[ITK-users] ITKModuleTemplate and external modules for use with python
<[email protected]> Thu, 12 Jul 2018 11:36:06 +0000
| Newsgroups | gmane.comp.lib.itk.user |
|---|---|
| Message-ID | <[email protected]> |
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Hi All,
I'm revisiting making my own external ITK module (for use in Python) after =
an initial attempt a while back. This time I've managed to get much further=
and have managed to successfully create python wheels following the direct=
ions on https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/=
master/docs/Build_ITK_Module_Python_packages.rst , I've created Windows wh=
eels via AppVeyor and linux wheels with CircleCI in addition to locally bui=
lt versions via the docker based method. All tests are passed successfully.
However, after installing them with pip in a fresh virtual environment in a=
Python 3.6 instance (Anaconda), I seem to always get a kernel crash (segme=
ntation fault) when I try and actually use or create one of my custom filte=
rs.
To strip everything back to basics I generated a vanilla external module, u=
sing only default values with:
python -m cookiecutter gh:InsightSoftwareConsortium/ITKModuleTemplate
I then built the wheels as described and installed them into the virtual en=
vironment.
Using the following basic python script below results in a seg fault,
import itk
InputType =3D itk.Image[itk.F,2]
OutputType =3D itk.Image[itk.F,2]
test =3D itk.MinimalStandardRandomVariateGenerator.New()
I get the same result if I try and create any of the classes defined in ITK=
ModuleTemplate, however I can successfully create standard itk filters.
After running the script with gdb I see that it crashes in the call as foll=
ows:
#1 0x00007fffe7405373 in PyInit__ModuleTemplatePython () from /home/tho78s=
/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_ModuleTemplate=
Python.so
I'm currently out of ideas as to where the problem lies and I seem to get t=
he identical problem in Windows too.
Any help or pointers in to what is going wrong would be greatly appreciated=
!
I you want any extra info, feel free to contact me.
Regards,
Darren
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<p class=3D"MsoNormal">Hi All,<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">I’m revisiting making my own external ITK modu=
le (for use in Python) after an initial attempt a while back. This time I&#=
8217;ve managed to get much further and have managed to successfully create=
python wheels following the directions on
<a href=3D"https://github.com/InsightSoftwareConsortium/ITKPythonPackage/bl=
ob/master/docs/Build_ITK_Module_Python_packages.rst">
https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/d=
ocs/Build_ITK_Module_Python_packages.rst</a> , I’ve created Win=
dows wheels via AppVeyor and linux wheels with CircleCI in addition to loca=
lly built versions via the docker based method.
All tests are passed successfully.<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">However, after installing them with pip in a fresh v=
irtual environment in a Python 3.6 instance (Anaconda), I seem to always ge=
t a kernel crash (segmentation fault) when I try and actually use or create=
one of my custom filters.
<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">To strip everything back to basics I generated a van=
illa external module, using only default values with:
<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">python -m cookiecutter gh:InsightSoftwareConsortium/=
ITKModuleTemplate<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">I then built the wheels as described and installed t=
hem into the virtual environment.<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">Using the following basic python script below result=
s in a seg fault,
<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal"><span style=3D"font-family:"Courier New"">=
import itk<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:"Courier New"">=
InputType =3D itk.Image[itk.F,2]<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:"Courier New"">=
OutputType =3D itk.Image[itk.F,2]<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:"Courier New"">=
test =3D itk.MinimalStandardRandomVariateGenerator.New()
<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">I get the same result if I try and create any of the=
classes defined in ITKModuleTemplate, however I can successfully create st=
andard itk filters.<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">After running the script with gdb I see that it cras=
hes in the call as follows:<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal"><span style=3D"font-family:"Courier New"">=
#1 0x00007fffe7405373 in PyInit__ModuleTemplatePython () from /home/t=
ho78s/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_ModuleTem=
platePython.so<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">I’m currently out of ideas as to where the pro=
blem lies and I seem to get the identical problem in Windows too.<o:p></o:p=
></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">Any help or pointers in to what is going wrong would=
be greatly appreciated!<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">I you want any extra info, feel free to contact me.<=
o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">Regards,<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">Darren<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
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