How can I batch process creating masks from the color thresholder function?

Question

I created a mask function using the color thresholder app. I would like to run multiple images through the function instead of each image individually. For example, 'Control_1 Negative P001(30).png', 'Control_1 Positive P001(30).png', etc until Control_41 Positive and Negative .png files. I assume you would use a for loop but I am not sure where to go from there.

function [BW,maskedRGBImage] = GlassBrainMask(RGB)
%createMask  Threshold RGB image using auto-generated code from colorThresholder app.
%  [BW,MASKEDRGBIMAGE] = createMask(RGB) thresholds image RGB using
%  auto-generated code from the colorThresholder app. The colorspace and
%  range for each channel of the colorspace were set within the app. The
%  segmentation mask is returned in BW, and a composite of the mask and
%  original RGB images is returned in maskedRGBImage.

% Auto-generated by colorThresholder app on 19-Feb-2021
%------------------------------------------------------

% Convert RGB image to chosen color space
I = rgb2hsv(RGB);

% Define thresholds for channel 1 based on histogram settings
channel1Min = 0.002;
channel1Max = 0.119;

% Define thresholds for channel 2 based on histogram settings
channel2Min = 0.322;
channel2Max = 1.000;

% Define thresholds for channel 3 based on histogram settings
channel3Min = 0.000;
channel3Max = 1.000;

% Create mask based on chosen histogram thresholds
sliderBW = (I(:,:,1) >= channel1Min ) & (I(:,:,1) <= channel1Max) & ...
    (I(:,:,2) >= channel2Min ) & (I(:,:,2) <= channel2Max) & ...
    (I(:,:,3) >= channel3Min ) & (I(:,:,3) <= channel3Max);
BW = sliderBW;

% Initialize output masked image based on input image.
maskedRGBImage = RGB;

% Set background pixels where BW is false to zero.
maskedRGBImage(repmat(~BW,[1 1 3])) = 0;

end

contdir = dir('Control_*');

for i = 1:length(contdir)
    RGB =     % Control_* .png file
    [BW Control_*, maskedControl_*Image] = GlassBrainMask(RGB)
end

Answer 1

To read in the respective files the .name property/member of the object returned by the dir() function can be used in conjunction with the imread() function. To store the outputs of the GlassBrainMask() function a struct() is used.

Files = dir('Control_*');
Results_Structure = struct('BW',[],'maskedRGBImage',[]);

for i = 1:length(Files)
    RGB = imread(Files(i).name);
    [Output_BW, Output_maskedRGBImage] = GlassBrainMask(RGB);
    Results_Structure(i).BW = Output_BW;
    Results_Structure(i).maskedRGBImage = Output_maskedRGBImage; 
end

%Showing the first result%
Image_Number = 1;
subplot(1,2,1); imshow(Results_Structure(Image_Number).BW);
subplot(1,2,2); imshow(Results_Structure(Image_Number).maskedRGBImage);