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OpenCV Java - Changing pixel color

I am trying to determine a way to change the pixel color of my masks from black to a different color. Unfortunately, I have not be able to determine a way to do this task. Essentially, what I am trying to do is take this image:
and convert the black portions to a color with values (255, 160, 130). I have tried several methods to try and achieve my goal. These include draw contours, setTo, and looping through the matrix. Unfortunately all of these attempts have failed. I have included the code and the resulting outcomes below.
Draw Contours method
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
Mat img = Imgcodecs.imread(
"C:\\Users\\Hassan\\Documents\\School\\Me\\COMP5900 Y\\Project\\Project\\src\\resources\\face.jpg");
Mat img_grey = new Mat();
Mat grad = new Mat(), grad_x = new Mat(), grad_y = new Mat();
Mat abs_grad_x = new Mat(), abs_grad_y = new Mat();
int ddepth = CvType.CV_32F;
int scale = 1;
int delta = 0;
Imgproc.GaussianBlur(img, img, new Size(3, 3), 0, 0, Core.BORDER_CONSTANT);
Imgproc.cvtColor(img, img_grey, Imgproc.COLOR_BGR2GRAY);
// Apply Sobel
Imgproc.Sobel(img_grey, grad_x, ddepth, 1, 0, 3, scale, delta, Core.BORDER_DEFAULT);
Imgproc.Sobel(img_grey, grad_y, ddepth, 0, 1, 3, scale, delta, Core.BORDER_DEFAULT);
// converting back to CV_8U
Core.convertScaleAbs(grad_x, abs_grad_x);
Core.convertScaleAbs(grad_y, abs_grad_y);
// Total Gradient (approximate)
Core.addWeighted(abs_grad_x, 0.5, abs_grad_y, 0.5, 0, grad);
Photo.fastNlMeansDenoising(grad, grad);
Imgproc.GaussianBlur(grad, grad, new Size(3, 3), 0, 0, Core.BORDER_CONSTANT);
// isolate background
Mat background = new Mat();
Imgproc.threshold(grad, background, 2, 255, Imgproc.THRESH_BINARY);
// draw contours
List<MatOfPoint> contours = new ArrayList<>();
Mat hierarchy = new Mat();
Imgproc.findContours(background, contours, hierarchy, Imgproc.RETR_TREE, Imgproc.CHAIN_APPROX_NONE);
Mat drawing = Mat.zeros(background.size(), CvType.CV_8UC3);
List<MatOfPoint> hullList = new ArrayList<>();
for (MatOfPoint contour : contours) {
MatOfInt hull = new MatOfInt();
Imgproc.convexHull(contour, hull);
Point[] contourArray = contour.toArray();
Point[] hullPoints = new Point[hull.rows()];
List<Integer> hullContourIdxList = hull.toList();
for (int i = 0; i < hullContourIdxList.size(); i++) {
hullPoints[i] = contourArray[hullContourIdxList.get(i)];
}
hullList.add(new MatOfPoint(hullPoints));
}
for (int i = 0; i < contours.size(); i++) {
Scalar color = new Scalar(255, 160, 130);
Imgproc.drawContours(drawing, contours, i, color);
//Imgproc.drawContours(drawing, hullList, i, color );
}
Note here, that I also tried using Imgproc.RETR_EXTERNAL as well, but that produced a completely black image. Also the name of the HighGui window is called "flood fill", but I just forgot to update the name.
setTo
// replace find and draw contours portion of code above
Mat out = new Mat();
background.copyTo(out);
out.setTo(new Scalar(255, 160, 130), background);
Iterating through matrix
// replace draw contours portion of code above
for (a = 0; a < background.rows(); a++) {
for(b = 0; b < background.cols(); b++) {
if(background.get(a,b)[0] == 0) {
//background.put(a, b, CvType.CV_16F, new Scalar(255, 160, 130));
double[] data = {255, 160, 130};
background.put(a, b, data);
}
}
}
The loop is promising, but I know it will not be efficient as I have 2 other masks that I would like to update as well. Could you please suggest an efficient method, that allows me to set the value for all three channels?
Thanks

I am not sure why you are doing many operations on the image but to me it looks like applying the mask and replacing the color efficiently. So if there are other complexities than please let me know.
Below is the code I was looking for in Java.
public static void main(String s[]) {
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
Mat matr =Imgcodecs.imread("/home/shariq/Desktop/test.png");
Mat result = new Mat();
//create a mask based on range
Core.inRange(matr, new Scalar(0), new Scalar(50), result);
Imgcodecs.imwrite("/home/shariq/Desktop/test_in.png", result);
//apply the mask with color you are looking for, note here scalar is in hsv
matr.setTo(new Scalar(130,160,255),result);
Imgcodecs.imwrite("/home/shariq/Desktop/result.png", matr);
}
We are creating a mask for the pixel values between 0-50 for black color using inRange method.
Core.inRange(matr, new Scalar(0), new Scalar(50), result);
This mask in result variable is than applied to original matrix using setTo method. The replacement color value is provided in HSV format through Scalar object. new Scalar(a,b,c) in HSV can be understand in RGB like this Red = c, Green = b and Blue = a.
matr.setTo(new Scalar(130,160,255),result);
Its quite fast compared to iterating the pixels one by one.

How to apply Canny edge detector effectively on image using Opencv in Android?

I am making an Android application to detect multiple objects from an image, then process those objects and compare them with reference objects to detect anomalies. I tested different image edge detectors in python and Prewitt operator gave me the best result as shown below https://i.imgur.com/4iwOx9s.png For android, I used Canny edge detector, but the result is not as good as Prewitt as shown below https://i.imgur.com/Bax1Wxw.png
The purpose of applying Canny edge detector is the detect the largest contour first then extract this contour and detect every object found in this contour (which in my case 3 objects).
Here is the java code I tried
Bitmap bmp = BitmapFactory.decodeResource(getResources(), R.drawable.coffret);
//compress bitmap
bmp = getResizedBitmap(bmp, 500);
Mat rgbMat = new Mat();
Utils.bitmapToMat(bmp, rgbMat);
Mat grayMat = new Mat();
Mat bwMat = new Mat();
Imgproc.cvtColor(rgbMat, grayMat, Imgproc.COLOR_RGB2GRAY);
Imgproc.equalizeHist(grayMat, grayMat);
//Imgproc.adaptiveThreshold(grayMat, grayMat, 255, Imgproc.ADAPTIVE_THRESH_MEAN_C, Imgproc.THRESH_BINARY, 15, 40);
Imgproc.Canny(grayMat, bwMat, 50, 200, 3, false);
//find largest contour
List<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Imgproc.findContours(bwMat, contours, new Mat(), Imgproc.RETR_LIST, Imgproc.CHAIN_APPROX_NONE);
double maxArea = -1;
int maxAreaIdx = -1;
if (contours.size() > 0) {
MatOfPoint temp_contour = contours.get(0); //the largest is at the index 0 for starting point
MatOfPoint2f approxCurve = new MatOfPoint2f();
Mat largest_contour = contours.get(0);
List<MatOfPoint> largest_contours = new ArrayList<MatOfPoint>();
for (int idx = 0; idx < contours.size(); idx++) {
temp_contour = contours.get(idx);
double contourarea = Imgproc.contourArea(temp_contour);
//compare this contour to the previous largest contour found
if (contourarea > maxArea) {
//check if this contour is a square
MatOfPoint2f new_mat = new MatOfPoint2f( temp_contour.toArray() );
int contourSize = (int)temp_contour.total();
Imgproc.approxPolyDP(new_mat, approxCurve, contourSize*0.05, true);
if (approxCurve.total() == 4) {
maxArea = contourarea;
maxAreaIdx = idx;
largest_contours.add(temp_contour);
largest_contour = temp_contour;
}
}
}
if (largest_contours.size() >= 1) {
MatOfPoint temp_largest = largest_contours.get(largest_contours.size()-1);
largest_contours = new ArrayList<MatOfPoint>();
largest_contours.add(temp_largest);
Imgproc.cvtColor(bwMat, bwMat, Imgproc.COLOR_BayerBG2RGB);
Imgproc.drawContours(bwMat, largest_contours, -1, new Scalar(0, 255, 0), 1);
}
}
Utils.matToBitmap(bwMat, bmp);
Matrix matrix = new Matrix();
matrix.postRotate(180);
bmp = Bitmap.createBitmap(bmp, 0, 0, bmp.getWidth(), bmp.getHeight(), matrix, true);
imgView.setImageBitmap(bmp);
As you can notice, using the Prewitt operator the text is clear and contours are more defined.
I think I am not applying Canny correctly that's why the largest contour is not detected. What am I doing wrong?
Edit:
Here is the original image
https://i.imgur.com/BtyZOvj.jpg

It seems that you are applying Canny edge detector correct. However, sometimes, it could be trick to define proper minimum and maximum values to threshold the edges.
Maybe the interval you are using (i.e., 50 to 200) is large for your purpose. You could try higher minimum and maximum values with tight intervals, for instance, 175 to 200.
As the image gets complex you need to take special care of these parameters. Sometimes, different sections of your image will require different minimum and maximum thresholds. Take a look at this reference, it contains a decent explanation about Improvement on Canny edge detection. At the end of this page, there is a explanation of how to determine the dual-threshold value.

How to remove overlapping contours

I am working on a program where I am trying to extract the colored squares from a puzzle. I take a frame from a video capture then find the all contours. I then remove contours that aren't in the shape of a square (This works alright but looking for a better method). The main problem I am facing is that there are overlapping contours. I use RETR_TREE to get all contours but when using RETR_EXTERNAL The contours become harder to detect. Is there a way I can improve the detection of squares? Or a way that I can remove the overlapping contours in the image.
Here is an image of where there are overlapping contours:
There were 11 contours found in this image but I want only 9.(I draw the rects to see the overlapping a little easier)
. How can I remove the inner contours?
Here is my code:
public Mat captureFrame(Mat capturedFrame){
Mat newFrame = new Mat();
capturedFrame.copyTo(newFrame);
//Gray
Mat gray = new Mat();
Imgproc.cvtColor(capturedFrame, gray, Imgproc.COLOR_RGB2GRAY);
//Blur
Mat blur = new Mat();
Imgproc.blur(gray, blur, new Size(3,3));
//Canny image
Mat canny = new Mat();
Imgproc.Canny(blur, canny, 20, 40, 3, true);
//Dilate image to increase size of lines
Mat kernel = Imgproc.getStructuringElement(1, new Size(3,3));
Mat dilated = new Mat();
Imgproc.dilate(canny,dilated, kernel);
List<MatOfPoint> contours = new ArrayList<>();
List<MatOfPoint> squareContours = new ArrayList<>();
//find contours
Imgproc.findContours(dilated, contours, new Mat(), Imgproc.RETR_TREE, Imgproc.CHAIN_APPROX_NONE);
//Remove contours that aren't close to a square shape.
//Wondering if there is a way I can improve this?
for(int i = 0; i < contours.size(); i++){
double area = Imgproc.contourArea( contours.get(i));
MatOfPoint2f contour2f = new MatOfPoint2f(contours.get(i).toArray());
double perimeter = Imgproc.arcLength(contour2f, true);
//Found squareness equation on wiki...
//https://en.wikipedia.org/wiki/Shape_factor_(image_analysis_and_microscopy)
double squareness = 4 * Math.PI * area / Math.pow(perimeter, 2);
//add contour to new List if it has a square shape.
if(squareness >= 0.7 && squareness <= 0.9 && area >= 3000){
squareContours.add(contours.get(i));
}
}
MatOfPoint2f approxCurve = new MatOfPoint2f();
for(int n = 0; n < squareContours.size(); n++){
//Convert contours(n) from MatOfPoint to MatOfPoint2f
MatOfPoint2f contour2f = new MatOfPoint2f( squareContours.get(n).toArray());
//Processing on mMOP2f1 which is in type MatOfPoint2f
double approxDistance = Imgproc.arcLength(contour2f, true)*0.02;
Imgproc.approxPolyDP(contour2f, approxCurve, approxDistance, true);
//Convert back to MatOfPoint
MatOfPoint points = new MatOfPoint( approxCurve.toArray());
// Get bounding rect of contour
Rect rect = Imgproc.boundingRect(points);
//length and width should be about the same
if(rect.height - rect.width < Math.abs(10)){
System.out.printf("%s , %s \n", rect.height, rect.width);
}
// draw enclosing rectangle (all same color, but you could use variable i to make them unique)
Imgproc.rectangle(newFrame, new Point(rect.x,rect.y), new Point(rect.x+rect.width,rect.y+rect.height),new Scalar (255, 0, 0, 255), 3);
}
return newFrame;
}

Fortunately, cv::findContours also provides us with hierarchy matrix, which you have ignored in your snippet, the hierarchy is very useful for all modes other than RETR_EXTERNAL, You may find the detailed doc of hierarchy matrix here.
Hierarchy matrix contains the data in the format [Next, Previous, First_Child, Parent] for each contour. Now you may filter contours, which a logic such as select only those contours where parent == -1, this will eliminate the sub contours inside the parent contour.
To make use of the hierarchy matrix you need to call cv::findContours as:
cv::Mat hierarchy;
Imgproc.findContours(dilated, contours, hierarchy, Imgproc.RETR_TREE, Imgproc.CHAIN_APPROX_NONE);

Estimation of euler angels (camera pose) using images from camera and opencv library

I'm working on a android application and I need to estimate online camera rotation in 3D-plan using images from camera and opencv library. I like to calculate Euler angles.
I have read this and this page and I can estimate homography matrix like here.
My first question is, should I really know the camera intrinsic matrix from camera calibrtion or is the homography matrix (camera extrinsic) enough to estimate euler angles (pitch, roll, yaw)?
If homography matrix is enough, how can I do it exactly?
Sorry, I am really beginner with opencv and cannot decompose "Mat" of homography to rotation matrix and translation matrix like describes here. How can I implement euler angles in android?
You can see my code using solvePnPRansac() and decomposeProjectionMatrix to calculate euler angles.
But it returns just a null-vector as double[] eulerArray = {0,0,0}!!! Can somebody help me?! What is wrong there?
Thank you very much for any response!
public double[] findEulerAngles(MatOfKeyPoint keypoints1, MatOfKeyPoint keypoints2, MatOfDMatch matches){
KeyPoint[] k1 = keypoints1.toArray();
KeyPoint[] k2 = keypoints2.toArray();
List<DMatch> matchesList = matches.toList();
List<KeyPoint> referenceKeypointsList = keypoints2.toList();
List<KeyPoint> sceneKeypointsList = keypoints1.toList();
// Calculate the max and min distances between keypoints.
double maxDist = 0.0;
double minDist = Double.MAX_VALUE;
for(DMatch match : matchesList) {
double dist = match.distance;
if (dist < minDist) {
minDist = dist;
}
if (dist > maxDist) {
maxDist = dist;
}
}
// Identify "good" keypoints based on match distance.
List<Point3> goodReferencePointsList = new ArrayList<Point3>();
ArrayList<Point> goodScenePointsList = new ArrayList<Point>();
double maxGoodMatchDist = 1.75 * minDist;
for(DMatch match : matchesList) {
if (match.distance < maxGoodMatchDist) {
Point kk2 = k2[match.queryIdx].pt;
Point kk1 = k1[match.trainIdx].pt;
Point3 point3 = new Point3(kk1.x, kk1.y, 0.0);
goodReferencePointsList.add(point3);
goodScenePointsList.add( kk2);
sceneKeypointsList.get(match.queryIdx).pt);
}
}
if (goodReferencePointsList.size() < 4 || goodScenePointsList.size() < 4) {
// There are too few good points to find the pose.
return;
}
MatOfPoint3f goodReferencePoints = new MatOfPoint3f();
goodReferencePoints.fromList(goodReferencePointsList);
MatOfPoint2f goodScenePoints = new MatOfPoint2f();
goodScenePoints.fromList(goodScenePointsList);
MatOfDouble mRMat = new MatOfDouble(3, 3, CvType.CV_32F);
MatOfDouble mTVec = new MatOfDouble(3, 1, CvType.CV_32F);
//TODO: solve camera intrinsic matrix
Mat intrinsics = Mat.eye(3, 3, CvType.CV_32F); // dummy camera matrix
intrinsics.put(0, 0, 400);
intrinsics.put(1, 1, 400);
intrinsics.put(0, 2, 640 / 2);
intrinsics.put(1, 2, 480 / 2);
Calib3d.solvePnPRansac(goodReferencePoints, goodScenePoints, intrinsics, new MatOfDouble(), mRMat, mTVec);
MatOfDouble rotCameraMatrix1 = new MatOfDouble(3, 1, CvType.CV_32F);
double[] rVecArray = mRMat.toArray();
// Calib3d.Rodrigues(mRMat, rotCameraMatrix1);
double[] tVecArray = mTVec.toArray();
MatOfDouble projMatrix = new MatOfDouble(3, 4, CvType.CV_32F); //projMatrix 3x4 input projection matrix P.
projMatrix.put(0, 0, rVecArray[0]);
projMatrix.put(0, 1, rVecArray[1]);
projMatrix.put(0, 2, rVecArray[2]);
projMatrix.put(0, 3, 0);
projMatrix.put(1, 0, rVecArray[3]);
projMatrix.put(1, 1, rVecArray[4]);
projMatrix.put(1, 2, rVecArray[5]);
projMatrix.put(1, 3, 0);
projMatrix.put(2, 0, rVecArray[6]);
projMatrix.put(2, 1, rVecArray[7]);
projMatrix.put(2, 2, rVecArray[8]);
projMatrix.put(2, 3, 0);
MatOfDouble cameraMatrix = new MatOfDouble(3, 3, CvType.CV_32F); //cameraMatrix Output 3x3 camera matrix K.
MatOfDouble rotMatrix = new MatOfDouble(3, 3, CvType.CV_32F); //rotMatrix Output 3x3 external rotation matrix R.
MatOfDouble transVect = new MatOfDouble(4, 1, CvType.CV_32F); //transVect Output 4x1 translation vector T.
MatOfDouble rotMatrixX = new MatOfDouble(3, 3, CvType.CV_32F); //rotMatrixX a rotMatrixX
MatOfDouble rotMatrixY = new MatOfDouble(3, 3, CvType.CV_32F); //rotMatrixY a rotMatrixY
MatOfDouble rotMatrixZ = new MatOfDouble(3, 3, CvType.CV_32F); //rotMatrixZ a rotMatrixZ
MatOfDouble eulerAngles = new MatOfDouble(3, 1, CvType.CV_32F); //eulerAngles Optional three-element vector containing three Euler angles of rotation in degrees.
Calib3d.decomposeProjectionMatrix( projMatrix,
cameraMatrix,
rotMatrix,
transVect,
rotMatrixX,
rotMatrixY,
rotMatrixZ,
eulerAngles);
double[] eulerArray = eulerAngles.toArray();
return eulerArray;
}

Homography relates images of the same planar surface, so it works only if there is a dominant plane in the image and you can find enough feature points lying on the plane in both images and successfully match them. Minimum number of matches is four and the math will work under the assumption, that the matches are 100% correct. With the help of robust estimation like RANSAC, you can get the result even if some elements in your set of feature point matches are obvious mismatches or are not placed on a plane.
For a more general case of a set of macthed features without the planarity assumption, you will need to find an essential matrix. The exact definition of the matrix can be found here. In short, it works more or less like homography - it relates corresponding points in two images. The minimum number of matches required to compute the essential matrix is five. To get the result from such a minimum sample, you need to make sure that the established matches are 100% correct. Again, robust estimation can help if there are outliers in your correspondence set -- and with automatic feature detection and matching there usually are.
OpenCV 3.0 has a function for essential matrix computation, conveniently integrated with RANSAC robust estimation. The essential matrix can be decomposed to the rotation matrix and translation vector as shown in the Wikipedia article I linked before. OpenCV 3.0 has a readily available function for this, too.

Now works the flowing code for me and I have decomposed the euler angles from homography matrix! I have some values for pitch, roll and yaw, which I don't know, whether there are correct. Have somebody any Idee, how can I test it?!
private static MatOfDMatch filterMatchesByHomography(MatOfKeyPoint keypoints1, MatOfKeyPoint keypoints2, MatOfDMatch matches){
List<Point> lp1 = new ArrayList<Point>(500);
List<Point> lp2 = new ArrayList<Point>(500);
KeyPoint[] k1 = keypoints1.toArray();
KeyPoint[] k2 = keypoints2.toArray();
List<DMatch> matchesList = matches.toList();
if (matchesList.size() < 4){
MatOfDMatch mat = new MatOfDMatch();
return mat;
}
// Add matches keypoints to new list to apply homography
for(DMatch match : matchesList){
Point kk1 = k1[match.queryIdx].pt;
Point kk2 = k2[match.trainIdx].pt;
lp1.add(kk1);
lp2.add(kk2);
}
MatOfPoint2f srcPoints = new MatOfPoint2f(lp1.toArray(new Point[0]));
MatOfPoint2f dstPoints = new MatOfPoint2f(lp2.toArray(new Point[0]));
//---------------------------------------
Mat mask = new Mat();
Mat homography = Calib3d.findHomography(srcPoints, dstPoints, Calib3d.RANSAC, 0.2, mask); // Finds a perspective transformation between two planes. ---Calib3d.LMEDS
Mat pose = cameraPoseFromHomography(homography);
//Decomposing a rotation matrix to eulerangle
pitch = Math.atan2(pose.get(2, 1)[0], pose.get(2, 2)[0]); // arctan2(r32, r33)
roll = Math.atan2(-1*pose.get(2, 0)[0], Math.sqrt( Math.pow(pose.get(2, 1)[0], 2) + Math.pow(pose.get(2, 2)[0], 2)) ); // arctan2(-r31, sqrt(r32^2 + r33^2))
yaw = Math.atan2(pose.get(2, 0)[0], pose.get(0, 0)[0]);
List<DMatch> matches_homo = new ArrayList<DMatch>();
int size = (int) mask.size().height;
for(int i = 0; i < size; i++){
if ( mask.get(i, 0)[0] == 1){
DMatch d = matchesList.get(i);
matches_homo.add(d);
}
}
MatOfDMatch mat = new MatOfDMatch();
mat.fromList(matches_homo);
return mat;
}
This is my camera pose from homography matrix (see this page too):
private static Mat cameraPoseFromHomography(Mat h) {
//Log.d("DEBUG", "cameraPoseFromHomography: homography " + matToString(h));
Mat pose = Mat.eye(3, 4, CvType.CV_32FC1); // 3x4 matrix, the camera pose
float norm1 = (float) Core.norm(h.col(0));
float norm2 = (float) Core.norm(h.col(1));
float tnorm = (norm1 + norm2) / 2.0f; // Normalization value
Mat normalizedTemp = new Mat();
Core.normalize(h.col(0), normalizedTemp);
normalizedTemp.convertTo(normalizedTemp, CvType.CV_32FC1);
normalizedTemp.copyTo(pose.col(0)); // Normalize the rotation, and copies the column to pose
Core.normalize(h.col(1), normalizedTemp);
normalizedTemp.convertTo(normalizedTemp, CvType.CV_32FC1);
normalizedTemp.copyTo(pose.col(1));// Normalize the rotation and copies the column to pose
Mat p3 = pose.col(0).cross(pose.col(1)); // Computes the cross-product of p1 and p2
p3.copyTo(pose.col(2));// Third column is the crossproduct of columns one and two
Mat temp = h.col(2);
double[] buffer = new double[3];
h.col(2).get(0, 0, buffer);
pose.put(0, 3, buffer[0] / tnorm); //vector t [R|t] is the last column of pose
pose.put(1, 3, buffer[1] / tnorm);
pose.put(2, 3, buffer[2] / tnorm);
return pose;
}

java.lang.IndexOutOfBoundsException error when applying OpenCV methods in Android

The code is about finding the largest rectangle in an Android device's camera using OpenCV. The app always force close but I can't find the trouble.
The input of the method is a Mat obtained by CvCameraViewFrame.rgba().
private Mat findLargestRectangle(Mat original_image)
{
Mat imgSource = original_image;
// convert the image to black and white
Imgproc.cvtColor(imgSource, imgSource, Imgproc.COLOR_BGR2GRAY);
// convert the image to black and white does (8 bit)
Imgproc.Canny(imgSource, imgSource, 50, 50);
// apply gaussian blur to smoothen lines of dots
Imgproc.GaussianBlur(imgSource, imgSource, new Size(5, 5), 5);
// find the contours
List<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Imgproc.findContours(imgSource, contours, new Mat(), Imgproc.RETR_LIST, Imgproc.CHAIN_APPROX_SIMPLE);
double maxArea = -1;
int maxAreaIdx = -1;
MatOfPoint temp_contour = contours.get(0); // the largest is at the
// index 0 for starting
// point
MatOfPoint2f approxCurve = new MatOfPoint2f();
Mat largest_contour = contours.get(0);
List<MatOfPoint> largest_contours = new ArrayList<MatOfPoint>();
for (int idx = 0; idx < contours.size(); idx++)
{
temp_contour = contours.get(idx);
double contourarea = Imgproc.contourArea(temp_contour);
// compare this contour to the previous largest contour found
if (contourarea > maxArea)
{
// check if this contour is a square
MatOfPoint2f new_mat = new MatOfPoint2f(temp_contour.toArray());
int contourSize = (int) temp_contour.total();
Imgproc.approxPolyDP(new_mat, approxCurve, contourSize * 0.05, true);
if (approxCurve.total() == 4)
{
maxArea = contourarea;
maxAreaIdx = idx;
largest_contours.add(temp_contour);
largest_contour = temp_contour;
}
}
}
MatOfPoint temp_largest = largest_contours.get(largest_contours.size() - 1);
largest_contours = new ArrayList<MatOfPoint>();
largest_contours.add(temp_largest);
Imgproc.cvtColor(imgSource, imgSource, Imgproc.COLOR_BayerBG2RGB);
Imgproc.drawContours(imgSource, largest_contours, -1, new Scalar(0, 255, 0), 1);
// create the new image here using the largest detected square
Toast.makeText(getApplicationContext(), "Largest Contour: ", Toast.LENGTH_LONG).show();
return imgSource;
}
Here are the error information in LogCat:
error opening trace file: No such file or directory (2)
Tegra Version detected: 0
FATAL EXCEPTION: Thread-14346
java.lang.IndexOutOfBoundsException: Invalid index 0, size is 0
at java.util.ArrayList.throwIndexOutOfBoundsException(ArrayList.java:251)
at java.util.ArrayList.get(ArrayList.java:304)
at org.opencv.samples.tutorial2.Tutorial2Activity.findLargestRectangle(Tutorial2Activity.java:221)
at org.opencv.samples.tutorial2.Tutorial2Activity.onCameraFrame(Tutorial2Activity.java:169)
at org.opencv.android.CameraBridgeViewBase.deliverAndDrawFrame(CameraBridgeViewBase.java:387)
at org.opencv.android.JavaCameraView$CameraWorker.run(JavaCameraView.java:328)
at java.lang.Thread.run(Thread.java:856)
And the 221st line of the Tutorial2Avctivity is:
MatOfPoint temp_contour = contours.get(0);
Please tell me what the errors are. Thanks a lot!

This simply means that the size of the ArrayList of contours is empty.
I would suggest adding a conditional block to allow your application cope with the scenario that no contours could be found in the input image.
If you're consistently getting no contours, regardless of the input image, you may want to review the documentation (or Javadoc):
image – Source, an 8-bit single-channel image. Non-zero pixels are treated as 1’s. Zero pixels remain 0’s, so the image is treated as binary . You can use compare() , inRange() , threshold() , adaptiveThreshold() , Canny() , and others to create a binary image out of a grayscale or color one.
Perhaps the threshold values in your Canny() function is not yielding any edges.
If you're still having no luck, perhaps you could test with the input image and values from this blog post.

Try with this,
List<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Imgproc.findContours(imgSource, contours, new Mat(), Imgproc.RETR_LIST, Imgproc.CHAIN_APPROX_SIMPLE);
You have to add some value into counter before below line
MatOfPoint temp_contour = contours.get(0);