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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkGDCMSeriesStreamReadImageWrite.cxx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkPipelineMonitorImageFilter.h"
#include "itkStreamingImageFilter.h"
/// \brief is comparison with a percentage tollerance
///
/// returns true of the current value is with in tol percentage of m);
///
/// | u - v | <= e * |u| or | u - v | <= e * |v|
/// defines a "close with tolerance e" relationship between u and v
/// this is a symetric comparison
///
/// Also it is check to see if the u an v are both less then
/// epsilon for the type
static bool IsEqualTolerant(const float lm, const float rm, double tol) {
tol = vcl_fabs(tol);
float temp = vcl_fabs(lm - rm);
return temp <= tol*vcl_fabs(lm) ||
temp <= tol*vcl_fabs(rm) ||
(vcl_fabs(lm) < vcl_numeric_limits<float>::epsilon() &&
vcl_fabs(rm) < vcl_numeric_limits<float>::epsilon());
}
int main( int argc, char* argv[] )
{
if( argc < 6 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " DicomDirectory outputFile ";
std::cerr << " spacingX spacingY spacingZ [ force-no-streaming 1|0]" << std::endl;
return EXIT_FAILURE;
}
typedef itk::Image<unsigned short,3> ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames SeriesFileNames;
unsigned int numberOfDataPieces = 4;
ImageType::SpacingType expectedSpacing;
expectedSpacing[0] = atof(argv[3]);
expectedSpacing[1] = atof(argv[4]);
expectedSpacing[2] = atof(argv[5]);
bool forceNoStreaming = true;
if( argc > 6 )
{
if( atoi(argv[6]) != 1 )
{
forceNoStreaming = false;
}
}
bool expectedToStream = !forceNoStreaming;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
SeriesFileNames::Pointer filenameGenerator = SeriesFileNames::New();
filenameGenerator->SetInputDirectory( argv[1] );
ReaderType::Pointer reader = ReaderType::New();
const ReaderType::FileNamesContainer & filenames =
filenameGenerator->GetInputFileNames();
reader->SetFileNames( filenames );
reader->SetImageIO( gdcmIO );
typedef itk::PipelineMonitorImageFilter<ImageType> MonitorFilter;
MonitorFilter::Pointer monitor = MonitorFilter::New();
monitor->SetInput( reader->GetOutput() );
typedef itk::StreamingImageFilter<ImageType, ImageType> StreamingFilter;
StreamingFilter::Pointer streamer = StreamingFilter::New();
streamer->SetInput( monitor->GetOutput() );
streamer->SetNumberOfStreamDivisions( numberOfDataPieces );
try
{
if( forceNoStreaming )
{
// no streaming
reader->UseStreamingOff();
streamer->Update();
}
else
{
// stream based on the number of z-slices
reader->UseStreamingOn();
reader->UpdateOutputInformation();
numberOfDataPieces = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[2];
streamer->SetNumberOfStreamDivisions( numberOfDataPieces );
streamer->Update();
}
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
std::cerr << monitor;
return EXIT_FAILURE;
}
// verify things executed as expected
bool passed = true;
if( expectedToStream )
{
if( !monitor->VerifyAllInputCanStream(numberOfDataPieces) )
{
passed = false;
}
}
else
{
if( !monitor->VerifyAllIputCanNotStream() )
{
passed = false;
}
}
if( !passed )
{
std::cerr << monitor << std::endl;
std::cerr << "pipeline did not execute as expected!" << std::endl;
return EXIT_FAILURE;
}
std::cout << "Origin: " << reader->GetOutput()->GetOrigin() << std::endl;
std::cout << "direction: " << reader->GetOutput()->GetDirection() << std::endl;
std::cout << "Spacing: " << reader->GetOutput()->GetSpacing() << std::endl;
std::cout << "Expected Spacing: " << expectedSpacing << std::endl;
ImageType::SpacingType spacing = reader->GetOutput()->GetSpacing();
// we only give 4 bits of tolerence, IEEE float a 24-bit mantissa
const double percentTolerance = 1.0 / double ( (unsigned int)(1) << 18);
if (!IsEqualTolerant(spacing[0], expectedSpacing[0], percentTolerance) ||
!IsEqualTolerant(spacing[1], expectedSpacing[1], percentTolerance) ||
!IsEqualTolerant(spacing[2], expectedSpacing[2], percentTolerance))
{
std::cerr << "Spacing does not match expected" << std::endl;
return EXIT_FAILURE;
}
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[2] );
writer->SetInput( reader->GetOutput() );
try
{
writer->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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