1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
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.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
21 #include <vtkSmartPointer.h>
22 #include <vtkFloatArray.h>
23 #include <vtkPointData.h>
24 #include <vtkPolyData.h>
25 #include <vtkPolyDataReader.h>
26 #include <vtkOBJReader.h>
27 #include <vtkImageData.h>
28 #include "clitkCommon.h"
30 #include <vtkImageStencil.h>
31 #include <vtkLinearExtrusionFilter.h>
32 #include <vtkPolyDataToImageStencil.h>
33 #include <vtkMarchingCubes.h>
34 #include <itksys/SystemTools.hxx>
36 #include <vtkMetaImageWriter.h>
43 void vvMesh::AddMesh(vtkPolyData* p)
45 vtkPolyData * mesh=vtkPolyData::New();
47 meshes.push_back(mesh);
50 void vvMesh::ReadFromVTK(const char * filename)
53 std::string extension=itksys::SystemTools::GetFilenameLastExtension(std::string(filename));
54 if (extension == ".vtk" || extension== ".VTK") {
55 assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
56 vtkSmartPointer<vtkPolyDataReader> r=vtkSmartPointer<vtkPolyDataReader>::New();
57 r->SetFileName(filename);
59 assert(r->GetOutput());
60 AddMesh(r->GetOutput());
61 } else if (extension == ".obj" || extension== ".OBJ") {
62 assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
63 vtkSmartPointer<vtkOBJReader> r=vtkSmartPointer<vtkOBJReader>::New();
64 r->SetFileName(filename);
66 assert(r->GetOutput());
67 AddMesh(r->GetOutput());
69 assert (false) ; //shouldn't happen
71 assert(GetNumberOfMeshes() != 0); ///We assume the object is empty
72 structure_name=filename;
75 void vvMesh::RemoveMeshes()
77 for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++)
79 meshes.erase(meshes.begin(),meshes.end());
82 void vvMesh::AddMask(vtkImageData* im)
84 assert(im->GetScalarType() == VTK_UNSIGNED_CHAR);
85 vtkImageData* image=vtkImageData::New();
86 image->ShallowCopy(im);
87 masks.push_back(image);
90 void vvMesh::RemoveMasks()
92 for (std::vector<vtkImageData*>::const_iterator i=masks.begin(); i!=masks.end(); i++)
94 masks.erase(masks.begin(),masks.end());
103 void vvMesh::CopyInformation(vvMesh::Pointer input)
108 structure_name=input->structure_name;
109 slice_spacing=input->slice_spacing;
112 void vvMesh::Print() const
114 std::cout << this << " : " << structure_name << std::endl << "RGB: " << r << "," << g << "," << b << std::endl;
115 for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++) {
116 std::cout << (*i)->GetNumberOfPoints() << " points, " << (*i)->GetNumberOfCells() << " cells." << std::endl;
117 DDV((*i)->GetBounds(),6);
119 std::cout << "-------------------------" << std::endl << std::endl;
122 void vvMesh::ComputeMasks(vtkImageData* sample,bool extrude)
125 for (std::vector<vtkPolyData*>::iterator i=meshes.begin(); i!=meshes.end(); i++) {
126 vtkPolyData* mesh=*i;
127 double *bounds=mesh->GetBounds();
129 vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
130 binary_image->SetScalarTypeToUnsignedChar();
131 ///Use the smallest mask in which the mesh fits
132 // Add two voxels on each side to make sure the mesh fits
133 double * samp_origin=sample->GetOrigin();
134 double * spacing=sample->GetSpacing();
135 binary_image->SetSpacing(spacing);
136 /// Put the origin on a voxel to avoid small skips
137 binary_image->SetOrigin(floor((bounds[0]-samp_origin[0])/spacing[0]-2)*spacing[0]+samp_origin[0],
138 floor((bounds[2]-samp_origin[1])/spacing[1]-2)*spacing[1]+samp_origin[1],
139 floor((bounds[4]-samp_origin[2])/spacing[2]-2)*spacing[2]+samp_origin[2]);
140 double * origin=binary_image->GetOrigin();
141 binary_image->SetExtent(0,ceil((bounds[1]-origin[0])/spacing[0]+4),
142 0,ceil((bounds[3]-origin[1])/spacing[1]+4),
143 0,ceil((bounds[5]-origin[2])/spacing[2])+4);
144 binary_image->AllocateScalars();
145 memset(binary_image->GetScalarPointer(),0,binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
148 vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
149 //The following line is extremely important
150 //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
151 sts->SetTolerance(0);
152 sts->SetInformationInput(binary_image);
155 vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
156 extrude->SetInput(mesh);
157 ///We extrude in the -slice_spacing direction to respect the FOCAL convention
158 extrude->SetVector(0, 0, -slice_spacing);
159 sts->SetInput(extrude->GetOutput());
163 vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
164 stencil->SetStencil(sts->GetOutput());
165 stencil->SetInput(binary_image);
167 this->AddMask(stencil->GetOutput());
168 //vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
169 //w->SetInput(stencil->GetOutput());
170 //w->SetFileName("binary.mhd");
175 void vvMesh::ComputeMeshes()
177 this->RemoveMeshes();
178 for (std::vector<vtkImageData*>::iterator i=masks.begin(); i!=masks.end(); i++) {
179 vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
180 marching->SetInput(*i);
181 marching->SetValue(0,0.5);
183 this->AddMesh(marching->GetOutput());
187 void vvMesh::propagateContour(vvImage::Pointer vf)
189 assert(this->GetNumberOfMeshes() == 1);
190 std::vector<vtkImageData*> sgrids=vf->GetVTKImages();
191 vtkSmartPointer<vtkPolyData> reference_mesh = vtkSmartPointer<vtkPolyData>::New();
192 reference_mesh->ShallowCopy(this->GetMesh(0));
193 this->RemoveMeshes();
195 for (std::vector<vtkImageData*>::iterator i=sgrids.begin();
196 i!=sgrids.end(); i++) {
197 vtkPolyData* new_mesh=vtkPolyData::New();
198 new_mesh->DeepCopy(reference_mesh);
199 double Ox=vf->GetOrigin()[0];
200 double Oy=vf->GetOrigin()[1];
201 double Oz=vf->GetOrigin()[2];
202 double Sx=vf->GetSpacing()[0];
203 double Sy=vf->GetSpacing()[1];
204 double Sz=vf->GetSpacing()[2];
205 int *dims=vf->GetVTKImages()[0]->GetDimensions();
206 assert((*i)->GetScalarType() == VTK_FLOAT); //vfs are assumed to be of float type
207 assert((*i)->GetNumberOfScalarComponents() == 3);
208 float * vector_data=reinterpret_cast<float*>((*i)->GetScalarPointer());
209 for (int j=0; j<new_mesh->GetNumberOfPoints(); j++) {
210 double* old=new_mesh->GetPoint(j);
211 int ix=(old[0]-Ox)/Sx;
212 int iy=(old[1]-Oy)/Sy;
213 int iz=(old[2]-Oz)/Sz;
214 float* vector=vector_data+(ix+iy*vf->GetSize()[0]+iz*vf->GetSize()[0]*vf->GetSize()[1])*3;
215 if (ix>=0 && ix < dims[0]
216 && iy>=0 && iy < dims[1]
217 && iz>=0 && iz < dims[2])
218 new_mesh->GetPoints()->SetPoint(j,old[0]+vector[0],old[1]+vector[1],old[2]+vector[2]);
220 this->AddMesh(new_mesh);
222 if (GetNumberOfMasks()) { //If the input mesh has a mask, use it to compute the warped meshes' masks
223 vtkSmartPointer<vtkImageData> ref_mask = vtkSmartPointer<vtkImageData>::New();
224 ref_mask->ShallowCopy(GetMask(0));
225 this->ComputeMasks(ref_mask);