ADD: Added the ReducedFullSampler

Common/ImageSamplers/itkImageReducedFullSampler.h

@@ -0,0 +1,123 @@
+/*=========================================================================
+ *
+ *  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 __ImageReducedFullSampler_h
+#define __ImageReducedFullSampler_h
+
+#include "itkImageSamplerBase.h"
+
+namespace itk
+{
+/** \class ImageReducedFullSampler
+ *
+ * \brief Samples all voxels in the InputImageRegion for groupwise registration.
+ *
+ * This ImageSampler samples all voxels in the InputImageRegion.
+ * If a mask is given: only those voxels within the mask AND the
+ * InputImageRegion.
+ *
+ * \ingroup ImageSamplers
+ */
+
+template< class TInputImage >
+class ImageReducedFullSampler :
+  public ImageSamplerBase< TInputImage >
+{
+public:
+
+  /** Standard ITK-stuff. */
+  typedef ImageReducedFullSampler         Self;
+  typedef ImageSamplerBase< TInputImage > Superclass;
+  typedef SmartPointer< Self >            Pointer;
+  typedef SmartPointer< const Self >      ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro( Self );
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro( ImageReducedFullSampler, ImageSamplerBase );
+
+  /** Typedefs inherited from the superclass. */
+  typedef typename Superclass::DataObjectPointer            DataObjectPointer;
+  typedef typename Superclass::OutputVectorContainerType    OutputVectorContainerType;
+  typedef typename Superclass::OutputVectorContainerPointer OutputVectorContainerPointer;
+  typedef typename Superclass::InputImageType               InputImageType;
+  typedef typename Superclass::InputImagePointer            InputImagePointer;
+  typedef typename Superclass::InputImageConstPointer       InputImageConstPointer;
+  typedef typename Superclass::InputImageRegionType         InputImageRegionType;
+  typedef typename Superclass::InputImagePixelType          InputImagePixelType;
+  typedef typename Superclass::ImageSampleType              ImageSampleType;
+  typedef typename Superclass::ImageSampleContainerType     ImageSampleContainerType;
+  typedef typename Superclass::ImageSampleContainerPointer  ImageSampleContainerPointer;
+  typedef typename Superclass::MaskType                     MaskType;
+
+  /** The input image dimension. */
+  itkStaticConstMacro( InputImageDimension, unsigned int, Superclass::InputImageDimension );
+
+  itkStaticConstMacro( ReducedInputImageDimension, unsigned int, Superclass::InputImageDimension - 1 );
+
+  /** Other typdefs. */
+  typedef typename InputImageType::IndexType InputImageIndexType;
+  typedef typename InputImageType::SizeType  InputImageSizeType;
+  typedef typename InputImageType::PointType InputImagePointType;
+
+  /** Selecting new samples makes no sense if nothing changed.
+   * The same samples would be selected anyway.
+   */
+  virtual bool SelectNewSamplesOnUpdate( void )
+  {
+    return false;
+  }
+
+
+  /** Returns whether the sampler supports SelectNewSamplesOnUpdate(). */
+  virtual bool SelectingNewSamplesOnUpdateSupported( void ) const
+  {
+    return false;
+  }
+
+
+protected:
+
+  /** The constructor. */
+  ImageReducedFullSampler() {}
+  /** The destructor. */
+  virtual ~ImageReducedFullSampler() {}
+
+  /** PrintSelf. */
+  void PrintSelf( std::ostream & os, Indent indent ) const;
+
+  /** Function that does the work. */
+  virtual void GenerateData( void );
+
+private:
+
+  /** The private constructor. */
+  ImageReducedFullSampler( const Self & );          // purposely not implemented
+  /** The private copy constructor. */
+  void operator=( const Self & );            // purposely not implemented
+
+};
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkImageReducedFullSampler.hxx"
+#endif
+
+#endif // end #ifndef __ImageReducedFullSampler_h

Common/ImageSamplers/itkImageReducedFullSampler.hxx

@@ -0,0 +1,150 @@
+/*=========================================================================
+ *
+ *  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 __ImageReducedFullSampler_txx
+#define __ImageReducedFullSampler_txx
+
+#include "itkImageReducedFullSampler.h"
+
+#include "itkImageRegionConstIteratorWithIndex.h"
+
+namespace itk
+{
+
+/**
+ * ******************* GenerateData *******************
+ */
+
+template< class TInputImage >
+void
+ImageReducedFullSampler< TInputImage >
+::GenerateData( void )
+{
+
+  /** Get handles to the input image, output sample container, and the mask. */
+  InputImageConstPointer inputImage = this->GetInput();
+  typename ImageSampleContainerType::Pointer sampleContainer = this->GetOutput();
+  typename MaskType::ConstPointer mask                       = this->GetMask();
+
+  /** Clear the container. */
+  sampleContainer->Initialize();
+
+  /** Set up a region iterator within the user specified image region. */
+  typedef ImageRegionConstIteratorWithIndex< InputImageType > InputImageIterator;
+  InputImageIndexType index = this->GetCroppedInputImageRegion().GetIndex();
+  index[ ReducedInputImageDimension ] = 0;
+  InputImageSizeType size = this->GetCroppedInputImageRegion().GetSize();
+  size[ ReducedInputImageDimension ] = 1;
+  InputImageRegionType region;
+  region.SetIndex( index );
+  region.SetSize( size );
+  InputImageIterator iter( inputImage, region );
+
+  /** Fill the sample container. */
+  if( mask.IsNull() )
+  {
+    /** Try to reserve memory. If no mask is used this can raise std
+     * exceptions when the input image is large.
+     */
+    try
+    {
+      sampleContainer->Reserve( region
+        .GetNumberOfPixels() );
+    }
+    catch( std::exception & excp )
+    {
+      std::string message = "std: ";
+      message += excp.what();
+      message += "\nERROR: failed to allocate memory for the sample container.";
+      const char * message2 = message.c_str();
+      itkExceptionMacro( << message2 );
+    }
+    catch( ... )
+    {
+      itkExceptionMacro( << "ERROR: failed to allocate memory for the sample container." );
+    }
+
+    /** Simply loop over the image and store all samples in the container. */
+    ImageSampleType tempSample;
+    unsigned long   ind = 0;
+    for( iter.GoToBegin(); !iter.IsAtEnd(); ++iter, ++ind )
+    {
+      /** Get sampled index */
+      InputImageIndexType index = iter.GetIndex();
+
+      /** Translate index to point */
+      inputImage->TransformIndexToPhysicalPoint( index,
+        tempSample.m_ImageCoordinates );
+
+      /** Get sampled image value */
+      tempSample.m_ImageValue = iter.Get();
+
+      /** Store in container */
+      sampleContainer->SetElement( ind, tempSample );
+
+    } // end for
+  }   // end if no mask
+  else
+  {
+    if( mask->GetSource() )
+    {
+      mask->GetSource()->Update();
+    }
+
+    /** Loop over the image and check if the points falls within the mask. */
+    ImageSampleType tempSample;
+    for( iter.GoToBegin(); !iter.IsAtEnd(); ++iter )
+    {
+      /** Get sampled index. */
+      InputImageIndexType index = iter.GetIndex();
+
+      /** Translate index to point. */
+      inputImage->TransformIndexToPhysicalPoint( index,
+        tempSample.m_ImageCoordinates );
+
+      if( mask->IsInside( tempSample.m_ImageCoordinates ) )
+      {
+        /** Get sampled image value. */
+        tempSample.m_ImageValue = iter.Get();
+
+        /** Store in container. */
+        sampleContainer->push_back( tempSample );
+
+      } // end if
+    }   // end for
+  }     // end else (if mask exists)
+
+} // end GenerateData()
+
+
+/**
+ * ******************* PrintSelf *******************
+ */
+
+template< class TInputImage >
+void
+ImageReducedFullSampler< TInputImage >
+::PrintSelf( std::ostream & os, Indent indent ) const
+{
+  Superclass::PrintSelf( os, indent );
+} // end PrintSelf()
+
+
+} // end namespace itk
+
+#endif // end #ifndef __ReducedImageFullSampler_txx

Components/ImageSamplers/ReducedFull/CMakeLists.txt

@@ -0,0 +1,5 @@
+ADD_ELXCOMPONENT( ReducedFullSampler
+  elxReducedFullSampler.h
+  elxReducedFullSampler.hxx
+  elxReducedFullSampler.cxx
+)

Components/ImageSamplers/ReducedFull/elxReducedFullSampler.cxx

@@ -0,0 +1,17 @@
+/*======================================================================
+
+  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.
+
+======================================================================*/
+
+#include "elxReducedFullSampler.h"
+
+elxInstallMacro( ReducedFullSampler );