2011/11/3 Carnë Draug <carandraug+...@gmail.com>: > On 3 November 2011 11:14, Kris Thielemans <kris.f.thielem...@gmail.com> wrote: >> Hi >> I discovered that Andy Buckle has made some routines available for DICOM >> support in Octave. See also http://wiki.octave.org/wiki.pl?CategoryDicom. >> Thanks Andy! >> >> I've made some changes to the files currently in svn >> (octave-forge/extra/dicom/). However, I don't have write access to the svn, >> so I've attached them to this email as a patch. I'd be very happy if this >> would be committed. >> >> This code works fine for me on Ubuntu 11.04 and allows me to read GE Dicom >> PET and CT images, and GE raw data, which was a very pleasant surprise. With >> this update, I think this dicom package is much closer to being ready and >> compatible with matlab. I haven't looked at dicomwrite though. Also, there's >> a TODO in dicominfo.cpp related to error handling if a dictionary is not >> found. I also have some doubts if the code properly handles different >> endianness, but am not familiar enough with gdcm to know for sure (and don't >> seem to have the data to check it). >> >> Note that I'm rather new to octave, so I'm sure that the C++ code can be >> improved. Also, I'm not quite sure about conventions to be used for the >> texinfo documentation (e.g.: how do you write an argument that's a string?) >> so somebody should/could correct this. >> >> Here's a summary of the changes >> ------------------------------------------------------------ >> All files: changed include of gdcm files to use gdcm-2.0/ path, which is I >> think how it should be done. That also meant I don't have to add an include >> flag anymore after installing the gdcm package on Ubuntu. >> >> dicomread.cpp: >> - support usage where 1st argument is a structure with a field Filename >> (such as returned by dicominfo) for matlab compatibility. >> >> dicomdict.cpp: >> - make sure that 'get' and 'set' behaviour works correctly. To do that, >> there's now a static variable storing the current dictionary name and a >> function get_current_dict() to access it. I didn't remove Andy's disabled >> code for using a dictionary object, but I don't think it's necessary as we >> can get away with a string. >> - updated doc-string >> >> dicomdict.h: >> - moved declaration of load_dict() here to make it accessible in the other >> routines >> - declare new function get_current_dict() >> >> dicominfo.cpp: >> - support usage dicominfo(filename, 'dictionary', dictname) >> - support FL, FD and SL VRs, which means that many more fields are now read >> correctly from the dicom file. >> - check if the VR in the file is the same as the one in the dictionary. If >> not, issue a warning but use the VR from the file. >> - assign values to private dicom fields >> - changed convention for private fields to use lower-case for the >> hexadecimal numbers to be compatible with Matlab >> - if an entry is not in the dictionary, determine its VR from the file (if >> possible) and assign anyway. >> - updated doc-string >> >> Makefile: >> - set include flag empty >> - removed a few gdcm components that aren't installed with the gdcm ubuntu >> package (do they still exist?) and aren't necessary anyway. >> -------------------------------------------------------- >> >> Finally, a comment for the wiki at >> http://wiki.octave.org/wiki.pl?CategoryDicom >> >> Question: Octave (and Matlab) stores images (y,x) and DICOM is intrinsically >> (x,y). Does Matlab transpose images when it loads them? >> >> Answer: 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 hope this is useful for someone. Andy's code (and Octave!) was certainly >> useful for me. > > Hi Kris > > I added your note to the wiki. Also, if no one objects to your patch > in 3 days, I'll apply (or ping us back if for some reason it's not > done). Thank you > > Carnë
I feel guilty for not having made some time to fix this earlier. My next aim is to make a first release of the dicom package, probably without dicomwrite in the first instance. I would also like to make sure it works with mingw builds, prepare NSIS packages, and then advertise it to colleagues in my world (medical physics). I have not reviewed, yet, but it all sounds very sensible. I think Kris and I will be the only users for a while, so no one will be onconvenienced if something is not quite right. I have just re-installed the linux system I mostly use for this. So I need to build GDCM and Octave on it. So, Carnë, if you could go ahead and commit it (or Kris could have access to do it), please do. I had a little help from Judd Storrs to start, but it has mostly been me chugging away on my own, learning C++, as I go. Kris, maybe you could make some notes here too http://wiki.octave.org/wiki.pl?CategoryDicom -- /* andy buckle */ ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Octave-dev mailing list Octave-dev@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/octave-dev
