vv/vvMesh.cxx

   1 /*=========================================================================
   2
   3  Program:   vv
   4  Language:  C++
   5  Author :   Joel Schaerer (joel.schaerer@insa-lyon.fr)
   6
   7 Copyright (C) 2008
   8 Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
   9 CREATIS-LRMN http://www.creatis.insa-lyon.fr
  10
  11 This program is free software: you can redistribute it and/or modify
  12 it under the terms of the GNU General Public License as published by
  13 the Free Software Foundation, version 3 of the License.
  14
  15 This program is distributed in the hope that it will be useful,
  16 but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 GNU General Public License for more details.
  19
  20 You should have received a copy of the GNU General Public License
  21 along with this program.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 =========================================================================*/
  24
  25 #include <sstream>
  26 #include <cassert>
  27 #include <vector>
  28 #include <vtkSmartPointer.h>
  29 #include <vtkFloatArray.h>
  30 #include <vtkPointData.h>
  31 #include <vtkPolyData.h>
  32 #include <vtkPolyDataReader.h>
  33 #include <vtkImageData.h>
  34 #include "clitkCommon.h"
  35 #include "vvMesh.h"
  36 #include <vtkImageStencil.h>
  37 #include <vtkLinearExtrusionFilter.h>
  38 #include <vtkPolyDataToImageStencil.h>
  39 #include <vtkMarchingCubes.h>
  40
  41 #include <vtkMetaImageWriter.h>
  42
  43 vvMesh::vvMesh() :
  44     r(1),g(0),b(0),
  45     slice_spacing(-1)
  46 {}
  47
  48 void vvMesh::AddMesh(vtkPolyData* p)
  49 {
  50     vtkPolyData * mesh=vtkPolyData::New();
  51     mesh->ShallowCopy(p);
  52     meshes.push_back(mesh);
  53 }
  54
  55 void vvMesh::ReadFromVTK(const char * filename)
  56 {
  57     assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
  58     vtkSmartPointer<vtkPolyDataReader> r=vtkSmartPointer<vtkPolyDataReader>::New();
  59     r->SetFileName(filename);
  60     r->Update();
  61     AddMesh(r->GetOutput());
  62     structure_name=filename;
  63 }
  64
  65 void vvMesh::RemoveMeshes()
  66 {
  67     for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin();i!=meshes.end();i++)
  68         (*i)->Delete();
  69     meshes.erase(meshes.begin(),meshes.end());
  70 }
  71
  72 void vvMesh::AddMask(vtkImageData* im)
  73 {
  74     assert(im->GetScalarType() == VTK_UNSIGNED_CHAR);
  75     vtkImageData* image=vtkImageData::New();
  76     image->ShallowCopy(im);
  77     masks.push_back(image);
  78 }
  79
  80 void vvMesh::RemoveMasks()
  81 {
  82     for (std::vector<vtkImageData*>::const_iterator i=masks.begin();i!=masks.end();i++)
  83         (*i)->Delete();
  84     masks.erase(masks.begin(),masks.end());
  85 }
  86
  87 vvMesh::~vvMesh()
  88 {
  89     RemoveMeshes();
  90     RemoveMasks();
  91 }
  92
  93 void vvMesh::CopyInformation(vvMesh::Pointer input)
  94 {
  95     r=input->r;
  96     g=input->g;
  97     b=input->b;
  98     structure_name=input->structure_name;
  99     slice_spacing=input->slice_spacing;
 100 }
 101
 102 void vvMesh::Print() const
 103 {
 104     std::cout << this << " : " << structure_name << std::endl << "RGB: " << r << "," << g << "," << b << std::endl;
 105     for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin();i!=meshes.end();i++)
 106     {
 107         std::cout << (*i)->GetNumberOfPoints() << " points, " << (*i)->GetNumberOfCells() << " cells." << std::endl;
 108         DDV((*i)->GetBounds(),6);
 109     }
 110     std::cout << "-------------------------" << std::endl << std::endl;
 111 }
 112
 113 void vvMesh::ComputeMasks(vtkImageData* sample,bool extrude)
 114 {
 115     this->RemoveMasks();
 116     for (std::vector<vtkPolyData*>::iterator i=meshes.begin();i!=meshes.end();i++)
 117     {
 118         vtkPolyData* mesh=*i;
 119         double *bounds=mesh->GetBounds();
 120
 121         vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
 122         binary_image->SetScalarTypeToUnsignedChar();
 123         ///Use the smallest mask in which the mesh fits
 124         // Add two voxels on each side to make sure the mesh fits
 125         double * samp_origin=sample->GetOrigin();
 126         double * spacing=sample->GetSpacing();
 127         binary_image->SetSpacing(spacing);
 128         /// Put the origin on a voxel to avoid small skips
 129         binary_image->SetOrigin(floor((bounds[0]-samp_origin[0])/spacing[0]-2)*spacing[0]+samp_origin[0],
 130                 floor((bounds[2]-samp_origin[1])/spacing[1]-2)*spacing[1]+samp_origin[1],
 131                 floor((bounds[4]-samp_origin[2])/spacing[2]-2)*spacing[2]+samp_origin[2]);
 132         double * origin=binary_image->GetOrigin();
 133         binary_image->SetExtent(0,ceil((bounds[1]-origin[0])/spacing[0]+4),
 134             0,ceil((bounds[3]-origin[1])/spacing[1]+4),
 135             0,ceil((bounds[5]-origin[2])/spacing[2])+4);
 136         binary_image->AllocateScalars();
 137         memset(binary_image->GetScalarPointer(),0,binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
 138
 139
 140         vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 141         //The following line is extremely important
 142         //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 143         sts->SetTolerance(0);
 144         sts->SetInformationInput(binary_image);
 145
 146         if (extrude)
 147         {
 148             vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 149             extrude->SetInput(mesh);
 150             ///We extrude in the -slice_spacing direction to respect the FOCAL convention
 151             extrude->SetVector(0, 0, -slice_spacing);
 152             sts->SetInput(extrude->GetOutput());
 153         }
 154         else
 155             sts->SetInput(mesh);
 156
 157         vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 158         stencil->SetStencil(sts->GetOutput());
 159         stencil->SetInput(binary_image);
 160         stencil->Update();
 161         this->AddMask(stencil->GetOutput());
 162         //vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 163         //w->SetInput(stencil->GetOutput());
 164         //w->SetFileName("binary.mhd");
 165         //w->Write();
 166     }
 167 }
 168
 169 void vvMesh::ComputeMeshes()
 170 {
 171     this->RemoveMeshes();
 172     for (std::vector<vtkImageData*>::iterator i=masks.begin();i!=masks.end();i++)
 173     {
 174         vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
 175         marching->SetInput(*i);
 176         marching->SetValue(0,0.5);
 177         marching->Update();
 178         this->AddMesh(marching->GetOutput());
 179     }
 180 }
 181
 182 void vvMesh::propagateContour(vvImage::Pointer vf)
 183 {
 184     assert(this->GetNumberOfMeshes() == 1);
 185     std::vector<vtkImageData*> sgrids=vf->GetVTKImages();
 186     vtkSmartPointer<vtkPolyData> reference_mesh = vtkSmartPointer<vtkPolyData>::New();
 187     reference_mesh->ShallowCopy(this->GetMesh(0));
 188     this->RemoveMeshes();
 189
 190     for (std::vector<vtkImageData*>::iterator i=sgrids.begin();
 191             i!=sgrids.end();i++)
 192     {
 193         vtkPolyData* new_mesh=vtkPolyData::New();
 194         new_mesh->DeepCopy(reference_mesh);
 195         double Ox=vf->GetOrigin()[0];
 196         double Oy=vf->GetOrigin()[1];
 197         double Oz=vf->GetOrigin()[2];
 198         double Sx=vf->GetSpacing()[0];
 199         double Sy=vf->GetSpacing()[1];
 200         double Sz=vf->GetSpacing()[2];
 201         int *dims=vf->GetVTKImages()[0]->GetDimensions();
 202         assert((*i)->GetScalarType() == VTK_FLOAT); //vfs are assumed to be of float type
 203         assert((*i)->GetNumberOfScalarComponents() == 3);
 204         float * vector_data=reinterpret_cast<float*>((*i)->GetScalarPointer());
 205         for (int j=0;j<new_mesh->GetNumberOfPoints();j++)
 206         {
 207             double* old=new_mesh->GetPoint(j);
 208             int ix=(old[0]-Ox)/Sx;
 209             int iy=(old[1]-Oy)/Sy;
 210             int iz=(old[2]-Oz)/Sz;
 211             float* vector=vector_data+(ix+iy*vf->GetSize()[0]+iz*vf->GetSize()[0]*vf->GetSize()[1])*3;
 212             if (ix>=0 && ix < dims[0]
 213                     && iy>=0 && iy < dims[1]
 214                     && iz>=0 && iz < dims[2])
 215                 new_mesh->GetPoints()->SetPoint(j,old[0]+vector[0],old[1]+vector[1],old[2]+vector[2]);
 216         }
 217         this->AddMesh(new_mesh);
 218     }
 219     if (GetNumberOfMasks()) //If the input mesh has a mask, use it to compute the warped meshes' masks
 220     {
 221         vtkSmartPointer<vtkImageData> ref_mask = vtkSmartPointer<vtkImageData>::New();
 222         ref_mask->ShallowCopy(GetMask(0));
 223         this->ComputeMasks(ref_mask);
 224     }
 225 }