[ITK-users] Simple ITK Python not working on Mac El Capitan (10.11)

paniwani paniwani at gmail.com
Fri Jun 17 14:55:26 EDT 2016 

I had several versions of Python installed. I removed the version at
/Library/Frameworks and reinstalled Python 2.7 using Homebrew. I then
followed the advice of the guide and setup a virtual environment within my
project (called ecvenv), installed pip, upgraded pip, and used it to
install SimpleITK. It installed the one you recommended earlier, v0.9.1.

(ecvenv) *➜  **econtour* *git:(**master**) **✗* pip install  --trusted-host
www.simpleitk.org -f
http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
SimpleITK

Collecting SimpleITK

  Downloading
https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
(72.6MB)

    100% |████████████████████████████████| 72.6MB 43.5MB/s

Installing collected packages: SimpleITK

Successfully installed SimpleITK-0.9.1


However, I continue to run into a "Fatal Python Error" when trying to load
simple itk from within python. See below:

(ecvenv) *➜  **econtour* *git:(**master**) **✗* which python

/Users/neil/work/Meteor/econtour/ecvenv/bin/python

(ecvenv) *➜  **econtour* *git:(**master**) **✗* which pip

/Users/neil/work/Meteor/econtour/ecvenv/bin/pip

(ecvenv) *➜  **econtour* *git:(**master**) **✗* pip list

pip (8.1.2)

setuptools (23.0.0)

SimpleITK (0.9.1)

wheel (0.29.0)

(ecvenv) *➜  **econtour* *git:(**master**) **✗* python

Python 2.7.11 (default, Jan 22 2016, 08:29:18)

[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import SimpleITK as sitk

Fatal Python error: PyThreadState_Get: no current thread

[1]    2805 abort      python




On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] <
ml-node+s7n37269h95 at n7.nabble.com> wrote:

> Hi,
>
> Where did you get you python from? You are using a version from
> /Library/Framework/Python.frameworks, which is not the system version.
>
> The error with the first command gives you a suggestion on how to solve
> the problem.
>
> The second error appears to be a binary compatibility issue with the
> distribution you have of python.
>
> Please read the guidance on the wiki with the different distributions of
> python, along with following the recommendation to setup a virtual
> environment.
>
> https://itk.org/Wiki/SimpleITK/GettingStarted
>
> Good luck,
> Brad
>
>
>
>
> > On Jun 17, 2016, at 11:20 AM, paniwani <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=37269&i=0>> wrote:
> >
> > Hi,
> >
> > It appears the code that I pasted did not show up in the email version
> of
> > the mailing list. I've re-pasted below. I'm using system Python 2.7 and
> Mac
> > OSX El Capitan. Thank you!
> >
> > -----
> >
> > I was using simple ITK with python in my application with no problems
> until
> > I recently upgraded to El Capitan on my Mac. Since then, I have received
> > error messages regarding 64-bit issues. I've tried to reinstall simple
> ITK
> > multiple times using the python binaries as stated here
> > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with
> both
> > pip and easy_install. However, I continue to run into issues running
> > simpleITK.
> >
> > I am on OSX El Capitan (10.11) and Python 2.7.
> >
> > Here is the output when I try to install the latest via pip and and use
> it:
> >
> > ➜  Downloads sudo pip install  --trusted-host www.simpleitk.org -f
> > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
> > SimpleITK
> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
> directory
> > is not owned by the current user and the cache has been disabled. Please
> > check the permissions and owner of that directory. If executing pip with
> > sudo, you may want sudo's -H flag.
> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
> is
> > not owned by the current user and caching wheels has been disabled.
> check
> > the permissions and owner of that directory. If executing pip with sudo,
> you
> > may want sudo's -H flag.
> > Collecting SimpleITK
> >  Downloading
> >
> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
> > (72.6MB)
> >    100% |████████████████████████████████| 72.6MB 41.9MB/s
> > Installing collected packages: SimpleITK
> > Successfully installed SimpleITK-0.9.1
> > ➜  Downloads python
> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import SimpleITK as sitk
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1,
> in
> > <module>
> >    from .SimpleITK import *
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 28,
> > in <module>
> >    _SimpleITK = swig_import_helper()
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 24,
> > in swig_import_helper
> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
> no
> > appropriate 64-bit architecture (see "man python" for running in 32-bit
> > mode)
> >>>>
> >
> > I also tried to download a separate binary which I thought would be more
> > applicable for El Capitan (Mac OSX v10.11):
> >
> >
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> >
> > However, I received the same error message:
> >
> > ➜  Downloads sudo pip install
> >
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
> directory
> > is not owned by the current user and the cache has been disabled. Please
> > check the permissions and owner of that directory. If executing pip with
> > sudo, you may want sudo's -H flag.
> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
> is
> > not owned by the current user and caching wheels has been disabled.
> check
> > the permissions and owner of that directory. If executing pip with sudo,
> you
> > may want sudo's -H flag.
> > Processing
> >
> ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> > Installing collected packages: SimpleITK
> > Successfully installed SimpleITK-0.9.0
> > ➜  Downloads python
> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import SimpleITK as sitk
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1,
> in
> > <module>
> >    from .SimpleITK import *
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 28,
> > in <module>
> >    _SimpleITK = swig_import_helper()
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 24,
> > in swig_import_helper
> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
> no
> > appropriate 64-bit architecture (see "man python" for running in 32-bit
> > mode)
> >>>>
> >
> > Any help to get simpleITK in python working again would be appreciated.
> > Thanks in advance!
> >
> > Neil
> >
> >
> >
> > --
> > View this message in context:
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-- 
Neil Panjwani
Duke University | B.S.E. 2010
Tel: (760) 486-0765




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