using threshold on 3D images to creat mask for training Unet
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I am using this code for 128x128x128 3D mirco CT image
% Open input and output files
fid3DOCT = fopen('SampleA_128x3_#1.raw','r');
fid3DOCTout = fopen('SampleA_128x3_#1_segmented.raw','w');
% Define image dimensions
nx = 128;
ny = 128;
nz = 128;
% Read input image
A = fread(fid3DOCT,nx*ny*nz, 'uint8');
A = uint8(reshape(A,nx,ny,nz));
%Define thresholds for segmentation
threshold1 = 48; % Threshold for class 1
threshold2 = 58; % Threshold for class 2
% You can adjust these thresholds as needed
% Apply segmentation
outputImage = zeros(size(A)); % Initialize segmented image
outputImage(A <= threshold1) = 1; % Class 1
outputImage(A > threshold1 & A <= threshold2) = 2; % Class 2
outputImage(A > threshold2) = 3; % Class 3
% Write segmented image to output file
for i = 1:nz
fwrite(fid3DOCTout, outputImage(:,:,i), 'uint8');
end
but what I get is a black image
I attached the image I am working on it is actually .raw but I saved as .png so I can attach it
Can you please see why the result is black
2 comentarios
Walter Roberson
el 21 de Abr. de 2024
You will get out a file that is uint8 1, 2 or 3. That is going to look black unless you use imagesc()
Respuestas (1)
Thomas
el 21 de Abr. de 2024
Your segmentation routine is correct. However, the issue is that the visualization of a uint8 or double composed of index values of [1, 2, 3] will 'appear' black without scaling. For example using your raster image:
im = imread('SampleA_128x3_#1.png');
%Define thresholds for segmentation
threshold1 = 48; % Threshold for class 1
threshold2 = 58; % Threshold for class 2
% Apply segmentation
outputImage = zeros(size(im)); % Initialize segmented image
outputImage(im <= threshold1) = 1; % Class 1
outputImage(im > threshold1 & im <= threshold2) = 2; % Class 2
outputImage(im > threshold2) = 3; % Class 3
% display thresholded image with scaling
imagesc(outputImage);
![](https://www.mathworks.com/matlabcentral/answers/uploaded_files/1675186/image.png)
2 comentarios
Walter Roberson
el 22 de Abr. de 2024
Change to
outputImage = zeros(size(A), 'uint8'); % Initialize segmented image
and imwrite() outputImage
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