ADD: Addition of point to surface metric to Elastix.

gokhangg · gokhangunay01 · commit 163a13b8ab28 · 2021-02-05T14:20:00.000+01:00
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.
diff --git a/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.cxx b/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.cxx
@@ -1,16 +1,20 @@
-/*======================================================================
-
-  This file is part of the elastix software.
-
-  Copyright (c) University Medical Center Utrecht. All rights reserved.
-  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
-  details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE. See the above copyright notices for more information.
-
-======================================================================*/
+/*=========================================================================
+ *
+ *  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"
 
diff --git a/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.h b/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.h
@@ -1,16 +1,20 @@
-/*======================================================================
-
-  This file is part of the elastix software.
-
-  Copyright (c) University Medical Center Utrecht. All rights reserved.
-  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
-  details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE. See the above copyright notices for more information.
-
-======================================================================*/
+/*=========================================================================
+ *
+ *  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__
 
@@ -21,8 +25,6 @@ namespace elastix
 {
 
 /**
- * \class TransformRigidityPenalty
- * \brief A penalty term based on non-rigidity.
  *
  * For more information check the paper:\n
  * Gunay, G. , Luu, M. H., Moelker, A. , Walsum, T. and Klein, S. (2017), 
@@ -61,17 +63,14 @@ class PointToSurfaceDistanceMetric :
 public:
 
   using Self = PointToSurfaceDistanceMetric;
-  /** The private constructor. */
-  PointToSurfaceDistanceMetric(const Self &) = delete;
-  /** The private copy constructor. */
-  void operator=(const Self &) = delete;
 
   /** 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 );
 
@@ -143,8 +142,6 @@ class PointToSurfaceDistanceMetric :
    */
   virtual void BeforeRegistration();
 
-/** Function to read the corresponding points. */
-/** Function to read the corresponding points. */
   using ImageConstPointer = typename Superclass1::ImageType::ConstPointer;
 
   unsigned int ReadLandmarks( const std::string & landmarkFileName, typename PointSetType::Pointer & pointSet, typename FixedImageType::ConstPointer image );
@@ -155,9 +152,9 @@ class PointToSurfaceDistanceMetric :
 protected:
 
   /** The constructor. */
-  PointToSurfaceDistanceMetric(){}
+  PointToSurfaceDistanceMetric() = default;
   /** The destructor. */
-  virtual ~PointToSurfaceDistanceMetric() {}
+  virtual ~PointToSurfaceDistanceMetric() = default;
 
 };
 
diff --git a/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.hxx b/Components/Metrics/PointToSurfaceDistance/elxPointToSurfaceDistanceMetric.hxx
@@ -1,16 +1,20 @@
-/*======================================================================
-
-  This file is part of the elastix software.
-
-  Copyright (c) University Medical Center Utrecht. All rights reserved.
-  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
-  details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE. See the above copyright notices for more information.
-
-======================================================================*/
+/*=========================================================================
+ *
+ *  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_HXX__
 #define __elxPointToSurfaceDistanceMetric_HXX__
@@ -57,15 +61,15 @@ PointToSurfaceDistanceMetric< TElastix >
 
   /** Check for appearance of parameter "PointToSurfaceDistanceAverage". */
   std::string PointToSurfaceDistanceAverageStr = "true";
-  this->m_AvPointWeigh=true;
-  if (this->m_Configuration->CountNumberOfParameterEntries( "PointToSurfaceDistanceAverage" )==1)
+  this->m_AvPointWeigh = true;
+  if (this->m_Configuration->CountNumberOfParameterEntries( "PointToSurfaceDistanceAverage" ) == 1)
   {
     this->m_Configuration->ReadParameter( PointToSurfaceDistanceAverageStr, "PointToSurfaceDistanceAverage", 0 );
-    if (PointToSurfaceDistanceAverageStr=="false") this->m_AvPointWeigh=false;
+    if (PointToSurfaceDistanceAverageStr == "false") this->m_AvPointWeigh = false;
   }
 
   elxout << "\nAverage of points in annotation set : "
-         << PointToSurfaceDistanceAverageStr<<"\n"
+         << PointToSurfaceDistanceAverageStr <<"\n"
          <<  std::endl;
 
   /** Check for appearance of "-fp". */
diff --git a/Components/Metrics/PointToSurfaceDistance/itkPointToSurfaceDistanceMetric.h b/Components/Metrics/PointToSurfaceDistance/itkPointToSurfaceDistanceMetric.h
@@ -1,16 +1,20 @@
-/*======================================================================
-
-  This file is part of the elastix software.
-
-  Copyright (c) University Medical Center Utrecht. All rights reserved.
-  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
-  details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE. See the above copyright notices for more information.
-
-======================================================================*/
+/*=========================================================================
+ *
+ *  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 __itkPointToSurfaceDistanceMetric_h
 #define __itkPointToSurfaceDistanceMetric_h
 
@@ -79,16 +83,16 @@ class PointToSurfaceDistanceMetric :
     /** Run-time type information (and related methods). */
     itkTypeMacro( PointToSurfaceDistanceMetric, SingleValuedPointSetToPointSetMetric );//OK
     /**  Initialize. */
-    virtual void Initialize() noexcept(false);
+    virtual void Initialize();
 
     /**  Get the value for single valued optimizers. */
-    MeasureType GetValue( const TransformParametersType & parameters ) const noexcept(false);
+    MeasureType GetValue( const TransformParametersType & parameters ) const;
 
     /** Get the derivatives of the match measure. */
-    void GetDerivative( const TransformParametersType & parameters, DerivativeType & Derivative ) const noexcept(false);
+    void GetDerivative( const TransformParametersType & parameters, DerivativeType & Derivative ) const;
 
     /**  Get value and derivatives for multiple valued optimizers. */
-    void GetValueAndDerivative( const TransformParametersType & parameters, MeasureType & Value, DerivativeType & Derivative ) const noexcept(false);
+    void GetValueAndDerivative( const TransformParametersType & parameters, MeasureType & Value, DerivativeType & Derivative ) const;
 
     /** Set input Segmented Image File **/
     void SetSegImageIn( const std::string  str ) ;
@@ -105,15 +109,15 @@ class PointToSurfaceDistanceMetric :
 protected:
 
     PointToSurfaceDistanceMetric();
-    virtual ~PointToSurfaceDistanceMetric() {}
-    bool m_AvPointWeigh;
+    virtual ~PointToSurfaceDistanceMetric() = default;
+    bool m_AvPointWeigh{true};
 
 private:
 
     PointToSurfaceDistanceMetric( const Self & );
-    std::string m_SegFileIn,m_DTFileIn,m_DTFileOut;
-    typename ImageType::Pointer m_ADTimage;
-    typename InterpolatorType::Pointer m_interpolator;    
+    std::string m_segmentationFileIn, m_distanceTransformFileIn, m_distanceTransformFileOut;
+    typename ImageType::Pointer m_internalDistanceTransformImage;
+    typename InterpolatorType::Pointer m_interpolator;
 
 };
 
diff --git a/Components/Metrics/PointToSurfaceDistance/itkPointToSurfaceDistanceMetric.hxx b/Components/Metrics/PointToSurfaceDistance/itkPointToSurfaceDistanceMetric.hxx
