Using same thresholding in different images to create binary

Hello all,

I am on the process to analyze RGB pictures of grass cover. We grew the grass homogeneusly before applying some treatments. I used the color thresholding app to create threshold for the baseline (homogeneous cover) filtering out small black spaces between leaves and consider all the rest as green. From this I extracted this code:

function [BW,maskedRGBImage] = createMask(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 17-Mar-2023

%------------------------------------------------------

% Convert RGB image to chosen color space

I = RGB;

% Define thresholds for channel 1 based on histogram settings

channel1Min = 35.000;

channel1Max = 109.000;

% Define thresholds for channel 2 based on histogram settings

channel2Min = 50.000;

channel2Max = 149.000;

% Define thresholds for channel 3 based on histogram settings

channel3Min = 23.000;

channel3Max = 131.000;

% 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

Now I want to use those treshold to identify green area in the treatments. Some grass is alive and green some other dead and brown. How can I apply this threshold to other images to have binary of them all so I can transform them in a matrix for further analysis? Is there any color detection app or code I can use?

Thank you all in advance for any suggestion.

Cheers

Answer 1

[Ranjeet]

Hi Enrico,

Since, you already have exported the createMask function by thresholding a baseline image having grass cover, you can use the function with other RGB images as the output of the function is a binary (BW) along with RGB (maskedRGBImage) image.

Here is a mask function that I exported by using some example images with grass cover and tuned to filter green patches, you may use this or try experimenting with the Color Thresholder App.

function [BW,maskedRGBImage] = createMask(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 11-Apr-2023
%------------------------------------------------------


% Convert RGB image to chosen color space
I = RGB;

% Define thresholds for channel 1 based on histogram settings
channel1Min = 38.000;
channel1Max = 187.000;

% Define thresholds for channel 2 based on histogram settings
channel2Min = 82.000;
channel2Max = 255.000;

% Define thresholds for channel 3 based on histogram settings
channel3Min = 0.000;
channel3Max = 188.000;

% 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