Examples of model.MARK_II.Neocortex

model.MARK_II.Neocortex
Neocortex is a tree(undirected graph) of Regions. Each Region in the Neocortex can have as many children Regions as necessary. Each Region can receive input from input SensorCellLayers, a lower Region, or a higher Region. Input to Neocortex: activity of Cells within VisionCellLayer, AudioCellLayer, etc. Output from Neocortex: activity of Cells/Columns within root Region. @author Quinn Liu (quinnliu@vt.edu) @author Michael Cogswell (cogswell@vt.edu) @version July 12, 2014

        final int LAYER_4_CELLS_PER_COLUMN = 4;
        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();

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        return nervousSystem;
    }


    public void test_HowToRunSingleLearningAlgorithmOnNervousSystem() throws IOException {
        Neocortex neocortex = this.partialNervousSystem.getCNS().getBrain().getCerebrum().getCerebralCortex().getNeocortex();


        ImageViewer imageViewer = new ImageViewer("imageOfHumanFace1000x1000pixels.bmp",
                this.partialNervousSystem.getPNS().getSNS().getRetina());


        final int NUMBER_OF_TIMES_TO_RUN_LEARNING_ALGORITHM = 1000;
        for (int i = 0; i < NUMBER_OF_TIMES_TO_RUN_LEARNING_ALGORITHM; i++) {


            neocortex.runSingleLearningAlgorithmOneTimeStep();


            Layer5Region layer5Region = (Layer5Region) neocortex.getRegion("M");
            Point3D nextRetinaPosition = layer5Region
                    .getMotorOutput(imageViewer.getBoxRetinaIsStuckIn());
            imageViewer.saccadeRetinaToNewPositionAndGetWhatItSees(nextRetinaPosition);
        }

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        this.gson = new Gson();
    }


    private NervousSystem constructConnectedNervousSystem() {
        Neocortex unconnectedNeocortex = new Neocortex(new Region("V1", 4, 4,
                4, 50, 3), new RegionToRegionRectangleConnect());


        LGN unconnectedLGN = new LGN(new Region("LGN", 8, 8, 1, 50, 3));


        Retina unconnectedRetina = new Retina(66, 66);


        NervousSystem nervousSystem = new NervousSystem(unconnectedNeocortex,
                unconnectedLGN, unconnectedRetina);


        // connect OldRetina to LGN
        Retina retina = nervousSystem.getPNS().getSNS().getRetina();
        LGN LGN = nervousSystem.getCNS().getBrain().getThalamus().getLGN();
        AbstractSensorCellsToRegionConnect opticNerve = new SensorCellsToRegionRectangleConnect();
        opticNerve.connect(retina.getVisionCells(), LGN.getRegion(), 0, 0);


        // connect LGN to very small part of V1 Region of Neocortex
        Neocortex neocortex = nervousSystem.getCNS().getBrain().getCerebrum()
                .getCerebralCortex().getNeocortex();
        AbstractRegionToRegionConnect regionToRegionConnect = new RegionToRegionRectangleConnect();
        regionToRegionConnect.connect(LGN.getRegion(),
                neocortex.getCurrentRegion(), 0, 0);


        return nervousSystem;
    }

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model.MARK_II.vision.HowMARK_II_FitsInToBrainAnatomy

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