Difference between revisions of "Dicom package"

From Octave
Jump to navigation Jump to search
(→‎Features: remove dicomwrite)
Line 44: Line 44:
 
*dicomanon
 
*dicomanon
 
*dicomuid
 
*dicomuid
 +
*dicomwrite
  
 
===Questions===
 
===Questions===

Revision as of 13:12, 20 December 2011

At an early development stage. octave-forge svn

  • Maintainer: Andy Buckle [1]
  • Currently worked on by: Kris Thielemans

Supporting library

GCDM. You can usually get this via your package manager,e e.g. on Ubuntu

sudo apt-get install libgdcm2.0

Alternatively, build it yourself. Get the source with subversion.

svn co https://gdcm.svn.sourceforge.net/svnroot/gdcm/branches/gdcm-2-0

cmake and g++ are required. create a gdcmbin directory parallel to the gdcm-2-0 directory. Change to gdcmbin and then run cmake (Linux/cygwin).

> mkdir gdcmbin
> ls
gdcmbin gdcm-2-0
> cd gdcmbin
> cmake -DGDCM_BUILD_SHARED_LIBS=ON ../gdcm-2-0/

This creates a Makefile in your gdcmbin directory. You can easily edit cmake options with "make edit_cache", for example to build applications like gdcmdump. "make help" is also very useful.

make install

On my system, I also had to add this to my ~/.bashrc.

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

Mingw32 is similar. Get openSSL: Win32 Openssl v1.0.0a Light

cmake -G "MinGW Makefile" -DGDCM_BUILD_SHARED_LIBS=ON ..\gdcm-2-0
mingw32-make all

Features

All of these still need work, but they exist, and are usable to some extent.

  • dicomdict (load different dict - file follows same format as Matlab's)
  • dicominfo (load metadata into octave struct. nasty bug in SQ loading)
  • dicomlookup (keyword <-> tag)
  • dicomread (load pixel data, 2D or 3D int types. Does not yield colormaps, yet.)

Todo

  • dicomanon
  • dicomuid
  • dicomwrite

Questions

I don't have a Matlab license available. I would like to make this package compatible with the dicom functions in Matlab's image processing toolbox, as far as possible.

  • Octave (and Matlab) stores images (y,x) and DICOM is intrinsically (x,y). Does Matlab transpose images when it loads them?
    • matlab reads the data from the dicom file as if it's a raw block of numbers (and then converts if necessary). Therefore, current Octave/dicom behaviour is compatible with matlab.
  • I would like people to try m-files that worked with Matlab to let me know of problems.
  • (not necessarily) Matlab related: I need examples of odd DICOM files. I have plenty with complex metadata, but I need some with unusual images.
    • More than one sample per pixel
    • Colour
    • Float types
  • DA (date) VR: does Matlab turn them into a string?
  • if the user supplies metadata (eg HighBit?, BitsStored?) that describe the type of the pixels and this is not in agreement with the type of the image matrix supplied, does Matlab
    • silently convert the image pixel type to match the metadata?
    • silently convert the metadata to match the pixel type?
    • error and do nothing?
  • What does dicominfo do when a tag is not in its dictionary: skip it or give error? I was wondering about turning the tag into a variable name, something like Tag_3243_0010. (Matlab 6.5 (2002): Private__3243_0010)
  • dicominfo: Items in sequences are not necessarily the same, so cannot be stored in arrays of structs. (Matlab 6.5 (2002): makes nested structs like dcm.RTDoseROISequence?.Item_1.DoseUnits?)