%% ===== BEC-Droplets-Stripes Settings =====

% Specify data location to run analysis on
dataSources = {
    struct('sequence', 'StructuralPhaseTransition', ...
           'date', '2025/08/16', ...
           'runs', [8]) % specify run numbers as a string in "" or just as a numeric value
};

options = struct();

% File / paths
options.baseDataFolder  = '//DyLabNAS/Data';
options.measurementName = 'DropletsToStripes';
scriptFullPath          = mfilename('fullpath');
options.saveDirectory   = fileparts(scriptFullPath);

% Camera / imaging
options.cam            = 5;
options.angle          = 0;
options.center         = [1420, 2050];
options.span           = [200, 200];
options.fraction       = [0.1, 0.1];
options.pixel_size     = 5.86e-6;       % in meters
options.magnification  = 24.6;
options.removeFringes  = false;
options.ImagingMode    = 'HighIntensity';
options.PulseDuration  = 5e-6;          % in s

% Fourier analysis settings
options.theta_min         = deg2rad(0);
options.theta_max         = deg2rad(180);
options.N_radial_bins     = 500;
options.Radial_Sigma      = 2;
options.Radial_WindowSize = 5;          % odd number

options.k_min              = 1.2771;    % μm⁻¹
options.k_max              = 2.5541;    % μm⁻¹
options.N_angular_bins     = 180;
options.Angular_Threshold  = 75;
options.Angular_Sigma      = 2;
options.Angular_WindowSize = 5;
options.zoom_size          = 50;

% Scan parameter
options.scan_parameter = 'ps_rot_mag_fin_pol_angle';

switch options.measurementName
    case 'BECToDroplets'
        options.scan_reference_values = [2.40, 2.39, 2.38, 2.37, 2.35, 2.34, 2.32, 2.30, 2.28, 2.26, 2.24, 2.22, 2.2, 2.15, 2.10, 2.05, 2, 1.95, 1.90, 1.85, 1.8];
        options.titleString           = 'BEC to Droplets';
    case 'BECToStripes'
        options.scan_reference_values = [2.45, 2.44, 2.43, 2.42, 2.4, 2.39, 2.38, 2.37, 2.36, 2.35, 2.34, 2.32, 2.3, 2.28, 2.25, 2.2, 2.15, 2.10, 2.0, 1.90, 1.8];
        options.titleString           = 'BEC to Stripes';
    case 'DropletsToStripes'
        options.scan_reference_values = [0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40];
        options.titleString           = 'Droplets to Stripes';
    case 'StripesToDroplets'
        options.scan_reference_values = fliplr([0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40]);
        options.titleString           = 'Stripes to Droplets';
end

% Flags
options.skipNormalization         = false;
options.skipUnshuffling           = false;
options.skipPreprocessing         = true;
options.skipMasking               = true;
options.skipIntensityThresholding = true;
options.skipBinarization          = true;
options.skipSaveFigures           = false;
options.skipLivePlot              = false;
options.showProgressBar           = true;

% Extras
options.font = 'Bahnschrift';

%% ===== Run Batch Analysis =====
results_all = Helper.batchAnalyze(dataSources, options);