TEST(binary, Shanbhag){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
auto b = denoise->BinaryShanbhag(r);
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(b->GetOutput(), 1, "BinaryShanbhag");
if (VFLAG) viewer.Visualize();
}
int main(int argc, char* argv[]) {
ImageType::Pointer image = ImageType::New();
GenerateImage(image);
QuickView viewer;
viewer.AddImage(image.GetPointer());
viewer.Visualize();
return EXIT_SUCCESS;
}
TEST(fileIO, write){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
auto d1 = denoise->AnisotropicFilterCurvature(r, 10, 0.044, 2);
string outFile = "./testResults/M1045_11_20_denoised.tiff";
denoise->Write(d1->GetOutput(), outFile);
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(d1->GetOutput(), 1, "Denoised");
if (VFLAG) viewer.Visualize();
}
TEST(binary, threshold){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
unsigned int threshold = 90;
auto b = denoise->BinaryThreshold(r, threshold);
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(b->GetOutput(), 1, "BinaryThreshold");
if (VFLAG) viewer.Visualize();
string outFile = "./testResults/pectin_threshold.tiff";
denoise->Write(b->GetOutput(), outFile);
}
TEST(regionGrowth, connectedThreshold){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
auto d1 = denoise->AnisotropicFilterCurvature(r, 5, 0.044, 5);
auto rg = denoise->RegionGrowth(d1->GetOutput(), 0, 100);
itk::Index<2> s1 = {{309,185}};
rg->SetSeed(s1);
rg->Update();
auto rgo = rg->GetOutput();
// Visualize
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(d1->GetOutput(), 1, "Denoised");
viewer.AddImage(rgo, 1, "Rgrowth");
if (VFLAG) viewer.Visualize();
}
TEST(holeFilling, binary){
const string img{"./testResults/pectin_threshold.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
using HoleFilter = itk::BinaryFillholeImageFilter<Denoise::InputImageType>;
auto fillFilter = HoleFilter::New();
fillFilter->SetInput(r.GetPointer());
fillFilter->SetForegroundValue( itk::NumericTraits< Denoise::InputPixelType>::min());
fillFilter->Update();
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(fillFilter->GetOutput(), 1, "BinaryThreshold");
if (VFLAG) viewer.Visualize();
string outFile = "./testResults/pectin_threshold_hole_filled.tiff";
denoise->Write(fillFilter->GetOutput(), outFile);
}
TEST(morphological, opening){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
auto mo10 = denoise->MorphologicalOpening(r, 10);
auto mo5 = denoise->MorphologicalOpening(r, 5);
auto mo20 = denoise->MorphologicalOpening(r, 20);
auto mo3 = denoise->MorphologicalOpening(r, 3);
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage(mo10->GetOutput(), 1, "Morphological Opening, r=10");
viewer.AddImage(mo5->GetOutput(), 1, "Morphological Opening, r=5");
viewer.AddImage(mo20->GetOutput(), 1, "Morphological Opening, r=20");
viewer.AddImage(mo3->GetOutput(), 1, "Morphological Opening, r=3");
auto d1 = denoise->AnisotropicFilterCurvature(mo3->GetOutput(), 5, 0.044, 5);
if (VFLAG) viewer.Visualize();
}
TEST(anisotropic, InPectinSubSet){
const string img{"./fixtures/M1045_11_20.tiff"};
auto denoise = make_shared<Denoise>() ;
auto r = denoise->Read(img);
auto outSmart = denoise->AnisotropicFilterCurvature(r, 5, 0.044, 2);
// // Visualize
QuickView viewer;
viewer.AddImage(r.GetPointer(), 1, img);
viewer.AddImage( outSmart->GetOutput(), 1 , "Anisotropic Filter");
auto outSmart2 = denoise->AnisotropicFilterCurvature(outSmart->GetOutput(), 5, 0.044, 5);
viewer.AddImage( outSmart2->GetOutput(), 1 , "Anisotropic Filterx2");
auto outSmart3 = denoise->AnisotropicFilterCurvature(outSmart2->GetOutput(), 10, 0.044, 2);
viewer.AddImage( outSmart3->GetOutput(), 1 , "Anisotropic Filterx3");
if (VFLAG) viewer.Visualize();
}
int main(int, char **)
{
char inputFile[] = "C:/Users/bmi/Documents/GitHub/Lab3/HR_081507_L_1003.tif";
unsigned int maximum = 65535;
typedef itk::Image<unsigned int, 2> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
// register TIFF
itk::TIFFImageIOFactory::RegisterOneFactory();
ReaderType::Pointer reader = ReaderType::New();
//read file
reader->SetFileName(inputFile);
reader->Update();
/////////////////////////////////////////
/// binary threshold filter
/////////////////////////////////////////
/*
typedef itk::BinaryThresholdImageFilter <ImageType, ImageType> BinaryThresholdImageFilterType;
BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
unsigned int lowerBinaryThreshold = 42000;
unsigned int upperBinaryThreshold = maximum;
thresholdFilter->SetInput(reader->GetOutput());
thresholdFilter->SetLowerThreshold(lowerBinaryThreshold);
thresholdFilter->SetUpperThreshold(upperBinaryThreshold);
thresholdFilter->SetInsideValue(maximum);
thresholdFilter->SetOutsideValue(0);
// view the images
QuickView viewer;
viewer.AddImage(reader->GetOutput(),
true,
"Original Image");
viewer.AddImage(thresholdFilter->GetOutput(),
true,
"Binary Threshold Filter");
viewer.Visualize();
*/
/////////////////////////////////////////
/// Threshold Filter
/////////////////////////////////////////
/*
typedef itk::ThresholdImageFilter <ImageType> ThresholdImageFilterType;
ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
unsigned int lowerThreshold = 42000;
unsigned int upperThreshold = maximum;
thresholdFilter->SetInput(reader->GetOutput());
thresholdFilter->ThresholdOutside(lowerThreshold, upperThreshold);
thresholdFilter->SetOutsideValue(0);
// view the images
QuickView viewer;
viewer.AddImage(reader->GetOutput(),
true,
"Original Image");
viewer.AddImage(thresholdFilter->GetOutput(),
true,
"Threshold Filter");
viewer.Visualize();
*/
/////////////////////////////////////////
/// Intensity mapping
/////////////////////////////////////////
/*
typedef itk::RescaleIntensityImageFilter< ImageType, ImageType > RescaleFilterType;
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(reader->GetOutput());
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(3);
// view the images
QuickView viewer;
viewer.AddImage(reader->GetOutput(),
true,
"Original Image");
viewer.AddImage(rescaleFilter->GetOutput(),
true,
"Intensity Mapping Filter");
viewer.Visualize();
*/
/////////////////////////////////////////
/// Mean Filter
/////////////////////////////////////////
/*
typedef itk::MedianImageFilter<ImageType, ImageType > FilterType;
FilterType::Pointer medianFilter = FilterType::New();
FilterType::InputSizeType radius;
QuickView viewer;
viewer.AddImage(reader->GetOutput(),
true,
"Original Image");
// r = 1;
radius.Fill( 1.4142f );
medianFilter->SetRadius(radius);
medianFilter->SetInput( reader->GetOutput() );
medianFilter->Update();
viewer.AddImage(medianFilter->GetOutput(),
true,
"Median Filter: x=1, y=1, r=1.4142f");
// r = 2
radius.Fill( 2.9155f );
medianFilter->SetRadius(radius);
medianFilter->SetInput( reader->GetOutput() );
medianFilter->Update();
viewer.AddImage(medianFilter->GetOutput(),
true,
"Median Filter: x=2, y=2, r=2.9155f");
// r = 3;
radius.Fill( 4.3012f );
medianFilter->SetRadius(radius);
medianFilter->SetInput( reader->GetOutput() );
medianFilter->Update();
viewer.AddImage(medianFilter->GetOutput(),
true,
"Median Filter: x=3, y=3, r=4.3012f");
// r = 4
radius.Fill( 5.7009f );
medianFilter->SetRadius(radius);
medianFilter->SetInput( reader->GetOutput() );
medianFilter->Update();
viewer.AddImage(medianFilter->GetOutput(),
true,
"Median Filter: x=4, y=4, r=5.7009f");
//r = 5
radius.Fill( 7.1063f );
medianFilter->SetRadius(radius);
medianFilter->SetInput( reader->GetOutput() );
medianFilter->Update();
viewer.AddImage(medianFilter->GetOutput(),
true,
"Median Filter: x=5, y=5, r=7.1063f");
// view the images
viewer.Visualize();
*/
/////////////////////////////////////////
/// Smoothing Filter
/////////////////////////////////////////
typedef itk::DiscreteGaussianImageFilter< ImageType, ImageType > filterType;
double variance;
filterType::Pointer gaussianFilter = filterType::New();
gaussianFilter->SetInput( reader->GetOutput() );
QuickView viewer;
viewer.AddImage(reader->GetOutput(),
true,
"Original Image");
variance = 2.9;
gaussianFilter->SetMaximumKernelWidth(14);
gaussianFilter->SetVariance(variance);
gaussianFilter->Update();
viewer.AddImage(gaussianFilter->GetOutput(),
true,
"Gaussian Filter, variance=2.9, width=14");
variance = 7.825;
gaussianFilter->SetMaximumKernelWidth(16);
gaussianFilter->SetVariance(variance);
gaussianFilter->Update();
viewer.AddImage(gaussianFilter->GetOutput(),
true,
"Gaussian Filter, variance=7.825, width=16");
variance = 1.1;
gaussianFilter->SetMaximumKernelWidth(25);
gaussianFilter->SetVariance(variance);
gaussianFilter->Update();
viewer.AddImage(gaussianFilter->GetOutput(),
true,
"Gaussian Filter, variance=1.1, width=25");
variance = 22;
gaussianFilter->SetMaximumKernelWidth(60);
gaussianFilter->SetVariance(variance);
gaussianFilter->Update();
viewer.AddImage(gaussianFilter->GetOutput(),
true,
"Gaussian Filter, variance=22, width=60");
variance = 22;
gaussianFilter->SetMaximumKernelWidth(20);
gaussianFilter->SetVariance(variance);
gaussianFilter->Update();
viewer.AddImage(gaussianFilter->GetOutput(),
true,
"Gaussian Filter, variance=22, width=20");
// view the images
viewer.Visualize();
}
