how to save my 3d matrix in X,Y,Z coordinates

I have 134* 2d matrix (86*86 each) and they make 86*86*134 matrix.

I need to generate a point cloud of this matrix and that is why I must save the Matrix in xyz coordinates.

how can I save the matrix (I) in xyz table

my matrix (I) was generated by the following code

clear all
close all
names=dir('inter the name of your file\*.tiff');
for iii=1:size(names,1) 
       
I(:,:,iii)=imread(strcat('inter the name of your file\',names(iii).name));
  
for j=1:size(names,1)
   
Img_3D=surface('XData',[0 355;0 355],'YData',[0 0;355 355],'ZData',[29.85*j 29.85*j;29.85*j 29.85*j], 'CData' ,flipdim(im2double(I(:,:,iii)),1),'FaceColor','texturemap','EdgeColor','none');
colormap(gray) 
xlabel('x')
ylabel('y')
zlabel('z µm')
end
end

Answer 1

[arushi]

Hi Mohannad,

I understand that you want to convert a 3d matrix into XYZ coordinates.

To save the matrix `I` in XYZ coordinates, you can use the `writematrix` function in MATLAB. Here is how you can save the matrix in an XYZ table format:

% Assuming I is your 3D matrix of size 86x86x134
% Reshape the matrix to a 2D matrix of size 7396x134
I_reshaped = reshape(I, [], size(I, 3));

% Generate XYZ coordinates
[X, Y, Z] = meshgrid(1:size(I, 1), 1:size(I, 2), 1:size(I, 3));

% Reshape the coordinates to a 2D matrix of size 7396x134
X_reshaped = reshape(X, [], size(I, 3));
Y_reshaped = reshape(Y, [], size(I, 3));
Z_reshaped = reshape(Z, [], size(I, 3));

% Combine the coordinates and intensity values
xyz_data = [X_reshaped(:), Y_reshaped(:), Z_reshaped(:), I_reshaped(:)];

% Save the data as an XYZ table
% Combine the coordinates and data into a matrix
xyz_data = [X_reshaped, Y_reshaped, Z_reshaped, data_reshaped];

% Save the data as a space-separated text file
dlmwrite('data.txt', xyz_data, 'delimiter', ' '); 

In this code, the `I` matrix is reshaped into a 2D matrix, and XYZ coordinates are generated using `meshgrid`. Then, the XYZ coordinates and intensity values are combined into a single matrix `xyz_data`. Finally, the `writematrix` function is used to save the data as an XYZ table, where each row represents a point with its XYZ coordinates and intensity value.

You can adjust the file name and delimiter (`' '`) according to your requirements. Optionally, you can specify column headers in the XYZ table by providing the `VariableNames` argument in the `writematrix` function.

Please refer to the following MATLAB documentation to know more about the ‘meshgrid,’ ‘dlmwrite’ and ‘reshape’ functions:

https://in.mathworks.com/help/matlab/ref/meshgrid.html

https://in.mathworks.com/help/matlab/ref/dlmwrite.html

https://in.mathworks.com/help/matlab/ref/reshape.html

Hope this helps.