diff --git a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runAngularSpectralDistributionAnalysis.m b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runAngularSpectralDistributionAnalysis.m index d4d1d83..9212b2e 100644 --- a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runAngularSpectralDistributionAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runAngularSpectralDistributionAnalysis.m @@ -155,7 +155,8 @@ Plotter.plotSpectralDistributionCumulants(results, ... 'FontSize', 14, ... 'FigNum', 3, ... 'SkipSaveFigures', false, ... - 'SaveFileName', 'SpectralCumulants.fig'); + 'SaveFileName', 'SpectralCumulants.fig', ... + 'SaveDirectory', options.saveDirectory); %% ------------------ 4. Fit shifted Angular Spectral Distribution Curves ------------------ [fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(... @@ -242,6 +243,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ... 'FigNum', 4, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -259,6 +261,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ... 'FigNum', 5, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakPositionPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -276,6 +279,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ... 'FigNum', 6, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakWidthPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -333,31 +337,41 @@ for i = 1:N_params end end -% --- Plot using plotMeanWithSE --- +% --- 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); + 'FontSize', 16, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryPeakAmplitudeMeanWithSEM.fig', ... + 'SaveDirectory', options.saveDirectory); -% --- Plot using plotMeanWithSE --- +% --- 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); + '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); + 'FontSize', 16, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ... + 'SaveDirectory', options.saveDirectory); %% Inspect individual realizations of a single parameter diff --git a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runCorrelationAnalysis.m b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runCorrelationAnalysis.m index c27e3d2..05ce4e2 100644 --- a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runCorrelationAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runCorrelationAnalysis.m @@ -117,14 +117,13 @@ analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, o options.skipLivePlot = true; options.skipSaveFigures = true; -saveDirectory = 'C:\Users\Karthik-OfficePC\Documents\GitRepositories\Calculations\Data-Analyzer\+Scripts'; Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ... 'FontName', options.font, ... 'FontSize', 14, ... 'ShowOverlays', true, ... - 'RepsPerPage', 5, ... % paginate 10 repetitions per figure - 'SaveDirectory', saveDirectory, ... + 'RepsPerPage', 5, ... + 'SaveDirectory', options.saveDirectory , ... 'SkipLivePlot', options.skipLivePlot, ... 'SkipSaveFigures', options.skipSaveFigures); @@ -138,7 +137,7 @@ Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals, 'FigNum', 1, ... 'FontName', options.font, ... 'SaveFileName', 'RadialSpectralContrast.fig', ... - 'SaveDirectory', pwd, ... % save figures inside dataset-specific folder + 'SaveDirectory', options.saveDirectory , ... 'SkipSaveFigures', options.skipSaveFigures); %% Plot distribution of anisotropy @@ -154,7 +153,7 @@ Plotter.plotPDF(grouped_data, ... 'FontName', options.font, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ... - 'SaveDirectory', pwd, ... + 'SaveDirectory', options.saveDirectory , ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... 'DataRange', [0 10], ... diff --git a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runRadialSpectralDistributionAnalysis.m b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runRadialSpectralDistributionAnalysis.m index f637d95..0101717 100644 --- a/Data-Analyzer/+Scripts/BECToDropletsToStripes/runRadialSpectralDistributionAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToDropletsToStripes/runRadialSpectralDistributionAnalysis.m @@ -201,6 +201,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ... 'FigNum', 4, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -218,6 +219,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ... 'FigNum', 5, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakPositionPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -234,6 +236,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ... 'FigNum', 6, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakWidthPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -252,6 +255,9 @@ Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... 'Colormap', @Colormaps.coolwarm, ... - 'OverlayMeanSEM', true); + 'OverlayMeanSEM', true, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryGaussianRange.fig', ... + 'SaveDirectory', options.saveDirectory); diff --git a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runAngularSpectralDistributionAnalysis.m b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runAngularSpectralDistributionAnalysis.m index 09c9e68..85d81ba 100644 --- a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runAngularSpectralDistributionAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runAngularSpectralDistributionAnalysis.m @@ -155,7 +155,8 @@ Plotter.plotSpectralDistributionCumulants(results, ... 'FontSize', 14, ... 'FigNum', 3, ... 'SkipSaveFigures', false, ... - 'SaveFileName', 'SpectralCumulants.fig'); + 'SaveFileName', 'SpectralCumulants.fig', ... + 'SaveDirectory', options.saveDirectory); %% ------------------ 4. Fit shifted Angular Spectral Distribution Curves ------------------ [fitResults, rawCurves] = Analyzer.fitTwoGaussianCurvesToAngularSpectralDistribution(... @@ -242,6 +243,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ... 'FigNum', 4, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -259,6 +261,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ... 'FigNum', 5, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakPositionPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -276,6 +279,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ... 'FigNum', 6, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakWidthPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -333,31 +337,41 @@ for i = 1:N_params end end -% --- Plot using plotMeanWithSE --- +% --- 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); + 'FontSize', 16, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryPeakAmplitudeMeanWithSEM.fig', ... + 'SaveDirectory', options.saveDirectory); -% --- Plot using plotMeanWithSE --- +% --- 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); + '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); + 'FontSize', 16, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ... + 'SaveDirectory', options.saveDirectory); %% Inspect individual realizations of a single parameter diff --git a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runCorrelationAnalysis.m b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runCorrelationAnalysis.m index d447b5b..1fdfeb7 100644 --- a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runCorrelationAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runCorrelationAnalysis.m @@ -97,7 +97,7 @@ end [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 @@ -107,11 +107,7 @@ 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.deviationThreshold = 0.30; -options.minEllipseFraction = 0.30; -options.angleLimit = deg2rad(45); -options.angleTolerance = deg2rad(5); +options.fitDeviationThreshold = 0.9; % Plot control options.skipLivePlot = true; @@ -121,13 +117,13 @@ analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, o options.skipLivePlot = true; options.skipSaveFigures = true; -saveDirectory = 'C:\Users\Karthik-OfficePC\Documents\GitRepositories\Calculations\Data-Analyzer\+Scripts'; + Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ... 'FontName', options.font, ... 'FontSize', 14, ... 'ShowOverlays', true, ... - 'RepsPerPage', 5, ... % paginate 10 repetitions per figure - 'SaveDirectory', saveDirectory, ... + 'RepsPerPage', 5, ... + 'SaveDirectory', options.saveDirectory , ... 'SkipLivePlot', options.skipLivePlot, ... 'SkipSaveFigures', options.skipSaveFigures); @@ -135,13 +131,13 @@ Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals, ... 'Title', options.titleString, ... - 'YLim', [0,10], ... + 'YLim', [0,6], ... 'XLabel', '\alpha (degrees)', ... 'YLabel', 'Anisotropy of correlation peaks', ... 'FigNum', 1, ... 'FontName', options.font, ... 'SaveFileName', 'RadialSpectralContrast.fig', ... - 'SaveDirectory', pwd, ... % save figures inside dataset-specific folder + 'SaveDirectory', options.saveDirectory , ... 'SkipSaveFigures', options.skipSaveFigures); %% Plot distribution of anisotropy @@ -157,10 +153,10 @@ Plotter.plotPDF(grouped_data, ... 'FontName', options.font, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ... - 'SaveDirectory', pwd, ... + 'SaveDirectory', options.saveDirectory , ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... - 'DataRange', [0 15], ... + 'DataRange', [0 10], ... 'Colormap', @Colormaps.coolwarm, ... 'XLim', [min(scan_reference_values) max(scan_reference_values)]); @@ -188,4 +184,4 @@ function groupedData = groupDataByScan(scan_values, data_values) groupedData{i} = data_values(idx == i); end end -end +end \ No newline at end of file diff --git a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runRadialSpectralDistributionAnalysis.m b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runRadialSpectralDistributionAnalysis.m index 4caf1fe..023ef11 100644 --- a/Data-Analyzer/+Scripts/BECToStripesToDroplets/runRadialSpectralDistributionAnalysis.m +++ b/Data-Analyzer/+Scripts/BECToStripesToDroplets/runRadialSpectralDistributionAnalysis.m @@ -201,6 +201,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ... 'FigNum', 4, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakAmplitudePDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -218,6 +219,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ... 'FigNum', 5, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakPositionPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -234,6 +236,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ... 'FigNum', 6, ... 'SkipSaveFigures', options.skipSaveFigures, ... 'SaveFileName', 'SecondaryPeakWidthPDF.fig', ... + 'SaveDirectory', options.saveDirectory, ... 'PlotType', 'histogram', ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... @@ -252,6 +255,9 @@ Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ... 'NumberOfBins', 20, ... 'NormalizeHistogram', true, ... 'Colormap', @Colormaps.coolwarm, ... - 'OverlayMeanSEM', true); + 'OverlayMeanSEM', true, ... + 'SkipSaveFigures', options.skipSaveFigures, ... + 'SaveFileName', 'SecondaryGaussianRange.fig', ... + 'SaveDirectory', options.saveDirectory);