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

Bradley Lowekamp blowekamp at mail.nih.gov
Thu Sep 11 20:36:50 EDT 2014 

From [1] did you try:

conda install --use-local simpleitk
Brad

[1] http://conda.pydata.org/docs/build_tutorials/pkgs.html

On Sep 11, 2014, at 1:06 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> Hi All,
> I think python PythonPackage/setup.py installed wasn't in the location that the recipe calls for. I manually went to the location and ran the command. It was in the following folder
> 
> /Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping
> 
> After that when I checked for simpleITK in /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found
> 
> 
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK
> 
> Now, when I try to import simpleitk, i get an error which is shown below. 
> 
> >>> import SimpleITK as sitk
> 
> Traceback (most recent call last):
> 
>   File "<stdin>", line 1, in <module>
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
> 
>     from .SimpleITK import *
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
> 
>     _SimpleITK = swig_import_helper()
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
> 
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> 
> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libjpeg.8.dylib
> 
>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
> 
>   Reason: image not found
> 
> 
> 
> I am guessing that's a progress from where I was. Any ideas to fix this one?
> 
> 
> 
> Vishwa
> 
> 
> On Thu, Sep 11, 2014 at 11:18 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> Hi, 
> I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find the simpleitk directory. I ran the conda build again and saved the log file. I am attaching here for your reference. Hopefully, that should tell us something.
> 
> Vishwa
> 
> On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 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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>> 
>> 
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>> NAML
>> 
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> 
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