I've computed the following mask of an image containing corn:
the problem is, now i have black parts inside the seeds. Is there a way to get rid of them while making sure that seeds remain disconnected from each other?
My ultimate goal is to count the seeds on the picture, using watershed algorithm. I observed when the seeds are touching each other, it introduces a imprecision to the algorithm, so I tried to introduce gaps between seeds by using canny and subtracting the borders from the mask, which is the result above.
My code so far:
auto img = GetAreaOfInterest(orig, bt); // <- just a Gauss blur with OTSU thresh
{
cv::Mat gray, edges;
cv::cvtColor(orig, gray, cv::COLOR_BGR2GRAY);
// tried bilateralFIlter here, but things only got worse
cv::Canny(gray, edges, 40, 160);
cv::dilate(edges, edges,
cv::getStructuringElement(cv::MORPH_ELLIPSE, {5, 5}),
{-1, -1}, 1);
img.setTo(0, edges != 0);
}
cv::Mat background, foreground, unknown, markers;
cv::dilate(img, background,
cv::getStructuringElement(cv::MORPH_ELLIPSE, {3,3}));
/* Get area for which we are sure it's the foreground */
cv::distanceTransform(img, img, cv::DIST_L1, 3, CV_8U);
{
double max;
cv::minMaxLoc(img, nullptr, &max);
cv::threshold(img, img, 0.46 * max, 255, cv::THRESH_BINARY);
}
img.convertTo(foreground, CV_8UC3);
show_resized("distance", foreground, 0.5);
/* Mark unknown areas */
cv::subtract(background, foreground, unknown);
/* Set up markers */
cv::connectedComponents(foreground, markers);
markers = markers + 1;
markers.setTo(0, unknown == 255);
/* Expand markers */
cv::watershed(orig, markers);
// Count objects
original image:
the most problematic image:
Related
Problem : Watershed algorithm
I started app project, for image processing, using OpenCv 4.5.3 and Swift ( with C++ ). I'm fighting with watershaded alg. for a really long time... And i have no clue what did i do wrong. Just don't know...
Error :
libc++abi.dylib: terminating with uncaught exception of type cv::Exception: OpenCV(4.5.3)
/Volumes/build-storage/build/master_iOS-mac/opencv/modules/imgproc/src/segmentation.cpp:161:
error: (-215:Assertion failed) src.type()
== CV_8UC3 && dst.type() == CV_32SC1 in function 'watershed'
terminating with uncaught exception of type cv::Exception: OpenCV(4.5.3)
/Volumes/build-storage/build/master_iOS-mac/opencv/modules/imgproc/src/segmentation.cpp:161: error:
(-215:Assertion failed) src.type()
== CV_8UC3 && dst.type() == CV_32SC1 in function 'watershed'
In the definition of openCv's watershed we can find :
#param image Input 8-bit 3-channel image.
#param markers Input/output 32-bit single-channel image (map) of markers. It should have the same size as image .
Code
+(UIImage *) watershed:(UIImage *)src{
cv::Mat img, mask;
UIImageToMat(src, img);
// Change the background from white to black, since that will help later to extract
// better results during the use of Distance Transform
cv::inRange(img, cv::Scalar(255,255,255), cv::Scalar(255,255,255), mask);
img.setTo(cv::Scalar(0,0,0), mask);
// Create a kernel that we will use to sharpen our image
// an approximation of second derivative, a quite strong kernel
cv::Mat kernel = (cv::Mat_<float>(3,3) <<
1, 1, 1,
1, -8, 1,
1, 1, 1);
// do the laplacian filtering as it is
// well, we need to convert everything in something more deeper then CV_8U
// because the kernel has some negative values,
// and we can expect in general to have a Laplacian image with negative values
// BUT a 8bits unsigned int (the one we are working with) can contain values from 0 to 255
// so the possible negative number will be truncated
cv::Mat lapl;
cv::filter2D(img, lapl, CV_32F, kernel);
cv::Mat sharp;
img.convertTo(sharp, CV_32F);
cv::Mat result = sharp - lapl;
// convert back to 8bits gray scale
result.convertTo(result, CV_8UC3);
lapl.convertTo(lapl, CV_8UC3);
cv::Mat bw;
cv::cvtColor(result, bw, cv::COLOR_BGR2GRAY);
cv::threshold(bw, bw, 40, 255, cv::THRESH_BINARY | cv::THRESH_OTSU);
// Perform the distance transform algorithm
cv::Mat dist;
cv::distanceTransform(bw, dist, cv::DIST_L2, cv::DIST_MASK_3);
// Normalize the distance image for range = {0.0, 1.0}
// so we can visualize and threshold it
cv::normalize(dist, dist, 0, 1.0, cv::NORM_MINMAX);
// Threshold to obtain the peaks
// This will be the markers for the foreground objects
cv::threshold(dist, dist, 0.4, 1.0, cv::THRESH_BINARY);
// Dilate a bit the dist image
cv::Mat kernel1 = cv::Mat::ones(3, 3, CV_8U);
dilate(dist, dist, kernel1);
// Create the CV_8U version of the distance image
// It is needed for findContours()
cv::Mat dist_8u;
dist.convertTo(dist_8u, CV_8U);
// Find total markers
std::vector<std::vector<cv::Point> > contours;
findContours(dist_8u, contours, cv::RETR_EXTERNAL, cv::CHAIN_APPROX_SIMPLE);
// Create the marker image for the watershed algorithm
cv::Mat markers = cv::Mat::zeros(dist.size(), CV_32S);
// Draw the foreground markers
for (size_t i = 0; i < contours.size(); i++)
{
drawContours(markers, contours, static_cast<int>(i), cv::Scalar(static_cast<int>(i)+1), -1);
}
// Draw the background marker
circle(markers, cv::Point(5,5), 3, cv::Scalar(255), -1);
cv::Mat markers8u;
markers.convertTo(markers8u, CV_8U, 10);
// Perform the watershed algorithm
watershed(result, markers);
return MatToUIImage(result);
}
You can clearly see, that variables has proper type, as in descr. of function:
result.convertTo(result, CV_8UC3);
cv::Mat markers = cv::Mat::zeros(dist.size(), CV_32S);
The convertTo can not add channels as well can not reduce/convert image to image with smaller amount of channels.
The key in this case is to use :
cvtColor(src, src, COLOR_BGRA2BGR); // change 4 to 3 channels
I want to calculate numbers of all white pixels within every polygon area efficiently.
Given some processes:
// some codes for reading gray image
// cv::Mat gray = cv::imread("gray.jpg");
// given polygons
// vector< vector<cv::Point> > polygons;
cv::Mat cropped;
cv::Mat mask = cv::Mat::zeros(gray.size(), CV_8UC1);
cv::fillPoly(mask, polygons, cv::Scalar(255));
cv::bitwise_and(gray, gray, cropped, mask);
cv::Mat binary;
cv::threshold(cropped, binary, 20, 255, CV_THRESH_BINARY);
So until now, we can get a image with multiple polygon areas(say we have 3 areas) which have white( with value 255) pixels. Then after some operations we expect to get a vector like:
// some efficient operations
// ...
vector<int> pixelNums;
The size of pixelNums should be same with polygons which is 3 here. And if we print them we may get some outputs like(the values are basically depended on the pre-processes):
index: 0; value: 120
index: 1; value: 1389
index: 2; value: 0
Here is my thought. Counting every pixels within every polygon area with help of cv::countNonZero, but I need to call it within a loop which I don't think it's a efficient way, isn't it?
vector<int> pixelNums;
for(auto polygon : polygons)
{
vector< vector<cv::Point> > temp_polygons;
temp_polygons.push_back(polygon);
cv::Mat cropped;
cv::Mat mask = cv::Mat::zeros(gray.size(), CV_8UC1);
cv::fillPoly(mask, temp_polygons, cv::Scalar(255));
cv::bitwise_and(gray, gray, cropped, mask);
cv::Mat binary;
cv::threshold(cropped, binary, 20, 255, CV_THRESH_BINARY);
pixelNums.push_back(cv::countNonZero(binary));
}
If you have some better ways, please kindly answer this post. Here I say better way is consuming as little time as you can just in cpu environment.
There are some minor improvements that can be done, but all of them combined should provide a decent speedup.
Compute the threshold only once
Make most operations on smaller images, using the bounding box of your polygon to get the region of interest
Avoid unneeded copies in the for loop, use const auto&
Example code:
#include <vector>
#include <opencv2/opencv.hpp>
int main()
{
// Your image
cv::Mat1b gray = cv::imread("path/to/image", cv::IMREAD_GRAYSCALE);
// Your polygons
std::vector<std::vector<cv::Point>> polygons
{
{ {15,120}, {45,200}, {160,160}, {140, 60} },
{ {10,10}, {15,30}, {50,25}, {40, 15} },
// etc...
};
// Compute the threshold just once
cv::Mat1b thresholded = gray > 20;
std::vector<int> pixelNums;
for (const auto& polygon : polygons)
{
// Get bbox of polygon
cv::Rect bbox = cv::boundingRect(polygon);
// Make a new (small) mask
cv::Mat1b mask(bbox.height, bbox.width, uchar(0));
cv::fillPoly(mask, std::vector<std::vector<cv::Point>>{polygon}, cv::Scalar(255), 8, 0, -bbox.tl());
// Get crop
cv::Mat1b cropped = thresholded(bbox) & mask;
// Compute the number of white pixels only on the crop
pixelNums.push_back(cv::countNonZero(cropped));
}
return 0;
}
I am trying to make an average of two blobs in OpenCV. To achieve that I was planning to use watershed algorithm on the image preprocessed in the following way:
cv::Mat common, diff, processed, result;
cv::bitwise_and(blob1, blob2, common); //calc common area of the two blobs
cv::absdiff(blob1, blob2, diff); //calc area where they differ
cv::distanceTransform(diff, processed, CV_DIST_L2, 3); //idea here is that the highest intensity
//will be in the middle of the differing area
cv::normalize(processed, processed, 0, 255, cv::NORM_MINMAX, CV_8U); //convert floats to bytes
cv::Mat watershedMarkers, watershedOutline;
common.convertTo(watershedMarkers, CV_32S, 1. / 255, 1); //change background to label 1, common area to label 2
watershedMarkers.setTo(0, processed); //set 0 (unknown) for area where blobs differ
cv::cvtColor(processed, processed, CV_GRAY2RGB); //watershed wants 3 channels
cv::watershed(processed, watershedMarkers);
cv::rectangle(watershedMarkers, cv::Rect(0, 0, watershedMarkers.cols, watershedMarkers.rows), 1); //remove the outline
//draw the boundary in red (for debugging)
watershedMarkers.convertTo(watershedOutline, CV_16S);
cv::threshold(watershedOutline, watershedOutline, 0, 255, CV_THRESH_BINARY_INV);
watershedOutline.convertTo(watershedOutline, CV_8U);
processed.setTo(cv::Scalar(CV_RGB(255, 0, 0)), watershedOutline);
//convert computed labels back to mask (blob), less relevant but shows my ultimate goal
watershedMarkers.convertTo(watershedMarkers, CV_8U);
cv::threshold(watershedMarkers, watershedMarkers, 1, 0, CV_THRESH_TOZERO_INV);
cv::bitwise_not(watershedMarkers * 255, result);
My problem with the results is that the calculated boundary is (almost) always adjacent to the area common to both blobs. Here are the pictures:
Input markers (black = 0, gray = 1, white = 2)
Watershed input image (distance transform result) with resulting outline drawn in red:
I would expect the boundary to go along the maximum intensity region of the input (that is, along the middle of the differing area). Instead (as you can see) it mostly goes around the area marked as 2, with a bit shifted to touch the background (marked as 1). Do I do something wrong here, or did I misunderstand how watershed works?
Starting from this image:
You can get the correct result simply passing an all-zero image to watershed algorithm. The "basin" is then equally filled of "water" starting from each "side" (then just remember to remove the outer border which is set by default to -1 by watershed algorithm):
Code:
#include <opencv2\opencv.hpp>
using namespace cv;
using namespace std;
int main()
{
Mat1b img = imread("path_to_image", IMREAD_GRAYSCALE);
Mat1i markers(img.rows, img.cols, int(0));
markers.setTo(1, img == 128);
markers.setTo(2, img == 255);
Mat3b image(markers.rows, markers.cols, Vec3b(0,0,0));
markers.convertTo(markers, CV_32S);
watershed(image, markers);
Mat3b result;
cvtColor(img, result, COLOR_GRAY2BGR);
result.setTo(Scalar(0, 0, 255), markers == -1);
imshow("Result", result);
waitKey();
return(0);
}
I am processing video images and I would like to detect if the video contains any pixels of a certain range of red. Is this possible?
Here is the code I am adapting from a tutorial:
#ifdef __cplusplus
- (void)processImage:(Mat&)image;
{
cv::Mat orig_image = image.clone();
cv::medianBlur(image, image, 3);
cv::Mat hsv_image;
cv::cvtColor(image, hsv_image, cv::COLOR_BGR2HSV);
cv::Mat lower_red_hue_range;
cv::Mat upper_red_hue_range;
cv::inRange(hsv_image, cv::Scalar(0, 100, 100), cv::Scalar(10, 255, 255), lower_red_hue_range);
cv::inRange(hsv_image, cv::Scalar(160, 100, 100), cv::Scalar(179, 255, 255), upper_red_hue_range);
// Interpret values here
}
Interpreting values
I would like to detect if the results from the inRange operations are nil or not. In other words I want to understand if there are any matching pixels in the original image with a colour inRange from the given lower and upper red scale. How can I interpret the results?
First you need to OR the lower and upper mask:
Mat mask = lower_red_hue_range | upper_red_hue_range;
Then you can countNonZero to see if there are non zero pixels (i.e. you found something).
int number_of_non_zero_pixels = countNonZero(mask);
It could be better to first apply morphological erosion or opening to remove small (probably noisy) blobs:
Mat kernel = getStructuringElement(MORPH_ELLIPSE, Size(3, 3));
morphologyEx(mask, mask, MORPH_OPEN, kernel); // or MORPH_ERODE
or find connected components (findContours, connectedComponentsWithStats) and prune / search for according to some criteria:
vector<vector<Point>> contours
findContours(mask.clone(), contours, RETR_EXTERNAL, CHAIN_APPROX_SIMPLE);
double threshold_on_area = 100.0;
for(int i=0; i<contours.size(); ++i)
{
double area = countourArea(contours[i]);
if(area < threshold_on_area)
{
// don't consider this contour
continue;
}
else
{
// do something (e.g. drawing a bounding box around the contour)
Rect box = boundingRect(contours[i]);
rectangle(hsv_image, box, Scalar(0, 255, 255));
}
}
I have a program for segmentation of lesion. In part of my program I want rescaling the intensity values in the original image to cover the entire dynamic range.
my code:
cvtColor(src, gray, CV_RGB2GRAY);
Mat kernel = Mat::ones(5, 5, CV_32F)/21;
kernel.row(0).col(0) = 0;
kernel.row(0).col(4) = 0;
kernel.row(4).col(0) = 0;
kernel.row(4).col(4) = 0;
//circular averaging low pass filter with a radius of 5, using the pill-box point spread function
filter2D(gray, gray, -1, kernel, Point(-1,-1));
threshold(gray, dst, 0, 255, THRESH_BINARY | THRESH_OTSU);
I am looking for solution for to do. It should Before threshold Done.