ITK  5.2.0
Insight Toolkit
Examples/Iterators/ImageLinearIteratorWithIndex2.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* 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.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// This example shows how to use the \doxygen{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}
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
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;
}
// Software Guide : BeginLatex
//
// First we declare the types of the images, the 3D and 4D readers.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using PixelType = unsigned char;
using Image3DType = itk::Image<PixelType, 3>;
using Image4DType = itk::Image<PixelType, 4>;
using Reader4DType = itk::ImageFileReader<Image4DType>;
using Writer3DType = itk::ImageFileWriter<Image3DType>;
// Software Guide : EndCodeSnippet
Reader4DType::Pointer reader4D = Reader4DType::New();
reader4D->SetFileName(argv[1]);
try
{
reader4D->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Error reading the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
Image4DType::ConstPointer image4D = reader4D->GetOutput();
// Software Guide : BeginLatex
//
// Next, define the necessary types for indices, points, spacings, and size.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
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;
// Software Guide : EndCodeSnippet
Index3DType index3D;
Size3DType size3D;
Spacing3DType spacing3D;
Origin3DType origin3D;
Image4DType::RegionType region4D = image4D->GetBufferedRegion();
Index4DType index4D = region4D.GetIndex();
Size4DType size4D = region4D.GetSize();
Spacing4DType spacing4D = image4D->GetSpacing();
Origin4DType origin4D = image4D->GetOrigin();
// Software Guide : BeginLatex
//
// Here we make sure that the values for our resultant 3D mean image
// match up with the input 4D image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
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->SetSpacing(spacing3D);
image3D->SetOrigin(origin3D);
Region3DType region3D;
region3D.SetIndex(index3D);
region3D.SetSize(size3D);
image3D->SetRegions(region3D);
image3D->Allocate();
// Software Guide : EndCodeSnippet
const unsigned int timeLength = region4D.GetSize()[3];
// Software Guide : BeginLatex
//
// Next we iterate over time in the input image series, compute the average,
// and store that value in the corresponding pixel of the output 3D image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
IteratorType it(image4D, region4D);
it.SetDirection(3); // Walk along time dimension
it.GoToBegin();
while (!it.IsAtEnd())
{
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();
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// 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 every pixel, but do not enforce any particular
// order for the visits. The linear iterator guarantees it will
// visit the pixels along a line of the image in the order
// in which they are placed in the line, but does not state
// 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.
//
// Software Guide : EndLatex
Writer3DType::Pointer writer3D = Writer3DType::New();
writer3D->SetFileName(argv[2]);
writer3D->SetInput(image3D);
try
{
writer3D->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Error writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
itk::ImageRegion::GetIndex
const IndexType & GetIndex() const
Definition: itkImageRegion.h:160
itk::GTest::TypedefsAndConstructors::Dimension2::PointType
ImageBaseType::PointType PointType
Definition: itkGTestTypedefsAndConstructors.h:51
itkImageFileReader.h
itk::NumericTraits::AccumulateType
double AccumulateType
Definition: itkNumericTraits.h:74
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itk::Index::SetIndex
void SetIndex(const IndexValueType val[VDimension])
Definition: itkIndex.h:238
itkImage.h
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::GTest::TypedefsAndConstructors::Dimension2::IndexType
ImageBaseType::IndexType IndexType
Definition: itkGTestTypedefsAndConstructors.h:50
itkImageLinearConstIteratorWithIndex.h
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::GTest::TypedefsAndConstructors::Dimension2::RegionType
ImageBaseType::RegionType RegionType
Definition: itkGTestTypedefsAndConstructors.h:54
itkImageFileWriter.h
itk::NumericTraits::ZeroValue
static T ZeroValue()
Definition: itkNumericTraits.h:148
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::NumericTraits::RealType
double RealType
Definition: itkNumericTraits.h:84
itk::ImageLinearConstIteratorWithIndex
A multi-dimensional image iterator that visits image pixels within a region in a "scan-line" order.
Definition: itkImageLinearConstIteratorWithIndex.h:101