Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
#ifndef clitkBinarizeImageGenericFilter_cxx
#define clitkBinarizeImageGenericFilter_cxx
void BinarizeImageGenericFilter::SetArgsInfo(const args_info_type & a)
{
mArgsInfo=a;
- SetIOVerbose(mArgsInfo.verbose_flag);
- if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.verbose_given)
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_given && mArgsInfo.imagetypes_flag)
+ this->PrintAvailableImageTypes();
if (mArgsInfo.input_given) {
SetInputFilename(mArgsInfo.input_arg);
if (mArgsInfo.output_given) {
SetOutputFilename(mArgsInfo.output_arg);
}
+ if (mArgsInfo.percentage_given) {
+ SetPercentage(mArgsInfo.percentage_arg);
+ }
}
//--------------------------------------------------------------------
void
BinarizeImageGenericFilter::UpdateWithInputImageType()
{
+ if (mArgsInfo.percentage_given)
+ MaskOfIntegratedIntensity<InputImageType>();
+ else {
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
- // Reading input
- typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+ // Main filter
+ typedef typename InputImageType::PixelType PixelType;
+ typedef itk::Image<uchar, InputImageType::ImageDimension> OutputImageType;
- // Main filter
- typedef typename InputImageType::PixelType PixelType;
- typedef itk::Image<uchar, InputImageType::ImageDimension> OutputImageType;
-
- // Filter
- typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
- typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
- thresholdFilter->SetInput(input);
- thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
-
- if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
- if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
-
- /* Three modes :
- - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
- - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
- - both -> use FG and BG (real binary image)
- */
- if (mArgsInfo.mode_arg == std::string("both")) {
- thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
- thresholdFilter->Update();
- typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
- this->template SetNextOutput<OutputImageType>(outputImage);
- } else {
- typename InputImageType::Pointer outputImage;
- thresholdFilter->SetOutsideValue(0);
- if (mArgsInfo.mode_arg == std::string("BG")) {
- typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
- typename maskFilterType::Pointer maskFilter = maskFilterType::New();
- maskFilter->SetInput1(input);
- maskFilter->SetInput2(thresholdFilter->GetOutput());
- maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
- maskFilter->Update();
- outputImage = maskFilter->GetOutput();
+ // Filter
+ typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
+ typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
+ thresholdFilter->SetInput(input);
+ thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+ if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
+ if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
+
+ /* Three modes :
+ - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
+ - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
+ - both -> use FG and BG (real binary image)
+ */
+ if (mArgsInfo.mode_arg == std::string("both")) {
+ thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ thresholdFilter->Update();
+ typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(outputImage);
} else {
- typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
- typename maskFilterType::Pointer maskFilter = maskFilterType::New();
- maskFilter->SetInput1(input);
- maskFilter->SetInput2(thresholdFilter->GetOutput());
- maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
- maskFilter->Update();
- outputImage = maskFilter->GetOutput();
+ typename InputImageType::Pointer outputImage;
+ thresholdFilter->SetOutsideValue(0);
+ if (mArgsInfo.mode_arg == std::string("BG")) {
+ typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ } else {
+ typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ }
+ // Write/Save results
+ this->template SetNextOutput<InputImageType>(outputImage);
}
- // Write/Save results
- this->template SetNextOutput<InputImageType>(outputImage);
}
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+// https://stackoverflow.com/questions/1577475/c-sorting-and-keeping-track-of-indexes
+template <typename T>
+std::vector<size_t> sort_indexes(const std::vector<T> &v) {
+
+ // initialize original index locations
+ std::vector<size_t> idx(v.size());
+ std::vector<std::pair<T, size_t> > compVector(v.size());
+ for (size_t i = 0; i < v.size(); ++i) {
+ compVector[i].first = v[i];
+ compVector[i].second = i;
+ }
+
+ // sort indexes based on comparing values in v
+ std::sort(compVector.begin(), compVector.end(), comparator<T>);
+ for (size_t i = 0; i < v.size(); ++i) {
+ idx[i] = compVector[i].second;
+ }
+
+ return idx;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class InputImageType>
+void
+BinarizeImageGenericFilter::MaskOfIntegratedIntensity()
+{
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<unsigned char, InputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ typename MaskImageType::Pointer mask;
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(0);
+
+ // Get a vector of all values (will be easier to sort)
+ // And compute total sum of values
+ std::vector<double> values;
+ typedef itk::ImageRegionIterator<InputImageType> IteratorInputType;
+ IteratorInputType iter(input, input->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ double total = 0.0;
+ while (!iter.IsAtEnd()) {
+ values.push_back(iter.Get());
+ total += iter.Get();
+ ++iter;
+ }
+
+ // Sort (reverse)
+ std::vector<size_t> indices = sort_indexes(values);
+
+ // Get max index of pixel to reach xx percent
+ double current = 0.0;
+ double max = GetPercentage()/100.0*total;
+ int i=0;
+ int n = input->GetLargestPossibleRegion().GetNumberOfPixels();
+ std::vector<int> should_keep(values.size());;
+ std::fill(should_keep.begin(), should_keep.end(), 0);
+ while (current<max and i<n) { // loop by decreasing pixel values
+ current += values[indices[i]];
+ should_keep[indices[i]] = 1.0;
+ ++i;
+ }
+ int nb = i;
+
+ // Set mask values
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ itm.GoToBegin();
+ i = 0;
+ while (!iter.IsAtEnd()) {
+ if (should_keep[i]) itm.Set(1);
+ ++iter;
+ ++itm;
+ ++i;
+ }
+
+ // Verbose option
+ if (this->m_IOVerbose)
+ std::cout << "Sum of pixel values : " << total << std::endl
+ << "Percentage : " << GetPercentage() << "%" << std::endl
+ << "Number of pixels : " << nb << "/" << n << std::endl
+ << "Number of pixels : " << nb/n*100.0 << "%" << std::endl;
+
+ // Write/Save results
+ this->template SetNextOutput<MaskImageType>(mask);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <typename T>
+bool comparator ( const std::pair<T, size_t>& l, const std::pair<T, size_t>& r)
+ { return l.first > r.first; }
+//--------------------------------------------------------------------
+
}//end clitk
#endif //#define clitkBinarizeImageGenericFilter_cxx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff