.. _PhysiCell_java_ODEEnergy_Initial_java:

Initial.java
============

.. role:: raw-html(raw)
   :format: html

.. raw:: html

   <style>
   pre {
      white-space: pre-wrap !important;       /* Сохраняет пробелы, но разрешает перенос */
      word-wrap: break-word !important;       /* Переносит длинные слова */
      overflow-wrap: break-word !important;   /* Альтернатива для совместимости */
      hyphens: auto !important;               /* Перенос с тире */
   }
   </style>

.. code-block:: console

    import ru.biosoft.physicell.core.Model;
    import ru.biosoft.physicell.core.PhysiCellUtilities;
    import ru.biosoft.physicell.core.InitialCellsArranger;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellDefinition;
    import ru.biosoft.physicell.biofvm.Microenvironment;
    import ru.biosoft.physicell.biofvm.VectorUtil;
    import java.util.List;
    import java.util.ArrayList;

    public class Initial extends InitialCellsArranger
    {      
        @Override
        public void arrange(Model model) throws Exception
        {
            Microenvironment m = model.getMicroenvironment();
            int oxygenIndex = m.findDensityIndex( "oxygen" );
            int glucoseIndex = m.findDensityIndex( "glucose" );
            int lactateIndex = m.findDensityIndex( "lactate" );

            CellDefinition cd = model.getCellDefinition( "default" );
            double cellRadius = cd.phenotype.geometry.radius;
            double initialTumorRadius = 100;

            List<double[]> positions = createCirclePositions( cellRadius, initialTumorRadius );
            for( int i = 0; i < positions.size(); i++ )
            {
                Cell pCell = Cell.createCell( cd, model, positions.get( i ) );
                model.getSignals().setSingleBehavior( pCell, "custom:intra_oxy", model.getParameterDouble( "initial_internal_oxygen" ) );
                model.getSignals().setSingleBehavior( pCell, "custom:intra_glu", model.getParameterDouble( "initial_internal_glucose" ) );
                model.getSignals().setSingleBehavior( pCell, "custom:intra_lac", model.getParameterDouble( "initial_internal_lactate" ) );
                model.getSignals().setSingleBehavior( pCell, "custom:intra_energy", model.getParameterDouble( "initial_energy" ) );
                double cellVolume = pCell.phenotype.volume.total;
                double[] substrates = pCell.phenotype.molecular.internSubstrates;
                substrates[oxygenIndex] = model.getSignals().getSingleSignal( pCell, "custom:intra_oxy" ) * cellVolume;
                substrates[glucoseIndex] = model.getSignals().getSingleSignal( pCell, "custom:intra_glu" ) * cellVolume;
                substrates[lactateIndex] = model.getSignals().getSingleSignal( pCell, "custom:intra_lac" ) * cellVolume;
                pCell.phenotype.intracellular.start();
                pCell.phenotype.intracellular.setParameterValue( "$Intracellular.Energy", model.getSignals().getSingleSignal( pCell, "custom:intra_energy" ) );
            }
        }

        public static List<double[]> createCirclePositions(double cellRadius, double sphereRadius)
        {
            List<double[]> result = new ArrayList<>();
            int xc = 0;
            double xSpacing = cellRadius * Math.sqrt( 3 );
            double ySpacing = cellRadius * Math.sqrt( 3 );

            for( double x = -sphereRadius; x < sphereRadius; x += xSpacing, xc++ )
            {
                for( double y = -sphereRadius; y < sphereRadius; y += ySpacing )
                {
                    double[] tempPoint = new double[3];
                    tempPoint[1] = y + ( xc % 2 ) * cellRadius;
                    tempPoint[0] = x;
                    tempPoint[2] = 0;
                    if( Math.sqrt( VectorUtil.norm_squared( tempPoint ) ) < sphereRadius )
                    {
                        result.add( tempPoint );
                    }
                }
            }
            return result;
        }
    }