Modifications in batch analysis script to take sequence name, date and run number, to reuse data saved in workspace and enhancements to image viewer.
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f52666d929
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1f7526c594
@ -9,7 +9,7 @@ function results_all = batchAnalyze(dataSources, options)
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options.baseDataFolder = '//DyLabNAS/Data';
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end
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results_all = struct([]); % one element per folder
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results_all = {}; % one element per folder
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for i = 1:numel(dataSources)
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ds = dataSources{i};
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@ -63,7 +63,7 @@ function results_all = batchAnalyze(dataSources, options)
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result.results = analysisResults;
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% Append to output
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results_all(end+1,1) = result;
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results_all{end+1,1} = result;
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catch ME
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warning("Error processing %s/%s/%s: %s", ...
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@ -20,6 +20,15 @@ function [ordered_od_imgs, ordered_scan_parameter_values, ordered_file_list] = c
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% ordered_od_imgs : cell array of processed OD images (ordered)
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% ordered_scan_parameter_values: vector of scan parameter values (ordered)
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% ordered_file_list : cell array of file names (ordered)
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% --- Early exit if processed data already exist ---
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if evalin('base', 'exist(''od_imgs'',''var'') && exist(''scan_parameter_values'',''var'') && exist(''file_list'',''var'')')
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fprintf('\nReusing processed OD images, scan parameters, and file list from memory.\n');
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ordered_od_imgs = evalin('base','od_imgs');
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ordered_scan_parameter_values = evalin('base','scan_parameter_values');
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ordered_file_list = evalin('base','file_list');
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return; % ✅ skip rest of the function
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end
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% --- Check if the full OD dataset and scan parameters exist in workspace ---
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fullDataExists = evalin('base', 'exist(''full_od_imgs'', ''var'')') && ...
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@ -39,7 +48,7 @@ function [ordered_od_imgs, ordered_scan_parameter_values, ordered_file_list] = c
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fprintf('\nFull OD image dataset or scan parameters not found in memory.\n');
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(options);
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% Optionally save the full dataset into workspace for future reuse
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% Save raw full dataset for reuse
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assignin('base', 'full_od_imgs', full_od_imgs);
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assignin('base', 'full_bkg_imgs', full_bkg_imgs);
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assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
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@ -103,9 +112,9 @@ function [ordered_od_imgs, ordered_scan_parameter_values, ordered_file_list] = c
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ordered_file_list = cell(1, n_total);
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counter = 1;
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temp_scan_values = raw_scan_parameter_values; % copy for indexing
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temp_scan_values = raw_scan_parameter_values;
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temp_od_imgs = processed_od_imgs;
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temp_file_list = raw_file_list; % copy original file paths for reordering
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temp_file_list = raw_file_list;
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for rep = 1:n_reps
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for val = options.scan_reference_values
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@ -113,25 +122,25 @@ function [ordered_od_imgs, ordered_scan_parameter_values, ordered_file_list] = c
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if isempty(idx), continue; end
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ordered_scan_parameter_values(counter) = temp_scan_values(idx);
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ordered_od_imgs{counter} = temp_od_imgs{idx};
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ordered_file_list{counter} = temp_file_list{idx}; % reorder file list
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temp_scan_values(idx) = NaN; % mark as used
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ordered_file_list{counter} = temp_file_list{idx};
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temp_scan_values(idx) = NaN;
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temp_od_imgs{idx} = [];
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temp_file_list{idx} = [];
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counter = counter + 1;
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end
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end
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fprintf('\nImage reordering completed.\n');
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else
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% No unshuffling: keep original order
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ordered_od_imgs = processed_od_imgs;
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ordered_scan_parameter_values = raw_scan_parameter_values;
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ordered_file_list = raw_file_list;
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ordered_file_list = raw_file_list;
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end
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% Optionally save the full dataset into workspace for future reuse
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% --- Save processed dataset for reuse ---
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assignin('base', 'od_imgs', ordered_od_imgs);
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assignin('base', 'scan_parameter_values', ordered_scan_parameter_values);
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assignin('base', 'file_list', ordered_file_list);
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fprintf('\nOD image dataset ready for further analysis.\n');
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end
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@ -1,6 +1,10 @@
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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, results_all.spectral_analysis_results.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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@ -11,7 +15,7 @@ Plotter.plotMeanWithSE(scan_parameter_values, results_all.spectral_analysis_resu
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'SkipSaveFigures', options.skipSaveFigures);
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% Plot Angular Spectral Weight
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Plotter.plotMeanWithSE(scan_parameter_values, results_all.spectral_analysis_results.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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@ -22,7 +26,7 @@ Plotter.plotMeanWithSE(scan_parameter_values, results_all.spectral_analysis_resu
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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, results_all.custom_g_results.max_g2_all_per_scan_parameter_value, ...
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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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@ -34,9 +38,9 @@ Plotter.plotMeanWithSE(options.scan_reference_values, results_all.custom_g_resul
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'SkipSaveFigures', options.skipSaveFigures);
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%% ------------------ 2. g²(θ) across transition ------------------
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Plotter.plotG2(results_all.full_g2_results.g2_all, ...
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results_all.full_g2_results.g2_error_all, ...
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results_all.full_g2_results.theta_values, ...
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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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@ -50,7 +54,7 @@ Plotter.plotG2(results_all.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(results_all.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, 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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@ -67,7 +71,7 @@ Plotter.plotPDF(results_all.custom_g_results.max_g2_all_per_scan_parameter_value
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%% ------------------ 4. Cumulants across transition ------------------
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Plotter.plotCumulants(options.scan_reference_values, ...
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{results_all.custom_g_results.mean_max_g2, results_all.custom_g_results.var_max_g2, results_all.custom_g_results.skew_max_g2_angle, results_all.custom_g_results.fourth_order_cumulant_max_g2}, ...
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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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@ -136,7 +140,7 @@ compareMultipleDatasets(scanValsCell, meanValsCell, stderrValsCell, ...
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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(results_all, options.scan_groups, BFields, '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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@ -147,7 +151,7 @@ Plotter.plotHeatmap(results_all, options.scan_groups, BFields, 'mean_max_g2_valu
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'SaveDirectory', options.resultsDir);
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% Heatmap of radial_spectral_contrast
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Plotter.plotHeatmap(results_all, options.scan_groups, BFields, '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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@ -1,10 +1,19 @@
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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.folderPath = "//DyLabNAS/Data/StructuralPhaseTransition/2025/08/13/0062";
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options.baseDataFolder = '//DyLabNAS/Data';
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options.savefileName = 'BECToDroplets';
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options.saveDirectory = "Z:/Users/Karthik/Data-Analyzer/+Scripts";
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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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@ -19,41 +28,40 @@ options.ImagingMode = 'HighIntensity';
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options.PulseDuration = 5e-6; % in s
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% Fourier analysis settings
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% Radial Spectral Distribution
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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 for centered moving avg
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options.Radial_WindowSize = 5; % odd number
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% Angular Spectral Distribution
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options.k_min = 1.2771; % in μm⁻¹
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options.k_max = 2.5541; % in μm⁻¹
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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; % zoomed-in region around center
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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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if strcmp(options.savefileName, '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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elseif strcmp(options.savefileName, '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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elseif strcmp(options.savefileName, '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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elseif strcmp(options.savefileName, '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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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 = true;
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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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@ -62,14 +70,49 @@ 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.skipLivePlot = false;
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options.showProgressBar = true;
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% Optional extras
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% Extras
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options.font = 'Bahnschrift';
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%%
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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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%%
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Analyzer.runInteractiveODImageViewer(od_imgs, scan_parameter_values, file_list, options);
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