PottsMeshReader.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste 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.

Chaste 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. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#include "PottsMeshReader.hpp"
#include "Exception.hpp"

#include <sstream>

template<unsigned SPACE_DIM>
PottsMeshReader<SPACE_DIM>::PottsMeshReader(std::string pathBaseName)
    : mFilesBaseName(pathBaseName),
      mIndexFromZero(false), // initially assume that nodes are not numbered from zero
      mNumNodes(0),
      mNumElements(0),
      mNodesRead(0),
      mElementsRead(0),
      mNumElementAttributes(0)
{
    OpenFiles();
    ReadHeaders();
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumElements() const
{
    return mNumElements;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumNodes() const
{
    return mNumNodes;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumElementAttributes() const
{
    return mNumElementAttributes;
}

template<unsigned SPACE_DIM>
ElementData PottsMeshReader<SPACE_DIM>::GetNextFaceData()
{
    ElementData ret;
    ret.NodeIndices = std::vector<unsigned>();
    ret.AttributeValue = 0;
    return ret;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumFaces() const
{
    return 0;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::Reset()
{
    CloseFiles();
    OpenFiles();
    ReadHeaders();

    mNodesRead = 0;
    mElementsRead = 0;
}

template<unsigned SPACE_DIM>
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;
}

template<unsigned SPACE_DIM>
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;
    }
    else
    {
        element_data.AttributeValue = 0;
    }

    mElementsRead++;
    return element_data;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenFiles()
{
    OpenNodeFile();
    OpenElementsFile();
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenNodeFile()
{
    // Nodes definition
    std::string file_name = mFilesBaseName + ".node";
    mNodesFile.open(file_name.c_str());
    if (!mNodesFile.is_open())
    {
        EXCEPTION("Could not open data file: " + file_name);
    }
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenElementsFile()
{
    // Elements definition
    std::string file_name;
    file_name = mFilesBaseName + ".cell";

    mElementsFile.open(file_name.c_str());
    if (!mElementsFile.is_open())
    {
        EXCEPTION("Could not open data file: " + file_name);
    }
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::ReadHeaders()
{
    std::string buffer;

    GetNextLineFromStream(mNodesFile, buffer);
    std::stringstream buffer_stream(buffer);
    buffer_stream >> mNumNodes >> mNumNodeAttributes;

    // Get the next line to see if nodes are indexed from zero or not
    GetNextLineFromStream(mNodesFile, buffer);
    std::stringstream node_buffer_stream(buffer);

    unsigned first_index;
    node_buffer_stream >> first_index;
    assert(first_index == 0 || first_index == 1);
    mIndexFromZero = (first_index == 0);

    // Close, reopen, skip header
    mNodesFile.close();
    OpenNodeFile();
    GetNextLineFromStream(mNodesFile, buffer);

    GetNextLineFromStream(mElementsFile, buffer);
    std::stringstream element_buffer_stream(buffer);

    element_buffer_stream >> mNumElements >> mNumElementAttributes;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::CloseFiles()
{
    mNodesFile.close();
    mElementsFile.close();
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::GetNextLineFromStream(std::ifstream& fileStream, std::string& rawLine)
{
    bool line_is_blank;

    do
    {
        getline(fileStream, rawLine);

        if (fileStream.eof())
        {
            EXCEPTION("Cannot get the next line from node or element file due to incomplete data");
        }

        // Get rid of any comment
        rawLine = rawLine.substr(0,rawLine.find('#', 0));

        line_is_blank = (rawLine.find_first_not_of(" \t", 0) == std::string::npos);
    }
    while (line_is_blank);
}

// Explicit instantiation

template class PottsMeshReader<1>;
template class PottsMeshReader<2>;
template class PottsMeshReader<3>;