Editing Dicom package

Jump to navigation Jump to search
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.

The edit can be undone. Please check the comparison below to verify that this is what you want to do, and then publish the changes below to finish undoing the edit.

Latest revision Your text
Line 1: Line 1:
The {{Forge|dicom}} package is part of the [[Octave Forge]] project.  The package is currently maintained by John Donoghue.
At an early development stage. [http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/dicom/ octave-forge svn]
*Maintainer: Andy Buckle [http://sourceforge.net/sendmessage.php?touser=1760416contact]  
*Currently worked on by: Kris Thielemans


= What is the aim of this package? =
===Supporting library===
Digital communications in medicine (DICOM) is an information standard. Originally created for image transfer, the standard now deals with an large range of medical data. See http://medical.nema.org/ for more info.
[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


This package provides functions to read and write DICOM files. The functions in the package are intended to have similar usage as
sudo apt-get install libgdcm2.0
the dicom functions in the Matlab Image Processing Toolbox. In Octave they are separate: most image package users will not use dicom, and its dependency might be considered troublesome.


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


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


The {{Forge|dicom}} package requires the [[http://gdcm.sourceforge.net/wiki/index.php/Main_Page GDCM]] libraries and include files to be installed in order to compile.
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).


for fedora: yum install gdcm-devel
> mkdir gdcmbin
> ls
gdcmbin gdcm-2-0
> cd gdcmbin
> cmake -DGDCM_BUILD_SHARED_LIBS=ON ../gdcm-2-0/


for ubuntu: apt install libgdcm-dev
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


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


From octave commmand line:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib


>> pkg install -forge dicom
Mingw32 is similar. Get openSSL: [http://www.slproweb.com/products/Win32OpenSSL.html Win32 Openssl v1.0.0a Light]


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


Load it before any usage:
===Features===
 
All of these still need work, but they exist, and are usable to some extent.
>> pkg load dicom
 
 
=Features=
The following functions are available:
*dicomdict (load different dict - file follows same format as Matlab's)
*dicomdict (load different dict - file follows same format as Matlab's)
*dicominfo (load metadata into octave struct)
*dicominfo (load metadata into octave struct. nasty bug in SQ loading)
*dicomdisp (Display the structure of a dicom file)
*dicomlookup (keyword <-> tag)
*dicomlookup (keyword <-> tag)
*dicomread (load pixel data, 2D or 3D int types. Does not yield colormaps, yet.)
*dicomread (load pixel data, 2D or 3D int types. Does not yield colormaps, yet.)
*dicomwrite (write pixel data to a DICOM format file)
*dicomuid (generate a DICOM unique id)
*isdicom (verify if a file is a DICOM formatted file)
*dicomanon(anonomize a file)
*dicomfind(find an attribute in a file or dicom struct)
*dicomupdate(Update an attribute value in a dicom struct)


===Todo===
*dicomanon
*dicomuid
*dicomwrite
*isdicom
===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.


= See also =
*Octave (and Matlab) stores images (y,x) and DICOM is intrinsically (x,y). Does Matlab transpose images when it loads them?
* {{Forge|dicom}} at [[Octave Forge]].
**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.
* [https://sourceforge.net/projects/gdcm/ Grassroots DICOM].
*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?)


[[Category:Octave Forge]][[Category:Packages]]
[[Category:OctaveForge]]
[[Category:Packages]]
Please note that all contributions to Octave may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see Octave:Copyrights for details). Do not submit copyrighted work without permission!

To edit this page, please answer the question that appears below (more info):

Cancel Editing help (opens in new window)

Template used on this page:

Retrieved from "https://wiki.octave.org/Dicom_package"