source: other-projects/is-sheet-music-encore/trunk/image-identification-development/src/Main.java@ 33325

/*
                StartAndEndPoint l1 = parseArray[i];
                StartAndEndPoint l2 = parseArray[i+ 1];
                //CHECK WHICH line starts after the other
                //If l1 is starting after, then comparisons are based around l1.s
                //System.out.println("l1: " + l1.getP1().x);
                //System.out.println("l2: " + l2.getP1().x);

                System.out.println("1.0: L1S: " + l1.getP1().x + " larger than L2S: " + l2.getP1().x);
                if(l1.getP1().x > l2.getP1().x) {
                    System.out.println("1.1: Comparing L1S: " + l1.getP1().x + " less than L2E: " + l2.getP2().x);
                    if (l1.getP1().x < l2.getP2().x) {
                        //AND
                        System.out.println("1.2: Comparing L1S: " + l1.getP1().x + " larger than L2S: " + l2.getP1().x);
                        if (l1.getP1().x > l2.getP1().x) {
                            System.out.println("1: Success. NEXT");
                            //IT IS INTERSECTED
                            continue;
                        }
                        else {
                            //FAILED SECOND COMPARISON
                            System.out.println("1: Fail");
                        }
                    }
                    else {
                        System.out.println("Checking other line");
                    }
                    System.out.println("2.0: L2S: " + l2.getP1().x + " larger than  L1S: " + l1.getP1().x);
                }
                //If l2 is starting after, then comparisons are based around l2.s
                else if(l2.getP1().x > l1.getP1().x) {
                    System.out.println("2.1: Comparing L2S: " + l1.getP1().x + " less than L1E: " + l2.getP2().x);
                    if (l2.getP1().x < l1.getP2().x) {
                        //AND
                        System.out.println("2.2: Comparing L2S: " + l2.getP1().x + " larger than L1S: " + l1.getP1().x);
                        if (l2.getP1().x > l1.getP1().x) {
                            System.out.println("2: Success");
                            //IT IS INTERSECTED
                            //continue;
                        }
                        else {
                            //FAILED SECOND COMPARISON
                            System.out.println("2: Fail");
                            //return false;
                        }
                    }
                    else {
                        System.out.println("Failed second comparison RETURN FALSE");
                        return false;
                    }
                    //return false;
                }
                else{
                    System.out.println("NEITHER RETURN FALSE");
                    return false;
                }
  */

import org.opencv.core.*;
import org.opencv.core.Point;
import org.opencv.highgui.HighGui;
import org.opencv.imgcodecs.Imgcodecs;
import org.opencv.imgproc.Imgproc;
import org.opencv.photo.Photo;
import static org.opencv.imgcodecs.Imgcodecs.imwrite;
import java.awt.image.BufferedImage;
import java.awt.image.DataBufferByte;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import javax.imageio.ImageIO;

//REFERENCES:
//https://docs.opencv.org/3.4.3/d9/db0/tutorial_hough_lines.
//https://stackoverflow.com/questions/43443309/count-red-pixel-in-a-given-image
//https://www.wikihow.com/Calculate-Percentage-in-Java
//https://riptutorial.com/opencv/example/21963/converting-an-mat-object-to-an-bufferedimage-object
//https://beginnersbook.com/2013/12/java-arraylist-of-object-sort-example-comparable-and-comparator/
//https://www.programiz.com/java-programming/examples/standard-deviation
//https://www.geeksforgeeks.org/how-to-remove-duplicates-from-arraylist-in-java/
//https://stackoverflow.com/questions/7988486/how-do-you-calculate-the-variance-median-and-standard-deviation-in-c-or-java/7988556
//https://stackoverflow.com/questions/10396970/sort-a-list-that-contains-a-custom-class




//GOAL for 21st


//Classifier 01
//Have args so can call "java image-identification-classifier01 XX XX"
//args can be parameters in algorthim such as threshold or theta?
//Run on 5000 images.
//Record success rates
//All done with makefile


//But first understand houghline transform
//Know what the algorithm being used is doing.
//MAke constants for this classifier
//Make java be able to run on CMD line

public class Main {
    //DEPENDENT FUNCTIONS AND CLASSES
    static class StartAndEndPoint {
        //PRIVATES
        private Point _p1;
        private Point _p2;
        //CONSTRUCTOR
        public StartAndEndPoint(Point p1, Point p2){
            _p1 = p1;
            _p2 = p2;
        }
        //GETTERS
        public Point getP1(){
            return _p1;
        }
        public Point getP2(){
            return  _p2;
        }
        //SETTERS
        public void setP1(Point p1){
            _p1 = p1;
        }
        public void setP2(Point p2){
            _p2 = p2;
        }

        //ToString
        public  String toString(){
            return "Start: " + _p1 + " End: " + _p2;
        }
        /*
        //CompareToOverride
        //Compares start point y co ordinates of input PointArray
        //With this. start point y co ordinate
        @Override
        public double compareTo(StartAndEndPoint comparePointArray){
            Point comparePoint = (comparePointArray.getP1());
            return (this.getP1().y) - (comparePoint.y);
        }
        */
    }
    public static <T> ArrayList<T> removeDuplicates(ArrayList<T> list) {
        //DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED
        // Function to remove duplicates from an ArrayList
        // Create a new ArrayList
        ArrayList<T> newList = new ArrayList();
        // Traverse through the first list
        for (T element : list) {
            // If this element is not present in newList
            // then add it
            if (!newList.contains(element)) {
                newList.add(element);
            }
        }
        // return the new list
        return newList;
        //DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED//DIRECTLY COPIED
    }
    public static double StandardDeviation(double parseArray[]) {

        double mean;
        double sum =0.0;
        double standardDeviation = 0.0;
        //calculate sum of array
        for(int i =0; i < parseArray.length; i++){
            sum += parseArray[i];
        }
        //calculate mean of array
        mean = sum/parseArray.length;
        //calculate SD of array
        for(int j =0; j < parseArray.length; j++){
            standardDeviation += Math.pow(parseArray[j]-mean, 2);
        }
        return Math.sqrt(standardDeviation/parseArray.length);


    }
    public static double VarianceCalc(StartAndEndPoint parseArray[]){
        double sum =0;
        double temp =0;
        double mean, variance;
        int size = parseArray.length;
        //Calculate sum of array
        for(int i =0; i < parseArray.length; i++){
            sum += parseArray[i].getP1().y;
        }
        //Calculate mean of array
        mean = sum/parseArray.length;
        //Calculate variants
        for(int i =0; i < size; i++){
            temp += Math.pow((parseArray[i].getP1().y-mean),2);
        }
        variance = Math.abs(temp/(size -1));
        System.out.println("VARIANCE: " + variance);
        return variance;
    }
    public static Boolean lineComparison(double baseLineS, double compareLineS, double compareLineE ){
        if(baseLineS < compareLineE && baseLineS > compareLineS){
            return true;
        }
        return false;
    }
    public static Boolean ClusterCheck(StartAndEndPoint parseArray[]){
        try {
            System.out.println("LENGTH: " + parseArray.length);
            //MAKE THREE COMPARISONS
            //After clusters have been found.
            //Check if  their x positions intersect
            //Logic being
            //(L1.S < L2.E && L1.S > L2.S)
            //or
            //(L2.S < L1.E && L2.S > L1.S)
            //Variance is using Start of line point.
            //USING VARIANTS
            double variance = VarianceCalc(parseArray);
            Boolean consistent = false;
            if (variance <= CLUSTER_DISTANCE_MAX && variance > CLUSTER_DISTANCE_MIN) {
                for (int i = 0; i < parseArray.length - 1; i++) {
                    System.out.println(i);
                    double l1_S = parseArray[i].getP1().x;
                    double l1_E = parseArray[i].getP2().x;
                    double l2_S = parseArray[i + 1].getP1().x;
                    double l2_E = parseArray[i + 1].getP2().x;

                    //Check which starts after
                    if (l1_S >= l2_S) {
                        //baseLineStart is l1_S (call with lineComparison)
                        consistent = lineComparison(l1_S, l2_S, l2_E);

                    } else if (l2_S > l1_S) {
                        //baseLineStart is l2_S (call with lineComparison)
                        consistent = lineComparison(l2_S, l1_S, l1_E);
                    } else {
                        System.err.println("An error, comparing l1_S and l2_S, has occurred");
                    }

                    //Check if false was returned;
                    if (consistent == false) {
                        System.out.println(" X positions of two lines did not overlap each other" + '\t');
                        System.out.print("l1_S: " + l1_S + '\t');
                        System.out.print("l1_E: " + l1_E + '\t');
                        System.out.print("l2_S: " + l2_S + '\t');
                        System.out.print("l2_E: " + l2_E);
                        return false;
                    }
                }
                //Have been through for loop, maintaining consistent being true.
                //Have also meet the variance MIN and MAX requirement. Therefore it is a cluster
                return true;
            }
            System.out.println("Did not meet Cluster Distance Min and Max requirements, Variance = " + variance);
            return false;
        }
        catch (Exception e){
            System.err.println("           "+e.getMessage());
            return false;
        }
    }

    //GLOBAL_CONSTANTS
    static double CLUSTER_DISTANCE_MAX      = 15;
    static double CLUSTER_DISTANCE_MIN      = 2;
    static int CLASSIFIER_HOUGHLINESP_MIN   = 10;
    static int CLASSIFIER_HOUGHLINESP_MAX   = 65;
    static int HOUGHLINEP_THRESHOLD         = 10;
    static int STANDARD_DEVIATION_THRESHOLD = 6;
    static int MINLINECOUNT                 = 40;
    static int MAXLINEGAP                   = 1;  //4
    static double SLOPEGRADIENT             = 0.02;
    //SHOULD TURN INTO ARGS

    //CLASSIFYING FUNCTIONS
    private static  BufferedImage toBufferedImage(Mat mat){
        //MOSTLY COPY PASTE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        //MOSTLY COPY PASTE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        //https://riptutorial.com/opencv/example/21963/converting-an-mat-object-to-an-bufferedimage-object
        try{
            int type = BufferedImage.TYPE_3BYTE_BGR;
            int bufferSize = mat.channels() * mat.cols() * mat.rows();
            byte[] b = new byte[bufferSize];
            //get all the pixels
            mat.get(0, 0, b);
            BufferedImage image = new BufferedImage(mat.cols(), mat.rows(), type);
            final byte[] targetPixels = ((DataBufferByte) image.getRaster().getDataBuffer()).getData();
            System.arraycopy(b, 0, targetPixels, 0, b.length);
            return image;
        }
        catch(Exception e){
            System.err.println(e);
        }
        return null;
    }
    private static boolean ClassifierPixelCount(BufferedImage img){
        try {
            //Read file
            //BufferedImage img = ImageIO.read(new File(processedFile));
            int x = img.getWidth();
            int y = img.getHeight();
            int pixelCount  = 0;
            int redCount    = 0;
            float percentage = 0;

            //Go Thru every pixel
            for(int i=0; i < y; i++){
                for(int j=0;j < x; j++){
                    //Get value for current pixels RGB value
                    int currPixelRGB = img.getRGB(j, i);
                    //Check if pixel is red (hex value of red)
                    if(currPixelRGB == 0xFFFF0000){
                        redCount++;
                    }
                    pixelCount++;
                }
            }
            //Calculate percentage of Red in image
            percentage = ((float)redCount/(float)pixelCount)*(float)100;
            //If more than %10 and less than %50 then its sheet music!
            if(percentage > CLASSIFIER_HOUGHLINESP_MIN && percentage < CLASSIFIER_HOUGHLINESP_MAX){ //MAKE THESE CONSTANTS!!
                return true;}
        }
        catch (Exception e) {
            System.err.println(e);
        }
        return false;
    }
    private static boolean ClassifierLineCount(int lineCount){

           if(lineCount>MINLINECOUNT){
                return true;
            }
            else{
                return false;
            }
    }
    private static ArrayList ClassifierLineClusterOLD(BufferedImage img){
        ArrayList returnArray = new ArrayList();
        try {

            //IF THIS WORKS THEN IMPLEMENT A VERSION THAT USES POINTS from the draw line code.
            //ALSO CHECK OUT K NEAREST NEIGHBOR?
            //0xFFFF0000 = RED

            //go thru every pixel until find red pixel
            //get y pos of red pixel
            //continue with loop until find another red pixel
            //get y pos of red pixel
            //compare y pos (if close together then continue loop) else break

            int x = img.getWidth();
            int y = img.getHeight();
            int closeLineCount = 0;
            ArrayList<Integer> redPixelYpos = new ArrayList<Integer>();

            //Go Thru every pixel
            for(int i=0; i < y; i++){
                for(int j=0;j < x; j++){
                    //Get value for current pixels RGB value
                    int currPixelRGB = img.getRGB(j, i);
                    //Check if pixel is red (hex value of red)
                    if(currPixelRGB == 0xFFFF0000) {

                        //Store y pos of red pixel if there is no duplicate
                        if(!redPixelYpos.contains(i)){
                            redPixelYpos.add(i);
                            //System.out.println(i );
                        }
                    }
                }
            }
            //Check if any of the lines found are close together and that there has been more than one line found
            if(redPixelYpos.size()>1){
                //go through list and compare every value
                for(int i =0; i< redPixelYpos.size(); i++){
                    //System.out.println("i: " +redPixelYpos.get(i));
                    for(int j=0; j< redPixelYpos.size(); j++){
                        //System.out.println("j: "+redPixelYpos.get(j));
                        //Check if difference is less than 4 and the values are not duplicates.
                        if(Math.abs(redPixelYpos.get(i) - redPixelYpos.get(j)) < 4 && !redPixelYpos.get(j).equals(redPixelYpos.get(i))){
                            closeLineCount++;
                        }
                    }
                }
            }
            int clusterCount = closeLineCount/4;

            if(closeLineCount >= 4){
                returnArray.add(true);
                returnArray.add(closeLineCount);
                returnArray.add(clusterCount);
            }
            else{
                returnArray.add(false);
                returnArray.add(closeLineCount);
                returnArray.add(clusterCount);
            }
        }
        catch (Exception e) {
            System.err.println(e);
        }
    return returnArray;
    }
    private static ArrayList ClassifierLineCluster(ArrayList<StartAndEndPoint> linePointsArray, Mat clustersFoundRGB){

        /*
        ADDITION:
        After clusters have been found.
        Check if x positions intersect at all
            StartXPos of p1

        This will check for a cluster of lines that are close together.
        1. Go through the list of Y positions(start point) in parsed array.
            If, there is a small distance between them,
                then, add to closeLineArray.

        Have all Y positions that are close to each other now.
        Need to find the lines that are clustered together.

        Now check if there are four of these are close to each other.
        2.  Go through list of closeLine.
                Get first four lines, traversing down a step each iteration {0,1,2,3} -> {1,2,3,4} -> {2,3,4,5}
                If, those 4 lines are close together,
                    Then, add them to a new array that holds Line Cluster Values.
                    Go to line 4 positions down since, as do not want duplicates.

        3.
        */

        ArrayList returnArray = new ArrayList();
        ArrayList<Double> closeLineYPos = new ArrayList();
        ArrayList<double[]> clusterArray = new ArrayList();
        int clusterCount = 0;
        try {
            if(linePointsArray.size()> 1) {

                /*
                //Display input array TESTING PURPOSES
                for (int i = 0; i < linePointsArray.size(); i++) {
                    System.out.println(linePointsArray.get(i).toString());
                }
                */

                //1. Check if y points are close together
                //go thru list and compare values against each other
                for (int i = 0; i < linePointsArray.size(); i++){
                    //System.out.println("i: "+ linePointsArray.get(i).getP1().y);
                    for (int j = 0; j < linePointsArray.size(); j++) {
                        //System.out.println("j: "+ linePointsArray.get(j).getP1().y);
                        //Check if difference is less than 4 and the values are not duplicates.
                        if(Math.abs(linePointsArray.get(j).getP1().y - linePointsArray.get(i).getP1().y) < 5){
                            if(linePointsArray.get(j).getP1().y != linePointsArray.get(i).getP1().y){
                                closeLineYPos.add(linePointsArray.get(j).getP1().y);

                            }
                        }
                    }
                }
                /*for (double num : closeLineYPos){
                      System.out.println(num);
                } */

                //2. Now check if there are four of these are close to each other.
                //Go through all of the items in this list and check if four of them are close together
                //Check first four items, traverse down a step {0,1,2,3} -> {1,2,3,4} -> {2,3,4,5}
                //If 4 items are close together,
                    //Then add them to a new array that holds Line Cluster Values.
                    //Go down 4 positions down since, as do not want duplicates.

                //Now have an array of at least four lines that are close together.
                //Sort array and remove duplicates
                Collections.sort(closeLineYPos);



                closeLineYPos = removeDuplicates(closeLineYPos);

                //DISPLAYING AS EXCEPTED! WOO!

                for (double y : closeLineYPos){
                    System.out.println("CloseLineYPos: " + y);
                }
                if(closeLineYPos.size() >= 4) {
                    //FOR every item in array of CloseLines
                    for(int i= 0; i< closeLineYPos.size(); i++){
                        //If last comparator is at end of array.
                        if(i + 4 >= closeLineYPos.size()){
                            break;
                        }
                        else{

                            //Add 4 values of CloseLine Array to a tempArray
                            double[] tempArray = new double[4];
                            tempArray[0] = closeLineYPos.get(i);
                            tempArray[1] = closeLineYPos.get(i + 1);
                            tempArray[2] = closeLineYPos.get(i + 2);
                            tempArray[3] = closeLineYPos.get(i + 3);

                            //Check standard deviation between these 4 values.
                            //If it SD is less than 5 then it is considered to be a cluster of lines.


                            if(StandardDeviation(tempArray) < STANDARD_DEVIATION_THRESHOLD){
                                //System.out.println("tempArray PT: "+tempArray[0] + " , " + tempArray[1] + " , " + tempArray[2] + " , " + tempArray[3]);
                                //System.out.println("tempArray SD: " + StandardDeviation(tempArray));
                                //Store array
                                clusterArray.add(tempArray);
                                //If I + 4 is less than the size of the array then increment by 4
                                //Go down +4 positions in closeLineYPos array
                                if((i + 4 < closeLineYPos.size())){
                                    //System.out.println("IF, i = " + i + " -> "+ (i+4) + ", CloseLineYpos size= " + closeLineYPos.size());
                                    i = i+4;
                                }
                                else{
                                    //break
                                    //System.out.println("ELSE, i = " + i+ " closeLineYpos size= " + closeLineYPos.size());
                                    Thread.sleep(2000);
                                    break;
                                }
                            }
                        }
                    }
                }
                /*
                System.out.println("Cluster Coordinates: ");
                for(double[] items : clusterArray){
                    for(int i = 0; i <items.length; i++){
                        System.out.println("ITEMS: "+ items[i]);
                    }
                }
                */
                //Setup Drawing clusters found.
                //For every pt given the input array
                for(StartAndEndPoint pt : linePointsArray){
                    //Go through every the Arrays in the clusterArray(clustered lines)
                    for(int i =0; i < clusterArray.size(); i++){
                        //Go through every item in the array
                        for(double item : clusterArray.get(i)) {
                            //Check if the curr item is equal to current pt
                            if (item == pt.getP1().y){
                                //calculate a different colour for each line

                                //Draw a line
                                Imgproc.line(clustersFoundRGB, pt.getP1(), pt.getP2(), new Scalar(0, 255, 0), 1, Imgproc.LINE_4, 0);
                            }
                        }
                    }

                }

                clusterCount = clusterArray.size();
                //SETUP RETURN ARRAY
                if(clusterCount >= 1){
                    returnArray.add(true);
                    returnArray.add(closeLineYPos.size());
                    returnArray.add(clusterCount);
                    returnArray.add(clustersFoundRGB);
                }
                else{
                    returnArray.add(false);
                    returnArray.add(closeLineYPos.size());
                    returnArray.add(clusterCount);
                }
            }
        }
        catch (Exception e) {
            System.err.println(e);
        }
        return returnArray;
    }

    private static ArrayList ClassifierLineClusterPt(ArrayList<StartAndEndPoint> linePointsArray, Mat clustersFoundRGB){
        /*
        ADDITION:
        This will check for a cluster of lines that are close together.
        1. Go through the list of Y positions(start point) in parsed array.
            If, there is a small distance between them,
                then, add to closeLineArray.

        Have all Y positions that are close to each other now.
        Need to find the lines that are clustered together.

        Now check if there are four of these are close to each other.
        2.  Go through list of closeLine.
                Get first four lines, traversing down a step each iteration {0,1,2,3} -> {1,2,3,4} -> {2,3,4,5}
                If, those 4 lines are close together,
                    Then, add them to a new array that holds Line Cluster Values.
                    Go to line 4 positions down since, as do not want duplicates.

        3.
        */
        ArrayList returnArray = new ArrayList();
        ArrayList<StartAndEndPoint> closeLinePts = new ArrayList();
        ArrayList<StartAndEndPoint[]> clusterPtArray = new ArrayList();
        int clusterCount = 0;
        try {
            if(linePointsArray.size()> 1) {
                /*
                //Display input array TESTING PURPOSES
                for (int i = 0; i < linePointsArray.size(); i++) {
                    System.out.println(linePointsArray.get(i).toString());
                }
                */
                //1. Check if y points are close together
                //go thru list and compare values against each other
                for (int i = 0; i < linePointsArray.size(); i++){
                    //System.out.println("i: "+ linePointsArray.get(i).getP1().y);
                    for (int j = 0; j < linePointsArray.size(); j++) {
                        //System.out.println("j: "+ linePointsArray.get(j).getP1().y);
                        //Check if difference is less than 4 and the values are not duplicates.
                        if(Math.abs(linePointsArray.get(j).getP1().y - linePointsArray.get(i).getP1().y) < 5){
                            if(linePointsArray.get(j).getP1().y != linePointsArray.get(i).getP1().y){
                                closeLinePts.add(linePointsArray.get(i));
                            }
                        }
                    }
                }
                /*for (double num : closeLineYPos){
                      System.out.println(num);
                } */

                //2. Now check if there are four of these are close to each other.
                //Go through all of the items in this list and check if four of them are close together
                //Check first four items, traverse down a step {0,1,2,3} -> {1,2,3,4} -> {2,3,4,5}
                //If 4 items are close together,
                //Then add them to a new array that holds Line Cluster Values.
                //Go down 4 positions down since, as do not want duplicates.

                //Now have an array of at least four lines that are close together.
                //Sort array and remove duplicates
                Collections.sort(closeLinePts, new Comparator<StartAndEndPoint>() {
                    @Override
                    public int compare(StartAndEndPoint p1, StartAndEndPoint p2) {
                        return (int)(p1.getP1().y - p2.getP1().y);
                    }
                });
                closeLinePts = removeDuplicates(closeLinePts);
                /*DISPLAYING AS EXCEPTED! WOO!
                for (StartAndEndPoint pt : closeLinePts) {
                    System.out.println("CloseLinePTs: " + pt.getP1().y);
                }
                */

                if(closeLinePts.size() >= 4) {
                    //FOR every item in array of CloseLines
                    for(int i= 0; i< closeLinePts.size(); i++){
                        //If last comparator is at end of array.
                        if(i + 4 >= closeLinePts.size()){
                            break;
                        }
                        else{
                            //Add 4 values of CloseLinePt Array to a tempArray
                            StartAndEndPoint[] tempPtArray = new StartAndEndPoint[4];
                            tempPtArray[0] = closeLinePts.get(i);
                            tempPtArray[1] = closeLinePts.get(i + 1);
                            tempPtArray[2] = closeLinePts.get(i + 2);
                            tempPtArray[3] = closeLinePts.get(i + 3);

                            //Check standard deviation between these 4 values.
                            //If it SD is less than 5 then it is considered to be a cluster of lines.
                            if(ClusterCheck(tempPtArray)){
                                //System.out.println("tempArray PT: "+tempArray[0] + " , " + tempArray[1] + " , " + tempArray[2] + " , " + tempArray[3]);
                                //System.out.println("tempArray SD: " + StandardDeviation(tempArray));
                                //Store array
                                clusterPtArray.add(tempPtArray);
                                //If I + 4 is less than the size of the array then increment by 4
                                //Go down +4 positions in closeLineYPos array
                                if((i + 4 < closeLinePts.size())){
                                    //System.out.println("IF, i = " + i + " -> "+ (i+4) + ", CloseLineYpos size= " + closeLineYPos.size());
                                    i = i+4;
                                }
                                else{
                                    //break
                                    //System.out.println("ELSE, i = " + i+ " closeLineYpos size= " + closeLineYPos.size());
                                    Thread.sleep(2000);
                                    break;
                                }
                            }
                        }
                    }
                }
                /*
                System.out.println("Cluster Coordinates: ");
                for(double[] items : clusterArray){
                    for(int i = 0; i <items.length; i++){
                        System.out.println("ITEMS: "+ items[i]);
                    }
                }
                */
                //Setup Drawing clusters found.
                //For every pt given the input array
                for(StartAndEndPoint pt : linePointsArray){
                    //Go through every the Arrays in the clusterArray(clustered lines)
                    for(int i =0; i < clusterPtArray.size(); i++){
                        //Go through every item in the array
                        for(StartAndEndPoint item : clusterPtArray.get(i)) {
                            //Check if the curr item is equal to current pt
                            if (item.getP1().y == pt.getP1().y){
                                //calculate a different colour for each line
                                //Draw a line
                                Imgproc.line(clustersFoundRGB, pt.getP1(), pt.getP2(), new Scalar(0, 255, 0), 1, Imgproc.LINE_4, 0);
                            }
                        }
                    }

                }

                clusterCount = clusterPtArray.size();
                //SETUP RETURN ARRAY
                if(clusterCount >= 1){
                    returnArray.add(true);
                    returnArray.add(closeLinePts.size());
                    returnArray.add(clusterCount);
                    returnArray.add(clustersFoundRGB);
                }
                else{
                    returnArray.add(false);
                    returnArray.add(closeLinePts.size());
                    returnArray.add(clusterCount);
                }
            }
        }
        catch (Exception e) {
            System.err.println("          " +e.getMessage());
        }
        return returnArray;
    }



    public static void main(String[] args) {

        System.loadLibrary(Core.NATIVE_LIBRARY_NAME);

        try {
            ArrayList<StartAndEndPoint> pointArrayList = new ArrayList<>();

            //Variables
            Mat edgesDetected = new Mat();
            Mat edgesDetectedRGB = new Mat();
            Mat clustersFoundRGB = new Mat();
            String directory = "/Scratch/cpb16/is-sheet-music-encore/download-images/MU/";
            //!!!!!!!!!!!!!!!!!!!!!!!!!!!NOT!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
            //mdp.39015097852365-2.png 176 lines    Contents page.
            //mdp.39015097852555-3.png 76  lines
            //String default_file = directory+"SheetMusic/coo.31924062612282-9.png";
            //String default_file ="TestImages/NotNot/mdp.39015080972303-3.png";


            //System.out.println(default_file);
            String default_file = "TestImages/NotSheetMusic01.png";
            //String default_file = "TestImages/NotSheetMusic02.png";
            //String default_file = "TestImages/SheetMusic01.png";
            //String default_file = "TestImages/SheetMusic02.png";
            //String default_file = "TestImages/vLine.png";
            String filename = ((args.length > 0) ? args[0] : default_file);
            File file = new File(filename);
            if(!file.exists()){System.err.println("Image not found: "+ filename);}

            int horizontalLineCount =0;

            // Load an image
            Mat original = Imgcodecs.imread(filename, Imgcodecs.IMREAD_GRAYSCALE);
            // Edge detection
            Imgproc.adaptiveThreshold(original, edgesDetected,255, Imgproc.ADAPTIVE_THRESH_GAUSSIAN_C,Imgproc.THRESH_BINARY_INV, 15, 4);

            //Convert to RGB for future use
            Imgproc.cvtColor(edgesDetected, edgesDetectedRGB, Imgproc.COLOR_GRAY2BGR);
            clustersFoundRGB = edgesDetectedRGB.clone();

            Mat linesP = new Mat(); // will hold the results of the detection
            //(edgeDetectedImage, outputOfDetection(r,Ξ), resolution of rho, resolution of theta, threshold (minimum num of intersections)

            double minLineLength = edgesDetectedRGB.size().width/8;

            Imgproc.HoughLinesP(edgesDetected, linesP, 1, Math.PI / 720, HOUGHLINEP_THRESHOLD, minLineLength,MAXLINEGAP); // runs the actual detection
            //System.out.println("Before Gradient Filtering num lines: " + linesP.rows());

            // Draw the lines
            for (int x = 0; x < linesP.rows(); x++) {
                double[] l = linesP.get(x, 0);
                Point p1 = new Point(l[0], l[1]);
                Point p2 = new Point(l[2], l[3]);
                double m = Math.abs(p2.y - p1.y)/(p2.x - p1.x);

                if(m<=SLOPEGRADIENT) {
                    Imgproc.line(edgesDetectedRGB, p1, p2, new Scalar(0, 0, 255), 1, Imgproc.LINE_4, 0);
                    horizontalLineCount++;
                    pointArrayList.add(new StartAndEndPoint(p1, p2));
                }

            }
            //Point is a co ordinate (x, y)
            //Prove by finding number of points from one end to other:
            //Get width of image.
            File filenameTest = new File("TestImages/NotSheetMusic02.png");
            BufferedImage i = ImageIO.read(filenameTest);
            BufferedImage toBeClassifiedImg = toBufferedImage(edgesDetectedRGB);



            //Display Results
            //HighGui.imshow("Source", original);
            //HighGui.imshow("Just Edges", justEdges); //TESTING
            //HighGui.imshow("Detected Lines (in red) - positive", edgesDetectedRGB);
            if(ClassifierLineClusterPt(pointArrayList, clustersFoundRGB).get(3) != null) {
                HighGui.imshow("CLUSTERS FOUND", clustersFoundRGB);
            }
            //HighGui.imshow("Detected Lines (in red) - negative", edgesDetectedRGBProb);



            //System.out.println("LINE COUNT RESULT:   " +  ClassifierLineCount(horizontalLineCount) + '\t' +"LineCount: " + horizontalLineCount); //COUNT OF LINES CLASSIFICATION
            //System.out.println("LINE CLUSTER RESULT: " +  ClassifierLineClusterOLD(toBeClassifiedImg).get(0) + '\t' + "LinesFound: " + ClassifierLineClusterOLD(toBeClassifiedImg).get(1) + '\t' + "ClustersFound: " + ClassifierLineClusterOLD(toBeClassifiedImg).get(2));
            //System.out.println("NEW CLUSTER RESULTS: " +  ClassifierLineCluster(pointArrayList,clustersFoundRGB).get(0) + '\t' + "LinesFound: " + ClassifierLineCluster(pointArrayList,clustersFoundRGB).get(1) + '\t' + "ClustersFound: " + ClassifierLineCluster(pointArrayList,clustersFoundRGB).get(2));
            System.out.println(ClassifierLineClusterPt(pointArrayList, clustersFoundRGB));

            // Wait and Exit
            HighGui.waitKey();
            System.exit(0);
        }
        catch(Exception e){
            System.err.println(e);
        }
    }
}