I want to get a metric of straightness of contour in my binary image (relatively faster). The image looks as follows:
Now, the contours in the red box are the ones which I would like to be removed preferably. Since they are not straight. These are the things I have tried. I am as of now implementing in MATLAB.
1.Collect row and column coordinates of each contour and then take derivative. For straight objects (such as rectangle), derivative will be mostly low with a few spikes (along the corners of the rectangle).
Problem: The coordinates collected are not in order i.e. the order in which the contour will be traversed if we imaging it as a path. Therefore, derivative gives absurdly high values sometimes. Also, the contour is not absolutely straight, its an output of edge detection algorithm, so you can imagine that there might be some discontinuity (see the rectangle at the bottom, human eye can understand that it is a rectangle though it is not absolutely straight).
2.Tried to think about polyfit, but again this contour issue comes up. Since its a rectangle I don't know how to apply polyfit to that point set.
Also, I would like to remove contours which are distributed vertically/horizontally. Basically this is a lane detection algorithm. So lanes cannot be absolutely vertical/horizontal.
Any ideas?
You should look into the features of regionprops more. To be fair I stole the script from this answer, but here it is:
BW = imread('lanes.png');
BW = im2bw(BW);
figure(1),
subplot(1,2,1);
imshow(BW);
cc = bwconncomp(BW);
l = labelmatrix(cc);
a_rp = regionprops(CC,'Area','MajorAxisLength','MinorAxislength','Orientation','PixelList','Eccentricity');
idx = ([a_rp.Eccentricity] > 0.99 & [a_rp.Area] > 100 & [a_rp.Orientation] < 70 & [a_rp.Orientation] > -90);
BW2 = ismember(l,find(idx));
subplot(1,2,2);
imshow(BW2);
You can mess around with the properties. 'Orientation', 'Eccentricity', and 'Area' are probably the parameters you want to mess with. I also messed with the ratios of the major/minor axis lengths but eccentricity basically does this (eccentricity is a measure of how "circular" an ellipse is). Here's the output:
I actually saw a good video specifically from matlab for lane detection using regionprops. I'll try to see if I can find it and link it.
You can segment your image using bwlabel, then work separately on each bwlabel connected object, using find. This should help solve your order problem.
About a metric, the only thing that come to mind at the moment is to fit to an ellipse, and set the a/b (major axis/minor axis) ratio (basically eccentricity) a parameter. For example a straight line (even if not perfect) will be fitted to an ellipse with a very big major axis and a very small minor axis. So say you set a ratio threshold of >10 etc... Fitting to an ellipse can be done using this FEX submission for example.
Related
(I use MATLAB R2015a). I have a plot of edge points of an object (obtained using edge detection), and I have a plot of the template of the object. I want to rotate the template until it matches with the detected edge points. (Figure link included: solid blue - template, red dots - edge detected points; the rotation is subtle, but it's there.)
I plan to rotate the template in a loop about the centroid through different values of thetas (which I know how to do), and ask the code to 'stop executing when it matches with the edge' (which is what I want to know how) and return the corresponding theta.
The number of points making up the template and that making up the edges are not the same, so splitting the plots into 3 lines and 1 (half) ellipse and directly comparing does not work.
Using regionprops 'orientation' does not give the expected result for each frame because of the way the edges are being detected in each frame. (I can elaborate more on this if required)
I have intentionally plotted points using plot, rather than keeping the edge as a BW image because, otherwise, I'm having to round off indices while creating the template, and for my application, I cannot afford to lose precision like that.
I'm not lazy, I don't want somebody to just code it up for me. None of my ideas worked and I'm unable to think any differently, so perhaps somebody with a fresh mind and more experience in Matlab will have some idea.
Assuming both image and template are bitmaps (= template isn't given as 3x lines + half of ellipse), and you know the position and size of the template, just not the angle:
For each edge, find the closest point on the template, and sum all the distances, or perhaps sum of sqrt of distances, or some other metric that penalizes many small outliers - many points will be slightly wrong if rotation is slightly wrong. Few points that are completely wrong are noise to ignore. So, something like:
minDist = inf;
minAngle = -1;
for t = 1 : length(thetas)
templatePoints = ...; % calculate template points.
for i = 1 : length(edges)
edge = edges(i); % assuming this edge is (x, y) edge point
mind = inf; % Min distance
for j = 1 : length(templatePoints)
d = sum(sqrt((edge - templatePoints).^2));
if (d < mind)
mind = d;
end
end
end
currentDist = sum(mind);
if (currentDist < minDist)
...
end
When you complete the full circle of template rotation select the rotation with the lowest difference.
This procedure might be a bit problematic because you might have template rotated by 10.5 deg and you are going in a step of 1 deg, so you will not have totally optimal angle in the end. Plus you will try tons of completely wrong angles, slowing you down.
But to find the optimal angle you can change angle step, say you first try every 10 deg rotation, then every 1deg around the minimum, then every 0.1deg etc. Or use optimization method. Gradient descent should work fine if you don't have too much noise, use simulated annealing for noisy images. Use the same code as above, currentDist is a good enough optimization parameter - it should be as close to 0 as possible.
If you have unknown template size too, or unknown template position, you definitely should use simulated annealing, gradient descent will almost surely get stuck in a local minimum. Use code similar to above to calculate difference between the edges and template, and put all the unknown parameters to the method.
One option is to make an image of your result for each rotation, but do not make it binary, make it grayscale. There are ways of making this so the "maximum interpolated edge" is where your continuous function is (such as Xiaolin Wu's line algorithm, for example).
As you are matching an image, you are not loosing precision, but putting the precision of your target to the same level as your image.
Once you get this, for each rotation, use a metric to evaluate how the 2 grayscale (yes, not binary) images match, using i.e. correlation coefficient, mutual information, universal quality index (UQI), etc.
I'm using the function regionprops to detect the number of trees on a image taked by drone.
First I removed the ground using Blue NDVI:
Image with threshold:
Then I used the function regionprops to detect the number of trees on image:
But there are a problem on region 15, because all trees on that region are connected and it detects as one tree.
I tried to separate the trees on that region using Watershed Segmentation, but its not working:
Am I doing this the wrong way?
Is there a better method to separate the trees?
If anyone can help me with this problem I will appreciate. Here is the region 15 without the ground:
If it helps, here is the Gradient Magnitude image:
It has been some time since this question was asked. I hope it is not too late for an answer. I see a general problem of using watershed segmentation in similar questions. Sometimes the objects are apart, not touching each other like in this example . In such cases, only blurring the image is enough to use watershed segmentation. Sometimes the objects are located closely and touch each other, thus the boundaries of objects are not clear like in this example. In such cases, using distance transform-->blur-->watershed helps. In this question, the logical approach should be using distance transform. However, this time the boundaries are not clear due to shadows on and nearby the trees. In such cases, it is good to use any information that helps to separate the objects as in here or emphasise objects itself.
In this question, I suggest using colour information to emphasise tree pixels.
Here are the MATLAB codes and results.
im=imread('https://i.stack.imgur.com/aBHUL.jpg');
im=im(58:500,86:585,:);
imOrig=im;
%% Emphasize trees
im=double(im);
r=im(:,:,1);
g=im(:,:,2);
b=im(:,:,3);
tmp=((g-r)./(r-b));
figure
subplot(121);imagesc(tmp),axis image;colorbar
subplot(122);imagesc(tmp>0),axis image;colorbar
%% Transforms
% Distance transform
im_dist=bwdist(tmp<0);
% Blur
sigma=10;
kernel = fspecial('gaussian',4*sigma+1,sigma);
im_blured=imfilter(im_dist,kernel,'symmetric');
figure
subplot(121);imagesc(im_dist),axis image;colorbar
subplot(122);imagesc(im_blured),axis image;colorbar
% Watershed
L = watershed(max(im_blured(:))-im_blured);
[x,y]=find(L==0);
figure
subplot(121);
imagesc(imOrig),axis image
hold on, plot(y,x,'r.','MarkerSize',3)
%% Local thresholding
trees=zeros(size(im_dist));
centers= [];
for i=1:max(L(:))
ind=find(L==i & im_blured>1);
mask=L==i;
[thr,metric] =multithresh(g(ind),1);
trees(ind)=g(ind)>thr*1;
trees_individual=trees*0;
trees_individual(ind)=g(ind)>thr*1;
s=regionprops(trees_individual,'Centroid');
centers=[centers; cat(1,[],s.Centroid)];
end
subplot(122);
imagesc(trees),axis image
hold on, plot(y,x,'r.','MarkerSize',3)
subplot(121);
hold on, plot(centers(:,1),centers(:,2),'k^','MarkerFaceColor','r','MarkerSize',8)
You could try out a marker-based watershed. Vanilla watershed transforms never work out of the box in my experience. One way to perform one would be to first create a distance map of the segmented area by using imdist(). Then you could suppress local maxima by calling imhmax(). Then calling watershed() will usually perform noticeably better.
Here's a sample script on how to do it:
bwTrees = imopen(bwTrees, strel('disk', 10));
%stabilize the borders to lessen oversegmentation
distTrees = -bwDist(~bwTrees); %Distance transform
distTrees(~bwTrees) = -Inf; %set background to -Inf
distTrees = imhmin(distTrees, 3); %suppress local minima
basins = watershed(distTrees);
ridges = basins == 0;
segmentedTrees = bwTrees & ~ridges; %segment
segmentedTrees = imopen(segmentedTrees, strel('disk', 2));
%remove 'segmentation trash' caused by oversegmentation near the borders.
I fiddled around with the parameters for ~10min but got fairly poor results:
You'd need to pour work into this. Mostly in pre- and post-processing via the morphology. More curvature would help the segmentation, if you could lower the sensitivity of the segmentation in the first part. The size of the h-minima transform is also an paramater of interest. You can probably get adequate results this way.
Probably a better approach would come from the world of clustering techniques. If you have or can find a way to estimate the number of trees in the forest you should be able to use traditional clustering methods to segment out the trees. A Gaussian mixture model or a k-means with k-trees would probably work much better than a marker based watershed if you get even nearly the right amount of trees. Normally I'd estimate the number of trees based on the number of suppressed maxima on a h-maxima transform, but your labels might be a bit too sausagey for that. It's worth a try though.
I'm using the function regionprops to detect the number of trees on a image taked by drone.
First I removed the ground using Blue NDVI:
Image with threshold:
Then I used the function regionprops to detect the number of trees on image:
But there are a problem on region 15, because all trees on that region are connected and it detects as one tree.
I tried to separate the trees on that region using Watershed Segmentation, but its not working:
Am I doing this the wrong way?
Is there a better method to separate the trees?
If anyone can help me with this problem I will appreciate. Here is the region 15 without the ground:
If it helps, here is the Gradient Magnitude image:
It has been some time since this question was asked. I hope it is not too late for an answer. I see a general problem of using watershed segmentation in similar questions. Sometimes the objects are apart, not touching each other like in this example . In such cases, only blurring the image is enough to use watershed segmentation. Sometimes the objects are located closely and touch each other, thus the boundaries of objects are not clear like in this example. In such cases, using distance transform-->blur-->watershed helps. In this question, the logical approach should be using distance transform. However, this time the boundaries are not clear due to shadows on and nearby the trees. In such cases, it is good to use any information that helps to separate the objects as in here or emphasise objects itself.
In this question, I suggest using colour information to emphasise tree pixels.
Here are the MATLAB codes and results.
im=imread('https://i.stack.imgur.com/aBHUL.jpg');
im=im(58:500,86:585,:);
imOrig=im;
%% Emphasize trees
im=double(im);
r=im(:,:,1);
g=im(:,:,2);
b=im(:,:,3);
tmp=((g-r)./(r-b));
figure
subplot(121);imagesc(tmp),axis image;colorbar
subplot(122);imagesc(tmp>0),axis image;colorbar
%% Transforms
% Distance transform
im_dist=bwdist(tmp<0);
% Blur
sigma=10;
kernel = fspecial('gaussian',4*sigma+1,sigma);
im_blured=imfilter(im_dist,kernel,'symmetric');
figure
subplot(121);imagesc(im_dist),axis image;colorbar
subplot(122);imagesc(im_blured),axis image;colorbar
% Watershed
L = watershed(max(im_blured(:))-im_blured);
[x,y]=find(L==0);
figure
subplot(121);
imagesc(imOrig),axis image
hold on, plot(y,x,'r.','MarkerSize',3)
%% Local thresholding
trees=zeros(size(im_dist));
centers= [];
for i=1:max(L(:))
ind=find(L==i & im_blured>1);
mask=L==i;
[thr,metric] =multithresh(g(ind),1);
trees(ind)=g(ind)>thr*1;
trees_individual=trees*0;
trees_individual(ind)=g(ind)>thr*1;
s=regionprops(trees_individual,'Centroid');
centers=[centers; cat(1,[],s.Centroid)];
end
subplot(122);
imagesc(trees),axis image
hold on, plot(y,x,'r.','MarkerSize',3)
subplot(121);
hold on, plot(centers(:,1),centers(:,2),'k^','MarkerFaceColor','r','MarkerSize',8)
You could try out a marker-based watershed. Vanilla watershed transforms never work out of the box in my experience. One way to perform one would be to first create a distance map of the segmented area by using imdist(). Then you could suppress local maxima by calling imhmax(). Then calling watershed() will usually perform noticeably better.
Here's a sample script on how to do it:
bwTrees = imopen(bwTrees, strel('disk', 10));
%stabilize the borders to lessen oversegmentation
distTrees = -bwDist(~bwTrees); %Distance transform
distTrees(~bwTrees) = -Inf; %set background to -Inf
distTrees = imhmin(distTrees, 3); %suppress local minima
basins = watershed(distTrees);
ridges = basins == 0;
segmentedTrees = bwTrees & ~ridges; %segment
segmentedTrees = imopen(segmentedTrees, strel('disk', 2));
%remove 'segmentation trash' caused by oversegmentation near the borders.
I fiddled around with the parameters for ~10min but got fairly poor results:
You'd need to pour work into this. Mostly in pre- and post-processing via the morphology. More curvature would help the segmentation, if you could lower the sensitivity of the segmentation in the first part. The size of the h-minima transform is also an paramater of interest. You can probably get adequate results this way.
Probably a better approach would come from the world of clustering techniques. If you have or can find a way to estimate the number of trees in the forest you should be able to use traditional clustering methods to segment out the trees. A Gaussian mixture model or a k-means with k-trees would probably work much better than a marker based watershed if you get even nearly the right amount of trees. Normally I'd estimate the number of trees based on the number of suppressed maxima on a h-maxima transform, but your labels might be a bit too sausagey for that. It's worth a try though.
I want to detect edges (with sub-pixel accuracy) in images like the one displayed:
The resolution would be around 600 X 1000.
I came across a comment by Mark Ransom here, which mentions about edge detection algorithms for vertical edges. I haven't come across any yet. Will it be useful in my case (since the edge isn't strictly a straight line)? It will always be a vertical edge though. I want it to be accurate till 1/100th of a pixel at least. I also want to have access to these sub-pixel co-ordinate values.
I have tried "Accurate subpixel edge location" by Agustin Trujillo-Pino. But this does not give me a continuous edge.
Are there any other algorithms available? I will be using MATLAB for this.
I have attached another similar image which the algorithm has to work on:
Any inputs will be appreciated.
Thank you.
Edit:
I was wondering if I could do this:
Apply Canny / Sobel in MATLAB and get the edges of this image (note that it won't be a continuous line). Then, somehow interpolate this Sobel edges and get the co-ordinates in subpixel. Is it possible?
A simple approach would be to project your image vertically and fit the projected profile with an appropriate function.
Here is a try, with an atan shape:
% Load image
Img = double(imread('bQsu5.png'));
% Project
x = 1:size(Img,2);
y = mean(Img,1);
% Fit
f = fit(x', y', 'a+b*atan((x0-x)/w)', 'Startpoint', [150 50 10 150])
% Display
figure
hold on
plot(x, y);
plot(f);
legend('Projected profile', 'atan fit');
And the result:
I get x_0 = 149.6 pix for your first image.
However, I doubt you will be able to achieve a subpixel accuracy of 1/100th of pixel with those images, for several reasons:
As you can see on the profile, your whites are saturated (grey levels at 255). As you cut the real atan profile, the fit is biased. If you have control over the experiments, I suggest you do it again again with a smaller exposure time for instance.
There are not so many points on the transition, so there is not so many information on where the transition is. Typically, your resolution will be the square root of the width of the atan (or whatever shape you prefer). In you case this limits the subpixel resolution at 1/5th of a pixel, at best.
Finally, your edges are not stricly vertical, they are slightly titled. If you choose to use this projection method, to increase the accuracy you should look for a way to correct this tilt before projecting. This won't increase your accuracy by several orders of magnitude, though.
Best,
There is a problem with your image. At pixel level, it seems like there are four interlaced subimages (odd and even rows and columns). Look at this zoomed area close to the edge.
In order to avoid this artifact, I just have taken the even rows and columns of your image, and compute subpixel edges. And finally, I look for the best fitting straight line, using the function clsq whose code is in this page:
%load image
url='http://i.stack.imgur.com/bQsu5.png';
image = imread(url);
imageEvenEven = image(1:2:end,1:2:end);
imshow(imageEvenEven, 'InitialMagnification', 'fit');
% subpixel detection
threshold = 25;
edges = subpixelEdges(imageEvenEven, threshold);
visEdges(edges);
% compute fit line
A = [ones(size(edges.x)) edges.x edges.y];
[c n] = clsq(A,2);
y = [1,200];
x = -(n(2)*y+c) / n(1);
hold on;
plot(x,y,'g');
When executing this code, you can see the green line that best aproximate all the edge points. The line is given by the equation c + n(1)*x + n(2)*y = 0
Take into account that this image has been scaled by 1/2 when taking only even rows and columns, so the right coordinates must be scaled.
Besides, you can try with the other tree subimages (imageEvenOdd, imageOddEven and imageOddOdd) and combine the four straigh lines to obtain the best solution.
I have a multiple plants in a single binary image. How would I identify each leaf in the image assuming that each leaf is approximately elliptical?
example input: http://i.imgur.com/BwhLVmd.png
I was thinking a good place to start would be finding the tip of each leaf and then getting the center of each plant. Then I could fit the curves starting from the tip and then going to the center. I've been looking online and saw something involving a watershed method, but I do not know where to begin with that idea.
You should be aware that these things are tricky to get working robustly - there will always be a failure case.
This said, I think your idea is not bad.
You could start as follows:
Identify the boundary curve of each plant (i.e. pixels with both foreground and background in their neighbourhood).
Compute the centroid of each plant.
Convert each plant boundary to a polar coordinate system, with the centroid as the origin. This amounts to setting up a coordinate system with the distance of each boundary curve point on the Y axis and the angle on the X axis.
In this representation of the boundary curve, try to identify maxima; these are the tips of the leaves. You will probably need to do some smoothing. Use the parts of the curve before and after the maxima the start fitting your ellipses or some other shape.
Generally, a polar coordinate system is always useful for analysing stuff thats roughly circular.
To fit you ellipses, once you have a rough initial position, I would probably try an EM-style approach.
I would do something like this (I is your binary image)
I=bwmorph(bwmorph(I, 'bridge'), 'clean');
SK=bwmorph(I, 'skel', Inf);
endpts = bwmorph(SK,'endpoints');
props=regionprops(I, 'All');
And then connect every segment from the centroids listed in props.centroid to the elements of endpts that should give you your leaves (petals?).
A bit of filtering is probably necessary, bwmorph is your friend. Have fun!