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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 itkMultiInputImageRandomCoordinateSampler_hxx
#define itkMultiInputImageRandomCoordinateSampler_hxx
#include "itkMultiInputImageRandomCoordinateSampler.h"
#include <vnl/vnl_inverse.h>
#include "itkConfigure.h"
#include <itkDeref.h>
namespace itk
{
/**
* ******************* GenerateData *******************
*/
template <class TInputImage>
void
MultiInputImageRandomCoordinateSampler<TInputImage>::GenerateData()
{
/** Check. */
if (!this->CheckInputImageRegions())
{
itkExceptionMacro("ERROR: at least one of the InputImageRegions is not a subregion of the LargestPossibleRegion");
}
/** Get handles to the input image, output sample container, and mask. */
const InputImageType & inputImage = Deref(this->GetInput());
auto & samples = Deref(this->GetOutput()).CastToSTLContainer();
const MaskType * const mask = this->Superclass::GetMask();
typename InterpolatorType::Pointer interpolator = this->GetModifiableInterpolator();
/** Set up the interpolator. */
interpolator->SetInputImage(&inputImage);
/** Get the intersection of all sample regions. */
InputImageContinuousIndexType smallestContIndex;
InputImageContinuousIndexType largestContIndex;
this->GenerateSampleRegion(smallestContIndex, largestContIndex);
/** Reserve memory for the output. */
samples.resize(this->GetNumberOfSamples());
InputImageContinuousIndexType sampleContIndex;
/** Fill the sample container. */
if (mask == nullptr)
{
/** Start looping over the sample container. */
for (auto & sample : samples)
{
/** Make a reference to the current sample in the container. */
InputImagePointType & samplePoint = sample.m_ImageCoordinates;
ImageSampleValueType & sampleValue = sample.m_ImageValue;
/** Generate a point in the input image region. */
this->GenerateRandomCoordinate(smallestContIndex, largestContIndex, sampleContIndex);
/** Convert to point */
inputImage.TransformContinuousIndexToPhysicalPoint(sampleContIndex, samplePoint);
/** Compute the value at the contindex. */
sampleValue = static_cast<ImageSampleValueType>(this->m_Interpolator->EvaluateAtContinuousIndex(sampleContIndex));
} // end for loop
} // end if no mask
else
{
/** Update all masks. */
this->UpdateAllMasks();
/** Set up some variable that are used to make sure we are not forever
* walking around on this image, trying to look for valid samples.
*/
unsigned long numberOfSamplesTried = 0;
unsigned long maximumNumberOfSamplesToTry = 10 * this->GetNumberOfSamples();
/** Start looping over the sample container. */
for (auto & sample : samples)
{
/** Make a reference to the current sample in the container. */
InputImagePointType & samplePoint = sample.m_ImageCoordinates;
ImageSampleValueType & sampleValue = sample.m_ImageValue;
/** Walk over the image until we find a valid point. */
do
{
/** Check if we are not trying eternally to find a valid point. */
++numberOfSamplesTried;
if (numberOfSamplesTried > maximumNumberOfSamplesToTry)
{
/** Squeeze the sample container to the size that is still valid. */
samples.resize(&sample - samples.data());
itkExceptionMacro(
"Could not find enough image samples within reasonable time. Probably the mask is too small");
}
/** Generate a point in the input image region. */
this->GenerateRandomCoordinate(smallestContIndex, largestContIndex, sampleContIndex);
inputImage.TransformContinuousIndexToPhysicalPoint(sampleContIndex, samplePoint);
} while (!this->IsInsideAllMasks(samplePoint));
/** Compute the value at the contindex. */
sampleValue = static_cast<ImageSampleValueType>(this->m_Interpolator->EvaluateAtContinuousIndex(sampleContIndex));
} // end for loop
} // end if mask
} // end GenerateData()
/**
* ******************* GenerateSampleRegion *******************
*/
template <class TInputImage>
void
MultiInputImageRandomCoordinateSampler<TInputImage>::GenerateSampleRegion(
InputImageContinuousIndexType & smallestContIndex,
InputImageContinuousIndexType & largestContIndex)
{
/** Get handles to the number of inputs and regions. */
const unsigned int numberOfInputs = this->GetNumberOfInputs();
const unsigned int numberOfRegions = this->GetNumberOfInputImageRegions();
/** Check. */
if (numberOfRegions != numberOfInputs && numberOfRegions != 1)
{
itkExceptionMacro("ERROR: The number of regions should be 1 or the number of inputs.");
}
using DirectionType = typename InputImageType::DirectionType;
DirectionType dir0 = this->GetInput(0)->GetDirection();
typename DirectionType::InternalMatrixType dir0invtemp = vnl_inverse(dir0.GetVnlMatrix());
DirectionType dir0inv(dir0invtemp);
for (unsigned int i = 1; i < numberOfInputs; ++i)
{
DirectionType diri = this->GetInput(i)->GetDirection();
if (diri != dir0)
{
itkExceptionMacro("ERROR: All input images should have the same direction cosines matrix.");
}
}
/** Initialize the smallest and largest point. */
InputImagePointType smallestPoint;
InputImagePointType largestPoint;
smallestPoint.Fill(NumericTraits<InputImagePointValueType>::NonpositiveMin());
largestPoint.Fill(NumericTraits<InputImagePointValueType>::max());
/** Determine the intersection of all regions, assuming identical direction cosines,
* but possibly different origin/spacing.
* \todo: test this really carefully!
*/
const auto unitSize = InputImageSizeType::Filled(1);
for (unsigned int i = 0; i < numberOfRegions; ++i)
{
/** Get the outer indices. */
const InputImageIndexType smallestIndex = this->GetInputImageRegion(i).GetIndex();
const InputImageIndexType largestIndex = smallestIndex + this->GetInputImageRegion(i).GetSize() - unitSize;
/** Convert to points */
InputImagePointType smallestImagePoint;
InputImagePointType largestImagePoint;
this->GetInput(i)->TransformIndexToPhysicalPoint(smallestIndex, smallestImagePoint);
this->GetInput(i)->TransformIndexToPhysicalPoint(largestIndex, largestImagePoint);
/** apply inverse direction, so that next max-operation makes sense. */
smallestImagePoint = dir0inv * smallestImagePoint;
largestImagePoint = dir0inv * largestImagePoint;
/** Determine intersection. */
for (unsigned int j = 0; j < InputImageDimension; ++j)
{
/** Get the largest smallest point. */
smallestPoint[j] = std::max(smallestPoint[j], smallestImagePoint[j]);
/** Get the smallest largest point. */
largestPoint[j] = std::min(largestPoint[j], largestImagePoint[j]);
}
}
/** Convert to continuous index in input image 0. */
smallestPoint = dir0 * smallestPoint;
largestPoint = dir0 * largestPoint;
smallestContIndex = this->GetInput(0)->template TransformPhysicalPointToContinuousIndex<CoordRepType>(smallestPoint);
largestContIndex = this->GetInput(0)->template TransformPhysicalPointToContinuousIndex<CoordRepType>(largestPoint);
/** Support for localised mutual information. */
if (this->GetUseRandomSampleRegion())
{
/** Convert sampleRegionSize to continuous index space */
using CIndexVectorType = typename InputImageContinuousIndexType::VectorType;
CIndexVectorType sampleRegionSize;
for (unsigned int i = 0; i < InputImageDimension; ++i)
{
sampleRegionSize[i] = this->GetSampleRegionSize()[i] / this->GetInput()->GetSpacing()[i];
}
InputImageContinuousIndexType maxSmallestContIndex = largestContIndex;
maxSmallestContIndex -= sampleRegionSize;
this->GenerateRandomCoordinate(smallestContIndex, maxSmallestContIndex, smallestContIndex);
largestContIndex = smallestContIndex;
largestContIndex += sampleRegionSize;
}
} // end GenerateSampleRegion()
/**
* ******************* GenerateRandomCoordinate *******************
*/
template <class TInputImage>
void
MultiInputImageRandomCoordinateSampler<TInputImage>::GenerateRandomCoordinate(
const InputImageContinuousIndexType & smallestContIndex,
const InputImageContinuousIndexType & largestContIndex,
InputImageContinuousIndexType & randomContIndex)
{
for (unsigned int i = 0; i < InputImageDimension; ++i)
{
randomContIndex[i] = static_cast<InputImagePointValueType>(
this->m_RandomGenerator->GetUniformVariate(smallestContIndex[i], largestContIndex[i]));
}
} // end GenerateRandomCoordinate()
/**
* ******************* PrintSelf *******************
*/
template <class TInputImage>
void
MultiInputImageRandomCoordinateSampler<TInputImage>::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "Interpolator: " << this->m_Interpolator.GetPointer() << std::endl;
os << indent << "RandomGenerator: " << this->m_RandomGenerator.GetPointer() << std::endl;
} // end PrintSelf
} // end namespace itk
#endif // end #ifndef itkMultiInputImageRandomCoordinateSampler_hxx
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