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Hi Bryn,

Thanks for your interest in Cleaver! I am preparing to make a new release on git hub in early July. Improvements through git hub pull requests are very welcome, and I would be happy to merge the code you have using that interface. You can also add your feature requests to the list of git hub issues on the cleaver repo.

https://github.com/SCIInstitute/Cleaver2

We are currently hoping to solve a bug that is primarily associated with quadruple points creating flat tets. It sounds like your discovery is a different bug. It would be great if you could submit a detailed report on git hub for us.

Let me know if you have any questions.

Regards,

Brig Bagley
Research Software Engineer
SCI Institute, University of Utah
WEB 3616
brig@sci.utah.edu
801.613.7718

On 05/30/2015 02:09 PM, Bryn Lloyd wrote:

Hi Brig

I recently noticed that cleaver2 is open source. When I checked before it was still only available as an executable.

I have been playing around with cleaver2 and am accumulating small changes that might be useful "improvements":

1. Better implementation of the writeVtkUnstructuredGrid function (see below). Unlike the original code it saves real tetrahedra, instead of 4 triangles per tetrahedra. A single (binary) VTK file with labels attached as a cell data field would be even nicer (http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf).

2. Small example showing how to use the library with implicit functions derived from AbstractScalarField.

I noticed that some tetrahedra on the boundary are assigned to an "inside" material but should really have been "background". These tetrahedra have 3 nodes "on" the surface and one which is clearly outside. Are you aware of such problems.

I can send the example mentioned above, if you are interested in adding it to the repo.

Cheers, Bryn





void TetMesh::writeVtkUnstructuredGrid(const std::string &filename, bool verbose)
{
std::string path = filename.substr(0,filename.find_last_of("/")+1);
std::string name = filename.substr(filename.find_last_of("/")+1,filename.size() - 1);
if (path.empty()) {
char cCurrentPath[FILENAME_MAX];
if(GetCurrentDir(cCurrentPath, sizeof(cCurrentPath))){}
cCurrentPath[sizeof(cCurrentPath) - 1] = '\0';
path = std::string(cCurrentPath) + "/";
}
// get the number of files/mats
std::vector<std::ofstream*> output;
std::vector<size_t> numTetsPerMat;
for(size_t i = 0; i < this->tets.size(); i++) {
size_t label = tets.at(i)->mat_label;
if (label + 1 > numTetsPerMat.size())
numTetsPerMat.resize(label+1);
numTetsPerMat.at(label)++;
}
size_t num = 0;
std::vector<std::string> filenames;
while (numTetsPerMat.size() != filenames.size()) {
std::stringstream ss;
ss << path << name << num++ << ".vtk" ;
filenames.push_back(ss.str());
std::cout << "\t" << ss.str() << std:: endl;
}
if(verbose) {
std::cout << "Writing VTK mesh files(tets): \n";
for(size_t i = 0; i < filenames.size(); i++)
std::cout << "\t" << filenames.at(i) << std::endl;
}
//-----------------------------------
// Write Headers
//-----------------------------------
for(size_t i=0; i < numTetsPerMat.size(); i++) {
output.push_back(new std::ofstream(filenames.at(i).c_str()));
*output.at(i) << "# vtk DataFile Version 2.0\n";
*output.at(i) << filenames.at(i) << " Tet Mesh\n";
*output.at(i) << "ASCII\n";
*output.at(i) << "DATASET UNSTRUCTURED_GRID\n";
*output.at(i) << "POINTS " << this->verts.size() << " float\n";
}
//-----------------------------------
// Write Vertex List
//-----------------------------------
for(size_t f=0; f < numTetsPerMat.size(); f++) {
for(size_t i=0; i < this->verts.size(); i++)
{
*output.at(f) << this->verts[i]->pos().x << " "
<< this->verts[i]->pos().y << " "
<< this->verts[i]->pos().z << std::endl;
}
size_t num_tets = numTetsPerMat.at(f);
*output.at(f) << "CELLS " << num_tets << " " << num_tets*5 << "\n";
}
//-----------------------------------
// Write Cell/Face List
//-----------------------------------
for(size_t f=0; f < this->tets.size(); f++)
{
Tet* t = this->tets.at(f);

size_t v1 = t->verts[0]->tm_v_index;
size_t v2 = t->verts[1]->tm_v_index;
size_t v3 = t->verts[2]->tm_v_index;
size_t v4 = t->verts[3]->tm_v_index;

*output.at(t->mat_label) << 4 << " " << v1 << " " << v2 << " " << v3 << " " << v4 << "\n";
}

for(size_t f=0; f < numTetsPerMat.size(); f++) {
size_t num_tets = numTetsPerMat.at(f);
*output.at(f) << "CELL_TYPES " << num_tets << "\n";
}

for(size_t f=0; f < this->tets.size(); f++)
{
Tet* t = this->tets.at(f);
*output.at(t->mat_label) << 10 << "\n";
}

//CLOSE
for(size_t i=0; i < numTetsPerMat.size(); i++) {
(*output.at(i)).close();
delete output.at(i);
}
}

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• Re: [Cleaver] Cleaver2, Brig Bagley, 06/01/2015

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