this fork and the original gdcm (https://github.com/malaterre/GDCM) have been set up. Eventually there will be three kinds of itk/gdcm builds on the dashboard:

  • ITK with included gdcm
  • ITK with SYSTEM_GDCM using our fork
  • ITK with SYSTEM_GDCM using gdcm proper

Modifications should go to our fork of gdcm first, so we expect the ITK with GDCM FORK to be the greenest. Then, we should transfer those to ITK, and eventually upstream.

dev process:

  • modify code (this can be either in ITK or in GDCM FORK, depending on the modification)
  • (re) install GDCM FORK on the system (as ITK does not work with a build tree of gdcm)
  • check ITK with GDCM FORK (local-experimental-nightly)
  • push to itk-gerrit
  • check ITK proper builds
  • gerrit merge

That means, developers need to maintain both a SYSTEM GDCM FORK build and an ITK build locally.

Discussions and Brainstorming

Discussions about PACS Support

Discussion about Streaming

  • Original GDCM Milestone here
  • Overview (should be made JIRA tickets. Some of them are done already, to check)
    • Create a gdcm.StreamImageReader
    • Add support for extent to ImageCodec hierarchy
    • Make JPEG2000Codec Streamable
    • Make JPEGCodec Streamable
    • Make RAWCodec Streamable
    • Make RLECodec Streamable
    • Make JPEGLSCodec Streamable
    • Update CharLS for streaming capability
    • Add support for BasicOffsetTable
  • Malaterre: to the best of my knownledge they can be executed in this order. The goal being to import subportion of large file in ITK. For this one'll need to implement a new gdcm.ImageReader (I called it gdcm.StreamImageReader), I have explained the implementation details of this class in bug #53.
  • Once this class is done, you will start by making the RAW codec 'streamable'. It should only read a subportion of a RAW (uncompressed) DICOM file, then you'll move on to more complex one (JPEG, J2K, RLE and JPEG-LS).

Discussion about RT-Struct

  • there is an existing implementation in vtk. Reading should be easier than writing, the later requiring some DICOM knowledge.
    • vtkGDCMPolyDataReader here
      • The actual function needed is here int vtkGDCMPolyDataReader::RequestData_RTStructureSetStorage(gdcm::Reader const &reader, vtkInformationVector *outputVector)
    • vtkGDCMPolyDataWriter here
    • vtkRTStructSetProperties here
    • Examples/Cxx/GenerateRTSTRUCT
  • there is IJ papers to read and write RTSTRUCT
  • Some leftover GDCM milestone here

Roadmap

TCons

Meeting