I am doing bayessian hyperparameter search in Matlab. The process is infinite by nature, so I am showing the plot and have limits by number of iterations and time. Nevertheless, very often I see that the plot will not improve anymore and want to terminate the process. If I terminate script by force it will stop in random place and won't finish gracefully. I would like it to save best found combination so far.
Can I make a button or something, which could flag process to terminate gracefully and perform final operations?
Here is a simple example of how you could achieve this, from a figure with uicontrol helpers.
function pushbuttonPlot
f = figure;
ax = axes;
L = 160*membrane(1,100);
s = surface(L);
s.EdgeColor = 'none';
view(3)
ax.XLim = [1 201];
ax.YLim = [1 201];
ax.ZLim = [-53.4 160];
c = uicontrol;
c.String = 'Clean Up';
c.Callback = #cleanUpandExit;
function cleanUpandExit(src,event)
disp('Cleanup and exit');
% Save data and exit
close(f);
end
end
Related
I am writing a code for a real time experiment using psychtoolbox to present the stimulus. In my experiment, I need to show the subject a graph that indicates his performance. I have plotted the graph using this simple code:
% Draw the graph
figure('visible','off','color',[0 0 0]);
pcolor([0 Num_timepoint+2],[-10 0],ones(2,2));
hold on;
pcolor([0 Num_timepoint+2],[0 10],2*ones(2,2));
colormap([79 167 255;255 187 221]/256);
plot(1:subloop,value0,'*-',...
'color',[0,0,0],...
'LineWidth',1,...
'MarkerSize',5,...
'MarkerEdgeColor','k',...
'MarkerFaceColor',[0.5,0.5,0.5]);
axis([0,Num_timepoint+2,-10,10]);
saveas(gcf,'line_chart.png'); %save it
close(figure);
line_chart=imread('line_chart.png'); %read it
resized_plot=imresize(line_chart,0.5);
imageSize = size(resized_plot);
[imageHeight,imageWidth,colorChannels]=size(resized_plot);
bottomRect = [xCenter-imageWidth/1.5, yCenter+gapdown, xCenter+imageWidth/1.5, yCenter+gapdown+imageHeight];
imageDisplay=Screen('MakeTexture', win0, resized_plot);
Screen('DrawTexture', win0, imageDisplay, [], bottomRect);
Unfortunately, this simple code is very slow. In addition, I couldn't make the graph moving along x axis, as soon as the new value comes.
Any help would be Awesome. Thanks in advance for your efforts.
Why are you saving the figure and redisplaying as an image? Maybe I'm missing something but you should be able to accomplish what you need by updating the existing plot with the fresh data using the handles properties of the plot:
.... First time through we need the initial plot ....
% Set up figure with colormaps and such but leave as 'visible','on'
hPlot = plot(plot(1:subloop,value0,'*-',...
'color',[0,0,0],...
'LineWidth',1,...
'MarkerSize',5,...
'MarkerEdgeColor','k',...
'MarkerFaceColor',[0.5,0.5,0.5]);
hAxes = gca;
.... Loop over your real time updates ....
% Assuming value0 has subject's results from t=0 to t=now
hPlot.XData = value0; hPlot.YData = [1:subloop];
hAxes.XLim = [0 numTimePoints+2];
hAxes.YLim = [-10 10]
.... Continue test and update value0 ....
I think that should keep your plots current without having to save the figure as image to file then reopen the image to display to subject.
If you want to move your data one sample, you can use the circshift function. For example, if you want your new values to appear on the left hand side, you can shift all values 1 sample rightward, then add your new value in the first position.
For converting a MATLAB figure to a Psychtoolbox texture, you don't need to save, then load the temporary images. You can instead use the getframe function to capture the MATLAB figure data, which can then be given to MakeTexture to turn it into a Psychtoolbox texture.
I'm not sure what values you're actually using for subloop, value0, etc. but there is an example that I think might be close to what you want. In this example, 30 frames of figures are plotted, with each figure being on screen for 1 second. New data points are generated randomly and appear from the left hand side of the figure.
Depending on the details of your experiment, you may find that this approach is still too slow. You could also create the figure directly via Psychtoolbox drawing methods like DrawLines, etc. though that would require more effort.
try
win0 = Screen('OpenWindow', 0, 0);
Num_timepoint = 100;
subloop = 100;
value0 = zeros(1,100);
num_demo_frames = 30;
% Draw the graph
fig_h = figure('visible','off','color',[0 0 0]);
pcolor([0 Num_timepoint+2],[-10 0],ones(2,2));
hold on;
pcolor([0 Num_timepoint+2],[0 10],2*ones(2,2));
colormap([79 167 255;255 187 221]/256);
plot_h = plot(1:subloop,value0,'*-',...
'color',[0,0,0],...
'LineWidth',1,...
'MarkerSize',5,...
'MarkerEdgeColor','k',...
'MarkerFaceColor',[0.5,0.5,0.5]);
axis([0,Num_timepoint+2,-10,10]);
for f = 1:num_demo_frames
new_value = randn(1,1);
data_values = plot_h.YData;
data_values = circshift(data_values, 1);
data_values(1) = new_value;
plot_h.YData = data_values;
plot_values = getframe(fig_h);
imageDisplay=Screen('MakeTexture', win0, plot_values.cdata);
Screen('DrawTexture', win0, imageDisplay);
Screen('Flip', win0);
WaitSecs(1);
end
sca;
catch e
sca;
rethrow(e);
end
Hoping you may be able to assist me with this error. I am running some code to fit curves to ages using a cross validation regime. I iterate the curve fitting 1000 times to assess the best fit.
I define my models as:
linear_ft = fittype({'x', '1'});
monotonic_ft= fittype({'-1/x', '1'});
quadratic_ft = fittype('poly2');
I then run the following to iterate through different selections of data splitting, recording the residuals following the curve fit...
Data = randn(4,300,10,10);
Ages = randn(300,1);
for thisDim1 = 1:4
for thisDim2 = 1:10
for thisDim3 = 1:10
for nIts = 1:1000
RandomOrder = randperm(300,300);
Fit_Subs = RandomOrder(1:length(Ages)/2); % Take random subs to fit to
Test_Subs = RandomOrder(length(Ages)/2+1:300); % Take random subs to test fit to
Fit_Data = squeeze(Data(thisDim1,Fit_Subs,thisDim2,thisDim3)); % Take data to fit to
Test_Data = squeeze(Data(thisDim1,Test_Subs,thisDim2,thisDim3)); % Take data to test fit
Fit_Ages = Ages;
Fit_Ages(Fit_Subs) = []; %Take ages of Fit Subs only
Test_Ages = Ages;
Test_Ages(Test_Subs) = []; % Take ages of Test Subs only
Nsubs = (length(Ages)/2);
% Model Data using Curves
fFit_Lin = fit(Fit_Ages,Fit_Data',linear_ft);
fFit_Mon = fit(Fit_Ages,Fit_Data',monotonic_ft);
fFit_Quad = fit(Fit_Ages,Fit_Data',quadratic_ft);
% Fit Modelled Data to Test Data
tFit_Lin = fFit_Lin(Test_Ages);
tFit_Mon = fFit_Mon(Test_Ages);
tFit_Quad = fFit_Quad(Test_Ages);
% Calculate Median Residual
Lin_Med_Resid(nIts) = median(tFit_Lin - Test_Data');
Mon_Med_Resid(nIts) = median(tFit_Mon - Test_Data');
Quad_Med_Resid(nIts) = median(tFit_Quad - Test_Data');
end
end
end
end
If you run this with the fourth loop (nIts) as a for-loop it will run. If you run it as a parfor-loop it won't stating the error:
Error using fit>iFit (line 264)
The name 'lower' is not an accessible property for an instance of class
'llsqoptions'.
Error in fit (line 108) [fitobj, goodness, output, convmsg] = iFit(
xdatain, ydatain, fittypeobj, ...
Does anyone have any idea how to fix this? I would be most grateful for any advice!!
Thanks,
Ben
Try restarting MATLAB or typing clear all to see if it clears things up for you.
Your code works for me, but the parallel toolbox can be a bit finicky in my experience.
I am using the GUIDE for matlab gui.
The gui built in order to communicate with keithley current measurement device through GPIB.
When using a toggle button for Current measurement while loop, i am using a pause() function inside the while loop for each iteration and a ytranspose on the y array reading results.
function Measure_Callback(hObject, eventdata, handles)
global GPIB1
global filename
global timeStep
disp('Measurement in progress \n stopwatch starts!');
tic
x=0;
n=0;
while get(hObject,'Value')
fprintf(GPIB1, 'printnumber(smua.measure.i(smua.nvbuffer1))');
fprintf(GPIB1, 'printbuffer(1,1,nvbuffer1)');
A = fscanf(GPIB1);
if length(A)<20
x = x+1;
n = n+1;
t(n) = toc ;
y(x) = str2double(A);
plot(t,y,'-bo',...
'LineWidth',2,...
'MarkerEdgeColor','k',...
'MarkerFaceColor',[.49 1 .63],...
'MarkerSize',10);
grid on
hold on
end
title('Current vs Time','FontSize', 15)
xlabel('Time [s]','FontSize', 15)
ylabel('Current [A]','FontSize', 15)
a = timeStep;
pause(a)
end
disp('Measurement terminated');
disp('Elapsed time: ');
elapsedtime = toc;
elapsedtime_string = num2str(elapsedtime);
disp(elapsedtime_string);
ytrans = transpose(y);
csvwrite(filename,ytrans);
fprintf(GPIB1, 'smua.source.output = smua.OUTPUT_OFF');
For the pause function i'm geting error:
?? Error using ==> pause Error while evaluating uicontrol Callback
For the transpose(y) function i'm also getting a error:
its undefined y.
Cant understand why are those errors and could use some help.
Thank you!
First off, as people say, post the errors and the code. Do you know if length(A) is smaller than 20 in the first time you run the loop? Because if not, A is not defined and you can't transpose something that is not there. Initialize A before the loop to something and see if the error persists (or print out length(A) to make sure the loop gets entered the first run).
As for the pause error, make sure pause is an int or double, not a string. If you get your global timeStep from the GUI field, it is probably a string and you need to covert it to double first.
I am attempting to write a function that, if called before any animation, will handle the close events without extra code in the animation file.
function matlabStopFunction(varargin)
persistent runs
if runs==2
runs = [];
end
if isempty(runs)
evalin('base','figure(''DeleteFcn'',#matlabStopFunction);');
runs = 1;
else
assignin('base','play',false);
pause(1);
runs = 2;
end
end
Here's a sample animation code that I've been using:
function sampleAnimation
matlabStopFunction;
r = 5;
th = 0;
play = true;
while play
x = r * cosd(th);
y = r * -sind(th);
plot(x,y,'r*');
axis([-10 10 -10 10]);
th = th + 45;
pause(0.25);
end
end
The stop function works fine creating the figure, and when I close the figure, it calls the same function as expected (including the assignin on line 10). However, when stepping through, when I first get back to the base function (sampleAnimation), play is false as would be expected:
But when I step one more line, play is reset to true
Am I incorrectly assigning the value of play to false in the stop function, and if so, how could I correct this so that the animation stops when the figure is closed while keeping the code inside the animation to a minimum? I am trying to replicate the method on this blog except with all the code contained in a separate file.
I am running Matlab 2014b on Windows 8.1.
To answer your question - you are modifying the value play in the base workspace - where as the loop is in the workspace of the sampleAnimation function -> so you are not changing the required value to stop the animation. To verify this clear your variables in the base workspace clear before you run your code and you will see that the variable play is created and set to false.
By the way there is a much simpler way to do this, you animation can create a figure and then you can stop when it is deleted:
function sampleAnimation
h = figure;
r = 5;
th = 0;
while ishandle ( h )
x = r * cosd(th);
y = r * -sind(th);
plot(x,y,'r*');
axis([-10 10 -10 10]);
th = th + 45;
pause(0.25);
end
end
I am having a problem updating a waitbar in a MATLAB GUI.
I created a simple example that works as expected.
steps = 5;
hWaitBar = waitbar(0, 'Testing...');
for i = 1:steps
waitbar(i/steps, hWaitBar);
pause(1);
end
close(hWaitBar);
However when I use this construction in the GUI...
numSteps = %calculated
hWaitBar = waitbar(0, 'Processing...');
if %conditional
for i = 1:numSteps
waitbar(i/numSteps, hWaitBar)
% additional processing
end
else %conditional
% additional processing
end
close(hWaitBar);
...the waitbar only displays correctly for the first for loop iteration.
The second interation fails with the execption:
Error using waitbar(109)
Improper arguments for waitbar.
I have verified that the waitbar progress value does not exceed 1.
I have verified that the waitbar is not being closed until outside the if/else loop.
I found the solution -- I was misuing handle graphics.
In my original code:
numSteps = %calculated
hWaitBar = waitbar(0, 'Processing...');
if %conditional
for i = 1:numSteps
waitbar(i/numSteps, hWaitBar)
% additional processing
% *** call to imagesc caused the error
end
else %conditional
% additional processing
end
close(hWaitBar);
Using the debugger, I saw that the waitbar became the current figure and imagesc tried to plot to it instead of the axis on the main form. Setting the appropriate figure as current immediately before the referencing calls yielded proper behavior.
Corrected code:
numSteps = %calculated
hForm = gcf; % save the handle of the main form
hWaitBar = waitbar(0, 'Processing...');
if %conditional
for i = 1:numSteps
% set the waitbar to be the current figure before it is updated
% note: this syntax will ensure window order will be preserved
% with waitbar on top
set(0, 'CurrentFigure', hWaitBar);
waitbar(i/numSteps, hWaitBar);
% additional processing
set(0, 'CurrentFigure', hForm);
imagesc(...);
% more processing
end
else %conditional
% additional processing
end
close(hWaitBar);