206 lines
8.6 KiB
Matlab
206 lines
8.6 KiB
Matlab
%% ===== BEC-Stripes Settings =====
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% Specify data location to run analysis on
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dataSources = {
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struct('sequence', 'StructuralPhaseTransition', ...
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'date', '2025/08/15', ...
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'runs', [3]) % specify run numbers as a string in "" or just as a numeric value
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};
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options = struct();
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% File paths
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options.baseDataFolder = '//DyLabNAS/Data';
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options.FullODImagesFolder = 'E:/Data - Experiment/FullODImages/202508';
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options.measurementName = 'BECToStripes';
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scriptFullPath = mfilename('fullpath');
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options.saveDirectory = fileparts(scriptFullPath);
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% Camera / imaging settings
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options.cam = 4; % 1 - ODT_1_Axis_Camera; 2 - ODT_2_Axis_Camera; 3 - Horizontal_Axis_Camera;, 4 - Vertical_Axis_Camera;
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options.angle = 0; % angle by which image will be rotated
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options.center = [1420, 2050];
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options.span = [200, 200];
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options.fraction = [0.1, 0.1];
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options.pixel_size = 5.86e-6; % in meters
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options.magnification = 24.6;
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options.ImagingMode = 'HighIntensity';
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options.PulseDuration = 5e-6; % in s
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% Fourier analysis settings
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options.theta_min = deg2rad(0);
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options.theta_max = deg2rad(180);
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options.N_radial_bins = 500;
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options.Radial_Sigma = 2;
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options.Radial_WindowSize = 5; % odd number
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options.k_min = 1.2771; % μm⁻¹
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options.k_max = 2.5541; % μm⁻¹
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options.N_angular_bins = 180;
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options.Angular_Threshold = 75;
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options.Angular_Sigma = 2;
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options.Angular_WindowSize = 5;
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options.zoom_size = 50;
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% Flags
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options.skipUnshuffling = false;
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options.skipNormalization = false;
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options.skipFringeRemoval = true;
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options.skipPreprocessing = true;
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options.skipMasking = true;
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options.skipIntensityThresholding = true;
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options.skipBinarization = true;
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options.skipFullODImagesFolderUse = false;
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options.skipSaveData = false;
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options.skipSaveFigures = true;
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options.skipSaveProcessedOD = true;
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options.skipLivePlot = false;
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options.showProgressBar = true;
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% Extras
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options.font = 'Bahnschrift';
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switch options.measurementName
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case 'BECToDroplets'
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options.scan_parameter = 'rot_mag_field';
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options.flipSortOrder = true;
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options.scanParameterUnits = 'gauss';
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options.titleString = 'BEC to Droplets';
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case 'BECToStripes'
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options.scan_parameter = 'rot_mag_field';
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options.flipSortOrder = true;
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options.scanParameterUnits = 'gauss';
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options.titleString = 'BEC to Stripes';
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case 'DropletsToStripes'
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options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
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options.flipSortOrder = false;
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options.scanParameterUnits = 'degrees';
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options.titleString = 'Droplets to Stripes';
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case 'StripesToDroplets'
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options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
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options.flipSortOrder = false;
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options.scanParameterUnits = 'degrees';
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options.titleString = 'Stripes to Droplets';
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end
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%% ===== Collect Images and Launch Viewer =====
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[options.selectedPath, options.folderPath] = Helper.selectDataSourcePath(dataSources, options);
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[od_imgs, scan_parameter_values, scan_reference_values, file_list] = Helper.collectODImages(options);
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%% Conduct spectral analysis
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spectral_analysis_results = Analyzer.extractFullRadialSpectralDistribution(od_imgs, options);
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%% ------------------ 1. Plot of all Radial Spectral Distribution Curves ------------------
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Plotter.plotSpectralCurves( ...
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spectral_analysis_results.S_k_all, ...
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spectral_analysis_results.k_rho_vals, ...
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scan_reference_values, ... % correct scan params
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'Title', options.titleString, ...
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'XLabel', 'k_\rho', ...
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'YLabel', 'S(k_\rho)', ...
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'YScale', 'log', ...
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'XLim', [min(spectral_analysis_results.k_rho_vals), max(spectral_analysis_results.k_rho_vals)], ...
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'HighlightEvery', 10, ... % highlight every 10th repetition
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'FontName', options.font, ...
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'FigNum', 1, ...
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'TileTitlePrefix', 'B', ... % user-defined tile prefix
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'TileTitleSuffix', 'G', ... % user-defined suffix (e.g., degrees symbol)
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SpectralCurves.fig', ...
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'SaveDirectory', options.saveDirectory);
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%% ------------------ 2. Fit truncated Radial Spectral Distribution Curves ------------------
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[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToRadialSpectralDistribution(...
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spectral_analysis_results.S_k_all, ... % radial spectral curves
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spectral_analysis_results.k_rho_vals, ... % corresponding k_rho values
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'KRhoRange', [0, 3], ... % truncate curves to 0 <= k_rho <= 3
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'AmplitudeRange', [0, 0.5], ... % truncate curves to y >= 0 (all amplitudes)
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'ResidualThreshold', 0.15, ... % maximum allowed residual
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'PositionThreshold', 0.5, ... % minimum separation between peaks
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'AmplitudeThreshold', 0.015); % minimum secondary peak fraction
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%% ------------------ Plot Fits on Raw ------------------
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options.skipLivePlot = true;
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options.skipSaveFigures = false;
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Plotter.plotTwoModeGaussianFitsOnRaw(fitResults, rawCurves, 4, 6, ...
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'SkipLivePlot', options.skipLivePlot, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveDirectory', options.saveDirectory);
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%% ------------------ Interactive Fit Viewer ------------------
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Analyzer.runInteractiveRSDTwoGaussianFitGUI(spectral_analysis_results);
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%% ------------------ 3. Plot fit parameters - amplitude ------------------
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Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', 'Secondary peak amplitude', ...
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'FontName', options.font, ...
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'FontSize', 16, ...
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'FigNum', 4, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ...
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'SaveDirectory', options.saveDirectory, ...
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'PlotType', 'histogram', ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
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'YLim', [0, 0.025]);
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%% ------------------ 4. Plot fit parameters - position ------------------
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Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', 'Secondary peak position (\theta, rad)', ...
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'FontName', options.font, ...
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'FontSize', 16, ...
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'FigNum', 5, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakPositionPDF.fig', ...
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'SaveDirectory', options.saveDirectory, ...
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'PlotType', 'histogram', ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
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'YLim', [0, 2]);
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%% ------------------ 5. Plot fit parameters - width ------------------
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Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', 'Secondary peak width (\sigma, rad)', ...
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'FontName', options.font, ...
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'FontSize', 16, ...
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'FigNum', 6, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakWidthPDF.fig', ...
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'SaveDirectory', options.saveDirectory, ...
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'PlotType', 'histogram', ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'XLim', [min(scan_reference_values), max(scan_reference_values)], ...
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'YLim', [0, 1.5]);
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%% ------------------ 6. Plot secondary Gaussian range ------------------
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Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', '\mu_2 \pm \sigma_2 (rad)', ...
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'FontName', options.font, ...
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'FontSize', 16, ...
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'FigNum', 8, ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'OverlayMeanSEM', true, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryGaussianRange.fig', ...
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'SaveDirectory', options.saveDirectory);
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