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/*=========================================================================
*
* 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
*
* https://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 "itkGDCMImageIO.h"
#include "itkImageSeriesReader.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkSimpleFilterWatcher.h"
#include "itkTestingMacros.h"
int
itkImageSeriesWriterTest(int argc, char * argv[])
{
if (argc < 4)
{
std::cerr << "Missing Parameters." << std::endl;
std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv) << " DicomDirectory OutputDirectory FileSuffix"
<< std::endl;
return EXIT_FAILURE;
}
using ImageNDType = itk::Image<short, 3>;
using ReaderType = itk::ImageSeriesReader<ImageNDType>;
itk::GDCMImageIO::Pointer io = itk::GDCMImageIO::New();
// Get the DICOM filenames from the directory
itk::GDCMSeriesFileNames::Pointer nameGenerator = itk::GDCMSeriesFileNames::New();
nameGenerator->SetDirectory(argv[1]);
using SeriesIdContainer = std::vector<std::string>;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
std::string seriesIdentifier = seriesUID.begin()->c_str();
auto reader = ReaderType::New();
reader->SetFileNames(nameGenerator->GetFileNames(seriesIdentifier));
reader->SetImageIO(io);
itk::SimpleFilterWatcher watcher(reader);
ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());
reader->GetOutput()->Print(std::cout);
using WritePixelType = unsigned char;
using RescaleImageType = itk::Image<WritePixelType, 3>;
using OutputImageType = itk::Image<WritePixelType, 2>;
using RescaleFilterType = itk::RescaleIntensityImageFilter<ImageNDType, RescaleImageType>;
auto rescaler = RescaleFilterType::New();
rescaler->SetInput(reader->GetOutput());
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
rescaler->UpdateLargestPossibleRegion();
{ // This API is being deprecated. Please use NumericSeriesFileNames in the future
// for generating the list of filenames. This API will be removed after ITK 1.8
using WriterType = itk::ImageSeriesWriter<RescaleImageType, OutputImageType>;
auto writer = WriterType::New();
ITK_EXERCISE_BASIC_OBJECT_METHODS(writer, ImageSeriesWriter, ProcessObject);
itk::SimpleFilterWatcher watcher2(writer);
writer->SetInput(rescaler->GetOutput());
itk::SizeValueType startIndex = 1;
writer->SetStartIndex(startIndex);
ITK_TEST_SET_GET_VALUE(startIndex, writer->GetStartIndex());
itk::SizeValueType incrementIndex = 1;
writer->SetIncrementIndex(incrementIndex);
ITK_TEST_SET_GET_VALUE(incrementIndex, writer->GetIncrementIndex());
char format[4096];
snprintf(format, sizeof(format), "%s/series.%%d.%s", argv[2], argv[3]);
writer->SetSeriesFormat(format);
ITK_TEST_SET_GET_VALUE(std::string(format), std::string(writer->GetSeriesFormat()));
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
// Verify that attempting to use a MetaDataDictionary without setting the ImageIO
// should throw an exception.
writer->SetMetaDataDictionaryArray(reader->GetMetaDataDictionaryArray());
ITK_TRY_EXPECT_EXCEPTION(writer->Update());
writer->SetImageIO(io);
ITK_TEST_SET_GET_VALUE(io, writer->GetImageIO());
std::cout << "Old API PASSED !" << std::endl;
}
{ // This is the new API, using the NumericSeriesFileNames (or any other filename generator).
itk::NumericSeriesFileNames::Pointer fit = itk::NumericSeriesFileNames::New();
using WriterType = itk::ImageSeriesWriter<RescaleImageType, OutputImageType>;
auto writer = WriterType::New();
char format[4096];
snprintf(format, sizeof(format), "%s/series.%%d.%s", argv[2], argv[3]);
std::cout << "Format = " << format << std::endl;
ImageNDType::RegionType region = reader->GetOutput()->GetBufferedRegion();
ImageNDType::SizeType size = region.GetSize();
itk::SizeValueType startIndex = 0;
fit->SetStartIndex(startIndex);
ITK_TEST_SET_GET_VALUE(startIndex, fit->GetStartIndex());
itk::SizeValueType endIndex = size[2] - 1;
fit->SetEndIndex(endIndex); // The number of slices to write
ITK_TEST_SET_GET_VALUE(endIndex, fit->GetEndIndex());
itk::SizeValueType incrementIndex = 1;
fit->SetIncrementIndex(incrementIndex);
ITK_TEST_SET_GET_VALUE(incrementIndex, fit->GetIncrementIndex());
fit->SetSeriesFormat(format);
ITK_TEST_SET_GET_VALUE(std::string(format), std::string(fit->GetSeriesFormat()));
writer->SetInput(rescaler->GetOutput());
writer->SetFileNames(fit->GetFileNames());
// experiment the UseCompression methods and values
if (writer->GetUseCompression())
{
std::cerr << "Wrong default use compression value" << std::endl;
return EXIT_FAILURE;
}
bool useCompression = false;
ITK_TEST_SET_GET_BOOLEAN(writer, UseCompression, useCompression);
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
// Verify that attempting to use a MetaDataDictionary without setting the ImageIO
// should throw an exception.
writer->SetMetaDataDictionaryArray(reader->GetMetaDataDictionaryArray());
ITK_TRY_EXPECT_EXCEPTION(writer->Update());
std::cout << "Test with NumericSeriesFileNames PASSED !" << std::endl;
}
std::cout << "Test finished" << std::endl;
return EXIT_SUCCESS;
}
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