%% Parameters

% === Define folders and settings ===

% === Define folders and settings ===

baseFolder = '//DyLabNAS/Data/TwoDGas/2025/04/';

dates = ["01", "02"];  % Example: three folders
runs = {
    ["0059", "0060", "0061"],                        
    ["0007", "0008", "0009", "0010", "0011"]         
};

options.scan_parameter = 'rot_mag_fin_pol_angle';
options.scan_groups    = 0:10:50;
options.cam            = 5;

% Image cropping and alignment
options.angle          = 0;
options.center         = [1285, 2100];
options.span           = [200, 200];
options.fraction       = [0.1, 0.1];

% Imaging and calibration parameters
options.pixel_size     = 5.86e-6;         % in meters
options.magnification  = 23.94;
options.removeFringes  = false;
options.ImagingMode    = 'HighIntensity';
options.PulseDuration  = 5e-6;

% Fourier analysis: Radial
options.theta_min         = deg2rad(0);
options.theta_max         = deg2rad(180);
options.N_radial_bins     = 500;
options.Radial_Sigma      = 2;
options.Radial_WindowSize = 5;  % Must be odd

% Fourier analysis: Angular
options.r_min              = 10;
options.r_max              = 20;
options.k_min              = 1.2;    % in μm⁻¹
options.k_max              = 2.2;    % in μm⁻¹
options.N_angular_bins     = 180;
options.Angular_Threshold  = 75;
options.Angular_Sigma      = 2;
options.Angular_WindowSize = 5;

% Optional visualization / zooming
options.zoom_size = 50;

% Optional flags or settings struct
options.skipUnshuffling = false;
options.skipPreprocessing = true;
options.skipMasking = true;
options.skipIntensityThresholding = true;
options.skipBinarization = true;

% === Loop through folders and collect results ===

results_all = [];

assert(length(dates) == length(runs), ...
    'Each entry in `dates` must correspond to a cell in `runs`.');

for i = 1:length(dates)
    currentDate = dates(i);
    currentRuns = runs{i};
    
    for j = 1:length(currentRuns)
        runID = currentRuns(j);
        folderPath = fullfile(baseFolder, currentDate, runID);
        
        if ~endsWith(folderPath, filesep)
            options.folderPath = [char(folderPath) filesep];
        else
            options.folderPath = char(folderPath);
        end 
        
        try
            % Unpack options struct into name-value pairs
            args = [fieldnames(options), struct2cell(options)]';
            args = args(:)';
            
            results = analyzeFolder(args{:});
            results_all = [results_all; results];
        catch ME
            warning("Error processing %s/%s: %s", currentDate, runID, ME.message);
        end
    end
end


%%  Plotting heatmap of mean_max_g2_values

N_x = length(options.scan_groups);
N_y = length(results_all) / N_x;

% Preallocate
g2_matrix = zeros(N_y, N_x);
angle_matrix = zeros(N_y, N_x);

for i = 1:length(results_all)
    row = ceil(i / N_x); % outer parameter (e.g., date)
    col = mod(i-1, N_x) + 1; % inner scan parameter
    g2_matrix(row, col) = results_all(i).mean_max_g2_values(col);
    angle_matrix(row, col) = results_all(i).mean_max_g2_angle(col);
end

% Plot heatmap
figure;
imagesc(options.scan_groups, 1:N_y, g2_matrix);
xlabel('Scan Parameter (e.g. Angle)');
ylabel('Scan Set Index');
title('Mean g_2 Value Heatmap');
colorbar;