int main(int argc,char ** argv){
typedef itk::Image<float,3> ImageType;
typedef itk::Image<float,2> SliceType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<SliceType> WriterType;
typedef itk::BoundedReciprocalImageFilter<ImageType,ImageType> BoundedReciprocalType;
BoundedReciprocalType::Pointer boundedReciprocal = BoundedReciprocalType::New();
typedef ttt::AdvectiveDiffusion2DIterationImageFilter<SliceType,SliceType> AdvectionDiffusion2DIterationType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->UpdateOutputInformation();
typedef itk::ExtractImageFilter<ImageType,SliceType> ExtractorType;
ExtractorType::Pointer extractor = ExtractorType::New();
ImageType::RegionType extractionRegion = reader->GetOutput()->GetLargestPossibleRegion();
extractionRegion.SetSize(2,0);
boundedReciprocal->SetInput(reader->GetOutput());
extractor->SetInput(boundedReciprocal->GetOutput());
extractor->SetExtractionRegion(extractionRegion);
extractor->SetDirectionCollapseToIdentity();
AdvectionDiffusion2DIterationType::Pointer advectionDiffusionIteration =AdvectionDiffusion2DIterationType::New();
advectionDiffusionIteration->SetInput(extractor->GetOutput());
advectionDiffusionIteration->SetNumberOfThreads(1.0);
WriterType::Pointer sliceWriter = WriterType::New();
sliceWriter->SetInput(extractor->GetOutput());
sliceWriter->SetFileName(argv[2]);
sliceWriter->Update();
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[3]);
writer->SetInput(advectionDiffusionIteration->GetOutput());
writer->Update();
}
void writeMesh(MeshType* mesh, const char* filename) {
typedef itk::MeshFileWriter<MeshType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(mesh);
writer->SetFileName(filename);
writer->Update();
}
void writeBinaryImage(BinaryImageType* image, const char* filename) {
typedef itk::ImageFileWriter<BinaryImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(image);
writer->SetFileName(filename);
writer->Update();
}
void saveFile(char* filename, ImageType* image)
{
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename);
writer->SetInput(image);
writer->Update();
}
void NRRDTools::saveNRRDFile(const cleaver::FloatField *field, const std::string &name) {
auto dims = field->dataBounds().size;
ImageType::Pointer img = ImageType::New();
itk::Index<3> start; start.Fill(0);
ImageType::SizeType size;
size[0] = static_cast<size_t>(dims[0]);
size[1] = static_cast<size_t>(dims[1]);
size[2] = static_cast<size_t>(dims[2]);
ImageType::RegionType region(start, size);
img->SetRegions(region);
img->Allocate();
img->FillBuffer(0);
for (size_t i = 0; i < dims[0]; i++) {
for (size_t j = 0; j < dims[1]; j++) {
for (size_t k = 0; k < dims[2]; k++) {
ImageType::IndexType pixelIndex;
pixelIndex[0] = i;
pixelIndex[1] = j;
pixelIndex[2] = k;
auto data = ((cleaver::FloatField*)field)->data();
img->SetPixel(pixelIndex, data[i + size[0] * j + size[0] * size[1] * k]);
}
}
}
WriterType::Pointer write = WriterType::New();
write->SetFileName(name + ((name.find_first_of(".nrrd") == std::string::npos) ? ".nrrd" : ""));
write->SetInput(img);
write->Update();
}
void LidarSegmentationWidget::on_actionSaveSegmentation_triggered()
{
// Ask the user for a filename to save the segment mask image to
QString fileName = QFileDialog::getSaveFileName(this,
"Save Segment Mask Image", ".", "PNG Files (*.png)");
if(fileName.isEmpty())
{
return;
}
// Write the file (object is white)
typedef itk::ImageFileWriter<Mask> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(fileName.toStdString());
writer->SetInput(this->GraphCut.GetSegmentMask());
writer->Update();
/*
// Write the inverted file (object is black)
Mask::Pointer inverted = Mask::New();
Helpers::InvertBinaryImage(this->GraphCut.GetSegmentMask(), inverted);
//typedef itk::ImageFileWriter<ImageAdaptorType> WriterType;
typedef itk::ImageFileWriter<Mask> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(fileName.toStdString());
writer->SetInput(inverted);
writer->Update();
*/
}
void InnerWidget::actionSave_Segmentation_triggered()
{
// Ask the user for a filename to save the segment mask image to
QString fileName = QFileDialog::getSaveFileName(this,
tr("Save Segment Mask Image"), "/home/doriad", tr("Image Files (*.png *.bmp)"));
/*
// Convert the image from a 1D vector image to an unsigned char image
typedef itk::CastImageFilter< GrayscaleImageType,
itk::Image<itk::CovariantVector<unsigned char, 1>, 2 > > CastFilterType;
CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(this->GraphCut->GetSegmentMask());
typedef itk::NthElementImageAdaptor< itk::Image<itk:: CovariantVector<unsigned char, 1>, 2 >,
unsigned char> ImageAdaptorType;
ImageAdaptorType::Pointer adaptor = ImageAdaptorType::New();
adaptor->SelectNthElement(0);
adaptor->SetImage(castFilter->GetOutput());
*/
// Write the file
//typedef itk::ImageFileWriter< ImageAdaptorType > WriterType;
typedef itk::ImageFileWriter<Mask> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(fileName.toStdString());
//writer->SetInput(adaptor);
writer->SetInput(this->GraphCut->GetSegmentMask());
writer->Update();
}
void AppITKImage::Save()
{
std::cout << "Save()" << std::endl;
#if USE_CHANNEL_WEIGHTING
std::cout << "Output weights: ";
for (int c = 0; c < LfnIc::Image::Pixel::NUM_CHANNELS; c++)
{
std::cout << m_channelWeights[c] << " ";
}
std::cout << std::endl;
LfnIc::Image::Pixel* pixelPtr = AppITKImage::GetData();
for (int i = 0, n = GetWidth() * GetHeight(); i < n; ++i, ++pixelPtr)
{
LfnIc::Image::Pixel& pixel = *pixelPtr;
for (int c = 0; c < LfnIc::Image::Pixel::NUM_CHANNELS; ++c)
{
pixel.channel[c] /= m_channelWeights[c];
}
}
#endif
// If the image is RGB and unsigned char, write it to the specified output file (likely png)
typedef itk::ImageFileWriter<AppImageITKType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(m_image);
if (LfnIc::Image::PixelInfo::IS_24_BIT_RGB)
{
writer->SetFileName(m_filePath);
}
else
{
// If the image is not 3 channel and unsigned char, change file extension to ".mhd" so it can be written
#if 0
std::stringstream ss;
ss << m_filePath << ".mhd";
writer->SetFileName(ss.str());
#endif
wxFileName filename(m_filePath);
filename.SetExt("mhd");
writer->SetFileName(filename.GetFullName().ToAscii());
std::cout << "Writing " << filename.GetFullName().ToAscii() << std::endl;
}
writer->Update();
}
int main(int argc, char *argv[])
{
// Verify arguments
if(argc < 6)
{
std::cerr << "Required: outputFilename sizeX sizeY components value" << std::endl;
return EXIT_FAILURE;
}
// Parse arguments
std::string outputFilename = argv[1];
std::stringstream ss;
ss << argv[2] << " " << argv[3] << " " << argv[4];
itk::Size<2> size = {{0,0}};
unsigned int components = 0;
float value = 0.0f;
ss >> size[0] >> size[1] >> components >> value;
// Output arguments
std::cout << "outputFilename " << outputFilename << std::endl;
std::cout << "size " << size << std::endl;
std::cout << "value " << value << std::endl;
ImageType::Pointer image = ImageType::New();
itk::Index<2> index = {{0,0}};
itk::ImageRegion<2> region(index, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(components);
image->Allocate();
typename itk::ImageRegionIterator<ImageType> imageIterator(image, image->GetLargestPossibleRegion());
ImageType::PixelType pixel;
pixel.SetSize(components);
pixel.Fill(value);
while(!imageIterator.IsAtEnd())
{
imageIterator.Set(pixel);
++imageIterator;
}
// Write the result
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFilename);
writer->SetInput(image);
writer->Update();
return EXIT_SUCCESS;
}
int main(int argc, char** argv) {
if(argc != 3){
std::cout << "Usage: Test2DImage inputFilename outputFilename";
return 1;
}
typedef signed int InputPixelType;
const unsigned int Dimension = 2;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, 2> RGBImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typedef itk::ImageFileWriter<RGBImageType> WriterType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType,
InputImageType> DiffusionFilterType;
typedef itk::GradientMagnitudeImageFilter<InputImageType, InputImageType>
GradientMagnitudeFilterType;
typedef itk::Functor::ScalarToRGBPixelFunctor<int> ColorMapFunctorType;
typedef itk::UnaryFunctorImageFilter<InputImageType,
RGBImageType, ColorMapFunctorType> ColorMapFilterType;
typedef itk::JPEGImageIO JImageIOType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
ImageIOType::Pointer GDCMImageIO = ImageIOType::New();
JImageIOType::Pointer JPEGImageIO = JImageIOType::New();
ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
reader->SetFileName(argv[1]);
reader->SetImageIO(GDCMImageIO);
try {
reader->Update();
}
catch (itk::ExceptionObject & e) {
std::cerr << "exception in file reader " << std::endl;
std::cerr << e << std::endl;
return 1;
}
DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
diffusion->SetNumberOfIterations(1);
diffusion->SetConductanceParameter(4);
diffusion->SetTimeStep(0.125);
GradientMagnitudeFilterType::Pointer gradient = GradientMagnitudeFilterType::New();
diffusion->SetInput(reader->GetOutput());
gradient->SetInput(diffusion->GetOutput());
gradient->Update();
MyWatershedSegmenter<InputImageType> watershed(gradient->GetOutput());
watershed.buildLowerCompleteImage();
watershed.buildLabeledImage();
colormapper->SetInput(watershed.returnFinalImage());
writer->SetInput(colormapper->GetOutput());
writer->UseInputMetaDataDictionaryOff();
writer->SetImageIO(JPEGImageIO);
writer->SetFileName(argv[2]);
writer->Update();
}
int main( int argc, char * argv[] )
{
if( argc < 7 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << std::endl;
std::cerr << " <InputImage> <OutputImage> <LowerThreshold>";
std::cerr << " <UpperThreshold> <OutsideValue> <InsideValue>"
<< std::endl;
return EXIT_FAILURE;
}
const unsigned int Dimension = 2;
typedef unsigned char PixelType;
const char * InputImage = argv[1];
const char * OutputImage = argv[2];
const PixelType LowerThreshold = static_cast<PixelType>(atoi( argv[3] ) );
const PixelType UpperThreshold = static_cast<PixelType>(atoi( argv[4] ) );
const PixelType OutsideValue = static_cast<PixelType>(atoi( argv[5] ) );
const PixelType InsideValue = static_cast<PixelType>(atoi( argv[6] ) );
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( InputImage );
typedef itk::BinaryThresholdImageFilter< ImageType, ImageType >
FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( reader->GetOutput() );
filter->SetLowerThreshold( LowerThreshold );
filter->SetUpperThreshold( UpperThreshold );
filter->SetOutsideValue( OutsideValue );
filter->SetInsideValue( InsideValue );
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( OutputImage );
writer->SetInput( filter->GetOutput() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & e )
{
std::cerr << "Error: " << e << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
void MriWatcherGUI::Combine()
{
QString m_filename = QFileDialog::getSaveFileName(
this,
tr("Save As"),
QDir::currentPath(),
tr("*.gipl *.hdr *.mha *.mhd") );
if( m_filename.isEmpty() )
{
g_combine->setDown(false);
return;
}
if( m_filename.lastIndexOf(".") == -1 )
{
m_filename += ".gipl";
}
int xc; int yc; int zc;
m_imagemanager.GetCrosshair(&xc, &yc, &zc);
ImageType::Pointer m_newimage =
CreateNewImage(m_imagesize[0], m_imagesize[1], m_numberofimages, m_imagespacing[0], m_imagespacing[1],
m_imagespacing[2]);
IteratorType m_itnewimage(m_newimage, m_newimage->GetLargestPossibleRegion() );
m_itnewimage.GoToBegin();
for( int z = 0; z < m_numberofimages; z++ )
{
ImageType::Pointer m_image = m_imageframelist[z]->g_imageframe->GetInputImage2();
IteratorType m_itimage(m_image, m_image->GetLargestPossibleRegion() );
m_itimage.GoToBegin();
for( unsigned int i = 0; i < zc * m_imagesize[0] * m_imagesize[1]; i++ )
{
++m_itimage;
}
for( unsigned int y = 0; y < m_imagesize[0]; y++ )
{
for( unsigned int x = 0; x < m_imagesize[1]; x++ )
{
m_itnewimage.Set(m_itimage.Get() );
++m_itimage;
++m_itnewimage;
}
}
}
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(m_filename.toLatin1().constData() );
writer->SetInput(m_newimage);
writer->Update();
g_combine->setDown(false);
}
int main(int argc, char* argv[])
{
if( argc < 2 )
{
std::cerr<<argv[0]<<" InputImage"<<std::endl;
return EXIT_FAILURE;
}
typedef RGBImageType InputImageType;
typedef RGBImageType2D OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
//typedef itk::ImageFileReader< UCharImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
std::cout<<argv[1]<<std::endl;
try
{
reader->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
InputImageType::Pointer in = reader->GetOutput();
Focus *f = new Focus( in );
f->SetRadius(10);
//std::vector<float> vars = f->FindVariance(1.93,4.57,300);
f->MakeVarianceImage();
//OutputImageType::Pointer p = f->MakeProjection();
OutputImageType::Pointer p = f->MakeProjectionColor();
delete f;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( "best.tif" );
writer->SetInput( p );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
std::cerr << "PRESS ENTER TO EXIT\n";
getchar();
}
int main (int argc, char *argv[])
{
// Verify arguments
if(argc != 3)
{
std::cerr << "Required arguments: InputFileName OutputFileName" << std::endl;
return EXIT_FAILURE;
}
// Parse arguments
std::string inputFileName = argv[1];
std::string outputFileName = argv[2];
// Output arguments
std::cout << "Input image: " << inputFileName << std::endl;
std::cout << "Output image: " << outputFileName << std::endl;
//typedef itk::Image<unsigned char, 2> ImageType;
typedef itk::RGBPixel<float> RGBFloatPixelType; // We must use float pixels so that the averaging operation does not overflow
typedef itk::Image<RGBFloatPixelType> RGBFloatImageType;
typedef itk::ImageFileReader<RGBFloatImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);
reader->Update();
SmallHoleFiller<RGBFloatImageType> smallHoleFiller;
smallHoleFiller.SetImage(reader->GetOutput());
RGBFloatImageType::PixelType green;
green.SetRed(0);
green.SetGreen(255);
green.SetBlue(0);
smallHoleFiller.SetHolePixel(green);
smallHoleFiller.GenerateMaskFromImage();
smallHoleFiller.Fill();
typedef itk::RGBPixel<unsigned char> RGBUCharPixelType;
typedef itk::Image<RGBUCharPixelType> RGBUCharImageType;
typedef itk::CastImageFilter<RGBFloatImageType, RGBUCharImageType> CastFilterType;
CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(smallHoleFiller.GetOutput());
castFilter->Update();
typedef itk::ImageFileWriter< RGBUCharImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFileName);
writer->SetInput(castFilter->GetOutput());
writer->Update();
return EXIT_SUCCESS;
}
// ------------------------------------------------------------------------
void DicomParser::writeSeries(const DicomSeries &series, const QString &outputFolder)
{
// create the series name
QString name = QString::fromStdString(series.description);
name.replace(" ","_");
name += "_" + QString::number(series.images.front().seriesNumber);
name += ".nrrd";
QDir path(outputFolder);
QString fullPath = path.absoluteFilePath(name);
std::vector<DicomImage> images = series.images;
std::sort(images.begin(), images.end());
// write and build the output images
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::Image<unsigned short, 4> OutputImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::JoinSeriesImageFilter<ImageType, OutputImageType> JoinerType;
JoinerType::Pointer joiner = JoinerType::New();
ImageType::Pointer orig;
for(unsigned int i = 0; i < images.size(); i++)
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(images[i].filename);
std::cout << images[i].filename << std::endl;
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
ImageType::Pointer im = reader->GetOutput();
if(i == 0) orig = im;
im->SetOrigin(orig->GetOrigin());
im->SetDirection(orig->GetDirection());
im->SetSpacing(orig->GetSpacing());
joiner->SetInput(i, reader->GetOutput());
}
std::cout << joiner->GetOutput()->GetDirection() << std::endl;
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(joiner->GetOutput());
writer->SetFileName(fullPath.toStdString());
writer->SetImageIO(itk::NrrdImageIO::New());
writer->Update();
}
int main(int argc, char* *argv)
{
GetPot cl(argc, argv);
if( cl.size() == 1 || cl.search(2, "--help", "-h") )
{
std::cout << "Not enough arguments" << std::endl;
return -1;
}
const string image_n = cl.follow("NoFile", 1, "-i");
typedef itk::Image<float, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(image_n.c_str());
reader-> Update();
ImageType::Pointer image = reader->GetOutput();
typedef itk::ImageRegionIterator<ImageType> ImageIterator;
ImageIterator it(image, image->GetLargestPossibleRegion());
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
if (it.Get() < -5 )
{
it.Set(1.0);
std::cout << it.GetIndex() << std::endl;
}
else if (it.Get() > 5 )
{
it.Set(1.0);
std::cout << it.GetIndex() << std::endl;
}
else
{
it.Set(0.0);
}
}
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("Trace_mask.nii.gz");
writer->SetInput(image);
writer->Update();
return 0;
}
ImageType::Pointer vesselnessFilter(ImageType::Pointer im, float typeImageFactor_, double alpha, double beta, double gamma, double sigmaMinimum, double sigmaMaximum, unsigned int numberOfSigmaSteps, double sigmaDistance)
{
typedef itk::ImageDuplicator< ImageType > DuplicatorTypeIm;
DuplicatorTypeIm::Pointer duplicator = DuplicatorTypeIm::New();
duplicator->SetInputImage(im);
duplicator->Update();
ImageType::Pointer clonedImage = duplicator->GetOutput();
typedef itk::SymmetricSecondRankTensor< double, 3 > HessianPixelType;
typedef itk::Image< HessianPixelType, 3 > HessianImageType;
typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType, ImageType > ObjectnessFilterType;
ObjectnessFilterType::Pointer objectnessFilter = ObjectnessFilterType::New();
objectnessFilter->SetBrightObject( 1-typeImageFactor_ );
objectnessFilter->SetScaleObjectnessMeasure( false );
objectnessFilter->SetAlpha( alpha );
objectnessFilter->SetBeta( beta );
objectnessFilter->SetGamma( gamma );
objectnessFilter->SetObjectDimension(1);
typedef itk::MultiScaleHessianBasedMeasureImageFilter< ImageType, HessianImageType, ImageType > MultiScaleEnhancementFilterType;
MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter =
MultiScaleEnhancementFilterType::New();
multiScaleEnhancementFilter->SetInput( clonedImage );
multiScaleEnhancementFilter->SetHessianToMeasureFilter( objectnessFilter );
multiScaleEnhancementFilter->SetSigmaStepMethodToLogarithmic();
multiScaleEnhancementFilter->SetSigmaMinimum( sigmaMinimum );
multiScaleEnhancementFilter->SetSigmaMaximum( sigmaMaximum );
multiScaleEnhancementFilter->SetNumberOfSigmaSteps( numberOfSigmaSteps );
multiScaleEnhancementFilter->Update();
ImageType::Pointer vesselnessImage = multiScaleEnhancementFilter->GetOutput();
WriterType::Pointer writerVesselNess = WriterType::New();
itk::NiftiImageIO::Pointer ioV = itk::NiftiImageIO::New();
writerVesselNess->SetImageIO(ioV);
writerVesselNess->SetInput( vesselnessImage );
writerVesselNess->SetFileName("imageVesselNessFilter.nii.gz");
try {
writerVesselNess->Update();
}
catch( itk::ExceptionObject & e )
{
cout << "Exception thrown ! " << endl;
cout << "An error ocurred during Writing 1" << endl;
cout << "Location = " << e.GetLocation() << endl;
cout << "Description = " << e.GetDescription() << endl;
}
return vesselnessImage;
}
int main(int argc, char *argv[])
{
if(argc < 3)
{
std::cerr << "Required: inputFilename outputFilename" << std::endl;
return EXIT_FAILURE;
}
std::string inputFilename = argv[1];
std::string outputFilename = argv[2];
std::cout << "inputFilename " << inputFilename << std::endl;
std::cout << "outputFilename " << outputFilename << std::endl;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFilename);
reader->Update();
typedef itk::DerivativeImageFilter<ImageType, ImageType> DerivativeImageFilterType;
DerivativeImageFilterType::Pointer xDerivativeFilter = DerivativeImageFilterType::New();
xDerivativeFilter->SetDirection(0);
xDerivativeFilter->SetOrder(1);
xDerivativeFilter->SetInput(reader->GetOutput());
xDerivativeFilter->Update();
DerivativeImageFilterType::Pointer yDerivativeFilter = DerivativeImageFilterType::New();
yDerivativeFilter->SetOrder(1);
yDerivativeFilter->SetDirection(1);
yDerivativeFilter->SetInput(reader->GetOutput());
yDerivativeFilter->Update();
typedef itk::ComposeImageFilter<ImageType, GradientImageType> ComposeImageFilterType;
ComposeImageFilterType::Pointer composeFilter = ComposeImageFilterType::New();
composeFilter->SetInput1(xDerivativeFilter->GetOutput());
composeFilter->SetInput2(yDerivativeFilter->GetOutput());
composeFilter->Update();
typedef itk::ImageFileWriter<GradientImageType> WriterType;
WriterType::Pointer xWriter = WriterType::New();
xWriter->SetFileName(outputFilename);
xWriter->SetInput(composeFilter->GetOutput());
xWriter->Update();
return EXIT_SUCCESS;
}
void write_snapshot_image(string fname)
{
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(fname.c_str());
writer->SetInput(g_snapshot_image);
try {
writer->Update();
give_wide_permissions(fname.c_str());
}
catch (itk::ExceptionObject &err) {
std::cout << "ExceptionObject caught !" << std::endl;
std::cout << err << std::endl;
assert(false);
}
}
void Cell::WriteImage(const std::string & filename, const itk::Image< double , 3 >::Pointer & image)
{
std::cout << "Writing " << filename << std::endl;
typedef itk::ImageFileWriter< itk::Image< double, 3 > > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(image); //image is from function parameters!
writer->SetFileName(filename);
try
{
writer->Update();
//ftk::TimeStampOverflowSafeUpdate( writer.GetPointer() );
}
catch (itk::ExceptionObject &err)
{
std::cerr << "writer Exception: " << filename << " " << err << std::endl;
std::cerr << writer << std::endl;
}
}
void ScaleSpaceExplorer::SavePlateness(){
QFileDialog dialog;
dialog.setAcceptMode(QFileDialog::AcceptSave);
dialog.setNameFilter("Image files (*.ome.tif)");
dialog.setFileMode(QFileDialog::AnyFile);
if(dialog.exec()){
QString fileName = dialog.selectedFiles().first();
typedef itk::ImageFileWriter<VertexnessImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
itk::SCIFIOImageIO::Pointer iodriver = itk::SCIFIOImageIO::New();
writer->SetImageIO(iodriver);
writer->SetFileName(fileName.toStdString());
writer->SetInput(m_PlatenessImages[m_CurrentPlateness]);
writer->Update();
}
}
void Histogram::save_as(const char * fname)
{
if(!histImage)
return;
typedef itk::Image< unsigned char, 3 > UcharImageType;
typedef itk::RescaleIntensityImageFilter< HistImageType, UcharImageType > RescaleFlUcType;
RescaleFlUcType::Pointer rescale = RescaleFlUcType::New();
rescale->SetOutputMaximum( 255 );
rescale->SetOutputMinimum( 0 );
rescale->SetInput( histImage );
rescale->Update();
typedef itk::ImageFileWriter< UcharImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( fname );
writer->SetInput( rescale->GetOutput() );
writer->Update();
}
void segmentation::on_filterButton_clicked()
{
typedef float InputPixelType;
typedef float OutputPixelType;
typedef itk::Image< InputPixelType, 3 > InputImageType;
typedef itk::Image< OutputPixelType, 3> OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::CurvatureAnisotropicDiffusionImageFilter<
InputImageType, OutputImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( inputFileName);
filter->SetInput( reader->GetOutput() );
const unsigned int numberOfIterations = 3;//5
const double timeStep = 0.0625; //timeStep=0.125(for 2D), 0.0625(for 3D)
const double conductance = 3;//3
filter->SetNumberOfIterations( numberOfIterations );
filter->SetTimeStep( timeStep );
filter->SetConductanceParameter( conductance );
filter->Update();//time-costing
typedef unsigned short WritePixelType;//unsigned char
typedef itk::Image< WritePixelType, 3 > WriteImageType;
typedef itk::RescaleIntensityImageFilter<
OutputImageType, WriteImageType > RescaleFilterType;
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 65535 );//255 for CNV, for PED
typedef itk::ImageFileWriter< WriteImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
filePrefix = filePrefix + "_filter.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
writer->SetFileName(outputFileName);
rescaler->SetInput( filter->GetOutput() );
writer->SetInput( rescaler->GetOutput() );
writer->Update();
//将结果图返回主窗口显示
emit returnOutputFileName(outputFileName);//发出信号
}
// ------------------------------------------------------------------------
void OpenCVValve::ConvertImage(const ImageType::Pointer &input, MatPtr &mat)
{
// cast the image to uchar
typedef itk::Image<unsigned char, 2> OutputImageType;
typedef itk::RescaleIntensityImageFilter<ImageType, OutputImageType> CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetOutputMaximum(255);
caster->SetOutputMinimum(0);
caster->SetInput(input);
caster->Update();
OutputImageType::Pointer output = caster->GetOutput();
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(itk::PNGImageIO::New());
writer->SetInput(output);
writer->SetFileName("test.png");
writer->Update();
ImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
unsigned int rows = size[1];
unsigned int cols = size[0];
mat = new MatType(rows,cols, CV_8UC1);
itk::ImageRegionConstIterator<OutputImageType> it(output, output->GetLargestPossibleRegion());
it.GoToBegin();
while(!it.IsAtEnd())
{
OutputImageType::IndexType index = it.GetIndex();
unsigned char val = it.Get();
mat->at<unsigned char>(cv::Point(index[0], index[1])) = val;
++it;
}
}
void LidarSegmentationWidget::on_action_Selections_SaveAsImage_triggered()
{
QString filename = QFileDialog::getSaveFileName(this,
"Save Image", ".", "PNG Files (*.png)");
if(filename.isEmpty())
{
return;
}
RGBImageType::Pointer selectionsImage = RGBImageType::New();
selectionsImage->SetRegions(this->ImageRegion);
selectionsImage->Allocate();
RGBPixelType whitePixel;
whitePixel.SetRed(255);
whitePixel.SetGreen(255);
whitePixel.SetBlue(255);
selectionsImage->FillBuffer(whitePixel);
RGBPixelType greenPixel;
greenPixel.SetRed(0);
greenPixel.SetGreen(255);
greenPixel.SetBlue(0);
ITKHelpers::SetPixels(selectionsImage.GetPointer(), this->Sources, greenPixel);
RGBPixelType redPixel;
redPixel.SetRed(255);
redPixel.SetGreen(0);
redPixel.SetBlue(0);
ITKHelpers::SetPixels(selectionsImage.GetPointer(), this->Sinks, redPixel);
typedef itk::ImageFileWriter< RGBImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename.toStdString());
writer->SetInput(selectionsImage);
writer->Update();
}
int main(int argc, char* argv[])
{
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->Update();
typedef itk::SLICSegmentation<ImageType, LabelImageType> SLICSegmentationType;
SLICSegmentationType::Pointer slicSegmentation = SLICSegmentationType::New();
slicSegmentation->SetNumberOfSuperPixels(200);
slicSegmentation->SetSpatialDistanceWeight(5.0);
slicSegmentation->SetInput(reader->GetOutput());
slicSegmentation->Update();
typedef itk::ImageFileWriter<LabelImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[2]);
writer->SetInput(slicSegmentation->GetOutput());
writer->Update();
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
if(argc < 3)
{
std::cerr << "Required: inputFilename outputFilename" << std::endl;
return EXIT_FAILURE;
}
std::string inputFilename = argv[1];
std::string outputFilename = argv[2];
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFilename.c_str());
reader->Update();
ImageType::Pointer output = ImageType::New();
output->SetNumberOfComponentsPerPixel(reader->GetOutput()->GetNumberOfComponentsPerPixel());
output->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
output->Allocate();
itk::ImageRegionIterator<ImageType> outputIterator(output, output->GetLargestPossibleRegion());
while(!outputIterator.IsAtEnd())
{
outputIterator.Set(reader->GetOutput()->GetPixel(outputIterator.GetIndex()));
++outputIterator;
}
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFilename);
writer->SetInput(output);
writer->Update();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[])
{
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->Update();
typedef itk::SuperPixelSegmentation<ImageType, LabelImageType> SuperPixelSegmentationType;
SuperPixelSegmentationType::Pointer superPixelSegmentation = SuperPixelSegmentationType::New();
superPixelSegmentation->SetSigma(.5);
superPixelSegmentation->SetK(500);
superPixelSegmentation->SetMinSize(50);
superPixelSegmentation->SetInput(reader->GetOutput());
superPixelSegmentation->Update();
typedef itk::ImageFileWriter<LabelImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[2]);
writer->SetInput(superPixelSegmentation->GetOutput());
writer->Update();
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
// Verify arguments
if(argc < 3)
{
std::cerr << "Required: inputFilename outputFilename" << std::endl;
return EXIT_FAILURE;
}
// Parse arguments
std::string inputFilename = argv[1];
std::string outputFilename = argv[2];
// Output arguments
std::cout << "inputFilename " << inputFilename << std::endl;
std::cout << "outputFilename " << outputFilename << std::endl;
// Read file
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFilename);
reader->Update();
typedef itk::ClampImageFilter< ImageType, ImageType > ClampFilterType;
ClampFilterType::Pointer clampFilter = ClampFilterType::New();
clampFilter->SetInput(reader->GetOutput());
clampFilter->Update();
// Write the result
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFilename);
writer->SetInput(clampFilter->GetOutput());
writer->Update();
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]) {
if (argc != 4) {
std::cout << "ERROR: Incorrrect number of arguments <Intensity_LR> <edgement_HR> <output>" << std::endl;
}
FFTWInit(""); //Just use the default in the home account
itk::TimeProbe tp;
tp.Start();
typedef itk::ImageFileReader<FloatImageType> ReaderType;
typedef itk::ImageFileWriter<FloatImageType> WriterType;
const std::string edgeFileName = argv[2];
ReaderType::Pointer edgeReader = ReaderType::New();
edgeReader->SetFileName(edgeFileName);
edgeReader->Update();
FloatImageType::Pointer highResEdgeImage = edgeReader->GetOutput();
const std::string lriFileName = argv[1];
ReaderType::Pointer intensityReader = ReaderType::New();
intensityReader->SetFileName(lriFileName);
intensityReader->Update();
FloatImageType::Pointer lriImage = intensityReader->GetOutput();
FloatImageType::Pointer X_lr = NormalizeDataComponent(lriImage);
lriImage=nullptr;
FloatImageType::Pointer SRImage = OpWeightedL2(X_lr, highResEdgeImage);
const std::string hriFileName = argv[3];
WriterType::Pointer hriWriter = WriterType::New();
hriWriter->SetInput(SRImage);
hriWriter->SetFileName(hriFileName);
hriWriter->Update();
tp.Stop();
std::cout << tp.GetTotal() << tp.GetUnit() << std::endl;
return EXIT_SUCCESS;
}