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/*
* Copyright (C) 2005-2020 Centre National d'Etudes Spatiales (CNES)
*
* This file is part of Orfeo Toolbox
*
* https://www.orfeo-toolbox.org/
*
* 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
*
* 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.
*/
// This example shows how to use the \doxygen{itk}{ImageLinearIteratorWithIndex} for
// computing the mean across time of a 4D image where the first three
// dimensions correspond to spatial coordinates and the fourth dimension
// corresponds to time. The result of the mean across time is to be stored in a
// 3D image.
//
// \index{Iterators!and 4D images}
// \index{ImageLinearIteratorWithIndex!4D images}
#include "otbImage.h"
#include "itkImageLinearConstIteratorWithIndex.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
int main(int argc, char* argv[])
{
// Verify the number of parameters on the command line.
if (argc < 3)
{
std::cerr << "Missing parameters. " << std::endl;
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " input4DImageFile output3DImageFile" << std::endl;
return EXIT_FAILURE;
}
// First we declare the types of the images
using PixelType = unsigned char;
using Image3DType = otb::Image<PixelType, 3>;
using Image4DType = otb::Image<PixelType, 4>;
using Reader4DType = otb::ImageFileReader<Image4DType>;
using Writer3DType = otb::ImageFileWriter<Image3DType>;
Reader4DType::Pointer reader4D = Reader4DType::New();
reader4D->SetFileName(argv[1]);
try
{
reader4D->Update();
}
catch (itk::ExceptionObject& excp)
{
std::cerr << "Error writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
Image4DType::ConstPointer image4D = reader4D->GetOutput();
Image3DType::Pointer image3D = Image3DType::New();
using Index3DType = Image3DType::IndexType;
using Size3DType = Image3DType::SizeType;
using Region3DType = Image3DType::RegionType;
using Spacing3DType = Image3DType::SpacingType;
using Origin3DType = Image3DType::PointType;
using Index4DType = Image4DType::IndexType;
using Size4DType = Image4DType::SizeType;
using Spacing4DType = Image4DType::SpacingType;
using Origin4DType = Image4DType::PointType;
Index3DType index3D;
Size3DType size3D;
Spacing3DType spacing3D;
Origin3DType origin3D;
Image4DType::RegionType region4D = image4D->GetBufferedRegion();
Index4DType index4D = region4D.GetIndex();
Size4DType size4D = region4D.GetSize();
Spacing4DType spacing4D = image4D->GetSignedSpacing();
Origin4DType origin4D = image4D->GetOrigin();
for (unsigned int i = 0; i < 3; ++i)
{
size3D[i] = size4D[i];
index3D[i] = index4D[i];
spacing3D[i] = spacing4D[i];
origin3D[i] = origin4D[i];
}
image3D->SetSignedSpacing(spacing3D);
image3D->SetOrigin(origin3D);
Region3DType region3D;
region3D.SetIndex(index3D);
region3D.SetSize(size3D);
image3D->SetRegions(region3D);
image3D->Allocate();
using SumType = itk::NumericTraits<PixelType>::AccumulateType;
using MeanType = itk::NumericTraits<SumType>::RealType;
const unsigned int timeLength = region4D.GetSize()[3];
using IteratorType = itk::ImageLinearConstIteratorWithIndex<Image4DType>;
IteratorType it(image4D, region4D);
it.SetDirection(3); // Walk along time dimension
it.GoToBegin();
while (!it.IsAtEnd())
{
SumType sum = itk::NumericTraits<SumType>::Zero;
it.GoToBeginOfLine();
index4D = it.GetIndex();
while (!it.IsAtEndOfLine())
{
sum += it.Get();
++it;
}
MeanType mean = static_cast<MeanType>(sum) / static_cast<MeanType>(timeLength);
index3D[0] = index4D[0];
index3D[1] = index4D[1];
index3D[2] = index4D[2];
image3D->SetPixel(index3D, static_cast<PixelType>(mean));
it.NextLine();
}
// As you can see, we avoid to use a 3D iterator to walk
// over the mean image. The reason is that there is no
// guarantee that the 3D iterator will walk in the same
// order as the 4D. Iterators just adhere to their contract
// of visiting all the pixel, but do not enforce any particular
// order for the visits. The linear iterator guarantees to
// visit the pixels along a line of the image in the order
// in which they are placed in the line, but do not states
// in what order one line will be visited with respect to
// other lines. Here we simply take advantage of knowing
// the first three components of the 4D iterator index,
// and use them to place the resulting mean value in the
// output 3D image.
Writer3DType::Pointer writer3D = Writer3DType::New();
writer3D->SetFileName(argv[2]);
writer3D->SetInput(image3D);
try
{
writer3D->Update();
}
catch (itk::ExceptionObject& excp)
{
std::cerr << "Error writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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