ITK  5.3.0
Insight Toolkit
SphinxExamples/src/IO/ImageBase/ProcessImageChunks/Code.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.
*
*=========================================================================*/
int
main(int argc, char * argv[])
{
if (argc != 3)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0];
std::cerr << " <InputFileName> <OutputFileName>";
std::cerr << std::endl;
return EXIT_FAILURE;
}
const char * inputFileName = argv[1];
const char * outputFileName = argv[2];
const int xDiv = 6;
const int yDiv = 4;
const int zDiv = 1; // 1 for 2D input
constexpr unsigned int Dimension = 3;
using PixelType = unsigned char;
const auto input = itk::ReadImage<ImageType>(inputFileName);
ImageType::RegionType fullRegion = input->GetLargestPossibleRegion();
ImageType::SizeType fullSize = fullRegion.GetSize();
// when reading image from file, start index is always 0
MedianType::Pointer median = MedianType::New();
median->SetInput(input);
median->SetRadius(2);
using WriterType = itk::ImageFileWriter<ImageType>;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFileName);
// Use for loops to split the image into chunks.
// This way of splitting gives us easy control over it.
// For example, we could make the regions always be of equal size
// in order to create samples for a deep learning algorithm.
// ImageRegionSplitterMultidimensional has a similar
// functionality to what is implemented below.
for (int z = 0; z < zDiv; z++)
{
start[2] = fullSize[2] * double(z) / zDiv;
end[2] = fullSize[2] * (z + 1.0) / zDiv;
size[2] = end[2] - start[2];
for (int y = 0; y < yDiv; y++)
{
start[1] = fullSize[1] * double(y) / yDiv;
end[1] = fullSize[1] * (y + 1.0) / yDiv;
size[1] = end[1] - start[1];
for (int x = 0; x < xDiv; x++)
{
start[0] = fullSize[0] * double(x) / xDiv;
end[0] = fullSize[0] * (x + 1.0) / xDiv;
size[0] = end[0] - start[0];
region.SetIndex(start);
region.SetSize(size);
// now that we have our chunk, request the filter to only process that
median->GetOutput()->SetRequestedRegion(region);
median->Update();
ImageType::Pointer result = median->GetOutput();
// only needed in case of further manual processing
result->DisconnectPipeline();
// possible additional non-ITK pipeline processing
writer->SetInput(result);
// convert region into IO region
ioRegion.SetIndex(0, start[0]);
ioRegion.SetIndex(1, start[1]);
ioRegion.SetIndex(2, start[2]);
ioRegion.SetSize(0, region.GetSize()[0]);
ioRegion.SetSize(1, region.GetSize()[1]);
ioRegion.SetSize(2, region.GetSize()[2]);
// tell the writer this is only a chunk of a larger image
writer->SetIORegion(ioRegion);
try
{
writer->Update();
}
catch (itk::ExceptionObject & error)
{
std::cerr << "Exception for chunk: " << x << ' ' << y << ' ' << z << error << std::endl;
return EXIT_FAILURE;
}
}
}
}
return EXIT_SUCCESS;
}
itk::ImageIORegion::SetIndex
void SetIndex(const IndexType &index)
itkMedianImageFilter.h
itkImageFileReader.h
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itk::ImageIORegion
An ImageIORegion represents a structured region of data.
Definition: itkImageIORegion.h:52
itk::GTest::TypedefsAndConstructors::Dimension2::IndexType
ImageBaseType::IndexType IndexType
Definition: itkGTestTypedefsAndConstructors.h:50
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:88
itk::GTest::TypedefsAndConstructors::Dimension2::RegionType
ImageBaseType::RegionType RegionType
Definition: itkGTestTypedefsAndConstructors.h:54
itkImageFileWriter.h
itk::ImageRegion::SetIndex
void SetIndex(const IndexType &index)
Definition: itkImageRegion.h:153
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:88
itk::MedianImageFilter
Applies a median filter to an image.
Definition: itkMedianImageFilter.h:53
itk::ImageIORegion::SetSize
void SetSize(const SizeType &size)
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44
itk::Size::GetSize
const SizeValueType * GetSize() const
Definition: itkSize.h:169