Contour results are not accurate with detection binary mask edges [closed] - opencv

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Now I have this mask generated based on the size of an image and I have a set of rectangles to know where are these rectangles so I tried to extract contours to know where are these rectangles ...
mask = np.zeros((image.shape[0], image.shape[1]), dtype=np.uint8) # Mask of original image
#some process to draw these rectangles merged...
_, bw = cv2.threshold(mask, 0, 255, cv2.THRESH_BINARY)
img, contours, hierarchy = cv2.findContours(bw.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
for j in range(len(contours)):
outputBoxes.append(cv2.boundingRect(contours[j]))
Another trial
_, bws = cv2.threshold(mask, 0, 255, cv2.THRESH_BINARY)
img, contours, hierarchy = cv2.findContours(bws, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE, offset=(0,0))
cv2.drawContours(bws, contours,-1,(255,255,0))
img, contours, hierarchy = cv2.findContours(bws, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE, offset=(0,0))
but with no vain
I can't get the rect dimensions exactly or even approximately
** NOTE This generated image is small part of long process
first one I detected some rects so I merged them as one in the second one then I should take this white one dimensions to be determined in the original one
As seen, it is not accurate too
Python or c++ are good for me
opencv 3.x

Here is the results I get:
Obviously from here you have pretty clear contours and you can just print out the lengths.
With this code:
Mat origImage = mat;
Mat canny_output = mat;
vector<vector<Point> > contours;
vector<Vec4i> hierarchy;
cv::Mat greyMat, colorMat;
cv::cvtColor(mat, greyMat, CV_BGR2GRAY);
int thresh = 100;
RNG rng(12345);
///// Detect edges using canny
Canny(greyMat, canny_output, thresh, thresh * 2, 3);
/// Find contours
findContours(canny_output, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, Point(0, 0));
int largest_area = 0;
int largest_contour_index = 0;
Rect bounding_rect;
/// Draw contours
Mat drawing = Mat::zeros(canny_output.size(), CV_8UC3);
for (int i = 0; i< contours.size(); i++)
{
Scalar color = Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255));
drawContours(drawing, contours, i, color, 2, 8, hierarchy, 0, Point());
double a=contourArea( contours[i],false); // Find the area of contour
if(a>largest_area){
largest_area=a;
largest_contour_index=i; //Store the index of largest contour
bounding_rect=boundingRect(contours[i]); // Find the bounding rectangle for biggest contour
}
}
rectangle(origImage, bounding_rect, Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255)),2);
/// Show in a window
namedWindow("Contours", CV_WINDOW_AUTOSIZE);
resize(drawing, drawing, Size(640, 480));
resize(mat, mat, Size(640, 480));
resize(origImage, origImage, Size(640, 480));
imshow("Contours", drawing);
cv::namedWindow("img");
cv::imshow("mat", mat);
cv::imshow("mat", origImage);
cv::imshow("mat123", drawing);
cv::waitKey(0);

Related

Draw lines connecting centroids of objects using OpenCV

I have found out the centroid of multiple objects in my image using the code provided here OpenCV examples
Here is the code which found the centroid and stored them in a vector.
cv::Mat InputImage;
cv::Mat CannyOutput;
vector<vector<cv::Point> > contours;
vector<Vec4i> hierarchy;
RNG rng(12345);
InputImage = cv::imread("Untitled.jpg");
//Edge detection
Canny(InputImage, CannyOutput, 100, 150);
//Contour detection
cv::findContours(CannyOutput, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, cv::Point(0, 0));
//Finding Moments
vector<Moments> mu(contours.size());
for (int i = 0; i < contours.size(); i++)
{
mu[i] = moments(contours[i], false);
}
//Calculating Centroid
vector<Point2f> mc(contours.size());
for (int i = 0; i < contours.size(); i++)
{
mc[i] = Point2f(mu[i].m10 / mu[i].m00, mu[i].m01 / mu[i].m00);
}
// Drawing
Mat drawing = Mat::zeros(CannyOutput.size(), CV_8UC3);
for (int i = 0; i< contours.size(); i++)
{
Scalar color = Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255));
//Drawing contour
drawContours(drawing, contours, i, color, 2, 8, hierarchy, 0, cv::Point());
//Drawing circles with centroid as centre
circle(drawing, mc[i], 4, color, -1, 8, 0);
}
What I want to do is draw a polygon with the centroid as the vertices. I used drawcontours, polyline and line functions but not getting the desired result. Is there a way to achieve this? . I need it to be achieved in C++
Output image
Desired image
Also, on another note, the code doesnt seem to be displaying the centroid if am replacing the 'color' variable with BGR value. Seems like both contour and centroid has to be of same color if i want to see the centroid. When i gave (0,255,255) for contour and (255,255,0) for centroid, the centroid was not displaying .
For the given sample image, you can use convexhull to obtain the order of centers, and then draw them with polylines.

OpenCV: How can I remove unwanted blobs or how can I copy wanted parts into an empty image?

From the following image, how could I find the result image?
The images shown here are threshold images. I have tried using morphological operators but they even remove the blob I want. How could I solve this problem?
Any hints?
Following is the result image I am interested to get/find:
import cv2
diff = cv2.imread('Image.png',0)
ret, thresh = cv2.threshold(diff, 12.5, 255, cv2.THRESH_BINARY)
thresh = cv2.dilate(thresh, None, iterations = 1)
cv2.imshow('img', thresh) # This is the first picture I have shown
cv2.waitKey(0)
You are most of the way there, all you need to do now is find the blobs, add some contours and find the biggest one. Easy! below is the code in C++, ill leave it up to you to work out how to convert it to Python:
cv::Mat mat = imread("g0cVU.png");
Mat origImage = mat;
Mat canny_output = mat;
vector<vector<Point> > contours;
vector<Vec4i> hierarchy;
cv::Mat greyMat, colorMat;
cv::cvtColor(mat, greyMat, CV_BGR2GRAY);
int thresh = 100;
RNG rng(12345);
///// Detect edges using canny
Canny(greyMat, canny_output, thresh, thresh * 2, 3);
/// Find contours
findContours(canny_output, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, Point(0, 0));
int largest_area = 0;
int largest_contour_index = 0;
Rect bounding_rect;
/// Draw contours
Mat drawing = Mat::zeros(canny_output.size(), CV_8UC3);
for (int i = 0; i< contours.size(); i++)
{
Scalar color = Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255));
drawContours(drawing, contours, i, color, 2, 8, hierarchy, 0, Point());
double a=contourArea( contours[i],false); // Find the area of contour
if(a>largest_area){
largest_area=a;
largest_contour_index=i; //Store the index of largest contour
bounding_rect=boundingRect(contours[i]); // Find the bounding rectangle for biggest contour
}
}
rectangle(origImage, bounding_rect, Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255)),2);
/// Show in a window
namedWindow("Contours", CV_WINDOW_AUTOSIZE);
imshow("Contours", drawing);
cv::namedWindow("img");
cv::imshow("mat", mat);
cv::imshow("mat", origImage);
cv::imshow("mat123", drawing);
cv::waitKey(0);
Which gives this results:
You can see in the bottom image the largest contor has a brown rectangle drawn around it.
o and obviously once you have the largest blob (or whatever blob you deem "the correct one") you can just set everything else to black which is fairly straightforward.

findcontours finds too many contours

Is it normal that find contours finds so many contours where there are obviously only 3 contours ?
The original image and after drawing found contours are shown below :
The code is :
Mat image;
vector<vector<Point> > contours;
vector<Vec4i> hierarchy;
image = imread(argv[1], 0); // Read the file
findContours(image, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, Point(0, 0));
cout << contours.size();
RNG rng(12345);
Mat drawing = Mat::zeros(image.size(), CV_8UC3);
for (int i = 0; i< contours.size(); i++)
{
Scalar color = Scalar(rng.uniform(0, 255), rng.uniform(0, 255), rng.uniform(0, 255));
drawContours(drawing, contours, i, color, 2, 8, hierarchy, 0, Point());
}
/// Show in a window
namedWindow("Contours", CV_WINDOW_AUTOSIZE);
imshow("Contours", drawing);
namedWindow("Display window", WINDOW_AUTOSIZE);// Create a window for display.
imshow("Display window", image); // Show our image inside it.
I think you are Reading a Jpeg or any other compressed version of your actual input image which adds these noise. Find contours needs Binary image. If you want to process this image simple apply threshold before finding contours! Note that your source image is working fine for me!

Find overlapping/complex circles with OpenCV

I want to compute the red circles radius (fig 2). I have troubles finding these circles using HoughCircles from OpenCV. As you can see in fig. 2 I can only find the little circles in center which are shown in black using HoughCircles.
original fig 2.
Since I know the center of the red circles (which are the same as the red ones), is there a way to compute simply the radius of the red circles ?
Is it also possible to have a generic way of computing radius of circles on a more complex image such as this one :
Edit : Here the interesting part of my code after obtaining fig 2 :
threshold(maskedImage, maskedImage, thresh, 255, THRESH_BINARY_INV | THRESH_OTSU);
std::vector<Vec3f> circles;
// Canny(maskedImage, maskedImage, thresh, thresh * 2, 3);
HoughCircles(maskedImage, circles, CV_HOUGH_GRADIENT, 1, src_gray.rows / 4, cannyThreshold, accumulatorThreshold, 0, 0);
Mat display = src_display.clone();
for (size_t i = 0; i < circles.size(); i++)
{
Point center(cvRound(circles[i][0]), cvRound(circles[i][1]));
int radius = cvRound(circles[i][2]);
// circle center
circle(display, center, 3, Scalar(0, 255, 0), -1, 8, 0);
// circle outline
circle(display, center, radius, Scalar(0, 0, 255), 3, 8, 0);
}
I have tried to use play with cannyThreshold and accumulator without results. Real images are 5x biggers. Here a link for example 1 after threshold.
Thanks
You already know the smaller circles in the image(which you have drawn in black).
Prepare a mask image using these circles so the areas having smaller circles will have non-zero pixels. We'll call it mask:
In the original image, fill these circle areas in a dark color(say black). This will result in an image like your fig 2. We'll call it filled
Threshold the filled image to obtain the dark areas. We'll call it binary. You can use Otsu thresholding for this. Result will look something like this:
Take the distance transform of this binary image. Use an accurate distance estimation method for this. We'll call this dist. It'll look something like this. The colored one is just a heat map for more clarity:
Use the mask to obtain the peak regions from dist. The max value of each such region should give you the radius of the larger circle. You can also do some processing on these regions to arrive at a more reasonable value for radius rather than just picking up the max.
For selecting the regions, you can either find the contours of the mask and then extract that region from dist image, or, since you already know the smaller circles from applying hough-circle transform, prepare a mask from each of those circles and extract that region from dist image. I'm not sure if you can calculate max or other stats by giving a mask. Max will definitely work because the rest of the pixels are 0. You might be able calculate the stats of the region if you extract those pixels to another array.
Figures below show such mask and the extracted region from dist. For this I get a max around 29 which is consistent with the radius of that circle. Note that the images are not to scale.
mask for a circle, extracted region from dist
Here's the code (I'm not using hough-circles transform):
Mat im = imread(INPUT_FOLDER_PATH + string("ex1.jpg"));
Mat gray;
cvtColor(im, gray, CV_BGR2GRAY);
Mat bw;
threshold(gray, bw, 0, 255, CV_THRESH_BINARY|CV_THRESH_OTSU);
// filtering smaller circles: not using hough-circles transform here.
// you can replace this part with you hough-circles code.
vector<int> circles;
vector<vector<Point>> contours;
vector<Vec4i> hierarchy;
findContours(bw, contours, hierarchy, CV_RETR_CCOMP, CV_CHAIN_APPROX_SIMPLE, Point(0, 0));
for(int idx = 0; idx >= 0; idx = hierarchy[idx][0])
{
Rect rect = boundingRect(contours[idx]);
if (abs(1.0 - ((double)rect.width/rect.height) < .1))
{
Mat mask = Mat::zeros(im.rows, im.cols, CV_8U);
drawContours(mask, contours, idx, Scalar(255, 255, 255), -1);
double area = sum(mask).val[0]/255;
double rad = (rect.width + rect.height)/4.0;
double circArea = CV_PI*rad*rad;
double dif = abs(1.0 - area/circArea);
if (dif < .5 && rad < 50 && rad > 30) // restrict the radius
{
circles.push_back(idx); // store smaller circle contours
drawContours(gray, contours, idx, Scalar(0, 0, 0), -1); // fill circles
}
}
}
threshold(gray, bw, 0, 255, CV_THRESH_BINARY_INV|CV_THRESH_OTSU);
Mat dist, distColor, color;
distanceTransform(bw, dist, CV_DIST_L2, 5);
double max;
Point maxLoc;
minMaxLoc(dist, NULL, &max);
dist.convertTo(distColor, CV_8U, 255.0/max);
applyColorMap(distColor, color, COLORMAP_JET);
imshow("", color);
waitKey();
// extract dist region corresponding to each smaller circle and find max
for(int idx = 0; idx < (int)circles.size(); idx++)
{
Mat masked;
Mat mask = Mat::zeros(im.rows, im.cols, CV_8U);
drawContours(mask, contours, circles[idx], Scalar(255, 255, 255), -1);
dist.copyTo(masked, mask);
minMaxLoc(masked, NULL, &max, NULL, &maxLoc);
circle(im, maxLoc, 4, Scalar(0, 255, 0), -1);
circle(im, maxLoc, (int)max, Scalar(0, 0, 255), 2);
cout << "rad: " << max << endl;
}
imshow("", im);
waitKey();
Results(scaled):
Hope this helps.

OpenCV - find bounding box of largest blob in binary image

What is the most efficient way to find the bounding box of the largest blob in a binary image using OpenCV? Unfortunately, OpenCV does not have specific functionality for blob detection. Should I just use findContours() and search for the largest in the list?
Here. It. Is.
(FYI: try not to be lazy and figure out what happens in my function below.
cv::Mat findBiggestBlob(cv::Mat & matImage){
int largest_area=0;
int largest_contour_index=0;
vector< vector<Point> > contours; // Vector for storing contour
vector<Vec4i> hierarchy;
findContours( matImage, contours, hierarchy,CV_RETR_CCOMP, CV_CHAIN_APPROX_SIMPLE ); // Find the contours in the image
for( int i = 0; i< contours.size(); i++ ) {// iterate through each contour.
double a=contourArea( contours[i],false); // Find the area of contour
if(a>largest_area){
largest_area=a;
largest_contour_index=i; //Store the index of largest contour
//bounding_rect=boundingRect(contours[i]); // Find the bounding rectangle for biggest contour
}
}
drawContours( matImage, contours, largest_contour_index, Scalar(255), CV_FILLED, 8, hierarchy ); // Draw the largest contour using previously stored index.
return matImage;
}
If you want to use OpenCV libs, check out OpenCVs SimpleBlobDetector. Here's another stack overflow showing a small tutorial of it: How to use OpenCV SimpleBlobDetector
This only gives you key points though. You could use this as an initial search to find the blob you want, and then possibly use the findContours algorithm around the most likely blobs.
Also the more information you know about your blob, you can provide parameters to filter out the blobs you don't want. You might want to test out the area parameters of the SimpleBlobDetector. Possibly could could compute the area based on the size of the area of the image and then iteratively allow for a smaller blob if the algorithm does not detect any blobs.
Here is the link to the main OpenCV documentation: http://docs.opencv.org/modules/features2d/doc/common_interfaces_of_feature_detectors.html#simpleblobdetector
To find the bounding box of the largest blob, I used findContours, followed by the following code:
double maxArea = 0;
for (MatOfPoint contour : contours) {
double area = Imgproc.contourArea(contour);
if (area > maxArea) {
maxArea = area;
largestContour = contour;
}
}
Rect boundingRect = Imgproc.boundingRect(largestContour);
Since no one has posted a complete OpenCV solution, here's a simple approach using thresholding + contour area filtering
Input image
Largest blob/contour highlighted in green
import cv2
# Load image, grayscale, Gaussian blur, and Otsu's threshold
image = cv2.imread('1.png')
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY_INV + cv2.THRESH_OTSU)[1]
# Find contours and sort using contour area
cnts = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
cnts = sorted(cnts, key=cv2.contourArea, reverse=True)
for c in cnts:
# Highlight largest contour
cv2.drawContours(image, [c], -1, (36,255,12), 3)
break
cv2.imshow('thresh', thresh)
cv2.imshow('image', image)
cv2.waitKey()
TimZaman, your code has a bug but I can't comment so I start a new and correct answer.
Here is my solution based on 1"'s and TimZaman's ideas:
Mat measure::findBiggestBlob(cv::Mat &src){
int largest_area=0;
int largest_contour_index=0;
Mat temp(src.rows,src.cols,CV_8UC1);
Mat dst(src.rows,src.cols,CV_8UC1,Scalar::all(0));
src.copyTo(temp);
vector<vector<Point>> contours; // storing contour
vector<Vec4i> hierarchy;
findContours( temp, contours, hierarchy,CV_RETR_CCOMP, CV_CHAIN_APPROX_SIMPLE );
for( int i = 0; i< contours.size(); i++ ) // iterate
{
double a=contourArea( contours[i],false); //Find the largest area of contour
if(a>largest_area)
{
largest_area=a;
largest_contour_index=i;
}
}
drawContours( dst, contours,largest_contour_index, Scalar(255), CV_FILLED, 8, hierarchy );
// Draw the largest contour
return dst;
}

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