Re: Dicom package on Mac OS X

[Andy Buckle]

On 16 June 2014 18:35, Miloslav <address@hidden> wrote:

Hi again,

thanks to everyone for their responses. It seems that I made it work! I had to do the following:

1. uninstall Octave (which was installed from dmg file)
2. install Homebrew (http://brew.sh/)
  2a. brew doctor (here it complained about previously installed static GDCM libraries, so I deleted them)
3. followed guide to install Octave for Mac using Homebrew (http://wiki.octave.org/Octave_for_MacOS_X#Homebrew)
  3a. minor exception is that I was not able to install gfortran, instead it suggested installing gcc (brew install gcc)
4. before I could start with installation of Octave I had to download and install LaTeX for mac (MacTex-2014)
5. install Octave (brew install octave)

The installation ran for about an hour. When done, I was able to launch Octave from the Terminal with:
 octave --force-gui
However, at this point there was a problem with plotting and launching X11. This was fixed by creating .octaverc file in my home directory and adding the line:
setenv ("GNUTERM", "X11”)

6. Installed again the supporting GDCM library from source code through Makefile as described here: http://wiki.octave.org/Dicom_package
Here I decided to go with an older version of the library (gdcm-2.0.19)

7. Exported the path to the library with
  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/lib
  7a. Here I checked again with
        echo $DYLD_LIBRARY_PATH
        that gave the right answer:
        :/usr/local/lib
        It is a bit weird, because this information should be stored in .bashrc file in the home directory. There was no such file, so I created it. But even after exporting the path, the file contained no information. So, where is the path stored? Nevertheless, it works somehow.

8. I took the dicom package and did the corrections that Sebastian suggested earlier (I omitted the one line that was only required when working with gdcm 2.4, because I decided to use gdcm 2.0):

#extract package
tar -zxvf dicom-0.1.1.tar.gz
#add correct include and libdirs
perl -pi -e 's/INCDIRFLAGS =.*/INCDIRFLAGS =\t-I\/usr\/local\/include/' dicom/src/Makefile
perl -pi -e 's/LIBDIRFLAGS =.*/LIBDIRFLAGS =\t-L\/usr\/local\/lib/' dicom/src/Makefile

# repack
tar -zcvf dicom-0.1.1patched.tar.gz dicom

9. Launched Octave (octave --force-gui) and installed the patched package with:
  pkg install dicom-0.1.1patched.tar.gz
It gave me some warnings (see below), but the package seems to be installed and working. I tried some real data that I have from an MRI scanner and it was able to load the dicom information and the imaging data correctly. Basically, I have no idea what I was doing, but I am happy that I can work with dicom files on my Mac now :-)

Miloslav


The warnings that I got during Dicom package installation:

>> pkg install dicom-0.1.1patched.tar.gz

dicominfo.cpp:79:1: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
Octave_map dump(const char filename[], int chatty);
^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:80:18: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth);
                 ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:82:18: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void dumpElement(Octave_map *om, const gdcm::DataElement * elem, int chatty, int sequenceDepth);
                 ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:166:2: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
        Octave_map om=dump(filename.c_str(),chatty);
        ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:175:1: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
Octave_map dump(const char filename[], int chatty) {
^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:177:2: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
        Octave_map om;
        ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:205:18: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth) {
                 ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:215:18: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void dumpElement(Octave_map *om, const gdcm::DataElement * elem,
                 ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:456:2: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
        Octave_map om;
        ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicominfo.cpp:459:3: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
                Octave_map subom;
                ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
10 warnings generated.
dicomwrite.cpp:46:55: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth);
                                                      ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicomwrite.cpp:135:2: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
        Octave_map om=ov.map_value();
        ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicomwrite.cpp:182:55: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth) {
                                                      ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicomwrite.cpp:190:3: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
                Octave_map subom = cell(0).map_value();
                ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
dicomwrite.cpp:292:3: warning: 'Octave_map' is deprecated [-Wdeprecated-declarations]
                Octave_map subom = ov->map_value();
                ^
/usr/local/Cellar/octave/3.8.1/include/octave-3.8.1/octave/oct-map.h:484:1: note: 'Octave_map' declared here
Octave_map
^
5 warnings generated.

A lot of those warnings are just becuase I have not updated the dicom package in a few years. what can i say, kids get in the way.

thanks for posting the detailed how-to. may well be useful for someone else.

--
/* andy buckle */