Minor bugfixes, coding inconsistency fixes and aesthetic changes.
This commit is contained in:
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e671d12969
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c24ab3e994
@ -155,7 +155,8 @@ Plotter.plotSpectralDistributionCumulants(results, ...
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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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'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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@ -242,6 +243,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
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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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@ -259,6 +261,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
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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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@ -276,6 +279,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
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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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@ -333,31 +337,41 @@ for i = 1:N_params
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end
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end
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% --- Plot using plotMeanWithSE ---
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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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'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 using plotMeanWithSE ---
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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);
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'FontSize', 16, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakPositionMeanWithSEM.fig', ...
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'SaveDirectory', options.saveDirectory);
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% --- Plot peak width mean with SEM ---
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Plotter.plotMeanWithSE(scan_reference_values, sigma2_vals, ...
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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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'FigNum', 9, ...
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'FontName', options.font, ...
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'FontSize', 16);
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'FontSize', 16, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ...
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'SaveDirectory', options.saveDirectory);
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%% Inspect individual realizations of a single parameter
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@ -117,14 +117,13 @@ analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, o
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options.skipLivePlot = true;
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options.skipSaveFigures = true;
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saveDirectory = 'C:\Users\Karthik-OfficePC\Documents\GitRepositories\Calculations\Data-Analyzer\+Scripts';
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Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ...
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'FontName', options.font, ...
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'FontSize', 14, ...
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'ShowOverlays', true, ...
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'RepsPerPage', 5, ... % paginate 10 repetitions per figure
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'SaveDirectory', saveDirectory, ...
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'RepsPerPage', 5, ...
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'SaveDirectory', options.saveDirectory , ...
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'SkipLivePlot', options.skipLivePlot, ...
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'SkipSaveFigures', options.skipSaveFigures);
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@ -138,7 +137,7 @@ Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals,
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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', pwd, ... % save figures inside dataset-specific folder
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'SaveDirectory', options.saveDirectory , ...
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'SkipSaveFigures', options.skipSaveFigures);
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%% Plot distribution of anisotropy
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@ -154,7 +153,7 @@ Plotter.plotPDF(grouped_data, ...
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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', pwd, ...
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'SaveDirectory', options.saveDirectory , ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'DataRange', [0 10], ...
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@ -201,6 +201,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
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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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@ -218,6 +219,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
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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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@ -234,6 +236,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
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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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@ -252,6 +255,9 @@ Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'OverlayMeanSEM', true);
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'OverlayMeanSEM', true, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryGaussianRange.fig', ...
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'SaveDirectory', options.saveDirectory);
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@ -155,7 +155,8 @@ Plotter.plotSpectralDistributionCumulants(results, ...
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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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'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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@ -242,6 +243,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
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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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@ -259,6 +261,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
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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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@ -276,6 +279,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
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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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@ -333,31 +337,41 @@ for i = 1:N_params
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end
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end
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% --- Plot using plotMeanWithSE ---
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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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'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 using plotMeanWithSE ---
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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);
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'FontSize', 16, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakPositionMeanWithSEM.fig', ...
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'SaveDirectory', options.saveDirectory);
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% --- Plot peak width mean with SEM ---
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Plotter.plotMeanWithSE(scan_reference_values, sigma2_vals, ...
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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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'FigNum', 9, ...
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'FontName', options.font, ...
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'FontSize', 16);
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'FontSize', 16, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryPeakWidthMeanWithSEM.fig', ...
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'SaveDirectory', options.saveDirectory);
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%% Inspect individual realizations of a single parameter
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@ -97,7 +97,7 @@ end
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[od_imgs, scan_parameter_values, scan_reference_values, file_list] = Helper.collectODImages(options);
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%% Conduct correlation analysis
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options.skipLivePlot = true;
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g2_analysis_results = Analyzer.conductCorrelationAnalysis(od_imgs, scan_parameter_values, options);
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%% Analyze G2 matrices
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@ -107,11 +107,7 @@ options.roi.center = [3, 3]; % center of ROI in µm (x0, y0)
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options.roi.size = [3, 11]; % width and height in µm
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options.roi.angle = pi/4; % rotation angle (radians, CCW)
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options.threshold = 0.85;
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options.deviationThreshold = 0.30;
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options.minEllipseFraction = 0.30;
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options.angleLimit = deg2rad(45);
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options.angleTolerance = deg2rad(5);
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options.fitDeviationThreshold = 0.9;
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% Plot control
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options.skipLivePlot = true;
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@ -121,13 +117,13 @@ analysis_results = Analyzer.analyzeG2Structures(g2_analysis_results, o
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options.skipLivePlot = true;
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options.skipSaveFigures = true;
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saveDirectory = 'C:\Users\Karthik-OfficePC\Documents\GitRepositories\Calculations\Data-Analyzer\+Scripts';
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Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results, analysis_results, options, ...
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'FontName', options.font, ...
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'FontSize', 14, ...
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'ShowOverlays', true, ...
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'RepsPerPage', 5, ... % paginate 10 repetitions per figure
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'SaveDirectory', saveDirectory, ...
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'RepsPerPage', 5, ...
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'SaveDirectory', options.saveDirectory , ...
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'SkipLivePlot', options.skipLivePlot, ...
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'SkipSaveFigures', options.skipSaveFigures);
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@ -135,13 +131,13 @@ Plotter.plotODG2withAnalysis(od_imgs, scan_parameter_values, g2_analysis_results
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Plotter.plotMeanWithSE(scan_parameter_values, analysis_results.anisotropy_vals, ...
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'Title', options.titleString, ...
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'YLim', [0,10], ...
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'YLim', [0,6], ...
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'XLabel', '\alpha (degrees)', ...
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'YLabel', 'Anisotropy of correlation peaks', ...
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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', pwd, ... % save figures inside dataset-specific folder
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'SaveDirectory', options.saveDirectory , ...
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'SkipSaveFigures', options.skipSaveFigures);
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%% Plot distribution of anisotropy
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@ -157,10 +153,10 @@ Plotter.plotPDF(grouped_data, ...
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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', pwd, ...
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'SaveDirectory', options.saveDirectory , ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'DataRange', [0 15], ...
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'DataRange', [0 10], ...
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'Colormap', @Colormaps.coolwarm, ...
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'XLim', [min(scan_reference_values) max(scan_reference_values)]);
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@ -188,4 +184,4 @@ function groupedData = groupDataByScan(scan_values, data_values)
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groupedData{i} = data_values(idx == i);
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end
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end
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end
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end
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@ -201,6 +201,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'A2', ...
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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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@ -218,6 +219,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'mu2', ...
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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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@ -234,6 +236,7 @@ Plotter.plotFitParameterPDF(fitResults, scan_reference_values, 'sigma2', ...
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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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@ -252,6 +255,9 @@ Plotter.plotSecondaryGaussianRange(fitResults, scan_reference_values, ...
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'NumberOfBins', 20, ...
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'NormalizeHistogram', true, ...
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'Colormap', @Colormaps.coolwarm, ...
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'OverlayMeanSEM', true);
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'OverlayMeanSEM', true, ...
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'SecondaryGaussianRange.fig', ...
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'SaveDirectory', options.saveDirectory);
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