Editing Dicom package

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

===Supporting library===
[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

 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: [http://www.slproweb.com/products/Win32OpenSSL.html 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. possible 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
*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.

*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). We think that 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. Answer: assign to a field like Private_3243_0010 (as Matlab)
*dicominfo: Items in sequences are not necessarily the same, so are stored as nested structs like dcm.RTDoseROISequence?.Item_1.DoseUnits?(as Matlab)

[[Category:OctaveForge]]
[[Category:Packages]]
@@ Line 1: / Line 1: @@
-The {{Forge|dicom}} package is part of the [[Octave Forge]] project.  The package is at an early development stage and it is maintained by Andy Buckle with contributions by Judd Storrs and Kris Thielemans.
+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 (eventually) write DICOM files. The functions in the package are intended to have similar usage as
-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.
-== Platforms ==
-{{Warning|The information of this section needs be reviewed (June 2019).}}
-*Linux. Tested on OpenSuSE 11.4 and Ubuntu. No known issues. GDCM is required: see below.
-*mingw
-**Ben Lindner's Octave 3.2.4 and the mingw build environment (gcc 4.4.0): dicom package 0.1.1 does not build against this older version of the Octave API.
-**Tatsuro/Nitzan's Octave 3.4.3 and mingw build environment (gcc 4.5.2): gdcm and dicom package build OK. Get segfault in ntdll.dll when one of the dicom*.oct files calls something from a gdcm*.dll.
-**mxe-octave: dicom and gdcm distributed as part of the installed package.
-*Cygwin: Panic when oct file called (or maybe when oct file uses gdcm dll). Need to try rebaseall
-==Supporting library==
-[http://gdcm.sourceforge.net/wiki/index.php/Main_Page GDCM]. You can usually get this via your package manager, e.g. on Ubuntu
   sudo apt-get install libgdcm2.0
-Alternatively, build it yourself. Get the source with git.
+Alternatively, build it yourself. Get the source with subversion.
-  git clone https://git.code.sf.net/p/gdcm/gdcm
+  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).
@@ Line 47: / Line 33: @@
   mingw32-make all
-On Cygwin gdcm 2.0.18 (and maybe some other versions) may have a problem with newer cmake. This kludge persuades cmake to define WIN32.
+===Features===
- cmake -DGDCM_BUILD_SHARED_LIBS=ON -DCMAKE_CXX_COMPILER=g++.exe -DCMAKE_LEGACY_CYGWIN_WIN32=1 ../gdcm-2.0.18/
-==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)
@@ Line 57: / Line 39: @@
 *dicomlookup (keyword <-> tag)
 *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)
-==Todo==
+===Todo===
 *dicomanon
+*dicomuid
+*dicomwrite
+*isdicom
-==Questions==
+===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.
@@ Line 80: / Line 62: @@
 **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. Answer: assign to a field like Private_3243_0010 (as Matlab)
+*dicominfo: Items in sequences are not necessarily the same, so are stored as nested structs like dcm.RTDoseROISequence?.Item_1.DoseUnits?(as Matlab)
-== Answered ==
+[[Category:OctaveForge]]
-*dicominfo: Items in sequences are not necessarily the same, so are stored as nested structs like dcm.RTDoseROISequence.Item_1.DoseUnits(as Matlab)
+[[Category:Packages]]
-*What does dicominfo do when a tag is not in its dictionary? Answer: assign to a field like Private_3243_0010 (as Matlab)
-== See also ==
-* {{Forge|dicom}} at [[Octave Forge]].
-* [https://sourceforge.net/projects/gdcm/ Grassroots DICOM].
-[[Category:Octave Forge]]