static
void ApplyTransforms(const mxArray *In, mxArray *Out)
{
double *Input = mxGetPr(In);
double *Output = mxGetPr(Out);
size_t nPixels = GetNumberOfPixels(In);;
cmsDoTransform(hColorTransform, Input, Output, nPixels );
}
std::vector<cleaver::AbstractScalarField*>
NRRDTools::loadNRRDFiles(std::vector<std::string> files,
double sigma) {
std::vector<cleaver::AbstractScalarField*> fields;
size_t num = 0;
for (auto file : files) {
// read file using ITK
if (file.find(".nrrd") != std::string::npos) {
itk::NrrdImageIOFactory::RegisterOneFactory();
} else if (file.find(".mha") != std::string::npos) {
itk::MetaImageIOFactory::RegisterOneFactory();
}
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(file);
reader->Update();
//do some blurring
GaussianBlurType::Pointer blur = GaussianBlurType::New();
blur->SetInput(reader->GetOutput());
blur->SetVariance(sigma * sigma);
blur->Update();
ImageType::Pointer img = blur->GetOutput();
//convert the image to a cleaver "abstract field"
auto region = img->GetLargestPossibleRegion();
auto numPixel = region.GetNumberOfPixels();
float *data = new float[numPixel];
auto x = region.GetSize()[0], y = region.GetSize()[1], z = region.GetSize()[2];
fields.push_back(new cleaver::FloatField(data, x, y, z));
auto beg = file.find_last_of("/") + 1;
auto name = file.substr(beg, file.size() - beg);
fields[num]->setName(name);
itk::ImageRegionConstIterator<ImageType> imageIterator(img, region);
size_t pixel = 0;
while (!imageIterator.IsAtEnd()) {
// Get the value of the current pixel
float val = static_cast<float>(imageIterator.Get());
((cleaver::FloatField*)fields[num])->data()[pixel++] = val;
++imageIterator;
}
((cleaver::FloatField*)fields[num])->setScale(cleaver::vec3(1., 1., 1.));
num++;
}
return fields;
}
std::vector<cleaver::AbstractScalarField*>
NRRDTools::segmentationToIndicatorFunctions(std::string filename, double sigma) {
// read file using ITK
if (filename.find(".nrrd") != std::string::npos) {
itk::NrrdImageIOFactory::RegisterOneFactory();
} else if (filename.find(".mha") != std::string::npos) {
itk::MetaImageIOFactory::RegisterOneFactory();
}
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(filename);
reader->Update();
ImageType::Pointer image = reader->GetOutput();
//determine the number of labels in the segmentations
ImageCalculatorFilterType::Pointer imageCalculatorFilter
= ImageCalculatorFilterType::New();
imageCalculatorFilter->SetImage(reader->GetOutput());
imageCalculatorFilter->Compute();
auto maxLabel = static_cast<size_t>(imageCalculatorFilter->GetMaximum());
auto minLabel = static_cast<size_t>(imageCalculatorFilter->GetMinimum());
std::vector<cleaver::AbstractScalarField*> fields;
//extract images from each label for an indicator function
for (size_t i = minLabel, num = 0; i <= maxLabel; i++, num++) {
//pull out this label
ThreshType::Pointer thresh = ThreshType::New();
thresh->SetInput(image);
thresh->SetOutsideValue(0);
thresh->ThresholdOutside(static_cast<double>(i) - 0.001,
static_cast<double>(i) + 0.001);
thresh->Update();
//change the values to be from 0 to 1
MultiplyImageFilterType::Pointer multiplyImageFilter =
MultiplyImageFilterType::New();
multiplyImageFilter->SetInput(thresh->GetOutput());
multiplyImageFilter->SetConstant(1. / static_cast<double>(i));
multiplyImageFilter->Update();
//do some blurring
GaussianBlurType::Pointer blur = GaussianBlurType::New();
blur->SetInput(multiplyImageFilter->GetOutput());
blur->SetVariance(sigma * sigma);
blur->Update();
//find the average value between
ImageCalculatorFilterType::Pointer calc =
ImageCalculatorFilterType::New();
calc->SetImage(blur->GetOutput());
calc->Compute();
float mx = calc->GetMaximum();
float mn = calc->GetMinimum();
auto md = (mx + mn) / 2.f;
//create a distance map with that minimum value as the levelset
DMapType::Pointer dm = DMapType::New();
dm->SetInput(blur->GetOutput());
dm->SetInsideValue(md + 0.1f);
dm->SetOutsideValue(md -0.1f);
dm->Update();
//MultiplyImageFilterType::Pointer mult =
// MultiplyImageFilterType::New();
//mult->SetInput(blur->GetOutput());
//mult->SetConstant(-20. / (mx - mn));
//mult->Update();
/*SubtractImageFilterType::Pointer subtractFilter
= SubtractImageFilterType::New();
subtractFilter->SetInput1(mult->GetOutput());
subtractFilter->SetConstant2(1.);
subtractFilter->Update();*/
//convert the image to a cleaver "abstract field"
auto img = dm->GetOutput();
auto region = img->GetLargestPossibleRegion();
auto numPixel = region.GetNumberOfPixels();
float *data = new float[numPixel];
auto x = region.GetSize()[0], y = region.GetSize()[1], z = region.GetSize()[2];
fields.push_back(new cleaver::FloatField(data, x, y, z));
auto beg = filename.find_last_of("/") + 1;
auto name = filename.substr(beg, filename.size() - beg);
auto fin = name.find_last_of(".");
name = name.substr(0, fin);
std::stringstream ss;
ss << name << i;
fields[num]->setName(ss.str());
itk::ImageRegionConstIterator<ImageType> imageIterator(img, region);
size_t pixel = 0;
while (!imageIterator.IsAtEnd()) {
// Get the value of the current pixel
float val = static_cast<float>(imageIterator.Get());
((cleaver::FloatField*)fields[num])->data()[pixel++] = -val;
++imageIterator;
}
auto spacing = img->GetSpacing();
((cleaver::FloatField*)fields[num])->setScale(
cleaver::vec3(spacing[0], spacing[1], spacing[2]));
//NRRDTools::saveNRRDFile(fields[num], "a" + std::to_string(num));
}
return fields;
}
