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/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* 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 <iomanip>
#include "itkUseMevisDicomTiff.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkImageIOBase.h"
#include <string>
#include "itkMath.h"
#include "itkTestingComparisonImageFilter.h"
//-------------------------------------------------------------------------------------
// This test tests the itkMevisDicomTiffImageIO library. The test is performed
// in 2D, 3D, and 4D, for a unsigned char image. An artificial image is generated,
// written to disk, read from disk, and compared to the original.
template< unsigned int Dimension >
int
testMevis( void )
{
std::cerr << "Testing write/read of " << Dimension << "D image..." << std::endl;
/** Some basic type definitions. */
typedef unsigned char PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileWriter< ImageType > WriterType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::Testing::ComparisonImageFilter<
ImageType, ImageType > ComparisonFilterType;
typedef typename ImageType::SizeType SizeType;
typedef typename ImageType::SpacingType SpacingType;
typedef typename ImageType::PointType OriginType;
typedef typename ImageType::DirectionType DirectionType;
typedef itk::ImageRegionIterator< ImageType > IteratorType;
typename WriterType::Pointer writer = WriterType::New();
typename ReaderType::Pointer reader = ReaderType::New();
typename ImageType::Pointer inputImage = ImageType::New();
SizeType size;
SpacingType spacing;
OriginType origin;
DirectionType direction;
direction.Fill( 0.0 );
for( unsigned int i = 0; i < Dimension; ++i )
{
size[ i ] = 20 + i;
spacing[ i ] = 0.5 + 0.1 * i;
origin[ i ] = 5 + 3 * i;
direction[ i ][ i ] = 1.0; // default, will be changed below
}
// 4th dimension origin/spacing are lost using dcm/tiff format!
if( Dimension == 4 )
{
// default values
spacing[ 3 ] = 1.0;
origin[ 3 ] = 0.0;
}
// Difficult direction cosines:
if( Dimension == 2 )
{
// Test flips
direction[ 0 ][ 0 ] = 1; direction[ 0 ][ 1 ] = 0;
direction[ 1 ][ 0 ] = 0; direction[ 1 ][ 1 ] = -1;
}
else if( Dimension == 3 )
{
// Test axis permutations
// RM: won't work, because dicom always assume right hand
// coordinate system when reconstructing the third direction
/*
direction[0][0] = 1; direction[0][1] = 0; direction[0][2] = 0;
direction[1][0] = 0; direction[1][1] = 0; direction[1][2] = 1;
direction[2][0] = 0; direction[2][1] = 1; direction[2][2] = 0;
*/
// this works:
direction[ 0 ][ 0 ] = 1; direction[ 0 ][ 1 ] = 0; direction[ 0 ][ 2 ] = 0;
direction[ 1 ][ 0 ] = 0; direction[ 1 ][ 1 ] = 0; direction[ 1 ][ 2 ] = -1;
direction[ 2 ][ 0 ] = 0; direction[ 2 ][ 1 ] = 1; direction[ 2 ][ 2 ] = 0;
}
else if( Dimension == 4 )
{
// Test 4D. RM: also make sure it is a right hand coordinate system
direction[ 0 ][ 0 ] = 1; direction[ 0 ][ 1 ] = 0; direction[ 0 ][ 2 ] = 0; direction[ 0 ][ 3 ] = 0;
direction[ 1 ][ 0 ] = 0; direction[ 1 ][ 1 ] = 0; direction[ 1 ][ 2 ] = -1; direction[ 1 ][ 3 ] = 0;
direction[ 2 ][ 0 ] = 0; direction[ 2 ][ 1 ] = 1; direction[ 2 ][ 2 ] = 0; direction[ 2 ][ 3 ] = 0;
direction[ 3 ][ 0 ] = 0; direction[ 3 ][ 1 ] = 0; direction[ 3 ][ 2 ] = 0; direction[ 3 ][ 3 ] = 1;
}
/** Generate image with gradually increasing pixel values. */
inputImage->SetRegions( size );
inputImage->SetSpacing( spacing );
inputImage->SetOrigin( origin );
inputImage->SetDirection( direction );
try
{
inputImage->Allocate();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: Failed to allocate test image" << std::endl;
std::cerr << err << std::endl;
return 1;
}
IteratorType it( inputImage, inputImage->GetLargestPossibleRegion() );
unsigned long nrPixels = inputImage->GetLargestPossibleRegion().GetNumberOfPixels();
double factor = itk::NumericTraits< PixelType >::max() / static_cast< double >( nrPixels );
PixelType pixval = 0;
unsigned long pixnr = 0;
for( it.GoToBegin(); !it.IsAtEnd(); ++it )
{
pixval = static_cast< PixelType >(
itk::Math::Floor< double >( pixnr * factor ) );
it.Set( pixval );
++pixnr;
}
std::string testfile( "testimageMevisDicomTiff.tif" );
writer->SetFileName( testfile );
writer->SetInput( inputImage );
reader->SetFileName( testfile );
std::string task( "" );
try
{
task = "Writing";
writer->Update();
task = "Reading";
reader->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: " << task << " mevis dicomtiff failed." << std::endl;
std::cerr << err << std::endl;
return 1;
}
std::cerr << "\nPrintSelf():\n" << std::endl;
typename itk::ImageIOBase::Pointer mevisIO = reader->GetImageIO();
mevisIO->Print( std::cerr, 2 );
typename ImageType::Pointer outputImage = reader->GetOutput();
bool same = true;
same &= size == outputImage->GetLargestPossibleRegion().GetSize();
same &= spacing == outputImage->GetSpacing();
same &= origin == outputImage->GetOrigin();
same &= direction == outputImage->GetDirection();
if( !same )
{
std::cerr << "ERROR: image properties are not preserved" << std::endl;
std::cerr << "Original properties:" << std::endl;
inputImage->Print( std::cerr, 0 );
std::cerr << "After write/read:" << std::endl;
outputImage->Print( std::cerr, 0 );
return 1;
}
typename ComparisonFilterType::Pointer comparisonFilter = ComparisonFilterType::New();
comparisonFilter->SetTestInput( outputImage );
comparisonFilter->SetValidInput( inputImage );
comparisonFilter->Update();
unsigned long nrDiffPixels = comparisonFilter->GetNumberOfPixelsWithDifferences();
if( nrDiffPixels > 0 )
{
std::cerr << "ERROR: the pixel values are not correct after write/read" << std::endl;
return 1;
}
return 0;
} // end templated function
int
main( int argc, char * argv[] )
{
/** Support Mevis Dicom Tiff (if selected in cmake) */
RegisterMevisDicomTiff();
#ifdef _ELASTIX_USE_MEVISDICOMTIFF
/** Test for 2d, 3d, and 4d images */
int ret2d = testMevis< 2 >();
int ret3d = testMevis< 3 >();
int ret4d = testMevis< 4 >();
/** Return a value. */
return ( ret2d | ret3d | ret4d );
#else
std::cerr << "Elastix was not built with Mevis DicomTiff support, so this test is not relevant." << std::endl;
return 0;
#endif
} // end main
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