ITK  5.2.0
Insight Toolkit
Examples/IO/DicomImageReadWrite.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
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*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to read a single DICOM slice and write it
// back as another DICOM slice. In the process an intensity rescaling is also
// applied.
//
// In order to read and write the slice we use the \doxygen{GDCMImageIO}
// class which encapsulates a connection to the underlying GDCM library. In
// this way we gain access from ITK to the DICOM functionalities offered by
// GDCM. The GDCMImageIO object is connected as the ImageIO object to be used
// by the \doxygen{ImageFileWriter}.
//
// We should first include the following header files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkGDCMImageIO.h"
// Software Guide : EndCodeSnippet
#include <list>
#include <fstream>
int
main(int argc, char * argv[])
{
// Verify the number of parameters in the command line
if (argc < 5)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " DicomImage OutputDicomImage ";
std::cerr << " OutputImage RescaleDicomImage\n";
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Then we declare the pixel type and image dimension, and use them for
// instantiating the image type to be read.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InputPixelType = signed short;
constexpr unsigned int InputDimension = 2;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// With the image type we can instantiate the type of the reader, create
// one, and set the filename of the image to be read.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// GDCMImageIO is an ImageIO class for reading and writing DICOM v3 and
// ACR/NEMA images. The GDCMImageIO object is constructed here and connected
// to the ImageFileReader.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ImageIOType = itk::GDCMImageIO;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO(gdcmImageIO);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// At this point we can trigger the reading process by invoking the
// \code{Update()} method. Since this reading process may eventually throw
// an exception, we place the invocation inside a \code{try/catch} block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
reader->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "exception in file reader " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now have the image in memory and can get access to it using the
// \code{GetOutput()} method of the reader. In the remainder of this current
// example, we focus on showing how to save this image again in DICOM
// format in a new file.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// First, we must instantiate an ImageFileWriter type. Then, we construct
// one, set the filename to be used for writing, and connect the input image
// to be written. Since in this example we write the image in different
// ways, and in each case use a different writer, we enumerated the variable
// names of the writer objects as well as their types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
Writer1Type::Pointer writer1 = Writer1Type::New();
writer1->SetFileName(argv[2]);
writer1->SetInput(reader->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We need to explicitly set the proper image IO (GDCMImageIO) to the
// writer filter since the input DICOM dictionary is being passed along the
// writing process. The dictionary contains all necessary information that
// a valid DICOM file should contain, like Patient Name, Patient ID,
// Institution Name, etc.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer1->SetImageIO(gdcmImageIO);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The writing process is triggered by invoking the \code{Update()} method.
// Since this execution may result in exceptions being thrown we place the
// \code{Update()} call inside a \code{try/catch} block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer1->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "exception in file writer " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We will now rescale the image using the RescaleIntensityImageFilter. For
// this purpose we use a better suited pixel type: \code{unsigned char}
// instead of \code{signed short}. The minimum and maximum values of the
// output image are explicitly defined in the rescaling filter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using WritePixelType = unsigned char;
using WriteImageType = itk::Image<WritePixelType, 2>;
using RescaleFilterType =
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We create a second writer object that will save the rescaled image into a
// new file, which is not in DICOM format. This is done only for the sake of
// verifying the image against the one that will be saved in DICOM format
// later in this example.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
Writer2Type::Pointer writer2 = Writer2Type::New();
writer2->SetFileName(argv[3]);
rescaler->SetInput(reader->GetOutput());
writer2->SetInput(rescaler->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The writer can be executed by invoking the \code{Update()} method from
// inside a \code{try/catch} block.
//
// Software Guide : EndLatex
try
{
writer2->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "exception in file writer " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// We proceed now to save the same rescaled image into a file in DICOM
// format. For this purpose we just need to set up a
// \doxygen{ImageFileWriter} and pass to it the rescaled image as input.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
Writer3Type::Pointer writer3 = Writer3Type::New();
writer3->SetFileName(argv[4]);
writer3->SetInput(rescaler->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now need to explicitly set the proper image IO (GDCMImageIO), but also
// we must tell the ImageFileWriter to not use the MetaDataDictionary from
// the input but from the GDCMImageIO since this is the one that contains
// the DICOM specific information
//
// The GDCMImageIO object will automatically detect the pixel type, in this
// case \code{unsigned char} and it will update the DICOM header information
// accordingly.
// \index{itk::ImageFileWriter!UseInputMetaDataDictionaryOff()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer3->UseInputMetaDataDictionaryOff();
writer3->SetImageIO(gdcmImageIO);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we trigger the execution of the DICOM writer by invoking the
// Update() method from inside a try/catch block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer3->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}
itkImageFileReader.h
itkGDCMImageIO.h
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itkRescaleIntensityImageFilter.h
itk::GDCMImageIO
ImageIO class for reading and writing DICOM V3.0 and ACR/NEMA 1&2 uncompressed images....
Definition: itkGDCMImageIO.h:111
itkImageFileWriter.h
itk::RescaleIntensityImageFilter
Applies a linear transformation to the intensity levels of the input Image.
Definition: itkRescaleIntensityImageFilter.h:154
itk::Math::e
static constexpr double e
Definition: itkMath.h:54
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86