Change in magnification, added scripts to analyse BEC to Droplets dataset.
This commit is contained in:
parent
1f7526c594
commit
1a99ff2c2a
@ -22,7 +22,7 @@ options.center = [1420, 2050];
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options.span = [200, 200];
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options.span = [200, 200];
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options.fraction = [0.1, 0.1];
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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.pixel_size = 5.86e-6; % in meters
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options.magnification = 23.94;
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options.magnification = 24.6;
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options.removeFringes = false;
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options.removeFringes = false;
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options.ImagingMode = 'HighIntensity';
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options.ImagingMode = 'HighIntensity';
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options.PulseDuration = 5e-6; % in s
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options.PulseDuration = 5e-6; % in s
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163
Data-Analyzer/+Scripts/BECToStripes/plotAnalysisResults.m
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163
Data-Analyzer/+Scripts/BECToStripes/plotAnalysisResults.m
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idx = 1;
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compiled_results = results_all{idx}.results;
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options.skipSaveFigures = false;
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%% ------------------ 1. Mean ± Std Plots ------------------
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% Plot Radial Spectral Contrast
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Plotter.plotMeanWithSE(scan_parameter_values, compiled_results.spectral_analysis_results.radial_spectral_contrast, ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', 'Radial Spectral Contrast', ...
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'FigNum', 1, ...
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'FontName', options.font, ...
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'SaveFileName', 'RadialSpectralContrast.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'SkipSaveFigures', options.skipSaveFigures);
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% Plot Angular Spectral Weight
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Plotter.plotMeanWithSE(scan_parameter_values, compiled_results.spectral_analysis_results.angular_spectral_weight, ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', 'Angular Spectral Weight', ...
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'FigNum', 2, ...
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'FontName', options.font, ...
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'SaveFileName', 'AngularSpectralWeight.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'SkipSaveFigures', options.skipSaveFigures);
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% Plot Peak Offset Angular Correlation
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Plotter.plotMeanWithSE(options.scan_reference_values, compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
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'FigNum', 3, ...
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'YLim', [0 1], ...
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'FontName', options.font, ...
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'SaveFileName', 'PeakOffsetAngularCorrelation.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'SkipSaveFigures', options.skipSaveFigures);
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%% ------------------ 2. g²(θ) across transition ------------------
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Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
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compiled_results.full_g2_results.g2_error_all, ...
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compiled_results.full_g2_results.theta_values, ...
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options.scan_reference_values, ...
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'rot_mag_field', ...
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'Title', options.titleString, ...
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'XLabel', '$\delta\theta / \pi$', ...
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'YLabel', '$g^{(2)}(\delta\theta)$', ...
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'FigNum', 4, ...
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'FontName', options.font, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'G2ThetaAcrossTransition.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'Colormap', @Colormaps.coolwarm);
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%% ------------------ 3. PDF of max g² across transition ------------------
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Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, options.scan_reference_values, ...
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'Title', options.titleString, ...
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'XLabel', 'B (G)', ...
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'YLabel', '$\mathrm{max}[g^{(2)}]$', ...
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'FigNum', 5, ...
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'FontName', options.font, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'NumPoints', 200, ...
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'DataRange', [0 1.5], ...
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'Colormap', @Colormaps.coolwarm, ...
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'XLim', [min(options.scan_reference_values) max(options.scan_reference_values)]);
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%% ------------------ 4. Cumulants across transition ------------------
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Plotter.plotCumulants(options.scan_reference_values, ...
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{compiled_results.custom_g_results.mean_max_g2, compiled_results.custom_g_results.var_max_g2, compiled_results.custom_g_results.skew_max_g2_angle, compiled_results.custom_g_results.fourth_order_cumulant_max_g2}, ...
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'Title', 'Cumulants of Peak Offset Angular Correlation', ...
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'XLabel', 'B (G)', ...
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'FigNum', 6, ...
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'FontName', options.font, ...
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'MarkerSize', 6, ...
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'LineWidth', 1.5, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'CumulantOfPeakOffsetAngularCorrelation.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results']);
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%{
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%% ------------------ 6. Average of Spectra Plots ------------------
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Plotter.plotAverageSpectra(scan_parameter_values, ...
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spectral_analysis_results, ...
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'ScanParameterName', scan_parameter, ...
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'FigNum', 7, ...
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'ColormapPS', Colormaps.coolwarm(), ...
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'Font', 'Bahnschrift', ...
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'SaveFileName', 'avgSpectra.fig', ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'SkipSaveFigures', options.skipSaveFigures);
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%% ------------------ 7. Compare quantities ------------------
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% Load Droplets → Stripes data
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Data = load(dtsFile, ...
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'unique_scan_parameter_values', ...
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'mean_max_g2_values', ...
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'std_error_g2_values');
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dts_scan_parameter_values = Data.unique_scan_parameter_values;
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dts_mean_mg2 = Data.mean_max_g2_values;
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dts_stderr_mg2 = Data.std_error_g2_values;
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% Load Stripes → Droplets data
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Data = load(stdFile, ...
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'unique_scan_parameter_values', ...
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'mean_max_g2_values', ...
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'std_error_g2_values');
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std_scan_parameter_values = Data.unique_scan_parameter_values;
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std_mean_mg2 = Data.mean_max_g2_values;
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std_stderr_mg2 = Data.std_error_g2_values;
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% Prepare cell arrays for multiple datasets
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scanValsCell = {dts_scan_parameter_values, std_scan_parameter_values};
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meanValsCell = {dts_mean_mg2, std_mean_mg2};
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stderrValsCell = {dts_stderr_mg2, std_stderr_mg2};
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% Compare datasets
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compareMultipleDatasets(scanValsCell, meanValsCell, stderrValsCell, ...
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'FigNum', 8, ...
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'FontName', 'Bahnschrift', ...
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'MarkerSize', 6, ...
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'LineWidth', 1.5, ...
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'CapSize', 5, ...
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'YLim', [0 1], ...
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'Labels', {'Droplets → Stripes', 'Stripes → Droplets'}, ...
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'Title', 'AngularCorrelation_Comparison', ...
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'XLabel', 'B (G)', ...
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'YLabel', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveDirectory', [options.saveDirectory '/Results'], ...
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'SaveFileName', 'AngularCorrelation_Comparison.fig');
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%% ------------------ 8. Heatmaps ------------------
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BFields = [2.35, 2.15, 2.0, 1.85, 1.7, 1.55, 1.4, 1.35];
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% Heatmap of mean_max_g2_values
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Plotter.plotHeatmap(compiled_results, options.scan_groups, BFields, 'mean_max_g2_values', ...
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'Colormap', @sky, ...
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'CLim', [0 1], ...
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'XLabel', '\alpha (degrees)', ...
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'YLabel', 'BField (G)', ...
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'Title', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
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'FigNum', 9, ...
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'SaveFileName', 'Heatmap_MaxG2.fig', ...
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'SaveDirectory', options.resultsDir);
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% Heatmap of radial_spectral_contrast
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Plotter.plotHeatmap(compiled_results, options.scan_groups, BFields, 'radial_spectral_contrast', ...
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'Colormap', @sky, ...
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'CLim', [0 0.008], ...
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'XLabel', '\alpha (degrees)', ...
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'YLabel', 'BField (G)', ...
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'Title', 'Radial Spectral Contrast', ...
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'FigNum', 10, ...
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'SaveFileName', 'Heatmap_RadialSpectralContrast.fig', ...
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'SaveDirectory', options.resultsDir);
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%}
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118
Data-Analyzer/+Scripts/BECToStripes/plotImages.m
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118
Data-Analyzer/+Scripts/BECToStripes/plotImages.m
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@ -0,0 +1,118 @@
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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.savefileName = 'BECToDroplets';
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scriptFullPath = mfilename('fullpath');
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options.saveDirectory = fileparts(scriptFullPath);
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% Camera / imaging
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options.cam = 5;
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options.angle = 0;
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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 = 23.94;
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options.removeFringes = false;
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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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% Scan parameter
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options.scan_parameter = 'rot_mag_field';
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switch options.savefileName
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case 'BECToDroplets'
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options.scan_reference_values = [2.40, 2.39, 2.38, 2.37, 2.35, 2.34, 2.32, 2.30, 2.28, 2.26, 2.24, 2.22, 2.2, 2.15, 2.10, 2.05, 2, 1.95, 1.90, 1.85, 1.8];
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options.titleString = 'BEC to Droplets';
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case 'BECToStripes'
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options.scan_reference_values = [2.45, 2.44, 2.43, 2.42, 2.4, 2.39, 2.38, 2.37, 2.36, 2.35, 2.34, 2.32, 2.3, 2.28, 2.25, 2.2, 2.15, 2.10, 2.0, 1.90, 1.8];
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options.titleString = 'BEC to Stripes';
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case 'DropletsToStripes'
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options.scan_reference_values = [0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40];
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options.titleString = 'Droplets to Stripes';
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case 'StripesToDroplets'
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options.scan_reference_values = fliplr([0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40]);
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options.titleString = 'Stripes to Droplets';
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end
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% Flags
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options.skipNormalization = false;
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options.skipUnshuffling = false;
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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.skipMovieRender = true;
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options.skipSaveFigures = true;
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options.skipSaveOD = 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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%% ===== Build Paths from Data Sources =====
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allPaths = {}; % initialize
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for i = 1:length(dataSources)
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ds = dataSources{i};
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% Split the date string into year/month/day
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dateParts = strsplit(ds.date, '/');
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for run = ds.runs
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runStr = sprintf('%04d', run); % 4-digit run number
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fullPath = fullfile(options.baseDataFolder, ds.sequence, dateParts{:}, runStr);
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if isfolder(fullPath) % only include valid directories
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allPaths{end+1} = fullPath;
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else
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warning('Path does not exist: %s', fullPath);
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end
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end
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end
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% Let user select a single path
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set(0,'DefaultUicontrolFontSize',10); % increase default font size
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[selectedIndex, tf] = listdlg('PromptString','Select a path to analyze:', ...
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'SelectionMode','single', ...
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'ListString', allPaths, ...
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'ListSize',[400, 300]); % width x height in pixels
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if tf
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options.folderPath = allPaths{selectedIndex}; % ✅ store in options
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fprintf('Path set to selection: %s\n', options.folderPath);
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else
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error('No path selected. Aborting.');
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end
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%% ===== Collect Images and Launch Viewer =====
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[od_imgs, scan_parameter_values, file_list] = Helper.collectODImages(options);
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Analyzer.runInteractiveODImageViewer(od_imgs, scan_parameter_values, file_list, options);
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80
Data-Analyzer/+Scripts/BECToStripes/runFullAnalysis.m
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80
Data-Analyzer/+Scripts/BECToStripes/runFullAnalysis.m
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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', '2025/08/15', ...
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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.savefileName = 'BECToStripes';
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scriptFullPath = mfilename('fullpath');
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options.saveDirectory = fileparts(scriptFullPath);
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% Camera / imaging
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options.cam = 5;
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options.angle = 0;
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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.removeFringes = false;
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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;
|
||||||
|
options.Angular_WindowSize = 5;
|
||||||
|
options.zoom_size = 50;
|
||||||
|
|
||||||
|
% Scan parameter
|
||||||
|
options.scan_parameter = 'rot_mag_field';
|
||||||
|
|
||||||
|
switch options.savefileName
|
||||||
|
case 'BECToDroplets'
|
||||||
|
options.scan_reference_values = [2.40, 2.39, 2.38, 2.37, 2.35, 2.34, 2.32, 2.30, 2.28, 2.26, 2.24, 2.22, 2.2, 2.15, 2.10, 2.05, 2, 1.95, 1.90, 1.85, 1.8];
|
||||||
|
options.titleString = 'BEC to Droplets';
|
||||||
|
case 'BECToStripes'
|
||||||
|
options.scan_reference_values = [2.45, 2.44, 2.43, 2.42, 2.4, 2.39, 2.38, 2.37, 2.36, 2.35, 2.34, 2.32, 2.3, 2.28, 2.25, 2.2, 2.15, 2.10, 2.0, 1.90, 1.8];
|
||||||
|
options.titleString = 'BEC to Stripes';
|
||||||
|
case 'DropletsToStripes'
|
||||||
|
options.scan_reference_values = [0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40];
|
||||||
|
options.titleString = 'Droplets to Stripes';
|
||||||
|
case 'StripesToDroplets'
|
||||||
|
options.scan_reference_values = fliplr([0, 5, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40]);
|
||||||
|
options.titleString = 'Stripes to Droplets';
|
||||||
|
end
|
||||||
|
|
||||||
|
% Flags
|
||||||
|
options.skipNormalization = false;
|
||||||
|
options.skipUnshuffling = false;
|
||||||
|
options.skipPreprocessing = true;
|
||||||
|
options.skipMasking = true;
|
||||||
|
options.skipIntensityThresholding = true;
|
||||||
|
options.skipBinarization = true;
|
||||||
|
options.skipMovieRender = true;
|
||||||
|
options.skipSaveFigures = true;
|
||||||
|
options.skipSaveOD = true;
|
||||||
|
options.skipLivePlot = false;
|
||||||
|
options.showProgressBar = true;
|
||||||
|
|
||||||
|
% Extras
|
||||||
|
options.font = 'Bahnschrift';
|
||||||
|
|
||||||
|
%% ===== Run Batch Analysis =====
|
||||||
|
results_all = Helper.batchAnalyze(dataSources, options);
|
||||||
Loading…
Reference in New Issue
Block a user