Difference between revisions of "Dicom package"
(move stuff from "code" page)
Revision as of 16:54, 1 December 2011
At an early development stage. octave-forge svn
- Maintainer: Andy Buckle 
- Currently worked on by: Kris Thielemans
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.
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.
On my system, I also had to add this to my ~/.bashrc.
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
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.)
- dicomwrite (only does some 2D int types, ATM. No metadata control, yet)
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
- 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?)