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| ==Digital communications in medicine (DICOM)== | | ==Digital communications in medicine (DICOM)== |
| There is a DICOM package hosted on sourceforge: [[dicom | more information]]. | | There is a DICOM package hosted on sourceforge: [[dicom | more information]]. |
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| At an early development stage. [http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/dicom/ octave-forge svn]
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| *Maintainer: Andy Buckle [http://sourceforge.net/sendmessage.php?touser=1760416contact]
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| *Currently worked on by: Kris Thielemans
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| ===Supporting library===
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| [http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Main_Page GCDM]. You can usually get this via your package manager,e e.g. on Ubuntu
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| sudo apt-get install libgdcm2.0
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| Alternatively, build it yourself. Get the source with subversion.
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| svn co https://gdcm.svn.sourceforge.net/svnroot/gdcm/branches/gdcm-2-0
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| 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).
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| > mkdir gdcmbin
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| > ls
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| gdcmbin gdcm-2-0
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| > cd gdcmbin
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| > cmake -DGDCM_BUILD_SHARED_LIBS=ON ../gdcm-2-0/
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| 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.
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| make install
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| On my system, I also had to add this to my ~/.bashrc.
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| export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
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| Mingw32 is similar. Get openSSL: [http://www.slproweb.com/products/Win32OpenSSL.html Win32 Openssl v1.0.0a Light]
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| cmake -G "MinGW Makefile" -DGDCM_BUILD_SHARED_LIBS=ON ..\gdcm-2-0
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| mingw32-make all
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| ===Features===
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| All of these still need work, but they exist, and are usable to some extent.
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| *dicomdict (load different dict - file follows same format as Matlab's)
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| *dicominfo (load metadata into octave struct. nasty bug in SQ loading)
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| *dicomlookup (keyword <-> tag)
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| *dicomread (load pixel data, 2D or 3D int types. Does not yield colormaps, yet.)
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| *dicomwrite (only does some 2D int types, ATM. No metadata control, yet)
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| ===Todo===
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| *dicomanon
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| *dicomuid
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| ===Questions===
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| 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.
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| *Octave (and Matlab) stores images (y,x) and DICOM is intrinsically (x,y). Does Matlab transpose images when it loads them?
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| **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.
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| *I would like people to try m-files that worked with Matlab to let me know of problems.
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| *(not necessarily) Matlab related: I need examples of odd DICOM files. I have plenty with complex metadata, but I need some with unusual images.
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| **More than one sample per pixel
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| **Colour
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| **Float types
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| *DA (date) VR: does Matlab turn them into a string?
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| *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
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| **silently convert the image pixel type to match the metadata?
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| **silently convert the metadata to match the pixel type?
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| **error and do nothing?
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| *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)
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| *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?)
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| == Fixed point toolbox == | | == Fixed point toolbox == |