Added routines to analyze BEC to Droplets, BEC to Stripes.
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%% ===== BEC-Droplets 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', '2025/08/13', ...
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'runs', [62]) % 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 = 'BECToDroplets';
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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.extractFullAngularSpectralDistribution(od_imgs, options);
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%% ------------------ 1. Plot of all Angular Spectral Distribution Curves ------------------
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Plotter.plotSpectralCurves( ...
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spectral_analysis_results.S_theta_norm_all, ...
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spectral_analysis_results.theta_vals/pi, ... % correct θ values
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scan_reference_values, ... % correct scan params
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'Title', options.titleString, ...
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'XLabel', '\theta / \pi', ...
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'YLabel', 'S(\theta)', ...
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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', '\alpha', ... % user-defined tile prefix
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'TileTitleSuffix', '^\circ', ... % 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. Plot of all Angular Spectral Distribution Curves shifted ------------------
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% --- Recenter curves first ---
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results = Analyzer.recenterSpectralCurves(spectral_analysis_results.S_theta_norm_all, ...
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spectral_analysis_results.theta_vals/pi, ...
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scan_reference_values, ...
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'SearchRange', [0 90]); % degrees
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% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
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thetaMin = 0; % in units of pi (since you divided by pi)
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thetaMax = 1; % corresponds to pi/2
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mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
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results.x_values = results.x_values(mask);
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% Apply the same mask to each curve set
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for i = 1:numel(results.curves)
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results.curves{i} = results.curves{i}(:, mask);
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results.curves_mean{i} = results.curves_mean{i}(mask);
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results.curves_error{i}= results.curves_error{i}(mask);
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end
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Plotter.plotSpectralCurvesRecentered( ...
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results, ...
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scan_reference_values, ... % correct scan params
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'Title', options.titleString, ...
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'XLabel', '\theta / \pi', ...
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'YLabel', 'S(\theta)', ...
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'HighlightEvery', 10, ... % highlight every 10th repetition
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'FontName', options.font, ...
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'FigNum', 2, ...
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'TileTitlePrefix', '\alpha', ... % user-defined tile prefix
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'TileTitleSuffix', '^\circ', ... % 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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%% ------------------ 3. Plot cumulants from shifted Angular Spectral Distribution Curves ------------------
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Plotter.plotSpectralDistributionCumulants(results, ...
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'Title', options.titleString, ...
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'XLabel', '\alpha (degrees)', ...
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'FontName', options.font, ...
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'FontSize', 14, ...
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'FigNum', 3, ...
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'SkipSaveFigures', false, ...
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'SaveFileName', 'SpectralCumulants.fig', ...
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'SaveDirectory', options.saveDirectory);
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%% ------------------ 4. Fit shifted Angular Spectral Distribution Curves ------------------
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[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
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spectral_analysis_results.S_theta_norm_all, ...
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spectral_analysis_results.theta_vals, ...
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'MaxTheta', pi/2, ...
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'ResidualThreshold', 0.15, ...
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'PositionThreshold', pi/15, ...
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'AmplitudeThreshold', 0.15);
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%{
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% --- Function call ---
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plotTwoGaussianFitsOnRaw(fitResults, rawCurves, 8, 12); % 8×12 subplots per page
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% --- Function definition ---
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function plotTwoGaussianFitsOnRaw(fitResults, rawCurves, nRows, nCols)
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% plotTwoGaussianFitsOnRaw - Plots raw curves and overlays valid two-Gaussian fits.
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%
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% Inputs:
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% fitResults - struct array from fitTwoGaussianCurvesToAngularSpectralDistribution (may contain fits)
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% rawCurves - struct array with fields:
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% .x - raw curve
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% .theta - corresponding theta values
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% nRows - number of subplot rows per page (default: 4)
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% nCols - number of subplot columns per page (default: 6)
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if nargin < 3, nRows = 4; end
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if nargin < 4, nCols = 6; end
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Ncurves = numel(rawCurves);
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plotsPerPage = nRows * nCols;
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pageNum = 1;
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for k = 1:Ncurves
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% --- New figure/page if needed ---
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if mod(k-1, plotsPerPage) == 0
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figure('Name', sprintf('Curves Page %d', pageNum), ...
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'NumberTitle', 'off', 'Color', 'w');
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pageNum = pageNum + 1;
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end
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% --- Select subplot ---
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subplot(nRows, nCols, mod(k-1, plotsPerPage)+1);
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hold on; grid on; box on;
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% --- Plot raw curve ---
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xRaw = rawCurves(k).x;
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thetaRaw = rawCurves(k).theta;
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if ~isempty(xRaw) && ~isempty(thetaRaw) && all(isfinite(xRaw))
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plot(thetaRaw, xRaw, 'k.-', 'LineWidth', 1, 'DisplayName', 'Raw data');
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end
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% --- Overlay fit if valid ---
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if k <= numel(fitResults)
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fit = fitResults(k);
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if isfield(fit, 'isValid') && fit.isValid ...
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&& ~isempty(fit.yFit) && ~isempty(fit.thetaFine)
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plot(fit.thetaFine, fit.yFit, 'r-', 'LineWidth', 1.2, 'DisplayName', 'Two-Gaussian fit');
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end
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end
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% --- Formatting ---
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xlabel('\theta (rad)');
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ylabel('Normalized amplitude');
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title(sprintf('Curve %d', k), 'FontSize', 10);
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% --- Legend once per page ---
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if mod(k-1, plotsPerPage) == 0
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legend('Location', 'best', 'FontSize', 8);
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end
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hold off;
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end
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end
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%}
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%% ------------------ 5. 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', '\alpha (degrees)', ...
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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, 1.6]);
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%% ------------------ 6. 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', '\alpha (degrees)', ...
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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, 1.6]);
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%% ------------------ 7. 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', '\alpha (degrees)', ...
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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, 1.6]);
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%% ------------------ 8. Plot fit parameters of mean shifted Angular Spectral Distribution Curves ------------------
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% --- Recenter curves first ---
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results = Analyzer.recenterSpectralCurves(spectral_analysis_results.S_theta_norm_all, ...
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spectral_analysis_results.theta_vals/pi, ...
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scan_reference_values, ...
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'SearchRange', [0 90]); % degrees
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% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
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thetaMin = 0; % in units of pi (since you divided by pi)
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thetaMax = 1; % corresponds to pi/2
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mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
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results.x_values = results.x_values(mask);
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% Apply the same mask to each curve set
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for i = 1:numel(results.curves)
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results.curves_mean{i} = results.curves_mean{i}(mask);
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end
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% --- Fit two-Gaussian model to mean curves ---
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[fitResultsMean, ~] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
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results.curves_mean, ...
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results.x_values*pi, ...
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'MaxTheta', pi/2, ...
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'ResidualThreshold', 0.15, ...
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'PositionThreshold', pi/15, ...
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'AmplitudeThreshold', 0.15, ...
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'RecenterCurves', false);
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% --- Prepare parameter values ---
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N_params = numel(fitResultsMean);
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amp2_vals = nan(1, N_params);
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mu2_vals = nan(1, N_params);
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sigma2_vals = nan(1, N_params);
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for i = 1:N_params
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pFit = fitResultsMean(i).pFit;
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if all(~isnan(pFit))
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% Successful fit → use fitted values
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amp2_vals(i) = pFit(4);
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mu2_vals(i) = pFit(5);
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sigma2_vals(i) = pFit(6);
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else
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% Fit failed → leave as NaN (skipped automatically)
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continue;
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end
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end
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% --- Plot peak amplitude mean with SEM ---
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Plotter.plotMeanWithSE(scan_reference_values, amp2_vals, ...
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'Title', options.titleString, ...
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'XLabel', '\alpha (degrees)', ...
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'YLabel', 'Secondary peak amplitude', ...
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'FigNum', 7, ...
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'FontName', options.font, ...
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'FontSize', 16, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakAmplitudeMeanWithSEM.fig', ...
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'SaveDirectory', options.saveDirectory);
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% --- Plot peak position mean with SEM ---
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Plotter.plotMeanWithSE(scan_reference_values, mu2_vals, ...
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'Title', options.titleString, ...
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'XLabel', '\alpha (degrees)', ...
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'YLabel', 'Secondary peak position (\theta, rad)', ...
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'FigNum', 8, ...
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'FontName', options.font, ...
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||||||
|
'FontSize', 16, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SecondaryPeakPositionMeanWithSEM.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
% --- Plot peak width mean with SEM ---
|
||||||
|
Plotter.plotMeanWithSE(scan_reference_values, sigma2_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Secondary peak width (\sigma, rad)', ...
|
||||||
|
'FigNum', 9, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 16, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
%% Inspect individual realizations of a single parameter
|
||||||
|
|
||||||
|
% --- Recenter curves first ---
|
||||||
|
results = Analyzer.recenterSpectralCurves( ...
|
||||||
|
spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals/pi, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'SearchRange', [0 90]); % degrees
|
||||||
|
|
||||||
|
% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
|
||||||
|
thetaMin = 0; % in units of pi (since you divided by pi)
|
||||||
|
thetaMax = 1; % corresponds to pi/2
|
||||||
|
|
||||||
|
mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
|
||||||
|
results.x_values = results.x_values(mask);
|
||||||
|
|
||||||
|
% --- Apply the same mask to each curve set (1x10 cell, each 60x180) ---
|
||||||
|
for i = 1:numel(results.curves)
|
||||||
|
results.curves{i} = results.curves{i}(:, mask);
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Convert selected curve set (e.g., 5th) into 1x60 cell array of 1xN row vectors ---
|
||||||
|
paramIdx = 1; % <-- choose which scan point or curve set to analyze
|
||||||
|
curves_matrix = results.curves{paramIdx}; % 60xN numeric
|
||||||
|
curves_cell = num2cell(curves_matrix, 2); % 1x60 cell array
|
||||||
|
curves_cell = cellfun(@(x) x(:).', curves_cell, 'UniformOutput', false); % ensure 1xN row vectors
|
||||||
|
|
||||||
|
% --- Fit two-Gaussian model to these curves ---
|
||||||
|
[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
|
||||||
|
curves_cell, ...
|
||||||
|
results.x_values*pi, ...
|
||||||
|
'MaxTheta', pi/2, ...
|
||||||
|
'ResidualThreshold', 0.15, ...
|
||||||
|
'PositionThreshold', pi/15, ...
|
||||||
|
'AmplitudeThreshold', 0.15, ...
|
||||||
|
'RecenterCurves', false);
|
||||||
181
Data-Analyzer/+Scripts/BECToDroplets/runCorrelationAnalysis.m
Normal file
181
Data-Analyzer/+Scripts/BECToDroplets/runCorrelationAnalysis.m
Normal file
@ -0,0 +1,181 @@
|
|||||||
|
%% ===== BEC-Droplets Settings =====
|
||||||
|
|
||||||
|
% Specify data location to run analysis on
|
||||||
|
dataSources = {
|
||||||
|
struct('sequence', 'StructuralPhaseTransition', ...
|
||||||
|
'date', '2025/08/13', ...
|
||||||
|
'runs', [62]) % 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 = 'BECToDroplets';
|
||||||
|
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 correlation analysis
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
g2_analysis_results = Analyzer.conductCorrelationAnalysis(od_imgs, scan_parameter_values, options);
|
||||||
|
|
||||||
|
%% Analyze G2 matrices
|
||||||
|
|
||||||
|
% ROI definition
|
||||||
|
options.roi.center = [3, 3]; % center of ROI in µm (x0, y0)
|
||||||
|
options.roi.size = [3, 11]; % width and height in µm
|
||||||
|
options.roi.angle = pi/4; % rotation angle (radians, CCW)
|
||||||
|
options.threshold = 0.85;
|
||||||
|
options.fitDeviationThreshold = 0.9;
|
||||||
|
|
||||||
|
% Plot control
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, options);
|
||||||
|
|
||||||
|
%% Plot raw OD images and the corresponding real space g2 matrix
|
||||||
|
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
options.skipSaveFigures = true;
|
||||||
|
|
||||||
|
Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 14, ...
|
||||||
|
'ShowOverlays', true, ...
|
||||||
|
'RepsPerPage', 5, ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'SkipLivePlot', options.skipLivePlot, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures);
|
||||||
|
|
||||||
|
%% Plot mean and standard error of anisotropy
|
||||||
|
|
||||||
|
Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'YLim', [0,6], ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Anisotropy of correlation peaks', ...
|
||||||
|
'FigNum', 1, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'SaveFileName', 'RadialSpectralContrast.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures);
|
||||||
|
|
||||||
|
%% Plot distribution of anisotropy
|
||||||
|
grouped_data = groupDataByScan(scan_parameter_values, analysis_results.anisotropy_vals);
|
||||||
|
|
||||||
|
% call plotPDF
|
||||||
|
Plotter.plotPDF(grouped_data, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Anisotropy of correlation peaks', ...
|
||||||
|
'FigNum', 2, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'NumberOfBins', 20, ...
|
||||||
|
'NormalizeHistogram', true, ...
|
||||||
|
'DataRange', [0 10], ...
|
||||||
|
'Colormap', @Colormaps.coolwarm, ...
|
||||||
|
'XLim', [min(scan_reference_values) max(scan_reference_values)]);
|
||||||
|
|
||||||
|
function groupedData = groupDataByScan(scan_values, data_values)
|
||||||
|
%% groupByScanValues
|
||||||
|
% Groups data according to unique scan parameter values.
|
||||||
|
%
|
||||||
|
% Inputs:
|
||||||
|
% scan_values : array of scan parameters (length = N_reps * N_scan)
|
||||||
|
% data_values : numeric array or cell array of measured values
|
||||||
|
% (same length as scan_values)
|
||||||
|
%
|
||||||
|
% Output:
|
||||||
|
% groupedData : 1 x N_unique cell array, each containing all repetitions
|
||||||
|
% corresponding to a unique scan value
|
||||||
|
|
||||||
|
[unique_vals, ~, idx] = unique(scan_values, 'stable'); % preserve order
|
||||||
|
groupedData = cell(1, numel(unique_vals));
|
||||||
|
|
||||||
|
for i = 1:numel(unique_vals)
|
||||||
|
if iscell(data_values)
|
||||||
|
group = data_values(idx == i);
|
||||||
|
groupedData{i} = [group{:}]; % concatenate if nested cells
|
||||||
|
else
|
||||||
|
groupedData{i} = data_values(idx == i);
|
||||||
|
end
|
||||||
|
end
|
||||||
|
end
|
||||||
@ -0,0 +1,263 @@
|
|||||||
|
%% ===== BEC-Droplets Settings =====
|
||||||
|
|
||||||
|
% Specify data location to run analysis on
|
||||||
|
dataSources = {
|
||||||
|
struct('sequence', 'StructuralPhaseTransition', ...
|
||||||
|
'date', '2025/08/13', ...
|
||||||
|
'runs', [62]) % 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 = 'BECToDroplets';
|
||||||
|
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', '\alpha', ... % user-defined tile prefix
|
||||||
|
'TileTitleSuffix', '^\circ', ... % 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
|
||||||
|
%%
|
||||||
|
%{
|
||||||
|
% --- Function call ---
|
||||||
|
plotTwoGaussianFitsOnRaw(fitResults, rawCurves, 8, 12); % 8×12 subplots per page
|
||||||
|
|
||||||
|
% --- Function definition ---
|
||||||
|
function plotTwoGaussianFitsOnRaw(fitResults, rawCurves, nRows, nCols)
|
||||||
|
%% plotTwoGaussianFitsOnRaw
|
||||||
|
% Plots raw radial spectral curves with their two-Gaussian fits.
|
||||||
|
%
|
||||||
|
% Inputs:
|
||||||
|
% fitResults - struct array from fitTwoGaussianCurvesToRadialSpectralDistribution
|
||||||
|
% rawCurves - struct array with fields:
|
||||||
|
% .x - raw normalized amplitudes
|
||||||
|
% .k - corresponding k_rho values
|
||||||
|
% nRows - number of subplot rows per page (default: 8)
|
||||||
|
% nCols - number of subplot columns per page (default: 12)
|
||||||
|
|
||||||
|
if nargin < 3, nRows = 8; end
|
||||||
|
if nargin < 4, nCols = 12; end
|
||||||
|
|
||||||
|
Ncurves = numel(rawCurves);
|
||||||
|
plotsPerPage = nRows * nCols;
|
||||||
|
pageNum = 1;
|
||||||
|
|
||||||
|
for k = 1:Ncurves
|
||||||
|
% --- Create new figure page if needed ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
figure('Name', sprintf('Radial Spectra Page %d', pageNum), ...
|
||||||
|
'NumberTitle', 'off', 'Color', 'w', ...
|
||||||
|
'Position', [50 50 1600 900]);
|
||||||
|
pageNum = pageNum + 1;
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Subplot selection ---
|
||||||
|
subplot(nRows, nCols, mod(k-1, plotsPerPage) + 1);
|
||||||
|
hold on; grid on; box on;
|
||||||
|
|
||||||
|
% --- Plot raw curve ---
|
||||||
|
if isfield(rawCurves, 'x') && isfield(rawCurves, 'k') && ...
|
||||||
|
~isempty(rawCurves(k).x) && all(isfinite(rawCurves(k).x))
|
||||||
|
plot(rawCurves(k).k, rawCurves(k).x, 'k.-', ...
|
||||||
|
'LineWidth', 1, 'DisplayName', 'Raw data');
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Overlay fit if valid ---
|
||||||
|
if k <= numel(fitResults)
|
||||||
|
fit = fitResults(k);
|
||||||
|
if isfield(fit, 'isValid') && fit.isValid && ...
|
||||||
|
isfield(fit, 'kFine') && isfield(fit, 'yFit') && ...
|
||||||
|
~isempty(fit.kFine) && all(isfinite(fit.yFit))
|
||||||
|
plot(fit.kFine, fit.yFit, 'r-', ...
|
||||||
|
'LineWidth', 1.2, 'DisplayName', 'Two-Gaussian fit');
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Labels and title ---
|
||||||
|
xlabel('k_\rho', 'FontSize', 10);
|
||||||
|
ylabel('Normalized amplitude', 'FontSize', 10);
|
||||||
|
title(sprintf('Curve %d', k), 'FontSize', 9, 'Interpreter', 'none');
|
||||||
|
|
||||||
|
% --- Legend on first subplot of each page ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
legend('Location', 'best', 'FontSize', 8);
|
||||||
|
end
|
||||||
|
|
||||||
|
hold off;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
%}
|
||||||
|
%% ------------------ 3. Plot fit parameters - amplitude ------------------
|
||||||
|
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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);
|
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,411 @@
|
|||||||
|
%% ===== 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.extractFullAngularSpectralDistribution(od_imgs, options);
|
||||||
|
|
||||||
|
%% ------------------ 1. Plot of all Angular Spectral Distribution Curves ------------------
|
||||||
|
Plotter.plotSpectralCurves( ...
|
||||||
|
spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals/pi, ... % correct θ values
|
||||||
|
scan_reference_values, ... % correct scan params
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\theta / \pi', ...
|
||||||
|
'YLabel', 'S(\theta)', ...
|
||||||
|
'HighlightEvery', 10, ... % highlight every 10th repetition
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FigNum', 1, ...
|
||||||
|
'TileTitlePrefix', '\alpha', ... % user-defined tile prefix
|
||||||
|
'TileTitleSuffix', '^\circ', ... % user-defined suffix (e.g., degrees symbol)
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SpectralCurves.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
%% ------------------ 2. Plot of all Angular Spectral Distribution Curves shifted ------------------
|
||||||
|
|
||||||
|
% --- Recenter curves first ---
|
||||||
|
results = Analyzer.recenterSpectralCurves(spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals/pi, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'SearchRange', [0 90]); % degrees
|
||||||
|
|
||||||
|
% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
|
||||||
|
thetaMin = 0; % in units of pi (since you divided by pi)
|
||||||
|
thetaMax = 1; % corresponds to pi/2
|
||||||
|
|
||||||
|
mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
|
||||||
|
results.x_values = results.x_values(mask);
|
||||||
|
|
||||||
|
% Apply the same mask to each curve set
|
||||||
|
for i = 1:numel(results.curves)
|
||||||
|
results.curves{i} = results.curves{i}(:, mask);
|
||||||
|
results.curves_mean{i} = results.curves_mean{i}(mask);
|
||||||
|
results.curves_error{i}= results.curves_error{i}(mask);
|
||||||
|
end
|
||||||
|
|
||||||
|
Plotter.plotSpectralCurvesRecentered( ...
|
||||||
|
results, ...
|
||||||
|
scan_reference_values, ... % correct scan params
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\theta / \pi', ...
|
||||||
|
'YLabel', 'S(\theta)', ...
|
||||||
|
'HighlightEvery', 10, ... % highlight every 10th repetition
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FigNum', 2, ...
|
||||||
|
'TileTitlePrefix', '\alpha', ... % user-defined tile prefix
|
||||||
|
'TileTitleSuffix', '^\circ', ... % user-defined suffix (e.g., degrees symbol)
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SpectralCurves.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
%% ------------------ 3. Plot cumulants from shifted Angular Spectral Distribution Curves ------------------
|
||||||
|
Plotter.plotSpectralDistributionCumulants(results, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 14, ...
|
||||||
|
'FigNum', 3, ...
|
||||||
|
'SkipSaveFigures', false, ...
|
||||||
|
'SaveFileName', 'SpectralCumulants.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
%% ------------------ 4. Fit shifted Angular Spectral Distribution Curves ------------------
|
||||||
|
[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
|
||||||
|
spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals, ...
|
||||||
|
'MaxTheta', pi/2, ...
|
||||||
|
'ResidualThreshold', 0.15, ...
|
||||||
|
'PositionThreshold', pi/15, ...
|
||||||
|
'AmplitudeThreshold', 0.15);
|
||||||
|
|
||||||
|
%{
|
||||||
|
% --- Function call ---
|
||||||
|
plotTwoGaussianFitsOnRaw(fitResults, rawCurves, 8, 12); % 8×12 subplots per page
|
||||||
|
|
||||||
|
% --- Function definition ---
|
||||||
|
function plotTwoGaussianFitsOnRaw(fitResults, rawCurves, nRows, nCols)
|
||||||
|
% plotTwoGaussianFitsOnRaw - Plots raw curves and overlays valid two-Gaussian fits.
|
||||||
|
%
|
||||||
|
% Inputs:
|
||||||
|
% fitResults - struct array from fitTwoGaussianCurvesToAngularSpectralDistribution (may contain fits)
|
||||||
|
% rawCurves - struct array with fields:
|
||||||
|
% .x - raw curve
|
||||||
|
% .theta - corresponding theta values
|
||||||
|
% nRows - number of subplot rows per page (default: 4)
|
||||||
|
% nCols - number of subplot columns per page (default: 6)
|
||||||
|
|
||||||
|
if nargin < 3, nRows = 4; end
|
||||||
|
if nargin < 4, nCols = 6; end
|
||||||
|
|
||||||
|
Ncurves = numel(rawCurves);
|
||||||
|
plotsPerPage = nRows * nCols;
|
||||||
|
pageNum = 1;
|
||||||
|
|
||||||
|
for k = 1:Ncurves
|
||||||
|
% --- New figure/page if needed ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
figure('Name', sprintf('Curves Page %d', pageNum), ...
|
||||||
|
'NumberTitle', 'off', 'Color', 'w');
|
||||||
|
pageNum = pageNum + 1;
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Select subplot ---
|
||||||
|
subplot(nRows, nCols, mod(k-1, plotsPerPage)+1);
|
||||||
|
hold on; grid on; box on;
|
||||||
|
|
||||||
|
% --- Plot raw curve ---
|
||||||
|
xRaw = rawCurves(k).x;
|
||||||
|
thetaRaw = rawCurves(k).theta;
|
||||||
|
if ~isempty(xRaw) && ~isempty(thetaRaw) && all(isfinite(xRaw))
|
||||||
|
plot(thetaRaw, xRaw, 'k.-', 'LineWidth', 1, 'DisplayName', 'Raw data');
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Overlay fit if valid ---
|
||||||
|
if k <= numel(fitResults)
|
||||||
|
fit = fitResults(k);
|
||||||
|
if isfield(fit, 'isValid') && fit.isValid ...
|
||||||
|
&& ~isempty(fit.yFit) && ~isempty(fit.thetaFine)
|
||||||
|
plot(fit.thetaFine, fit.yFit, 'r-', 'LineWidth', 1.2, 'DisplayName', 'Two-Gaussian fit');
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Formatting ---
|
||||||
|
xlabel('\theta (rad)');
|
||||||
|
ylabel('Normalized amplitude');
|
||||||
|
title(sprintf('Curve %d', k), 'FontSize', 10);
|
||||||
|
|
||||||
|
% --- Legend once per page ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
legend('Location', 'best', 'FontSize', 8);
|
||||||
|
end
|
||||||
|
|
||||||
|
hold off;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
%}
|
||||||
|
|
||||||
|
%% ------------------ 5. Plot fit parameters - amplitude ------------------
|
||||||
|
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'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, 1.6]);
|
||||||
|
|
||||||
|
%% ------------------ 6. Plot fit parameters - position ------------------
|
||||||
|
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'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', [0, 1.6]);
|
||||||
|
|
||||||
|
%% ------------------ 7. Plot fit parameters - width ------------------
|
||||||
|
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'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, 1.6]);
|
||||||
|
|
||||||
|
%% ------------------ 8. Plot fit parameters of mean shifted Angular Spectral Distribution Curves ------------------
|
||||||
|
|
||||||
|
% --- Recenter curves first ---
|
||||||
|
results = Analyzer.recenterSpectralCurves(spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals/pi, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'SearchRange', [0 90]); % degrees
|
||||||
|
|
||||||
|
% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
|
||||||
|
thetaMin = 0; % in units of pi (since you divided by pi)
|
||||||
|
thetaMax = 1; % corresponds to pi/2
|
||||||
|
|
||||||
|
mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
|
||||||
|
results.x_values = results.x_values(mask);
|
||||||
|
|
||||||
|
% Apply the same mask to each curve set
|
||||||
|
for i = 1:numel(results.curves)
|
||||||
|
results.curves_mean{i} = results.curves_mean{i}(mask);
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Fit two-Gaussian model to mean curves ---
|
||||||
|
[fitResultsMean, ~] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
|
||||||
|
results.curves_mean, ...
|
||||||
|
results.x_values*pi, ...
|
||||||
|
'MaxTheta', pi/2, ...
|
||||||
|
'ResidualThreshold', 0.15, ...
|
||||||
|
'PositionThreshold', pi/15, ...
|
||||||
|
'AmplitudeThreshold', 0.15, ...
|
||||||
|
'RecenterCurves', false);
|
||||||
|
|
||||||
|
% --- Prepare parameter values ---
|
||||||
|
N_params = numel(fitResultsMean);
|
||||||
|
amp2_vals = nan(1, N_params);
|
||||||
|
mu2_vals = nan(1, N_params);
|
||||||
|
sigma2_vals = nan(1, N_params);
|
||||||
|
|
||||||
|
for i = 1:N_params
|
||||||
|
pFit = fitResultsMean(i).pFit;
|
||||||
|
if all(~isnan(pFit))
|
||||||
|
% Successful fit → use fitted values
|
||||||
|
amp2_vals(i) = pFit(4);
|
||||||
|
mu2_vals(i) = pFit(5);
|
||||||
|
sigma2_vals(i) = pFit(6);
|
||||||
|
|
||||||
|
else
|
||||||
|
% Fit failed → leave as NaN (skipped automatically)
|
||||||
|
continue;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Plot peak amplitude mean with SEM ---
|
||||||
|
Plotter.plotMeanWithSE(scan_reference_values, amp2_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Secondary peak amplitude', ...
|
||||||
|
'FigNum', 7, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 16, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SecondaryPeakAmplitudeMeanWithSEM.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
% --- Plot peak position mean with SEM ---
|
||||||
|
Plotter.plotMeanWithSE(scan_reference_values, mu2_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Secondary peak position (\theta, rad)', ...
|
||||||
|
'FigNum', 8, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 16, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SecondaryPeakPositionMeanWithSEM.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
% --- Plot peak width mean with SEM ---
|
||||||
|
Plotter.plotMeanWithSE(scan_reference_values, sigma2_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Secondary peak width (\sigma, rad)', ...
|
||||||
|
'FigNum', 9, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 16, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory);
|
||||||
|
|
||||||
|
%% Inspect individual realizations of a single parameter
|
||||||
|
|
||||||
|
% --- Recenter curves first ---
|
||||||
|
results = Analyzer.recenterSpectralCurves( ...
|
||||||
|
spectral_analysis_results.S_theta_norm_all, ...
|
||||||
|
spectral_analysis_results.theta_vals/pi, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'SearchRange', [0 90]); % degrees
|
||||||
|
|
||||||
|
% --- Restrict to desired theta range (e.g., 0 to 0.5*pi) ---
|
||||||
|
thetaMin = 0; % in units of pi (since you divided by pi)
|
||||||
|
thetaMax = 1; % corresponds to pi/2
|
||||||
|
|
||||||
|
mask = results.x_values >= thetaMin & results.x_values <= thetaMax;
|
||||||
|
results.x_values = results.x_values(mask);
|
||||||
|
|
||||||
|
% --- Apply the same mask to each curve set (1x10 cell, each 60x180) ---
|
||||||
|
for i = 1:numel(results.curves)
|
||||||
|
results.curves{i} = results.curves{i}(:, mask);
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Convert selected curve set (e.g., 5th) into 1x60 cell array of 1xN row vectors ---
|
||||||
|
paramIdx = 1; % <-- choose which scan point or curve set to analyze
|
||||||
|
curves_matrix = results.curves{paramIdx}; % 60xN numeric
|
||||||
|
curves_cell = num2cell(curves_matrix, 2); % 1x60 cell array
|
||||||
|
curves_cell = cellfun(@(x) x(:).', curves_cell, 'UniformOutput', false); % ensure 1xN row vectors
|
||||||
|
|
||||||
|
% --- Fit two-Gaussian model to these curves ---
|
||||||
|
[fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(...
|
||||||
|
curves_cell, ...
|
||||||
|
results.x_values*pi, ...
|
||||||
|
'MaxTheta', pi/2, ...
|
||||||
|
'ResidualThreshold', 0.15, ...
|
||||||
|
'PositionThreshold', pi/15, ...
|
||||||
|
'AmplitudeThreshold', 0.15, ...
|
||||||
|
'RecenterCurves', false);
|
||||||
181
Data-Analyzer/+Scripts/BECToStripes/runCorrelationAnalysis.m
Normal file
181
Data-Analyzer/+Scripts/BECToStripes/runCorrelationAnalysis.m
Normal file
@ -0,0 +1,181 @@
|
|||||||
|
%% ===== 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 correlation analysis
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
g2_analysis_results = Analyzer.conductCorrelationAnalysis(od_imgs, scan_parameter_values, options);
|
||||||
|
|
||||||
|
%% Analyze G2 matrices
|
||||||
|
|
||||||
|
% ROI definition
|
||||||
|
options.roi.center = [3, 3]; % center of ROI in µm (x0, y0)
|
||||||
|
options.roi.size = [3, 11]; % width and height in µm
|
||||||
|
options.roi.angle = pi/4; % rotation angle (radians, CCW)
|
||||||
|
options.threshold = 0.85;
|
||||||
|
options.fitDeviationThreshold = 0.9;
|
||||||
|
|
||||||
|
% Plot control
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, options);
|
||||||
|
|
||||||
|
%% Plot raw OD images and the corresponding real space g2 matrix
|
||||||
|
|
||||||
|
options.skipLivePlot = true;
|
||||||
|
options.skipSaveFigures = true;
|
||||||
|
|
||||||
|
Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'FontSize', 14, ...
|
||||||
|
'ShowOverlays', true, ...
|
||||||
|
'RepsPerPage', 5, ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'SkipLivePlot', options.skipLivePlot, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures);
|
||||||
|
|
||||||
|
%% Plot mean and standard error of anisotropy
|
||||||
|
|
||||||
|
Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'YLim', [0,6], ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Anisotropy of correlation peaks', ...
|
||||||
|
'FigNum', 1, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'SaveFileName', 'RadialSpectralContrast.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures);
|
||||||
|
|
||||||
|
%% Plot distribution of anisotropy
|
||||||
|
grouped_data = groupDataByScan(scan_parameter_values, analysis_results.anisotropy_vals);
|
||||||
|
|
||||||
|
% call plotPDF
|
||||||
|
Plotter.plotPDF(grouped_data, ...
|
||||||
|
scan_reference_values, ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'YLabel', 'Anisotropy of correlation peaks', ...
|
||||||
|
'FigNum', 2, ...
|
||||||
|
'FontName', options.font, ...
|
||||||
|
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||||
|
'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
|
||||||
|
'SaveDirectory', options.saveDirectory , ...
|
||||||
|
'NumberOfBins', 20, ...
|
||||||
|
'NormalizeHistogram', true, ...
|
||||||
|
'DataRange', [0 10], ...
|
||||||
|
'Colormap', @Colormaps.coolwarm, ...
|
||||||
|
'XLim', [min(scan_reference_values) max(scan_reference_values)]);
|
||||||
|
|
||||||
|
function groupedData = groupDataByScan(scan_values, data_values)
|
||||||
|
%% groupByScanValues
|
||||||
|
% Groups data according to unique scan parameter values.
|
||||||
|
%
|
||||||
|
% Inputs:
|
||||||
|
% scan_values : array of scan parameters (length = N_reps * N_scan)
|
||||||
|
% data_values : numeric array or cell array of measured values
|
||||||
|
% (same length as scan_values)
|
||||||
|
%
|
||||||
|
% Output:
|
||||||
|
% groupedData : 1 x N_unique cell array, each containing all repetitions
|
||||||
|
% corresponding to a unique scan value
|
||||||
|
|
||||||
|
[unique_vals, ~, idx] = unique(scan_values, 'stable'); % preserve order
|
||||||
|
groupedData = cell(1, numel(unique_vals));
|
||||||
|
|
||||||
|
for i = 1:numel(unique_vals)
|
||||||
|
if iscell(data_values)
|
||||||
|
group = data_values(idx == i);
|
||||||
|
groupedData{i} = [group{:}]; % concatenate if nested cells
|
||||||
|
else
|
||||||
|
groupedData{i} = data_values(idx == i);
|
||||||
|
end
|
||||||
|
end
|
||||||
|
end
|
||||||
@ -0,0 +1,263 @@
|
|||||||
|
%% ===== 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', '\alpha', ... % user-defined tile prefix
|
||||||
|
'TileTitleSuffix', '^\circ', ... % 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
|
||||||
|
%%
|
||||||
|
%{
|
||||||
|
% --- Function call ---
|
||||||
|
plotTwoGaussianFitsOnRaw(fitResults, rawCurves, 8, 12); % 8×12 subplots per page
|
||||||
|
|
||||||
|
% --- Function definition ---
|
||||||
|
function plotTwoGaussianFitsOnRaw(fitResults, rawCurves, nRows, nCols)
|
||||||
|
%% plotTwoGaussianFitsOnRaw
|
||||||
|
% Plots raw radial spectral curves with their two-Gaussian fits.
|
||||||
|
%
|
||||||
|
% Inputs:
|
||||||
|
% fitResults - struct array from fitTwoGaussianCurvesToRadialSpectralDistribution
|
||||||
|
% rawCurves - struct array with fields:
|
||||||
|
% .x - raw normalized amplitudes
|
||||||
|
% .k - corresponding k_rho values
|
||||||
|
% nRows - number of subplot rows per page (default: 8)
|
||||||
|
% nCols - number of subplot columns per page (default: 12)
|
||||||
|
|
||||||
|
if nargin < 3, nRows = 8; end
|
||||||
|
if nargin < 4, nCols = 12; end
|
||||||
|
|
||||||
|
Ncurves = numel(rawCurves);
|
||||||
|
plotsPerPage = nRows * nCols;
|
||||||
|
pageNum = 1;
|
||||||
|
|
||||||
|
for k = 1:Ncurves
|
||||||
|
% --- Create new figure page if needed ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
figure('Name', sprintf('Radial Spectra Page %d', pageNum), ...
|
||||||
|
'NumberTitle', 'off', 'Color', 'w', ...
|
||||||
|
'Position', [50 50 1600 900]);
|
||||||
|
pageNum = pageNum + 1;
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Subplot selection ---
|
||||||
|
subplot(nRows, nCols, mod(k-1, plotsPerPage) + 1);
|
||||||
|
hold on; grid on; box on;
|
||||||
|
|
||||||
|
% --- Plot raw curve ---
|
||||||
|
if isfield(rawCurves, 'x') && isfield(rawCurves, 'k') && ...
|
||||||
|
~isempty(rawCurves(k).x) && all(isfinite(rawCurves(k).x))
|
||||||
|
plot(rawCurves(k).k, rawCurves(k).x, 'k.-', ...
|
||||||
|
'LineWidth', 1, 'DisplayName', 'Raw data');
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Overlay fit if valid ---
|
||||||
|
if k <= numel(fitResults)
|
||||||
|
fit = fitResults(k);
|
||||||
|
if isfield(fit, 'isValid') && fit.isValid && ...
|
||||||
|
isfield(fit, 'kFine') && isfield(fit, 'yFit') && ...
|
||||||
|
~isempty(fit.kFine) && all(isfinite(fit.yFit))
|
||||||
|
plot(fit.kFine, fit.yFit, 'r-', ...
|
||||||
|
'LineWidth', 1.2, 'DisplayName', 'Two-Gaussian fit');
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% --- Labels and title ---
|
||||||
|
xlabel('k_\rho', 'FontSize', 10);
|
||||||
|
ylabel('Normalized amplitude', 'FontSize', 10);
|
||||||
|
title(sprintf('Curve %d', k), 'FontSize', 9, 'Interpreter', 'none');
|
||||||
|
|
||||||
|
% --- Legend on first subplot of each page ---
|
||||||
|
if mod(k-1, plotsPerPage) == 0
|
||||||
|
legend('Location', 'best', 'FontSize', 8);
|
||||||
|
end
|
||||||
|
|
||||||
|
hold off;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
%}
|
||||||
|
%% ------------------ 3. Plot fit parameters - amplitude ------------------
|
||||||
|
Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
|
||||||
|
'Title', options.titleString, ...
|
||||||
|
'XLabel', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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', '\alpha (degrees)', ...
|
||||||
|
'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);
|
||||||
|
|
||||||
|
|
||||||
Loading…
Reference in New Issue
Block a user