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ADD: Addition of point to surface metric to Elastix.
COMP: Remove cmake* from .gitignore Having cmake* in there stopped Gokhan Gunay from adding his CMakeLists file to pull request #236 (Addition of PointToSurface metric). Addition of PointToSurface metric ADD: Addition of point to surface metric to Elastix. In this commit addition of point to surface metric is done. This metric essentially considers how surface of an masked organ is aligned with the points provided from the surface of the organ. Therefore, it is used to improve alignment of the organ under interest.
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‎.gitignore‎

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# Generated files and
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help/
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cmake*
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Makefile
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CMakeFiles/
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CTestTestfile.cmake

‎Components/Metrics/PointToSurfaceDistance/CMakeLists.txt‎

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ADD_ELXCOMPONENT( PointToSurfaceDistanceMetric ON
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elxPointToSurfaceDistanceMetric.h
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elxPointToSurfaceDistanceMetric.hxx
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elxPointToSurfaceDistanceMetric.cxx
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itkPointToSurfaceDistanceMetric.h
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itkPointToSurfaceDistanceMetric.hxx )
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‎Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.cxx‎

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/*=========================================================================
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*
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* Copyright UMC Utrecht and contributors
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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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*
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*=========================================================================*/
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#include "elxPointToSurfaceDistanceMetric.h"
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elxInstallMacro( PointToSurfaceDistanceMetric );

‎Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.h‎

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/*=========================================================================
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*
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* Copyright UMC Utrecht and contributors
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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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*
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*=========================================================================*/
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#ifndef __elxPointToSurfaceDistanceMetric_H__
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#define __elxPointToSurfaceDistanceMetric_H__
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#include "elxIncludes.h" // include first to avoid MSVS warning
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#include "itkPointToSurfaceDistanceMetric.h"
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namespace elastix
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{
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/**
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*
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* For more information check the paper:\n
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* Gunay, G. , Luu, M. H., Moelker, A. , Walsum, T. and Klein, S. (2017),
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* "Semiautomated registration of pre‐ and intraoperative CT for image‐guided percutaneous
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* liver tumor ablation interventions," Med. Phys., 44: 3718-3725.
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*
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* The parameters used in this class are:\n
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* \parameter Metric: Select this metric as follows:
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* </tt>(Metric "PointToSurfaceDistance")</tt>
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*
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* \parameter PointToSurfaceDistanceAverage: A parameter to get average of the points by dividing the weight of the penalty with the number of the points included.
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* example: </tt>(PointToSurfaceDistanceAverage "true")</tt> \n
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* Default is "true".
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*
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* \Command line parameters
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* \parameter -fp "file" : Elastix pointset file.
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* example:
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* \parameter -dt "file" : Distance transform (file) of segmentation of the organ under interest in the moving image.
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* \parameter -seg "file" : Segmentation (file) of the organ under interest in the moving image. With this parameter the algorithm internally computes the distance transform.
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* \parameter -dtout "file" : If the user wants to get the distance transform from organ segmentation, this parameter is called with the name of the distance transform image file to write .
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*
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*
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* \ingroup Metrics
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*
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*/
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template< class TElastix >
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class PointToSurfaceDistanceMetric :
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public
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itk::PointToSurfaceDistanceMetric <
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typename MetricBase< TElastix >::FixedPointSetType,
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typename MetricBase< TElastix >::MovingPointSetType >,
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public MetricBase< TElastix >
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{
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public:
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using Self = PointToSurfaceDistanceMetric;
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/** Standard ITK-stuff. */
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using Superclass1 = itk::PointToSurfaceDistanceMetric<typename MetricBase< TElastix >::FixedPointSetType, typename MetricBase< TElastix >::MovingPointSetType >;
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using Superclass2 = MetricBase< TElastix >;
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using Pointer = itk::SmartPointer< Self >;
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using ConstPointer = itk::SmartPointer< const Self >;
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ITK_DISALLOW_COPY_AND_ASSIGN(PointToSurfaceDistanceMetric);
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/** Method for creation through the object factory. */
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itkNewMacro( Self );
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/** Run-time type information (and related methods). */
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itkTypeMacro( PointToSurfaceDistanceMetric, itk::PointToSurfaceDistanceMetric );
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/** Name of this class.
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* Use this name in the parameter file to select this specific metric. \n
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* example: <tt>(Metric "PointToSurfaceDistance")</tt>\n
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*/
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elxClassNameMacro( "PointToSurfaceDistance" );
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/** Typedefs from the superclass. */
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using CoordinateRepresentationType = typename Superclass1::CoordinateRepresentationType;
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using FixedPointSetType = typename Superclass1::FixedPointSetType;
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using FixedPointSetConstPointer = typename Superclass1::FixedPointSetConstPointer;
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using MovingPointSetType = typename Superclass1::MovingPointSetType;
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using MovingPointSetConstPointer = typename Superclass1::MovingPointSetConstPointer;
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using TransformType = typename Superclass1::TransformType;
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using TransformPointer = typename Superclass1::TransformPointer;
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using InputPointType = typename Superclass1::InputPointType;
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using OutputPointType = typename Superclass1::OutputPointType;
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using TransformParametersType = typename Superclass1::TransformParametersType;
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using TransformJacobianType = typename Superclass1::TransformJacobianType;
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using FixedImageMaskType = typename Superclass1::FixedImageMaskType;
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using FixedImageMaskPointer = typename Superclass1::FixedImageMaskPointer;
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using MovingImageMaskType = typename Superclass1::MovingImageMaskType;
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using MovingImageMaskPointer = typename Superclass1::MovingImageMaskPointer;
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using MeasureType = typename Superclass1::MeasureType;
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using DerivativeType = typename Superclass1::DerivativeType;
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using ParametersType = typename Superclass1::ParametersType;
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/** Typedefs inherited from elastix. */
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using ElastixType = typename Superclass2::ElastixType;
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using ElastixPointer = typename Superclass2::ElastixPointer;
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using ConfigurationType = typename Superclass2::ConfigurationType;
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using ConfigurationPointer = typename Superclass2::ConfigurationPointer;
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using RegistrationType = typename Superclass2::RegistrationType;
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using RegistrationPointer = typename Superclass2::RegistrationPointer;
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using ITKBaseType = typename Superclass2::ITKBaseType;
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using FixedImageType = typename Superclass2::FixedImageType;
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using MovingImageType = typename Superclass2::MovingImageType;
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/** The fixed image dimension. */
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itkStaticConstMacro( FixedImageDimension, unsigned int, FixedImageType::ImageDimension );
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/** The moving image dimension. */
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itkStaticConstMacro( MovingImageDimension, unsigned int, MovingImageType::ImageDimension );
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using PointSetType = FixedPointSetType;
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using ImageType = typename Superclass1::ImageType;
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/** Sets up a timer to measure the initialisation time and
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* calls the Superclass' implementation.
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*/
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virtual void Initialize();
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/**
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* Do some things before all:
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* \li Check and print the command line arguments fp and mp.
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* This should be done in BeforeAllBase and not BeforeAll.
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*/
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virtual int BeforeAllBase();
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/**
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* Do some things before registration:
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* \li Load and set the pointsets.
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*/
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virtual void BeforeRegistration();
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using ImageConstPointer = typename Superclass1::ImageType::ConstPointer;
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unsigned int ReadLandmarks( const std::string & landmarkFileName, typename PointSetType::Pointer & pointSet, typename FixedImageType::ConstPointer image );
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/** Overwrite to silence warning. */
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virtual void SelectNewSamples( void ){}
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protected:
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/** The constructor. */
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PointToSurfaceDistanceMetric() = default;
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/** The destructor. */
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virtual ~PointToSurfaceDistanceMetric() = default;
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};
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} // end namespace elastix
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#ifndef ITK_MANUAL_INSTANTIATION
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#include "elxPointToSurfaceDistanceMetric.hxx"
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#endif
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#endif

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