[ITK] Python wrapper for first order ITKTextureFeatures
Matt McCormick
matt.mccormick at kitware.com
Mon Sep 18 11:06:00 EDT 2017
Hi Yannick,
Great progress.
This error:
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.
occurs because FirstOrderTextureFeaturesImageFilter depends on
MovingHistogramImageFilter (it is its parent class):
https://github.com/InsightSoftwareConsortium/ITKTextureFeatures/blob/c1039d5ab834d8dba77ae4b9a3cc96a60788686b/include/itkFirstOrderTextureFeaturesImageFilter.h#L53-L57
The lines above show the relationship between the types. The second
template argument, TOutputImage, for
FirstOrderTextureFeaturesImageFilter, is the second template argument
for MovingHistogramImageFilter. So, in the wrapping for
MovingHistogramImageFilter, change
${ITKM_I${t}${d}}${ITKM_I${t}${d}}
${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}
to
${ITKM_I${t}${d}}${ITKM_VI${ITKM_F}${d}}
${ITKT_I${t}${d}}, ${ITKT_VI${ITKM_F}${d}}
to match the arguments that were used for FirstOrderTextureFeaturesImageFilter.
Hope this helps,
Mat
On Mon, Sep 18, 2017 at 10:09 AM, <yannick.suter at istb.unibe.ch> wrote:
> Dear Matt,
>
> Thank you for helping!
> The link to the structuring element example was very useful.
>
> I ran into a new issue where I would appreciate some help:
> The FirstOrderTextureFeaturesImageFilter uses the "MovingHistogramImageFilter", and I have some issues wrapping it correctly. I get the following error for each type I want to wrap:
>
> Warning 401: Nothing known about base class 'itk::MovingHistogramImageFilter< itk::Image< short,2 >,itk::VectorImage< float,2 >,itk::FlatStructuringElement< 2 >,itk::Function::FirstOrderTextureHistogram< short,itk::VariableLengthVector< float > > >'. Ignored.
> /home/yannick/Projects/PhD/ITK/ITK/bin/Wrapping/Typedefs/itkFirstOrderTextureFeaturesImageFilter.i:99: Warning 401: Maybe you forgot to instantiate 'itk::MovingHistogramImageFilter< itk::Image< short,2 >,itk::VectorImage< float,2 >,itk::FlatStructuringElement< 2 >,itk::Function::FirstOrderTextureHistogram< short,itk::VariableLengthVector< float > > >' using %template.
>
> Even though I put the MovingHistogramImageFilter in the .wrap file and tried including the base class itkMovingHistogramImageFilterBase as well.
>
> Could you take a look?
> Here's my itkFirstOrderTextureFeaturesImageFilter.wrap file:
> ----------------------------------------------------
> set(OutputVectorDim 8)
> itk_wrap_class("itk::FixedArray")
> itk_wrap_template("${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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>>
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