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     /// Put the origin on a voxel to avoid small skips
 145     binary_image->SetOrigin(floor((bounds[0]-samp_origin[0])/spacing[0]-2)*spacing[0]+samp_origin[0],
 146                             floor((bounds[2]-samp_origin[1])/spacing[1]-2)*spacing[1]+samp_origin[1],
 147                             floor((bounds[4]-samp_origin[2])/spacing[2]-2)*spacing[2]+samp_origin[2]);
 148     double * origin=binary_image->GetOrigin();
 149     binary_image->SetExtent(0,ceil((bounds[1]-origin[0])/spacing[0]+4),
 150                             0,ceil((bounds[3]-origin[1])/spacing[1]+4),
 151                             0,ceil((bounds[5]-origin[2])/spacing[2])+4);
 152     binary_image->AllocateScalars();
 153     memset(binary_image->GetScalarPointer(),0,binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
 154
 155
 156     vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 157     //The following line is extremely important
 158     //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 159     sts->SetTolerance(0);
 160     sts->SetInformationInput(binary_image);
 161
 162     if (extrude) {
 163       vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 164       extrude->SetInput(mesh);
 165       ///We extrude in the -slice_spacing direction to respect the FOCAL convention
 166       extrude->SetVector(0, 0, -slice_spacing);
 167       sts->SetInput(extrude->GetOutput());
 168     } else
 169       sts->SetInput(mesh);
 170
 171     vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 172     stencil->SetStencil(sts->GetOutput());
 173     stencil->SetInput(binary_image);
 174     stencil->Update();
 175     this->AddMask(stencil->GetOutput());
 176     //vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 177     //w->SetInput(stencil->GetOutput());
 178     //w->SetFileName("binary.mhd");
 179     //w->Write();
 180   }
 181 }
 182
 183 void vvMesh::ComputeMeshes()
 184 {
 185   this->RemoveMeshes();
 186   for (std::vector<vtkImageData*>::iterator i=masks.begin(); i!=masks.end(); i++) {
 187     vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
 188     marching->SetInput(*i);
 189     marching->SetValue(0,0.5);
 190     marching->Update();
 191     this->AddMesh(marching->GetOutput());
 192   }
 193 }
 194
 195 void vvMesh::propagateContour(vvImage::Pointer vf)
 196 {
 197   assert(this->GetNumberOfMeshes() == 1);
 198   std::vector<vtkImageData*> sgrids=vf->GetVTKImages();
 199   vtkSmartPointer<vtkPolyData> reference_mesh = vtkSmartPointer<vtkPolyData>::New();
 200   reference_mesh->ShallowCopy(this->GetMesh(0));
 201   this->RemoveMeshes();
 202
 203   for (std::vector<vtkImageData*>::iterator i=sgrids.begin();
 204        i!=sgrids.end(); i++) {
 205     vtkPolyData* new_mesh=vtkPolyData::New();
 206     new_mesh->DeepCopy(reference_mesh);
 207     double Ox=vf->GetOrigin()[0];
 208     double Oy=vf->GetOrigin()[1];
 209     double Oz=vf->GetOrigin()[2];
 210     double Sx=vf->GetSpacing()[0];
 211     double Sy=vf->GetSpacing()[1];
 212     double Sz=vf->GetSpacing()[2];
 213     int *dims=vf->GetVTKImages()[0]->GetDimensions();
 214     assert((*i)->GetScalarType() == VTK_FLOAT); //vfs are assumed to be of float type
 215     assert((*i)->GetNumberOfScalarComponents() == 3);
 216     float * vector_data=reinterpret_cast<float*>((*i)->GetScalarPointer());
 217     for (int j=0; j<new_mesh->GetNumberOfPoints(); j++) {
 218       double* old=new_mesh->GetPoint(j);
 219       int ix=(old[0]-Ox)/Sx;
 220       int iy=(old[1]-Oy)/Sy;
 221       int iz=(old[2]-Oz)/Sz;
 222       float* vector=vector_data+(ix+iy*vf->GetSize()[0]+iz*vf->GetSize()[0]*vf->GetSize()[1])*3;
 223       if (ix>=0 && ix < dims[0]
 224           && iy>=0 && iy < dims[1]
 225           && iz>=0 && iz < dims[2])
 226         new_mesh->GetPoints()->SetPoint(j,old[0]+vector[0],old[1]+vector[1],old[2]+vector[2]);
 227     }
 228     this->AddMesh(new_mesh);
 229   }
 230   if (GetNumberOfMasks()) { //If the input mesh has a mask, use it to compute the warped meshes' masks
 231     vtkSmartPointer<vtkImageData> ref_mask = vtkSmartPointer<vtkImageData>::New();
 232     ref_mask->ShallowCopy(GetMask(0));
 233     this->ComputeMasks(ref_mask);
 234   }
 235 }