std::vector<double> PottsMeshReader<SPACE_DIM>::GetNextNode()
{
std::vector<double> node_data;
std::string buffer;
GetNextLineFromStream(mNodesFile, buffer);
std::stringstream buffer_stream(buffer);
unsigned index;
buffer_stream >> index;
unsigned offset = mIndexFromZero ? 0 : 1;
if (index != mNodesRead + offset)
{
EXCEPTION("Data for node " << mNodesRead << " missing");
}
double node_value;
for (unsigned i=0; i<SPACE_DIM+1; i++)
{
buffer_stream >> node_value;
node_data.push_back(node_value);
}
mNodesRead++;
return node_data;
}
ElementData PottsMeshReader<SPACE_DIM>::GetNextElementData()
{
// Create data structure for this element
ElementData element_data;
std::string buffer;
GetNextLineFromStream(mElementsFile, buffer);
std::stringstream buffer_stream(buffer);
unsigned element_index;
buffer_stream >> element_index;
unsigned offset = mIndexFromZero ? 0 : 1;
if (element_index != mElementsRead + offset)
{
EXCEPTION("Data for element " << mElementsRead << " missing");
}
unsigned num_nodes_in_element;
buffer_stream >> num_nodes_in_element;
// Store node indices owned by this element
unsigned node_index;
for (unsigned i=0; i<num_nodes_in_element; i++)
{
buffer_stream >> node_index;
element_data.NodeIndices.push_back(node_index - offset);
}
if (mNumElementAttributes > 0)
{
assert(mNumElementAttributes==1);
unsigned attribute_value;
buffer_stream >> attribute_value;
element_data.AttributeValue = attribute_value;
}
void TrianglesMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadHeaders()
{
/*
* Reading node file header
*/
std::string buffer;
GetNextLineFromStream(mNodesFile, buffer);
std::stringstream node_header_line(buffer);
unsigned dimension;
node_header_line >> mNumNodes >> dimension >> mNumNodeAttributes >> mMaxNodeBdyMarker;
if (SPACE_DIM != dimension)
{
EXCEPTION("SPACE_DIM != dimension read from file ");
}
// Is there anything else on the header line?
std::string extras;
node_header_line >> extras;
if (extras == "BIN")
{
mFilesAreBinary = true;
mNodeFileDataStart = mNodesFile.tellg(); // Record the position of the first byte after the header.
mNodeItemWidth = SPACE_DIM * sizeof(double);
// We enforce that all binary files (written by Chaste) are indexed from zero
mIndexFromZero = true;
}
else
{
// #1621 - ncl files are only supported in binary read mode.
assert(!mNclFileAvailable);
// Get the next line to see if it is indexed from zero or not
GetNextLineFromStream(mNodesFile, buffer);
std::stringstream node_first_line(buffer);
unsigned first_index;
node_first_line >> first_index;
assert(first_index == 0 || first_index == 1);
mIndexFromZero = (first_index == 0);
// Close, reopen, skip header
mNodesFile.close();
OpenNodeFile();
GetNextLineFromStream(mNodesFile, buffer);
}
/*
* Reading element file header
*/
GetNextLineFromStream(mElementsFile, buffer);
std::stringstream element_header_line(buffer);
unsigned extra_attributes = 0;
if (ELEMENT_DIM == SPACE_DIM)
{
element_header_line >> mNumElements >> mNumElementNodes >> mNumElementAttributes;
extra_attributes = mNumElementAttributes;
// Is there anything else on the header line?
std::string element_extras;
element_header_line >> element_extras;
if (element_extras == "BIN")
{
// Double check for binaryness
assert (mFilesAreBinary);
}
else if (element_extras == "HEX")
{
mMeshIsHexahedral = true;
if ( ELEMENT_DIM == 2 )
{
mNodesPerElement = 4;
mNodesPerBoundaryElement = 2;
}
if ( ELEMENT_DIM == 3 )
{
mNodesPerElement = 8;
mNodesPerBoundaryElement = 4;
}
}
else
{
assert (element_extras == "");
}
// The condition below allows the writer to cope with a NodesOnlyMesh
if (mNumElements != 0)
{
if (mNumElementNodes != mNodesPerElement)
{
EXCEPTION("Number of nodes per elem, " << mNumElementNodes << ", does not match "
<< "expected number, " << mNodesPerElement << " (which is calculated given "
<< "the order of elements chosen, " << mOrderOfElements << " (1=linear, 2=quadratics)");
}
}
}
