[ITK] Fwd: ITK and python wrap problem
gowith king
gowithking at googlemail.com
Sat Aug 23 10:08:43 EDT 2014
That means the mismatching is not really matter and the essential problem
is the valence of idconfig activation.
So I will write a summary to end our discussion to emailling list and
recommend your wrapping protocol, which should also work on Ubuntu.
have a nice weekend.
On Sat, Aug 23, 2014 at 3:41 PM, 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
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>
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