Re: [ITK-users] ITKModuleTemplate and external modules for use with python

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Hi Darren,

can you please re-post this question on the forum
<https://discourse.itk.org/>? Many of us were on vacation in the last few
weeks.

Regards,
D=C5=BEenan

On Thu, Jul 12, 2018 at 7:47 AM <[email protected]> wrote:

> Hi All,
>
>
>
> I=E2=80=99m revisiting making my own external ITK module (for use in Pyth=
on) after
> an initial attempt a while back. This time I=E2=80=99ve managed to get mu=
ch further
> and have managed to successfully create python wheels following the
> directions on
> https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master=
/docs/Build_ITK_Module_Python_packages.rst
>  , I=E2=80=99ve created Windows wheels via AppVeyor and linux wheels with=
 CircleCI
> in addition to locally built 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
> (segmentation fault) when I try and actually use or create one of my cust=
om
> filters.
>
>
>
> To strip everything back to basics I generated a vanilla external module,
> using only default values with:
>
>
>
> python -m cookiecutter gh:InsightSoftwareConsortium/ITKModuleTemplate
>
>
>
> I then built the wheels as described and installed them into the virtual
> environment.
>
>
>
> 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
> ITKModuleTemplate, however I can successfully create standard itk filters=
.
>
>
>
> After running the script with gdb I see that it crashes in the call as
> follows:
>
>
>
> #1  0x00007fffe7405373 in PyInit__ModuleTemplatePython () from
> /home/tho78s/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_=
ModuleTemplatePython.so
>
>
>
> I=E2=80=99m currently out of ideas as to where the problem lies and I see=
m to get
> the 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
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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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>

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<div dir=3D"ltr"><div class=3D"gmail_default" style=3D"font-family:verdana,=
sans-serif;font-size:small">Hi Darren,</div><div class=3D"gmail_default" st=
yle=3D"font-family:verdana,sans-serif;font-size:small"><br></div><div class=
=3D"gmail_default" style=3D"font-family:verdana,sans-serif;font-size:small"=
>can you please re-post this question on the <a href=3D"https://discourse.i=
tk.org/">forum</a>? Many of us were on vacation in the last few weeks.</div=
><div class=3D"gmail_default" style=3D"font-family:verdana,sans-serif;font-=
size:small"><br></div><div class=3D"gmail_default" style=3D"font-family:ver=
dana,sans-serif;font-size:small">Regards,</div><div class=3D"gmail_default"=
 style=3D"font-family:verdana,sans-serif;font-size:small">D=C5=BEenan</div>=
</div><br><div class=3D"gmail_quote"><div dir=3D"ltr">On Thu, Jul 12, 2018 =
at 7:47 AM &lt;[email protected]&gt; wrote:<br></div><blockquote cla=
ss=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;pa=
dding-left:1ex">





<div lang=3D"EN-AU" link=3D"#0563C1" vlink=3D"#954F72">
<div class=3D"m_1997716889707673519WordSection1">
<p class=3D"MsoNormal">Hi All,<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">I=E2=80=99m revisiting making my own external ITK mo=
dule (for use in Python) after an initial attempt a while back. This time I=
=E2=80=99ve managed to get much further and have managed to successfully cr=
eate python wheels following the directions on
<a href=3D"https://github.com/InsightSoftwareConsortium/ITKPythonPackage/bl=
ob/master/docs/Build_ITK_Module_Python_packages.rst" target=3D"_blank">
https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/d=
ocs/Build_ITK_Module_Python_packages.rst</a> =C2=A0, I=E2=80=99ve created W=
indows wheels via AppVeyor and linux wheels with CircleCI in addition to lo=
cally built versions via the docker based method.
 All tests are passed successfully.<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></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.
<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">To strip everything back to basics I generated a van=
illa external module, using only default values with:
<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">python -m cookiecutter gh:InsightSoftwareConsortium/=
ITKModuleTemplate<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">I then built the wheels as described and installed t=
hem into the virtual environment.<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Using the following basic python script below result=
s in a seg fault,
<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Courier New&quot;">=
import itk<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Courier New&quot;">=
InputType =3D itk.Image[itk.F,2]<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Courier New&quot;">=
OutputType =3D itk.Image[itk.F,2]<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Courier New&quot;">=
test =3D itk.MinimalStandardRandomVariateGenerator.New()
<u></u><u></u></span></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></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.<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">After running the script with gdb I see that it cras=
hes in the call as follows:<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Courier New&quot;">=
#1=C2=A0 0x00007fffe7405373 in PyInit__ModuleTemplatePython () from /home/t=
ho78s/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_ModuleTem=
platePython.so<u></u><u></u></span></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">I=E2=80=99m currently out of ideas as to where the p=
roblem lies and I seem to get the identical problem in Windows too.<u></u><=
u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Any help or pointers in to what is going wrong would=
 be greatly appreciated!<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">I you want any extra info, feel free to contact me.<=
u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Regards,<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Darren<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
</div>
</div>

The ITK community is transitioning from this mailing list to <a href=3D"htt=
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</blockquote></div>

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The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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