[Insight-users] SimpleITK / jar wrapper?
Bradley Lowekamp
blowekamp at mail.nih.gov
Thu Apr 19 09:44:08 EDT 2012
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:
> 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> 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 It appears that the Wrapping read me is a bit out of date.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 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://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://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://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
>>
>>
>>
>>
========================================================
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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