[Insight-users] SimpleITK / jar wrapper?

Thu Apr 19 15:11:11 EDT 2012

Thanks Brad. Just another question: I used the setPixelAsInt16 method, but it works per voxel. The issue is that I have to loop over 3 dimensions from within Matlab to call this method to construct an image object. This looping is extremely time consuming in Matlab. So a method where I can pass the entire 3D matrix would be very efficient for Matlab.

Registration wrappers would be great and we all certainly look forward to having them.

- Aditya

On 4/19/12 9:44 AM, "Bradley Lowekamp" <blowekamp at mail.nih.gov> wrote:

Hello,

There are examples in the MICCAI 2011 tutorial presentation:

http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011

And there are those that are in the source code and in the Doxygen:

http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011

Registration is still underdevelopment and it forthcoming. We have gone through a few prototypes and have settled on one but there is still a good bit of work to do.

Brad

On Apr 18, 2012, at 5:16 PM, aptea at mskcc.org wrote:

Re: [Insight-users] SimpleITK / jar wrapper?
Thanks Brad. It works like a charm!!

I tested it by reading in a Dicom image and calculating statistics on it. I am specifically interested in image Registration and Segmentation. Are there any examples for those?

Thanks,
Aditya

On 4/18/12 4:29 PM, "Bradley Lowekamp" <blowekamp at mail.nih.gov <x-msg://25/blowekamp@mail.nih.gov> > wrote:

Hello,

It appears that the Wrapping read me is a bit out of date. It would be good if you could add this issue to the SimpleITK issue tracker:

https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK

This visual guide is mostly current:

http://www.vtk.org/Wiki/A_visual_guide_to_SimpleITK_in_Java

I believe the bit you need are:

SimpleITK-build/Wrapping/simpleitk-0.5.0.jar
SimpleITK-build/Wrapping/simpleitk-javadoc-0.5.0.jar
SimpleITK-build/Wrapping/simpleitk-source-0.5.0.jar

Then there is the needed java native shared library which currently is here:

SimpleITK-build/lib/libSimpleITKJava.jnilib

Which has moved since the release version from SimpleITK-build/Wrapping.

On Apr 18, 2012, at 4:08 PM, aptea at mskcc.org <x-msg://25/aptea@mskcc.org>  wrote:

Re: [Insight-users] SimpleITK / jar wrapper?
Hello Brad,

Thanks for your reply. I tried to build SimpleITK using the following procedure:
git clone --recursive  http://itk.org/SimpleITK.git
mkdir SimpleITK-build
cd SimpleITK-build

Then, I used “make” to build SimpleITK. It ran until 32% completion, and gave the following message:

Linking CXX shared module ../lib/simpleitk.bundle
ld: framework not found ruby
collect2: ld returned 1 exit status
make[5]: *** [lib/simpleitk.bundle] Error 1
make[4]: *** [Wrapping/CMakeFiles/simpleitk.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
make: *** [all] Error 2

It did create simpleitk-0.4.0.jar file under SimpleITK-build/Wrapper directory. Then, I tried to use this .jar file within Matlab. For this, I added  the file to classpath, but I am not able to load the classes within this file as described in the examples. For example, org.itk.simple.ImageFileReader could not be accessed and so on. The documentation under http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html mentions that I should get org.itk.simple.jar file that contains the required classes. But I did not get this file when I built SimpleITK. So I am confused about where to find the java classes that wrap ITK functions.

Thanks,
Aditya

On 4/18/12 3:49 PM, "Bradley Lowekamp" <blowekamp at mail.nih.gov <x-msg://25/blowekamp@mail.nih.gov>  <x-msg://497/blowekamp@mail.nih.gov <x-msg://497/blowekamp@mail.nih.gov> > > wrote:

Hello,

The SimpleITK Getting Started wiki page a a section for Binaries:

http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Binaries

Which points to SourceForge for the Java Binaries:

http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/

Where there is a download for Java for MacOSX 10.6:

SimpleITK-0.4.0-Java-maxosx-10.6-intel.zip <http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/SimpleITK-0.4.0-Java-maxosx-10.6-intel.zip/download>

This would likely also work for macOSX 10.7 as well.

I also would like to know what was the issue when you tried to compile SimpleITK on OSX.

Thanks,
Brad

On Apr 18, 2012, at 3:32 PM, aptea at mskcc.org <x-msg://25/aptea@mskcc.org>  <x-msg://497/aptea@mskcc.org <x-msg://497/aptea@mskcc.org> >  wrote:

SimpleITK / jar wrapper?
Are SimpleITK Wrapper .jar files available for download?
I failed to build SimpleITK for Mac OS X, so was wondering if I could use the binaries directly?
Many thanks!

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========================================================

Bradley Lowekamp

Medical Science and Computing for

Office of High Performance Computing and Communications

National Library of Medicine

blowekamp at mail.nih.gov <x-msg://25/blowekamp@mail.nih.gov>  <x-msg://497/blowekamp@mail.nih.gov <x-msg://497/blowekamp@mail.nih.gov> >

========================================================

Bradley Lowekamp

Medical Science and Computing for

Office of High Performance Computing and Communications

National Library of Medicine

blowekamp at mail.nih.gov <x-msg://25/blowekamp@mail.nih.gov>

========================================================

Bradley Lowekamp

Medical Science and Computing for

Office of High Performance Computing and Communications

National Library of Medicine

blowekamp at mail.nih.gov

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