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itkbasics.cpp
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itkbasics.cpp
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#include <iostream>
#include <exception>
#include "itkbasics.h"
#include "itkImportImageFilter.h"
#include "itkIntensityWindowingImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkIdentityTransform.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageSeriesWriter.h"
#include "itkTimeProbesCollectorBase.h"
#include "itkResampleImageFilter.h"
#include "itkSubtractImageFilter.h"
#include "itkScalarToRGBPixelFunctor.h"
#include "itkUnaryFunctorImageFilter.h"
#ifdef useFastMemoryHungryGaussian
#include "itkRecursiveGaussianImageFilter.h"
#else
#include "itkDiscreteGaussianImageFilter.h"
#endif
namespace itkBasic {
typedef itk::IdentityTransform< double, Dimension > IdentityTransformType;
typedef itk::LinearInterpolateImageFunction< FilterImageType, double > InterpolatorType;
typedef itk::RecursiveGaussianImageFilter< FilterImageType, FilterImageType > GaussFilterType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
typedef itk::ResampleImageFilter< FilterImageType, FilterImageType > ResampleFilterType;
typedef itk::SubtractImageFilter< FilterImageType, FilterImageType, FilterImageType > SubtractFilter;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, Dimension> RGBImageType;
typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long> ColorMapFunctorType;
typedef itk::UnaryFunctorImageFilter<LabeledImageType, RGBImageType, ColorMapFunctorType> ColorMapFilterType;
typedef itk::PermuteAxesImageFilter< FilterImageType > PermuteAxesFilter;
typedef itk::FlipImageFilter< FilterImageType > FlipFilter;
typedef itk::GDCMImageIO ImageIOType;
void memtest(void) {
long unsigned size = 0;
long unsigned asize = 1024*1024*1024;
long unsigned max = asize;
long unsigned min = 0;
std::list< void * > plist;
bool working = true;
while( working ) {
void *t = malloc(asize);
if (t!=NULL) {
if (asize == 1024*1024*1024) {
size += asize;
plist.push_back( t );
} else {
free( t );
if ((max - min)> 1024) {
min = asize;
asize = (asize + max) / 2;
} else {
size += asize;
working = false;
}
}
} else {
max = asize;
asize = (asize + min) / 2;
}
}
std::cerr << "could allocate " << size/ (1024.0*1024.0) << " MB" << std::endl;
for( std::list< void * >::iterator i = plist.begin(); i!=plist.end(); ++i) free( *i );
}
void replaceMetaData( ReaderType::DictionaryArrayRawPointer dictArrayPointer, const std::string tag, const std::string newvalue, bool additive) {
for( ReaderType::DictionaryArrayType::const_iterator it = dictArrayPointer->begin(); it != dictArrayPointer->end(); ++it) {
ReaderType::DictionaryRawPointer dp = *it;
std::string val;
if (additive) {
ExposeMetaData( *dp, tag, val);
}
val += newvalue;
EncapsulateMetaData( *dp, tag, val);
}
}
DicomInputImageType::Pointer getDicomSerie(const FileNamesContainer &filenames, ReaderType *reader, unsigned int scaleValue) {
ReaderType::Pointer smart_reader;
if (reader == NULL) {
smart_reader = ReaderType::New();
reader = smart_reader;
}
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
reader->SetFileNames(filenames);
try {
reader->Update();
}catch( itk::ExceptionObject & excep ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
DicomInputImageType::Pointer result = reader->GetOutput();
if (scaleValue > 1) result = ImageShrink( result, scaleValue );
return result;
}
void SeriesReader::getSeriesFileNames(unsigned int num, FileNamesContainer &fc) {
if (slist.size() > num) fc = slist[num];
else fc.clear();
};
void SeriesReader::readSeriesData(unsigned int minSlices) {
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( inputDir );
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while( seriesItr != seriesEnd ) {
FileNamesContainer fileNames = nameGenerator->GetFileNames(seriesItr->c_str());
if (fileNames.size() >= minSlices)
slist.push_back( fileNames );
seriesItr++;
}
}
/*
void saveCoroImage(const std::string &fname, FilterImageType::ConstPointer image, int windowWidth, int windowLevel) {
PermuteAxesFilter::Pointer permutator = PermuteAxesFilter::New();
permutator->SetInput( image );
PermuteAxesFilter::PermuteOrderArrayType order;
order[0] = 0; order[1] = 2; order[2] = 1;
permutator->SetOrder( order );
FlipFilter::Pointer flipper = FlipFilter::New();
flipper->SetInput( permutator->GetOutput() );
FlipFilter::FlipAxesArrayType faxes;
faxes[0] = false; faxes[1] = true; faxes[2] = false;
flipper->SetFlipAxes( faxes );
try {
flipper->Update();
}catch( itk::ExceptionObject & excep ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
saveImage(fname, flipper->GetOutput(), windowWidth, windowLevel);
}
*/
void saveCoroSubtractionImage(const std::string &fname, FilterImageType::ConstPointer minuent, FilterImageType::ConstPointer subtrahent) {
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
SubtractFilter::Pointer subtractor = SubtractFilter::New();
subtractor->SetInput1( minuent );
subtractor->SetInput2( subtrahent );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try {
subtractor->Update();
}catch( itk::ExceptionObject & excep ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
PermuteAxesFilter::Pointer permutator = PermuteAxesFilter::New();
permutator->SetInput( subtractor->GetOutput() );
PermuteAxesFilter::PermuteOrderArrayType order;
order[0] = 0; order[1] = 2; order[2] = 1;
permutator->SetOrder( order );
FlipFilter::Pointer flipper = FlipFilter::New();
flipper->SetInput( permutator->GetOutput() );
FlipFilter::FlipAxesArrayType faxes;
faxes[0] = false; faxes[1] = true; faxes[2] = false;
flipper->SetFlipAxes( faxes );
try {
flipper->Update();
}catch( itk::ExceptionObject & excep ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
FilterImageType::Pointer flipImage = flipper->GetOutput();
ImageSave(flipImage, fname);
}
/*
FilterImageType::Pointer gaussianScale(const FilterImageType::Pointer sourceImage, double scaleValue, float gaussSigma) {
FilterImageType::SizeType destSize;
for(unsigned int i = 0; i < Dimension; ++i)
destSize[i] = static_cast<FilterImageType::SizeType::SizeValueType>(sourceImage->GetBufferedRegion().GetSize(i) * scaleValue);
return gaussTransform(sourceImage, destSize, gaussSigma);
}
*/
FilterImageType::Pointer gaussTransform(const FilterImageType::Pointer sourceImage, FilterImageType::SizeType destSize,
float gaussSigma, const BaseTransformType *transform) {
std::cerr << "Filter, Transformation and Output start" << std::endl;
itk::TimeProbesCollectorBase collector;
collector.Start( "Filter, Transformation and Output" );
collector.Start( "Filter" );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::SizeType sourceSize = sourceImage->GetBufferedRegion().GetSize();
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::ConstPointer temp;
#ifdef useFastMemoryHungryGaussian
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 0 ); // 0 --> X direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( sourceImage );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 1 ); // 1 --> Y direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 2 ); // 2 --> Z direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
#else
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetUseImageSpacingOn();
filter->SetVariance( std::sqrt(gaussSigma) );
filter->SetInput( sourceImage );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
#endif
collector.Stop( "Filter" );
InterpolatorType::Pointer interpolator = InterpolatorType::New();
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInterpolator( interpolator );
IdentityTransformType::Pointer identPointer;
if (transform == NULL) {
identPointer = IdentityTransformType::New();
transform = identPointer;
}
resampler->SetTransform( transform );
FilterImageType::SpacingType destSpacing;
for(unsigned int i = 0; i < Dimension; ++i) {
destSpacing[i] = sourceImage->GetSpacing()[i] * float(sourceSize[i]) / float(destSize[i]);
}
resampler->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
resampler->SetSize( destSize );
resampler->SetOutputSpacing( destSpacing );
resampler->SetOutputOrigin( sourceImage->GetOrigin() );
resampler->SetDefaultPixelValue( 0 );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::Pointer result;
try { resampler->Update(); result = resampler->GetOutput(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
collector.Stop( "Filter, Transformation and Output" );
collector.Report();
std::cerr << "Filter, Transformation and Output end" << std::endl;
return result;
}
SeriesFilelist getSeriesFileNames(const std::string &inputDir, unsigned int minSlices) {
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( inputDir );
SeriesFilelist slist;
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while( seriesItr != seriesEnd ) {
FileNamesContainer fileNames = nameGenerator->GetFileNames(seriesItr->c_str());
if (fileNames.size() >= minSlices)
slist.push_back( fileNames );
seriesItr++;
}
return slist;
}
FilterImageType::Pointer getImage(const FileNamesContainer &filenames, DictionaryArray &dictArray) {
typedef itk::ImageSeriesReader< FilterImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
reader->SetFileNames(filenames);
reader->Update();
ReaderType::DictionaryArrayRawPointer dict;
dict = reader->GetMetaDataDictionaryArray();
for( ReaderType::DictionaryArrayType::const_iterator it = dict->begin(); it != dict->end(); ++it) {
dictArray.push_back( **it );
}
return reader->GetOutput();
}
void writeLabelImage( LabeledImageType::Pointer image, const std::string &fname) {
try {
ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
colormapper->SetInput( image );
colormapper->Update();
RGBImageType::ConstPointer colorImage = colormapper->GetOutput();
colormapper = NULL;
typedef itk::Image< RGBPixelType, 2 > OutputImage2DType;
typedef itk::ImageSeriesWriter< RGBImageType, OutputImage2DType > WriterType;
WriterType::Pointer writer = WriterType::New();
typedef itk::NumericSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetSeriesFormat( fname.c_str() );
nameGenerator->SetStartIndex( 1 );
nameGenerator->SetEndIndex( colorImage->GetBufferedRegion().GetSize()[2] );
writer->SetFileNames( nameGenerator->GetFileNames() );
writer->SetInput( colorImage );
writer->Update();
} catch( itk::ExceptionObject & exp ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << exp << std::endl;
}
}
}