How can I plot a histogram for each of the multiple .mat files located in a folder outside of MATLAB?

I am new to using MATLAB to analyze and visualize many individual files of data.

Here is the situation: I have multiple (20+ but can certainly extend to the 50-60+ range) .mat files that are typically (but not always) in the form of a 1024x1024 matrix. These .mat files are automatically placed in a folder outside of MATLAB (the folder's location is specified as the save file path in a seperate script). Each of those codes share a common naming tag (ie. an identifying text that can be used to readily identify the targeted .mat files).

I would like to be able to produce a reusable code that can take all of the selected .mat files in that filepath and produce a histogram for each .mat at the same time. The values of the matricies can differ so I wouldn't want to put any restraints on axises or rows/columns.

The code I have so far is as follows:

clear all

%The Code below specifies the filepath on my computer where said .mat files are located in
directory = '/Users/NAME/Desktop/selectedmatricies/';
realdata = dir(directory);

%MATLAB Version: 9.7.0.1261785 (R2019b) Update 3

I am unsure where to go from here, or even if the code I listed above is even needed for what I am intending. I do have some suspiscion that a for loop would play a role in the code that would be generated, but I do not know how to structure it.

I have scoured MathWorks for previously asked questions in a similiar predicament to mine, however my efforts were fruitless. I am very much open to any ideas or codes that the community can provide! Thank you so much everyone!

TLDR; I would like to take multiple .mat files in an outside folder and run them through MATLAB code to produce a histogram per file

Answer 1

[Kevin Holly]

Here is one method you can use:

directory = '/Users/NAME/Desktop/selectedmatricies/'; %Alternatively, could use: directory = uigetdir()
files=dir(fullfile(directory,'*.mat')); % This gets all the .mat files in the directory. * is a wild card

save_directory=uigetdir('C:\'); % Where you want to save your histograms

%let's analyze each file
for i = 1:length(files)
    matrix = load([file(i).folder,filesep,file(i).name],'-mat');
    histogram(matrix)
    xlabel('X label')
    ylabel('Y label')
    title('title')
    saveas(gcf,[save_directory,filesep,strrep(file(i).name,'.mat','.fig')],'fig'); %save figure (can also save as an image (e.g. .png or .tif))
    % Could use the line below if you want to save the figure with the word histogram
    %saveas(gcf,[save_directory,filesep,strrep(file(i).name,'.mat','_histogram.fig')],'fig'); %save figure
end

[bobby]

Thank you for responding in such a timely manner! It is very much appreciated!

I have a couple questions about the code after I set a filepath for the save directory:

• When running the code, a popup comes up which wants me to open up a folder. What is the purpose of this popup and why does it ask for me to open a folder?
• In the command window, I get an error from within the for loop seen below. Changing everywhere that is listed as 'file' to 'files' does not fix this error. Any solutions to this problem?

Unrecognized function or variable 'file'

Error in histogramFunction, (note that 'histogramFunction is the name of the script)

matrix = load([file(i).folder,filesep,file(i).name],'-mat');"

[Kevin Holly]

I made a few changes:

directory = '/Users/NAME/Desktop/selectedmatricies/'; %Alternatively, could use: directory = uigetdir()
files=dir(fullfile(directory,'*.mat')); % This gets all the .mat files in the directory. * is a wild card

uiwait(msgbox('Please select the folder in which you want to save the histogram files'))
save_directory=uigetdir('C:\'); % Where you want to save your histograms
%let's analyze each file
for i = 1:length(files)
    Data = load([files(i).folder,filesep,files(i).name],'-mat');
    histogram(Data.matrix) %Note "matrix" needs to be replaced with the variable you want to load in the .mat file.
    xlabel('X label')
    ylabel('Y label')
    title('title')
    saveas(gcf,[save_directory,filesep,strrep(files(i).name,'.mat','.fig')],'fig'); %save figure (can also save as an image (e.g. .png or .tif))
    % gcf stands for get current figure. strrep() is a string replace
    % function. I replaced '.mat' with '.fig' in this case.
    % Could use the line below if you want to save the figure with the word histogram
    %saveas(gcf,[save_directory,filesep,strrep(file(i).name,'.mat','_histogram.fig')],'fig'); %save figure
end

I added a step, so you can choose where you want to save your histograms. See comments in the code. I added a message box for clarity.

[bobby]

Thank you! I am a little bit confused on your comment that says

"Note "matrix" needs to be replaced with the variable you want to load in the .mat file."

Could you explain what that means? Is that where I would be putting the 'string of text' that all of the .mat files share?

[Image Analyst]

I think matrix is actually a structure, not a matrix. Just leave off the semicolon and see what appears in the command window:

matrix = load(fullfile(file(i).folder, file(i).name))

What do you see? By the way, you can use a simplified call to load() like I did.

[Kevin Holly]

Yes, it was a structure as Image Analyst stated. That why I changed it to the variable name Data. Then I called the matrix by using Data.matrix. I do not have your data, so I don't know how the matrix you want to load is saved in the .mat file. I don't know the variable name.

[bobby]

Doing it Kevin Holly's way, the code is listed below. Running that exact code, I get an error that is as shown:

Reference to non-existent field 'matrix'.

Error in histogramFunction (line 16)

histogram(Data.matrix)

for i = 1:length(files)
    
    Data = load([files(i).folder,filesep,files(i).name],'-mat')
    histogram(Data.matrix) %this is wear the error occurs aka line 16
    xlabel('X label')
    ylabel('Y label')
    title('title')
    
    %gcf stands for get current figure. strrep() is a string replace
    saveas(gcf,[save_directory,filesep,strrep(files(i).name,'.mat','.fig')],'fig'); %save figure (can also save as an image (e.g. .png or .tif))

end

Doing it Image Analyst's way, the code is listed below. Running that exact code, I get an error that is as shown:

Unrecognized function or variable 'file'.

Error in histogramFunction (line 14)

matrix = load(fullfile(file(i).folder, file(i).name))

for i = 1:length(files)
    
    matrix = load(fullfile(file(i).folder, file(i).name))
    histogram(Data.matrix)
    xlabel('X label')
    ylabel('Y label')
    title('title')
    
    %gcf stands for get current figure. strrep() is a string replace
    saveas(gcf,[save_directory,filesep,strrep(files(i).name,'.mat','.fig')],'fig'); %save figure (can also save as an image (e.g. .png or .tif))

end

[Kevin Holly]

Run the following and tell us what you see:

Data = load(fullfile(files(i).folder, files(i).name))

[bobby]

@Kevin Holly, How can I tell how the matrix is saved in my .mat file? It is entirely composed of numbers. I thought that all matricies were saved the same way?

When you say "don't know the variable name", are you referring to the 'string of text' that all of the .mat files share? If so, that "string of text" would be just the date, so for example for today it would be 09292021...., that "..." would then be the other characters in the name that would probably be different for each .mat

[Kevin Holly]

The .mat files are files that save your workspace variables. Please see link below.

https://www.mathworks.com/help/matlab/matlab_env/save-load-and-delete-workspace-variables.html#mw_093429e0-f588-4d9b-8eae-00bddea902a4

[bobby]

After replacing and running the code with the function, I get the following error

Reference to non-existent field 'matrix'.

Error in histogramFunction (line 16)

histogram(Data.matrix)

Currently, I think all of the .mat files save under the same workspace variable name. Is there a way to have each of them save under its own workspace variable name?

[Kevin Holly]

That is because there is no workspace variable named "matrix". The workspace variable saved in your Mat-files will be different.

If you run:

Data = load(fullfile(files(i).folder, files(i).name))

In isolation without a semicolon at the end. We can see what variables the structure contains. Or simply type Data in your command window if you have already run the above command. The structure Data should already be saved in your workspace.

[Image Analyst]

@bobby, run this and copy and paste what shows up in the command window back here in your reply:

clc;
files = dir('*.mat')
for k = 1:length(files)
    storedStructure = load(fullfile(files(k).folder, files(k).name))	% No semicolon
end

[bobby]

@Image Analyst, When running the attached code on a seperate script, in the command window I get the following:

storedStructure =

struct with fields:

IntensityImagedataCh1: [1024×1024 double]

That message above is repeated 24 times.

[bobby]

@Kevin Holly, Given your most recent response, would I have to fix the error with the workspace variable names before continuing to write the code?

[Kevin Holly]

@bobby Now replace matrix with IntensityImagedataCh1 in the code. IntensityImagedataCh1 is your workspace variable.

for i = 1:length(files)
    
    Data = load(fullfile(files(i).folder, files(i).name))
    histogram(Data.IntensityImagedataCh1)
    xlabel('X label')
    ylabel('Y label')
    title('title')
    
    %gcf stands for get current figure. strrep() is a string replace
    saveas(gcf,[save_directory,filesep,strrep(files(i).name,'.mat','.fig')],'fig'); %save figure (can also save as an image (e.g. .png or .tif))
end

[Image Analyst]

I'd just add

drawnow;

after histogram() to make sure it paints the screen every time. Otherwise you might just see the latest histogram only.

[bobby]

@Kevin Holly and @Image Analyst, thank you for sticking with me through this issue and lending your expert suggestions! From your guidance and expertise, I was able to figure out the code that would be able to work with my current script! Thank you both so very much!

Answer 2

[Image Analyst]

The answer to this and lots of other good stuff can be found in the FAQ:

https://matlab.fandom.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

[bobby]

Thank you! I see that the first example would be most relevant but how would I change that code to analyze .mat files into histograms, rather than it analyzing a group of .png files as seen in the example? Would the code still be the same?