CsvGzExporter.cpp

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/*
 * Copyright 2011-2016 Universiteit Antwerpen
 *
 * Licensed under the EUPL, Version 1.1 or  as soon they will be approved by
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl5
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing
 * permissions and limitations under the Licence.
 */
#include "CsvGzExporter.h"

#include "bio/Cell.h"
#include "bio/Mesh.h"
#include "bio/Wall.h"
#include "math/MeshGeometry.h"
#include "sim/CoreData.h"
#include "sim/SimInterface.h"

#include <QFile>
#include <QString>
#include <QTextStream>
#include <fstream>
#include <tuple>

namespace SimPT_Shell {

using namespace std;
using namespace SimPT_Sim;

bool CsvGzExporter::Export(shared_ptr<SimPT_Sim::SimInterface> sim, string const& file_path, bool overwrite)
{
        if (ifstream(file_path).good()) {
                if (overwrite) {
                        // Qt doesn't overwrite by default, must delete file first
                        QFile::remove(QString::fromStdString(file_path));
                } else {
                        return false; // Don't overwrite
                }
        }

        bool status = false;
        QFile file(QString::fromStdString(file_path));
        if (file.open(QIODevice::WriteOnly)) {
                const auto mesh = sim->GetCoreData().m_mesh.get();
                QTextStream stream(&file);
                StreamCellData(mesh, stream);
                StreamWallData(mesh, stream);
                StreamMeshData(mesh, stream);
                file.close();
                status = true;
        }
        return status;
}

string CsvGzExporter::GetFileExtension()
{
        return "csv.gz";
}

void CsvGzExporter::StreamCellData(const Mesh* mesh, QTextStream& csv_stream)
{
        csv_stream << "\"Cell Index\",\"Center of mass (x)\",\"Center of mass (y)\",\"Cell area\",\"Cell length\"";

        const unsigned int num_chem = mesh->GetNumChemicals();

        for (unsigned int c = 0; c < num_chem; c++) {
                csv_stream << ",\"Chemical " << c << "\"";
        }
        csv_stream << endl;
        for (auto const& cell : mesh->GetCells()) {
                auto centroid = cell->GetCentroid();
                csv_stream << cell->GetIndex() << ", " << centroid[0] << ", " << centroid[1] << ", "
                                << cell->GetArea() << ", " << get<0>(cell->GetGeoData().GetEllipseAxes());
                for (unsigned int c = 0; c < num_chem; c++) {
                        csv_stream << ", " << cell->GetChemical(c);
                }
                csv_stream << endl;
        }
}

void CsvGzExporter::StreamMeshData(const Mesh* mesh, QTextStream& csv_stream)
{
        csv_stream << "\"Morph area\",\"Number of cells\",\"Number of nodes\",\"Compactness\",\"Hull area\",\"Morph circumference\",\"Hull circumference\""
                        << endl;

        auto res_tuple = MeshGeometry::Compactness(mesh);
        const double res_compactness      = get<0>(res_tuple);
        const double res_area             = get<1>(res_tuple);
        const double hull_circumference   = get<2>(res_tuple);
        const double morph_circumference  = mesh->GetBoundaryPolygon()->GetCircumference();
        const double mesh_area            = mesh->GetBoundaryPolygon()->GetArea();

        csv_stream << mesh_area << ", " << mesh->GetCells().size() << ", " << mesh->GetNodes().size()
                        << ", " << res_compactness << ", " << res_area << ", "
                        << morph_circumference << ", " << hull_circumference << endl;
}

void CsvGzExporter::StreamWallData(const Mesh* mesh, QTextStream& csv_stream)
{
        csv_stream << "\"Wall Index\",\"Cell A\",\"Cell B\",\"Length\"";

        const unsigned int num_chem = mesh->GetNumChemicals();

        for (unsigned int c = 0; c < num_chem; c++) {
                csv_stream << ",\"Transporter A:" << c << "\"";
        }
        for (unsigned int c = 0; c < num_chem; c++) {
                csv_stream << ",\"Transporter B:" << c << "\"";
        }
        csv_stream << endl;
        for (auto const& wall : mesh->GetWalls()) {
                csv_stream << wall->GetIndex() << "," << wall->GetC1()->GetIndex() << ","
                                << wall->GetC2()->GetIndex() << "," << wall->GetLength();
                for (unsigned int c = 0; c < num_chem; c++) {
                        csv_stream << "," << wall->GetTransporters1(c);
                }
                for (unsigned int c = 0; c < num_chem; c++) {
                        csv_stream << "," << wall->GetTransporters2(c);
                }
                csv_stream << endl;
        }
}

} // namespace