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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://oncora1.lyon.fnclcc.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   DD("hello!");
62   std::string extension=itksys::SystemTools::GetFilenameLastExtension(std::string(filename));
63   if (extension == ".vtk" || extension== ".VTK") {
64     assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
65     vtkSmartPointer<vtkPolyDataReader> r=vtkSmartPointer<vtkPolyDataReader>::New();
66     r->SetFileName(filename);
67     r->Update();
68     assert(r->GetOutput());
69     AddMesh(r->GetOutput());
70   } else if (extension == ".obj" || extension== ".OBJ") {
71     assert(GetNumberOfMeshes() == 0); ///We assume the object is empty
72     vtkSmartPointer<vtkOBJReader> r=vtkSmartPointer<vtkOBJReader>::New();
73     r->SetFileName(filename);
74     r->Update();
75     assert(r->GetOutput());
76     AddMesh(r->GetOutput());
77   } else
78     assert (false) ; //shouldn't happen
79
80   assert(GetNumberOfMeshes() != 0); ///We assume the object is empty
81   structure_name=filename;
82 }
83
84 void vvMesh::RemoveMeshes()
85 {
86   for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++)
87     (*i)->Delete();
88   meshes.erase(meshes.begin(),meshes.end());
89 }
90
91 void vvMesh::AddMask(vtkImageData* im)
92 {
93   assert(im->GetScalarType() == VTK_UNSIGNED_CHAR);
94   vtkImageData* image=vtkImageData::New();
95   image->ShallowCopy(im);
96   masks.push_back(image);
97 }
98
99 void vvMesh::RemoveMasks()
100 {
101   for (std::vector<vtkImageData*>::const_iterator i=masks.begin(); i!=masks.end(); i++)
102     (*i)->Delete();
103   masks.erase(masks.begin(),masks.end());
104 }
105
106 vvMesh::~vvMesh()
107 {
108   RemoveMeshes();
109   RemoveMasks();
110 }
111
112 void vvMesh::CopyInformation(vvMesh::Pointer input)
113 {
114   r=input->r;
115   g=input->g;
116   b=input->b;
117   structure_name=input->structure_name;
118   slice_spacing=input->slice_spacing;
119 }
120
121 void vvMesh::Print() const
122 {
123   std::cout << this << " : " << structure_name << std::endl << "RGB: " << r << "," << g << "," << b << std::endl;
124   for (std::vector<vtkPolyData*>::const_iterator i=meshes.begin(); i!=meshes.end(); i++) {
125     std::cout << (*i)->GetNumberOfPoints() << " points, " << (*i)->GetNumberOfCells() << " cells." << std::endl;
126     DDV((*i)->GetBounds(),6);
127   }
128   std::cout << "-------------------------" << std::endl << std::endl;
129 }
130
131 void vvMesh::ComputeMasks(vtkImageData* sample,bool extrude)
132 {
133   this->RemoveMasks();
134   for (std::vector<vtkPolyData*>::iterator i=meshes.begin(); i!=meshes.end(); i++) {
135     vtkPolyData* mesh=*i;
136     double *bounds=mesh->GetBounds();
137
138     vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
139     binary_image->SetScalarTypeToUnsignedChar();
140     ///Use the smallest mask in which the mesh fits
141     // Add two voxels on each side to make sure the mesh fits
142     double * samp_origin=sample->GetOrigin();
143     double * spacing=sample->GetSpacing();
144     binary_image->SetSpacing(spacing);
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     //vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
178     //w->SetInput(stencil->GetOutput());
179     //w->SetFileName("binary.mhd");
180     //w->Write();
181   }
182 }
183
184 void vvMesh::ComputeMeshes()
185 {
186   this->RemoveMeshes();
187   for (std::vector<vtkImageData*>::iterator i=masks.begin(); i!=masks.end(); i++) {
188     vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
189     marching->SetInput(*i);
190     marching->SetValue(0,0.5);
191     marching->Update();
192     this->AddMesh(marching->GetOutput());
193   }
194 }
195
196 void vvMesh::propagateContour(vvImage::Pointer vf)
197 {
198   assert(this->GetNumberOfMeshes() == 1);
199   std::vector<vtkImageData*> sgrids=vf->GetVTKImages();
200   vtkSmartPointer<vtkPolyData> reference_mesh = vtkSmartPointer<vtkPolyData>::New();
201   reference_mesh->ShallowCopy(this->GetMesh(0));
202   this->RemoveMeshes();
203
204   for (std::vector<vtkImageData*>::iterator i=sgrids.begin();
205        i!=sgrids.end(); i++) {
206     vtkPolyData* new_mesh=vtkPolyData::New();
207     new_mesh->DeepCopy(reference_mesh);
208     double Ox=vf->GetOrigin()[0];
209     double Oy=vf->GetOrigin()[1];
210     double Oz=vf->GetOrigin()[2];
211     double Sx=vf->GetSpacing()[0];
212     double Sy=vf->GetSpacing()[1];
213     double Sz=vf->GetSpacing()[2];
214     int *dims=vf->GetVTKImages()[0]->GetDimensions();
215     assert((*i)->GetScalarType() == VTK_FLOAT); //vfs are assumed to be of float type
216     assert((*i)->GetNumberOfScalarComponents() == 3);
217     float * vector_data=reinterpret_cast<float*>((*i)->GetScalarPointer());
218     for (int j=0; j<new_mesh->GetNumberOfPoints(); j++) {
219       double* old=new_mesh->GetPoint(j);
220       int ix=(old[0]-Ox)/Sx;
221       int iy=(old[1]-Oy)/Sy;
222       int iz=(old[2]-Oz)/Sz;
223       float* vector=vector_data+(ix+iy*vf->GetSize()[0]+iz*vf->GetSize()[0]*vf->GetSize()[1])*3;
224       if (ix>=0 && ix < dims[0]
225           && iy>=0 && iy < dims[1]
226           && iz>=0 && iz < dims[2])
227         new_mesh->GetPoints()->SetPoint(j,old[0]+vector[0],old[1]+vector[1],old[2]+vector[2]);
228     }
229     this->AddMesh(new_mesh);
230   }
231   if (GetNumberOfMasks()) { //If the input mesh has a mask, use it to compute the warped meshes' masks
232     vtkSmartPointer<vtkImageData> ref_mask = vtkSmartPointer<vtkImageData>::New();
233     ref_mask->ShallowCopy(GetMask(0));
234     this->ComputeMasks(ref_mask);
235   }
236 }