.. _PhysiCell_java_Heterogeneity_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.biofvm.Microenvironment;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellDefinition;
    import ru.biosoft.physicell.core.Model;
    import ru.biosoft.physicell.ui.Visualizer;
    import ru.biosoft.physicell.core.InitialCellsArranger;

    public class Initial extends InitialCellsArranger
    {      
        private static final String CUSTOM_ONCOPROTEIN = "custom:oncoprotein";

        @Override
        public void arrange(Model model) throws Exception
        {
            CellDefinition pCD = model.getCellDefinition( "cancer cell" );
            double cellRadius = pCD.phenotype.geometry.radius;
            pCD.parameters.o2_proliferation_saturation = 38;
            pCD.parameters.o2_reference = 38;
            double cellSpacing = 0.95 * 2.0 * cellRadius;
            double tumorRadius = model.getParameterDouble( "tumor_radius" ); // 250.0; 
            double x = 0.0;
            double xOuter = tumorRadius;
            double y = 0.0;
            double pMean = model.getParameterDouble( "oncoprotein_mean" );
            double pSD = model.getParameterDouble( "oncoprotein_sd" );
            double pMin = model.getParameterDouble( "oncoprotein_min" );
            double pMax = model.getParameterDouble( "oncoprotein_max" );
            Cell cell;
            int n = 0;
            while( y < tumorRadius )
            {
                x = 0.0;
                if( n % 2 == 1 )
                    x = 0.5 * cellSpacing;
                xOuter = Math.sqrt( tumorRadius * tumorRadius - y * y );

                while( x < xOuter )
                {
                    cell = Cell.createCell( pCD, model, new double[] {x, y, 0.0} ); // tumor cell 
                    double p = model.getRNG().NormalRestricted( pMean, pSD, pMin, pMax );
                    model.signals.setSingleBehavior( cell, CUSTOM_ONCOPROTEIN, p );

                    if( Math.abs( y ) > 0.01 )
                    {
                        cell = Cell.createCell( pCD, model, new double[] {x, -y, 0.0} ); // tumor cell 
                        p = model.getRNG().NormalRestricted( pMean, pSD, pMin, pMax );
                        model.signals.setSingleBehavior( cell, CUSTOM_ONCOPROTEIN, p );
                    }
                    if( Math.abs( x ) > 0.01 )
                    {
                        cell = Cell.createCell( pCD, model, new double[] { -x, y, 0} ); // tumor cell 
                        p = model.getRNG().NormalRestricted( pMean, pSD, pMin, pMax );
                        model.signals.setSingleBehavior( cell, CUSTOM_ONCOPROTEIN, p );

                        if( Math.abs( y ) > 0.01 )
                        {
                            cell = Cell.createCell( pCD, model, new double[] { -x, -y, 0} ); // tumor cell
                            p = model.getRNG().NormalRestricted( pMean, pSD, pMin, pMax );
                            model.signals.setSingleBehavior( cell, CUSTOM_ONCOPROTEIN, p );
                        }
                    }
                    x += cellSpacing;
                }
                y += cellSpacing * Math.sqrt( 3.0 ) / 2.0;
                n++;
            }
        }
    }