Creating a 3D-array out of a 2D-array

I have a large 2D-array (31100 x 4) built up like this:

Intensity | X | Y | Z

out of this array I would like to create a 3D-array to visualize it as a 3D-image.

I would somehow have to transform the 2D into a 3D-array. Since there will be plenty of points where there is no intensity value available all of these points should be zero values.

Side information:

min(x) = -152.0120; max(x) = 161.4350; min(y) = -256.2560; max (y) = -52.3801; min(z) = -428.5920; max (z) = -152.4210;

Because of the larger number of decimal places I might have to round up. Yet, this would possibly lead to several intensities being assigned to the same coordinate combination. Logically, I would have to add up the intensities in these cases.

This makes everything really complicated.

I would be happy if someone could teach me how to transform a 2D into a 3D array with zero-values for spots without intensity values.

Thanks for reading.

Answer 1

[Raghava S N]

Hi,

To create the 3D array that displays the accumulated intensity at particular co-ordinates, you can create an empty 3D array (filled with zeros), and then loop through the "Intensity" column and add each intensity to its respective co-ordinate. This way, if there are duplicate co-ordinates generated due to rounding, the intensities add up, and empty co-ordinates will have zero intensity.

Here is some sample code to get you started-

% Sample data (replace this with your actual data)
data = rand(31100, 4); % Replace with your actual 2D array

Extract the data -

% Extract columns
intensity = data(:, 1);
X = data(:, 2);
Y = data(:, 3);
Z = data(:, 4);

Define the grid ranges and size -

% Define grid ranges
x_min = floor(min(X));
x_max = ceil(max(X));
y_min = floor(min(Y));
y_max = ceil(max(Y));
z_min = floor(min(Z));
z_max = ceil(max(Z));

% Define the size of the 3D array
x_size = round((x_max - x_min)) + 1;
y_size = round((y_max - y_min)) + 1;
z_size = round((z_max - z_min)) + 1;
% Initialize the 3D array
volume = zeros(x_size, y_size, z_size);

Map the Intensities -

% Map intensities to the 3D grid
for i = 1:length(intensity)
    % Calculate grid indices
    x_idx = round((X(i) - x_min)) + 1;
    y_idx = round((Y(i) - y_min)) + 1;
    z_idx = round((Z(i) - z_min)) + 1;
    
    % Accumulate intensity values
    volume(x_idx, y_idx, z_idx) = volume(x_idx, y_idx, z_idx) + intensity(i);
end

To plot the 3D grid, "volume", you can refer to this link - https://www.mathworks.com/matlabcentral/answers/1682834-how-can-i-create-a-3d-intensity-map-or-3d-scatter-plot-where-colour-represents-intensity.

Hope this helps!