[ITK] Fwd: ITK and python wrap problem
Michka Popoff
michkapopoff at gmail.com
Sat Aug 23 09:49:09 EDT 2014
Yes, these warnings are known, it’s because we did not finish and clean up all the wrappings.
I changed the code some time ago for the warnings, you may disable them following the instructions below.
This is a temporary solution, until we get this sorted out.
Users can now disable warnings with the following lines before importing ITK :
import warnings
warnings.filterwarnings("ignore”)
import itk
or by running python with : python -W ignore foo.py
On 23 août 2014, at 15:41, gowith king <gowithking at googlemail.com> wrote:
> update :
> following Mr. Popoff 's instruction, I add these few command to active ldconfig
> cd /etc/ld.so.conf.d/
> add a file called itk-46.conf, which should contain only one line: /usr/local/lib
> ldconfig # tells the system to read the files in ld.so.conf.d
> then python
> import itk
> itk.image
> lots warning reported :
> Warning: Unknown parameter 'itk::Matrix< float, 2, 2 >' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::Matrix< double, 2, 2 >' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::Matrix< float, 3, 3 >' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::Matrix< double, 3, 3 >' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< float,2,2,float,float >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultDynamicMeshTraits< float,2,2,float,float >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< float,3,3,float,float >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultDynamicMeshTraits< float,3,3,float,float >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< double,2,2,double,double,double >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< double,3,3,double,double,double >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< itk::Matrix <double,2,2>,2,2,float,float,itk::Matrix <double,2,2> >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< itk::Matrix <double,3,3>,3,3,float,float,itk::Matrix <double,3,3> >' in template 'itk::PointSet'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< float,2,2,float,float >' in template 'itk::Mesh'
> Warning: Unknown parameter 'itk::DefaultDynamicMeshTraits< float,2,2,float,float >' in template 'itk::Mesh'
> Warning: Unknown parameter 'itk::DefaultStaticMeshTraits< float,3,3,float,float >' in template 'itk::Mesh'
> Warning: Unknown parameter 'itk::DefaultDynamicMeshTraits< float,3,3,float,float >' in template 'itk::Mesh'
> Warning: Unknown parameter 'itk::CellInterface< float, itk::CellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,2 >,itk::MapContainer< unsigned long,itk::Point< float,2 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::MapContainer'
> Warning: Unknown parameter 'itk::CellInterface< double, itk::CellTraitsInfo< 2,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,2 >,itk::MapContainer< unsigned long,itk::Point< double,2 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::MapContainer'
> Warning: Unknown parameter 'itk::CellInterface< float, itk::CellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,3 >,itk::MapContainer< unsigned long,itk::Point< float,3 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::MapContainer'
> Warning: Unknown parameter 'itk::CellInterface< double, itk::CellTraitsInfo< 3,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,3 >,itk::MapContainer< unsigned long,itk::Point< double,3 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::MapContainer'
> Warning: Unknown parameter 'itk::CellInterface< float, itk::CellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,2 >,itk::MapContainer< unsigned long,itk::Point< float,2 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::CellInterface< double, itk::CellTraitsInfo< 2,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,2 >,itk::MapContainer< unsigned long,itk::Point< double,2 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::CellInterface< float, itk::CellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,3 >,itk::MapContainer< unsigned long,itk::Point< float,3 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::CellInterface< double, itk::CellTraitsInfo< 3,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,3 >,itk::MapContainer< unsigned long,itk::Point< double,3 > >, std::set< unsigned long, std::less< unsigned long > > > > *' in template 'itk::VectorContainer'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,2 >,itk::MapContainer< unsigned long,itk::Point< float,2 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterfaceVisitor'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 2,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,2 >,itk::MapContainer< unsigned long,itk::Point< double,2 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterfaceVisitor'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,3 >,itk::MapContainer< unsigned long,itk::Point< float,3 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterfaceVisitor'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 3,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,3 >,itk::MapContainer< unsigned long,itk::Point< double,3 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterfaceVisitor'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,2 >,itk::MapContainer< unsigned long,itk::Point< float,2 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterface'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 2,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,2 >,itk::MapContainer< unsigned long,itk::Point< double,2 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterface'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned long,itk::Point< float,3 >,itk::MapContainer< unsigned long,itk::Point< float,3 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterface'
> Warning: Unknown parameter 'itk::CellTraitsInfo< 3,double,double,unsigned long,unsigned long,unsigned long,itk::Point< double,3 >,itk::MapContainer< unsigned long,itk::Point< double,3 > >, std::set< unsigned long, std::less< unsigned long > > >' in template 'itk::CellInterface'
> Warning: Unknown parameter 'itk::Mesh< float,2,itk::DefaultStaticMeshTraits< float,2,2,float > >' in template 'itk::MeshToMeshFilter'
> Warning: Unknown parameter 'itk::Mesh< float,2,itk::DefaultDynamicMeshTraits< float,2,2,float > >' in template 'itk::MeshToMeshFilter'
> Warning: Unknown parameter 'itk::Mesh< float,3,itk::DefaultStaticMeshTraits< float,3,3,float > >' in template 'itk::MeshToMeshFilter'
> Warning: Unknown parameter 'itk::Mesh< float,3,itk::DefaultDynamicMeshTraits< float,3,3,float > >' in template 'itk::MeshToMeshFilter'
>
>
>
>
> On Fri, Aug 22, 2014 at 6:13 PM, gowith king <gowithking at googlemail.com> wrote:
> I recorded my procedure as follow:
> cd ~
> git clone git://itk.org/ITK.git
> cd ITK
> git pull
> mkdir BUILD
> cd BUILD
> ccmake ..
> in the ccmake configure options the follow flags were selected:
> BUILD_EXAMPLES OFF
> BUILD_SHARED_LIBS ON
> BUILD_TESTING OFF
> CMAKE_BUILD_TYPE Release
> ITK_WRAP_PERL OFF
> ITK_WRAP_PYTHON ON
> PERL_EXECUTABLE /usr/bin/perl
> PYTHON_EXECUTABLE /usr/bin/python
> PYTHON_INCLUDE_DIR /usr/include/python2.7
> PYTHON_LIBRARY /usr/lib/libpython2.7.so
> PY_SITE_PACKAGES_PATH /usr/lib/python2.7/dist-packages
> SCPCOMMAND /usr/bin/scp
>
> Then the configure warning of executable and library mismatch comes, ignore the warning
> g to generation
> sudo make
> sudo make install
>
> for the test :
> python
> >>>import itk
> >>> inputimage=itk.Image[itk.UC,3] --- errors report here :
> in eclispe : undefined variable from import UC
> in terminal :Traceback (most recent call last):
>
> File "<stdin>", line 1, in <module>
> File "/usr/local/lib/ITK-4.7/Python/itkLazy.py", line 42, in __getattribute__
> itkBase.LoadModule(module, namespace)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
> LoadModule(dep, namespace)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
> LoadModule(dep, namespace)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
> LoadModule(dep, namespace)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
> LoadModule(dep, namespace)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 118, in LoadModule
> module = loader.load(swigModuleName)
> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 224, in load
> return imp.load_module(name, fp, pathname, description)
> File "/usr/local/lib/ITK-4.7/Python/ITKCommonPython.py", line 32, in <module>
> _ITKCommonPython = swig_import_helper()
> File "/usr/local/lib/ITK-4.7/Python/ITKCommonPython.py", line 28, in swig_import_helper
> _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
> ImportError: libitkvnl_algo-4.7.so.1: cannot open shared object file: No such file or directory
>
>
>
>
>
>
> On Fri, Aug 22, 2014 at 5:55 PM, gowith king <gowithking at googlemail.com> wrote:
> Please keep the discussion on the mailing list :)
>
> This is my first post in mailing list system " if this is a sort of system, :)"
> I guess that means I should always do not forget to cc to community? or what else should I do to keep it?
>
>
> Okay, so you will have to find the paths to the right folders/files to be consistent in your python choice.
>
>
> I have no idea Howto identify the python2.7.3 working library, normally they are lots of .pyr files in the folder of /usr/lib/python2.7 . I find a similar .so file in /usr/lib/libpython2.7.so .
> However in your instruction :PYTHON_LIBRARY = /usr/lib64/libpython2.7.so.1.0
> The file "libpython2.7.so.1.0" also present in the same path : /usr/lib/libpython2.7.so.1.0 ; should I use this file?
>
> I would be happy if you could communicate me the paths for Ubuntu 12.04, so I could extend the installation procedure.
>
> How could I send you the path of ubuntu 12.04? I can try to switch on a remote assistant if necessary.
>
>
> Seems on ubuntu the procedure is the same for loading the shared libraries:
> http://unix.stackexchange.com/questions/67781/use-shared-libraries-in-usr-local-lib
> On Ubuntu you should have a /etc/ld.so.conf file. Then you should run ldconfig.
>
>
> On Fri, Aug 22, 2014 at 5:30 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Please keep the discussion on the mailing list :)
>
> Okay, so you will have to find the paths to the right folders/files to be consistent in your python choice.
> I would be happy if you could communicate me the paths for Ubuntu 12.04, so I could extend the installation procedure.
>
> Seems on ubuntu the procedure is the same for loading the shared libraries:
> http://unix.stackexchange.com/questions/67781/use-shared-libraries-in-usr-local-lib
> On Ubuntu you should have a /etc/ld.so.conf file. Then you should run ldconfig.
>
> Michka
>
> On 22 août 2014, at 17:21, gowith king <gowithking at googlemail.com> wrote:
>
>> Dear Popoff
>> I am using Ubuntu 12.04 LTS. the warning is the mismatching of python library and python executable : python executable "2.7.3" and library "" is mismatched. Here is the option setting:
>>
>>
>> PYTHON_EXECUTABLE /usr/bin/python
>> PYTHON_INCLUDE_DIR /usr/include/python2.7
>> PYTHON_LIBRARY /usr/lib/libpython2.7.so
>> PY_SITE_PACKAGES_PATH /usr/lib/python2.7/dist-packages
>>
>> The libitkvnl_algo-4.7.so file exist in /usr/local/lib .
>>
>> I do have few python versions been installed in the same OS.
>> The flags in the instruction of 'http://www.itk.org/Wiki/ITK_Release_4/Wrapping/WrapITK_Installation' are not exact as the same as the description. I will try your instruction step be step in my system.
>> By the way, your instruction is so practical.
>>
>> Have a nice day.
>>
>>
>>
>>
>>
>> On Fri, Aug 22, 2014 at 4:15 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
>> Hi
>>
>> Some important questions first:
>>
>> What was the warning for the library mismatch ?
>> On what OS are you installing ?
>> Is the libitkvnl_algo-4.7.so file present in /usr/local/lib ?
>>
>> If the warnings were about the python library, it is quite important.
>> It may happen that you have two different python installations, and cmake is not able to find the right libraries.
>>
>> I wrote some instructions to install ITK with python wrapping on Fedora http://www.itk.org/Wiki/ITK/WrapITKInstallFedora
>> There is a list of cmake flags you can set to help cmake find the right python, if it’s the problem you had.
>> I think the error is just because the library is not in your path. If you are using Fedora, just follow the instructions I wrote down.
>> For other OS’es there are ways to do this, like setting the LD_LIBRARY_PATH for example (you'll have to google this)
>>
>> Feedback is welcome so I can improve the installation instructions :)
>>
>> Michka
>>
>> On 22 août 2014, at 16:06, gowith king <gowithking at googlemail.com> wrote:
>>
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: gowith king <gowithking at googlemail.com>
>>> Date: Fri, Aug 22, 2014 at 1:32 PM
>>> Subject: ITK and python wrap problem
>>> To: community at itk.org
>>>
>>>
>>> Dear ITK friends
>>> I am not sure this is an appropriate place to issue my problem in the wrapping process:
>>> I followed the instruction of 'http://www.itk.org/Wiki/ITK_Release_4/Wrapping/WrapITK_Installation' to finish the compiling and installing process. it look good so far except a warning of mismatching library version, I think it could be ignored.
>>> Then I tried one line for test :
>>> >>> import itk
>>> >>> inputimage=itk.Image[itk.UC,3]
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File "/usr/local/lib/ITK-4.7/Python/itkLazy.py", line 42, in __getattribute__
>>> itkBase.LoadModule(module, namespace)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
>>> LoadModule(dep, namespace)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
>>> LoadModule(dep, namespace)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
>>> LoadModule(dep, namespace)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 108, in LoadModule
>>> LoadModule(dep, namespace)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 118, in LoadModule
>>> module = loader.load(swigModuleName)
>>> File "/usr/local/lib/ITK-4.7/Python/itkBase.py", line 224, in load
>>> return imp.load_module(name, fp, pathname, description)
>>> File "/usr/local/lib/ITK-4.7/Python/ITKCommonPython.py", line 32, in <module>
>>> _ITKCommonPython = swig_import_helper()
>>> File "/usr/local/lib/ITK-4.7/Python/ITKCommonPython.py", line 28, in swig_import_helper
>>> _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
>>> ImportError: libitkvnl_algo-4.7.so.1: cannot open shared object file: No such file or directory
>>>
>>> I got totally lost for this, what should I do to fix this?
>>> Any suggestion would be appreciated
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20140823/4ad615bc/attachment-0002.html>
More information about the Community
mailing list