[ITK] [ITK-users] Simpleitk installation on Mac 10.9.2

[Bradley Lowekamp]

Hello Chao,

The "Fatal Python error: PyThreadState_Get: no current thread" error, frequently occurs when the SimpleITK binary was compiled against an incompatible version of python to what you are running. 

What python distribution are you using? Do you have any third party python interpreters installed? (Your error message below indicates that you are not using the system python!)


On OSX this frequently occurs when there is a Third Party version of Python installed. The distributed binary are not compatible with Enthought or Mac Ports  installation of python. It's work with the system python and the python distributed from python.org.

Regarding compiling:

1) I recommend disabling the languages you don't need. Such as R.
2) For python review which executable, library, and headers are used. Ensure that they are consistent with the version and installation of python you will be using.

hope that helps,
Brad

On Apr 16, 2014, at 5:43 PM, Chao Wang <dynastywang1010 at gmail.com> wrote:

> Hi, Dave,
> 
> I gave up building it by myself. For the binary installation on Mac, I did 'sudo easy_install SimplyITK'. 
> 
> I believe it is successfully installed. But when I entered python, it gave me an error like the above. 
> 
> Please direct me to where it can be solved. 
> 
> Thanks,
> 
> Chao
> 
> 
> On Wed, Apr 16, 2014 at 2:28 PM, David Welch <david.m.welch at gmail.com> wrote:
> Hi Chao,
> 
> Let's keep this on the mailing list.  I assumed from your original message you were trying to build with R wrapping, not Python.  That was probably your original problem - just turn off R_WRAPPING (or whatever it is in the CMake GUI).
> 
> For your first error: if you Google "Fatal Python error: PyThreadState_Get: no current thread" there are a TON of hits.  What have you tried?
> 
> Ubuntu is a different issue, so let's take it one OS at a time.
> 
> Cheers,
> Dave
> 
> 
> On Wed, Apr 16, 2014 at 2:47 PM, Chao Wang <dynastywang1010 at gmail.com> wrote:
> I also tried in ubuntu, after sudo easy_install SimpleITK, and import SimpleITK as sitk,
> 
> 
> Python still cannot find the package. 
> 
> Thanks,
> 
> Chao
> 
> 
> On Wed, Apr 16, 2014 at 11:52 AM, Chao Wang <dynastywang1010 at gmail.com> wrote:
> 
> Hi, David, 
> 
> I switched to binary install and it was successful, I hope. 
> 
> But, when I open python and tried to import SimpleITK as import SimpleITK as sitk
> sitk
> Fatal Python error: PyThreadState_Get: no current thread
> Abort trap: 6
> 
> 
> 
> Process:         Python [90787]
> Path:            /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
> Identifier:      Python
> Version:         2.7.3 (2.7.3)
> Code Type:       X86-64 (Native)
> Parent Process:  bash [90730]
> Responsible:     Terminal [200]
> User ID:         501
> 
> Date/Time:       2014-04-16 11:51:19.463 -0700
> OS Version:      Mac OS X 10.9.2 (13C64)
> Report Version:  11
> Anonymous UUID:  D20752B2-FC7D-334A-7483-EAC1C469DF11
> 
> Sleep/Wake UUID: 619C0566-6D47-4938-8E49-BD544C13CF52
> 
> Crashed Thread:  0  Dispatch queue: com.apple.main-thread
> 
> Exception Type:  EXC_CRASH (SIGABRT)
> Exception Codes: 0x0000000000000000, 0x0000000000000000
> 
> Application Specific Information:
> abort() called
> 
> I wonder if the path is wrong or something else happened? 
> 
> 
> Thanks,
> 
> 
> Chao
> 
> On Wed, Apr 16, 2014 at 9:37 AM, David Welch <david.m.welch at gmail.com> wrote:
> Hi Chao,
> 
> It looks like your path to the R framework is incorrect in your CMake build.  Can you email the values for R in your CMakeCache file?
>  
> Cheers,
> Dave
> 
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> 
> 
> 
> -- 
> Chao Wang
> 
> 
> 
> -- 
> Chao Wang
> 
> 
> 
> 
> -- 
> Chao Wang
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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