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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 elxRegistrationBase_h
#define elxRegistrationBase_h
/** Needed for the macros */
#include "elxMacro.h"
#include "elxBaseComponentSE.h"
#include "itkMultiResolutionImageRegistrationMethod2.h"
/** Mask support. */
#include "itkImageMaskSpatialObject.h"
#include "itkErodeMaskImageFilter.h"
namespace elastix
{
/**
* \class RegistrationBase
* \brief This class is the elastix base class for all Registration schemes.
*
* This class contains all the common functionality for Registrations.
*
* \parameter ErodeMask: a flag to determine if the masks should be eroded
* from one resolution level to another. Choose from {"true", "false"} \n
* example: <tt>(ErodeMask "false")</tt> \n
* The default is "true". The parameter may be specified for each
* resolution differently, but that's not obliged. The actual amount of
* erosion depends on the image pyramid. \n
* Erosion of the mask prevents the border / edge of the mask taken into account.
* This can be useful for example for ultrasound images,
* where you don't want to take into account values outside
* the US-beam, but where you also don't want to match the
* edge / border of this beam.
* For example for MRI's of the head, the borders of the head
* may be wanted to match, and there erosion should be avoided.
* \parameter ErodeFixedMask: a flag to determine if the fixed mask(s) should be eroded
* from one resolution level to another. Choose from {"true", "false"} \n
* example: <tt>(ErodeFixedMask "true" "false")</tt>
* This setting overrules ErodeMask.\n
* \parameter ErodeMovingMask: a flag to determine if the moving mask(s) should be eroded
* from one resolution level to another. Choose from {"true", "false"} \n
* example: <tt>(ErodeMovingMask "true" "false")</tt>
* This setting overrules ErodeMask.\n
* \parameter ErodeFixedMask\<i\>: a flag to determine if the i-th fixed mask should be eroded
* from one resolution level to another. Choose from {"true", "false"} \n
* example: <tt>(ErodeFixedMask2 "true" "false")</tt>
* This setting overrules ErodeMask and ErodeFixedMask.\n
* \parameter ErodeMovingMask\<i\>: a flag to determine if the i-th moving mask should be eroded
* from one resolution level to another. Choose from {"true", "false"} \n
* example: <tt>(ErodeMovingMask2 "true" "false")</tt>
* This setting overrules ErodeMask and ErodeMovingMask.\n
*
* \ingroup Registrations
* \ingroup ComponentBaseClasses
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT RegistrationBase : public BaseComponentSE<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(RegistrationBase);
/** Standard ITK stuff. */
using Self = RegistrationBase;
using Superclass = BaseComponentSE<TElastix>;
/** Run-time type information (and related methods). */
itkTypeMacro(RegistrationBase, BaseComponentSE);
/** Typedef's from Elastix. */
using typename Superclass::ElastixType;
using typename Superclass::RegistrationType;
/** Other typedef's. */
using FixedImageType = typename ElastixType::FixedImageType;
using MovingImageType = typename ElastixType::MovingImageType;
/** Get the dimension of the fixed image. */
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
/** Get the dimension of the moving image. */
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
/** Typedef for ITKBaseType. */
using ITKBaseType = itk::MultiResolutionImageRegistrationMethod2<FixedImageType, MovingImageType>;
/** Typedef for mask erosion options */
using UseMaskErosionArrayType = std::vector<bool>;
/** Retrieves this object as ITKBaseType. */
ITKBaseType *
GetAsITKBaseType()
{
return &(this->GetSelf());
}
/** Retrieves this object as ITKBaseType, to use in const functions. */
const ITKBaseType *
GetAsITKBaseType() const
{
return &(this->GetSelf());
}
/** Function to read the mask parameters from the configuration object.
* \todo: move to RegistrationBase
* Input:
* \li an array that will contain a bool for each mask, saying if it needs erosion or not
* \li the number of masks
* \li whichMask: "Fixed" or "Moving"
* \li the current resolution level
* Output:
* \li The function returns a bool that says if any mask needs erosion. If the number of masks
* is zero, this bool will be false.
* \li The useMaskErosionArray, which indicates for each mask whether it should be eroded.
* If the number of masks is zero, this array will be empty.
*
* The function first checks Erode<Fixed,Moving>Mask\<i\>, with i the mask number,
* then Erode<Fixed,Moving>Mask, and finally ErodeMask. So, if you do not specify
* Erode<Fixed,Moving>Mask\<i\>, Erode<Fixed,Moving>Mask is tried, and then ErodeMask.
* If you specify ErodeMask, that option will be used for all masks, fixed and moving!
* All options can be specified for each resolution specifically, or at once for all
* resolutions.
*/
virtual bool
ReadMaskParameters(UseMaskErosionArrayType & useMaskErosionArray,
const unsigned int nrOfMasks,
const std::string & whichMask,
const unsigned int level) const;
protected:
/** The constructor. */
RegistrationBase() = default;
/** The destructor. */
~RegistrationBase() override = default;
/** Typedef's for mask support. */
using MaskPixelType = typename ElastixType::MaskPixelType;
using FixedMaskImageType = typename ElastixType::FixedMaskType;
using MovingMaskImageType = typename ElastixType::MovingMaskType;
using FixedMaskImagePointer = typename FixedMaskImageType::Pointer;
using MovingMaskImagePointer = typename MovingMaskImageType::Pointer;
using FixedMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::FixedImageDimension>;
using MovingMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::MovingImageDimension>;
using FixedMaskSpatialObjectPointer = typename FixedMaskSpatialObjectType::Pointer;
using MovingMaskSpatialObjectPointer = typename MovingMaskSpatialObjectType::Pointer;
using FixedImagePyramidType = typename ITKBaseType::FixedImagePyramidType;
using MovingImagePyramidType = typename ITKBaseType::MovingImagePyramidType;
/** Some typedef's used for eroding the masks */
using FixedMaskErodeFilterType = itk::ErodeMaskImageFilter<FixedMaskImageType>;
using FixedMaskErodeFilterPointer = typename FixedMaskErodeFilterType::Pointer;
using MovingMaskErodeFilterType = itk::ErodeMaskImageFilter<MovingMaskImageType>;
using MovingMaskErodeFilterPointer = typename MovingMaskErodeFilterType::Pointer;
/** Generate a spatial object from a mask image, possibly after eroding the image
* Input:
* \li the mask as an image, consisting of 1's and 0's;
* \li a boolean that determines whether mask erosion is needed
* \li the image pyramid, which is needed to determines the amount of erosion
* (can be set to 0 if useMaskErosion == false
* \li the resolution level
* Output:
* \li the mask as a spatial object, which can be set in a metric for example
*
* This function is used by the registration components
*/
FixedMaskSpatialObjectPointer
GenerateFixedMaskSpatialObject(const FixedMaskImageType * maskImage,
bool useMaskErosion,
const FixedImagePyramidType * pyramid,
unsigned int level) const;
/** Generate a spatial object from a mask image, possibly after eroding the image
* Input:
* \li the mask as an image, consisting of 1's and 0's;
* \li a boolean that determines whether mask erosion is needed
* \li the image pyramid, which is needed to determines the amount of erosion
* (can be set to 0 if useMaskErosion == false
* \li the resolution level
* Output:
* \li the mask as a spatial object, which can be set in a metric for example
*
* This function is used by the registration components
*/
MovingMaskSpatialObjectPointer
GenerateMovingMaskSpatialObject(const MovingMaskImageType * maskImage,
bool useMaskErosion,
const MovingImagePyramidType * pyramid,
unsigned int level) const;
private:
elxDeclarePureVirtualGetSelfMacro(ITKBaseType);
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxRegistrationBase.hxx"
#endif
#endif // end #ifndef elxRegistrationBase_h
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