[ITK-users] using simpleITK with anaconda python distribution

[Bradley Lowekamp]

Hello,

You need to use the conda build environment. Look at the readme in this repo[1].

Basically you'll need to do the following:

$ conda install conda-build
$ cd src
$ git clone https://github.com/thewtex/conda-recipes.git
$ git checkout simpleitk-clone-url
$ conda build simpleitk



[1] https://github.com/conda/conda-recipes

On Sep 10, 2014, at 11:01 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> Thanks very much for the information. I looked at the conda recipe. There are three files. 
> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile..
> 
> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. 
> 
> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. 
> 
> Best regards,
> Vishwa
> 
> 
> 
> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> This error message frequently happens when SimpleITK is compiled against a different version of  Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.
> 
> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.
> 
> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.
> 
> Also you can inspect the runtime libraries:
> 
>  otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
> 	@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
> 	/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)
> 	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)
> 
> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme
> 
> Hope this helps,
> Brad
> 
> On Sep 9, 2014, at 10:55 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> 
>> import SimpleITK as sitk
>> 
>> Fatal Python error: PyThreadState_Get: no current thread
>> 
>> 
>> Abort trap: 6
>> 
> 
> 
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