elxElastixMain.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 elxElastixMain_h
#define elxElastixMain_h
 
#include "elxComponentDatabase.h"
 
#include "elxElastixBase.h"
#include "itkParameterMapInterface.h"
 
#include <itkObject.h>
 
// Standard C++ header files:
#include <fstream>
#include <iostream>
#include <string>
 
 
namespace elastix
{
 
 
extern int
xoutSetup(const char * logfilename, bool setupLogging, bool setupCout);
 
 
class xoutManager
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(xoutManager);
 
  explicit xoutManager(const std::string & logfilename, const bool setupLogging, const bool setupCout);
 
  xoutManager() = default;
 
  ~xoutManager() = default;
 
private:
  struct Guard
  {
    ITK_DISALLOW_COPY_AND_MOVE(Guard);
    Guard() = default;
    ~Guard();
  };
 
  const Guard m_Guard{};
};
 
 
class ElastixMain : public itk::Object
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(ElastixMain);
 
  using Self = ElastixMain;
  using Superclass = itk::Object;
  using Pointer = itk::SmartPointer<Self>;
  using ConstPointer = itk::SmartPointer<const Self>;
 
  itkNewMacro(Self);
 
  itkTypeMacro(ElastixMain, Object);
 
  using ObjectPointer = itk::Object::Pointer;
  using DataObjectPointer = itk::DataObject::Pointer;
 
  using ArgumentMapType = Configuration::CommandLineArgumentMapType;
  using ConfigurationPointer = Configuration::Pointer;
  using ObjectContainerType = ElastixBase::ObjectContainerType;
  using DataObjectContainerType = ElastixBase::DataObjectContainerType;
  using ObjectContainerPointer = ElastixBase::ObjectContainerPointer;
  using DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer;
  using FlatDirectionCosinesType = ElastixBase::FlatDirectionCosinesType;
 
  using ComponentDatabasePointer = ComponentDatabase::Pointer;
  using PtrToCreator = ComponentDatabase::PtrToCreator;
  using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType;
  using PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType;
  using ImageDimensionType = ComponentDatabase::ImageDimensionType;
  using DBIndexType = ComponentDatabase::IndexType;
 
  using ParameterMapType = itk::ParameterMapInterface::ParameterMapType;
 
  itkSetMacro(FixedImagePixelType, PixelTypeDescriptionType);
  itkSetMacro(MovingImagePixelType, PixelTypeDescriptionType);
  itkSetMacro(FixedImageDimension, ImageDimensionType);
  itkSetMacro(MovingImageDimension, ImageDimensionType);
  itkGetConstMacro(FixedImagePixelType, PixelTypeDescriptionType);
  itkGetConstMacro(MovingImagePixelType, PixelTypeDescriptionType);
  itkGetConstMacro(FixedImageDimension, ImageDimensionType);
  itkGetConstMacro(MovingImageDimension, ImageDimensionType);
 
  itkSetObjectMacro(FixedImageContainer, DataObjectContainerType);
  itkSetObjectMacro(MovingImageContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(FixedImageContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(MovingImageContainer, DataObjectContainerType);
 
  itkSetObjectMacro(FixedMaskContainer, DataObjectContainerType);
  itkSetObjectMacro(MovingMaskContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(FixedMaskContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(MovingMaskContainer, DataObjectContainerType);
 
  itkSetObjectMacro(ResultImageContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(ResultImageContainer, DataObjectContainerType);
 
  itkSetObjectMacro(ResultDeformationFieldContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(ResultDeformationFieldContainer, DataObjectContainerType);
 
  itkSetObjectMacro(Configuration, Configuration);
  itkGetModifiableObjectMacro(Configuration, Configuration);
 
  itkGetModifiableObjectMacro(Elastix, itk::Object);
 
  ElastixBase &
  GetElastixBase() const;
 
  itkGetModifiableObjectMacro(FinalTransform, itk::Object);
 
  itkSetObjectMacro(InitialTransform, itk::Object);
  itkGetModifiableObjectMacro(InitialTransform, itk::Object);
 
  virtual void
  SetOriginalFixedImageDirectionFlat(const FlatDirectionCosinesType & arg);
 
  virtual const FlatDirectionCosinesType &
  GetOriginalFixedImageDirectionFlat() const;
 
  void
  SetElastixLevel(unsigned int level);
 
  unsigned int
  GetElastixLevel();
 
  void
  SetTotalNumberOfElastixLevels(unsigned int levels);
 
  unsigned int
  GetTotalNumberOfElastixLevels();
 
  itkGetConstMacro(DBIndex, DBIndexType);
 
  virtual void
  EnterCommandLineArguments(const ArgumentMapType & argmap);
 
  virtual void
  EnterCommandLineArguments(const ArgumentMapType & argmap, const ParameterMapType & inputMap);
 
  // Version used when elastix is used as a library.
  virtual void
  EnterCommandLineArguments(const ArgumentMapType & argmap, const std::vector<ParameterMapType> & inputMaps);
 
  virtual int
  Run();
 
  virtual int
  Run(const ArgumentMapType & argmap);
 
  virtual int
  Run(const ArgumentMapType & argmap, const ParameterMapType & inputMap);
 
  virtual void
  SetProcessPriority() const;
 
  virtual void
  SetMaximumNumberOfThreads() const;
 
  static const ComponentDatabase &
  GetComponentDatabase();
 
  virtual ParameterMapType
  GetTransformParametersMap() const;
 
protected:
  ElastixMain();
  ~ElastixMain() override;
 
  ObjectPointer m_Elastix{ nullptr };
 
  ConfigurationPointer m_Configuration{ Configuration::New() };
 
  std::vector<ConfigurationPointer> m_Configurations{};
 
  PixelTypeDescriptionType m_FixedImagePixelType{};
  ImageDimensionType       m_FixedImageDimension{ 0 };
  PixelTypeDescriptionType m_MovingImagePixelType{};
  ImageDimensionType       m_MovingImageDimension{ 0 };
 
  DBIndexType m_DBIndex{ 0 };
 
  DataObjectContainerPointer m_FixedImageContainer{ nullptr };
  DataObjectContainerPointer m_MovingImageContainer{ nullptr };
  DataObjectContainerPointer m_FixedMaskContainer{ nullptr };
  DataObjectContainerPointer m_MovingMaskContainer{ nullptr };
  DataObjectContainerPointer m_ResultImageContainer{ nullptr };
  DataObjectContainerPointer m_ResultDeformationFieldContainer{ nullptr };
 
  ObjectPointer m_FinalTransform{ nullptr };
 
  ObjectPointer m_InitialTransform{ nullptr };
 
  ParameterMapType m_TransformParametersMap{};
 
  FlatDirectionCosinesType m_OriginalFixedImageDirection{};
 
  virtual int
  InitDBIndex();
 
  virtual ObjectPointer
  CreateComponent(const ComponentDescriptionType & name);
 
  virtual ObjectContainerPointer
  CreateComponents(const ComponentDescriptionType & key,
                   const ComponentDescriptionType & defaultComponentName,
                   int &                            errorcode,
                   bool                             mandatoryComponent = true);
 
  void
  GetImageInformationFromFile(const std::string & filename, ImageDimensionType & imageDimension) const;
};
 
} // end namespace elastix
 
#endif // end #ifndef elxElastixMain_h