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ENH: Add BlockMatching registration Python wrappings + example
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‎examples/itkBlockMatchingMultiResolutionImageRegistrationMethodTest.py‎

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#!/usr/bin/env python
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# Copyright NumFOCUS
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0.txt
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import os
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from urllib.request import urlretrieve
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import itk
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# Verify wrapping succeeded
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assert 'MultiResolutionFixedBlockRadiusCalculator' in dir(itk.Ultrasound)
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# Get image input for registration
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FIXED_IMAGE_PATH = 'Input/rf_pre15.mha'
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MOVING_IMAGE_PATH = 'Input/rf_post15.mha'
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if not os.path.exists(FIXED_IMAGE_PATH):
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url = 'https://data.kitware.com/api/v1/file/58ee3b778d777f16d095fd8a/download'
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urlretrieve(url, FIXED_IMAGE_PATH)
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if not os.path.exists(MOVING_IMAGE_PATH):
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url = 'https://data.kitware.com/api/v1/file/58ee3b758d777f16d095fd87/download'
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urlretrieve(url, MOVING_IMAGE_PATH)
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fixed_image = itk.imread(FIXED_IMAGE_PATH, itk.D)
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moving_image = itk.imread(MOVING_IMAGE_PATH, itk.D)
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dimension = fixed_image.GetImageDimension()
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displacement_image_type = itk.Image[itk.Vector[itk.D,dimension],dimension]
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block_radius_calculator = itk.Ultrasound.MultiResolutionFixedBlockRadiusCalculator[type(fixed_image)].New()
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block_radius_calculator.SetRadius([12,4])
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# Create schedule for iterative registration
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search_region_source = itk.Ultrasound.MultiResolutionFixedSearchRegionImageSource[type(fixed_image),
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type(fixed_image),
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displacement_image_type].New()
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pyramid_schedule = itk.Array2D[itk.UI]()
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pyramid_schedule.SetSize(3,2)
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pyramid_schedule.SetElement(0,0,3)
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pyramid_schedule.SetElement(0,1,2)
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pyramid_schedule.SetElement(1,0,2)
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pyramid_schedule.SetElement(1,1,1)
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pyramid_schedule.SetElement(2,0,1)
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pyramid_schedule.SetElement(2,1,1)
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search_region_source.SetPyramidSchedule(pyramid_schedule)
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search_region_source.SetSearchRegionRadiusSchedule([50,6])
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search_region_source.SetOverlapSchedule(1.0)
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metric_image_filter = itk.Ultrasound.NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter[type(fixed_image),
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type(fixed_image),
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type(fixed_image)].New()
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level_registration_method = itk.Ultrasound.ImageRegistrationMethod[type(fixed_image),
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type(fixed_image),
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type(fixed_image),
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displacement_image_type,
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itk.D].New()
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level_registration_method.SetMetricImageFilter(metric_image_filter)
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# Set up the multi-resolution registration object
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multi_res_registration_method = itk.Ultrasound.MultiResolutionImageRegistrationMethod[type(fixed_image),
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type(fixed_image),
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type(fixed_image),
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displacement_image_type,
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itk.D].New()
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multi_res_registration_method.SetFixedImage(fixed_image)
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multi_res_registration_method.SetMovingImage(moving_image)
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multi_res_registration_method.SetBlockRadiusCalculator(block_radius_calculator)
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multi_res_registration_method.SetSearchRegionImageSource(search_region_source)
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multi_res_registration_method.SetSchedules(pyramid_schedule, pyramid_schedule)
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multi_res_registration_method.SetImageRegistrationMethod(level_registration_method)
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# Run the actual registration
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multi_res_registration_method.Update()
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# Write out results
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itk.imwrite(multi_res_registration_method.GetOutput(), 'Output/rf_post15_registered.mha')

‎wrapping/CMakeLists.txt‎

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itk_wrap_module(Ultrasound)
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set(WRAPPER_LIBRARY_GROUPS
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itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator
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itkBlockMatchingMetricImageToDisplacementCalculator
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itkBlockMatchingBayesianRegularizationDisplacementCalculator
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itkBlockMatchingMultiResolutionFixedSearchRegionImageSource
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itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter
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itkBlockMatchingMultiResolutionImageRegistrationMethod
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itkSpectra1DSupportWindowImageFilter
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itkCurvilinearArraySpecialCoordinatesImage
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itkFrequencyDomain1DFilterFunction

‎wrapping/itkBlockMatchingBayesianRegularizationDisplacementCalculator.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkImage.h")
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# Wrap desired class
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itk_wrap_include("itkBlockMatchingBayesianRegularizationDisplacementCalculator.h")
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itk_wrap_class("itk::BlockMatching::BayesianRegularizationDisplacementCalculator" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_V${ITKM_${t}}${d}}${d}"
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"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_V${ITKM_${t}}${d}},${d}>")
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endforeach()
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endforeach()
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itk_end_wrap_class()

‎wrapping/itkBlockMatchingMetricImageToDisplacementCalculator.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkBlockMatchingMetricImageToDisplacementCalculator.h")
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itk_wrap_class("itk::BlockMatching::MetricImageToDisplacementCalculator" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(t2 ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_V${t2}${d}}${d}"
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"${ITKT_I${ITKM_${t}}${d}}, ${ITKT_I${ITKM_V${t2}${d}}${d}}")
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endforeach()
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endforeach()
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endforeach()
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itk_end_wrap_class()

‎wrapping/itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkImage.h")
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itk_wrap_include("itkBlockMatchingMultiResolutionBlockRadiusCalculator.h")
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itk_wrap_class("itk::BlockMatching::MultiResolutionBlockRadiusCalculator" POINTER)
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foreach(t ${WRAP_ITK_SCALAR})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("I${ITKM_${t}}${d}" "itk::Image<${ITKT_${t}},${d}>")
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endforeach()
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endforeach()
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itk_end_wrap_class()
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itk_wrap_include("itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator.h")
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itk_wrap_class("itk::BlockMatching::MultiResolutionFixedBlockRadiusCalculator" POINTER)
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foreach(t ${WRAP_ITK_SCALAR})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("I${ITKM_${t}}${d}" "itk::Image<${ITKT_${t}},${d}>")
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endforeach()
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endforeach()
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itk_end_wrap_class()

‎wrapping/itkBlockMatchingMultiResolutionFixedSearchRegionImageSource.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkVector.h")
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itk_wrap_include("itkImage.h")
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itk_wrap_include("itkImageRegion.h")
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# Wrap for class template
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itk_wrap_include("itkImageRegion.h")
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itk_wrap_class("itk::Image" POINTER)
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("IR${d}${d}" "itk::ImageRegion<${d}>, ${d}")
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endforeach()
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itk_end_wrap_class()
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itk_wrap_include("itkImageSource.h")
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itk_wrap_class("itk::ImageSource" POINTER)
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("IIR${d}${d}" "itk::Image<itk::ImageRegion<${d}>,${d}>")
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endforeach()
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itk_end_wrap_class()
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# Wrap class hierarchy
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itk_wrap_include("itkBlockMatchingMultiResolutionSearchRegionImageSource.h")
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itk_wrap_class("itk::BlockMatching::MultiResolutionSearchRegionImageSource" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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foreach(vt ${WRAP_ITK_VECTOR_REAL})
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itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_${t}}${d}I${ITKM_${vt}${d}}${d}"
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"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${vt}${d}},${d}>")
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endforeach()
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endforeach()
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endforeach()
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itk_end_wrap_class()
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# Wrap class
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itk_wrap_include("itkBlockMatchingMultiResolutionFixedSearchRegionImageSource.h")
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itk_wrap_class("itk::BlockMatching::MultiResolutionFixedSearchRegionImageSource" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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foreach(vt ${WRAP_ITK_VECTOR_REAL})
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itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_${t}}${d}I${ITKM_${vt}${d}}${d}"
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"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${vt}${d}},${d}>")
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endforeach()
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endforeach()
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endforeach()
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itk_end_wrap_class()

‎wrapping/itkBlockMatchingMultiResolutionImageRegistrationMethod.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkPoint.h")
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itk_wrap_include("itkSmartPointer.h")
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itk_wrap_include("itkImage.h")
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itk_wrap_include("itkImageRegion.h")
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# Wrap base classes for itk::BlockMatching::MetricImageToDisplacementCalculator public members
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#itk_wrap_class("itk::SmartPointer")
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# foreach(t ${WRAP_ITK_REAL})
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# foreach(d ${ITK_WRAP_IMAGE_DIMS})
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# itk_wrap_template("I${ITKM_${t}}${d}" "itk::Image<${ITKT_${t}},${d}>")
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# endforeach()
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# endforeach()
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#itk_end_wrap_class()
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itk_wrap_class("itk::Image" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("P${ITKM_${t}}${d}${d}" "itk::Point<${ITKT_${t}},${d}>, ${d}")
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itk_wrap_template("SPI${ITKM_${t}}${d}${d}" "itk::SmartPointer<itk::Image<${ITKT_${t}},${d}>>, ${d}")
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endforeach()
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endforeach()
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itk_end_wrap_class()
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# Wrap class hierarchy
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itk_wrap_include("itkImageToImageFilter.h")
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itk_wrap_class("itk::ImageToImageFilter" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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itk_wrap_template("IIR${d}${d}I${ITKM_V${t}${d}}${d}"
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"itk::Image<itk::ImageRegion<${d}>,${d}>, itk::Image<${ITKT_V${t}${d}},${d}>")
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endforeach()
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endforeach()
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itk_end_wrap_class()
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itk_wrap_include("itkBlockMatchingImageRegistrationMethod.h")
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itk_wrap_class("itk::BlockMatching::ImageRegistrationMethod" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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foreach(vt ${WRAP_ITK_VECTOR_REAL})
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set(img_m "I${ITKM_${t}}${d}")
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set(img_t "itk::Image<${ITKT_${t}}, ${d}>")
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itk_wrap_template("${img_m}${img_m}${img_m}I${ITKM_${vt}${d}}${d}"
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"${img_t}, ${img_t}, ${img_t}, itk::Image<${ITKT_${vt}${d}},${d}>, ${ITKT_${t}}")
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endforeach()
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endforeach()
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endforeach()
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itk_end_wrap_class()
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# Wrap target class
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itk_wrap_include("itkBlockMatchingMultiResolutionImageRegistrationMethod.h")
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itk_wrap_class("itk::BlockMatching::MultiResolutionImageRegistrationMethod" POINTER)
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foreach(t ${WRAP_ITK_REAL})
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foreach(d ${ITK_WRAP_IMAGE_DIMS})
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set(img_m "I${ITKM_${t}}${d}")
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set(img_t "itk::Image<${ITKT_${t}}, ${d}>")
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itk_wrap_template("${img_m}${img_m}${img_m}I${ITKM_${vt}${d}}${d}"
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"${img_t}, ${img_t}, ${img_t}, itk::Image<${ITKT_V${t}${d}},${d}>, ${ITKT_${t}}")
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endforeach()
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endforeach()
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itk_end_wrap_class()

‎wrapping/itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter.wrap‎

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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
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itk_wrap_include("itkBlockMatchingMetricImageFilter.h")
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itk_wrap_class("itk::BlockMatching::MetricImageFilter" POINTER)
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itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
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itk_end_wrap_class()
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itk_wrap_include("itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter.h")
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itk_wrap_class("itk::BlockMatching::NormalizedCrossCorrelationMetricImageFilter" POINTER)
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itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
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itk_end_wrap_class()
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itk_wrap_include("itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter.h")
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itk_wrap_class("itk::BlockMatching::NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter" POINTER)
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itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
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itk_end_wrap_class()

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