ADD: Addition of point to surface metric to elastix.

.gitignore

@@ -33,7 +33,6 @@
 
 # Generated files and
 help/
-cmake*
 Makefile
 CMakeFiles/
 CTestTestfile.cmake

Components/Metrics/PointToSurfaceDistance/CMakeLists.txt

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+
+ADD_ELXCOMPONENT( PointToSurfaceDistanceMetric ON
+ elxPointToSurfaceDistanceMetric.h
+ elxPointToSurfaceDistanceMetric.hxx
+ elxPointToSurfaceDistanceMetric.cxx
+ itkPointToSurfaceDistanceMetric.h
+ itkPointToSurfaceDistanceMetric.hxx )
+

Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.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 "elxPointToSurfaceDistanceMetric.h"
+
+elxInstallMacro( PointToSurfaceDistanceMetric );

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