In this tutorial, an ellipse will be outlined. As you can see, a red border will be drawn around. Form such result, how can we fill such surrounded border with white, and the rest of the image as black?
Thanks.
A little Google search with the words fill and Matlab would tell you that there is a function called fill which performs what you want(check here).
In the example, putting it right after the call to plot gives something like the following. I put the whole code for the for-loop:
for k = 1:length(s)
xbar = s(k).Centroid(1);
ybar = s(k).Centroid(2);
a = s(k).MajorAxisLength/2;
b = s(k).MinorAxisLength/2;
theta = pi*s(k).Orientation/180;
R = [ cos(theta) sin(theta)
-sin(theta) cos(theta)];
xy = [a*cosphi; b*sinphi];
xy = R*xy;
x = xy(1,:) + xbar;
y = xy(2,:) + ybar;
plot(x,y,'r','LineWidth',2);
fill(x,y,rand(1,3)) %// Here is the important line.
end
I'll let you discover how you can fill the ellipses with white instead of random colors.
Related
I am detecting circles in an image. I return circle radii and X,Y of the axis. I know how to crop 1 circle no problem with formula:
X-radius, Y-radius, width=2*r,height=2*r using imcrop.
My problem is when I get returned more than 1 circle.
I get returned circle radii in an array radiiarray.
I get returned circle centers in centarray.
When i disp(centarray), It looks like this:
146.4930 144.4943
610.0317 142.1734
When I check size(centarray) and disp it i get:
2 2
So I understand first column is X and second is Y axis values. So first circle center would be 146,144.
I made a loop that works for only 1 circle. "-------" is where I'm unsure what to use to get:
note: radius = r
1st circle)
X = centarray(1)-r;
Y = centarray(3)-r;
Width =2*r;
Width =2*r;
2nd circle)
X = centarray(2);
Y = centarray(4);
Width =2*r;
Width =2*r;
How would I modify the "------" parts for my code? I also would like that if there are 3+ circles the loop would work as Im getting sometimes up to 9 circles from an image.
B = imread('p5.tif');
centarray = [];
centarray = [centarray,centers];
radiiarray = [];
radiiarray = [radiiarray,radii];
for j=1:length(radiiarray)
x = centarray((------))-radiiarray(j); %X value to crop
y = centarray((------))-radiiarray(j); %Y value to crop
width = 2*radiiarray(j); %WIDTH
height = 2*radiiarray(j); %HEIGHT
K = imcrop(B, [x y width height]);
end
My full code, which doesnt work, as I realized why when i saw the way values are stored...:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DETECT + GET X Y WIDTH HEIGHT OF CIRCLES
I = imread('p5.tif');
subplot(2,2,1);imshow(I);title('Original Image');
%sharpen edges
B = imsharpen(I);
subplot(2,2,2);imshow(B);title('sharpened edges');
%find circles
Img = im2bw(B(:,:,3));
minRad = 20;
maxRad = 90;
[centers, radii] = imfindcircles(Img, [minRad maxRad], ...
'ObjectPolarity','bright','sensitivity',0.84);
imagesc(Img);
viscircles(centers, radii,'Color','green');
%nuber of circles found
%arrays to store values for radii and centers
centarray = [];
centarray = [centarray,centers];
radiiarray = [];
radiiarray = [radiiarray,radii];
sc = size(centarray);
disp(sc)
disp(centarray)
disp(radiiarray)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CROP USING VALUE FROM ARRAYS NUMBER OF TIMES THERE ARE CENTERS(number of
%circles)
for j=1:length(radiiarray)
x = centarray((2*j)-1)-radiiarray(j); %X value to crop
y = centarray((2*j))-radiiarray(j); %Y value to crop
width = 2*radiiarray(j); %WIDTH
height = 2*radiiarray(j); %HEIGHT
disp(x)
disp(y)
disp(centarray)
%crop using values
K = imcrop(B, [x y width height]);
%togray
gray = rgb2gray(K);
subplot(2,2,3);imshow(K);title('cropped before bw');
Icorrected = imtophat(gray, strel('disk', 15));
%to black and white
black = im2bw(Icorrected);
subplot(2,2,4);imshow(black);title('sharpened edges');
%read
results = ocr(black);
number = results.Text;
%display value
disp(number)
end
Any help on how to create this kind of loop is appreciated as I just have no more ideas or cant find answer to this..
EDIT
SOLUTION
Hi, answer is to treat matrix as 2 dimensional.
for j=1:length(radiiarray)
x=centarray(j,1)
y=centarray(j,2)
width = radiiarray(j)
height = radiiarray(j)
end
as j increases values update correctly now.
answer is to treat matrix as 2 dimensional.
for j=1:length(radiiarray)
x=centarray(j,1)
y=centarray(j,2)
width = radiiarray(j)
height = radiiarray(j)
end
as j increases values update correctly now.
Thanks for #beaker for his comment! Thats why I figured it out
I currently have to create a sphere from a stack of 2D slices (2D matrices in MATLAB, which represent 2D gray scale images). I have created a bunch of slices using the code below. To create the sphere I have repeatedly created slices of circles of increasing size till 100, and then of decreasing sizes. All of these slices are added to a 3D matrix.
Circle = ones(200,400,400);
for i = 1:100
[rr cc] = meshgrid(1:400);
C = sqrt((rr-200).^2+(cc-200).^2)<=i;
for j = 1:400
for k = 1:400
Circle(i,j,k) = C(j,k);
end
end
end
index = 100;
for i = 1:100
[rr cc] = meshgrid(1:400);
C = sqrt((rr-200).^2+(cc-200).^2)<=index;
for j = 1:400
for k = 1:400
Circle(i+100,j,k) = C(j,k);
end
end
index = index - 1;
end
viewer3d(Circle);
viewer3d is 3rd part library that helps you view your 3D image stacks of slices as 3d objects. Once I visualized this 'supposed' sphere, I realized that it is a diamond shape top and not a sphere.
Therefore I do not understand how to vary the size of circles till the center point of the sphere in the y plane and then decrease it with the same algorithm.
Thank you for your answers and please do not hesitate to ask me to clarify anything within this question.
Alternatively, create a sphere directly, without using loops:
Circle = zeros(200,400,400);
[x,y,z]=meshgrid(1:size(Circle,1),1:size(Circle,2),1:size(Circle,3));
radius=??; %// e.g. radius=100;
%//this sphere is centered in the middle of the image
Circle(sqrt((x-size(Circle,1)/2).^2+(y-size(Circle,2)/2).^2..
+(z-size(Circle,2)/2).^2)<radius)=1;
Yes, the radius along the Z axis is not linear but varies with cos/sin function. Using this representation:
your radius is "Radius = r sin(Theta)", with "Theta = arccos(r / z)". So "r" is the radius of your sphere, and "z" the level/slice you want to draw in. Don't forget to that "z" goes from -"r" to "r". I've tested the formulae and it works fine for an image stack (slices).
Just a quick question. I've an image and I've extracted a certain point (feature), I know the coordinates of that point in every frame.
Say x1 and y1.
I need a circular ROI form that point on the image with a radius that I chose.
I tried impoly and roipoly - not sure how to use either of these when I know the point in the image.
Thanks
Since you know the coordinates of the center of the ROI along with the radius, you can modify a bit the code provided by #Jonas here to create a circular mask in a quite efficient way.
Example:
clc;clear
Im = imread('coins.png');
[rNum,cNum,~] = size(Im);
%// Define coordinates and radius
x1 = 60;
y1 = 100;
radius = 40;
%// Generate grid with binary mask representing the circle. Credit to Jonas for original code.
[xx,yy] = ndgrid((1:rNum)-y1,(1:cNum)-x1);
mask = (xx.^2 + yy.^2)<radius^2;
%// Mask the original image
Im(mask) = uint8(0);
imshow(Im)
Output:
EDIT
If you want to see only the outer edge of the ROI to see the center, add a logical condition with some tolerance for the radius of a smaller circle. Something like this:
mask = (xx.^2 + yy.^2)<radius^2 & (xx.^2 + yy.^2)>(radius-tol)^2;
With a tol of 2 it looks like this:
I'm trying to create a dataset of raw volumetric data consisting of geometrical shapes. The point is to use volume ray casting to project them in 2D but first I want to create the volume manually.
The geometry is consisting of one cylinder that is in the middle of the volume, along the Z axis and 2 smaller cylinders that are around the first one, deriving from rotations around the axes.
Here is my function so far:
function cyl= createCylinders(a, b, c, rad1, h1, rad2, h2)
% a : data width
% b : data height
% c : data depth
% rad1: radius of the big center cylinder
% rad2: radius of the smaller cylinders
% h1: height of the big center cylinder
% h2: height of the smaller cylinders
[Y X Z] =meshgrid(1:a,1:b,1:c); %matlab saves in a different order so X must be Y
centerX = a/2;
centerY = b/2;
centerZ = c/2;
theta = 0; %around y
fi = pi/4; %around x
% First cylinder
cyl = zeros(a,b,c);
% create for infinite height
R = sqrt((X-centerX).^2 + (Y-centerY).^2);
startZ = ceil(c/2) - floor(h1/2);
endZ = startZ + h1 - 1;
% then trim it to height = h1
temp = zeros(a,b,h1);
temp( R(:,:,startZ:endZ)<rad1 ) = 255;
cyl(:,:,startZ:endZ) = temp;
% Second cylinder
cyl2 = zeros(a,b,c);
A = (X-centerX)*cos(theta) + (Y-centerY)*sin(theta)*sin(fi) + (Z-centerZ)*cos(fi)*sin(theta);
B = (Y-centerY)*cos(fi) - (Z-centerZ)*sin(fi);
% create again for infinite height
R2 = sqrt(A.^2+B.^2);
cyl2(R2<rad2) = 255;
%then use 2 planes to trim outside of the limits
N = [ cos(fi)*sin(theta) -sin(fi) cos(fi)*cos(theta) ];
P = (rad2).*N + [ centerX centerY centerZ];
T = (X-P(1))*N(1) + (Y-P(2))*N(2) + (Z-P(3))*N(3);
cyl2(T<0) = 0;
P = (rad2+h2).*N + [ centerX centerY centerZ];
T = (X-P(1))*N(1) + (Y-P(2))*N(2) + (Z-P(3))*N(3);
cyl2(T>0) = 0;
% Third cylinder
% ...
cyl = cyl + cyl2;
cyl = uint8(round(cyl));
% ...
The concept is that the first cylinder is created and then "cut" according to the z-axis value, to define its height. The other cylinder is created using the relation A2 + B 2 = R2 where A and B are rotated accordingly using the rotation matrices only around x and y axes, using Ry(θ)Rx(φ) as described here.
Until now everything seems to be working, because I have implemented code (tested that it works well) to display the projection and the cylinders seem to have correct rotation when they are not "trimmed" from infinite height.
I calculate N which is the vector [0 0 1] aka z-axis rotated in the same way as the cylinder. Then I find two points P of the same distances that I want the cylinder's edges to be and calculate the plane equations T according to that points and normal vector. Lastly, I trim according to that equality. Or at least that's what I think I'm doing, because after the trimming I usually don't get anything (every value is zero). Or, the best thing I could get when I was experimenting was cylinders trimmed, but the planes of the top and bottom where not oriented well.
I would appreciate any help or corrections at my code, because I've been looking at the geometry equations and I can't find where the mistake is.
Edit:
This is a quick screenshot of the object I'm trying to create. NOTE that the cylinders are opaque in the volume data, all the inside is considered as homogeneous material.
I think instead of:
T = (X-P(1))*N(1) + (Y-P(2))*N(2) + (Z-P(3))*N(3);
you should try the following at both places:
T = (X-P(1)) + (Y-P(2)) + (Z-P(3));
Multiplying by N is to account for the direction of the axis of the 2nd cylinder which you have already done just above that step.
I want to stretch an elliptical object in an image until it forms a circle. My program currently inputs an image with an elliptical object (eg. coin at an angle), thresholds and binarizes it, isolates the region of interest using edge-detect/bwboundaries(), and performs regionprops() to calculate major/minor axis lengths.
Essentially, I want to use the 'MajorAxisLength' as the diameter and stretch the object on the minor axis to form a circle. Any suggestions on how I should approach this would be greatly appreciated. I have appended some code for your perusal (unfortunately I don't have enough reputation to upload an image, the binarized image looks like a white ellipse on a black background).
EDIT: I'd also like to apply this technique to the gray-scale version of the image, to examine what the stretch looks like.
code snippet:
rgbImage = imread(fullFileName);
redChannel = rgbImage(:, :, 1);
binaryImage = redChannel < 90;
labeledImage = bwlabel(binaryImage);
area_measurements = regionprops(labeledImage,'Area');
allAreas = [area_measurements.Area];
biggestBlobIndex = find(allAreas == max(allAreas));
keeperBlobsImage = ismember(labeledImage, biggestBlobIndex);
measurements = regionprops(keeperBlobsImage,'Area','MajorAxisLength','MinorAxisLength')
You know the diameter of the circle and you know the center is the location where the major and minor axes intersect. Thus, just compute the radius r from the diameter, and for every pixel in your image, check to see if that pixel's Euclidean distance from the cirlce's center is less than r. If so, color the pixel white. Otherwise, leave it alone.
[M,N] = size(redChannel);
new_image = zeros(M,N);
for ii=1:M
for jj=1:N
if( sqrt((jj-center_x)^2 + (ii-center_y)^2) <= radius )
new_image(ii,jj) = 1.0;
end
end
end
This can probably be optimzed by using the meshgrid function combined with logical indices to avoid the loops.
I finally managed to figure out the transform required thanks to a lot of help on the matlab forums. I thought I'd post it here, in case anyone else needed it.
stats = regionprops(keeperBlobsImage, 'MajorAxisLength','MinorAxisLength','Centroid','Orientation');
alpha = pi/180 * stats(1).Orientation;
Q = [cos(alpha), -sin(alpha); sin(alpha), cos(alpha)];
x0 = stats(1).Centroid.';
a = stats(1).MajorAxisLength;
b = stats(1).MinorAxisLength;
S = diag([1, a/b]);
C = Q*S*Q';
d = (eye(2) - C)*x0;
tform = maketform('affine', [C d; 0 0 1]');
Im2 = imtransform(redChannel, tform);
subplot(2, 3, 5);
imshow(Im2);