-#include <iostream>
-using std::cout;
-using std::endl;
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
-#include <itkImageFileReader.h>
-#include <itkImageFileWriter.h>
-#include <itkMinimumMaximumImageCalculator.h>
-#include <itkShiftScaleImageFilter.h>
-#include <itkImageConstIteratorWithIndex.h>
-#include <itkChangeInformationImageFilter.h>
-#include <itkSignedDanielssonDistanceMapImageFilter.h>
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================*/
#include "clitkGammaIndex_ggo.h"
+#include "clitkIO.h"
+#include "clitkDD.h"
+
+#include <iostream>
+#include <cmath>
+#include <cassert>
+
+#include <vtkPoints.h>
+#include <vtkCellArray.h>
+#include <vtkPointData.h>
+#include <vtkImageData.h>
+#include <vtkMetaImageReader.h>
+#include <vtkMetaImageWriter.h>
+#include <vtkPNGReader.h>
+#include <vtkPolyData.h>
+#include <vtkCellLocator.h>
+
+#include <vvImage.h>
+#include <vvImageReader.h>
+#include <vvImageWriter.h>
+
+#include <itkImage.h>
+#include <itkImageRegionIterator.h>
+typedef itk::Image<double> OutputImageType;
+typedef itk::ImageRegionIterator<OutputImageType> OutputImageIterator;
+
+using std::endl;
+using std::cout;
-const unsigned int image_dim = 2;
-
-typedef itk::Image<float,image_dim> Image;
-typedef itk::ImageRegionIteratorWithIndex<Image> ImageIterator;
-typedef itk::ImageRegionConstIteratorWithIndex<Image> ImageConstIterator;
-typedef itk::ImageFileReader<Image> Reader;
-typedef itk::MinimumMaximumImageCalculator<Image> MinMaxer;
-typedef itk::ShiftScaleImageFilter<Image,Image> Normalizer;
-typedef itk::ChangeInformationImageFilter<Image> Scaler;
-
-typedef itk::Image<unsigned char,image_dim+1> ImageBin;
-typedef itk::Image<float,image_dim+1> ImageMap;
-typedef itk::SignedDanielssonDistanceMapImageFilter<ImageBin,ImageMap> Mapper;
-
-template <typename ImageType>
-void SaveImage(const ImageType *image, const std::string &filename) {
- typedef typename itk::ImageFileWriter<ImageType> Writer;
- typename Writer::Pointer writer = Writer::New();
- writer->SetFileName(filename);
- writer->SetInput(image);
- writer->Update();
+vtkImageData* loadImage(const std::string& filename)
+{
+ vvImageReader::Pointer reader = vvImageReader::New();
+ reader->SetInputFilename(filename);
+ reader->Update();
+ vvImage::Pointer vvimage = reader->GetOutput();
+ if (!vvimage) { cerr << "can't load " << filename << endl; return NULL; }
+
+ vtkImageData *image = vtkImageData::New();
+ image->DeepCopy(vvimage->GetFirstVTKImageData());
+ return image;
}
-ImageBin::Pointer AllocateImageBin(const Image *reference, const Image *target, unsigned int dose_size, float dose_max) {
- const Image::RegionType reference_region = reference->GetLargestPossibleRegion();
- const Image::RegionType target_region = target->GetLargestPossibleRegion();
- const Image::SpacingType reference_spacing = reference->GetSpacing();
- const Image::SpacingType target_spacing = target->GetSpacing();
- const Image::PointType reference_origin = reference->GetOrigin();
- const Image::PointType target_origin = target->GetOrigin();
-
- assert(reference_region == target_region);
- assert(reference_spacing == target_spacing);
- assert(reference_origin == target_origin);
-
- ImageBin::RegionType region;
- ImageBin::SpacingType spacing;
- ImageBin::PointType origin;
- for (unsigned long kk=0; kk<Image::GetImageDimension(); kk++) {
- region.SetSize(kk,reference_region.GetSize(kk));
- region.SetIndex(kk,reference_region.GetIndex(kk));
- spacing[kk] = reference_spacing[kk];
- origin[kk] = reference_origin[kk];
- }
- const unsigned long dose_dimension = Image::GetImageDimension();
- region.SetSize(dose_dimension,dose_size);
- region.SetIndex(dose_dimension,0);
- spacing[dose_dimension] = dose_max/(dose_size-1);
- origin[dose_dimension] = 0;
-
- ImageBin::Pointer map = ImageBin::New();
- map->SetRegions(region);
- map->SetSpacing(spacing);
- map->SetOrigin(origin);
- map->Allocate();
- map->FillBuffer(0);
-
- return map;
+void saveImage(OutputImageType* image,const std::string &filename) {
+ vvImage::Pointer vvimage = vvImage::New();
+ vvimage->AddItkImage(image);
+
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetOutputFileName(filename.c_str());
+ writer->SetInput(vvimage);
+ writer->Update();
}
-Image::Pointer AllocateImageGamma(const Image *target) {
- const Image::RegionType target_region = target->GetLargestPossibleRegion();
- const Image::SpacingType target_spacing = target->GetSpacing();
- const Image::PointType target_origin = target->GetOrigin();
- Image::Pointer gamma = Image::New();
- gamma->SetRegions(target_region);
- gamma->SetSpacing(target_spacing);
- gamma->SetOrigin(target_origin);
- gamma->Allocate();
- gamma->FillBuffer(0);
+void insertTriangles(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[4]) {
+ double p0[3]; points->GetPoint(ids[0],p0);
+ double p1[3]; points->GetPoint(ids[1],p1);
+ double p2[3]; points->GetPoint(ids[2],p2);
+ double p3[3]; points->GetPoint(ids[3],p3);
+ //cout << "----------------------------------" << endl;
+ //cout << "p0=[" << p0[0] << "," << p0[1] << "," << p0[2] << "]" << endl;
+ //cout << "p1=[" << p1[0] << "," << p1[1] << "," << p1[2] << "]" << endl;
+ //cout << "p2=[" << p2[0] << "," << p2[1] << "," << p2[2] << "]" << endl;
+ //cout << "p3=[" << p3[0] << "," << p3[1] << "," << p3[2] << "]" << endl;
+
+ double center[] = {0,0,0};
+ for (int kk=0; kk<3; kk++) {
+ center[kk] += p0[kk];
+ center[kk] += p1[kk];
+ center[kk] += p2[kk];
+ center[kk] += p3[kk];
+ center[kk] /= 4.;
+ }
+
+ vtkIdType center_id = points->InsertNextPoint(center);
+ //cout << "center=[" << center[0] << "," << center[1] << "," << center[2] << "]" << endl;
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(ids[1]);
+ cells->InsertCellPoint(center_id);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[1]);
+ cells->InsertCellPoint(ids[3]);
+ cells->InsertCellPoint(center_id);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[3]);
+ cells->InsertCellPoint(ids[2]);
+ cells->InsertCellPoint(center_id);
- return gamma;
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[2]);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(center_id);
}
-void FillImageBin(ImageBin *image_bin, const Image *reference) {
- ImageConstIterator iterator(reference,reference->GetLargestPossibleRegion());
- iterator.GoToBegin();
- while (!iterator.IsAtEnd()) {
- Image::PixelType value = iterator.Get();
- Image::PointType point;
- reference->TransformIndexToPhysicalPoint(iterator.GetIndex(),point);
-
- ImageBin::PointType point_bin;
- for (unsigned long kk=0; kk<Image::GetImageDimension(); kk++) {
- point_bin[kk] = point[kk];
- }
- point_bin[Image::GetImageDimension()] = value;
+void insertLine(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[2]) {
+ cells->InsertNextCell(2);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(ids[1]);
+}
- ImageBin::IndexType index_bin;
-#ifdef NDEBUG
- image_bin->TransformPhysicalPointToIndex(point_bin,index_bin);
-#else
- bool found = image_bin->TransformPhysicalPointToIndex(point_bin,index_bin);
- assert(found);
-#endif
+double getMaximum(vtkImageData *image) {
+ bool first = true;
+ double maximum = 0;
+
+ vtkPointData* point_data = image->GetPointData();
+ assert(point_data);
+ vtkDataArray* scalars = point_data->GetScalars();
+ assert(scalars);
+
+ for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
+ double value = scalars->GetTuple1(kk);
+
+ if (first) {
+ maximum = value;
+ first = false;
+ continue;
+ }
- while (index_bin[Image::GetImageDimension()] >=0 ) {
- image_bin->SetPixel(index_bin,255);
- index_bin[Image::GetImageDimension()]--;
+ if (maximum<value) maximum = value;
}
-
- ++iterator;
- }
+
+ return maximum;
}
-void FillImageGamma(Image *gamma, const Image *target, const ImageMap *distance) {
- ImageIterator gamma_iterator(gamma,gamma->GetLargestPossibleRegion());
- ImageConstIterator target_iterator(target,target->GetLargestPossibleRegion());
- gamma_iterator.GoToBegin();
- target_iterator.GoToBegin();
- while (!target_iterator.IsAtEnd()) {
- assert(!gamma_iterator.IsAtEnd());
-
- Image::PixelType value = target_iterator.Get();
- Image::PointType point;
- target->TransformIndexToPhysicalPoint(target_iterator.GetIndex(),point);
-
- ImageMap::PointType point_map;
- point_map.Fill(0);
- for (unsigned long kk=0; kk<Image::GetImageDimension(); kk++) {
- point_map[kk] = point[kk];
- }
- point_map[Image::GetImageDimension()] = value;
- ImageMap::IndexType index_map;
-#ifdef NDEBUG
- distance->TransformPhysicalPointToIndex(point_map,index_map);
+vtkPolyData *buildPlane(vtkImageData *image,double spatial_margin,double dose_margin) {
+ vtkPoints *points = vtkPoints::New();
+ for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
+ double *point = image->GetPoint(kk);
+ double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
+ assert(value>=0);
+ assert(point[2]==0);
+ point[2] = value;
+
+ point[0] /= spatial_margin;
+ point[1] /= spatial_margin;
+ point[2] /= dose_margin;
+
+#ifndef NDEBUG
+ vtkIdType point_id = points->InsertNextPoint(point);
+ assert(kk==point_id);
#else
- bool found = distance->TransformPhysicalPointToIndex(point_map,index_map);
- assert(found);
+ points->InsertNextPoint(point);
#endif
+ }
- gamma_iterator.Set(fabsf(distance->GetPixel(index_map)));
-
- ++gamma_iterator;
- ++target_iterator;
- }
-}
+ vtkCellArray *cells = vtkCellArray::New();
+ for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
+ vtkCell *cell = image->GetCell(kk);
-void TuneScaler(Scaler *scaler,float space_margin) {
- Scaler::InputImageType::PointType origin = scaler->GetInput()->GetOrigin();
- Scaler::InputImageType::SpacingType spacing = scaler->GetInput()->GetSpacing();
- for (unsigned int kk=0; kk<Scaler::InputImageType::GetImageDimension(); kk++) {
- origin[kk] /= space_margin;
- spacing[kk] /= space_margin;
- }
-
- scaler->SetOutputSpacing(spacing);
- scaler->SetOutputOrigin(origin);
- scaler->ChangeSpacingOn();
- scaler->ChangeOriginOn();
-}
+ if (cell->GetNumberOfPoints()==4) {
+ insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
-Image::PixelType GetImageMaximum(const Image *image) {
- MinMaxer::Pointer minmaxer = MinMaxer::New();
- minmaxer->SetImage(image);
- minmaxer->ComputeMaximum();
- return minmaxer->GetMaximum();
-}
-
-void ComputeGammaRatio(const Image *image) {
- ImageConstIterator iterator(image,image->GetLargestPossibleRegion());
- iterator.GoToBegin();
- unsigned long total = 0;
- unsigned long over_one = 0;
- while (!iterator.IsAtEnd()) {
- Image::PixelType value = iterator.Get();
+ if (cell->GetNumberOfPoints()==2) {
+ insertLine(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
- if (value>1) over_one++;
- total++;
+ assert(false);
+ }
- ++iterator;
- }
+ vtkPolyData *data = vtkPolyData::New();
+ data->SetPoints(points);
+ data->SetPolys(cells);
+ points->Delete();
+ cells->Delete();
- cout << "total=" << total << endl;
- cout << "over_one=" << over_one << endl;
- cout << "ratio=" << static_cast<float>(over_one)/total << endl;
+ return data;
}
int main(int argc,char * argv[])
{
- args_info_clitkGammaIndex args_info;
-
- if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
- exit(1);
-
- if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
- std::cerr << "Specify either relative or absolute dose margin" << endl;
- exit(1);
- }
-
- if (args_info.isodose_number_arg <= 0) {
- std::cerr << "Specify a valid isodose number (>0)" << endl;
- exit(1);
- }
-
- bool verbose = args_info.verbose_flag;
-
- std::string reference_filename(args_info.reference_arg);
- std::string target_filename(args_info.target_arg);
- std::string gamma_filename(args_info.output_arg);
- float space_margin = args_info.spatial_margin_arg;
- float dose_rel_margin = args_info.relative_dose_margin_arg;
- float dose_margin = args_info.absolute_dose_margin_arg;
- bool use_dose_margin = args_info.absolute_dose_margin_given;
- unsigned int dose_size = args_info.isodose_number_arg;
-
- if (verbose) {
- cout << "reference_filename=" << reference_filename << endl;
- cout << "target_filename=" << target_filename << endl;
- cout << "gamma_filename=" << gamma_filename << endl;
- cout << "dose_size=" << dose_size << endl;
- cout << "space_margin=" << space_margin << endl;
- if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
- else cout << "dose_rel_margin=" << dose_rel_margin << endl;
- }
-
- // load images
- Reader::Pointer reference_reader = Reader::New();
- Reader::Pointer target_reader = Reader::New();
- {
- reference_reader->SetFileName(reference_filename);
- target_reader->SetFileName(target_filename);
- reference_reader->Update();
- target_reader->Update();
- }
-
- // intensity normalisation
- if (!use_dose_margin) {
- MinMaxer::PixelType reference_max = GetImageMaximum(reference_reader->GetOutput());
- //MinMaxer::PixelType target_max = GetImageMaximum(target_reader->GetOutput());
-
- dose_margin = reference_max*dose_rel_margin;
-
- if (verbose) cout << "dose_margin=" << dose_margin << endl;
- }
-
- // scale intensity
- Normalizer::Pointer reference_normalizer = Normalizer::New();
- Normalizer::Pointer target_normalizer = Normalizer::New();
- {
- reference_normalizer->SetShift(0);
- reference_normalizer->SetScale(1/dose_margin);
- reference_normalizer->SetInput(reference_reader->GetOutput());
- reference_normalizer->Update();
-
- target_normalizer->SetShift(0);
- target_normalizer->SetScale(1/dose_margin);
- target_normalizer->SetInput(target_reader->GetOutput());
- target_normalizer->Update();
-
- //cout << "scale=" << reference_normalizer->GetScale() << "/" << target_normalizer->GetScale() << endl;
- //cout << "shift=" << reference_normalizer->GetShift() << "/" << target_normalizer->GetShift() << endl;
- }
-
- // normalize space coordinates
- Scaler::Pointer reference_scaler = Scaler::New();
- Scaler::Pointer target_scaler = Scaler::New();
- {
- reference_scaler->SetInput(reference_normalizer->GetOutput());
- TuneScaler(reference_scaler,space_margin);
- reference_scaler->Update();
-
- target_scaler->SetInput(target_normalizer->GetOutput());
- TuneScaler(target_scaler,space_margin);
- target_scaler->Update();
-
- //SaveImage(reference_scaler->GetOutput(),"norm_reference.mhd");
- //SaveImage(reference_scaler->GetOutput(),"norm_target.mhd");
- }
-
- // compute hyper surface plane
- float reference_dose_scaled_max = GetImageMaximum(reference_scaler->GetOutput());
- float target_dose_scaled_max = GetImageMaximum(target_scaler->GetOutput());
- float dose_scaled_max = reference_dose_scaled_max > target_dose_scaled_max ? reference_dose_scaled_max : target_dose_scaled_max;
- ImageBin::Pointer image_bin = AllocateImageBin(reference_scaler->GetOutput(),target_scaler->GetOutput(),dose_size,dose_scaled_max);
- FillImageBin(image_bin,reference_scaler->GetOutput());
- //SaveImage(image_bin.GetPointer(),"surface.mhd");
-
- // compute distance map
- Mapper::Pointer mapper = Mapper::New();
- mapper->InsideIsPositiveOn();
- mapper->UseImageSpacingOn();
- mapper->SetInput(image_bin);
- mapper->Update();
- //SaveImage(mapper->GetOutput(),"distance.mhd");
-
- // extract gamma index from distance map
- Image::Pointer image_gamma = AllocateImageGamma(target_normalizer->GetOutput());
- FillImageGamma(image_gamma,target_scaler->GetOutput(),mapper->GetOutput());
- SaveImage(image_gamma.GetPointer(),gamma_filename);
-
- if (verbose) ComputeGammaRatio(image_gamma);
-
- return 0;
-}
+ clitk::RegisterClitkFactories();
+
+ args_info_clitkGammaIndex args_info;
+
+ if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
+ exit(1);
+
+ if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
+ std::cerr << "Specify either relative or absolute dose margin" << endl;
+ exit(1);
+ }
+
+ bool verbose = args_info.verbose_flag;
+
+ std::string reference_filename(args_info.reference_arg);
+ std::string target_filename(args_info.target_arg);
+ std::string gamma_filename(args_info.output_arg);
+ double space_margin = args_info.spatial_margin_arg;
+ double dose_rel_margin = args_info.relative_dose_margin_arg;
+ double dose_margin = args_info.absolute_dose_margin_arg;
+ bool use_dose_margin = args_info.absolute_dose_margin_given;
+
+ if (verbose) {
+ cout << "reference_filename=" << reference_filename << endl;
+ cout << "target_filename=" << target_filename << endl;
+ cout << "gamma_filename=" << gamma_filename << endl;
+ cout << "space_margin=" << space_margin << endl;
+ if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
+ else cout << "dose_rel_margin=" << dose_rel_margin << endl;
+ }
+ // load reference
+ vtkImageData* reference = loadImage(reference_filename);
+ assert(reference);
+
+ // translate target with arguments values
+ // reference is translated instead of target so that the output space stay the same as target
+ {
+ double reference_origin[3];
+ reference->GetOrigin(reference_origin);
+ reference_origin[0] -= args_info.translation_x_arg;
+ reference_origin[1] -= args_info.translation_y_arg;
+ reference_origin[2] -= args_info.translation_z_arg;
+ reference->SetOrigin(reference_origin);
+ }
+
+ // intensity normalisation
+ if (!use_dose_margin) {
+ dose_margin = getMaximum(reference)*dose_rel_margin;
+ if (verbose) cout << "dose_margin=" << dose_margin << endl;
+ }
+
+ // build surface
+ vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
+ reference->Delete();
+
+ vtkAbstractCellLocator *locator = vtkCellLocator::New();
+ locator->SetDataSet(data);
+ DD("here");
+ // data->Delete();
+ locator->CacheCellBoundsOn();
+ locator->AutomaticOn();
+ DD("BuildLocator");
+ locator->BuildLocator();
+ DD("end BuildLocator");
+
+ // load target
+ vtkImageData* target = loadImage(target_filename);
+ assert(target);
+
+
+ // allocate output
+ OutputImageType::Pointer output = OutputImageType::New();
+ {
+ OutputImageType::SizeType::SizeValueType output_array_size[2];
+ output_array_size[0] = target->GetDimensions()[0];
+ output_array_size[1] = target->GetDimensions()[1];
+ OutputImageType::SizeType output_size;
+ output_size.SetSize(output_array_size);
+ output->SetRegions(OutputImageType::RegionType(output_size));
+ output->SetOrigin(target->GetOrigin());
+ output->SetSpacing(target->GetSpacing());
+ output->Allocate();
+ }
+
+ // fill output
+ unsigned long kk = 0;
+ unsigned long over_one = 0;
+ OutputImageIterator iter(output,output->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ DD("loop");
+ while (!iter.IsAtEnd()) {
+ double *point = target->GetPoint(kk);
+ double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
+ assert(value>=0);
+ assert(point[2]==0);
+ point[2] = value;
+
+ point[0] /= space_margin;
+ point[1] /= space_margin;
+ point[2] /= dose_margin;
+
+ double closest_point[3] = {0,0,0};
+ vtkIdType cell_id = 0;
+ int foo = 0;
+ double squared_distance = 0;
+
+ locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
+ double distance = sqrt(squared_distance);
+ iter.Set(distance);
+
+ if (distance>1) over_one++;
+ kk++;
+ ++iter;
+ }
+
+ if (verbose) {
+ cout << "total=" << kk << endl;
+ cout << "over_one=" << over_one << endl;
+ cout << "ratio=" << static_cast<float>(over_one)/kk << endl;
+ }
+
+ locator->Delete();
+ target->Delete();
+
+ saveImage(output,gamma_filename);
+
+ return 0;
+}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff