float PropagatedDeformableModel::computeContrast(Referential& refInitial)
{
// Calcul du profil de la moelle et du LCR perpendiculairement au tube
CVector3 pointS, indexS;
vector<float> contrast(resolutionRadiale_);
float angle;
CMatrix3x3 trZ;
CMatrix4x4 transformationFromOrigin = refInitial.getTransformationInverse();
float factor = image3D_->getTypeImageFactor();
for (int k=0; k<resolutionRadiale_; k++)
{
vector<float> profilIntensite;
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
for (int l=0; l<2.5*rayon_; l++) {
pointS = transformationFromOrigin*(trZ*CVector3(l,0.0,0.0));
if (image3D_->TransformPhysicalPointToIndex(pointS,indexS))
profilIntensite.push_back(factor*image3D_->GetPixelOriginal(indexS));
}
float min = 0.0, max = 0.0, maxVal = 0.0, valCourante;
unsigned int m = 0;
for (unsigned int i=1; i<profilIntensite.size(); i++) {
valCourante = profilIntensite[i]-profilIntensite[i-1];
if (maxVal <= valCourante) {
maxVal = valCourante;
m = i;
}
}
if (profilIntensite.size() > 0)
{
min = profilIntensite[m];
for (unsigned int j=0; j<m; j++) {
valCourante = profilIntensite[j];
if (min > valCourante) min = valCourante;
}
max = profilIntensite[m];
for (unsigned int j=m+1; j<profilIntensite.size(); j++) {
valCourante = profilIntensite[j];
if (max < valCourante) max = valCourante;
}
}
contrast[k] = abs(max-min);
}
float result = 0.0;
for (unsigned int i=0; i<contrast.size(); i++)
result += contrast[i];
result /= contrast.size();
return result;
}
void PropagatedDeformableModel::computeNewBand(SpinalCord* mesh, CVector3 initialPoint, CVector3 nextPoint, int resolution)
{
CMatrix4x4 transformationFromOrigin;
double angle;
CMatrix3x3 trZ;
CVector3 point, normale;
CVector3 directionCourante = nextPoint-initialPoint, lastNormal = (nextPoint-initialPoint).Normalize(), directionCourantePerpendiculaire;
if (lastNormal[2] == 0.0) directionCourantePerpendiculaire = CVector3(0.0,0.0,1.0);
else directionCourantePerpendiculaire = CVector3(1.0,2.0,-(lastNormal[0]+2*lastNormal[1])/lastNormal[2]).Normalize();
CVector3 stretchingFactorWorld = image3D_->TransformContinuousIndexToPhysicalPoint(CVector3((1-1.0/stretchingFactor_), 0.0, 0.0))-image3D_->getOrigine();
int offsetTriangles = mesh->getNbrOfPoints()-resolutionRadiale_;
for (int len=1; len<=resolution; len++)
{
CVector3 pointIntermediaire = initialPoint + len*directionCourante/(double)resolutionAxiale_;
Referential refCourant = Referential(lastNormal^directionCourantePerpendiculaire, directionCourantePerpendiculaire, lastNormal, pointIntermediaire);
transformationFromOrigin = refCourant.getTransformationInverse();
for (int k=0; k<resolutionRadiale_; k++)
{
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
point = transformationFromOrigin*(trZ*CVector3(rayon_,0.0,0.0));
CVector3 vecPoint = initialPoint - point;
point[0] += stretchingFactorWorld[0]*vecPoint[0];
point[1] += stretchingFactorWorld[1]*vecPoint[1];
point[2] += stretchingFactorWorld[2]*vecPoint[2];
mesh->addPoint(new Vertex(point,(point-pointIntermediaire).Normalize()));
}
// Ajout des triangles - attention � la structure en cercle
for (int k=0; k<resolutionRadiale_-1; k++)
{
mesh->addTriangle(offsetTriangles+(len-1)*resolutionRadiale_+k,offsetTriangles+(len-1)*resolutionRadiale_+k+1,offsetTriangles+len*resolutionRadiale_+k);
mesh->addTriangle(offsetTriangles+(len-1)*resolutionRadiale_+k+1,offsetTriangles+len*resolutionRadiale_+k+1,offsetTriangles+len*resolutionRadiale_+k);
}
// Ajout des deux derniers triangles pour fermer le tube
mesh->addTriangle(offsetTriangles+(len-1)*resolutionRadiale_+resolutionRadiale_-1,offsetTriangles+(len-1)*resolutionRadiale_,offsetTriangles+len*resolutionRadiale_+resolutionRadiale_-1);
mesh->addTriangle(offsetTriangles+(len-1)*resolutionRadiale_,offsetTriangles+len*resolutionRadiale_,offsetTriangles+len*resolutionRadiale_+resolutionRadiale_-1);
}
}
void PropagatedDeformableModel::computeMeshInitial()
{
// centerline can be added to be followed. Points of centerline have to be added from bottom to top
if (propCenterline_) {
if (centerline.size() < 1) {
cerr << "Error: Not enought points in centerline" << endl;
return;
} else {
//int init = centerline.size()*init_position_;
/******************************************************************************************
* If a centerline is used for the orientation computation, we compute its BSpline approximation. This approximation is used for centerline position and orientation extraction
* The parameter range is the centerline approximation accuracy
*****************************************************************************************/
initial_centerline = centerline;
centerline_approximator = BSplineApproximation(&initial_centerline);
initialPoint_ = centerline_approximator.EvaluateBSpline(init_position_);
initialNormal1_ = -centerline_approximator.EvaluateGradient(init_position_-0.01).Normalize();
initialNormal2_ = centerline_approximator.EvaluateGradient(init_position_+0.01).Normalize();;
//initialNormal1_ = (centerline[init-1]-centerline[init]).Normalize();
//initialNormal2_ = (centerline[init+1]-centerline[init]).Normalize();
hasInitialPointAndNormals_ = true;
}
}
if (centerline.size() < 1 && !hasInitialPointAndNormals_) {
cerr << "Error: Not enought points in centerline" << endl;
}
else if (centerline.size() == 2) {
initialTube1 = new SpinalCord;
CVector3 directionInitiale = (centerline[1]-centerline[0]).Normalize(), directionInitialePerpendiculaire;
if (directionInitiale[2] == 0.0) directionInitialePerpendiculaire = CVector3(0.0,0.0,1.0);
else directionInitialePerpendiculaire = CVector3(1.0,2.0,-(directionInitiale[0]+2*directionInitiale[1])/directionInitiale[2]).Normalize();
Referential refInitial = Referential(directionInitiale^directionInitialePerpendiculaire, directionInitialePerpendiculaire, directionInitiale, centerline[0]);
CMatrix4x4 transformationFromOrigin = refInitial.getTransformationInverse();
double angle;
CMatrix3x3 trZ;
CVector3 point, normale;
// Compute initial disk
for (int k=0; k<resolutionRadiale_; k++)
{
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
point = transformationFromOrigin*(trZ*CVector3(rayon_,0.0,0.0));
initialTube1->addPoint(new Vertex(point,(point-centerline[0]).Normalize()));
}
CVector3 nextPoint = centerline[0] + deplacementAxial_*directionInitiale;
computeNewBand(initialTube1,centerline[0],nextPoint,resolutionAxiale_+2);
initialTube1->computeConnectivity();
initialTube1->computeTrianglesBarycentre();
isMeshInitialized = true;
meanContrast = computeContrast(refInitial);
//cout << "Contrast = " << contrast << endl;
}
else if (hasInitialPointAndNormals_) {
initialTube1 = new SpinalCord;
CVector3 directionInitiale = initialNormal1_, directionInitialePerpendiculaire;
if (directionInitiale[2] == 0.0) directionInitialePerpendiculaire = CVector3(0.0,0.0,1.0);
else directionInitialePerpendiculaire = CVector3(1.0,2.0,-(directionInitiale[0]+2*directionInitiale[1])/directionInitiale[2]).Normalize();
Referential refInitial = Referential(directionInitiale^directionInitialePerpendiculaire, directionInitialePerpendiculaire, directionInitiale, initialPoint_);
CMatrix4x4 transformationFromOrigin = refInitial.getTransformationInverse();
double angle;
CMatrix3x3 trZ;
CVector3 point, normale;
CVector3 stretchingFactorWorld = image3D_->TransformContinuousIndexToPhysicalPoint(CVector3((1.0-1.0/stretchingFactor_), 0.0, 0.0))-image3D_->getOrigine();
// Compute initial disk
for (int k=0; k<resolutionRadiale_; k++)
{
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
point = transformationFromOrigin*(trZ*CVector3(rayon_,0.0,0.0));
CVector3 vecPoint = initialPoint_ - point;
point[0] += stretchingFactorWorld[0]*vecPoint[0];
point[1] += stretchingFactorWorld[1]*vecPoint[1];
point[2] += stretchingFactorWorld[2]*vecPoint[2];
initialTube1->addPoint(new Vertex(point,(point-initialPoint_).Normalize()));
}
CVector3 nextPoint = initialPoint_ + deplacementAxial_*directionInitiale;
computeNewBand(initialTube1,initialPoint_,nextPoint,resolutionAxiale_+2);
initialTube1->computeConnectivity();
initialTube1->computeTrianglesBarycentre();
initialTube2 = new SpinalCord;
directionInitiale = initialNormal2_;
if (directionInitiale[2] == 0.0) directionInitialePerpendiculaire = CVector3(0.0,0.0,1.0);
else directionInitialePerpendiculaire = CVector3(1.0,2.0,-(directionInitiale[0]+2*directionInitiale[1])/directionInitiale[2]).Normalize();
refInitial = Referential(directionInitiale^directionInitialePerpendiculaire, directionInitialePerpendiculaire, directionInitiale, initialPoint_);
transformationFromOrigin = refInitial.getTransformationInverse();
// Compute initial disk
for (int k=0; k<resolutionRadiale_; k++)
{
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
point = transformationFromOrigin*(trZ*CVector3(rayon_,0.0,0.0));
CVector3 vecPoint = initialPoint_ - point;
point[0] += stretchingFactorWorld[0]*vecPoint[0];
point[1] += stretchingFactorWorld[1]*vecPoint[1];
point[2] += stretchingFactorWorld[2]*vecPoint[2];
initialTube2->addPoint(new Vertex(point,(point-initialPoint_).Normalize()));
}
nextPoint = initialPoint_ + deplacementAxial_*directionInitiale;
computeNewBand(initialTube2,initialPoint_,nextPoint,resolutionAxiale_+2);
initialTube2->computeConnectivity();
initialTube2->computeTrianglesBarycentre();
isMeshInitialized = true;
meanContrast = computeContrast(refInitial);
}
else {
initialTube1 = new SpinalCord;
CVector3 directionInitiale = (centerline[1]-centerline[0]).Normalize(), directionInitialePerpendiculaire;
if (directionInitiale[2] == 0.0) directionInitialePerpendiculaire = CVector3(0.0,0.0,1.0);
else directionInitialePerpendiculaire = CVector3(1.0,2.0,-(directionInitiale[0]+2*directionInitiale[1])/directionInitiale[2]).Normalize();
Referential refInitial = Referential(directionInitiale^directionInitialePerpendiculaire, directionInitialePerpendiculaire, directionInitiale, centerline[0]);
CMatrix4x4 transformationFromOrigin = refInitial.getTransformationInverse();
double angle;
CMatrix3x3 trZ;
CVector3 point, normale;
// Compute initial disk
for (int k=0; k<resolutionRadiale_; k++)
{
angle = 2*M_PI*k/(double)resolutionRadiale_;
trZ[0] = cos(angle), trZ[1] = sin(angle), trZ[3] = -sin(angle), trZ[4] = cos(angle);
point = transformationFromOrigin*(trZ*CVector3(rayon_,0.0,0.0));
initialTube1->addPoint(new Vertex(point,(point-centerline[0]).Normalize()));
}
for (unsigned int i=1; i<centerline.size(); i++)
{
computeNewBand(initialTube1,centerline[i-1],centerline[i],resolutionAxiale_);
}
initialTube1->computeConnectivity();
initialTube1->computeTrianglesBarycentre();
isMeshInitialized = true;
}
}