tools/clitkGammaIndex.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================*/
  18 #include <vtkPoints.h>
  19 #include <vtkCellArray.h>
  20 #include <vtkPointData.h>
  21 #include <vtkImageData.h>
  22 #include <vtkMetaImageReader.h>
  23 #include <vtkMetaImageWriter.h>
  24 #include <vtkPNGReader.h>
  25 #include <vtkPolyData.h>
  26 #include <vtkCellLocator.h>
  27 #include <iostream>
  28 #include <cmath>
  29 #include <cassert>
  30 using std::endl;
  31 using std::cout;
  32
  33 #include "clitkGammaIndex_ggo.h"
  34
  35 #include <vvImage.h>
  36 #include <vvImageReader.h>
  37
  38 void saveImage(vtkImageData *image,const std::string &filename) {
  39     cout << "saving " << filename << endl;
  40     vtkImageWriter *writer = vtkMetaImageWriter::New();
  41     writer->SetFileName(filename.c_str());
  42     writer->SetInput(image);
  43     writer->Write();
  44     writer->Delete();
  45 }
  46
  47
  48 void insertTriangles(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[4]) {
  49     double p0[3]; points->GetPoint(ids[0],p0);
  50     double p1[3]; points->GetPoint(ids[1],p1);
  51     double p2[3]; points->GetPoint(ids[2],p2);
  52     double p3[3]; points->GetPoint(ids[3],p3);
  53     //cout << "----------------------------------" << endl;
  54     //cout << "p0=[" << p0[0] << "," << p0[1] << "," << p0[2] << "]" << endl;
  55     //cout << "p1=[" << p1[0] << "," << p1[1] << "," << p1[2] << "]" << endl;
  56     //cout << "p2=[" << p2[0] << "," << p2[1] << "," << p2[2] << "]" << endl;
  57     //cout << "p3=[" << p3[0] << "," << p3[1] << "," << p3[2] << "]" << endl;
  58
  59     double center[] = {0,0,0};
  60     for (int kk=0; kk<3; kk++) {
  61         center[kk] += p0[kk];
  62         center[kk] += p1[kk];
  63         center[kk] += p2[kk];
  64         center[kk] += p3[kk];
  65         center[kk] /= 4.;
  66     }
  67
  68     vtkIdType center_id = points->InsertNextPoint(center);
  69     //cout << "center=[" << center[0] << "," << center[1] << "," << center[2] << "]" << endl;
  70
  71     cells->InsertNextCell(3);
  72     cells->InsertCellPoint(ids[0]);
  73     cells->InsertCellPoint(ids[1]);
  74     cells->InsertCellPoint(center_id);
  75
  76     cells->InsertNextCell(3);
  77     cells->InsertCellPoint(ids[1]);
  78     cells->InsertCellPoint(ids[3]);
  79     cells->InsertCellPoint(center_id);
  80
  81     cells->InsertNextCell(3);
  82     cells->InsertCellPoint(ids[3]);
  83     cells->InsertCellPoint(ids[2]);
  84     cells->InsertCellPoint(center_id);
  85
  86     cells->InsertNextCell(3);
  87     cells->InsertCellPoint(ids[2]);
  88     cells->InsertCellPoint(ids[0]);
  89     cells->InsertCellPoint(center_id);
  90 }
  91
  92 double getMaximum(vtkImageData *image) {
  93     bool first = true;
  94     double maximum = 0;
  95
  96     for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
  97         double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
  98
  99         if (first) {
 100             maximum = value;
 101             first = false;
 102             continue;
 103         }
 104
 105         if (maximum<value) maximum = value;
 106     }
 107
 108     return maximum;
 109 }
 110
 111
 112 vtkPolyData *buildPlane(vtkImageData *image,double spatial_margin,double dose_margin) {
 113     vtkPoints *points = vtkPoints::New();
 114     for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
 115         double *point = image->GetPoint(kk);
 116         double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
 117         assert(value>=0);
 118         assert(point[2]==0);
 119         point[2] = value;
 120
 121         point[0] /= spatial_margin;
 122         point[1] /= spatial_margin;
 123         point[2] /= dose_margin;
 124
 125 #ifndef NDEBUG
 126         vtkIdType point_id = points->InsertNextPoint(point);
 127         assert(kk==point_id);
 128 #else
 129         points->InsertNextPoint(point);
 130 #endif
 131     }
 132
 133     vtkCellArray *cells = vtkCellArray::New();
 134     for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
 135         vtkCell *cell = image->GetCell(kk);
 136         assert(cell->GetNumberOfPoints()==4);
 137         insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
 138     }
 139
 140     vtkPolyData *data = vtkPolyData::New();
 141     data->SetPoints(points);
 142     data->SetPolys(cells);
 143     points->Delete();
 144     cells->Delete();
 145
 146     return data;
 147 }
 148
 149 int main(int argc,char * argv[])
 150 {
 151     args_info_clitkGammaIndex args_info;
 152
 153     if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
 154         exit(1);
 155
 156     if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
 157         std::cerr << "Specify either relative or absolute dose margin" << endl;
 158         exit(1);
 159     }
 160
 161     bool verbose = args_info.verbose_flag;
 162
 163     std::string reference_filename(args_info.reference_arg);
 164     std::string target_filename(args_info.target_arg);
 165     std::string gamma_filename(args_info.output_arg);
 166     double space_margin = args_info.spatial_margin_arg;
 167     double dose_rel_margin = args_info.relative_dose_margin_arg;
 168     double dose_margin = args_info.absolute_dose_margin_arg;
 169     bool use_dose_margin = args_info.absolute_dose_margin_given;
 170
 171     if (verbose) {
 172         cout << "reference_filename=" << reference_filename << endl;
 173         cout << "target_filename=" << target_filename << endl;
 174         cout << "gamma_filename=" << gamma_filename << endl;
 175         cout << "space_margin=" << space_margin << endl;
 176         if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
 177         else cout << "dose_rel_margin=" << dose_rel_margin << endl;
 178     }
 179
 180     // load reference
 181     vtkImageData* reference = NULL;
 182     {
 183         vvImageReader::Pointer reader = vvImageReader::New();
 184         reader->SetInputFilename(reference_filename);
 185         reader->Update();
 186         vvImage::Pointer vvimage = reader->GetOutput();
 187         reference = vvimage->GetFirstVTKImageData();
 188     }
 189
 190     // intensity normalisation
 191     if (!use_dose_margin) {
 192         dose_margin = getMaximum(reference)*dose_rel_margin;
 193         if (verbose) cout << "dose_margin=" << dose_margin << endl;
 194     }
 195
 196     // build surface
 197     vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
 198     reference->Delete();
 199
 200     vtkAbstractCellLocator *locator = vtkCellLocator::New();
 201     locator->SetDataSet(data);
 202     data->Delete();
 203     locator->CacheCellBoundsOn();
 204     locator->AutomaticOn();
 205     locator->BuildLocator();
 206
 207     // load target
 208     vtkImageData *target = NULL;
 209     {
 210         vvImageReader::Pointer reader = vvImageReader::New();
 211         reader->SetInputFilename(target_filename);
 212         reader->Update();
 213         vvImage::Pointer vvimage = reader->GetOutput();
 214         target = vvimage->GetFirstVTKImageData();
 215     }
 216
 217     // allocate output
 218     vtkImageData *output = vtkImageData::New();
 219     output->SetExtent(target->GetWholeExtent());
 220     output->SetOrigin(target->GetOrigin());
 221     output->SetSpacing(target->GetSpacing());
 222     output->SetScalarTypeToFloat();
 223     output->AllocateScalars();
 224
 225     // fill output
 226     unsigned long total = 0;
 227     unsigned long over_one = 0;
 228     for (int kk=0; kk<target->GetNumberOfPoints(); kk++) {
 229         double *point = target->GetPoint(kk);
 230         double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
 231         assert(value>=0);
 232         assert(point[2]==0);
 233         point[2] = value;
 234
 235         point[0] /= space_margin;
 236         point[1] /= space_margin;
 237         point[2] /= dose_margin;
 238
 239         double closest_point[3] = {0,0,0};
 240         vtkIdType cell_id = 0;
 241         int foo = 0;
 242         double squared_distance = 0;
 243
 244         locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
 245
 246         double distance = sqrt(squared_distance);
 247         output->GetPointData()->GetScalars()->SetTuple1(kk,distance);
 248
 249         if (value>1) over_one++;
 250         total++;
 251
 252     }
 253
 254     if (verbose) {
 255         cout << "total=" << total << endl;
 256         cout << "over_one=" << over_one << endl;
 257         cout << "ratio=" << static_cast<float>(over_one)/total << endl;
 258     }
 259
 260     locator->Delete();
 261     target->Delete();
 262
 263     saveImage(output,gamma_filename);
 264     output->Delete();
 265
 266     return 0;
 267 }
 268