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MeshGmshLoader.cpp
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MeshGmshLoader.cpp
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/******************************************************************************
* SOFA, Simulation Open-Framework Architecture *
* (c) 2006 INRIA, USTL, UJF, CNRS, MGH *
* *
* This program is free software; you can redistribute it and/or modify it *
* under the terms of the GNU Lesser General Public License as published by *
* the Free Software Foundation; either version 2.1 of the License, or (at *
* your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, but WITHOUT *
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
* for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*******************************************************************************
* Authors: The SOFA Team and external contributors (see Authors.txt) *
* *
* Contact information: contact@sofa-framework.org *
******************************************************************************/
#include <sofa/component/io/mesh/config.h>
#include <sofa/core/ObjectFactory.h>
#include <sofa/component/io/mesh/MeshGmshLoader.h>
#include <sofa/core/visual/VisualParams.h>
#include <iostream>
#include <fstream>
#include <sofa/helper/io/Mesh.h>
namespace sofa::component::io::mesh
{
using namespace sofa::type;
using namespace sofa::defaulttype;
using namespace sofa::helper;
using std::string;
using std::stringstream;
int MeshGmshLoaderClass = core::RegisterObject("Specific mesh loader for Gmsh file format.")
.add< MeshGmshLoader >()
;
bool MeshGmshLoader::doLoad()
{
string cmd;
unsigned int gmshFormat = 0;
if (!canLoad())
{
msg_error(this) << "Can't load file " << d_filename.getFullPath().c_str();
return false;
}
// -- Loading file
const char* filename = d_filename.getFullPath().c_str();
std::ifstream file(filename);
// -- Looking for Gmsh version of this file.
std::getline(file, cmd);
if (cmd.length() >= 11 && cmd.substr(0, 11) == "$MeshFormat") // Reading gmsh
{
// NB: .msh file header line for version >= 2 can be "$MeshFormat", "$MeshFormat\r", "$MeshFormat \r"
string version;
std::getline(file, version); // Getting the version line (e.g. 4.1 0 8)
gmshFormat = std::stoul( version.substr( 0, version.find(" ")) ); // Retrieving the mesh format, keeping only the integer part
std::getline(file, cmd); // $EndMeshFormat
if (cmd.length() < 14 || cmd.substr(0, 14) != string("$EndMeshFormat")) // it should end with "$EndMeshFormat" or "$EndMeshFormat\r"
{
msg_error() << "No $EndMeshFormat flag found at the end of the file. Closing File";
file.close();
return false;
}
else
{
// Reading the file until the node section is hit. In recent versions of MSH file format,
// we may encounter various sections between $MeshFormat and $Nodes
while (cmd.length() < 6 || cmd.substr(0, 6) != std::string("$Nodes")) // can be "$Nodes" or "$Nodes\r"
{
std::getline(file, cmd); // First Command
if (file.eof())
{
msg_error() << "End of file reached without finding the $Nodes section expected in MSH file format. Closing file.";
file.close();
return false;
}
}
}
}
else if (cmd.length() >= 4 && cmd.substr(0, 4) == "$NOD")
{
// Legacy MSh format version 1 directly starts with the Nodes section
// https://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format-version-1-_0028Legacy_0029
// NB: corresponding line can be "$NOD", "$NOD\r"
gmshFormat = 1;
}
else // If the first line is neither "$MeshFormat" or "$NOD", then the file is not in a registered MSH format
{
msg_error() << "File '" << d_filename << "' finally appears not to be a Gmsh file (first line doesn't match known formats).";
file.close();
return false;
}
std::istringstream nodeReader(cmd);
string node;
nodeReader >> node;
// -- Reading file
// By default for Gmsh file format, create subElements except if specified not to.
if (!d_createSubelements.isSet())
d_createSubelements.setValue(true);
// TODO 2018-04-06: temporary change to unify loader API
//fileRead = readGmsh(file, gmshFormat);
(void)gmshFormat;
file.close();
helper::io::Mesh* _mesh = helper::io::Mesh::Create("gmsh", filename);
copyMeshToData(*_mesh);
delete _mesh;
return true;
}
void MeshGmshLoader::doClearBuffers()
{
/// Nothing to do if no output is added to the "filename" dataTrackerEngine.
}
void MeshGmshLoader::addInGroup(type::vector< sofa::core::loader::PrimitiveGroup>& group,int tag,int /*eid*/) {
for (auto& group_i : group) {
if (tag == group_i.p0) {
group_i.nbp++;
return;
}
}
stringstream ss;
const string s;
ss << tag;
group.push_back(sofa::core::loader::PrimitiveGroup(tag,1,s,s,-1));
}
void MeshGmshLoader::normalizeGroup(type::vector< sofa::core::loader::PrimitiveGroup>& group) {
int start = 0;
for (auto& group_i : group) {
group_i.p0 = start;
start += group_i.nbp;
}
}
bool MeshGmshLoader::readGmsh(std::ifstream &file, const unsigned int gmshFormat)
{
dmsg_info() << "Reading Gmsh file: " << gmshFormat;
string cmd;
unsigned int npoints = 0;
unsigned int nelems = 0;
// Accessors to complete the loader data
auto my_positions = getWriteOnlyAccessor(d_positions);
auto my_edges = getWriteOnlyAccessor(d_edges);
auto my_triangles = getWriteOnlyAccessor(d_triangles);
auto my_quads = getWriteOnlyAccessor(d_quads);
auto my_tetrahedra = getWriteOnlyAccessor(d_tetrahedra);
auto my_hexahedra = getWriteOnlyAccessor(d_hexahedra);
auto my_highOrderEdgePositions = getWriteOnlyAccessor(d_highOrderEdgePositions);
auto my_edgesGroups = getWriteOnlyAccessor(d_edgesGroups);
auto my_trianglesGroups = getWriteOnlyAccessor(d_trianglesGroups);
auto my_tetrahedraGroups = getWriteOnlyAccessor(d_tetrahedraGroups);
auto my_hexahedraGroups = getWriteOnlyAccessor(d_hexahedraGroups);
if (gmshFormat <= 2)
{
// --- Loading Vertices ---
file >> npoints; //nb points
std::vector<unsigned int> pmap; // map for reordering vertices possibly not well sorted
for (unsigned int i = 0; i < npoints; ++i)
{
unsigned int index = i;
double x, y, z;
file >> index >> x >> y >> z;
my_positions.push_back(Vec3(x, y, z));
if (pmap.size() <= index)
pmap.resize(index + 1);
pmap[index] = i; // In case of hole or switch
}
file >> cmd;
if (cmd.length() < 7 || cmd.substr(0, 7) != "$ENDNOD") // can be "$ENDNOD" or "$ENDNOD\r"
{
if (cmd.length() < 9 || cmd.substr(0, 9) != "$EndNodes") // can be "$EndNodes" or "$EndNodes\r"
{
msg_error() << "'$ENDNOD' or '$EndNodes' expected, found '" << cmd << "'";
file.close();
return false;
}
}
// --- Loading Elements ---
file >> cmd;
if (cmd.length() < 4 || cmd.substr(0, 4) != "$ELM") // can be "$ELM" or "$ELM\r"
{
if (cmd.length() < 9 || cmd.substr(0, 9) != "$Elements") // can be "$ELM" or "$ELM\r"
{
msg_error() << "'$ELM' or '$Elements' expected, found '" << cmd << "'";
file.close();
return false;
}
}
file >> nelems; //Loading number of Element
for (unsigned int i = 0; i < nelems; ++i) // for each elem
{
int index, etype, rphys, relem, nnodes, ntags, tag = 0; // TODO: i don't know if tag must be set to 0, but if it's not, the application assert / crash on Windows (uninitialized value)
if (gmshFormat == 1)
{
// version 1.0 format is
// elm-number elm-type reg-phys reg-elem number-of-nodes <node-number-list ...>
file >> index >> etype >> rphys >> relem >> nnodes;
}
else /*if (gmshFormat == 2)*/
{
// version 2.0 format is
// elm-number elm-type number-of-tags < tag > ... node-number-list
file >> index >> etype >> ntags;
for (int t = 0; t < ntags; t++)
{
file >> tag;
}
switch (etype)
{
case 15: //point
nnodes = 1;
break;
case 1: // Line
nnodes = 2;
break;
case 2: // Triangle
nnodes = 3;
break;
case 3: // Quad
nnodes = 4;
break;
case 4: // Tetra
nnodes = 4;
break;
case 5: // Hexa
nnodes = 8;
break;
case 8: // Quadratic edge
nnodes = 3;
break;
case 9: // Quadratic Triangle
nnodes = 6;
break;
case 11: // Quadratic Tetrahedron
nnodes = 10;
break;
default:
msg_warning() << "Elements of type 1, 2, 3, 4, 5, or 6 expected. Element of type " << etype << " found.";
nnodes = 0;
}
}
//store real index of node and not line index
type::vector <unsigned int> nodes;
nodes.resize(nnodes);
const unsigned int edgesInQuadraticTriangle[3][2] = { {0,1}, {1,2}, {2,0} };
const unsigned int edgesInQuadraticTetrahedron[6][2] = { {0,1}, {1,2}, {0,2},{0,3},{2,3},{1,3} };
std::set<Edge> edgeSet;
size_t j;
for (int n = 0; n < nnodes; ++n)
{
int t = 0;
file >> t;
nodes[n] = (((unsigned int)t) < pmap.size()) ? pmap[t] : 0;
}
switch (etype)
{
case 1: // Line
addInGroup(my_edgesGroups.wref(), tag, my_edges.size());
addEdge(my_edges.wref(), Edge(nodes[0], nodes[1]));
break;
case 2: // Triangle
addInGroup(my_trianglesGroups.wref(), tag, my_triangles.size());
addTriangle(my_triangles.wref(), Triangle(nodes[0], nodes[1], nodes[2]));
break;
case 3: // Quad
addQuad(my_quads.wref(), Quad(nodes[0], nodes[1], nodes[2], nodes[3]));
break;
case 4: // Tetra
addInGroup(my_tetrahedraGroups.wref(), tag, my_tetrahedra.size());
addTetrahedron(my_tetrahedra.wref(), Tetrahedron(nodes[0], nodes[1], nodes[2], nodes[3]));
break;
case 5: // Hexa
addInGroup(my_hexahedraGroups.wref(), tag, my_hexahedra.size());
addHexahedron(my_hexahedra.wref(), Hexahedron(nodes[0], nodes[1], nodes[2], nodes[3], nodes[4], nodes[5], nodes[6], nodes[7]));
break;
case 8: // quadratic edge
addInGroup(my_edgesGroups.wref(), tag, my_edges.size());
addEdge(my_edges.wref(), Edge(nodes[0], nodes[1]));
{
HighOrderEdgePosition hoep;
hoep[0] = nodes[2];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
break;
case 9: // quadratic triangle
addInGroup(my_trianglesGroups.wref(), tag, my_triangles.size());
addTriangle(my_triangles.wref(), Triangle(nodes[0], nodes[1], nodes[2]));
{
HighOrderEdgePosition hoep;
for (j = 0; j < 3; ++j) {
size_t v0 = std::min(nodes[edgesInQuadraticTriangle[j][0]],
nodes[edgesInQuadraticTriangle[j][1]]);
size_t v1 = std::max(nodes[edgesInQuadraticTriangle[j][0]],
nodes[edgesInQuadraticTriangle[j][1]]);
Edge e(v0, v1);
if (edgeSet.find(e) == edgeSet.end()) {
edgeSet.insert(e);
addEdge(my_edges.wref(), v0, v1);
hoep[0] = nodes[j + 3];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
}
}
break;
case 11: // quadratic tetrahedron
addInGroup(my_tetrahedraGroups.wref(), tag, my_tetrahedra.size());
addTetrahedron(my_tetrahedra.wref(), Tetrahedron(nodes[0], nodes[1], nodes[2], nodes[3]));
{
HighOrderEdgePosition hoep;
for (j = 0; j < 6; ++j) {
size_t v0 = std::min(nodes[edgesInQuadraticTetrahedron[j][0]],
nodes[edgesInQuadraticTetrahedron[j][1]]);
size_t v1 = std::max(nodes[edgesInQuadraticTetrahedron[j][0]],
nodes[edgesInQuadraticTetrahedron[j][1]]);
Edge e(v0, v1);
if (edgeSet.find(e) == edgeSet.end()) {
edgeSet.insert(e);
addEdge(my_edges.wref(), v0, v1);
hoep[0] = nodes[j + 4];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
}
}
break;
default:
//if the type is not handled, skip rest of the line
string tmp;
std::getline(file, tmp);
}
}
}
else // gmshFormat >= 4
{
// --- Parsing the $Nodes section --- //
std::getline(file, cmd); // Getting first line of $Nodes
std::istringstream nodesHeader(cmd);
unsigned int nbEntityBlocks, nbNodes, minNodeTag, maxNodeTag;
nodesHeader >> nbEntityBlocks >> nbNodes >> minNodeTag >> maxNodeTag;
for (unsigned int entityIndex = 0; entityIndex < nbEntityBlocks; entityIndex++) // looping over the entity blocks
{
std::getline(file, cmd); // Reading the entity line
std::istringstream entitySummary(cmd);
unsigned int entityDim, entityTag, parametric, nbNodesInBlock;
entitySummary >> entityDim >> entityTag >> parametric >> nbNodesInBlock;
for (unsigned int nodeIndex = 0; nodeIndex < nbNodesInBlock; nodeIndex++)
std::getline(file, cmd); // Reading the node indices lines
for (unsigned int nodeIndex = 0; nodeIndex < nbNodesInBlock; nodeIndex++)
{
std::getline(file, cmd); // Reading the node coordinates
std::istringstream coordinates(cmd);
double x, y, z;
coordinates >> x >> y >> z;
my_positions.push_back(Vec3(x, y, z));
}
}
std::getline(file, cmd);
if (cmd != "$EndNodes")
{
msg_error("MeshGmshLoader") << "'$EndNodes' expected, found '" << cmd << "'";
return false;
}
// --- Parsing the $Elements section --- //
std::getline(file, cmd);
if (cmd != "$Elements")
{
msg_error("MeshGmshLoader") << "'$Elements' expected, found '" << cmd << "'";
return false;
}
std::getline(file, cmd); // Getting first line of $Elements
std::istringstream elementsHeader(cmd);
unsigned int nbElements, minElementTag, maxElementTag;
elementsHeader >> nbEntityBlocks >> nbElements >> minElementTag >> maxElementTag;
// Common information to add second order triangles (elementType = 9) and tetrahedra (elementType = 11)
const unsigned int edgesInQuadraticTriangle[3][2] = { {0,1}, {1,2}, {2,0} };
const unsigned int edgesInQuadraticTetrahedron[6][2] = { {0,1}, {1,2}, {0,2},{0,3},{2,3},{1,3} };
std::set<Edge> edgeSet;
for (unsigned int entityIndex = 0; entityIndex < nbEntityBlocks; entityIndex++) // looping over the entity blocks
{
std::getline(file, cmd); // Reading the entity line
std::istringstream entitySummary(cmd);
unsigned int entityDim, entityTag, nbElementsInBlock, elementType;
entitySummary >> entityDim >> entityTag >> elementType >> nbElementsInBlock;
unsigned int nnodes = 0;
switch (elementType)
{
case 1: // Line
nnodes = 2;
break;
case 2: // Triangle
nnodes = 3;
break;
case 3: // Quadrangle
nnodes = 4;
break;
case 4: // Tetrahedron
nnodes = 4;
break;
case 5: // Hexahedron
nnodes = 8;
break;
case 6: // Prism
nnodes = 6;
break;
case 8: // Second order line
nnodes = 3;
break;
case 9: // Second order triangle
nnodes = 6;
break;
case 11: // Second order tetrahedron
nnodes = 10;
break;
case 15: // Point
nnodes = 1;
break;
default:
msg_error("MeshGmshLoader") << "Elements of type 1, 2, 3, 4, 5, 8, 9, 11 or 15 expected. Element of type " << elementType << " found.";
// nnodes = 0;
}
for (unsigned int elemIndex = 0; elemIndex < nbElementsInBlock; elemIndex++)
{
std::getline(file, cmd); // Reading the element info
std::istringstream elementInfo(cmd);
unsigned int elementTag;
elementInfo >> elementTag;
type::vector<unsigned int> nodes;
unsigned int nodeId = 0;
nodes.resize(nnodes);
for (unsigned int i = 0; i < nnodes; i++)
{
elementInfo >> nodeId;
nodes[i] = nodeId - 1; //To account for the fact that node indices in the MSH file format start with 1 instead of 0
}
switch (elementType)
{
case 1: // Line
addInGroup(my_edgesGroups.wref(), elementTag, my_edges.size());
addEdge(my_edges.wref(), Edge(nodes[0], nodes[1]));
break;
case 2: // Triangle
addInGroup(my_trianglesGroups.wref(), elementTag, my_triangles.size());
addTriangle(my_triangles.wref(), Triangle(nodes[0], nodes[1], nodes[2]));
break;
case 3: // Quadrangle
addQuad(my_quads.wref(), Quad(nodes[0], nodes[1], nodes[2], nodes[3]));
break;
case 4: // Tetrahedron
addInGroup(my_tetrahedraGroups.wref(), elementTag, my_tetrahedra.size());
addTetrahedron(my_tetrahedra.wref(), Tetrahedron(nodes[0], nodes[1], nodes[2], nodes[3]));
break;
case 5: // Hexahedron
addInGroup(my_hexahedraGroups.wref(), elementTag, my_hexahedra.size());
addHexahedron(my_hexahedra.wref(), Hexahedron(nodes[0], nodes[1], nodes[2], nodes[3], nodes[4], nodes[5], nodes[6], nodes[7]));
break;
case 8: // Second order line
addInGroup(my_edgesGroups.wref(), elementTag, my_edges.size());
addEdge(my_edges.wref(), Edge(nodes[0], nodes[1]));
{
HighOrderEdgePosition hoep;
hoep[0] = nodes[2];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
break;
case 9: // Second order triangle
addInGroup(my_trianglesGroups.wref(), elementTag, my_triangles.size());
addTriangle(my_triangles.wref(), Triangle(nodes[0], nodes[1], nodes[2]));
{
HighOrderEdgePosition hoep;
for (size_t j = 0; j < 3; ++j)
{
size_t v0 = std::min(nodes[edgesInQuadraticTriangle[j][0]],
nodes[edgesInQuadraticTriangle[j][1]]);
size_t v1 = std::max(nodes[edgesInQuadraticTriangle[j][0]],
nodes[edgesInQuadraticTriangle[j][1]]);
Edge e(v0, v1);
if (edgeSet.find(e) == edgeSet.end())
{
edgeSet.insert(e);
addEdge(my_edges.wref(), v0, v1);
hoep[0] = nodes[j + 3];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
}
}
break;
case 11: // Second order tetrahedron
addInGroup(my_tetrahedraGroups.wref(), elementTag, my_tetrahedra.size());
addTetrahedron(my_tetrahedra.wref(), Tetrahedron(nodes[0], nodes[1], nodes[2], nodes[3]));
{
HighOrderEdgePosition hoep;
for (size_t j = 0; j < 6; ++j)
{
size_t v0 = std::min(nodes[edgesInQuadraticTetrahedron[j][0]],
nodes[edgesInQuadraticTetrahedron[j][1]]);
size_t v1 = std::max(nodes[edgesInQuadraticTetrahedron[j][0]],
nodes[edgesInQuadraticTetrahedron[j][1]]);
Edge e(v0, v1);
if (edgeSet.find(e) == edgeSet.end())
{
edgeSet.insert(e);
addEdge(my_edges.wref(), v0, v1);
hoep[0] = nodes[j + 4];
hoep[1] = my_edges.size() - 1;
hoep[2] = 1;
hoep[3] = 1;
my_highOrderEdgePositions.push_back(hoep);
}
}
}
break;
// default: if the type is not handled, nothing to be done
}
} // end of loop over the elements in one entity block
} //end of loop over the entity blocks
}
normalizeGroup(my_edgesGroups.wref());
normalizeGroup(my_trianglesGroups.wref());
normalizeGroup(my_tetrahedraGroups.wref());
normalizeGroup(my_hexahedraGroups.wref());
file >> cmd;
if (cmd != "$ENDELM" && cmd != "$EndElements")
{
msg_error("MeshGmshLoader") << "'$ENDELM' or '$EndElements' expected, found '" << cmd << "'";
file.close();
return false;
}
file.close();
return true;
}
} //namespace sofa::component::io::mesh