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[SofaBaseTopology] Fix SparseGridTopology initialization with an input mesh #670

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merged 6 commits into from
Aug 1, 2018
Merged

[SofaBaseTopology] Fix SparseGridTopology initialization with an input mesh #670

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7f55b08
FIX issue #308 with initialization of SparseGridTopology with a mesh
hugtalbot May 29, 2018
6458f7f
FIX minor typo
hugtalbot May 29, 2018
92cd417
FIX messages format
hugtalbot Jun 7, 2018
c9a86bd
Merge branch 'master' into fix_issue_308_sparsegrid
epernod Jul 3, 2018
0f2e89f
Merge remote-tracking branch 'upstream' into fix_issue_308_sparsegrid
hugtalbot Jul 30, 2018
0c92a17
FIX scene with error due to comparison of double value
hugtalbot Jul 31, 2018
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70 changes: 39 additions & 31 deletions SofaKernel/modules/SofaBaseTopology/SparseGridTopology.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -273,22 +273,18 @@ void SparseGridTopology::buildAsFinest( )
// seqPoints, seqHexahedra.getValue(), nbPoints
if(_filename.length() > 4 && _filename.compare(_filename.length()-4, 4, ".obj")==0)
{
// std::cout << "SparseGridTopology: using mesh "<<_filename<<std::endl;
buildFromTriangleMesh(_filename);
}
else if(_filename.length() > 6 && _filename.compare(_filename.length()-6, 6, ".trian")==0)
{
// std::cout << "SparseGridTopology: using mesh "<<_filename<<std::endl;
buildFromTriangleMesh(_filename);
}
else if(_filename.length() > 4 && _filename.compare(_filename.length()-4, 4, ".stl")==0)
{
// std::cout << "SparseGridTopology: using mesh "<<_filename<<std::endl;
buildFromTriangleMesh(_filename);
}
else if(_filename.length() > 4 && _filename.compare(_filename.length()-4, 4, ".raw")==0)
{
// std::cout << "SparseGridTopology: using mesh "<<_filename<<std::endl;
_usingMC = true;

buildFromRawVoxelFile(_filename);
Expand Down Expand Up @@ -785,13 +781,9 @@ void SparseGridTopology::buildFromTriangleMesh(const std::string& filename)
SReal xMin, xMax, yMin, yMax, zMin, zMax;
computeBoundingBox(mesh->getVertices(), xMin, xMax, yMin, yMax, zMin, zMax);

// increase the box a little
Vector3 diff ( xMax-xMin, yMax - yMin, zMax - zMin );
diff /= 100.0;

_min.setValue(Vector3( xMin - diff[0], yMin - diff[1], zMin - diff[2] ));
_max.setValue(Vector3( xMax + diff[0], yMax + diff[1], zMax + diff[2] ));
sout << "BBox size: " << (_max.getValue() - _min.getValue()) << sendl;
_min.setValue(Vector3( xMin, yMin, zMin ));
_max.setValue(Vector3( xMax, yMax, zMax ));
msg_info() << "BBox size: " << (_max.getValue() - _min.getValue());
}

// if cellWidth is given, update n
Expand All @@ -800,7 +792,7 @@ void SparseGridTopology::buildFromTriangleMesh(const std::string& filename)
SReal w = _cellWidth.getValue();
Vector3 diff = _max.getValue() - _min.getValue();
setN(Vec3i((int)ceil(diff[0] / w)+1, (int)ceil(diff[1] / w)+1, (int)ceil(diff[2] / w)+1));
sout << "Grid size: " << n.getValue() << sendl;
msg_info() << "Grid size: " << n.getValue();
}

_regularGrid->setSize(getNx(),getNy(),getNz());
Expand All @@ -811,7 +803,7 @@ void SparseGridTopology::buildFromTriangleMesh(const std::string& filename)

buildFromRegularGridTypes(_regularGrid, regularGridTypes);

sout << "Mesh Loaded" << sendl;
msg_info() << "Mesh Loaded";

delete mesh;
}
Expand Down Expand Up @@ -840,38 +832,45 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
const helper::vector< Vector3 >& vertices = mesh->getVertices();
const size_t vertexSize = vertices.size();
helper::vector< int > verticesHexa(vertexSize);
helper::vector< bool > facetDone;
const Vector3 delta = (regularGrid->getDx() + regularGrid->getDy() + regularGrid->getDz()) / 2;
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Not sure about this Delta value, If I understand well. If one of the direction is very big and the other are small. You could miss some points in the "big" resolution direction in your test below.

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this could explain the crashing scene, but I don't get why actually. Why could I miss some points in the "big" resolution direction?

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not sure to remember exactly what mean Dx, Dy and Dz as they are 3D.
But in a general way in 1 dimension, if for example: Dx = 1000 and Dy = Dz = 10.
delta = 1020/2 = 510.
So when looking at next point in Dx direction, if the scale is ~1000, your delta of 510 is too small.


// Compute the grid element for each mesh vertex
for (size_t i = 0; i < vertexSize; ++i)
{
const Vector3& vertex = vertices[i];
int index = regularGrid->findHexa(vertex);

if (index > 0)
regularGridTypes[index] = BOUNDARY;

// Case where 'findHexa' did not find the right hexa
// Here we test the case where the point is close the surface (delta /2)
// Useful when the point is on the boundary
if (index == -1)
{
Vector3 vertex2 = vertex;
const Vector3 gmin = regularGrid->getMin();
const Vector3 gmax = regularGrid->getMax();

if (vertex2[0] < gmin[0])
vertex2[0] = gmin[0];
else if (vertex2[0] > gmax[0])
if (vertex2[0] <= gmin[0])
vertex2[0] = gmin[0] + delta[0];
else if (vertex2[0] >= gmax[0])
vertex2[0] = gmax[0] - delta[0];

if (vertex2[1] < gmin[1])
vertex2[1] = gmin[1];
else if (vertex2[1] > gmax[1])
if (vertex2[1] <= gmin[1])
vertex2[1] = gmin[1] + delta[1];
else if (vertex2[1] >= gmax[1])
vertex2[1] = gmax[1] - delta[1];

if (vertex2[2] < gmin[2])
vertex2[2] = gmin[2];
else if (vertex2[2] > gmax[2])
if (vertex2[2] <= gmin[2])
vertex2[2] = gmin[2] + delta[2];
else if (vertex2[2] >= gmax[2])
vertex2[2] = gmax[2] - delta[2];

index = regularGrid->findHexa(vertex2);

if(index == -1)
msg_error() << "vertex "<<i<<" not found in hexahedral topology";
}

verticesHexa[i] = index;
Expand All @@ -897,6 +896,7 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
const Vector3 i0 = regularGrid->getCubeCoordinate(c0);
const Vector3 i1 = regularGrid->getCubeCoordinate(c1);
const Vector3 i2 = regularGrid->getCubeCoordinate(c2);

const Vector3 iMin( std::min(i0[0],std::min(i1[0],i2[0])),
std::min(i0[1],std::min(i1[1],i2[1])),
std::min(i0[2],std::min(i1[2],i2[2])));
Expand All @@ -912,13 +912,16 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
{
// if already inserted discard
unsigned int index = regularGrid->getCubeIndex(x,y,z);

if(regularGridTypes[index]==BOUNDARY)
continue;

Hexa c = regularGrid->getHexaCopy(index);

CubeCorners corners;
for(int k=0; k<8; ++k)
corners[k] = regularGrid->getPoint( c[k] );

#ifdef SOFA_NEW_HEXA
Vector3 cubeDiagonal = corners[6] - corners[0];
#else
Expand All @@ -932,6 +935,7 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,

// Scale the triangle to the unit cube matching
float points[3][3];

for (unsigned short w=0; w<3; ++w)
{
points[0][w] = (float) ((A[w]-cubeCenter[w])/cubeDiagonal[w]);
Expand All @@ -952,6 +956,7 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
}
}


// TODO: regarder les cellules pleines, et les ajouter
vector<bool> alreadyTested(regularGrid->getNbHexahedra(),false);
std::stack< Vec3i > seed;
Expand All @@ -963,6 +968,7 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
launchPropagationFromSeed(Vec3i(0,y,z), regularGrid, regularGridTypes, alreadyTested,seed );
launchPropagationFromSeed(Vec3i(regularGrid->getNx()-2,y,z), regularGrid, regularGridTypes, alreadyTested,seed );
}

// y==0 and y=ny-2
for(int x=0; x<regularGrid->getNx()-1; ++x)
{
Expand All @@ -971,6 +977,7 @@ void SparseGridTopology::voxelizeTriangleMesh(helper::io::Mesh* mesh,
launchPropagationFromSeed(Vec3i(x,0,z), regularGrid, regularGridTypes, alreadyTested,seed );
launchPropagationFromSeed(Vec3i(x,regularGrid->getNy()-2,z), regularGrid, regularGridTypes, alreadyTested,seed );
}

// z==0 and z==Nz-2
for(int y=0; y<regularGrid->getNy()-1; ++y)
{
Expand Down Expand Up @@ -1419,8 +1426,8 @@ void SparseGridTopology::buildVirtualFinerLevels()
_virtualFinerLevels[0]->_fillWeighted.setValue( _fillWeighted.getValue() );
_virtualFinerLevels[0]->init();

sout<<"SparseGridTopology "<<getName()<<" buildVirtualFinerLevels : ";
sout<<"("<<newnx<<"x"<<newny<<"x"<<newnz<<") -> "<< _virtualFinerLevels[0]->getNbHexahedra() <<" elements , ";
msg_info()<<"SparseGridTopology "<<getName()<<" buildVirtualFinerLevels : " << msgendl;
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There is no needs for msgendl at he end of message it is only to separate lines within a message.

msg_info()<<"("<<newnx<<"x"<<newny<<"x"<<newnz<<") -> "<< _virtualFinerLevels[0]->getNbHexahedra() <<" elements , " << msgendl;
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It is better (more efficient, more clear) to have a single message with multiple lines in it instead of two message.

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@damienmarchal damienmarchal May 30, 2018 •
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Here is an example of one message without line breaks.

 msg_info() <<"("<<newnx<<"x"<<newny<<"x"<<newnz<<") ->   "<<_virtualFinerLevels[0]->getNbHexahedra() <<" elements , " 

<<"("<<_virtualFinerLevels[i]->getNx()<<"x"<<_virtualFinerLevels[i]->getNy()

<<"x"<<_virtualFinerLevels[i]->getNz()<<") -> "<< _virtualFinerLevels[i]->getNbHexahedra() <<" elements , "

If you want linebreaks into a message...add msgendl where you want the break.

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Does my latest commit do what you expected @damienmarchal ?


for(int i=1; i<nb; ++i)
{
Expand All @@ -1431,11 +1438,9 @@ void SparseGridTopology::buildVirtualFinerLevels()

_virtualFinerLevels[i]->init();

sout<<"("<<_virtualFinerLevels[i]->getNx()<<"x"<<_virtualFinerLevels[i]->getNy()<<"x"<<_virtualFinerLevels[i]->getNz()<<") -> "<< _virtualFinerLevels[i]->getNbHexahedra() <<" elements , ";
msg_info()<<"("<<_virtualFinerLevels[i]->getNx()<<"x"<<_virtualFinerLevels[i]->getNy()<<"x"<<_virtualFinerLevels[i]->getNz()<<") -> "<< _virtualFinerLevels[i]->getNbHexahedra() <<" elements , "<<msgendl;
}

sout<<sendl;

this->setFinerSparseGrid(_virtualFinerLevels[nb-1].get());
}

Expand Down Expand Up @@ -1507,11 +1512,14 @@ int SparseGridTopology::findNearestCube(const Vector3& pos, SReal& fx, SReal &fy

helper::fixed_array<int,6> SparseGridTopology::findneighboorCubes( int indice )
{
sout<<"SparseGridTopology::findneighboorCubes : "<<indice<<" -> "<<_indicesOfCubeinRegularGrid[indice]<<sendl;
sout<<_indicesOfRegularCubeInSparseGrid[ _indicesOfCubeinRegularGrid[indice] ] <<sendl;
msg_info()<<"SparseGridTopology::findneighboorCubes : "<<indice<<" -> "<<_indicesOfCubeinRegularGrid[indice];
msg_info()<<_indicesOfRegularCubeInSparseGrid[ _indicesOfCubeinRegularGrid[indice] ];

helper::fixed_array<int,6> result;
Vector3 c = _regularGrid->getCubeCoordinate( _indicesOfCubeinRegularGrid[indice] );
sout<<c<<sendl;

msg_info()<<c;

result[0] = c[0]<=0 ? -1 : _indicesOfRegularCubeInSparseGrid[ _regularGrid->getCubeIndex( (int)c[0]-1,(int)c[1],(int)c[2] )];
result[1] = c[0]>=getNx()-2 ? -1 : _indicesOfRegularCubeInSparseGrid[ _regularGrid->getCubeIndex( (int)c[0]+1,(int)c[1],(int)c[2] )];
result[2] = c[1]<=0 ? -1 : _indicesOfRegularCubeInSparseGrid[ _regularGrid->getCubeIndex( (int)c[0],(int)c[1]-1,(int)c[2] )];
Expand Down
6 changes: 3 additions & 3 deletions modules/SofaGraphComponent/SceneChecks.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -159,9 +159,9 @@ void SceneCheckMissingRequiredPlugin::doPrintSummary()
tmp <<"]-->" << msgendl ;
}
msg_warning("SceneChecker")
<< "This scene is using component defined in plugins but are not importing the requierd plugins." << msgendl
<< "Your scene may not work on a sofa environment with different pre-loaded plugins." << msgendl
<< "To fix your scene and remove this warning you just need to cut & paste the following lines at the begining of your scene (if it is a .scn): " << msgendl
<< "This scene is using component defined in plugins but are not importing the required plugins." << msgendl
<< "Your scene may not work on a sofa environment regarding the currently pre-loaded plugins." << msgendl
<< "To fix your scene and remove this warning, you just need to cut & paste the following lines at the begining of your scene (if it is a .scn): " << msgendl
<< tmp.str() ;
}
}
Expand Down