Pull request 52 (ReducedFullSampler) updated

Common/ImageSamplers/itkImageReducedFullSampler.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 __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.
+   */
+  bool
+  SelectNewSamplesOnUpdate(void) override
+  {
+    return false;
+  }
+
+
+  /** Returns whether the sampler supports SelectNewSamplesOnUpdate(). */
+  bool
+  SelectingNewSamplesOnUpdateSupported(void) const override
+  {
+    return false;
+  }
+
+
+protected:
+  /** The constructor. */
+  ImageReducedFullSampler() {}
+  /** The destructor. */
+  ~ImageReducedFullSampler() override {}
+
+  /** PrintSelf. */
+  void
+  PrintSelf(std::ostream & os, Indent indent) const override;
+
+  /** Function that does the work. */
+  void
+  GenerateData(void) override;
+
+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

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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 __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->IsInsideInWorldSpace(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

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+ADD_ELXCOMPONENT( ReducedFullSampler
+  elxReducedFullSampler.h
+  elxReducedFullSampler.hxx
+  elxReducedFullSampler.cxx
+)

Components/ImageSamplers/ReducedFull/elxReducedFullSampler.cxx

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+/*======================================================================
+
+  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);