Modified PDF plotting to allow for plotting true histogram with and without normalization as default, with KDE as a choice. Modified function calls accordingly.
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@ -1,8 +1,11 @@
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function plotPDF(dataCell, referenceValues, varargin)
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%% plotPDF: Plots 2D heatmap of PDFs for grouped data
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%% plotPDF: Plots 2D heatmap of PDFs for grouped data (Histogram or KDE)
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%
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% Usage:
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% Plotter.plotPDF(dataCell, referenceValues, ...
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% 'PlotType', 'histogram', ... % 'histogram' (default) or 'kde'
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% 'NumBins', 50, ... % number of histogram bins
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% 'NormalizeHist', true, ... % normalize hist counts to probability density
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% 'Title', 'My Title', ...
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% 'XLabel', 'Scan Parameter', ...
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% 'YLabel', 'Data Values', ...
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@ -31,42 +34,77 @@ function plotPDF(dataCell, referenceValues, varargin)
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addParameter(p, 'DataRange', [], @(x) isempty(x) || numel(x)==2);
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addParameter(p, 'XLim', [], @(x) isempty(x) || numel(x)==2);
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addParameter(p, 'Colormap', @jet);
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addParameter(p, 'PlotType', 'histogram', @(x) any(validatestring(x,{'kde','histogram'})));
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addParameter(p, 'NumBins', 50, @isscalar);
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addParameter(p, 'NormalizeHist', true, @islogical);
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parse(p, varargin{:});
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opts = p.Results;
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N_params = numel(referenceValues);
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% --- Determine y-grid for PDF ---
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% --- Determine y-range ---
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if isempty(opts.DataRange)
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allData = cell2mat(dataCell(:));
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y_grid = linspace(min(allData), max(allData), opts.NumPoints);
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y_min = min(allData);
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y_max = max(allData);
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else
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y_grid = linspace(opts.DataRange(1), opts.DataRange(2), opts.NumPoints);
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y_min = opts.DataRange(1);
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y_max = opts.DataRange(2);
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end
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pdf_matrix = zeros(numel(y_grid), N_params);
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if strcmpi(opts.PlotType,'kde') % KDE
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y_grid = linspace(y_min, y_max, opts.NumPoints);
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pdf_matrix = zeros(numel(y_grid), N_params);
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else % Histogram
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edges = linspace(y_min, y_max, opts.NumBins+1);
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binCenters = (edges(1:end-1) + edges(2:end)) / 2;
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pdf_matrix = zeros(numel(binCenters), N_params);
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end
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% --- Compute PDFs ---
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for i = 1:N_params
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data = dataCell{i};
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data = data(~isnan(data));
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if isempty(data), continue; end
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f = ksdensity(data, y_grid);
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pdf_matrix(:, i) = f;
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if strcmpi(opts.PlotType,'kde') % KDE
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f = ksdensity(data, y_grid);
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pdf_matrix(:, i) = f;
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else % Histogram
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counts = histcounts(data, edges);
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if opts.NormalizeHist
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binWidth = edges(2) - edges(1);
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counts = counts / (sum(counts) * binWidth); % probability density
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end
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pdf_matrix(:, i) = counts(:);
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end
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end
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% --- Plot heatmap ---
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fig = figure(opts.FigNum); clf(fig);
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set(fig, 'Color', 'w', 'Position',[100 100 950 750]);
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imagesc(referenceValues, y_grid, pdf_matrix);
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if strcmpi(opts.PlotType,'kde')
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imagesc(referenceValues, y_grid, pdf_matrix);
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else
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imagesc(referenceValues, binCenters, pdf_matrix);
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end
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set(gca, 'YDir', 'normal', 'FontName', opts.FontName, 'FontSize', opts.FontSize);
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xlabel(opts.XLabel, 'Interpreter', 'latex', 'FontSize', opts.FontSize, 'FontName', opts.FontName);
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ylabel(opts.YLabel, 'Interpreter', 'latex', 'FontSize', opts.FontSize, 'FontName', opts.FontName);
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title(opts.Title, 'Interpreter', 'latex', 'FontSize', opts.FontSize + 2, 'FontWeight', 'bold');
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colormap(feval(opts.Colormap));
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c = colorbar;
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ylabel(c, 'PDF', 'Interpreter', 'latex', 'FontSize', opts.FontSize);
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if strcmpi(opts.PlotType,'kde')
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ylabel(c, 'PDF', 'Interpreter', 'latex', 'FontSize', opts.FontSize);
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else
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if opts.NormalizeHist
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ylabel(c, 'Probability Density', 'Interpreter', 'latex', 'FontSize', opts.FontSize);
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else
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ylabel(c, 'Counts', 'Interpreter', 'latex', 'FontSize', opts.FontSize);
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end
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end
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if ~isempty(opts.XLim)
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xlim(opts.XLim);
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@ -78,4 +116,4 @@ function plotPDF(dataCell, referenceValues, varargin)
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'SaveDirectory', opts.SaveDirectory, ...
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'SkipSaveFigures', opts.SkipSaveFigures);
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end
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end
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@ -79,7 +79,8 @@ Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
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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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Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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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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@ -88,7 +89,8 @@ Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
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'SaveDirectory', figSaveDir, ...
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'NumPoints', 200, ...
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'NumBins', 20, ...
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'NormalizeHist', true, ...
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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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@ -79,7 +79,8 @@ Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
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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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Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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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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@ -88,12 +89,12 @@ Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
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'SaveDirectory', figSaveDir, ...
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'NumPoints', 200, ...
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'NumBins', 20, ...
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'NormalizeHist', true, ...
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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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@ -79,7 +79,8 @@ Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
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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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Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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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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@ -88,7 +89,8 @@ Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
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'SaveDirectory', figSaveDir, ...
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'NumPoints', 200, ...
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'NumBins', 20, ...
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'NormalizeHist', true, ...
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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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@ -79,7 +79,8 @@ Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
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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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Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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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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@ -88,7 +89,8 @@ Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_
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'SkipSaveFigures', options.skipSaveFigures, ...
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'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
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'SaveDirectory', figSaveDir, ...
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'NumPoints', 200, ...
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'NumBins', 20, ...
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'NormalizeHist', true, ...
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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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@ -4,14 +4,14 @@
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dataSources = {
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struct('sequence', 'StructuralPhaseTransition', ...
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'date', '2025/08/18', ...
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'runs', [8]) % specify run numbers as a string in "" or just as a numeric value
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'runs', [8, 9, 10, 11, 12, 13]) % 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.measurementName = 'DropletsToStripes';
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options.measurementName = 'StripesToDroplets';
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scriptFullPath = mfilename('fullpath');
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options.saveDirectory = fileparts(scriptFullPath);
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