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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_hxx
#define elxRegistrationBase_hxx
#include "elxRegistrationBase.h"
#include <itkDeref.h>
namespace elastix
{
/**
* ********************* ReadMaskParameters ************************
*/
template <class TElastix>
bool
RegistrationBase<TElastix>::ReadMaskParameters(UseMaskErosionArrayType & useMaskErosionArray,
const unsigned int nrOfMasks,
const std::string & whichMask,
const unsigned int level) const
{
/** Read whether mask erosion is wanted, if any masks were supplied. */
/** Bool that remembers if mask erosion is wanted in any of the masks
* remains false when no masks are used. This bool will be output.
*/
bool useMaskErosion = false;
/** Array of bools, that remembers for each mask if erosion is wanted. */
useMaskErosionArray.resize(nrOfMasks, false);
/** "ErodeFixedMask" or "ErodeMovingMask". */
std::string whichErodeMaskOption("Erode");
whichErodeMaskOption += whichMask;
whichErodeMaskOption += "Mask";
/** Read the parameters. */
if (nrOfMasks > 0)
{
const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Default values for all masks. Look for ErodeMask, or Erode<Fixed,Moving>Mask. */
bool erosionOrNot = true;
configuration.ReadParameter(erosionOrNot, "ErodeMask", "", level, 0, false);
configuration.ReadParameter(erosionOrNot, whichErodeMaskOption, "", level, 0);
if (erosionOrNot)
{
/** fill with 'true's. */
useMaskErosionArray.clear();
useMaskErosionArray.resize(nrOfMasks, true);
}
/** Try to read an erode mask parameter given for a specified mask only:
* (ErodeFixedMask0 "true" "false" ) for example.
*/
for (unsigned int i = 0; i < nrOfMasks; ++i)
{
std::ostringstream makestring;
makestring << whichErodeMaskOption << i; // key for parameter file
bool erosionOrNot_i = erosionOrNot; // default value
configuration.ReadParameter(erosionOrNot_i, makestring.str(), "", level, 0, false);
if (erosionOrNot_i)
{
useMaskErosionArray[i] = true;
}
else
{
useMaskErosionArray[i] = false;
}
/** Check if mask erosion is wanted in any of the masks. */
useMaskErosion |= useMaskErosionArray[i];
}
} // end if nrOfMasks > 0
return useMaskErosion;
} // end ReadMaskParameters()
/**
* ******************* GenerateFixedMaskSpatialObject **********************
*/
template <class TElastix>
auto
RegistrationBase<TElastix>::GenerateFixedMaskSpatialObject(const FixedMaskImageType * maskImage,
bool useMaskErosion,
const FixedImagePyramidType * pyramid,
unsigned int level) const -> FixedMaskSpatialObjectPointer
{
FixedMaskSpatialObjectPointer fixedMaskSpatialObject; // default-constructed (null)
if (!maskImage)
{
return fixedMaskSpatialObject;
}
fixedMaskSpatialObject = FixedMaskSpatialObjectType::New();
/** Just convert to spatial object if no erosion is needed. */
if (!useMaskErosion || !pyramid)
{
fixedMaskSpatialObject->SetImage(maskImage);
fixedMaskSpatialObject->Update();
return fixedMaskSpatialObject;
}
/** Erode, and convert to spatial object. */
FixedMaskErodeFilterPointer erosion = FixedMaskErodeFilterType::New();
erosion->SetInput(maskImage);
erosion->SetSchedule(pyramid->GetSchedule());
erosion->SetIsMovingMask(false);
erosion->SetResolutionLevel(level);
/** Set output of the erosion to fixedImageMaskAsImage. */
FixedMaskImagePointer erodedFixedMaskAsImage = erosion->GetOutput();
/** Do the erosion. */
try
{
erodedFixedMaskAsImage->Update();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("RegistrationBase - UpdateMasks()");
std::string err_str = excp.GetDescription();
err_str += "\nError while eroding the fixed mask.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Release some memory. */
erodedFixedMaskAsImage->DisconnectPipeline();
fixedMaskSpatialObject->SetImage(erodedFixedMaskAsImage);
fixedMaskSpatialObject->Update();
return fixedMaskSpatialObject;
} // end GenerateFixedMaskSpatialObject()
/**
* ******************* GenerateMovingMaskSpatialObject **********************
*/
template <class TElastix>
auto
RegistrationBase<TElastix>::GenerateMovingMaskSpatialObject(const MovingMaskImageType * maskImage,
bool useMaskErosion,
const MovingImagePyramidType * pyramid,
unsigned int level) const -> MovingMaskSpatialObjectPointer
{
MovingMaskSpatialObjectPointer movingMaskSpatialObject; // default-constructed (null)
if (!maskImage)
{
return movingMaskSpatialObject;
}
movingMaskSpatialObject = MovingMaskSpatialObjectType::New();
/** Just convert to spatial object if no erosion is needed. */
if (!useMaskErosion || !pyramid)
{
movingMaskSpatialObject->SetImage(maskImage);
movingMaskSpatialObject->Update();
return movingMaskSpatialObject;
}
/** Erode, and convert to spatial object. */
MovingMaskErodeFilterPointer erosion = MovingMaskErodeFilterType::New();
erosion->SetInput(maskImage);
erosion->SetSchedule(pyramid->GetSchedule());
erosion->SetIsMovingMask(true);
erosion->SetResolutionLevel(level);
/** Set output of the erosion to movingImageMaskAsImage. */
MovingMaskImagePointer erodedMovingMaskAsImage = erosion->GetOutput();
/** Do the erosion. */
try
{
erodedMovingMaskAsImage->Update();
}
catch (itk::ExceptionObject & excp)
{
/** Add information to the exception. */
excp.SetLocation("RegistrationBase - UpdateMasks()");
std::string err_str = excp.GetDescription();
err_str += "\nError while eroding the moving mask.\n";
excp.SetDescription(err_str);
/** Pass the exception to an higher level. */
throw;
}
/** Release some memory */
erodedMovingMaskAsImage->DisconnectPipeline();
movingMaskSpatialObject->SetImage(erodedMovingMaskAsImage);
movingMaskSpatialObject->Update();
return movingMaskSpatialObject;
} // end GenerateMovingMaskSpatialObject()
} // end namespace elastix
#endif // end #ifndef elxRegistrationBase_hxx
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