cropping a serie of images and save only the cropped part of it

Hi guys, I would be grateful if someone kindly could help me with this.

I have a serie of frames of the same image (.tif). I would like to load all the images (they become matrixes 2000*2000) from the folder and crop all of them with the same pattern (I dont know the coordinates of cropping so I would like to be allowed to choose a rectangular square in one of them and apply it to all). Then I would like to save them in a new folder in the same path.

clc;

clear;

close all;

% cd('C:\Users\...\OT pics')

% Sample

dirName = uigetdir('./', 'Select data folder');

cd(dirName);

for i=484:487

image_{i}=imread(sprintf('SI380820191011130728_%03d.tif',i));

[J,rect]=imcrop(image_{i})

[x,y]=size(image_{i});

X=1:x;

Y=1:y;

[xx,yy]=meshgrid(Y,X);

figure;imshow([J,rect])

colormap (jet)

colorbar

caxis([0 45000]);

axis on

fullFileName = fullfile('C:\Users\..\OT pics\new', [J,rect]);

saveas(mfig,fullFileName);

end

This is the script i have been using but it gives back this error. Anyone helping? Thanks a lot

Error using horzcat

Dimensions of arrays being concatenated are not consistent.

Error in Untitled2 (line 43)

figure;imshow([J,rect])

[darova]

Can you explain what are you trying to do?

imshow([J,rect]) 

[Murstoe]

I would like to show the cropped images. So, that tool only returns me the coordinates, it does not actually croop it right?

[darova]

Use just

imshow(J)

[Murstoe]

thanks a lot. However, now it let me choose a rectangle for every of the 4 pics. is it possible to automatically apply the cropping to all the 4 pictures?

....

image_{i}=imread(sprintf('SI380820191011130728_%03d.tif',i));

J=imcrop(image_{i})

[x,y]=size(image_{i});

X=1:x;

Y=1:y;

[xx,yy]=meshgrid(Y,X);

figure;imshow(J)

...

Answer 1

[darova]

Tri this (not tested)

dirName = uigetdir('./', 'Select data folder');
cd(dirName); 
fname = sprintf('SI380820191011130728_%03d.tif',1)
image_{i} = imread(str);
[J,rect] = imcrop(image_{i})
for i = 2:487
    fname = sprintf('SI380820191011130728_%03d.tif',i)
    image_{i} = imread(str);
    J = imcrop(image_{i},rect)
    [x,y] = size(image_{i});
    X=1:x; 
    Y=1:y;
    [xx,yy]=meshgrid(Y,X);   
    figure
    imshow(J) 
    colormap (jet) 
    colorbar 
    caxis([0 45000]);
    axis on 
    fullFileName = fullfile('C:\Users\..\OT pics\new', [str num2str(i)]);
    imwrite(J,fullFileName)
end 

[Murstoe]

thank you very much.

it still gives back an error in this line: "Unrecognized function or variable 'str' ". what do you mean by str?

image_{i} = imread(str)

[darova]

I believe i made a mistake.(never happened before)

[darova]

please change according to this