ITK  5.2.0
Insight Toolkit
SphinxExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/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.
*
*=========================================================================*/
#include "itkImage.h"
#include "itkGDCMImageIO.h"
int
main(int argc, char * argv[])
{
if (argc < 2)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " [DicomDirectory [outputFileName [seriesName]]]";
std::cerr << "\nIf DicomDirectory is not specified, current directory is used\n";
}
std::string dirName = "."; // current directory by default
if (argc > 1)
{
dirName = argv[1];
}
using PixelType = signed short;
constexpr unsigned int Dimension = 3;
using NamesGeneratorType = itk::GDCMSeriesFileNames;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetGlobalWarningDisplay(false);
nameGenerator->SetDirectory(dirName);
try
{
using SeriesIdContainer = std::vector<std::string>;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
auto seriesItr = seriesUID.begin();
auto seriesEnd = seriesUID.end();
if (seriesItr != seriesEnd)
{
std::cout << "The directory: ";
std::cout << dirName << std::endl;
std::cout << "Contains the following DICOM Series: ";
std::cout << std::endl;
}
else
{
std::cout << "No DICOMs in: " << dirName << std::endl;
return EXIT_SUCCESS;
}
while (seriesItr != seriesEnd)
{
std::cout << seriesItr->c_str() << std::endl;
++seriesItr;
}
seriesItr = seriesUID.begin();
while (seriesItr != seriesUID.end())
{
std::string seriesIdentifier;
if (argc > 3) // If seriesIdentifier given convert only that
{
seriesIdentifier = argv[3];
seriesItr = seriesUID.end();
}
else // otherwise convert everything
{
seriesIdentifier = seriesItr->c_str();
seriesItr++;
}
std::cout << "\nReading: ";
std::cout << seriesIdentifier << std::endl;
using FileNamesContainer = std::vector<std::string>;
FileNamesContainer fileNames = nameGenerator->GetFileNames(seriesIdentifier);
ReaderType::Pointer reader = ReaderType::New();
using ImageIOType = itk::GDCMImageIO;
ImageIOType::Pointer dicomIO = ImageIOType::New();
reader->SetImageIO(dicomIO);
reader->SetFileNames(fileNames);
reader->ForceOrthogonalDirectionOff(); // properly read CTs with gantry tilt
using WriterType = itk::ImageFileWriter<ImageType>;
WriterType::Pointer writer = WriterType::New();
std::string outFileName;
if (argc > 2)
{
outFileName = argv[2];
}
else
{
outFileName = dirName + std::string("/") + seriesIdentifier + ".nrrd";
}
writer->SetFileName(outFileName);
writer->UseCompressionOn();
writer->SetInput(reader->GetOutput());
std::cout << "Writing: " << outFileName << std::endl;
try
{
writer->Update();
}
catch (itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
continue;
}
}
}
catch (itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
itk::ImageSeriesReader
Data source that reads image data from a series of disk files.
Definition: itkImageSeriesReader.h:45
itkImage.h
itkGDCMImageIO.h
itkImageSeriesReader.h
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::GDCMImageIO
ImageIO class for reading and writing DICOM V3.0 and ACR/NEMA 1&2 uncompressed images....
Definition: itkGDCMImageIO.h:109
itkImageFileWriter.h
itk::GDCMSeriesFileNames
Generate a sequence of filenames from a DICOM series.
Definition: itkGDCMSeriesFileNames.h:63
itkGDCMSeriesFileNames.h
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44