How can I make a scatter plot when the signal above a certain threshold in real time?

Hi all,

I am quite fresh in Matlab but want to design a program to simulate flowing paricles, the concept would close to flow cytometry.

The scenario is, the particle will induce several sine waves once it pass through the detecting zone. Each sine waves could be connected as a wave envelope since the particel transerving in the detection zone will have different sensitivity. Please see the fig1.

According to the sine wave amplitude, if the maximum value above a certain threshold which set by me, I can plot a dot on the XY scatter plot spontanously.

My question is, how can I modify my code for monitoring (real-time) measurement when I am scanning the particles?

I attached my code but they are just a sample for showing example, I think they should be more complicated if I want to use in my experiment.

Thanks! And hope everybody stay healthy and safe!

clc
close all
clear all
%Generate a similar signal
t=linspace(0,0.0025,10000);
fc= 5000;
fm= 200;
fs= 40000;
Am= 1;
Ac= 0.01;
m= Am/Ac;
wc= 2*pi*fc*t;
wm= 2*pi*fm*t;
ec= Ac*sin(wc);
em= Am*sin(wm);
y=Ac*(1+m*sin(wm).*sin(wc));
plot(t,y);
%Find the maximum amplitude and count it to make a XYscatter graph
[maxYvalue, indexAtmaxY]= max(y);
XvalueAtMaxYvalue= t(indexAtmaxY(1));
x= XvalueAtMaxYvalue.*1000;
scatter(x, maxYvalue)
xlabel('Time(us)')
ylabel('Voltage(a.u.)')

[darova]

Can you show something? Your code? Picture? Another attempts?

Something!

[Chen Kevin]

Hi Darova,

Thanks for the suggestions! I've edited more information, hope it can express my question clearly now.

Answer 1

[darova]

Here is my vision of your problem

x = -20:0.5:20;
f = @(x) sin(x).*sqrt(20^2-x.^2);
y = f(x);
ylim([-30 30])
cla
plot(x,y)        
hold on
h1 = plot(0,0);
h2 = scatter(0,0);
for i = 1:length(x)
    set(h2,'xdata',x(i),'ydata',f(x(i))*(f(x(i))>0));
    set(h1,'xdata',[0 0]+x(i),'ydata',[-30 30])
    xlim([-20 20]+x(i)) % move limits
    pause(0.1)          % wait a sec
    drawnow
end
hold off

[Chen Kevin]

Hi Darova,

Thanks! I thinks is useful and close now, but could it shows two graph seperately in the same time? (Analysing the peak + producing scatter)

[darova]

Here my new invention

clc,clear
close
ff = figure(1);
set(ff,'windowstyle','docked')
x = -20:0.5:20;
f = @(x) sin(x).*sqrt(20^2-x.^2);
y = f(x);
ylim([-30 30])
cla
ax1 = gca;
plot(x,y)        
hold on
h1 = plot(0,0);
h2 = scatter(0,0);
ax2 = axes('position',[.7 .7 .2 .2]);
h3 = scatter(0,0);
h4 = line(0,0);
h5 = line(0,0);
for i = 6:length(x)-5
    set(h1,'xdata',[0 0]+x(i),'ydata',[-30 30])             % large vertical line
    set(h2,'xdata',      x(i),'ydata',f(x(i))*(f(x(i))>0)); % scatter point
    set(h4,'xdata',x(i-5:i+5),'ydata',y(i-5:i+5))           % small part of data
    set(h3,'xdata',      x(i),'ydata',f(x(i))*(f(x(i))>0)); % scatter point
    set(h5,'xdata',[0 0]+x(i),'ydata',[-30 30])             % small vertical line
    xlim(ax1,[-20 20]+x(i)) % move limits main axes
    xlim(ax2,[-20 20]+x(i)) % move limits small axes
    pause(0.1)              % wait a sec
    % drawnow
end
hold off

[Chen Kevin]

Hi Darova,

Thanks! Closer now, but regarding to the inset, it is possible to make each peaks become "scatter dots" only?

Please take a look at the attachment which I used "findpeaks" function that I hope those peaks could be pulled out and become scatter dots graph.

[darova]

Once you used findpeaks why don't jsut use those indices?

[~,ix] = findpeaks(y);
scatter(x(ix),y(ix))

[Chen Kevin]

Hi Darova,

Thanks! I even changed to max(y) to find the maximum value of the series wave.

Last extra question, as I want to make the series wave closer to realistic, how could I make it to:

1. The series wave happen in 1.1ms
2. 55 sine waves (pulses) appear in 1.1ms interval, which means the pulse repitition rate is 50kHz.

Thanks!

[darova]

Try to change these lines

% x = -20:0.5:20;
% f = @(x) sin(x).*sqrt(20^2-x.^2);
x = linspace(0,1.1e-3,50);              % 50 points between 0 and 0.0011 sec
f = @(x) sin(50000*x);                  % sinus wave with 50kHz frequency

[Chen Kevin]

Hi Darova,

Thanks, closer now, but how could I make these series sine waves remain like the previous one? (amplitude start increasing before transerve to the center, start to decrease when it transerve from the center to the edge.) please find the attachment.

Second, the time interval(1.1ms) should have 55 sine waves (or you can say 55 pulse), but I only got 8... please also see the attachment.

[darova]

• Second, the time interval(1.1ms) should have 55 sine waves (or you can say 55 pulse), but I only got 8... please also see the attachment.

My bad, sorry. Forgot

y = sin(2*pi*5e4*x);

• how could I make these series sine waves remain like the previous one?

What frequency of changes?

y = sin(2*pi*5e4*x).*sin(2*pi*x * 1000);    % 1000 - frequency of changes

[Chen Kevin]

Perfect! It works, thanks!

But how do you save the file to animation? Like you responsed before with the comment.

[darova]

Example

clc,clear

	% GRAPHICAL DRIVER
	opengl software

x = linspace(0,5,20);
y = x.^2;

% axis([0 max(x) 0 max(y)])
h = plot(0,0,'or');
line(x,y)
filename = 'gif_animation.gif';
f = getframe(gcf); 
[im,map] = rgb2ind(f.cdata,256);
imwrite(im,map,filename,'DelayTime',0,'Loopcount',inf);
for i = 1:length(x)    
    set(h,'xdata',x(i),'ydata',y(i))
    pause(0.1)
    f = getframe(gcf); 
    [im,map] = rgb2ind(f.cdata,256);
    imwrite(im,map,filename,'DelayTime',0.1,'WriteMode','Append');
end

Answer 2

[Image Analyst]

Sometime you need to put a drawnow after your call() to plot to get the plot to show up in real time, otherwise, if it's in an intensive loop, it will only update the plot once the loop has finished:

plot(............)
drawnow; % Force screen to repaint immediately.

[darova]

Can you make a simple example? I've heard a lot about drawnow but never had a reason to use it

[Image Analyst]

It's easy to demonstrate. Run this code with the drawnow line commented out and see that it doesn't plot every single iteration. It only plots the whole thing once the loop exits:

for k = 1 : 1000
	plot(1:k, 'b*');
	%drawnow; % See # of points and y axis change as the loop runs, if not commented out.
end
fprintf('Done with loop now.\n');

Then uncomment the drawnow and see how it refreshes the screen at every single iteration.

[darova]

Does pause function force somehow to draw? Works ok with pause

[Image Analyst]

Yes, when pause hits, it gives time for the operating system to process other messages in the queue that have basically been held up while the OS is processing what it thinks are more important operations. So the MATLAB stuff like iterating on the loop and incrementing the loop counter (which it thinks are super important) are basically paused and it then gives it time to get around to handling the other messages that it considered lower priority, like updating the display. You might check out this Wikipedia article on message based computing: https://en.wikipedia.org/wiki/Message_queue

[darova]

thanks