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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 elxMainBase_h
#define elxMainBase_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
{
/**
* \class MainBase
* \brief Common (abstract) base class of ElastixMain and TransformixMain.
*
* \ingroup Kernel
*/
class MainBase : public itk::Object
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MainBase);
/** Standard itk. */
using Self = MainBase;
using Superclass = itk::Object;
using Pointer = itk::SmartPointer<Self>;
using ConstPointer = itk::SmartPointer<const Self>;
/** Run-time type information (and related methods). */
itkTypeMacro(MainBase, Object);
/** Typedef's.*/
/** ITK base objects. */
using ObjectPointer = itk::Object::Pointer;
using DataObjectPointer = itk::DataObject::Pointer;
/** elastix components. */
using ArgumentMapType = Configuration::CommandLineArgumentMapType;
using ObjectContainerType = ElastixBase::ObjectContainerType;
using DataObjectContainerType = ElastixBase::DataObjectContainerType;
using ObjectContainerPointer = ElastixBase::ObjectContainerPointer;
using DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer;
using FlatDirectionCosinesType = ElastixBase::FlatDirectionCosinesType;
/** Typedefs for the database that holds pointers to New() functions.
* Those functions are used to instantiate components, such as the metric etc.
*/
using ComponentDatabasePointer = ComponentDatabase::Pointer;
using PtrToCreator = ComponentDatabase::PtrToCreator;
using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType;
using PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType;
using ImageDimensionType = ComponentDatabase::ImageDimensionType;
using DBIndexType = ComponentDatabase::IndexType;
/** Typedef that is used in the elastix dll version. */
using ParameterMapType = itk::ParameterMapInterface::ParameterMapType;
/** Set/Get functions for the description of the image type. */
itkSetMacro(FixedImagePixelType, PixelTypeDescriptionType);
itkSetMacro(MovingImagePixelType, PixelTypeDescriptionType);
itkSetMacro(FixedImageDimension, ImageDimensionType);
itkSetMacro(MovingImageDimension, ImageDimensionType);
itkGetConstMacro(FixedImagePixelType, PixelTypeDescriptionType);
itkGetConstMacro(MovingImagePixelType, PixelTypeDescriptionType);
itkGetConstMacro(FixedImageDimension, ImageDimensionType);
itkGetConstMacro(MovingImageDimension, ImageDimensionType);
/** Set/Get functions for the moving images
* (if these are not used, elastix tries to read them from disk,
* according to the command line parameters).
*/
itkSetObjectMacro(MovingImageContainer, DataObjectContainerType);
itkGetModifiableObjectMacro(MovingImageContainer, DataObjectContainerType);
/** Set/Get functions for the result images
* (if these are not used, elastix tries to read them from disk,
* according to the command line parameters).
*/
itkSetObjectMacro(ResultImageContainer, DataObjectContainerType);
itkGetModifiableObjectMacro(ResultImageContainer, DataObjectContainerType);
itkSetObjectMacro(ResultDeformationFieldContainer, DataObjectContainerType);
itkGetModifiableObjectMacro(ResultDeformationFieldContainer, DataObjectContainerType);
/** Set/Get the configuration object. */
itkSetObjectMacro(Configuration, Configuration);
itkGetModifiableObjectMacro(Configuration, Configuration);
/** Functions to get pointers to the elastix components.
* The components are returned as Object::Pointer.
* Before calling this functions, call run().
*/
itkGetModifiableObjectMacro(Elastix, itk::Object);
/** Convenience function that returns the elastix component as
* a pointer to an ElastixBase. Use only after having called run()!
*/
ElastixBase &
GetElastixBase() const;
/** Returns the Index that is used in elx::ComponentDatabase. */
itkGetConstMacro(DBIndex, DBIndexType);
/** Start the registration
* run() without command line parameters; it assumes that
* EnterCommandLineParameters has been invoked already, or that
* m_Configuration is initialized in a different way.
*/
virtual int
Run() = 0;
/** Start the registration
* this version of 'run' first calls this->EnterCommandLineParameters(argc,argv)
* and then calls run().
*/
virtual int
Run(const ArgumentMapType & argmap);
virtual int
Run(const ArgumentMapType & argmap, const ParameterMapType & inputMap);
/** Set process priority, which is read from the command line arguments.
* Syntax:
* -priority \<high, belownormal\>
*/
virtual void
SetProcessPriority() const;
/** Set maximum number of threads, which is read from the command line arguments.
* Syntax:
* -threads \<int\>
*/
virtual void
SetMaximumNumberOfThreads() const;
/** Function to get the ComponentDatabase. */
static const ComponentDatabase &
GetComponentDatabase();
protected:
MainBase();
~MainBase() override = 0;
/** A pointer to elastix as an itk::object. In run() this
* pointer will be assigned to an ElastixTemplate<>.
*/
ObjectPointer m_Elastix{ nullptr };
/** A vector of configuration objects, needed when transformix is used as library. */
std::vector<Configuration::ConstPointer> m_TransformConfigurations{};
/** Description of the ImageTypes. */
PixelTypeDescriptionType m_FixedImagePixelType{};
ImageDimensionType m_FixedImageDimension{ 0 };
PixelTypeDescriptionType m_MovingImagePixelType{};
ImageDimensionType m_MovingImageDimension{ 0 };
DBIndexType m_DBIndex{ 0 };
/** The images and masks. */
DataObjectContainerPointer m_MovingImageContainer{ nullptr };
DataObjectContainerPointer m_ResultImageContainer{ nullptr };
DataObjectContainerPointer m_ResultDeformationFieldContainer{ nullptr };
/** InitDBIndex sets m_DBIndex by asking the ImageTypes
* from the Configuration object and obtaining the corresponding
* DB index from the ComponentDatabase.
*/
virtual int
InitDBIndex() = 0;
/** Create a component. Make sure InitDBIndex has been called before.
* The input is a string, e.g. "MattesMutualInformation".
*/
virtual ObjectPointer
CreateComponent(const ComponentDescriptionType & name);
/** Create components. Reads from the configuration object (using the provided key)
* the names of the components to create and store their instantiations in the
* provided ObjectContainer.
* The errorcode remains what it was if no error occurred. Otherwise it's set to 1.
* The 'key' is the entry inspected in the parameter file
* A component named 'defaultComponentName' is used when the key is not found
* in the parameter file. If "" is used, no default is assumed, and an error
* is given when the component was not specified. If the flag mandatoryComponent
* is set to false, no error is given, because the component may not be needed
* anyway.
*
* NB: this function should never be called with:
* ( !mandatoryComponent && defaultComponentName != "" ) == true
*
*/
virtual ObjectContainerPointer
CreateComponents(const ComponentDescriptionType & key,
const ComponentDescriptionType & defaultComponentName,
int & errorcode,
bool mandatoryComponent = true);
private:
/** The configuration object, containing the parameters and command-line arguments. */
Configuration::Pointer m_Configuration{ Configuration::New() };
};
} // end namespace elastix
#endif // end #ifndef elxMainBase_h
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