- 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 <vtkPNGReader.h>
#include <vtkPolyData.h>
#include <vtkCellLocator.h>
-#include <iostream>
-#include <cmath>
-#include <cassert>
-using std::endl;
-using std::cout;
-#include "clitkGammaIndex_ggo.h"
+#include <vvImage.h>
+#include <vvImageReader.h>
+#include <vvImageWriter.h>
-vtkImageData *loadImage(const std::string &filename) {
- vtkImageReader2 *reader = vtkMetaImageReader::New();
- //vtkImageReader2 *reader = vtkPNGReader::New();
- reader->SetFileName(filename.c_str());
- reader->Update();
+#include <itkImage.h>
+#include <itkImageRegionIterator.h>
+typedef itk::Image<double> OutputImageType;
+typedef itk::ImageRegionIterator<OutputImageType> OutputImageIterator;
- vtkImageData *image = reader->GetOutput();
- image->Register(NULL);
- reader->Delete();
+using std::endl;
+using std::cout;
- return image;
+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;
}
-void saveImage(vtkImageData *image,const std::string &filename) {
- cout << "saving " << filename << endl;
- vtkImageWriter *writer = vtkMetaImageWriter::New();
- writer->SetFileName(filename.c_str());
- writer->SetInput(image);
- writer->Write();
- writer->Delete();
+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();
}
+
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);
-
- cells->InsertNextCell(3);
- cells->InsertCellPoint(ids[2]);
- cells->InsertCellPoint(ids[0]);
- cells->InsertCellPoint(center_id);
+ 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);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[2]);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(center_id);
+}
+
+void insertLine(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[2]) {
+ cells->InsertNextCell(2);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(ids[1]);
}
double getMaximum(vtkImageData *image) {
- bool first = true;
- double maximum = 0;
+ bool first = true;
+ double maximum = 0;
- for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
- double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
+ vtkPointData* point_data = image->GetPointData();
+ assert(point_data);
+ vtkDataArray* scalars = point_data->GetScalars();
+ assert(scalars);
- if (first) {
- maximum = value;
- first = false;
- continue;
- }
+ for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
+ double value = scalars->GetTuple1(kk);
- if (maximum<value) maximum = value;
- }
+ if (first) {
+ maximum = value;
+ first = false;
+ continue;
+ }
- return maximum;
+ if (maximum<value) maximum = value;
+ }
+
+ return maximum;
}
+
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;
+ 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);
+ vtkIdType point_id = points->InsertNextPoint(point);
+ assert(kk==point_id);
#else
- points->InsertNextPoint(point);
+ points->InsertNextPoint(point);
#endif
- }
-
- vtkCellArray *cells = vtkCellArray::New();
- for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
- vtkCell *cell = image->GetCell(kk);
- assert(cell->GetNumberOfPoints()==4);
- insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
- }
-
- vtkPolyData *data = vtkPolyData::New();
- data->SetPoints(points);
- data->SetPolys(cells);
- points->Delete();
- cells->Delete();
-
- return data;
-}
+ }
-void assert2D(vtkImageData *image) {
-#ifndef NDEBUG
- int *extent = image->GetWholeExtent();
- assert(extent[4]==0);
- assert(extent[5]==0);
-#endif
+ vtkCellArray *cells = vtkCellArray::New();
+ for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
+ vtkCell *cell = image->GetCell(kk);
+
+ if (cell->GetNumberOfPoints()==4) {
+ insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
+
+ if (cell->GetNumberOfPoints()==2) {
+ insertLine(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
+
+ assert(false);
+ }
+
+ vtkPolyData *data = vtkPolyData::New();
+ data->SetPoints(points);
+ data->SetPolys(cells);
+ points->Delete();
+ cells->Delete();
+
+ 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);
- }
-
- 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);
- assert2D(reference);
-
- // 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);
- data->Delete();
- locator->CacheCellBoundsOn();
- locator->AutomaticOn();
- locator->BuildLocator();
-
- // load target
- vtkImageData *target = loadImage(target_filename);
- assert2D(target);
-
- // allocate output
- vtkImageData *output = vtkImageData::New();
- output->SetExtent(target->GetWholeExtent());
- output->SetOrigin(target->GetOrigin());
- output->SetSpacing(target->GetSpacing());
- output->SetScalarTypeToFloat();
- output->AllocateScalars();
-
- // fill output
- unsigned long total = 0;
- unsigned long over_one = 0;
- for (int kk=0; kk<target->GetNumberOfPoints(); kk++) {
- 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);
- output->GetPointData()->GetScalars()->SetTuple1(kk,distance);
-
- if (value>1) over_one++;
- total++;
-
- }
-
- if (verbose) {
- cout << "total=" << total << endl;
- cout << "over_one=" << over_one << endl;
- cout << "ratio=" << static_cast<float>(over_one)/total << endl;
- }
-
- locator->Delete();
- target->Delete();
-
- saveImage(output,gamma_filename);
- output->Delete();
-
- 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