I would like to kindly ask you for the help with the definition of the line thickness. I have the binary curve. I need to find out a distance of each point of the curve skeleton to line edge in the direction of the normal. So, I firstly computed skeleton of the binary curve. Consequently, for each pixel of the skeleton I computed normal. This situation is depicted on the figure, showing the skeleton and a map of normal vectors from each pixel. In this point, I do not know how to compute the distance for each skeleton pixel to curve edge in the normal direction. Practically, I need to count number of the pixels (logical 1) from the skeleton pixels to the line edge in the normal direction. It means I need to obtain the vector, containing distance for each skeleton point. I would like to thank you in advance for your help.
Code for generating skeleton with normals:
clc;clear all;close all
i=rgb2gray(imread('Bin_Lines.bmp'));
BW=bwskel(logical(i));
% BW = image sceleton
Orientations = skeletonOrientation(BW,5); %5x5 box
Onormal = Orientations+90; %easier to view normals
Onr = sind(Onormal); %vv
Onc = cosd(Onormal); %uu
[r,c] = find(BW); %row/cols
idx = find(BW); %Linear indices into Onr/Onc
figure()
imshow(BW,[]);
%Plotting normals of binary skeleton
hold on
quiver(c,r,-Onc(idx),Onr(idx));
Here is the link where I store source codes and binary line image:
https://www.dropbox.com/sh/j84ep3k1604hsza/AABm92TUBX6yIp29Gc0v_PHHa?dl=0
You can use distance transform to compute the distance of each interior pixel to the boundary. Matlab has bwdist to do that for you.
Then you can extract the information for the skeleton pixels.
img = rgb2gray(imread('Bin_Lines.bmp'));
bw = bwskel(img > 128);
dst = bwdist(img <= 128); % need opposite contrast
distance_of_skel_pixels_to_boundary = dst(bw)
The distance dst looks like:
Related
I use camera calibration in matlab to detect some checkerboard patterns, after
figure; showExtrinsics(cameraParams, 'CameraCentric');
Now, I want to rotate the checkerboard patterns around the x-axis such that all of them have nearly the same y coordinates in the camera frame.
Method:
I get the positions of all patterns in the camera's frame. Then I do optimization,where the objective function is to minimize variance in y and the variable is rotation about x ranging from o to 360.
Problem:
But when I plot the transformed y-coordinates, they are even nearly in a line.
Code:
Get the checkerboad points:
%% Get rotation and translation matrices for each image;
T_cw=cell(num_imgs,1); % stores camera to world rotation and translation for each image
pixel_coordinates=zeros(num_imgs,2); % stores the pixel coordinates of each checkerboard origin
for ii=1:num_imgs,
% Calibrate the camera
im=imread(list_imgs_path{ii});
[imagePoints, boardSize] = detectCheckerboardPoints(im);
[r_wc, t_wc] = extrinsics(imagePoints, worldPoints, cameraParams);
T_wc=[r_wc,t_wc';0 0 0 1];
% World to camera matrix
T_cw{ii} = inv(T_wc);
t_cw{ii}=T_cw{ii}(1:3,4); % x,y,z coordinates in camera's frame
end
Data(num_imgs=10):
t_cw
[-1072.01388542262;1312.20387622761;-1853.34408157349]
[-1052.07856598756;1269.03455126794;-1826.73576892251]
[-1091.85978641218;1351.08261414473;-1668.88197803184]
[-1337.56358084648;1373.78548638383;-1396.87603554914]
[-1555.19509876309;1261.60428874489;-1174.63047408086]
[-1592.39596647158;1066.82210015055;-1165.34417772659]
[-1523.84307918660;963.781819272748;-1207.27444716506]
[-1614.00792252030;893.962075837621;-1114.73528985018]
[-1781.83112607964;708.973204727939;-797.185326205240]
[-1781.83112607964;708.973204727939;-797.185326205240]
Main code (Optimization and transformation):
%% Get theta for rotation
f_obj = #(x)var_ycors(x,t_cw);
opt_theta = fminbnd(f_obj,0,360);
%% Plotting (rotate ycor and check to fix theta)
y_rotated=zeros(1,num_imgs);
for ii=1:num_imgs,
y_rotated(ii)=rotate_cor(opt_theta,t_cw{ii});
end
plot(1:numel(y_rotated),y_rotated);
function var_computed=var_ycors(theta,t_cw)
ycor=zeros(1,numel(t_cw));
for ii =1:numel(t_cw),
ycor(ii)=rotate_cor(theta,t_cw{ii});
end
var_computed=var(ycor);
end
function ycor=rotate_cor(theta,mat)
r_x=[1 0 0; 0 cosd(theta) -sind(theta); 0 sind(theta) cosd(theta)];
rotate_mat=mat'*r_x;
ycor=rotate_mat(2);
end
This is a clear eigenvector problem!
Take your centroids:
t_cw=[-1072.01388542262;1312.20387622761;-1853.34408157349
-1052.07856598756;1269.03455126794;-1826.73576892251
-1091.85978641218;1351.08261414473;-1668.88197803184
-1337.56358084648;1373.78548638383;-1396.87603554914
-1555.19509876309;1261.60428874489;-1174.63047408086
-1592.39596647158;1066.82210015055;-1165.34417772659
-1523.84307918660;963.781819272748;-1207.27444716506
-1614.00792252030;893.962075837621;-1114.73528985018
-1781.83112607964;708.973204727939;-797.185326205240
-1781.83112607964;708.973204727939;-797.185326205240];
t_cw=reshape(t_cw,[3,10])';
compute PCA on them, so we know the principal conponents:
[R]=pca(t_cw);
And.... thats it! R is now the transformation matrix between your original points and the rotated coordinate system. As an example, I will draw in red the old points and in blue the new ones:
hold on
plot3(t_cw(:,1),t_cw(:,2),t_cw(:,3),'ro')
trans=t_cw*R;
plot3(trans(:,1),trans(:,2),trans(:,3),'bo')
You can see that now the blue ones are in a plane, with the best possible fit to the X direction. If you want them in Y direction, just rotate 90 degrees in Z (I am sure you can figure out how to do this with 2 minutes of Google ;) ).
Note: This is mathematically the best possible fit. I know they are not as "in a row" as one would like, but this is because of the data, this is honestly the best possible fit, as that is what the eigenvectors are!
Calibration:
I have calibrated the camera using this vision toolbox in Matlab. I used checkerboard images to do so. After calibration I get the cameraParams
which contains:
Camera Extrinsics
RotationMatrices: [3x3x18 double]
TranslationVectors: [18x3 double]
and
Camera Intrinsics
IntrinsicMatrix: [3x3 double]
FocalLength: [1.0446e+03 1.0428e+03]
PrincipalPoint: [604.1474 359.7477]
Skew: 3.5436
Aim:
I have recorded trajectories of some objects in motion using this camera. Each object corresponds to a single point in a frame. Now, I want to project the points such that I get a top-view.
Note all these points I wish to transform are are the on the same plane.
ex: [xcor_i,ycor_i ]
-101.7000 -77.4040
-102.4200 -77.4040
KEYPOINT: This plane is perpendicular to one of images of checkerboard used for calibration. For that image(below), I know the height of origin of the checkerboard of from ground(193.040 cm). And the plane to project the points on is parallel to the ground and perpendicular to this image.
Code
(Ref:https://stackoverflow.com/a/27260492/3646408 and answer by #Dima below):
function generate_homographic_matrix()
%% Calibrate camera
% Define images to process
path=['.' filesep 'Images' filesep];
list_imgs=dir([path '*.jpg']);
list_imgs_path=strcat(path,{list_imgs.name});
% Detect checkerboards in images
[imagePoints, boardSize, imagesUsed] = detectCheckerboardPoints(list_imgs_path);
imageFileNames = list_imgs_path(imagesUsed);
% Generate world coordinates of the corners of the squares
squareSize = 27; % in units of 'mm'
worldPoints = generateCheckerboardPoints(boardSize, squareSize);
% Calibrate the camera
[cameraParams, imagesUsed, estimationErrors] = estimateCameraParameters(imagePoints, worldPoints, ...
'EstimateSkew', true, 'EstimateTangentialDistortion', true, ...
'NumRadialDistortionCoefficients', 3, 'WorldUnits', 'mm');
%% Compute homography for peripendicular plane to checkerboard
% Detect the checkerboard
im=imread(['.' filesep 'Images' filesep 'exp_19.jpg']); %exp_19.jpg is the checkerboard orthogonal to the floor
[imagePoints, boardSize] = detectCheckerboardPoints(im);
% Compute rotation and translation of the camera.
[Rc, Tc] = extrinsics(imagePoints, worldPoints, cameraParams);
% Rc(rotation of the calibration view w.r.t the camera) = [x y z])
%then the floor has rotation Rf = [z x -y].(Normal vector of the floor goes up.)
Rf=[Rc(:,3),Rc(:,1),Rc(:,2)*-1];
% Translate it to the floor
H=452;%distance btw origin and floor
Fc = Rc * [0; H; 0];
Tc = Tc + Fc';
% Combine rotation and translation into one matrix:
Rf(3, :) = Tc;
% Compute the homography between the checkerboard and the image plane:
H = Rf * cameraParams.IntrinsicMatrix;
save('homographic_matrix.mat','H')
end
%% Transform points
function [x_transf,y_transf] =transform_points(xcor_i,ycor_i)
% creates a projective2D object and then transforms the points forward to
% get a top-view
% xcor_i and ycor_i are 1d vectors comprising of the x-coordinates and
% y-coordinates of trajectories.
data=load('homographic_matrix.mat');
homo_matrix=data.H;
tform=projective2d(inv(homo_matrix));
[x_transf,y_transf] = transformPointsForward(tform,xcor_i,ycor_i);
end
Quoting text from OReilly Learning OpenCV Pg 412:
"Once we have the homography matrix and the height parameter set as we wish, we could
then remove the chessboard and drive the cart around, making a bird’s-eye view video
of the path..."
This what I essentially wish to achieve.
Abhishek,
I don't entirely understand what you are trying to do. Are your points on a plane, and are you trying to create a bird's eye view of that plane?
If so, then you need to know the extrinsics, R and t, describing the relationship between that plane and the camera. One way to get R and t is to place a checkerboard on the plane, and then use the extrinsics function.
After that, you can follow the directions in the question you cited to get the homography. Once you have the homography, you can create a projective2D object, and use its transformPointsForward method to transform your points.
Since you have the size of squares on the grid, then given 2 points that you know are connected by an edge of size E (in real world units), you can calculate their 3D position.
Taking the camera intrinsic matrix K and the 3D position C and the camera orientation matrix R, you can calculate a ray to each of the points p by doing:
D = R^T * K^-1 * p
Each 3D point is defined as:
P = C + t*D
and you have the constraint that ||P1-P2|| = E
then it's a matter of solving for t1,t2 and finding the 3D position of the two points.
In order to create a top view, you can take the 3D points and project them using a camera model for that top view to generate a new image.
If all your points are on a single plane, it's enough to calculate the position of 3 points, and you can extrapolate the rest.
If your points are located on a plane that you know one coordinate of, you can do it simply for each point. For example, if you know that your camera is located at height h=C.z, and you want to find the 3D location of points in the frame, given that they are on the floor (z=0), then all you have to do is calculate the direction D as above, and then:
t=abs( (h-0)/D.z )
The 0 represent the height of the plane. Substitute for any other value for other planes.
Now that you have the value of t, you can calculate the 3D position of each point: P=C+t*D.
Then, to create a top view, create a new camera position and rotation to match your required projection, and you can project each point onto this camera's image plane.
If you want a full image, you can interpolate positions and fill in the blanks where no feature point was present.
For more details, you can always read: http://www.robots.ox.ac.uk/~vgg/hzbook/index.html
I have a list of coordinates, which are generated from another program, and I have an image.
I'd like to load those coordinates (making circular regions of interest (ROIs) with a diameter of 3 pixels) onto my image, and extract the intensity of those pixels.
I can load/impose the coordinates on to the image by using;
imshow(file);
hold on
scatter(xCoords, yCoords, 'g')
But can not extract the intensity.
Can you guys point me in the right direction?
I am not sure what you mean by a circle with 3 pixels diameter since you are in a square grid (as mentioned by Ander Biguri). But you could use fspecial to create a disk filter and then normalize. Something like this:
r = 1.5; % for diameter = 3
h = fspecial('disk', r);
h = h/h(ceil(r),ceil(r));
You can use it as a mask to get the intensities at the given region of the image.
im = imread(file);
ROI = im(xCoord-1:xCoord+1; yCoord-1:yCoord+1);
I = ROI.*h;
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 have skeletonize binary image and the junction information. I want to draw circle at junction points as center and want to find the point of intersection of circle and binary image.
I have written the following code:
BW = imread('circles.png');
imshow(BW);
BW2 = bwmorph(BW,'remove');
figure, imshow(BW2)
BW3 = bwmorph(BW,'skel',Inf);
figure, imshow(BW3)
BW3t = bwmorph(BW3,'thin');
figure, imshow(BW3t)
[rj, cj, re, ce] = findendsjunctions(BW3t, 1);
hold on
plot(cj(1),rj(1),'ob')
hold on
circle([cj(1),rj(1)],4,50,':r');
findendsjunctions.m and dependent file show.m can downloaded from here: http://www.csse.uwa.edu.au/~pk/research/matlabfns/LineSegments/findendsjunctions.m and here http://www.csse.uwa.edu.au/~pk/research/matlabfns/Misc/show.m respectively.
And circle.m can be downloaded from here: http://www.mathworks.co.uk/matlabcentral/fileexchange/2876-draw-a-circle/content/circle.m
I want to find whether circle intersect 2, 3 or 4 vessels around it (marked as star in an image). Even if circle transverse many times a single vessel but output should be one intersection point per vessel.
Please suggest how can I find the intersection of circle and binary vessels.
Thanks
I have found the point of intersection of circle and Binary image and the coordinates of 3 points (marked as star in an image provided with my question). I have change the function circle.m (mentioned in my question above ) to give output of all X and Y coordinates of circumference of the circle and then I have written the following matlab code:
[H, X, Y]=circle([cj(1),rj(1)],4,50,':r');
c = improfile(BW3t,X,Y)
x=1:length(c)
figure
plot(x, c,'r')
[maxtab, mintab]=peakdet(c, 1)
[pks,locs] = findpeaks(c)
pt1=[X(locs(1)) Y(locs(1))]
pt2=[X(locs(2)) Y(locs(2))]
pt3=[X(locs(3)) Y(locs(3))]
hold on
plot(pt1(1),pt1(2),'om','LineWidth',2)
hold on
plot(pt2(1),pt2(2),'og','LineWidth',2)
hold on
plot(pt3(1),pt3(2),'ob','LineWidth',2)
pt1, pt2 pt3 are three points where circle cuts the binary image