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

% Specify data location to run analysis on
dataSources = {
    struct('sequence', 'StructuralPhaseTransition', ...
           'date', '2025/08/15', ...
           'runs', [3]) % specify run numbers as a string in "" or just as a numeric value
};

options = struct();

% File paths
options.baseDataFolder     = '//DyLabNAS/Data';
options.FullODImagesFolder = 'E:/Data - Experiment/FullODImages/202508';
options.measurementName    = 'BECToStripes';
scriptFullPath             = mfilename('fullpath');
options.saveDirectory      = fileparts(scriptFullPath);

% Camera / imaging settings
options.cam                = 4;             % 1 - ODT_1_Axis_Camera; 2 - ODT_2_Axis_Camera; 3 - Horizontal_Axis_Camera;, 4 - Vertical_Axis_Camera;
options.angle              = 0;             % angle by which image will be rotated
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.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;

% Flags
options.skipUnshuffling           = false;
options.skipNormalization         = false;

options.skipFringeRemoval         = true;
options.skipPreprocessing         = true;
options.skipMasking               = true;
options.skipIntensityThresholding = true;
options.skipBinarization          = true;

options.skipFullODImagesFolderUse = false;
options.skipSaveData              = false;
options.skipSaveFigures           = true;
options.skipSaveProcessedOD       = true;
options.skipLivePlot              = false;
options.showProgressBar           = true;

% Extras
options.font = 'Bahnschrift';
switch options.measurementName
    case 'BECToDroplets'
        options.scan_parameter        = 'rot_mag_field';
        options.flipSortOrder         = true;
        options.scanParameterUnits    = 'gauss';
        options.titleString           = 'BEC to Droplets';
    case 'BECToStripes'
        options.scan_parameter        = 'rot_mag_field';
        options.flipSortOrder         = true;
        options.scanParameterUnits    = 'gauss';
        options.titleString           = 'BEC to Stripes';
    case 'DropletsToStripes'
        options.scan_parameter        = 'ps_rot_mag_fin_pol_angle';
        options.flipSortOrder         = false;
        options.scanParameterUnits    = 'degrees';
        options.titleString           = 'Droplets to Stripes';
    case 'StripesToDroplets'
        options.scan_parameter        = 'ps_rot_mag_fin_pol_angle';
        options.flipSortOrder         = false;
        options.scanParameterUnits    = 'degrees';
        options.titleString           = 'Stripes to Droplets';
end

%% ===== Collect Images and Launch Viewer =====

[options.selectedPath, options.folderPath]                         = Helper.selectDataSourcePath(dataSources, options);

[od_imgs, scan_parameter_values, scan_reference_values, file_list] = Helper.collectODImages(options);

%% Conduct spectral analysis
spectral_analysis_results                                          = Analyzer.extractFullRadialSpectralDistribution(od_imgs, options);

%% ------------------ 1. Plot of all Radial Spectral Distribution Curves ------------------
Plotter.plotSpectralCurves( ...
    spectral_analysis_results.S_k_all, ...
    spectral_analysis_results.k_rho_vals, ...
    scan_reference_values, ...                   % correct scan params
    'Title', options.titleString, ...
    'XLabel', 'k_\rho', ...
    'YLabel', 'S(k_\rho)', ...
    'YScale', 'log', ...
    'XLim', [min(spectral_analysis_results.k_rho_vals), max(spectral_analysis_results.k_rho_vals)], ...
    'HighlightEvery', 10, ...                    % highlight every 10th repetition
    'FontName', options.font, ...
    'FigNum', 1, ...
    'TileTitlePrefix', 'B', ...             % user-defined tile prefix
    'TileTitleSuffix', 'G', ...             % user-defined suffix (e.g., degrees symbol)
    'SkipSaveFigures', options.skipSaveFigures, ...
    'SaveFileName', 'SpectralCurves.fig', ...
    'SaveDirectory', options.saveDirectory);

%% ------------------ 2. Fit truncated Radial Spectral Distribution Curves ------------------
[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToRadialSpectralDistribution(...
    spectral_analysis_results.S_k_all, ...        % radial spectral curves
    spectral_analysis_results.k_rho_vals, ...     % corresponding k_rho values
    'KRhoRange', [0, 3], ...                      % truncate curves to 0 <= k_rho <= 3
    'AmplitudeRange', [0, 0.5], ...               % truncate curves to y >= 0 (all amplitudes)
    'ResidualThreshold', 0.15, ...                % maximum allowed residual
    'PositionThreshold', 0.5, ...                 % minimum separation between peaks
    'AmplitudeThreshold', 0.015);                 % minimum secondary peak fraction

%% ------------------ Interactive Fit Viewer ------------------
Analyzer.runInteractiveRSDTwoGaussianFitGUI(spectral_analysis_results);

%% ------------------ 3. Plot fit parameters - amplitude ------------------
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
    'Title', options.titleString, ...
    'XLabel', 'B (G)', ...
    'YLabel', 'Secondary peak amplitude', ...
    'FontName', options.font, ...
    'FontSize', 16, ...
    'FigNum', 4, ...
    'SkipSaveFigures', options.skipSaveFigures, ...
    'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ...
    'SaveDirectory', options.saveDirectory, ...
    'PlotType', 'histogram', ...
    'NumberOfBins', 20, ...
    'NormalizeHistogram', true, ...
    'Colormap', @Colormaps.coolwarm, ...
    'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
    'YLim', [0, 0.06]);

%% ------------------ 4. Plot fit parameters - position ------------------
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
    'Title', options.titleString, ...
    'XLabel', 'B (G)', ...
    'YLabel', 'Secondary peak position (\theta, rad)', ...
    'FontName', options.font, ...
    'FontSize', 16, ...
    'FigNum', 5, ...
    'SkipSaveFigures', options.skipSaveFigures, ...
    'SaveFileName', 'SecondaryPeakPositionPDF.fig', ...
    'SaveDirectory', options.saveDirectory, ...
    'PlotType', 'histogram', ...
    'NumberOfBins', 20, ...
    'NormalizeHistogram', true, ...
    'Colormap', @Colormaps.coolwarm, ...
    'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
    'YLim', [1, 2]);
%% ------------------ 5. Plot fit parameters - width ------------------
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
    'Title', options.titleString, ...
    'XLabel', 'B (G)', ...
    'YLabel', 'Secondary peak width (\sigma, rad)', ...
    'FontName', options.font, ...
    'FontSize', 16, ...
    'FigNum', 6, ...
    'SkipSaveFigures', options.skipSaveFigures, ...
    'SaveFileName', 'SecondaryPeakWidthPDF.fig', ...
    'SaveDirectory', options.saveDirectory, ...
    'PlotType', 'histogram', ...
    'NumberOfBins', 20, ...
    'NormalizeHistogram', true, ...
    'Colormap', @Colormaps.coolwarm, ...
    'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
    'YLim', [0, 1.5]);

%% ------------------ 6. Plot secondary Gaussian range ------------------
Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ...
    'Title', options.titleString, ...
    'XLabel', 'B (G)', ...
    'YLabel', '\mu_2 \pm \sigma_2 (rad)', ...
    'FontName', options.font, ...
    'FontSize', 16, ...
    'FigNum', 8, ...
    'NumberOfBins', 20, ...
    'NormalizeHistogram', true, ...
    'Colormap', @Colormaps.coolwarm, ...
    'OverlayMeanSEM', true, ...
    'SkipSaveFigures', options.skipSaveFigures, ...
    'SaveFileName', 'SecondaryGaussianRange.fig', ...
    'SaveDirectory', options.saveDirectory);