Hello, I am new to MATLAB, i need to process around 2000 CT images which are in .tiff format. The image is of material with defect, i want to find the 3d size of the defect

Hello,

I am new to MATLAB ...

I wish to do following things ....

1. Read around 2000 CT images of a metal specimen.
2. defect in metal are dark in color. I wish to calculate the 3d size of the defect.

Please guide me for the following steps:

1. How to read 2000 CT images ..
2. how to set the threshold intensity for identification of defect in the CT image
3. how to calculate the 3D size of the defect and the CT image in which the 2d area of the inclusion is maximum.

[Rik]

This seems fairly easy to do in a loop. Determining the threshold is anything from trivial to impossible, but once you have it, it is as easy as using the less than operator.

What have you tried?

[Vikas Verma]

hi Rik, thanks for your reply.

i Have tried to read the file using the following codes.

clc;
image_folder = 'E:\spring 8 2021 January\testing '; 
filenames = dir(fullfile(image_folder, '*.tiff'));
total_images=numel(filenames);

for n=1:total_images
    f=fullfile(image_folder, filenames(n).name);
    outimages= imread(f);
    figure(n);
    show(outimages)
end

But the program is not running.

[Vikas Verma]

Error using imread>get_full_filename (line 567)

Cannot open file "E:\spring 8 2021 January\testing \ro0462.tif" for reading. You might not have read permission.

Error in imread (line 377)

fullname = get_full_filename(filename);

[Rik]

This is a bit strange. Apparently dir has reading permissions, but imread does not.

I do notice that the error mentions a file with .tif, while your code should only select files with .tiff (double f).

[Vikas Verma]

i already corrected .tiff to .tif

[Image Analyst]

Try

filenames = dir(fullfile(image_folder, '*.tif*'));

It will handle both .tif and .tiff extensions.

[Vikas Verma]

@Rik can you please tell me any other way to handle this error

[Rik]

This sounds more like a file system error than a coding error. You could try copying the file to the tempdir, but I'm not sure that will actually fix anything.

[Vikas Verma]

This did not work.

I will try to figure out.

BTW, can you please guide me how to calculate the size of the defect

[Rik]

If you're not able to read your files, questions about further processing are moot. You also already received an answer from Image Analyst. Did you read it?

Answer 1

[Image Analyst]

Can you fit the whole 3-D volumetric image into memory? If so use regionprops3 to ask for volume. If not, use regionprops to get the area of each slice and add them together. See my Fle Exchange for an image Segmentation Tutorial:

Image Analyst's File Exchange

[Vikas Verma]

thanks for the reply. I will go through the tutorial.