I am currently working the image to transform the sector part in the image to a rectangle shape.
I tried some ways but don't work well.
Any ideas on how to transform?
Create a destination image the height of which is the difference in the radii, and the width is the length of the perimeter at middle radius (this ensures square pixels along the middle arc).
Scan this image and for every pixel convert the coordinates (angle, radius) from Cartesian to polar, with a shift to the ROI center. This will give you the corresponding pixel in the source image, which you copy to the destination. Make sure to scale the angle and radius to match the destination image limits to the ROI edges.
As the source coordinates won't be integer, truncating and merely copying the source pixel achieves so-called nearest-neighbor resampling, which features visible artifacts. You can smoothen them by considering four neighboring pixels and interpolating bilinearly between them by means of the fractional parts of the coordinates.
You can even go for bicubic interpolation, using sixteen neighbors. But from my experience, the gain in quality is not so visible.
How do I separate the two connected circles in the image below, using MATLAB? I have tried using imerode, but this does not give good results. Eroding does not work, because in order to erode enough to separate the circles, the lines disappear or become mangled. In other starting pictures, a circle and a line overlap, so isolating the overlapping objects won't work either.
The image shows objects identified by bwboundaries, each object painted a different color. As you can see, the two light blue circles are joined, and I want to disjoin them, producing two separate circles. Thanks
I would recommend you use the Circular Hough Transform through imfindcircles. However, you need version 8 of the Image Processing Toolbox, which was available from version R2012a and onwards. If you don't have this, then unfortunately this won't work :(... but let's go with the assumption that you do have it. However, if you are using something older than R2012a, Dev-iL in his/her comment above linked to some code on MATLAB's File Exchange on an implementation of this, most likely created before the Circular Hough Transform was available: http://www.mathworks.com/matlabcentral/fileexchange/9168-detect-circles-with-various-radii-in-grayscale-image-via-hough-transform/
This is a special case of the Hough Transform where you are trying to find circles in your image rather than lines. The beauty with this is that you are able to find circles even when the circle is partially completed or overlapping.
I'm going to take the image that you provided above and do some post-processing on it. I'm going to convert the image to binary, and remove the border, which is white and contains the title. I'm also going to fill in any holes that result so that all of the objects are filled in with solid white. There is also some residual quantization noise after I do this step, so I'm going to a small opening with a 3 x 3 square element. After, I'm going to close the shapes with a 3 x 3 square element, as I see that there are noticeable gaps in the shapes. Therefore:
Therefore, directly reading in your image from where you've posted it:
im = imread('http://s29.postimg.org/spkab8oef/image.jpg'); %// Read in the image
im_gray = im2double(rgb2gray(im)); %// Convert to grayscale, then [0,1]
out = imclearborder(im_gray > 0.6); %// Threshold using 0.6, then clear the border
out = imfill(out, 'holes'); %// Fill in the holes
out = imopen(out, strel('square', 3));
out = imclose(out, strel('square', 3));
This is the image I get:
Now, apply the Circular Hough Transform. The general syntax for this is:
[centres, radii, metric] = imfindcircles(img, [start_radius, end_radius]);
img would be the binary image that contains your shapes, start_radius and end_radius would be the smallest and largest radius of the circles you want to find. The Circular Hough Transform is performed such that it will find any circles that are within this range (in pixels). The outputs are:
centres: Which returns the (x,y) positions of the centres of each circle detected
radii: The radius of each circle
metric: A measure of purity of the circle. Higher values mean that the shape is more probable to be a circle and vice-versa.
I searched for circles having a radius between 30 and 60 pixels. Therefore:
[centres, radii, metric] = imfindcircles(out, [30, 60]);
We can then demonstrate the detected circles, as well as the radii by a combination of plot and viscircles. Therefore:
imshow(out);
hold on;
plot(centres(:,1), centres(:,2), 'r*'); %// Plot centres
viscircles(centres, radii, 'EdgeColor', 'b'); %// Plot circles - Make edge blue
Here's the result:
As you can see, even with the overlapping circles towards the top, the Circular Hough Transform was able to detect two distinct circles in that shape.
Edit - November 16th, 2014
You wish to ensure that the objects are separated before you do bwboundaries. This is a bit tricky to do. The only way I can see you do this is if you don't even use bwboundaries at all and do this yourself. I'm assuming you'll want to analyze each shape's properties by themselves after all of this, so what I suggest you do is iterate through every circle you have, then place each circle on a new blank image, do a regionprops call on that shape, then append it to a separate array. You can also keep track of all of the circles by having a separate array that adds the circles one at a time to this array.
Once you've finished with all of the circles, you'll have a structure array that contains all of the measured properties for all of the measured circles you have found. You would use the array that contains only the circles from above, then use these and remove them from the original image so you get just the lines. You'd then call one more regionprops on this image to get the information for the lines and append this to your final structure array.
Here's the first part of the procedure I outlined above:
num_circles = numel(radii); %// Get number of circles
struct_reg = []; %// Save the shape analysis per circle / line here
%// For creating our circle in the temporary image
[X,Y] = meshgrid(1:size(out,2), 1:size(out,1));
%// Storing all of our circles in this image
circles_img = false(size(out));
for idx = 1 : num_circles %// For each circle we have...
%// Place our circle inside a temporary image
r = radii(idx);
cx = centres(idx,1); cy = centres(idx,2);
tmp = (X - cx).^2 + (Y - cy).^2 <= r^2;
% // Save in master circle image
circles_img(tmp) = true;
%// Do regionprops on this image and save
struct_reg = [struct_reg; regionprops(tmp)];
end
The above code may be a bit hard to swallow, but let's go through it slowly. I first figure out how many circles we have, which is simply looking at how many radii we have detected. I keep a separate array called struct_reg that will append a regionprops struct for each circle and line we have in our image. I use meshgrid to determine the (X,Y) co-ordinates with respect to the image containing our shapes so that I can draw one circle onto a blank image at each iteration. To do this, you simply need to find the Euclidean distance with respect to the centre of each circle, and set the pixels to true only if that location has its distance less than r. After doing this operation, you will have created only one circle and filtered all of them out. You would then use regionprops on this circle, add it to our circles_img array, which will only contain the circles, then continue with the rest of the circles.
At this point, we will have saved all of our circles. This is what circles_img looks like so far:
You'll notice that the circles drawn are clean, but the actual circles in the original image are a bit jagged. If we tried to remove the circles with this clean image, you will get some residual pixels along the border and you won't completely remove the circles themselves. To illustrate what I mean, this is what your image looks like if I tried to remove the circles with circles_img by itself:
... not good, right?
If you want to completely remove the circles, then do a morphological reconstruction through imreconstruct where you can use this image as the seed image, and specify the original image to be what we're working on. The job of morphological reconstruction is essentially a flood fill. You specify seed pixels, and an image you want to work on, and the job of imreconstruct is from these seeds, flood fill with white until we reach the boundaries of the objects that the seed pixels resided in. Therefore:
out_circles = imreconstruct(circles_img, out);
Therefore, we get this for our final reconstructed circles image:
Great! Now, use this and remove the circles from the original image. Once you do this, run regionprops again on this final image and append to your struct_reg variable. Obviously, save a copy of the original image before doing this:
out_copy = out;
out_copy(out_circles) = false;
struct_reg = [struct_reg; regionprops(out_copy)];
Just for sake of argument, this is what the image looks like with the circles removed:
Now, we have analyzed all of our shapes. Bear in mind I did the full regionprops call because I don't know exactly what you want in your analysis... so I just decided to give you everything.
Hope this helps!
erosion is the way to go. You should probably use a larger structuring element.
How about
1 erode
2 detect your objects
3 dilate each object for itself using the same structuring element
How to identify boundaries of a binary image to crop in matlab?
ie. the input binary image has no noises. only has one black object in white background.
You can use the edge command in MATLAB.
E = edge(I);
I would be an input grayscale or binary image. This will return a binary image with only the edges.
This can provide further assistance:
http://www.mathworks.com/help/images/ref/edge.html
If your image is just black-and-white and has a single object, you can likely make use of the Flood fill algorithm, for which Matlab has built-in support!
Try the imfill function (ref).
This should give you the extents of the object, which would allow you to crop at will.
You can also invert the image, then do regionprops to extract all of the properties for separate objects. You need to invert the image as regionprops assumes that the objects are white while the background is black. A good thing about this approach is that it generalizes for multiple objects and you only need about a few lines of code to do it.
As an example, let's artificially create a circle in the centre of an image that is black on a white background as you have suggested. Let's assume this is also a binary image.
im = true(200, 200);
[X,Y] = meshgrid(1:200, 1:200);
ind = (X-100).^2 + (Y-100).^2 <= 1000;
im(ind) = false;
imshow(im);
This is what your circle will look like:
Now let's go ahead and invert this so that it's a white circle on black background:
imInvert = ~im;
imshow(imInvert);
This is what your inverted circle will look like:
Now, invoke regionprops to find properties of all of the objects in our image. In this case, there should only be one.
s = regionProps(imInvert, 'BoundingBox');
As such, s contains a structure that is 1 element long, and has a single field called BoundingBox. This field is a 4 element array that is structured in the following way:
[x y w h]
x denotes the column/vertical co-ordinate while y denotes the row/horizontal co-ordinate of the top-left corner of the bounding box. w,h are the width and height of the rectangle. Our output of the above code is:
s =
BoundingBox: [68.5000 68.5000 63 63]
This means that the top-left corner of our bounding box is located at (x,y) = (68.5,68.5), and has a width and height of 63 each. Therefore, the span of our bounding box goes from rows (68.5,131.5) and columns (68.5,131.5). To make sure that we have the right bounding box, you can draw a rectangle around our shape by using the rectangle command.
imshow(im);
rectangle('Position', s.BoundingBox);
This is what your image will look like with a rectangle drawn around the object. As you can see, the bounding box given from regionprops is the minimum spanning bounding box required to fully encapsulate the object.
If you wish to crop the object, you can do the following:
imCrop = imcrop(imInvert, s.BoundingBox);
This should give you the cropped image that is defined by the bounding box that we talked about earlier.
Hope this is what you're looking for. Good luck!
I have this 3 points (x,y) and I need to obtain a mask with a triangle where vertices is the points. I should respect some parameters, like the pixel pitch and I need a grid from the minimum x cordinate to the maximum x coordinate (the same for the y).
I tried to do this in matlab with the function poly2mask but the problem is the resultant image: when I have negative coordinates, I cannot see the polygon.
So I tried to center the polygon but I loose the original coordinates and I cannot have they back again because I need to do some elaboration on the image.
How I can obtain a mask triangle from 3 points without modifying the points and respecting the parameters?
Is it possible to crop an image along a particular curve. for ex. I want to crop out the finger image out of this image, but i dont want to crop it along a rectangle.
you need a binary mask and apply that mask as alpha map
here is how it is usually done
s = 100;
h = imagesc(rand(s));%show some garbage
%prepare a circular mask
dummy = meshgrid(-s/2:s/2-1).^2;%squared distances from the center
mask = sqrt(dummy+dummy') < 20;%20 is the radius of your mask
%here you go, mask the image in a curved manner
set(h,'alphaData',mask);
exporting it as a png would do the job.
so in your case, you need to make your own mask, this means either threshold your bitmap image or parameterize the space (as I did it with the circle above).