function [IMGFFT, IMGPR] = computeFourierTransform(I, skipPreprocessing, skipMasking, skipIntensityThresholding, skipBinarization) % computeFourierSpectrum - Computes the 2D Fourier power spectrum % of binarized and enhanced lattice image features, with optional central mask. % % Inputs: % I - Grayscale or RGB image matrix % % Output: % F_mag - 2D Fourier power spectrum (shifted) if ~skipPreprocessing % Preprocessing: Denoise filtered = imgaussfilt(I, 10); IMGPR = I - filtered; % adjust sigma as needed else IMGPR = I; end if ~skipMasking [rows, cols] = size(IMGPR); [X, Y] = meshgrid(1:cols, 1:rows); % Elliptical mask parameters cx = cols / 2; cy = rows / 2; % Shifted coordinates x = X - cx; y = Y - cy; % Ellipse semi-axes rx = 0.4 * cols; ry = 0.2 * rows; % Rotation angle in degrees -> radians theta_deg = 30; % Adjust as needed theta = deg2rad(theta_deg); % Rotated ellipse equation cos_t = cos(theta); sin_t = sin(theta); x_rot = (x * cos_t + y * sin_t); y_rot = (-x * sin_t + y * cos_t); ellipseMask = (x_rot.^2) / rx^2 + (y_rot.^2) / ry^2 <= 1; % Apply cutout mask IMGPR = IMGPR .* ellipseMask; end if ~skipIntensityThresholding % Apply global intensity threshold mask intensity_thresh = 0.20; intensity_mask = IMGPR > intensity_thresh; IMGPR = IMGPR .* intensity_mask; end if ~skipBinarization % Adaptive binarization and cleanup IMGPR = imbinarize(IMGPR, 'adaptive', 'Sensitivity', 0.0); IMGPR = imdilate(IMGPR, strel('disk', 2)); IMGPR = imerode(IMGPR, strel('disk', 1)); IMGPR = imfill(IMGPR, 'holes'); F = fft2(double(IMGPR)); % Compute 2D Fourier Transform IMGFFT = abs(fftshift(F))'; % Shift zero frequency to center else F = fft2(double(IMGPR)); % Compute 2D Fourier Transform IMGFFT = abs(fftshift(F))'; % Shift zero frequency to center end end