vv/vvMesh.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
  19 //std
  20 #include <sstream>
  21 #include <cassert>
  22 #include <vector>
  23
  24 // clitk
  25 #include "clitkCommon.h"
  26
  27 // vv
  28 #include "vvMesh.h"
  29
  30 // itk
  31 #include <itksys/SystemTools.hxx>
  32
  33 // vtk
  34 #include <vtkSmartPointer.h>
  35 #include <vtkFloatArray.h>
  36 #include <vtkPointData.h>
  37 #include <vtkPolyData.h>
  38 #include <vtkPolyDataReader.h>
  39 #include <vtkOBJReader.h>
  40 #include <vtkImageData.h>
  41 #include <vtkImageStencil.h>
  42 #include <vtkLinearExtrusionFilter.h>
  43 #include <vtkPolyDataToImageStencil.h>
  44 #include <vtkMarchingCubes.h>
  45 #include <vtkMetaImageWriter.h>
  46
  47 vvMesh::vvMesh() :
  48   r(1),g(0),b(0),
  49   slice_spacing(-1)
  50 {}
  51
  52 void vvMesh::AddMesh(vtkPolyData* p)
  53 {
  54   vtkPolyData * mesh=vtkPolyData::New();
  55   mesh->ShallowCopy(p);
  56   meshes.push_back(mesh);
  57 }
  58
  59 void vvMesh::ReadFromVTK(const char * filename)
  60 {
  61   std::string extension=itksys::SystemTools::GetFilenameLastExtension(std::string(filename));
  62   if (extension == ".vtk" || extension== ".VTK") {
  63     assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
  64     vtkSmartPointer<vtkPolyDataReader> r=vtkSmartPointer<vtkPolyDataReader>::New();
  65     r->SetFileName(filename);
  66     r->Update();
  67     assert(r->GetOutput());
  68     AddMesh(r->GetOutput());
  69   } else if (extension == ".obj" || extension== ".OBJ") {
  70     assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
  71     vtkSmartPointer<vtkOBJReader> r=vtkSmartPointer<vtkOBJReader>::New();
  72     r->SetFileName(filename);
  73     r->Update();
  74     assert(r->GetOutput());
  75     AddMesh(r->GetOutput());
  76   } else
  77     assert (false) ; //shouldn't happen
  78
  79   assert(GetNumberOfMeshes() != 0); ///We assume the object is empty
  80   structure_name=filename;
  81 }
  82
  83 void vvMesh::RemoveMeshes()
  84 {
  85   for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++)
  86     (*i)->Delete();
  87   meshes.erase(meshes.begin(),meshes.end());
  88 }
  89
  90 void vvMesh::AddMask(vtkImageData* im)
  91 {
  92   assert(im->GetScalarType() == VTK_UNSIGNED_CHAR);
  93   vtkImageData* image=vtkImageData::New();
  94   image->ShallowCopy(im);
  95   masks.push_back(image);
  96 }
  97
  98 void vvMesh::RemoveMasks()
  99 {
 100   for (std::vector<vtkImageData*>::const_iterator i=masks.begin(); i!=masks.end(); i++)
 101     (*i)->Delete();
 102   masks.erase(masks.begin(),masks.end());
 103 }
 104
 105 vvMesh::~vvMesh()
 106 {
 107   RemoveMeshes();
 108   RemoveMasks();
 109 }
 110
 111 void vvMesh::CopyInformation(vvMesh::Pointer input)
 112 {
 113   r=input->r;
 114   g=input->g;
 115   b=input->b;
 116   structure_name=input->structure_name;
 117   slice_spacing=input->slice_spacing;
 118 }
 119
 120 void vvMesh::Print() const
 121 {
 122   std::cout << this << " : " << structure_name << std::endl << "RGB: " << r << "," << g << "," << b << std::endl;
 123   for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++) {
 124     std::cout << (*i)->GetNumberOfPoints() << " points, " << (*i)->GetNumberOfCells() << " cells." << std::endl;
 125     DDV((*i)->GetBounds(),6);
 126   }
 127   std::cout << "-------------------------" << std::endl << std::endl;
 128 }
 129
 130 void vvMesh::ComputeMasks(vtkImageData* sample,bool extrude)
 131 {
 132   this->RemoveMasks();
 133   for (std::vector<vtkPolyData*>::iterator i=meshes.begin(); i!=meshes.end(); i++) {
 134     vtkPolyData* mesh=*i;
 135     double *bounds=mesh->GetBounds();
 136
 137     vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
 138     binary_image->SetScalarTypeToUnsignedChar();
 139     ///Use the smallest mask in which the mesh fits
 140     // Add two voxels on each side to make sure the mesh fits
 141     double * samp_origin=sample->GetOrigin();
 142     double * spacing=sample->GetSpacing();
 143     binary_image->SetSpacing(spacing);
 144
 145     /// Put the origin on a voxel to avoid small skips
 146     binary_image->SetOrigin(floor((bounds[0]-samp_origin[0])/spacing[0]-2)*spacing[0]+samp_origin[0],
 147                             floor((bounds[2]-samp_origin[1])/spacing[1]-2)*spacing[1]+samp_origin[1],
 148                             floor((bounds[4]-samp_origin[2])/spacing[2]-2)*spacing[2]+samp_origin[2]);
 149     double * origin=binary_image->GetOrigin();
 150     binary_image->SetExtent(0,ceil((bounds[1]-origin[0])/spacing[0]+4),
 151                             0,ceil((bounds[3]-origin[1])/spacing[1]+4),
 152                             0,ceil((bounds[5]-origin[2])/spacing[2])+4);
 153     binary_image->AllocateScalars();
 154     memset(binary_image->GetScalarPointer(),0,binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
 155
 156
 157     vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 158     //The following line is extremely important
 159     //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 160     sts->SetTolerance(0);
 161     sts->SetInformationInput(binary_image);
 162
 163     if (extrude) {
 164       vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 165       extrude->SetInput(mesh);
 166       ///We extrude in the -slice_spacing direction to respect the FOCAL convention
 167       extrude->SetVector(0, 0, -slice_spacing);
 168       sts->SetInput(extrude->GetOutput());
 169     } else
 170       sts->SetInput(mesh);
 171
 172     vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 173     stencil->SetStencil(sts->GetOutput());
 174     stencil->SetInput(binary_image);
 175     stencil->Update();
 176     this->AddMask(stencil->GetOutput());
 177
 178     /*
 179       vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 180       w->SetInput(stencil->GetOutput());
 181       w->SetFileName("binary.mhd");
 182       w->Write();
 183     */
 184   }
 185 }
 186
 187 void vvMesh::ComputeMeshes()
 188 {
 189   this->RemoveMeshes();
 190   for (std::vector<vtkImageData*>::iterator i=masks.begin(); i!=masks.end(); i++) {
 191     vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
 192     marching->SetInput(*i);
 193     marching->SetValue(0,0.5);
 194     marching->Update();
 195     this->AddMesh(marching->GetOutput());
 196   }
 197 }
 198
 199 void vvMesh::propagateContour(vvImage::Pointer vf)
 200 {
 201   assert(this->GetNumberOfMeshes() == 1);
 202   std::vector<vtkImageData*> sgrids=vf->GetVTKImages();
 203   vtkSmartPointer<vtkPolyData> reference_mesh = vtkSmartPointer<vtkPolyData>::New();
 204   reference_mesh->ShallowCopy(this->GetMesh(0));
 205   this->RemoveMeshes();
 206
 207   for (std::vector<vtkImageData*>::iterator i=sgrids.begin();
 208        i!=sgrids.end(); i++) {
 209     vtkPolyData* new_mesh=vtkPolyData::New();
 210     new_mesh->DeepCopy(reference_mesh);
 211     double Ox=vf->GetOrigin()[0];
 212     double Oy=vf->GetOrigin()[1];
 213     double Oz=vf->GetOrigin()[2];
 214     double Sx=vf->GetSpacing()[0];
 215     double Sy=vf->GetSpacing()[1];
 216     double Sz=vf->GetSpacing()[2];
 217     int *dims=vf->GetVTKImages()[0]->GetDimensions();
 218     assert((*i)->GetScalarType() == VTK_FLOAT); //vfs are assumed to be of float type
 219     assert((*i)->GetNumberOfScalarComponents() == 3);
 220     float * vector_data=reinterpret_cast<float*>((*i)->GetScalarPointer());
 221     for (int j=0; j<new_mesh->GetNumberOfPoints(); j++) {
 222       double* old=new_mesh->GetPoint(j);
 223       int ix=(old[0]-Ox)/Sx;
 224       int iy=(old[1]-Oy)/Sy;
 225       int iz=(old[2]-Oz)/Sz;
 226       float* vector=vector_data+(ix+iy*vf->GetSize()[0]+iz*vf->GetSize()[0]*vf->GetSize()[1])*3;
 227       if (ix>=0 && ix < dims[0]
 228           && iy>=0 && iy < dims[1]
 229           && iz>=0 && iz < dims[2])
 230         new_mesh->GetPoints()->SetPoint(j,old[0]+vector[0],old[1]+vector[1],old[2]+vector[2]);
 231     }
 232     this->AddMesh(new_mesh);
 233   }
 234   if (GetNumberOfMasks()) { //If the input mesh has a mask, use it to compute the warped meshes' masks
 235     vtkSmartPointer<vtkImageData> ref_mask = vtkSmartPointer<vtkImageData>::New();
 236     ref_mask->ShallowCopy(GetMask(0));
 237     this->ComputeMasks(ref_mask);
 238   }
 239 }