.. _PhysiCell_java_CancerImmune_Initial_java:

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

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

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   <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.CellDefinition;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.biofvm.VectorUtil;
    import ru.biosoft.physicell.core.standard.StandardModels;
    import java.util.List;
    import java.util.ArrayList;

    public class Initial extends InitialCellsArranger
    {      
        @Override
        public void arrange(Model model) throws Exception
        {
            CellDefinition cd = model.getCellDefinition( "cancer cell" );
            double cellRadius = cd.phenotype.geometry.radius;
            //        double cell_spacing = 0.95 * 2.0 * cell_radius;

            double tumorRadius = 250;//model.getParameterDouble( "tumor_radius" );// 250.0;  
            boolean use2D = model.getMicroenvironment().options.simulate2D;
            List<double[]> positions = createSpherePositions( new double[] {750,750, 750}, cellRadius, tumorRadius, use2D );
            //        System.out.println( "creating " + positions.size() + " closely-packed tumor cells ... " );

            double imm_mean = model.getParameterDouble( "tumor_mean_immunogenicity" );
            double imm_sd = model.getParameterDouble( "tumor_immunogenicity_standard_deviation" );

            for( double[] position : positions )
            {
                Cell pCell = Cell.createCell( cd, model, position ); // tumor cell 
                double oncoprotein = Math.max( 0, model.getRNG().NormalRandom( imm_mean, imm_sd ) );
                pCell.customData.set( "oncoprotein", oncoprotein );
            }
        } 

        private List<double[]> createSpherePositions(double[] center, double cellRadius, double sphereRadius, boolean use2D)
        {
            List<double[]> cells = new ArrayList<>();
            int xc = 0, zc = 0;
            double xSpacing = cellRadius * Math.sqrt( 3 );
            double ySpacing = cellRadius * 2;
            double zSpacing = cellRadius * Math.sqrt( 3 );
            if( use2D )
            {
                for( double x = -sphereRadius; x < sphereRadius; x += xSpacing, xc++ )
                {
                    for( double y = -sphereRadius; y < sphereRadius; y += ySpacing )
                    {
                        double[] tempPoint = new double[3];
                        tempPoint[0] = x + ( zc % 2 ) * 0.5 * cellRadius  + center[0];
                        tempPoint[1] = y + ( xc % 2 ) * cellRadius  + center[1];
                        tempPoint[2] = 0;

                        if( VectorUtil.dist( tempPoint, center ) < sphereRadius )
                        {
                            cells.add( tempPoint );
                        }
                    }
                }
            }
            else
            {
                for( double z = -sphereRadius; z < sphereRadius; z += zSpacing, zc++ )
                {
                    for( double x = -sphereRadius; x < sphereRadius; x += xSpacing, xc++ )
                    {
                        for( double y = -sphereRadius; y < sphereRadius; y += ySpacing )
                        {
                            double[] tempPoint = new double[3];
                            tempPoint[0] = x + ( zc % 2 ) * 0.5 * cellRadius + center[0];
                            tempPoint[1] = y + ( xc % 2 ) * cellRadius + center[1];
                            tempPoint[2] = z + center[2];

                            if( VectorUtil.dist( tempPoint, center ) < sphereRadius )
                            {
                                cells.add( tempPoint );
                            }
                        }
                    }
                }
            }
            return cells;
        }
    }