[ITK] Fwd: ITK and python wrap problem

gowith king gowithking at googlemail.com
Sat Aug 23 09:41:01 EDT 2014 

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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