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WIP: ENH: Add BlockMatching registration Python wrappings + example #150

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WIP: ENH: Add BlockMatching registration Python wrappings + example #150

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3beeb9c
ENH: Add BlockMatching registration Python wrappings + example
tbirdso Jul 8, 2021
d863da8
WIP: Add image point wrapping for calculator member
tbirdso Jul 26, 2021
025ad39
ENH: Rename BlockMatchingImageRegistrationMethod to mitigate collisions
tbirdso Jul 23, 2021
8ac535a
Merge branch 'wrap-blockmatching-renaming' into wrap-blockmatching
tbirdso Jul 30, 2021
4481861
WIP: Replace MetricImage SmartPointer types with pointers for wrapping
tbirdso Jul 30, 2021
461879f
WIP: Fix ImageImagePointerType typename issue
tbirdso Jul 30, 2021
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91 changes: 91 additions & 0 deletions examples/itkBlockMatchingMultiResolutionImageRegistrationMethodTest.py
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#!/usr/bin/env python

# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import os
from urllib.request import urlretrieve

import itk

# Verify wrapping succeeded
assert 'MultiResolutionFixedBlockRadiusCalculator' in dir(itk.Ultrasound)

# Get image input for registration
FIXED_IMAGE_PATH = 'Input/rf_pre15.mha'
MOVING_IMAGE_PATH = 'Input/rf_post15.mha'

if not os.path.exists(FIXED_IMAGE_PATH):
url = 'https://data.kitware.com/api/v1/file/58ee3b778d777f16d095fd8a/download'
urlretrieve(url, FIXED_IMAGE_PATH)

if not os.path.exists(MOVING_IMAGE_PATH):
url = 'https://data.kitware.com/api/v1/file/58ee3b758d777f16d095fd87/download'
urlretrieve(url, MOVING_IMAGE_PATH)

fixed_image = itk.imread(FIXED_IMAGE_PATH, itk.D)
moving_image = itk.imread(MOVING_IMAGE_PATH, itk.D)

dimension = fixed_image.GetImageDimension()
displacement_image_type = itk.Image[itk.Vector[itk.D,dimension],dimension]

block_radius_calculator = itk.Ultrasound.MultiResolutionFixedBlockRadiusCalculator[type(fixed_image)].New()
block_radius_calculator.SetRadius([12,4])

# Create schedule for iterative registration
search_region_source = itk.Ultrasound.MultiResolutionFixedSearchRegionImageSource[type(fixed_image),
type(fixed_image),
displacement_image_type].New()
pyramid_schedule = itk.Array2D[itk.UI]()
pyramid_schedule.SetSize(3,2)
pyramid_schedule.SetElement(0,0,3)
pyramid_schedule.SetElement(0,1,2)
pyramid_schedule.SetElement(1,0,2)
pyramid_schedule.SetElement(1,1,1)
pyramid_schedule.SetElement(2,0,1)
pyramid_schedule.SetElement(2,1,1)

search_region_source.SetPyramidSchedule(pyramid_schedule)
search_region_source.SetSearchRegionRadiusSchedule([50,6])
search_region_source.SetOverlapSchedule(1.0)

metric_image_filter = itk.Ultrasound.NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter[type(fixed_image),
type(fixed_image),
type(fixed_image)].New()

level_registration_method = itk.Ultrasound.ImageRegistrationMethod[type(fixed_image),
type(fixed_image),
type(fixed_image),
displacement_image_type,
itk.D].New()
level_registration_method.SetMetricImageFilter(metric_image_filter)

# Set up the multi-resolution registration object
multi_res_registration_method = itk.Ultrasound.MultiResolutionImageRegistrationMethod[type(fixed_image),
type(fixed_image),
type(fixed_image),
displacement_image_type,
itk.D].New()
multi_res_registration_method.SetFixedImage(fixed_image)
multi_res_registration_method.SetMovingImage(moving_image)
multi_res_registration_method.SetBlockRadiusCalculator(block_radius_calculator)
multi_res_registration_method.SetSearchRegionImageSource(search_region_source)
multi_res_registration_method.SetSchedules(pyramid_schedule, pyramid_schedule)
multi_res_registration_method.SetImageRegistrationMethod(level_registration_method)

# Run the actual registration
multi_res_registration_method.Update()

# Write out results
itk.imwrite(multi_res_registration_method.GetOutput(), 'Output/rf_post15_registered.mha')
6 changes: 6 additions & 0 deletions wrapping/CMakeLists.txt
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itk_wrap_module(Ultrasound)
set(WRAPPER_LIBRARY_GROUPS
itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator
itkBlockMatchingMetricImageToDisplacementCalculator
itkBlockMatchingBayesianRegularizationDisplacementCalculator
itkBlockMatchingMultiResolutionFixedSearchRegionImageSource
itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter
itkBlockMatchingMultiResolutionImageRegistrationMethod
itkSpectra1DSupportWindowImageFilter
itkCurvilinearArraySpecialCoordinatesImage
itkFrequencyDomain1DFilterFunction
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13 changes: 13 additions & 0 deletions wrapping/itkBlockMatchingBayesianRegularizationDisplacementCalculator.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
itk_wrap_include("itkImage.h")

# Wrap desired class
itk_wrap_include("itkBlockMatchingBayesianRegularizationDisplacementCalculator.h")
itk_wrap_class("itk::BlockMatching::BayesianRegularizationDisplacementCalculator" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_V${ITKM_${t}}${d}}${d}"
"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_V${ITKM_${t}}${d}},${d}>")
endforeach()
endforeach()
itk_end_wrap_class()
13 changes: 13 additions & 0 deletions wrapping/itkBlockMatchingMetricImageToDisplacementCalculator.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)

itk_wrap_include("itkBlockMatchingMetricImageToDisplacementCalculator.h")
itk_wrap_class("itk::BlockMatching::MetricImageToDisplacementCalculator" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(t2 ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_V${t2}${d}}${d}"
"${ITKT_I${ITKM_${t}}${d}}, ${ITKT_I${ITKM_V${t2}${d}}${d}}")
endforeach()
endforeach()
endforeach()
itk_end_wrap_class()
20 changes: 20 additions & 0 deletions wrapping/itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
itk_wrap_include("itkImage.h")

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

itk_wrap_include("itkBlockMatchingMultiResolutionFixedBlockRadiusCalculator.h")
itk_wrap_class("itk::BlockMatching::MultiResolutionFixedBlockRadiusCalculator" POINTER)
foreach(t ${WRAP_ITK_SCALAR})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("I${ITKM_${t}}${d}" "itk::Image<${ITKT_${t}},${d}>")
endforeach()
endforeach()
itk_end_wrap_class()
46 changes: 46 additions & 0 deletions wrapping/itkBlockMatchingMultiResolutionFixedSearchRegionImageSource.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)

itk_wrap_include("itkVector.h")
itk_wrap_include("itkImage.h")
itk_wrap_include("itkImageRegion.h")

# Wrap for class template
itk_wrap_include("itkImageRegion.h")
itk_wrap_class("itk::Image" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IR${d}${d}" "itk::ImageRegion<${d}>, ${d}")
endforeach()
itk_end_wrap_class()

itk_wrap_include("itkImageSource.h")
itk_wrap_class("itk::ImageSource" POINTER)
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IIR${d}${d}" "itk::Image<itk::ImageRegion<${d}>,${d}>")
endforeach()
itk_end_wrap_class()

# Wrap class hierarchy
itk_wrap_include("itkBlockMatchingMultiResolutionSearchRegionImageSource.h")
itk_wrap_class("itk::BlockMatching::MultiResolutionSearchRegionImageSource" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(vt ${WRAP_ITK_VECTOR_REAL})
itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_${t}}${d}I${ITKM_${vt}${d}}${d}"
"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${vt}${d}},${d}>")
endforeach()
endforeach()
endforeach()
itk_end_wrap_class()

# Wrap class
itk_wrap_include("itkBlockMatchingMultiResolutionFixedSearchRegionImageSource.h")
itk_wrap_class("itk::BlockMatching::MultiResolutionFixedSearchRegionImageSource" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(vt ${WRAP_ITK_VECTOR_REAL})
itk_wrap_template("I${ITKM_${t}}${d}I${ITKM_${t}}${d}I${ITKM_${vt}${d}}${d}"
"itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${t}},${d}>, itk::Image<${ITKT_${vt}${d}},${d}>")
endforeach()
endforeach()
endforeach()
itk_end_wrap_class()
61 changes: 61 additions & 0 deletions wrapping/itkBlockMatchingMultiResolutionImageRegistrationMethod.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
itk_wrap_include("itkPoint.h")
itk_wrap_include("itkSmartPointer.h")
itk_wrap_include("itkImage.h")
itk_wrap_include("itkImageRegion.h")

# Wrap base classes for itk::BlockMatching::MetricImageToDisplacementCalculator public members
#itk_wrap_class("itk::SmartPointer")
# foreach(t ${WRAP_ITK_REAL})
# foreach(d ${ITK_WRAP_IMAGE_DIMS})
# itk_wrap_template("I${ITKM_${t}}${d}" "itk::Image<${ITKT_${t}},${d}>")
# endforeach()
# endforeach()
#itk_end_wrap_class()

itk_wrap_class("itk::Image" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("P${ITKM_${t}}${d}${d}" "itk::Point<${ITKT_${t}},${d}>, ${d}")
itk_wrap_template("SPI${ITKM_${t}}${d}${d}" "itk::SmartPointer<itk::Image<${ITKT_${t}},${d}>>, ${d}")
endforeach()
endforeach()
itk_end_wrap_class()

# Wrap class hierarchy
itk_wrap_include("itkImageToImageFilter.h")
itk_wrap_class("itk::ImageToImageFilter" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
itk_wrap_template("IIR${d}${d}I${ITKM_V${t}${d}}${d}"
"itk::Image<itk::ImageRegion<${d}>,${d}>, itk::Image<${ITKT_V${t}${d}},${d}>")
endforeach()
endforeach()
itk_end_wrap_class()
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Seeing the following warnings when instantiating any BlockMatching class at runtime:

Template itk::ImageToImageFilter<itk::Image<itk::Vector<double,2>,2>,itk::Image<itk::CovariantVector<double,2>,2>>
already defined as <class 'itk.itkImageToImageFilterAPython.itkImageToImageFilterIVD22ICVD22'>
is redefined as {cl}
Warning: template already defined 'itk::ImageToImageFilter<itk::Image<itk::Vector<double,2>,2>,itk::Image<itk::CovariantVector<double,2>,2>>'
Template itk::ImageToImageFilter<itk::Image<itk::Vector<double,3>,3>,itk::Image<itk::CovariantVector<double,3>,3>>
already defined as <class 'itk.itkImageToImageFilterAPython.itkImageToImageFilterIVD33ICVD33'>
is redefined as {cl}
Warning: template already defined 'itk::ImageToImageFilter<itk::Image<itk::Vector<double,3>,3>,itk::Image<itk::CovariantVector<double,3>,3>>'

The warnings are introduced with these changes, but we are not explicitly wrapping ImageToImageFilter for these templates. Any thoughts on where this could be coming from?

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😕 interesting. I do not see anything via inspection, either. 👁️ I will start a local build.

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@thewtex Were you able to reproduce by any chance?

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I did not reproduce these warnings locally.

I did get

itkBlockMatchingMultiResolutionImageRegistrationMethod: warning(4): ITK type not wrapped, or currently not known: itk::Image< itk::Point< double, 2 >, 2 >
itkBlockMatchingMultiResolutionImageRegistrationMethod: warning(4): ITK type not wrapped, or currently not known: itk::Image< itk::Point< double, 3 >, 3 >

at build time.

And,

>>> itk.Ultrasound.NormalizedCrossCorrelationMetricImageFilter.New()
Warning: Unknown parameter 'itk::SmartPointer<itk::Image<float,2>>' in template 'itk::Image'
Warning: Unknown parameter 'itk::SmartPointer<itk::Image<float,3>>' in template 'itk::Image'
Namespace already has a value for ImageRegistrationMethod, which is not an itkTemplate instance for class itk::BlockMatching::ImageRegistrationMethod. Overwriting old value.
Namespace already has a value for MultiResolutionImageRegistrationMethod, which is not an itkTemplate instance for class itk::BlockMatching::MultiResolutionImageRegistrationMethod. Overwriting old value.
<itk.ITKCommonBasePython.itkObject; proxy of <Swig Object of type 'itkObject *' at 0x7fa4d95d8660> >

at run time.

We could likely replace the SmartPointer's with raw pointers.

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Interesting, thanks for taking a look. I'll try a clean build over the weekend and see if warnings still appear on my end.

My guess is that the point wrapping warnings are related to my having ITK_WRAP_DOUBLE enabled locally, I'll take a closer look.

We could likely replace the SmartPointer's with raw pointers.
Will do. This would occur within the cxx classes as well as the wrapping files, right?


itk_wrap_include("itkBlockMatchingImageRegistrationMethod.h")
itk_wrap_class("itk::BlockMatching::ImageRegistrationMethod" POINTER)
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foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
foreach(vt ${WRAP_ITK_VECTOR_REAL})
set(img_m "I${ITKM_${t}}${d}")
set(img_t "itk::Image<${ITKT_${t}}, ${d}>")
itk_wrap_template("${img_m}${img_m}${img_m}I${ITKM_${vt}${d}}${d}"
"${img_t}, ${img_t}, ${img_t}, itk::Image<${ITKT_${vt}${d}},${d}>, ${ITKT_${t}}")
endforeach()
endforeach()
endforeach()
itk_end_wrap_class()

# Wrap target class
itk_wrap_include("itkBlockMatchingMultiResolutionImageRegistrationMethod.h")
itk_wrap_class("itk::BlockMatching::MultiResolutionImageRegistrationMethod" POINTER)
foreach(t ${WRAP_ITK_REAL})
foreach(d ${ITK_WRAP_IMAGE_DIMS})
set(img_m "I${ITKM_${t}}${d}")
set(img_t "itk::Image<${ITKT_${t}}, ${d}>")
itk_wrap_template("${img_m}${img_m}${img_m}I${ITKM_${vt}${d}}${d}"
"${img_t}, ${img_t}, ${img_t}, itk::Image<${ITKT_V${t}${d}},${d}>, ${ITKT_${t}}")
endforeach()
endforeach()
itk_end_wrap_class()
16 changes: 16 additions & 0 deletions ...ping/itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter.wrap
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set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)

itk_wrap_include("itkBlockMatchingMetricImageFilter.h")
itk_wrap_class("itk::BlockMatching::MetricImageFilter" POINTER)
itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
itk_end_wrap_class()

itk_wrap_include("itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter.h")
itk_wrap_class("itk::BlockMatching::NormalizedCrossCorrelationMetricImageFilter" POINTER)
itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
itk_end_wrap_class()

itk_wrap_include("itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter.h")
itk_wrap_class("itk::BlockMatching::NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter" POINTER)
itk_wrap_image_filter("${WRAP_ITK_REAL}" 3 2+)
itk_end_wrap_class()