<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I eventually got it working by re-installing python as above and then using homebrew to install simple itk. Thanks for your help!</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Neil</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 17, 2016 at 1:03 PM, Neil Panjwani <span dir="ltr"><<a href="/user/SendEmail.jtp?type=node&node=37271&i=0" target="_top" rel="nofollow" link="external">[hidden email]</a>></span> wrote:<br><blockquote style='border-left:2px solid #CCCCCC;padding:0 1em' class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default">
<p><font face="monospace, monospace"><span>(ecvenv) </span><span><b>➜ </b></span><span><b>econtour</b></span><span> </span><span><b>git:(</b></span><span><b>master</b></span><span><b>) </b></span><span><b>✗</b></span><span> pip install --trusted-host <a href="http://www.simpleitk.org" target="_blank" rel="nofollow" link="external">www.simpleitk.org</a> -f <a href="http://www.simpleitk.org/SimpleITK/resources/software.html" target="_blank" rel="nofollow" link="external">http://www.simpleitk.org/SimpleITK/resources/software.html</a> --timeout 30 SimpleITK</span></font></p><span class="">
<p><span><font face="monospace, monospace">Collecting SimpleITK</font></span></p>
<p><span><font face="monospace, monospace"> Downloading <a href="https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl" target="_blank" rel="nofollow" link="external">https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl</a> (72.6MB)</font></span></p>
</span><p><span><font face="monospace, monospace"> 100% |████████████████████████████████| 72.6MB 43.5MB/s </font></span></p><span class="">
<p><span><font face="monospace, monospace">Installing collected packages: SimpleITK</font></span></p>
<p><span><font face="monospace, monospace">Successfully installed SimpleITK-0.9.1</font></span></p></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">However, I continue to run into a "Fatal Python Error" when trying to load simple itk from within python. See below:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default">
<p><font face="monospace, monospace"><span>(ecvenv) </span><span><b>➜ </b></span><span><b>econtour</b></span><span> </span><span><b>git:(</b></span><span><b>master</b></span><span><b>) </b></span><span><b>✗</b></span><span> which python</span></font></p>
<p><span><font face="monospace, monospace">/Users/neil/work/Meteor/econtour/ecvenv/bin/python</font></span></p>
<p><font face="monospace, monospace"><span>(ecvenv) </span><span><b>➜ </b></span><span><b>econtour</b></span><span> </span><span><b>git:(</b></span><span><b>master</b></span><span><b>) </b></span><span><b>✗</b></span><span> which pip</span></font></p>
<p><span><font face="monospace, monospace">/Users/neil/work/Meteor/econtour/ecvenv/bin/pip</font></span></p>
<p><font face="monospace, monospace"><span>(ecvenv) </span><span><b>➜ </b></span><span><b>econtour</b></span><span> </span><span><b>git:(</b></span><span><b>master</b></span><span><b>) </b></span><span><b>✗</b></span><span> pip list</span></font></p>
<p><span><font face="monospace, monospace">pip (8.1.2)</font></span></p>
<p><span><font face="monospace, monospace">setuptools (23.0.0)</font></span></p>
<p><span><font face="monospace, monospace">SimpleITK (0.9.1)</font></span></p>
<p><span><font face="monospace, monospace">wheel (0.29.0)</font></span></p>
<p><font face="monospace, monospace"><span>(ecvenv) </span><span><b>➜ </b></span><span><b>econtour</b></span><span> </span><span><b>git:(</b></span><span><b>master</b></span><span><b>) </b></span><span><b>✗</b></span><span> python</span></font></p>
<p><span><font face="monospace, monospace">Python 2.7.11 (default, Jan 22 2016, 08:29:18) </font></span></p>
<p><span><font face="monospace, monospace">[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin</font></span></p><span class="">
<p><span><font face="monospace, monospace">Type "help", "copyright", "credits" or "license" for more information.</font></span></p>
<p><span><font face="monospace, monospace">>>> import SimpleITK as sitk</font></span></p>
</span><p><span><font face="monospace, monospace">Fatal Python error: PyThreadState_Get: no current thread</font></span></p>
<p><span><font face="monospace, monospace">[1] 2805 abort python</font></span></p><p><span><font face="monospace, monospace"><br></font></span></p><p><br></p></div></div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] <span dir="ltr"><<a href="/user/SendEmail.jtp?type=node&node=37271&i=1" target="_top" rel="nofollow" link="external">[hidden email]</a>></span> wrote:<br></span><blockquote style='border-left:2px solid #CCCCCC;padding:0 1em' class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><span>
Hi,
<br><br>Where did you get you python from? You are using a version from /Library/Framework/Python.frameworks, which is not the system version.
<br><br>The error with the first command gives you a suggestion on how to solve the problem.
<br><br>The second error appears to be a binary compatibility issue with the distribution you have of python.
<br><br>Please read the guidance on the wiki with the different distributions of python, along with following the recommendation to setup a virtual environment.
<br><br><a href="https://itk.org/Wiki/SimpleITK/GettingStarted" rel="nofollow" link="external" target="_blank">https://itk.org/Wiki/SimpleITK/GettingStarted</a><br><br>Good luck,
<br></span>Brad
<br><br><br><br></span><div><div class="h5"><div><div><div><div class='shrinkable-quote'><br>> On Jun 17, 2016, at 11:20 AM, paniwani <<a href="http:///user/SendEmail.jtp?type=node&node=37269&i=0" rel="nofollow" link="external" target="_blank">[hidden email]</a>> wrote:
<br>>
<br>> Hi,
<br>>
<br>> It appears the code that I pasted did not show up in the email version of
<br>> the mailing list. I've re-pasted below. I'm using system Python 2.7 and Mac
<br>> OSX El Capitan. Thank you!
<br>>
<br>> -----
<br>>
<br>> I was using simple ITK with python in my application with no problems until
<br>> I recently upgraded to El Capitan on my Mac. Since then, I have received
<br>> error messages regarding 64-bit issues. I've tried to reinstall simple ITK
<br>> multiple times using the python binaries as stated here
<br>> <a href="https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files" rel="nofollow" link="external" target="_blank">https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files</a> with both
<br>> pip and easy_install. However, I continue to run into issues running
<br>> simpleITK.
<br>>
<br>> I am on OSX El Capitan (10.11) and Python 2.7.
<br>>
<br>> Here is the output when I try to install the latest via pip and and use it:
<br>>
<br>> ➜ Downloads sudo pip install --trusted-host <a href="http://www.simpleitk.org" target="_blank" rel="nofollow" link="external">www.simpleitk.org</a> -f
<br>> <a href="http://www.simpleitk.org/SimpleITK/resources/software.html" rel="nofollow" link="external" target="_blank">http://www.simpleitk.org/SimpleITK/resources/software.html</a> --timeout 30
<br>> SimpleITK
<br>> The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
<br>> is not owned by the current user and the cache has been disabled. Please
<br>> check the permissions and owner of that directory. If executing pip with
<br>> sudo, you may want sudo's -H flag.
<br>> The directory '/Users/neil/Library/Caches/pip' or its parent directory is
<br>> not owned by the current user and caching wheels has been disabled. check
<br>> the permissions and owner of that directory. If executing pip with sudo, you
<br>> may want sudo's -H flag.
<br>> Collecting SimpleITK
<br>> Downloading
<br>> <a href="https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl" rel="nofollow" link="external" target="_blank">https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl</a><br>> (72.6MB)
<br>> 100% |████████████████████████████████| 72.6MB 41.9MB/s
<br>> Installing collected packages: SimpleITK
<br>> Successfully installed SimpleITK-0.9.1
<br>> ➜ Downloads python
<br>> Python 2.7.10 (default, Oct 23 2015, 19:19:21)
<br>> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
<br>> Type "help", "copyright", "credits" or "license" for more information.
<br>>>>> import SimpleITK as sitk
<br>> Traceback (most recent call last):
<br>> File "<stdin>", line 1, in <module>
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
<br>> <module>
<br>> from .SimpleITK import *
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
<br>> in <module>
<br>> _SimpleITK = swig_import_helper()
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
<br>> in swig_import_helper
<br>> _mod = imp.load_module('_SimpleITK', fp, pathname, description)
<br>> ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
<br>> appropriate 64-bit architecture (see "man python" for running in 32-bit
<br>> mode)
<br>>>>>
<br>>
<br>> I also tried to download a separate binary which I thought would be more
<br>> applicable for El Capitan (Mac OSX v10.11):
<br>>
<br>> 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
<br>>
<br>> However, I received the same error message:
<br>>
<br>> ➜ Downloads sudo pip install
<br>> 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
<br>> The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
<br>> is not owned by the current user and the cache has been disabled. Please
<br>> check the permissions and owner of that directory. If executing pip with
<br>> sudo, you may want sudo's -H flag.
<br>> The directory '/Users/neil/Library/Caches/pip' or its parent directory is
<br>> not owned by the current user and caching wheels has been disabled. check
<br>> the permissions and owner of that directory. If executing pip with sudo, you
<br>> may want sudo's -H flag.
<br>> Processing
<br>> ./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
<br>> Installing collected packages: SimpleITK
<br>> Successfully installed SimpleITK-0.9.0
<br>> ➜ Downloads python
<br>> Python 2.7.10 (default, Oct 23 2015, 19:19:21)
<br>> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
<br>> Type "help", "copyright", "credits" or "license" for more information.
<br>>>>> import SimpleITK as sitk
<br>> Traceback (most recent call last):
<br>> File "<stdin>", line 1, in <module>
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
<br>> <module>
<br>> from .SimpleITK import *
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
<br>> in <module>
<br>> _SimpleITK = swig_import_helper()
<br>> File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
<br>> in swig_import_helper
<br>> _mod = imp.load_module('_SimpleITK', fp, pathname, description)
<br>> ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
<br>> appropriate 64-bit architecture (see "man python" for running in 32-bit
<br>> mode)
<br>>>>>
<br>>
<br>> Any help to get simpleITK in python working again would be appreciated.
<br>> Thanks in advance!
<br>>
<br>> Neil
<br>>
<br>>
<br>>
</div></div></div>> --
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