Does findpeaks work with mat files?

Hi there

I have a very simple question. Does findpeaks work with matfile variables?

I run the following example below and I don't get any errors but my script doesn't detect any peaks. Essentially nothing happens if I run the following.

EPSCs_PYR_1= load('mytrace2131soma&syns.mat', 'mytrace2131syns');
EPSCs_PYR = mytrace2131syns(:,2);
time=mytrace2131syns(:,1);
findpeaks(EPSCs_PYR,time);

What do I do wrong? Similar scripts have worked in the past if I load .dat or .txt files

thank you!

[Stephen23]

You load the .mat file into a structure named EPSCs_PYR_1, but you never actually use EPSCs_PYR_1 for anything or refer to it again. Whatever data is imported from that file is ignored by your code.

[Fran]

Hello

that's a good point I will investigate, however it is not entirely true that the variable imported (mytrace2131syns) is ingnored by my code because I can plot this variable just fine using the script below. It is the peak detection that doesn't work on these data.

EPSCs_PYR_1= load('mytrace2131soma&syns.mat', 'mytrace2131syns');
EPSCs_PYR = mytrace2131syns(:,2);
time=mytrace2131syns(:,1);

findpeaks(EPSCs_PYR,time);
plot(time,EPSCs_PYR);

Answer 1

[Stephen23]

Most likely you need to actually refer to the structure that you imported the file data into:

S = load('mytrace2131soma&syns.mat', 'mytrace2131syns');
T = S.mytrace2131syns(:,1);
V = S.mytrace2131syns(:,2);
pks = findpeaks(V,T)

[Fran]

thanks, that looks more correct than what I did previously, however it produces the same output. The script plots my trace but the peakdetection on the trace doesn't work.

Answer 2

[Star Strider]

‘... my script doesn't plot my trace and doesn't detect any peaks ...’

You are overwriting the findpeaks plot.

Try this instead:

figure
findpeaks(EPSCs_PYR,time);

figure
plot(time,EPSCs_PYR);

Both plots should now appear in their respective figure objects.

[Fran]

Thanks for your reply.

For findpeaks a blank Figure window opens if I follow your suggestion. Plotting my trace works fine as it did from before.

[Star Strider]

My pleasure.

In the absence of your ‘mytrace2131soma&syns.mat’ file, this will likely remain a mystery.

Nothing I can do to simulate what I believe could be wrong reproduces the problem you report. Even if the argument has no variation at all, findpeaks will produce a plot (if you call it without outputs):

findpeaks(ones(1, 90))

If you give it a cell array or a structure (it only accepts single or double precision vectors), it will throw an error. Since you did not report it throwing any errors, I have no idea what the problem could be.

[Fran]

Thanks again Star

As a matter of fact my "mytrace2131soma&syns.mat" isn't all that mysterious. Just a voltage trace as a function of time which I can plot without issues. Interestingly running the line you just mentioned: "findpeaks(ones(1, 90))" doesn't generate any plot for me.

I am thinking that this might be a matter of updating my matlab from a 2017 version I am currently using to a 2019.

[Star Strider]

That findpeaks call creates a horizontal line at 1 when I run it (without outputs) in R2019a.

Be sure your MATLAB version has all the latest updates. Click on Add-Ons in the top toolstrip, then scroll down to Check for Updates, then click on Products. I described this procedure in detail in: 2018b Update 3. The problem you’re having with findpeaks could be a bug that was later corrected in your version.

Upgrading to 2019a would definitely be a good idea. (Check for Updates moved to Help in R2019a.)

[Fran]

awesome thanks so much!

[Star Strider]

My pleasure!

Did you do the updates?

If so, did they solve your problem?

[Fran]

I installed R2019a but our administator hasn't send me the licenses to update my matlab server yet, thus the R2019a is too new for my existing license files. I am now installing R2018b for the next month or so, at least until I update the server. I will let you know how it goes!

PS: in terms of updates, following your instructions everything appeared to be up-to-date in my previous 2017 version.

[Star Strider]

Please do!

I have no idea what the problem with findpeaks is in your R2017 installation. I never had any problems with it.