I have a drawn a random dot matrix on the screen using matlab/psychtoolbox like this:
Screen('DrawDots', wPtr, dotPositionMatrix, dotSizes, dotColors, dotCenter, 2);
Screen('Flip', wPtr, (stimVbl + STIMULUS_DURATION - .5 * ifi), 0);
Now I want to save the result somehow into a figure that I can print off. How do I do that? I have no idea where to start looking for this information i.e. to save what came up once on the screen. Any guidance much appreciated.
Try Screen('GetImage'). In your case, for example:
Screen('DrawDots', wPtr, dotPositionMatrix, dotSizes, dotColors, dotCenter, 2);
Screen('Flip', wPtr, (stimVbl + STIMULUS_DURATION - .5 * ifi), 0);
current_display = Screen('GetImage',wPtr);
The variable current_display will then be a 3D array of pixel values representing the screen at that moment. You can save this, export this, do whatever you want with it.
Related
so I am working for my disertation thesis and I have to detect the pupil from images using Hough Transform. So far I wrote a code that identifies 2 circles on my image, but right now I have to keep the black circle from the pupil.
When I run the code, it identifies me the pupil, but also a random circle on the cheek. My professor said that I should calculate the pixels mean and, considering the fact that the pupil is black, to keep the pixels from only that region. I don't know how to do this.
I will let my code here to have a look and if someone has an ideea on how should I write this and keep only the black pixels would be great. I also attached to this the final image to see what I obtained.
close all
clear all
path='C:\Users\Ioana PMEC\OneDrive\Ioana personal\Disertatie\test.jpg';
%Citire imagine initiala
xx = imread(path);
figure
imshow(xx)
title('Imagine initiala');% Binarizarea imaginii initiale
yy = rgb2gray(xx);
figure
imshow(yy);
title('Imagine binarizata');
e = edge(yy, 'canny');
imshow(e);
radii = 11:1:30;
h = circle_hough(e, radii, 'same', 'normalise');
peaks = circle_houghpeaks(h, radii, 'nhoodxy', 15, 'nhoodr', 21, 'npeaks', 2);
imshow(yy);
hold on;
for peak = peaks
[x, y]=circlepoints(peak(3));
plot(x+peak(1), y+peak(2), 'r-');
end
hold off
testimage
finalimage
I implemented something which should get the task done for you. The example is done with the image you provided.
Step 1: Read the file(s) and convert them to grayscale.
path = %user input;
RGB = imread(path);
lab = rgb2lab(RGB);
grayscale_image = rgb2gray(RGB);
Step 2: Do the Hough transformation with given parameters.
These, and also the sensitivity can be adapted according to your task. Hint: Play around in the Image Segmenter toolbox for fast parameter finding. Next, the inferred circles are converted to integer values, since these are required for indexing.
min_radius = 10;
max_radius = 50;
% Find circles
[centers,radii,~] = imfindcircles(RGB,[min_radius max_radius],'ObjectPolarity','dark','Sensitivity',0.95);
centers = uint16(centers);
radii = uint16(radii);
The annotated image appears as follows:
Step 3: Get the brightness values of the circles.
From the circle center and radius values, we infer their respective brightness. It is sufficient to only check for the x and y pixel values left/right and above/below the center. (-1 is just a safety margin to completely stay within the circles.)
brightness_checker = zeros(2, max(radii), 2);
for i=1:size(centers,1)
current_radii = radii(i)-1;
for j=1:current_radii
% X-center minus radius, step along x-axis
brightness_checker(i, j, 1) = grayscale_image((centers(i,2) - current_radii/2) + j,...
(centers(i,1) - radii(i)/2) + j);
% Y-center minus radius, step along y-axis
brightness_checker(i, j, 2) = grayscale_image((centers(i,2) - current_radii/2) + j,...
(centers(i,1) - current_radii/2) + j);
end
end
Step 4: Check which circle is a pupil.
The determined value of 30 could potentially be enhanced.
median_x = median(brightness_checker(:,:,1),2);
median_y = median(brightness_checker(:,:,2),2);
is_pupil = (median_x<30)&(median_y<30);
pupils_center = centers(is_pupil == true,:);
Step 5: Draw the pupils.
The marker can be changed. Refer to:
https://de.mathworks.com/help/matlab/ref/matlab.graphics.chart.primitive.line-properties.html
figure
imshow(grayscale_image);
hold on
plot(centers(:,1), centers(:,2), 'r+', 'MarkerSize', 20, 'LineWidth', 2);
hold on
plot(pupils_center(:,1), pupils_center(:,2), 'b+', 'MarkerSize', 20, 'LineWidth', 2);
This is the final output:
Is there a way to have a certain text/shape/image stays on the screen in front of other objects without flipping with the rest of objects on and off the screen? For example, I want to have a fixation crosshair always stays on the screen without changing with the images behind it.
In another word, can "Screen('Flip',window)" only flip certain shapes but not all that are on the screen?
Thanks!
You can indicate that the frame shouldn't be cleared after a Flip, by setting the don't clear Flag to 1:
Screen('Flip', wPtr, [], 1);
However, with this you can overlay new objects on the frame, but if you want to remove any of them, you have to remove them all - the next call to clip without the don't clear flag set to 1 will clear everything:
try
screenNum= max(Screen('Screens'));
Screen('Preference', 'SkipSyncTests', 1);
[wPtr, wRect]=Screen('OpenWindow', screenNum, 0);
% draw fixation, indicate that the frame buffer should not be cleared
DrawFormattedText(wPtr, '+', 'center', 'center', 255);
Screen('Flip', wPtr, [], 1);
WaitSecs(1);
% overlay a purple oval, in addition to the fixation
Screen('FillOval', wPtr, [128 0 128], [0 0 100 100])
Screen('Flip', wPtr, []);
WaitSecs(1);
% display an orange oval, this will be presented without the fixation
% unless the previous purple oval is also retained
Screen('FillOval', wPtr, [128 128 0], [100 100 200 200])
Screen('Flip', wPtr, []);
WaitSecs(1);
sca;
catch e
sca;
rethrow(e)
end
If you need to frequently draw the fixation cross, with other objects being added and removed, another option is to store the fixation as a texture, which can be more easily redrawn on every frame.
I would like to implement the fly-through effect as shown in this nice example. First I created a figure from matrix hm, a 300X300 matrix by using the surf function:
surf(hm);
Then, I defined an animated line from variables x, y, and z and displayed on the figure as follows:
curve = animatedline;
curve.LineWidth = 6;
curve.Color = [ 1 0 1];
for i = 1:length(x)
addpoints(curve, x(i), y(i), z(i));
drawnow;
end
Then, I wanted to implement the fly-through effect so that the camera will move along the line. I tried this code piece I took from the example above and I slightly modified it:
for i = 1:length(x)
campos([(x(i) -5), (y(i)-5), 0]);
camtarget([x(i), y(i), z(i)]);
drawnow;
end
But the camera doesn't move as I intended. What am I doing wrong?
If you want to mimic the behavior of the linked example, you need to have both the camera target and camera position moving along your curve defined by (x, y, z). The way you've written it above, the camera target moves along the curve, but the camera position is always offset from the target by (-5, -5) in the xy plane and sitting at z = 0. If you want the camera to follow the curve behind the target, you should try something like this:
for iPoint = 6:numel(x)
campos([x(iPoint-5) y(iPoint-5) z(iPoint-5)]); % Note the index is shifted, not the value
camtarget([x(iPoint) y(iPoint) z(iPoint)]);
drawnow;
end
If you don't want the camera moving along the same curve, and instead want it to always be at a fixed offset from your moving camera target, you could try this:
offset = [-5 -5 0]; % X, Y, and Z offset from target
for iPoint = 1:numel(x)
campos([x(iPoint)+offset(1) y(iPoint)+offset(2) z(iPoint)+offset(3)]);
camtarget([x(iPoint) y(iPoint) z(iPoint)]);
drawnow;
end
Finally, if you'd like to control the speed of the animation, you can replace the drawnow command with a call to pause. Note that a call to pause is equivalent to a call to drawnow in that it will force an update of graphics objects. You can also animate graphics using a timer object, as I illustrate in this answer.
I have data that records the x and y positions of an animal in a 2D assay over time stored in a matlab matrix. I can plot these co-ordinates over time, and extract the velocity information and plot this using cline.
The problem I am having at the moment is calculating the heading angle. It should be a trivial trigonometry question, but I am drawing a blank on the best way to start.
The data is stored in a matrix xy representing x and y co-ordinates:
796.995391705069 151.755760368664
794.490825688073 150.036697247706
788.098591549296 145.854460093897
786.617021276596 144.327659574468
781.125000000000 140.093750000000
779.297872340426 138.072340425532
775.294642857143 133.879464285714
What I would like to be able to do is know the angle of the line drawn from (796.995, 151.755) to (794.490, 150.036), and so on. My research suggests atan2 will be the appropriate function, but I am unsure how to call it correctly to give useful information.
difx = xy(1,1) - xy(2,1);
dify = xy(1,2) - xy(2,2);
angle = atan2(dify,difx);
angle = angle*180/pi % convert to degrees
The result is 34.4646. Is this correct?
If it is correct, how do I get the value to be in the range 0-360?
You can use the diff function to get all the differences at once:
dxy = diff(xy); % will contain [xy(2,1)-xy(1,1) xy(2,2)-xy(1,2); ...
Then you compute the angle using the atan2 function:
a = atan2(dxy(:,2), dxy(:,1));
You convert to degrees with
aDeg = 180 * a / pi;
And finally take the angle modulo 360 to get it between 0 and 360:
aDeg = mod(aDeg, 360);
So - you pretty much got it right, yes. Except that you have calculated the heading from point 2 to point 1, and I suspect you want to start at 1 and move towards 2. That would give you a negative number - or modulo 360, an angle of about 325 degrees.
Also, using the diff function gets you the entire array of headings all at once which is a slight improvement over your code.
[rc mi]=
EDIT the problem of "phase wrapping" - when the heading goes from 359 to 0 - is quite a common problem. If you are interested in knowing when a large change happens, you can try the following trick (using aDeg from above - angle in degrees).
dDeg1 = diff(aDeg); % the change in angle
dDeg2 = diff(mod(aDeg + 90, 360)); % we moved the phase wrap point by 180 degrees
dDeg12 = [dDeg1(:) dDeg2(:)]';
[rc mi]= min(abs(dDeg12));
indx = sub2ind(size(dDeg12), mi, 1:size(dDeg12, 2));
result = dDeg12(ii);
What I did there: one of the variables (dDeg or dDeg2) does not see the phase wrap, and the min function finds out which one (it will have a smaller absolute difference). The sub2ind looks up that number (it is either positive or negative - but it's the smaller one of the two), and that is the value that ends up in result.
You can verify the angle by plotting a little line that starts at the first point and end in the direction of the heading. If the angle is correct, it will point in the direction of the next point in xy. Everything depends on where yo define 0 degrees at (straight up, say) from and whether positive degrees is rotation counterclockwise (I do) or clockwise. In MATLAB you can get the numbers between 0 and 360 but using modulo---or you can just add 180 to your results but this will change the definition of where the 0 degree mark is.
I made the following script that is a bit complex but shows how to calculate the heading/angle for all points in vector format and then displays them.
xy =[ 796.995391705069 151.755760368664
794.490825688073 150.036697247706
788.098591549296 145.854460093897
786.617021276596 144.327659574468
781.125000000000 140.093750000000
779.297872340426 138.072340425532
775.294642857143 133.879464285714];
% t = linspace(0,3/2*pi, 14)';
% xy = [sin(t), cos(t)];
% calculate the angle:
myDiff = diff(xy);
myAngle = mod(atan2(myDiff(:,1), myDiff(:,2))*180/pi, 360);
% Plot the original Data:
figure(1);
clf;
subplot(1,3,1);
plot(xy(:,1), xy(:,2), '-bx', 'markersize', 12);
hold all
axis equal;grid on;
title('Original Data');
% Plot the calculated angle:
subplot(1,3,2);
plot(myAngle);
axis tight; grid on;
title('Heading');
% Now plot the result with little lines pointing int he heading:
subplot(1,3,3);
plot(xy(:,1), xy(:,2), '-bx', 'markersize', 12);
hold all
% Just for visualization:
vectorLength = max(.8, norm(xy(1,:)- xy(2,:)));
for ind = 1:length(xy)-1
startPoint = xy(ind,:)';
endPoint = startPoint + vectorLength*[sind(myAngle(ind)); cosd(myAngle(ind))];
myLine = [startPoint, endPoint];
plot(myLine(1,:), myLine(2, :), ':r ', 'linewidth', 2)
end
axis equal;grid on;
title('Original Data with Heading Drawn On');
For example, if you use my test data
t = linspace(0,3/2*pi, 14)';
xy = [sin(t), cos(t)];
You get the following:
and if you do yours you get
Note how the little red line starts at the original data point and moves in the direction of the next point---just like the original blue line connecting the points.
Also note that the use of diff in the code to difference all the points properly at once. This is faster and avoids any problems with the direction--looks like in your case it's swapped.
I have a figure of size 14 x 14 square drawn inside an axis of 20 x 20, in matlab.
I am trying to draw circles of radius 0.7 inside the square and need to arrange them evenly. I need to draw 233 circles. Please let me know how can I do it?
Currently I can draw them randomly but couldn't get 233 circle. Please see my below code.
Your reply is appreciated.
% Urban, sub urban, Rural areas
x_area =[3, 12, 6];
y_area = [6, 8, 16];
r_area = [1, 7, 2];
f = figure;
hAxs = axes('Parent',f);
hold on, box on, axis equal
xlabel('x')
ylabel('y','Rotation',0)
title('Compute the area of circles a vectorized way for several cicles')
axis([0 20 0 20])
rectangle('Position',[5,1,14,14])
rectangle('Position',[3,1,2,2])
rectangle('Position',[1,3,4,4])
hold on, box on, axis equal
a = 233;
x_base_urban = randi([6 18], 1, a);
b = rand([10 8], 1);
y_base_urban = randi([2 14],1, a);
r_base_urban = 0.9;
size_x = size(x_base_urban);
size_x = size_x(2);
size_y = size(y_base_urban);
size_y = size_y(2);
colour = rand(size_x,3);
for t = 1: size_x
plot(x_base_urban(t)+ r_base_urban.*cos(0:2*pi/100:2*pi),...
y_base_urban(t)+ r_base_urban.*sin(0:2*pi/100:2*pi),'parent',hAxs)
plot(x_base_urban(t),y_base_urban(t),'+','parent',hAxs)
end
Thanks
Randomly plotting everything won't work. Actually, if your circles can't overlap, nothing will work. To show that, just compare the results of following calculations:
lSquare = 14;
rCircle = 0.7;
nCircles = 233;
areaCircles = nCircles * pi * rCircle^2
areaSquare = lSquare^2
You will see that areaCircles > areaSquare, so it is impossible to fit them all in. On the other hand, if areaSquare >= areaCircles does not guarantee you that a solution exists!
Try your setup with a smaller example to come up with a solution. E.g. take a square box and a bunch of spherical objects (balls, marbles, oranges, apples, ... if need be) and try to fit as much of those in your box. If that works, you might even want to draw their positions on a sheet of paper before trying to implement it.
If you do this correctly, you will get an idea of how to stack round objects in a square container. That is also exactly what you need to do in your exercise. Then try to make a model/algorithm of what you did manually and implement that in MATLAB. It won't be hard, but you will need some small calculations: Pythagoras and intersection of circles.
I also suggest you use a function to draw a circle as #Andrey shows, so something of the form function drawCircle(center, radius). That allows you to keep complexity down.
If your circles can overlap, then the solution is quite easy: look at a circle as an object with a center point and distribute these center points evenly over the square. Don't use rand to do this, but calculate their positions yourself.
If you can't find a solution, I might expand my answer in a few days.
Without diving too deep into your code, I think that you need to add a hold function, after the first plot
for t = 1: size_x
plot(x_base_urban(t)+ r_base_urban.*cos(0:2*pi/100:2*pi),...
y_base_urban(t)+ r_base_urban.*sin(0:2*pi/100:2*pi),'parent',hAxs)
plot(x_base_urban(t),y_base_urban(t),'+','parent',hAxs)
hold(hAxs,'on');
end
By the way, the best way to draw circle is by using rectangle command.
rectangle('Curvature',[1 1],'Position',[1 3 4 5])
So you can create a PlotCircle function (like #EgonGeerardyn suggests) like this:
function plotCircle(x,y,r)
rectangle('Position',[x-r y-r 2*r 2*r],'Curvature',[1 1]);
end