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I have sequence of 10 frames. Images have black dots.
What I'm trying to do is saving every centroid co-ordinates (for all dots), but whenever it shows more than one centroid in image I get an error [Error using horzcat Dimensions of matrices being concatenated are not consistent.] My question might be stupid because of course the Error is clear and obvious, but still how to save the co-ordinates from every loop?
temp = [];
for j = 1:1:10
img = imread('img.tif, j);
grayImg = mat2gray(img);
bwImg = imbinarize(grayImg, Threshold);
s = regionprops(bwImg, 'centroid');
centroids = cat(1, s.Centroid);
temp2 = [temp2, centroids];
end
N.Cvala,
did you consider using cell arrays (see help cell)? I rewrote your code to accommodate that.
nCells = 10;
temp = cell(1, nCells);
for j = 1:nCells
img = imread('img.tif', j);
grayImg = mat2gray(img);
bwImg = imbinarize(grayImg, Threshold);
s = regionprops(bwImg, 'centroid');
centroids = cat(1, s.Centroid);
temp{j} = centroids;
end
% Access the centroids computed in the first iteration
temp{1}
Cells are nice because they are arrays which allow to store any type of data into them. If you would like a more structured way of store your data you could look into structures (doc struct)
I was trying to implement the IBVS algorithm (the one explained in the Introduction here) in MATLAB myself, but I am facing the following problem : The algorithm seems to work only for the cases that the camera does not have to change its orientation in respect to the world frame.For example, if I just try to make one vertex of the initial (almost) square go closer to its opposite vertex, the algorithm does not work, as can be seen in the following image
The red x are the desired projections, the blue circles are the initial ones and the green ones are the ones I get from my algorithm.
Also the errors are not exponentially dereasing as they should.
What am I doing wrong? I am attaching my MATLAB code which is fully runable. If anyone could take a look, I would be really grateful. I took out the code that was performing the plotting. I hope it is more readable now. Visual servoing has to be performed with at least 4 target points, because else the problem has no unique solution. If you are willing to help, I would suggest you take a look at the calc_Rotation_matrix() function to check that the rotation matrix is properly calculated, then verify that the line ds = vc; in euler_ode is correct. The camera orientation is expressed in Euler angles according to this convention. Finally, one could check if the interaction matrix L is properly calculated.
function VisualServo()
global A3D B3D C3D D3D A B C D Ad Bd Cd Dd
%coordinates of the 4 points wrt camera frame
A3D = [-0.2633;0.27547;0.8956];
B3D = [0.2863;-0.2749;0.8937];
C3D = [-0.2637;-0.2746;0.8977];
D3D = [0.2866;0.2751;0.8916];
%initial projections (computed here only to show their relation with the desired ones)
A=A3D(1:2)/A3D(3);
B=B3D(1:2)/B3D(3);
C=C3D(1:2)/C3D(3);
D=D3D(1:2)/D3D(3);
%initial camera position and orientation
%orientation is expressed in Euler angles (X-Y-Z around the inertial frame
%of reference)
cam=[0;0;0;0;0;0];
%desired projections
Ad=A+[0.1;0];
Bd=B;
Cd=C+[0.1;0];
Dd=D;
t0 = 0;
tf = 50;
s0 = cam;
%time step
dt=0.01;
t = euler_ode(t0, tf, dt, s0);
end
function ts = euler_ode(t0,tf,dt,s0)
global A3D B3D C3D D3D Ad Bd Cd Dd
s = s0;
ts=[];
for t=t0:dt:tf
ts(end+1)=t;
cam = s;
% rotation matrix R_WCS_CCS
R = calc_Rotation_matrix(cam(4),cam(5),cam(6));
r = cam(1:3);
% 3D coordinates of the 4 points wrt the NEW camera frame
A3D_cam = R'*(A3D-r);
B3D_cam = R'*(B3D-r);
C3D_cam = R'*(C3D-r);
D3D_cam = R'*(D3D-r);
% NEW projections
A=A3D_cam(1:2)/A3D_cam(3);
B=B3D_cam(1:2)/B3D_cam(3);
C=C3D_cam(1:2)/C3D_cam(3);
D=D3D_cam(1:2)/D3D_cam(3);
% computing the L matrices
L1 = L_matrix(A(1),A(2),A3D_cam(3));
L2 = L_matrix(B(1),B(2),B3D_cam(3));
L3 = L_matrix(C(1),C(2),C3D_cam(3));
L4 = L_matrix(D(1),D(2),D3D_cam(3));
L = [L1;L2;L3;L4];
%updating the projection errors
e = [A-Ad;B-Bd;C-Cd;D-Dd];
%compute camera velocity
vc = -0.5*pinv(L)*e;
%change of the camera position and orientation
ds = vc;
%update camera position and orientation
s = s + ds*dt;
end
ts(end+1)=tf+dt;
end
function R = calc_Rotation_matrix(theta_x, theta_y, theta_z)
Rx = [1 0 0; 0 cos(theta_x) -sin(theta_x); 0 sin(theta_x) cos(theta_x)];
Ry = [cos(theta_y) 0 sin(theta_y); 0 1 0; -sin(theta_y) 0 cos(theta_y)];
Rz = [cos(theta_z) -sin(theta_z) 0; sin(theta_z) cos(theta_z) 0; 0 0 1];
R = Rx*Ry*Rz;
end
function L = L_matrix(x,y,z)
L = [-1/z,0,x/z,x*y,-(1+x^2),y;
0,-1/z,y/z,1+y^2,-x*y,-x];
end
Cases that work:
Ad=2*A;
Bd=2*B;
Cd=2*C;
Dd=2*D;
Ad=A+1;
Bd=B+1;
Cd=C+1;
Dd=D+1;
Ad=2*A+1;
Bd=2*B+1;
Cd=2*C+1;
Dd=2*D+1;
Cases that do NOT work:
Rotation by 90 degrees and zoom out (zoom out alone works, but I am doing it here for better visualization)
Ad=2*D;
Bd=2*C;
Cd=2*A;
Dd=2*B;
Your problem comes from the way you move the camera from the resulting visual servoing velocity. Rather than
cam = cam + vc*dt;
you should compute the new camera position using the exponential map
cam = cam*expm(vc*dt)
I have a set of Dicom images on matlab and i would like to add a midline going through all the images
I am outputting the images via imshow3d function
thanks
Edit: here's what i have, the random points are not in the middle they just run through the image
>> clc;
>>clear;
>>%imports dicom images
>>run DicomImport.m;
>>%random points for shortest distance test
>>a = [1 10 200];
>>b = [500 512 300];
>>ab = b - a;
>>n = max(abs(ab)) + 1;
>>s = repmat(linspace(0, 1, n)', 1, 3);
>>for d = 1:3
>> s(:, d) = s(:, d) * ab(d) + a(d);
>>end
>>s = round(s);
>>Z = 593;
>>N = 512;
>>X = zeros(N, N, Z);
>>X(sub2ind(size(X), s(:, 1), s(:, 2), s(:, 3))) = 1;
>>C = find(X);
>>ans.Img(C) = 5000;
>> %shows image
>>imshow3D(ans.Img);
So it looks like ans.Img contains the 3D matrix consisting of your image stack. It looks like you've got something going, but allow me to do this a bit differently. Basically, you need to generate a set of coordinates where we can access the image stack and draw a vertical line in the middle of the each image in the image stack. Do something like this. First get the dimensions of the stack, then determine the halfway point for the columns. Next, generate a set of coordinates that will draw a line down the middle for one image. After you do this, repeat this for the rest of the slices and get the column major indices for these:
%// Get dimensions
[rows,cols,slices] = size(ans.Img);
%// Get halfway point for columns
col_half = floor(cols/2);
%// Generate coordinates for vertical line for one slice
coords_middle_row = (1:rows).';
coords_middle_col = repmat(col_half, rows, 1);
%// Generate column major indices for the rest of the slices:
ind = sub2ind(size(ans.Img), repmat(coords_middle_row, slices, 1), ...
repmat(coords_middle_col, slices, 1), ...
reshape(kron(1:slices, ones(rows, 1)), [], 1));
%// Set the pixels accordingly
ans.Img(ind) = 5000;
This code is quite similar to the answer I provided to one of your earlier question; i.e. I don't use imshow3D but the framework is similar and simpler to modify in order to suit your need. In this case, upon pressing a pushbutton a line appears at the middle of the stack and you can scroll through it with the slider. I hope this can be of help.
function LineDicom(~)
clc
clear
close all
%// Load demo data
S = load('mri');
%// Get dimensions and number of slices.
ImageHeight = S.siz(1); %// Not used here
ImageWidth = S.siz(2); %// Not used here
NumSlices = S.siz(3);
S.D = squeeze(S.D);
%// Create GUI
hFig = figure('Position',[100 100 400 400],'Units','normalized');
%// create axes with handle
handles.axes1 = axes('Position', [0.2 0.2 0.6 0.6]);
%// create y slider with handle
handles.y_slider = uicontrol('style', 'Slider', 'Min', 1, 'Max', NumSlices, 'Value',1, 'Units','normalized','position', [0.08 0.2 0.08 0.6], 'callback', #(s,e) UpdateY);
handles.SlideryListener = addlistener(handles.y_slider,'Value','PostSet',#(s,e) YListenerCallBack);
%// Create pusbutton to draw line
handles.DrawLineButton= uicontrol('style', 'push','position', [40 40 100 30],'String','Draw line', 'callback', {#DrawLine,handles});
%// Flag to know whether pushbutton has been pushed
handles.LineDrawn = false;
%// Show 1st slice
imshow(S.D(:,:,1))
guidata(hFig,handles);
%// Listeners callbacks followed by sliders callbacks. Used to display each
%// slice smoothly.
function YListenerCallBack
handles = guidata(hFig);
%// Get current slice
CurrentSlice = round(get(handles.y_slider,'value'));
hold on
imshow(S.D(:,:,CurrentSlice));
%// If button was button, draw line
if handles.LineDrawn
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
end
drawnow
guidata(hFig,handles);
end
function UpdateY(~)
handles = guidata(hFig); %// Get handles.
CurrentSlice = round(get(handles.y_slider,'value'));
hold on
imshow(S.D(:,:,CurrentSlice));
if handles.LineDrawn
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
end
drawnow
guidata(hFig,handles);
end
%// Pushbutton callback to draw line.
function DrawLine(~,~,handles)
line([round(ImageWidth/2) round(ImageWidth/2)],[1 ImageHeight],'Color','r','LineWidth',2);
handles.LineDrawn = true;
guidata(hFig,handles);
end
end
Sample output:
and after moving the slider up:
Is this what you meant? If not I'll remove that answer haha and sorry.
I have created a big heat map using matlab's imagesc command. It plots the error output for each combination of the values in x and y axes. As can be seen in the figure there are too many axes labels. This might become even denser as I plan to increase the number of points in both x and y axes - which means I will get more outputs on a finer grid.
I want to be flexible with the labels, and skip some of them. I want to do this for both X and Y. I also want to be flexible with the "ticks" and draw either all of them or maybe skip some of them. Keep in mind that both the X and Y values are not increasing in order, at first the increment is 0.01 for 9 points, then 0.1, then 1 or 3 or whatever. I will change these increments too.
I tried to show what I want the graph look like in the second image. I want roughly the labels shown in red boxes only. As I said these are not set values, and I will make the increments smaller which will lead to denser plot.
Thank you for your help.
OS: Windows 7, 8 (64 bit)
Matlab version: Matlab 2014 a
You can manipulate the ticks and labels like this:
ticksarray=[1 33 41 100 ...] % edit these to whatever you want
tickslabels={'1', '33', '41', '100'; ...} % match the size of both arrays
set(gca,'XTick',ticksarray)
set(gca,'XTickLabel',tickslabels)
The same thing applies to the y-axis.
Small working example:
x=1:100;
y=2*x.^2-3*x+2;
plot(x,y)
ticksarray=[1 33 41 100];
tickslabels={'1', '33', '41', '100'};
set(gca,'XTick',ticksarray)
set(gca,'XTickLabel',tickslabels)
Example:
figure(1)
load clown
subplot(211)
imagesc(X);
subplot(212)
imagesc(X);
h = gca;
Now you can either set a maximum number of labels per axis:
%// define maximum number of labels
maxLabel = 3;
h.XTick = linspace(h.xlim(1),h.xlim(2),maxLabel);
h.YTick = linspace(h.ylim(1),h.ylim(2),maxLabel);
or define how many labels should be skipped:
%// define number of labels to skip
skipLabel = 2;
h.XTick = h.XTick(1:skipLabel:end);
h.YTick = h.YTick(1:skipLabel:end)
You can also get a different number of ticks and labels, more complicated though:
maxLabel = 3;
maxTicks = 6;
h.XTick = linspace(h.xlim(1),h.xlim(2),maxTicks);
h.YTick = linspace(h.ylim(1),h.ylim(2),maxTicks);
h.XTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ) ) = repmat({''},1,maxTicks-maxLabel);
h.YTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ) ) = repmat({''},1,maxTicks-maxLabel);
If you use a prior version of Matlab 2014b, then you will need the set command to set all properties:
%// define maximum number of labels
maxLabel = 3;
Xlim = get(h,'Xlim');
Ylim = get(h,'Ylim');
set(h,'XTick', linspace(Xlim(1),Xlim(2),maxLabel));
set(h,'YTick', linspace(Ylim(1),Ylim(2),maxLabel));
%// or define number of labels to skip
skipLabel = 2;
XTick = get(h,'XTick');
YTick = get(h,'YTick');
set(h,'XTick', XTick(1:skipLabel:end));
set(h,'YTick', YTick(1:skipLabel:end));
%// or combined
maxLabel = 3;
maxTicks = 6;
Xlim = get(h,'Xlim');
Ylim = get(h,'Ylim');
set(h,'XTick', linspace(Xlim(1),Xlim(2),maxTicks));
set(h,'YTick', linspace(Ylim(1),Ylim(2),maxTicks));
XTickLabel = cellstr(get(h,'XTickLabel'));
YTickLabel = cellstr(get(h,'YTickLabel'));
XTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ),: ) = repmat({''},1,maxTicks-maxLabel);
YTickLabel( setdiff( 1:maxTicks, 1:maxTicks/maxLabel:maxTicks ),: ) = repmat({''},1,maxTicks-maxLabel);
set(h,'XTickLabel',XTickLabel);
set(h,'YTickLabel',YTickLabel);
After applying the second method proposed by #thewaywewalk I got the second figure below. Apparently the labels need to be structured as well, because they only take the first so many labels.
Then I tried to manipulate the labels as shown below, and got the third image.
skipLabel = 2;
XTick = get(h,'XTick');
YTick = get(h,'YTick');
set(h,'XTick', XTick(1:skipLabel:end));
set(h,'YTick', YTick(1:skipLabel:end));
XTickLabel = get(h,'XTickLabel');
labelsX = cell( length(1: skipLabel:length(XTick)) , 1);
j = 1;
for i = 1: skipLabel:length(XTick)
labelsX{j} = XTickLabel(i, :);
j = j + 1;
end
set(h,'XTickLabel', labelsX);
YTickLabel = get(h,'YTickLabel');
labelsY = cell( length(1: skipLabel:length(YTick)) , 1);
j = 1;
for i = 1: skipLabel:length(YTick)
labelsY{j} = YTickLabel(i, :);
j = j + 1;
end
set(h,'YTickLabel', labelsY);
The Y axis labels seem to be in place as before (right next to tick), however the X axis labels seem to be shifted to the left a little. How can I correct this?
Another note: How can I change the scientific values into normal numbers? Also, probably there is a better approach at manipulating the labels.
I have read in an image file to MATLAB and I am trying to stretch it in one direction, but a variable amount (sinusoidal). This would create an accordion affect on the image. I have toyed around with imresize, however that only resizes the image linearly. I would like the amount of "stretch" to vary for each image line. I tried to convey this with the following code:
periods = 10; % Number of "stretch" cycles
sz = size(original_image,2)/periods;
s = 0;
x = 0;
for index = 1:periods
B = original_image(:,round(s+1:s+sz));
if mod(index,2) == 0
amp = 1.5;
else
amp = 0.75;
end
xi = size(B,2)*amp;
new_image(:,x+1:x+xi) = imresize(B, [size(B,1) size(B,2)*amp]);
s = s + sz;
x = x+xi;
end
You can see that segments of the image are stretched, then compressed, then stretched, etc, like an accordion. However, each segment has a uniform amount of stretch, whereas I'd like it to be increasing then decreasing as you move along the image.
I have also looked at MATLAB's example of Applying a Sinusoidal Transformation to a Checkerboard which seems very applicable to my problem, however I have been trying and I cannot get this to produce the desired result for my image.
Any help is much appreciated.
UPDATE:
Thank you for Answer #1. I was unable to get it to work for me, but also realized it would resulted in loss of data, as the code only called for certian lines in the original image, and other lines would have been ignored.
After experimenting further, I developed the code below. I used a checkerboard as an example. While combersome, it does get the job done. However, upon trying the script with an actual high-resolution image, it was extremely slow and ended up failing due to running out of memory. I believe this is because of the excessive number of "imresize" commands that are used in loop.
I = checkerboard(10,50);
I = imrotate(I,90);
[X Y] = size(I);
k = 4; % Number of "cycles"
k = k*2;
x = 1;
y = 2;
z = 2;
F = [];
i = 1;
t = 0;
s = 0;
for j = 1:k/2
t = t + 1;
for inc = round(s+1):round(Y/k*t)
Yi = i + 1;
F(:,(x:y)) = imresize(I(:,(inc:inc)),[X Yi]);
x = y + 1;
y = x + z;
z = z + 1;
i = i + 1;
end
y = y - 2;
z = z - 4;
for inc = round(Y/k*t+1):round(Y/k*(t+1))
Yi = i - 1;
F(:,(x:y)) = imresize(I(:,(inc:inc)),[X Yi]);
x = y + 1;
y = x + z;
z = z - 1;
i = i - 1;
end
y = y + 2;
z = z + 4;
s = Y/k*(t+1);
t = t + 1;
end
Fn = imresize(F, [X Y]);
imshow(Fn);
Does anyone know of a simpler way to achieve this? If you run the code above, you can see the effect I am trying to achieve. Unfortunately, my method above does not allow me to adjust the amplitude of the "stretch" either, only the number of "cycles," or frequency. Help on this would also be appreciated. Much thanks!
Here is how I would approach it:
Determine how the coordinate of each point in your Final image F maps into your Initial image I of size (M,N)
Since you want to stretch horizontally only, given a point (xF,yF) in your final image, that point would be (xI,yI) in your initial image where xI and yI can be obtained as follows:
yI = yF;
xI = xF + Lsin(xFK);
Notes:
these equations do not guarantee that xI remains within the range [1:N] so cropping needs to be added
K controls the how many wrinkles you want to have in your accordion effect. For example, if you only want one wrinkle, K would be 2*pi/N
L controls how much stretching you want to apply
Then simply express your image F from image I with the transforms you have in 1.
Putting it all together, the code below creates a sample image I and generates the image F as follows:
% Generate a sample input image
N=500;
xF=1:N;
I=(1:4)'*xF/N*50;
% Set the parameters for your accordion transform
K=2*pi/N;
L=100;
% Apply the transform
F=I(:, round(min(N*ones(1,N), max(ones(1,N), (xF + L*sin(xF*K))))) );
% Display the input and output images side by side
image(I);
figure;
image(F);
If you run this exact code you get:
As you can see, the final image on the right stretches the center part of the image on the left, giving you an accordion effect with one wrinkle.
You can fiddle with K and L and adjust the formula to get the exact effect you want, but note how by expressing the transform in a matrix form MATLAB executes the code in a fraction of second. If there is one take away for you is that you should stay away from for loops and complex processing whenever you can.
Have fun!