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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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 "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkMRCImageIO.h"
#include "itkTestingMacros.h"
#include "itkMath.h"
static unsigned int m_CallNumber = 0;
template <typename TImageType>
class MRCImageIOTester
{
public:
virtual int Test(int argc, char* argv[] );
virtual ~MRCImageIOTester(){ }
static bool Write( const std::string &filePrefix, std::string &outputPath );
static bool Read( const std::string &filePrefix,
std::string &outputPath,
unsigned int index );
};
template <typename TImageType>
bool MRCImageIOTester<TImageType>
::Write( const std::string &filePrefix, std::string &outputPath )
{
try
{
++m_CallNumber;
typedef TImageType ImageType;
typedef typename ImageType::PixelType PixelType;
// allocate an 10x10x10 image
typename ImageType::Pointer image = ImageType::New();
typename ImageType::SizeType m_ImageSize;
m_ImageSize.Fill(10);
image->SetRegions( m_ImageSize );
image->Allocate();
unsigned int cnt = 0;
itk::ImageRegionIterator< ImageType > i( image, image->GetLargestPossibleRegion() );
i.GoToBegin();
while (!i.IsAtEnd() )
{
// fill the image switching between these pixels
switch (cnt%4)
{
case 0:
i.Set( itk::NumericTraits<PixelType>::ZeroValue() );
break;
case 1:
i.Set( itk::NumericTraits<PixelType>::OneValue() );
break;
case 2:
i.Set( itk::NumericTraits<PixelType>::min( PixelType() ) );
break;
case 3:
i.Set( itk::NumericTraits<PixelType>::max( PixelType() ) );
}
++cnt;
++i;
}
typedef itk::ImageFileWriter<ImageType> ImageFileWriterType;
typename ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
writer->SetInput( image );
// force use of MRCImageIO
typedef itk::MRCImageIO IOType;
IOType::Pointer mrcIO = IOType::New();
writer->SetImageIO(mrcIO);
std::ostringstream m_NameWithIndex;
m_NameWithIndex << filePrefix << "_" << m_CallNumber << ".mrc";
std::ostringstream m_OutputFileName;
#if defined(WIN32) // windows
// if it ends in \\ just append the name
if (outputPath[outputPath.size()-1] == '\\')
{
m_OutputFileName << outputPath << m_NameWithIndex.str();
}
else
{
m_OutputFileName << outputPath << "\\" << m_NameWithIndex.str();
}
#else /// POSIX UNIX
// if it ends in / just append the name
if (outputPath[outputPath.size()-1] == '/')
{
m_OutputFileName << outputPath << m_NameWithIndex.str();
}
// otherwise, add / and the name
else
{
m_OutputFileName << outputPath << "/" << m_NameWithIndex.str();
}
#endif
writer->SetFileName( m_OutputFileName.str() );
writer->Update();
// test the CanWriteFile function after the fact (should always be true at
// this point)
if (!mrcIO->CanWriteFile(m_OutputFileName.str().c_str() ) )
{
return false;
}
return true;
}
catch(itk::ExceptionObject &e)
{
std::cout << e.GetDescription() << std::endl;
return false;
}
}
template <typename TImageType>
bool MRCImageIOTester<TImageType>
::Read( const std::string &filePrefix,
std::string &outputPath,
unsigned int index )
{
try
{
typedef TImageType ImageType;
typedef typename ImageType::PixelType PixelType;
typedef itk::ImageFileReader<ImageType> ImageFileReaderType;
typename ImageFileReaderType::Pointer reader = ImageFileReaderType::New();
// force use of MRCImageIO
typedef itk::MRCImageIO IOType;
IOType::Pointer mrcIO = IOType::New();
reader->SetImageIO(mrcIO);
// construct the image filename
std::ostringstream m_NameWithIndex;
m_NameWithIndex << filePrefix << "_" << index << ".mrc";
std::ostringstream m_OutputFileName;
#if defined(WIN32) // windows
// if it ends in \\ just append the name
if (outputPath[outputPath.size()-1] == '\\')
{
m_OutputFileName << outputPath << m_NameWithIndex.str();
}
else
{
m_OutputFileName << outputPath << "\\" << m_NameWithIndex.str();
}
#else /// POSIX UNIX
// if it ends in / just append the name
if (outputPath[outputPath.size()-1] == '/')
{
m_OutputFileName << outputPath << m_NameWithIndex.str();
}
// otherwise, add / and the name
else
{
m_OutputFileName << outputPath << "/" << m_NameWithIndex.str();
}
#endif
reader->SetFileName( m_OutputFileName.str() );
// read the image
typename ImageType::Pointer image = reader->GetOutput();
reader->Update();
// test the CanReadFile function after the fact (should always be true at
// this point)
if (!mrcIO->CanReadFile(m_OutputFileName.str().c_str() ) )
{
return false;
}
// check the size
typename ImageType::RegionType region = image->GetLargestPossibleRegion();
typename ImageType::SizeType size = region.GetSize();
bool sizeGood = true;
for (unsigned int i = 0; i < ImageType::GetImageDimension(); i++)
{
if (size[i] != 10)
{
sizeGood = false;
break;
}
}
if (!sizeGood)
{
std::cout << "Error: Size didn't read properly" << std::endl;
return false;
}
// check each pixel
bool pixelsGood = true;
unsigned int cnt = 0;
itk::ImageRegionIterator< ImageType > iter( image, region );
iter.GoToBegin();
while (!iter.IsAtEnd() && pixelsGood)
{
// check image switching between these pixels
switch (cnt%4)
{
case 0:
if (itk::Math::NotExactlyEquals(iter.Get(), itk::NumericTraits<PixelType>::ZeroValue()) )
{
pixelsGood = false;
}
break;
case 1:
if (itk::Math::NotExactlyEquals(iter.Get(), itk::NumericTraits<PixelType>::OneValue()) )
{
pixelsGood = false;
}
break;
case 2:
if (itk::Math::NotExactlyEquals(iter.Get(), itk::NumericTraits<PixelType>::min( PixelType() )) )
{
pixelsGood = false;
}
break;
case 3:
if (itk::Math::NotExactlyEquals(iter.Get(), itk::NumericTraits<PixelType>::max( PixelType() )) )
{
pixelsGood = false;
}
}
++cnt;
++iter;
}
if (!pixelsGood)
{
std::cout << "Error: Pixels didn't read properly" << std::endl;
return false;
}
// reading successful, so return true
return true;
}
catch(itk::ExceptionObject &e)
{
std::cout << e.GetDescription() << std::endl;
return false;
}
}
// int MRCImageIOTester::Test(int argc, char* argv[] )
int itkMRCImageIOTest(int argc, char* argv[])
{
if( argc < 2 )
{
std::cerr << "Usage: " << argv[0] << " outputPath" << std::endl;
return EXIT_FAILURE;
}
std::string outputPath = argv[1];
std::string filePrefix = argv[0];
//
// test all usable pixeltypes
//
// unsigned char
typedef itk::Image<unsigned char, 3> ImageTypeUnsignedChar3;
if (!(MRCImageIOTester< ImageTypeUnsignedChar3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (unsighed char)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (unsighed char)" << std::endl;
if (!(MRCImageIOTester< ImageTypeUnsignedChar3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (unsighed char)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (unsighed char)" << std::endl;
// short
typedef itk::Image<short, 3> ImageTypeShort3;
if (!(MRCImageIOTester< ImageTypeShort3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (short)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (short)" << std::endl;
if (!(MRCImageIOTester< ImageTypeShort3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (short)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (short)" << std::endl;
// float
typedef itk::Image<float, 3> ImageTypeFloat3;
if (!(MRCImageIOTester< ImageTypeFloat3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (float)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (float)" << std::endl;
if (!(MRCImageIOTester< ImageTypeFloat3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (float)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (float)" << std::endl;
// unsigned short
typedef itk::Image<unsigned short, 3> ImageTypeUnsignedShort3;
if (!(MRCImageIOTester< ImageTypeUnsignedShort3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (unsighed short)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (unsighed short)" << std::endl;
if (!(MRCImageIOTester< ImageTypeUnsignedShort3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (unsighed short)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (unsighed short)" << std::endl;
// RGBPixel<unsigned char>
typedef itk::RGBPixel<unsigned char> PixelTypeRGB;
typedef itk::Image<PixelTypeRGB, 3> ImageTypeRGB3;
if (!(MRCImageIOTester< ImageTypeRGB3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (RGBPixel<unsighed char>)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (RGBPixel<unsigned char>)" << std::endl;
if (!(MRCImageIOTester< ImageTypeRGB3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (RGBPixel<unsigned char>)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (RGBPixel<unsigned char>)" << std::endl;
// complex<float>
typedef std::complex<float> PixelTypeComplexFloat;
typedef itk::Image<PixelTypeComplexFloat, 3> ImageTypeComplexFloat3;
if (!(MRCImageIOTester< ImageTypeComplexFloat3 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (complex<float>)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (complex<float>)" << std::endl;
if (!(MRCImageIOTester< ImageTypeComplexFloat3 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (complex<float>)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (complex<float>)" << std::endl;
//
// test additional usable dimensions
//
// 1D
typedef itk::Image<unsigned char, 1> ImageTypeUnsignedChar1;
if (!(MRCImageIOTester< ImageTypeUnsignedChar1 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (1D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (1D)" << std::endl;
if (!(MRCImageIOTester< ImageTypeUnsignedChar1 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (1D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (1D)" << std::endl;
// 2D
typedef itk::Image<unsigned char, 2> ImageTypeUnsignedChar2;
if (!(MRCImageIOTester< ImageTypeUnsignedChar2 >::Write(filePrefix, outputPath) ) )
{
std::cout << "[FAILED] writing (2D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] writing (2D)" << std::endl;
if (!(MRCImageIOTester< ImageTypeUnsignedChar2 >::Read(filePrefix, outputPath, m_CallNumber) ) )
{
std::cout << "[FAILED] reading (2D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] reading (2D)" << std::endl;
//
// expect exceptions with the following
//
typedef itk::Image<double> ImageTypeDouble;
if (MRCImageIOTester< ImageTypeDouble >::Write(filePrefix, outputPath) )
{
std::cout << "[FAILED] didn't throw exception (Image<double>)"
<< std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] threw exception (Image<double>)" << std::endl;
typedef itk::Image<int> ImageTypeInt;
if (MRCImageIOTester< ImageTypeInt >::Write(filePrefix, outputPath) )
{
std::cout << "[FAILED] didn't throw exception (Image<int>)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] threw exception (Image<int>)" << std::endl;
typedef itk::Image<unsigned long> ImageTypeUnsignedLong;
if (MRCImageIOTester< ImageTypeUnsignedLong >::Write(filePrefix, outputPath) )
{
std::cout << "[FAILED] didn't throw exception (Image<unsigned long>)"
<< std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] threw exception (Image<unsigned long>)" << std::endl;
//
// test unusable dimensions
//
typedef itk::Image<unsigned char, 4> ImageTypeUnsignedChar4;
if (MRCImageIOTester< ImageTypeUnsignedChar4 >::Write(filePrefix, outputPath) )
{
std::cout << "[FAILED] incorrectly returned true (4D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] threw exception (4D)" << std::endl;
typedef itk::Image<unsigned char, 5> ImageTypeUnsignedChar5;
if (MRCImageIOTester< ImageTypeUnsignedChar5 >::Write(filePrefix, outputPath) )
{
std::cout << "[FAILED] incorrectly returned true (5D)" << std::endl;
return EXIT_FAILURE;
}
std::cout << "[PASSED] threw exception (5D)" << std::endl;
//
// use print methods
//
typedef itk::MRCImageIO IOType;
IOType::Pointer mrcIO = IOType::New();
EXERCISE_BASIC_OBJECT_METHODS( mrcIO, MRCImageIO, StreamingImageIOBase );
//
// All tests succeeded
//
return EXIT_SUCCESS;
}
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