ImmersedBoundarySvgWriter.cpp

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#include "ImmersedBoundarySvgWriter.hpp"
#include "ImmersedBoundaryMesh.hpp"
 
template <unsigned DIM>
ImmersedBoundarySvgWriter<DIM>::ImmersedBoundarySvgWriter()
    : AbstractCellBasedSimulationModifier<DIM>(),
      mSamplingMultiple(100u),
      mSvgSize(1600.0),
      mOutputDirectory(""),
      mSvgHeader(""),
      mSvgFooter("")
{
}
 
template <unsigned DIM>
ImmersedBoundarySvgWriter<DIM>::~ImmersedBoundarySvgWriter()
{
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::UpdateAtEndOfTimeStep(
    AbstractCellPopulation<DIM, DIM>& rCellPopulation)
{
    if (SimulationTime::Instance()->GetTimeStepsElapsed() % mSamplingMultiple == 0)
    {
        ImmersedBoundaryMesh<DIM, DIM> *p_mesh = static_cast<ImmersedBoundaryMesh<DIM, DIM> *>(&(rCellPopulation.rGetMesh()));
 
        // Get the number of time steps elapsed to use in the file name, and zero-pad it
        std::stringstream time;
        time << std::setfill('0') << std::setw(6) << SimulationTime::Instance()->GetTimeStepsElapsed();
 
        // Open the svg file for writing
        std::string full_file_name = "results_" + time.str() + ".svg";
        OutputFileHandler results_handler(mOutputDirectory, false);
        out_stream svg_file = results_handler.OpenOutputFile(full_file_name);
 
        (*svg_file) << mSvgHeader;
 
        // Add all nodes to the svg file
        double node_rad = p_mesh->GetAverageNodeSpacingOfElement(0, false) * 0.35 * mSvgSize;
        for (auto it = p_mesh->GetNodeIteratorBegin();
             it != p_mesh->GetNodeIteratorEnd();
             ++it)
        {
            AddPointToSvgFile(svg_file, it->rGetLocation(), it->GetRegion(), node_rad);
        }
 
        (*svg_file) << mSvgFooter;
 
        svg_file->close();
    }
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::SetupSolve(
    AbstractCellPopulation<DIM, DIM>& rCellPopulation,
    std::string outputDirectory)
{
    mOutputDirectory = outputDirectory;
 
    // Define colours
    std::string bg_col = "darkgray";
    std::string region0_col = "#990000"; // dark red
    std::string region1_col = "#cc0000"; // light red
    std::string region2_col = "#e68a00"; // dark orange
    std::string region3_col = "#ff9900"; // light orange
    std::string region4_col = "#006666"; // dark teal
    std::string region5_col = "#009999"; // light teal
    std::string region6_col = "#000099"; // dark blue
    std::string region7_col = "#0000cc"; // light blue
    std::string region8_col = "#FFFFFF"; // white
    std::string glyph0_col = "DarkRed"; // white
    std::string glyph1_col = "DarkBlue"; // white
    std::string glyph2_col = "DarkGreen"; // white
 
    std::stringstream header;
 
    // Set precision so as not to write out too many decimal places of uncompressed text
    header << std::setprecision(5);
 
    // Output svg header to file
    header << "<svg version=\"1.1\" baseProfile=\"full\" width=\""
           << mSvgSize <<"px\" height=\"" << mSvgSize << "px\" "
           << "viewBox=\"0 0 " << mSvgSize << " " << mSvgSize << "\" "
           << "xmlns=\"http://www.w3.org/2000/svg\">" << "\n";
 
    // Add text/css style for elements
    header << "<style type=\"text/css\">" << "\n"
           << "\t.bg_rect{fill:" << bg_col << ";}" << "\n"
           << "\t.node_0{fill:" << region0_col << ";}" << "\n"
           << "\t.node_1{fill:" << region1_col << ";}" << "\n"
           << "\t.node_2{fill:" << region2_col << ";}" << "\n"
           << "\t.node_3{fill:" << region3_col << ";}" << "\n"
           << "\t.node_4{fill:" << region4_col << ";}" << "\n"
           << "\t.node_5{fill:" << region5_col << ";}" << "\n"
           << "\t.node_6{fill:" << region6_col << ";}" << "\n"
           << "\t.node_7{fill:" << region7_col << ";}" << "\n"
           << "\t.node_8{fill:" << region8_col << ";}" << "\n"
           << "\t.glyph_0{fill:" << glyph0_col << ";}" << "\n"
           << "\t.glyph_1{fill:" << glyph1_col << ";}" << "\n"
           << "\t.glyph_2{fill:" << glyph2_col << ";}" << "\n"
           << "</style>" << "\n";
 
    // Add background rectangle
    header << "<rect class=\"bg_rect\" width=\"" << mSvgSize << "\" height=\"" << mSvgSize << "\"/>" << "\n";
 
    mSvgHeader = header.str();
    mSvgFooter = "</svg>\n";
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::AddPointToSvgFile(
    out_stream& rSvgFile,
    c_vector<double, DIM> location,
    unsigned region,
    double rad)
{
    double scaled_x = location[0] * mSvgSize;
    double scaled_y = (1.0 - location[1]) * mSvgSize;
 
    (*rSvgFile) << "<circle class=\"node_" << region << "\" "
                << "cx=\"" << scaled_x << "\" "
                << "cy=\"" << scaled_y << "\" "
                << "r=\"" << rad << "\"/>" << "\n";
 
    // Account for possible wrap-around of glyph in x
    if (scaled_x < rad)
    {
        (*rSvgFile) << "<circle class=\"node_" << region << "\" "
                    << "cx=\"" << scaled_x + mSvgSize << "\" "
                    << "cy=\"" << scaled_y << "\" "
                    << "r=\"" << rad << "\"/>" << "\n";
    }
    else if (scaled_x > mSvgSize - rad)
    {
        (*rSvgFile) << "<circle class=\"node_" << region << "\" "
                    << "cx=\"" << scaled_x - mSvgSize << "\" "
                    << "cy=\"" << scaled_y << "\" "
                    << "r=\"" << rad << "\"/>" << "\n";
    }
 
    // Account for possible wrap-around of glyph in y
    if (scaled_y < rad)
    {
        (*rSvgFile) << "<circle class=\"node_" << region << "\" "
                    << "cx=\"" << scaled_x << "\" "
                    << "cy=\"" << scaled_y + mSvgSize << "\" "
                    << "r=\"" << rad << "\"/>" << "\n";
    }
    else if (scaled_y > mSvgSize - rad)
    {
        (*rSvgFile) << "<circle class=\"node_" << region << "\" "
                    << "cx=\"" << scaled_x << "\" "
                    << "cy=\"" << scaled_y - mSvgSize << "\" "
                    << "r=\"" << rad << "\"/>" << "\n";
    }
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::OutputSimulationModifierParameters(
    out_stream& rParamsFile)
{
    // Call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
 
template <unsigned DIM>
unsigned ImmersedBoundarySvgWriter<DIM>::GetSamplingMultiple() const
{
    return mSamplingMultiple;
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::SetSamplingMultiple(
    unsigned samplingMultiple)
{
    mSamplingMultiple = samplingMultiple;
}
 
template <unsigned DIM>
double ImmersedBoundarySvgWriter<DIM>::GetSvgSize() const
{
    return mSvgSize;
}
 
template <unsigned DIM>
void ImmersedBoundarySvgWriter<DIM>::SetSvgSize(double svgSize)
{
    mSvgSize = svgSize;
}
 
// Explicit instantiation
template class ImmersedBoundarySvgWriter<1>;
template class ImmersedBoundarySvgWriter<2>;
template class ImmersedBoundarySvgWriter<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundarySvgWriter)