final int LAYER_3_CELLS_PER_COLUMN = 1;
double percentMinimumOverlap = 20;
int desiredLocalActivity = 3;
Neocortex neocortex = new Neocortex(new Region("root", 60, 60, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), new RegionToRegionRectangleConnect());
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(29, 60)), new Region("A", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.addToCurrentRegion(new Rectangle(new Point(30, 0), new Point(60, 60)), new Region("B", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.changeCurrentRegionTo("A");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), new Region("C", 125, 125, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.changeCurrentRegionTo("B");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), new Region("D", 125, 125, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.changeCurrentRegionTo("C");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(62, 125)), new Region("E", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.addToCurrentRegion(new Rectangle(new Point(63, 0), new Point(125, 125)), new Region("F", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.changeCurrentRegionTo("D");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(62, 125)), new Region("G", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
neocortex.addToCurrentRegion(new Rectangle(new Point(63, 0), new Point(125, 125)), new Region("H", 125, 125, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity), 0, 0);
Region I = new Region("I", 250, 250, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity);
Layer5Region M = new Layer5Region("M", 250, 250, LAYER_4_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity);
neocortex.changeCurrentRegionTo("E");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), I, 0, 0);
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), M, 0, 0);
Region J = new Region("J", 250, 250, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity);
neocortex.changeCurrentRegionTo("F");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), J, 0, 0);
Region K = new Region("K", 250, 250, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity);
neocortex.changeCurrentRegionTo("G");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), K, 0, 0);
Region L = new Region("L", 250, 250, LAYER_3_CELLS_PER_COLUMN, percentMinimumOverlap, desiredLocalActivity);
neocortex.changeCurrentRegionTo("H");
neocortex.addToCurrentRegion(new Rectangle(new Point(0, 0), new Point(125, 125)), L, 0, 0);
// NOTE: I, J, K, & L are connected to different parts of the same Retina
Retina retina = new Retina(1000, 1000);
AbstractSensorCellsToRegionConnect opticNerve = new SensorCellsToRegionRectangleConnect();
opticNerve.connect(retina.getVisionCells(new Rectangle(new Point(0, 0), new Point(500, 500))), I, 0, 0); // .getVisionCells(topLeftPoint, bottomRightPoint)
opticNerve.connect(retina.getVisionCells(new Rectangle(new Point(0, 500), new Point(500, 1000))), J, 0, 0);
opticNerve.connect(retina.getVisionCells(new Rectangle(new Point(500, 0), new Point(1000, 500))), K, 0, 0);
opticNerve.connect(retina.getVisionCells(new Rectangle(new Point(500, 500), new Point(1000, 1000))), L, 0, 0);
NervousSystem nervousSystem = new NervousSystem(neocortex, null, retina); // no LGN with circle surround input for now
return nervousSystem;
}