Euler transform with optional upper/lower limits to each parameter

Components/Transforms/AdvancedLimitedEulerTransform/CMakeLists.txt

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+
+ADD_ELXCOMPONENT( AdvancedLimitedEulerTransformElastix
+ itkLimitedEulerTransform.h
+ itkAdvancedLimitedEuler3DTransform.h
+ itkAdvancedLimitedEuler3DTransform.hxx
+ elxAdvancedLimitedEulerTransform.h
+ elxAdvancedLimitedEulerTransform.hxx
+ elxAdvancedLimitedEulerTransform.cxx )
+

Components/Transforms/AdvancedLimitedEulerTransform/elxAdvancedLimitedEulerTransform.cxx

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+/*=========================================================================
+ *
+ *  Copyright UMC Utrecht and contributors
+ *
+ *  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.
+ *
+ *=========================================================================*/
+
+#include "elxAdvancedLimitedEulerTransform.h"
+
+elxInstallMacro( AdvancedLimitedEulerTransformElastix );

Components/Transforms/AdvancedLimitedEulerTransform/elxAdvancedLimitedEulerTransform.h

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+/*=========================================================================
+ *
+ *  Copyright UMC Utrecht and contributors
+ *
+ *  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.
+ *
+ *=========================================================================*/
+#ifndef __elxAdvancedLimitedEulerTransform_H__
+#define __elxAdvancedLimitedEulerTransform_H__
+
+#include "elxIncludes.h" // include first to avoid MSVS warning
+#include "itkAdvancedCombinationTransform.h"
+#include "itkLimitedEulerTransform.h"
+#include "itkCenteredTransformInitializer.h"
+
+namespace elastix
+{
+
+/**
+ * \class AdvancedLimitedEulerTransformElastix
+ * \brief A transform based on the itk LimitedEulerTransforms.
+ *
+ * This transform is a rigid body transformation.
+ *
+ * The parameters used in this class are:
+ * \parameter Transform: Select this transform as follows:\n
+ *    <tt>(%Transform "LimitedEulerTransform")</tt>
+ * \parameter UpperLimits: the upper limit value for the rotations and translations,
+ *    used in the optimizer. \n
+ *    example: <tt>(UpperLimits 3.14 3.14 3.14 100.00 100.00 100.00)</tt> \n
+ *    The number of arguments should be equal to the number of parameters: 
+ *    for each parameter its upper limit value. Arguments are in the order as for
+ *    the Euler transform parameters: <RotX RotY RotZ TraX TraY TraZ>. Set the limit 
+ *    value to extreme positive values to (e.g. 1e+3) to effectively disable the upper limits.
+ * \parameter LowerLimits: the lower limit values for the rotations and translations,
+ *    used in the optimizer. \n
+ *    example: <tt>(LowerLimits -3.14 -3.14 -3.14 -100.00 -100.00 -100.00)</tt> \n
+ *    The number of arguments should be equal to the number of parameters: 
+ *    for each parameter its lower limit value. Arguments are in the order as for
+ *    the Euler transform parameters: <RotX RotY RotZ TraX TraY TraZ>. Set the limit 
+ *    value to extreme negative values to (e.g. -1e+3) to effectively disable the upper limits.
+ * \parameter SharpnessOfLimits: the scale factor which determines the limit cutoff sharpness. \n
+ *    example: <tt>(LimitSharpness 25.0)</tt> \n
+ *    High values impose a sharp limit (e.g. 10.0--100.0), while lower values (1.0-10.0). 
+ *    Minimum value is 1.0, lower values will be clamped to 1.0. If this parameter option 
+ *    is not used, by default for the sharpness limit value is 25.0.* 
+ * \parameter Scales: the scale factor between the rotations and translations,
+ *    used in the optimizer. \n
+ *    example: <tt>(Scales 200000.0)</tt> \n
+ *    example: <tt>(Scales 100000.0 60000.0 ... 80000.0)</tt> \n
+ *    If only one argument is given, that factor is used for the rotations.
+ *    If more than one argument is given, then the number of arguments should be
+ *    equal to the number of parameters: for each parameter its scale factor.
+ *    If this parameter option is not used, by default the rotations are scaled
+ *    by a factor of 100000.0. See also the AutomaticScalesEstimation parameter.
+ * \parameter AutomaticScalesEstimation: if this parameter is set to "true" the Scales
+ *    parameter is ignored and the scales are determined automatically. \n
+ *    example: <tt>( AutomaticScalesEstimation "true" ) </tt> \n
+ *    Default: "false" (for backwards compatibility). Recommended: "true".
+ * \parameter CenterOfRotation: an index around which the image is rotated. \n
+ *    example: <tt>(CenterOfRotation 128 128 90)</tt> \n
+ *    By default the CenterOfRotation is set to the geometric center of the image.
+ * \parameter AutomaticTransformInitialization: whether or not the initial translation
+ *    between images should be estimated as the distance between their centers.\n
+ *    example: <tt>(AutomaticTransformInitialization "true")</tt> \n
+ *    By default "false" is assumed. So, no initial translation.
+ * \parameter AutomaticTransformInitializationMethod: how to initialize this
+ *    transform. Should be one of {GeometricalCenter, CenterOfGravity}.\n
+ *    example: <tt>(AutomaticTransformInitializationMethod "CenterOfGravity")</tt> \n
+ *    By default "GeometricalCenter" is assumed.\n
+ *
+ * The transform parameters necessary for transformix, additionally defined by this class, are:
+ * \transformparameter CenterOfRotation: stores the center of rotation as an index. \n
+ *    example: <tt>(CenterOfRotation 128 128 90)</tt>\n
+ *    <b>depecrated!</b> From elastix version 3.402 this is changed to CenterOfRotationPoint!
+ * \transformparameter CenterOfRotationPoint: stores the center of rotation, expressed in world coordinates. \n
+ *    example: <tt>(CenterOfRotationPoint 10.555 6.666 12.345)</tt>
+ *
+ * \ingroup Transforms
+ */
+
+template< class TElastix >
+class AdvancedLimitedEulerTransformElastix :
+  public itk::AdvancedCombinationTransform<
+  typename elx::TransformBase< TElastix >::CoordRepType,
+  elx::TransformBase< TElastix >::FixedImageDimension >,
+  public elx::TransformBase< TElastix >
+{
+public:
+
+  /** Standard ITK-stuff.*/
+  typedef AdvancedLimitedEulerTransformElastix Self;
+
+  typedef itk::AdvancedCombinationTransform<
+    typename elx::TransformBase< TElastix >::CoordRepType,
+    elx::TransformBase< TElastix >::FixedImageDimension >     Superclass1;
+
+  typedef elx::TransformBase< TElastix > Superclass2;
+
+  /** The ITK-class that provides most of the functionality, and
+   * that is set as the "CurrentTransform" in the CombinationTransform */
+  typedef itk::LimitedEulerTransform<
+    typename elx::TransformBase< TElastix >::CoordRepType,
+    elx::TransformBase< TElastix >::FixedImageDimension >     LimitedEulerTransformType;
+
+  // typedef itk::LimitedEuler3DTransform<
+  //   typename elx::TransformBase< TElastix >::CoordRepType >     LimitedEulerTransformType;
+
+  typedef itk::SmartPointer< Self >       Pointer;
+  typedef itk::SmartPointer< const Self > ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro( Self );
+
+  /** Run-time type information (and related methods). */
+  //itkTypeMacro( AdvancedLimitedEulerTransformElastix, LimitedEulerTransform );
+  itkTypeMacro( AdvancedLimitedEulerTransformElastix, itk::AdvancedCombinationTransform );
+
+  /** Name of this class.
+   * Use this name in the parameter file to select this specific transform. \n
+   * example: <tt>(Transform "AdvancedLimitedEulerTransform")</tt>\n
+   */
+  elxClassNameMacro( "AdvancedLimitedEulerTransform" );
+
+  /** Dimension of the fixed image. */
+  itkStaticConstMacro( SpaceDimension, unsigned int, Superclass2::FixedImageDimension );
+
+  /** Typedefs inherited from the superclass. */
+
+  /** These are both in Euler2D and Euler3D. */
+  typedef typename Superclass1::ScalarType             ScalarType;
+  typedef typename Superclass1::ParametersType         ParametersType;
+  typedef typename Superclass1::NumberOfParametersType NumberOfParametersType;
+  typedef typename Superclass1::JacobianType           JacobianType;
+
+  typedef typename Superclass1::InputPointType            InputPointType;
+  typedef typename Superclass1::OutputPointType           OutputPointType;
+  typedef typename Superclass1::InputVectorType           InputVectorType;
+  typedef typename Superclass1::OutputVectorType          OutputVectorType;
+  typedef typename Superclass1::InputCovariantVectorType  InputCovariantVectorType;
+  typedef typename Superclass1::OutputCovariantVectorType OutputCovariantVectorType;
+  typedef typename Superclass1::InputVnlVectorType        InputVnlVectorType;
+  typedef typename Superclass1::OutputVnlVectorType       OutputVnlVectorType;
+
+  typedef typename LimitedEulerTransformType::Pointer    LimitedEulerTransformPointer;
+  typedef typename LimitedEulerTransformType::OffsetType OffsetType;
+
+  /** Typedef's inherited from TransformBase. */
+  typedef typename Superclass2::ElastixType              ElastixType;
+  typedef typename Superclass2::ElastixPointer           ElastixPointer;
+  typedef typename Superclass2::ParameterMapType         ParameterMapType;
+  typedef typename Superclass2::ConfigurationType        ConfigurationType;
+  typedef typename Superclass2::ConfigurationPointer     ConfigurationPointer;
+  typedef typename Superclass2::RegistrationType         RegistrationType;
+  typedef typename Superclass2::RegistrationPointer      RegistrationPointer;
+  typedef typename Superclass2::CoordRepType             CoordRepType;
+  typedef typename Superclass2::FixedImageType           FixedImageType;
+  typedef typename Superclass2::MovingImageType          MovingImageType;
+  typedef typename Superclass2::ITKBaseType              ITKBaseType;
+  typedef typename Superclass2::CombinationTransformType CombinationTransformType;
+
+  /** Other typedef's. */
+  typedef typename FixedImageType::IndexType     IndexType;
+  typedef typename IndexType::IndexValueType     IndexValueType;
+  typedef typename FixedImageType::SizeType      SizeType;
+  typedef typename FixedImageType::PointType     PointType;
+  typedef typename FixedImageType::SpacingType   SpacingType;
+  typedef typename FixedImageType::RegionType    RegionType;
+  typedef typename FixedImageType::DirectionType DirectionType;
+
+  typedef itk::CenteredTransformInitializer<
+    LimitedEulerTransformType, FixedImageType, MovingImageType >  TransformInitializerType;
+  typedef typename TransformInitializerType::Pointer TransformInitializerPointer;
+
+  /** For scales setting in the optimizer */
+  typedef typename Superclass2::ScalesType ScalesType;
+
+  /** Execute stuff before the actual registration:
+   * \li Call InitializeTransform
+   * \li Set the scales.
+   */
+  void BeforeRegistration( void ) override;
+
+  /** Initialize Transform.
+   * \li Set all parameters to zero.
+   * \li Set center of rotation:
+   *  automatically initialized to the geometric center of the image, or
+   *   assigned a user entered voxel index, given by the parameter
+   *   (CenterOfRotation <index-x> <index-y> ...);
+   *   If an initial transform is present and HowToCombineTransforms is
+   *   set to "Compose", the initial transform is taken into account
+   *   while setting the center of rotation.
+   * \li Set initial translation:
+   *  the initial translation between fixed and moving image is guessed,
+   *  if the user has set (AutomaticTransformInitialization "true").
+   *
+   * It is not yet possible to enter an initial rotation angle.
+   */
+  virtual void InitializeTransform( void );
+
+  /** Set the scales
+   * \li If AutomaticScalesEstimation is "true" estimate scales
+   * \li If scales are provided by the user use those,
+   * \li Otherwise use some default value
+   * This function is called by BeforeRegistration, after
+   * the InitializeTransform function is called
+   */
+  virtual void SetScales( void );
+
+  /** Function to read transform-parameters from a file.
+   *
+   * It reads the center of rotation and calls the superclass' implementation.
+   */
+  void ReadFromFile( void ) override;
+
+  /** Function to create transform-parameters map.
+   * Creates the TransformParametersmap
+   */
+  ParameterMapType
+  CreateDerivedTransformParametersMap(void) const override;
+
+  void
+  AfterRegistration(void) override;
+
+protected:
+
+  /** The constructor. */
+  AdvancedLimitedEulerTransformElastix();
+  /** The destructor. */
+  ~AdvancedLimitedEulerTransformElastix() override {}
+
+  /** Try to read the CenterOfRotationPoint from the transform parameter file
+   * The CenterOfRotationPoint is already in world coordinates.
+   * Transform parameter files generated by elastix version > 3.402
+   * save the center of rotation in this way.
+   */
+  virtual bool ReadCenterOfRotationPoint( InputPointType & rotationPoint ) const;
+
+private:
+  elxOverrideGetSelfMacro;
+
+  /** The private constructor. */
+  AdvancedLimitedEulerTransformElastix( const Self & );  // purposely not implemented
+  /** The private copy constructor. */
+  void operator=( const Self & );         // purposely not implemented
+
+  LimitedEulerTransformPointer m_LimitedEulerTransform;
+
+};
+
+} // end namespace elastix
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "elxAdvancedLimitedEulerTransform.hxx"
+#endif
+
+#endif // end #ifndef __elxAdvancedLimitedEulerTransform_H__