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

Vishwa vishwanath.somashekar at gmail.com
Thu Sep 11 13:06:10 EDT 2014 

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]
>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=0>> 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]
>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=1>> 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]
>>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=2>> wrote:
>>>>
>>>> import SimpleITK as sitk
>>>>
>>>> Fatal Python error: PyThreadState_Get: no current thread
>>>>
>>>> Abort trap: 6
>>>>
>>>>
>>>>
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