[ITK-users] Fwd: using simpleITK with anaconda python distribution

[Bradley Lowekamp]

Hello,

First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory.

Brad
On Sep 11, 2014, at 12:43 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> 
> 
> I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. 
> 
> Any ideas?
> 
> Vishwa
> 
> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] <ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:
> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
>> 
>>> import SimpleITK as sitk
>>> 
>>> Fatal Python error: PyThreadState_Get: no current thread
>>> 
>>> 
>>> Abort trap: 6
>>> 
>> 
>> 
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