[ITK] Python wrapper for first order ITKTextureFeatures
yannick.suter at istb.unibe.ch
yannick.suter at istb.unibe.ch
Mon Sep 18 10:09:00 EDT 2017
Dear Matt,
Thank you for helping!
The link to the structuring element example was very useful.
I ran into a new issue where I would appreciate some help:
The FirstOrderTextureFeaturesImageFilter uses the "MovingHistogramImageFilter", and I have some issues wrapping it correctly. I get the following error for each type I want to wrap:
Warning 401: Nothing known about base class 'itk::MovingHistogramImageFilter< itk::Image< short,2 >,itk::VectorImage< float,2 >,itk::FlatStructuringElement< 2 >,itk::Function::FirstOrderTextureHistogram< short,itk::VariableLengthVector< float > > >'. Ignored.
/home/yannick/Projects/PhD/ITK/ITK/bin/Wrapping/Typedefs/itkFirstOrderTextureFeaturesImageFilter.i:99: Warning 401: Maybe you forgot to instantiate 'itk::MovingHistogramImageFilter< itk::Image< short,2 >,itk::VectorImage< float,2 >,itk::FlatStructuringElement< 2 >,itk::Function::FirstOrderTextureHistogram< short,itk::VariableLengthVector< float > > >' using %template.
Even though I put the MovingHistogramImageFilter in the .wrap file and tried including the base class itkMovingHistogramImageFilterBase as well.
Could you take a look?
Here's my itkFirstOrderTextureFeaturesImageFilter.wrap file:
----------------------------------------------------
set(OutputVectorDim 8)
itk_wrap_class("itk::FixedArray")
itk_wrap_template("${ITKM_F}${OutputVectorDim}" "${ITKT_F},${OutputVectorDim}")
itk_end_wrap_class()
itk_wrap_class("itk::Vector")
itk_wrap_template("${ITKM_F}${OutputVectorDim}" "${ITKT_F},${OutputVectorDim}")
itk_end_wrap_class()
WRAP_TYPE("itk::Image" "I" "itkImage.h")
foreach(d ${ITK_WRAP_IMAGE_DIMS})
ADD_TEMPLATE("V${ITKM_F}${OutputVectorDim}${d}" "itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}")
endforeach()
END_WRAP_TYPE()
itk_wrap_class("itk::Image" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("V${ITKM_F}${OutputVectorDim}${d}" "itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}")
endforeach()
itk_end_wrap_class()
itk_wrap_class("itk::ImageSource" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}" "itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
endforeach()
itk_end_wrap_class()
itk_wrap_class("itk::ImageToImageFilter" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(t ${WRAP_ITK_INT})
itk_wrap_template("${ITKM_I${t}${d}}IV${ITKM_F}${OutputVectorDim}${d}"
"${ITKT_I${t}${d}}, itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
endforeach()
endforeach()
itk_end_wrap_class()
itk_wrap_include("itkFlatStructuringElement.h")
WRAP_TYPE("itk::FlatStructuringElement" "SE")
foreach(d ${ITK_WRAP_IMAGE_DIMS})
ADD_TEMPLATE("${d}" "${d}")
endforeach()
END_WRAP_TYPE()
set(itk_Wrap_StructuringElement ${WRAPPER_TEMPLATES})
itk_wrap_simple_class("itk::ImageIOBase" )
itk_wrap_class("itk::KernelImageFilter" POINTER)
foreach(t ${WRAP_ITK_INT})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}${ITKM_SE${d}}" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, ${ITKT_SE${d}}")
endforeach()
endforeach()
itk_end_wrap_class()
itk_wrap_include("itkMovingHistogramImageFilterBase.h")
itk_wrap_class("itk::MovingHistogramImageFilterBase" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(t ${WRAP_ITK_INT})
itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}${ITKM_SE${d}}"
"${ITKT_I${t}${d}},${ITKT_I${t}${d}},${ITKT_SE${d}}")
endforeach()
endforeach()
itk_end_wrap_class()
itk_wrap_class("itk::ImageFileReader" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
"itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
endforeach()
itk_end_wrap_class()
itk_wrap_class("itk::ImageFileWriter" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
"itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
endforeach()
itk_end_wrap_class()
itk_wrap_include("itkFirstOrderTextureHistogram.h")
itk_wrap_class("itk::Function::FirstOrderTextureHistogram")
foreach(t ${WRAP_ITK_INT})
itk_wrap_template("${ITKM_${t}}${ITKM_${t}}" "${ITKT_${t}}, ${ITKT_${t}}")
endforeach()
itk_end_wrap_class()
itk_wrap_include("itkMovingHistogramImageFilter.h")
itk_wrap_class("itk::MovingHistogramImageFilter" POINTER)
foreach(t ${WRAP_ITK_INT})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}${ITKM_SE${d}}"
"${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, ${ITKT_SE${d}}, itk::Function::FirstOrderTextureHistogram< ${ITKT_${t}}, ${ITKT_${t}} >")
endforeach()
endforeach()
itk_end_wrap_class()
itk_wrap_class("itk::FirstOrderTextureFeaturesImageFilter" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(t ${WRAP_ITK_INT})
itk_wrap_template("${ITKM_I${t}${d}}${ITKM_VI${ITKM_F}${d}}${ITKM_SE${d}}"
"${ITKT_I${t}${d}}, ${ITKT_VI${ITKM_F}${d}}, ${ITKT_SE${d}}")
endforeach()
endforeach()
itk_end_wrap_class()
----------------------------------------------------
Best and thank you,
Best,
Yannick
________________________________________
Von: Matt McCormick [matt.mccormick at kitware.com]
Gesendet: Sonntag, 17. September 2017 20:48
An: Suter, Yannick Raphael (ISTB)
Cc: community at itk.org; Jean-Baptiste Vimort
Betreff: Re: [ITK] Python wrapper for first order ITKTextureFeatures
Dear Yannick,
It looks like you are close.
To find out what template parameters to pass, the class declaration
has this information:
https://github.com/InsightSoftwareConsortium/ITKTextureFeatures/blob/master/include/itkFirstOrderTextureFeaturesImageFilter.h#L51
template< class TInputImage, class TOutputImage, class TKernel >
There are three template parameters, the input image, the output
image, and the kernel. To see what kind of types are used for these
parameters, the test gives a hint:
https://github.com/InsightSoftwareConsortium/ITKTextureFeatures/blob/master/test/itkFirstOrderTextureFeaturesImageFilterTest.cxx#L28-L30
The KernelType is usually itk::FlatStructuringElement< ImageDimension
>. A grep through ITK's sources finds an example of how this is used
as a template parameter when wrapping:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/BinaryMathematicalMorphology/wrapping/itkBinaryDilateImageFilter.wrap
There is also a good wrapping reference in the ITK Software Guide to reach for:
https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x48-1540009.5
Please let use know if more help is needed. Contribution pull requests
are welcome and appreciated :-)
Thanks,
Matt
On Sat, Sep 16, 2017 at 12:45 PM, <yannick.suter at istb.unibe.ch> wrote:
> Dear all,
>
> I would like to use the the first order texture features of
> ITKTextureFeatures
> (https://github.com/InsightSoftwareConsortium/ITKTextureFeatures) in Python.
> Thanks to J.Vimort et al. for the great work!
> Since the coocurrence and run length features are already wrapped, I tried
> to take these as an example and wrap it myself (I'm very new to this).
>
> I would appreciate any help to point me into the right direction.
>
> That's what I've tried:
> - Created a .wrap file "itkFirstOrderTextureFeaturesImageFilter.wrap" and
> put it in the "/Modules/External/ITKTextureFeatures/wrapping" directory (see
> below)
> - Added "itkFirstOrderTextureFeaturesImageFilter" to the CMakeLists.txt in
> the "/Modules/External/ITKTextureFeatures/wrapping" directory, now looking
> like this:
>
> itk_wrap_module(TextureFeatures)
>
> set(WRAPPER_SUBMODULE_ORDER
> itkCoocurrenceTextureFeaturesImageFilter
> itkRunLengthTextureFeaturesImageFilter
> itkFirstOrderTextureFeaturesImageFilter)
>
> itk_auto_load_submodules()
> itk_end_wrap_module()
>
> This gives me the folowwing error for every datatype I set to wrap:
>>>
>>> /home/yannick/Projects/PhD/ITK/ITK/bin/Wrapping/itkFirstOrderTextureFeaturesImageFilter.cxx:79:18:
>>> error: too few template arguments for class template
>>> 'FirstOrderTextureFeaturesImageFilter'
>>> typedef itk::FirstOrderTextureFeaturesImageFilter< itk::Image< signed
>>> short,2 >, itk::Image<itk::Vector<float,8>,2> >
>>> itkFirstOrderTextureFeaturesImageFilterISS2IVF82;
> ^
>>>/home/yannick/Projects/PhD/ITK/ITK/Modules/External/ITKTextureFeatures/include/itkFirstOrderTextureFeaturesImageFilter.h:52:27:
>>> note: template is declared here
>>>class ITK_TEMPLATE_EXPORT FirstOrderTextureFeaturesImageFilter:
>
> Since the it's working if I use it in C++, I don't see where template
> arguments are missing.
>
> Best and thank you,
>
> Yannick
>
> That's my .wrap-file:
> ------------
> set(OutputVectorDim 8)
> itk_wrap_class("itk::FixedArray")
> itk_wrap_template("${ITKM_F}${OutputVectorDim}"
> "${ITKT_F},${OutputVectorDim}")
> itk_end_wrap_class()
>
> itk_wrap_class("itk::Vector")
> itk_wrap_template("${ITKM_F}${OutputVectorDim}"
> "${ITKT_F},${OutputVectorDim}")
> itk_end_wrap_class()
>
> WRAP_TYPE("itk::Image" "I" "itkImage.h")
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> ADD_TEMPLATE("V${ITKM_F}${OutputVectorDim}${d}"
> "itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}")
> endforeach()
> END_WRAP_TYPE()
>
> itk_wrap_class("itk::Image" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> itk_wrap_template("V${ITKM_F}${OutputVectorDim}${d}"
> "itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}")
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_class("itk::ImageSource" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
> "itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_class("itk::ImageToImageFilter" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> foreach(t ${WRAP_ITK_INT})
> itk_wrap_template("${ITKM_I${t}${d}}IV${ITKM_F}${OutputVectorDim}${d}"
> "${ITKT_I${t}${d}},
> itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> endforeach()
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_simple_class("itk::ImageIOBase" )
>
> itk_wrap_class("itk::ImageFileReader" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
>
> "itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_class("itk::ImageFileWriter" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
>
> "itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_class("itk::ImageFileWriter" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> itk_wrap_template("IV${ITKM_F}${OutputVectorDim}${d}"
>
> "itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> endforeach()
> itk_end_wrap_class()
>
> itk_wrap_class("itk::FirstOrderTextureFeaturesImageFilter" POINTER)
> foreach(d ${ITK_WRAP_IMAGE_DIMS})
> foreach(t ${WRAP_ITK_INT})
> itk_wrap_template("${ITKM_I${t}${d}}IV${ITKM_F}${OutputVectorDim}${d}"
> "${ITKT_I${t}${d}},
> itk::Image<itk::Vector<${ITKT_F},${OutputVectorDim}>,${d}>")
> itk_wrap_template("${ITKM_I${t}${d}}${ITKM_VI${ITKM_F}${d}}"
> "${ITKT_I${t}${d}}, ${ITKT_VI${ITKM_F}${d}}")
> endforeach()
> endforeach()
> itk_end_wrap_class()
>
>
>
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