Problem calling multiple files through for-loop
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This is the for-loop function, named spike_analysis_wrapper:
function spike_analysis_wrapper()
filepairs = {
'spike1.mat', 'footsignal_spike1.mat';
'spike2.mat', 'footsignal_spike2.mat'};
% Loop through each row of filepairs
for i = 1:size(filepairs)
% Send the 2 files in row "i" into the analysis
spike_analysis(filepairs{i,1},filepairs{i,2});
end
end
And this is the main function, named spike_analysis:
function spike_analysis (file1,file2)
load(file1)
%Plot the spike with a corrected baseline
A=spike1(:,1);
B=spike1(:,2);
B1=B-(min(B)); %Baseline is 0 if the minimum value is diferent than 0.
figure(1)
plot(A,B1)
ylabel('Intensity (pA)')
xlabel('Time(s)')
title('1st spike')
% The paramenters of the foot signal
load(file2)
A_f=footsignal_spike1(:,1);
B_f=footsignal_spike1(:,2);
figure (2)
plot(A_f,B_f)
ylabel('Intensity (pA)')
xlabel('Time(s)')
title('1st foot signal')
end
The for-loop execute the first set of files (spike1 & footsignal_spike1) but I got this error when the loop tries to execute the second set of files (spike2 & footsignal_spike2).
Undefined function or variable 'spike1'.
Error in spike_analysis (line 5)
A=spike1(:,1);
Error in spike_analysis_wrapper (line 8)
spike_analysis(filepairs{i,1},filepairs{i,2});
According to the error, the problem lies on the main function (spike_analysis) because of the variable spike1.
How can I fix this problem?
Thanks in advance!
1 Comment
Accepted Answer
The problem is caused by badly designed .mat files, where every .mat file contains variables with different names. Your code assumes that the second files contains variables of the same name/s as the first file, but clearly this is not the case.Parsing multiple .mat files in a loop is much simpler when every .mat file contains exactly the same variable names.
S = load(file1);
C = struct2cell(S);
A = C{1}(:,1);
B = C{1}(:,2);
And the same for file2.
If your .mat files contain multiple variables per file, then you can load into a structure and then use dynamic fieldnames:
10 Comments
Jose Rego Terol
on 1 Sep 2019
Jose Rego Terol
on 1 Sep 2019
Edited: Jose Rego Terol
on 1 Sep 2019
1) "How can I change the below code in order to load from the first set of spike to the last one?"
Essentially there are two ways to process multiple files: 1. read the filenames from folder/s, or 2. generate the filenames (e.g. using sprintf). Both of these are shown in the documentation:
"Is sprintf expression suitable for this purpose?"
Most likely, yes.
2) "In other words, name the plot with the same name as the file."
Use fileparts and sprintf.
3) "But I got this error:.. Too many output arguments."
You did not define your function to have any output arguments. Then you tried calling it with output arguments. Thus the error.
If you want your function to have output arguments, then you need to specify them:
PS: "I've tried this"
Is that code is supposed to process multiple files? Nowhere do you actually read the filenames from a folder (e.g. using dir) or generate the filenames (e.g. using sprintf).
You also define spike_analysis2 with one input argument, and then call it with two input arguments (neither of which are a filename, which is what you wrote the function to require).
Try something like this instead:
D = 'C:\Users\usuario\Desktop\Lab\Stackoverflow\Spikes from B2310\Spikes subtracted\spikes'
S = dir(fullfile(D,'spike*.mat'));
for k = 1:numel(S)
F = fullfile(D,S(k).name);
spike_analysis2(F);
end
Jose Rego Terol
on 2 Sep 2019
"Skip the second one and let's go fist to the third one."
fileparts is very simple:
[P,N,E] = fileparts(F)
or even just
[~,N,E] = fileparts(S(k).name)
I am sure you can handle the rest using sprintf.
"Honestly, I don't know what I should type as output in the spike_analysis2 function for the loop."
As you do not explain which variables you want to output from the function, I also have no idea what you should type as the output of the spike_analysis2 function.
But, for the sake of example, lets say you want to output Ti_f and Tf_f (in exactly that order), then you simply define your function with:
function [Ti_f,Tf_f] = spike_analysis2(file1,file2)
which is exactly what the documentation explains as well, which I why I gave you the link to read. Remember to then call the function with two output arguments, e.g.:
[X,Y] = spike_analysis2(...);
How to call functions (with multiple inputs/outputs) is covered in the introductory tutorials:
Jose Rego Terol
on 2 Sep 2019
You wrote spike_analysis_file1 to accept one input argument named file1, which should be a filename. Now look at how you call spike_analysis_file1: is the provided input argument a filename?:
spike_analysis_file1(k) % k is not a filename!
Most likely you want to call it something like this:
spike_analysis_file1(fullFileName)
Jose Rego Terol
on 3 Sep 2019
Jose Rego Terol
on 8 Sep 2019
"How can I save a table for all files loaded in the loop's script that contains all the outputs of the function for each file loaded in one .xlsx file?"
Using writetable or xlswrite, both of which let you specify the destination worksheet and/or range to save the data to (thus easily avoiding overwriting data).
"Obviusly, the file was overwriting everytime by the loop."
You forgot to write the new data to different sheets and/or ranges, to ensure that the data was not overwritten.
"...but the table only contains the first output of the function of the last file loaded."
In fact what your code shows is that you did not call your function with any output arguments at all (something that has been thoroughly discussed in previous comments). The table Table_parameters_spike is being displayed in the command window, and you have not defined it as an output of your function. You appear to be confusing some data being displayed in the command window with the output arguments of your function (none of which appear to be tables).
"Actually, the value of the function in the loop is only the first output of the function."
Because you did not allocate the function outputs to any variables, MATLAB allocates the first ouput argument to the default ans:
"It is abnormal because the function has 5 output and the loop should give all the outputs, right?"
Nope, not abnormal at all... in fact because you did not allocate any of the outputs to variables, I would not expect "all the outputs", I would expect only the first one allocated to the default ans.
Very basic MATLAB concepts, such as how to call functions with multiple output arguments, are explained in the introductory tutorials:
You need to decide if you want to:
- return the table from the function (in which case it needs to be an output argument AND you need to call the function with an appropriate number of output arguments AND you need to decide if you also save the table inside the loop (see point 2) or somehow join/concatenate the data into one table and save it after the loop)
- save the table inside the loop (in which case you need to decide what destination worksheet/range to use to prevent data from being overwritten).
So what would you prefer?
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