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Added EulerStackTransform to trunkpublic
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‎src/Components/Transforms/EulerStackTransform/CMakeLists.txt

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ADD_ELXCOMPONENT( EulerStackTransform
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elxEulerStackTransform.h
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elxEulerStackTransform.hxx
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elxEulerStackTransform.cxx)
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‎src/Components/Transforms/EulerStackTransform/elxEulerStackTransform.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 "elxEulerStackTransform.h"
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elxInstallMacro( EulerStackTransform );

‎src/Components/Transforms/EulerStackTransform/elxEulerStackTransform.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 __elxEulerStackTransform_h
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#define __elxEulerStackTransform_h
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#include "elxIncludes.h"
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/** Include itk transforms needed. */
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#include "itkAdvancedCombinationTransform.h"
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#include "itkStackTransform.h"
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#include "itkEulerTransform.h"
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namespace elastix
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{
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/**
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* \class EulerStackTransform
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* \brief A stack transform based on the itk EulerTransforms.
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*
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* This transform is a rigid body transformation. Calls to TransformPoint and GetJacobian are
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* redirected to the appropriate sub transform based on the last dimension (time) index.
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*
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* This transform uses the size, spacing and origin of the last dimension of the fixed
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* image to set the number of sub transforms, the origin of the first transform and the
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* spacing between the transforms.
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*
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*
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* The parameters used in this class are:
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* \parameter Transform: Select this transform as follows:\n
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* <tt>(%Transform "EulerStackTransform")</tt>
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* \parameter Scales: the scale factor between the rotations and translations,
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* used in the optimizer. \n
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* example: <tt>(Scales 200000.0)</tt> \n
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* example: <tt>(Scales 100000.0 60000.0 ... 80000.0)</tt> \n
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* If only one argument is given, that factor is used for the rotations.
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* If more than one argument is given, then the number of arguments should be
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* equal to the number of parameters: for each parameter its scale factor.
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* If this parameter option is not used, by default the rotations are scaled
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* by a factor of 100000.0. See also the AutomaticScalesEstimation parameter.
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* \parameter AutomaticScalesEstimation: if this parameter is set to "true" the Scales
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* parameter is ignored and the scales are determined automatically. \n
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* example: <tt>( AutomaticScalesEstimation "true" ) </tt> \n
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* Default: "false" (for backwards compatibility). Recommended: "true".
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* \parameter CenterOfRotation: an index around which the image is rotated. \n
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* example: <tt>(CenterOfRotation 128 128)</tt> \n
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*
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* The transform parameters necessary for transformix, additionally defined by this class, are:
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* \transformparameter CenterOfRotation: stores the center of rotation as an index. \n
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* example: <tt>(CenterOfRotation 128 128)</tt>
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* deprecated! From elastix version 3.402 this is changed to CenterOfRotationPoint!
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* \transformparameter CenterOfRotationPoint: stores the center of rotation, expressed in world coordinates. \n
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* example: <tt>(CenterOfRotationPoint 10.555 6.666)</tt>
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* \transformparameter StackSpacing: stores the spacing between the sub transforms. \n
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* exanoke: <tt>(StackSpacing 1.0)</tt>
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* \transformparameter StackOrigin: stores the origin of the first sub transform. \n
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* exanoke: <tt>(StackOrigin 0.0)</tt>
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* \transformparameter NumberOfSubTransforms: stores the number of sub transforms. \n
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* exanoke: <tt>(NumberOfSubTransforms 10)</tt>
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*
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* \todo It is unsure what happens when one of the image dimensions has length 1.
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* \todo The center of rotation point is not transformed with the initial transform yet.
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*
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* \ingroup Transforms
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*/
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template< class TElastix >
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class EulerStackTransform :
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public itk::AdvancedCombinationTransform<
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typename elx::TransformBase< TElastix >::CoordRepType,
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elx::TransformBase< TElastix >::FixedImageDimension >,
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public elx::TransformBase< TElastix >
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{
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public:
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/** Standard ITK-stuff. */
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typedef EulerStackTransform Self;
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typedef itk::AdvancedCombinationTransform<
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typename elx::TransformBase< TElastix >::CoordRepType,
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elx::TransformBase< TElastix >::FixedImageDimension > Superclass1;
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typedef elx::TransformBase< TElastix > Superclass2;
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typedef itk::SmartPointer< Self > Pointer;
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typedef itk::SmartPointer< const Self > ConstPointer;
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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( EulerStackTransform, itk::AdvancedCombinationTransform );
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/** Name of this class.
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* Use this name in the parameter file to select this specific transform. \n
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* example: <tt>(Transform "EulerStackTransform")</tt>\n
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*/
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elxClassNameMacro( "EulerStackTransform" );
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/** (Reduced) dimension of the fixed image. */
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itkStaticConstMacro( SpaceDimension, unsigned int, Superclass2::FixedImageDimension );
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itkStaticConstMacro( ReducedSpaceDimension, unsigned int, Superclass2::FixedImageDimension - 1 );
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/** The ITK-class that provides most of the functionality, and
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* that is set as the "CurrentTransform" in the CombinationTransform.
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*/
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typedef itk::EulerTransform<
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typename elx::TransformBase< TElastix >::CoordRepType,
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itkGetStaticConstMacro( SpaceDimension ) > EulerTransformType;
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typedef typename EulerTransformType::Pointer EulerTransformPointer;
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typedef typename EulerTransformType::InputPointType InputPointType;
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/** The ITK-class for the sub transforms, which have a reduced dimension. */
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typedef itk::EulerTransform<
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typename elx::TransformBase< TElastix >::CoordRepType,
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itkGetStaticConstMacro( ReducedSpaceDimension ) > ReducedDimensionEulerTransformType;
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typedef typename ReducedDimensionEulerTransformType::Pointer ReducedDimensionEulerTransformPointer;
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typedef typename ReducedDimensionEulerTransformType::OutputVectorType ReducedDimensionOutputVectorType;
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typedef typename ReducedDimensionEulerTransformType::InputPointType ReducedDimensionInputPointType;
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/** Typedef for stack transform. */
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typedef itk::StackTransform<
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typename elx::TransformBase< TElastix >::CoordRepType,
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itkGetStaticConstMacro( SpaceDimension ),
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itkGetStaticConstMacro( SpaceDimension ) > EulerStackTransformType;
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typedef typename EulerStackTransformType::Pointer EulerStackTransformPointer;
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/** Typedefs inherited from the superclass. */
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typedef typename Superclass1::ParametersType ParametersType;
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typedef typename Superclass1::NumberOfParametersType NumberOfParametersType;
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/** Typedef's from TransformBase. */
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typedef typename Superclass2::ElastixType ElastixType;
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typedef typename Superclass2::ElastixPointer ElastixPointer;
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typedef typename Superclass2::ConfigurationType ConfigurationType;
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typedef typename Superclass2::ConfigurationPointer ConfigurationPointer;
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typedef typename Superclass2::RegistrationType RegistrationType;
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typedef typename Superclass2::RegistrationPointer RegistrationPointer;
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typedef typename Superclass2::CoordRepType CoordRepType;
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typedef typename Superclass2::FixedImageType FixedImageType;
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typedef typename Superclass2::MovingImageType MovingImageType;
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typedef typename Superclass2::ITKBaseType ITKBaseType;
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typedef typename Superclass2::CombinationTransformType CombinationTransformType;
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/** Reduced Dimension typedef's. */
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typedef float PixelType;
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typedef itk::Image< PixelType,
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itkGetStaticConstMacro( ReducedSpaceDimension ) > ReducedDimensionImageType;
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typedef itk::ImageRegion<
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itkGetStaticConstMacro( ReducedSpaceDimension ) > ReducedDimensionRegionType;
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typedef typename ReducedDimensionImageType::PointType ReducedDimensionPointType;
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typedef typename ReducedDimensionImageType::SizeType ReducedDimensionSizeType;
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typedef typename ReducedDimensionRegionType::IndexType ReducedDimensionIndexType;
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typedef typename ReducedDimensionImageType::SpacingType ReducedDimensionSpacingType;
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typedef typename ReducedDimensionImageType::DirectionType ReducedDimensionDirectionType;
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typedef typename ReducedDimensionImageType::PointType ReducedDimensionOriginType;
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/** For scales setting in the optimizer */
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typedef typename Superclass2::ScalesType ScalesType;
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/** Other typedef's. */
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typedef typename FixedImageType::IndexType IndexType;
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typedef typename FixedImageType::SizeType SizeType;
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typedef typename FixedImageType::PointType PointType;
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typedef typename FixedImageType::SpacingType SpacingType;
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typedef typename FixedImageType::RegionType RegionType;
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typedef typename FixedImageType::DirectionType DirectionType;
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typedef typename itk::ContinuousIndex< CoordRepType, ReducedSpaceDimension > ReducedDimensionContinuousIndexType;
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typedef typename itk::ContinuousIndex< CoordRepType, SpaceDimension > ContinuousIndexType;
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/** Execute stuff before anything else is done:*/
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virtual int BeforeAll( void );
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/** Execute stuff before the actual registration:
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* \li Set the stack transform parameters.
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* \li Set initial sub transforms.
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* \li Create initial registration parameters.
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*/
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virtual void BeforeRegistration( void );
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/** Method initialize the parameters (to 0). */
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virtual void InitializeTransform( void );
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/** Set the scales
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* \li If AutomaticScalesEstimation is "true" estimate scales
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* \li If scales are provided by the user use those,
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* \li Otherwise use some default value
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* This function is called by BeforeRegistration, after
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* the InitializeTransform function is called
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*/
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virtual void SetScales( void );
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/** Function to read transform-parameters from a file. */
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virtual void ReadFromFile( void );
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/** Function to write transform-parameters to a file. */
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virtual void WriteToFile( const ParametersType & param ) const;
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/** Function to rotate center of rotation point using initial transformation. */
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virtual void InitialTransformCenter( ReducedDimensionInputPointType & point );
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protected:
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/** The constructor. */
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EulerStackTransform();
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/** The destructor. */
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virtual ~EulerStackTransform() {}
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/** Try to read the CenterOfRotation from the transform parameter file
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* This is an index value, and, thus, converted to world coordinates.
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* Transform parameter files generated by elastix version < 3.402
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* saved the center of rotation in this way.
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*/
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virtual bool ReadCenterOfRotationIndex( ReducedDimensionInputPointType & rotationPoint ) const;
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/** Try to read the CenterOfRotationPoint from the transform parameter file
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* The CenterOfRotationPoint is already in world coordinates.
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* Transform parameter files generated by elastix version > 3.402
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* save the center of rotation in this way.
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*/
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virtual bool ReadCenterOfRotationPoint( ReducedDimensionInputPointType & rotationPoint ) const;
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private:
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/** The private constructor and copy constructor. */
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EulerStackTransform( const Self & ); // purposely not implemented
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void operator=( const Self & ); // purposely not implemented
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/** The Affine stack transform. */
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EulerStackTransformPointer m_EulerStackTransform;
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/** Dummy sub transform to be used to set sub transforms of stack transform. */
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ReducedDimensionEulerTransformPointer m_EulerDummySubTransform;
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/** Stack variables. */
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unsigned int m_NumberOfSubTransforms;
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double m_StackOrigin, m_StackSpacing;
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/** Initialize the affine transform. */
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unsigned int InitializeEulerTransform();
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};
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} // end namespace elastix
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#ifndef ITK_MANUAL_INSTANTIATION
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#include "elxEulerStackTransform.hxx"
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#endif
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#endif // end #ifndef __elxEulerStackTransform_h

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