Added more verbose text to display in console, new scripts to analyse Stripe to Droplet transition.
This commit is contained in:
parent
b0f45aa7e6
commit
dc360ed659
@ -89,15 +89,22 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
|
||||
assignin('base', 'full_bkg_imgs', full_bkg_imgs);
|
||||
assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
|
||||
assignin('base', 'raw_file_list', raw_file_list);
|
||||
fprintf('\nCompleted computing OD images and will be stored in workspace for reuse.\n');
|
||||
fprintf('\nCompleted computing OD images. Images will be stored in workspace for reuse.\n');
|
||||
end
|
||||
|
||||
fprintf('\nCropping and subtracting background from images...\n');
|
||||
nFiles = size(full_od_imgs, 3);
|
||||
|
||||
% --- Preallocate arrays for processed images ---
|
||||
absimages = zeros(options.span(1)+1, options.span(2)+1, nFiles, 'single');
|
||||
refimages = zeros(options.span(1)+1, options.span(2)+1, nFiles, 'single');
|
||||
|
||||
% --- Progress bar ---
|
||||
if isfield(options, 'showProgressBar') && options.showProgressBar
|
||||
pb = Helper.ProgressBar();
|
||||
pb.run('Progress: ');
|
||||
end
|
||||
|
||||
% --- Process each image: crop and subtract background ---
|
||||
for k = 1:nFiles
|
||||
full_od_img = full_od_imgs(:,:,k); % original full OD image, never modified
|
||||
@ -122,6 +129,17 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
|
||||
% Store processed image (transpose to match orientation)
|
||||
absimages(:,:,k) = processed_absimage';
|
||||
refimages(:,:,k) = processed_refimage';
|
||||
|
||||
% Update progress bar
|
||||
if isfield(options, 'showProgressBar') && options.showProgressBar
|
||||
progressPercent = round(k / nFiles * 100);
|
||||
pb.run(progressPercent);
|
||||
end
|
||||
end
|
||||
|
||||
% Finish progress bar
|
||||
if isfield(options, 'showProgressBar') && options.showProgressBar
|
||||
pb.run(' Done!');
|
||||
end
|
||||
|
||||
% --- Optional fringe removal ---
|
||||
|
||||
@ -35,7 +35,7 @@ function [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list]
|
||||
% --- Progress bar ---
|
||||
if isfield(options, 'showProgressBar') && options.showProgressBar
|
||||
pb = Helper.ProgressBar();
|
||||
pb.run('Computing OD images | Progress: ');
|
||||
pb.run('Progress: ');
|
||||
end
|
||||
|
||||
raw_file_list = strings(1, nFiles); % store full file paths
|
||||
|
||||
@ -0,0 +1,163 @@
|
||||
idx = 1;
|
||||
compiled_results = results_all{idx}.results;
|
||||
options.skipSaveFigures = false;
|
||||
|
||||
%% ------------------ 1. Mean ± Std Plots ------------------
|
||||
% Plot Radial Spectral Contrast
|
||||
Plotter.plotMeanWithSE(scan_parameter_values, compiled_results.spectral_analysis_results.radial_spectral_contrast, ...
|
||||
'Title', options.titleString, ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'YLabel', 'Radial Spectral Contrast', ...
|
||||
'FigNum', 1, ...
|
||||
'FontName', options.font, ...
|
||||
'SaveFileName', 'RadialSpectralContrast.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'SkipSaveFigures', options.skipSaveFigures);
|
||||
|
||||
% Plot Angular Spectral Weight
|
||||
Plotter.plotMeanWithSE(scan_parameter_values, compiled_results.spectral_analysis_results.angular_spectral_weight, ...
|
||||
'Title', options.titleString, ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'YLabel', 'Angular Spectral Weight', ...
|
||||
'FigNum', 2, ...
|
||||
'FontName', options.font, ...
|
||||
'SaveFileName', 'AngularSpectralWeight.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'SkipSaveFigures', options.skipSaveFigures);
|
||||
|
||||
% Plot Peak Offset Angular Correlation
|
||||
Plotter.plotMeanWithSE(options.scan_reference_values, compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, ...
|
||||
'Title', options.titleString, ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'YLabel', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
|
||||
'FigNum', 3, ...
|
||||
'YLim', [0 1], ...
|
||||
'FontName', options.font, ...
|
||||
'SaveFileName', 'PeakOffsetAngularCorrelation.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'SkipSaveFigures', options.skipSaveFigures);
|
||||
|
||||
%% ------------------ 2. g²(θ) across transition ------------------
|
||||
Plotter.plotG2(compiled_results.full_g2_results.g2_all, ...
|
||||
compiled_results.full_g2_results.g2_error_all, ...
|
||||
compiled_results.full_g2_results.theta_values, ...
|
||||
options.scan_reference_values, ...
|
||||
'rot_mag_field', ...
|
||||
'Title', options.titleString, ...
|
||||
'XLabel', '$\delta\theta / \pi$', ...
|
||||
'YLabel', '$g^{(2)}(\delta\theta)$', ...
|
||||
'FigNum', 4, ...
|
||||
'FontName', options.font, ...
|
||||
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||
'SaveFileName', 'G2ThetaAcrossTransition.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'Colormap', @Colormaps.coolwarm);
|
||||
|
||||
%% ------------------ 3. PDF of max g² across transition ------------------
|
||||
Plotter.plotPDF(compiled_results.custom_g_results.max_g2_all_per_scan_parameter_value, options.scan_reference_values, ...
|
||||
'Title', options.titleString, ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'YLabel', '$\mathrm{max}[g^{(2)}]$', ...
|
||||
'FigNum', 5, ...
|
||||
'FontName', options.font, ...
|
||||
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||
'SaveFileName', 'PDF_MaxG2AcrossTransition.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'NumPoints', 200, ...
|
||||
'DataRange', [0 1.5], ...
|
||||
'Colormap', @Colormaps.coolwarm, ...
|
||||
'XLim', [min(options.scan_reference_values) max(options.scan_reference_values)]);
|
||||
|
||||
|
||||
%% ------------------ 4. Cumulants across transition ------------------
|
||||
Plotter.plotCumulants(options.scan_reference_values, ...
|
||||
{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}, ...
|
||||
'Title', 'Cumulants of Peak Offset Angular Correlation', ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'FigNum', 6, ...
|
||||
'FontName', options.font, ...
|
||||
'MarkerSize', 6, ...
|
||||
'LineWidth', 1.5, ...
|
||||
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||
'SaveFileName', 'CumulantOfPeakOffsetAngularCorrelation.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results']);
|
||||
%{
|
||||
|
||||
%% ------------------ 6. Average of Spectra Plots ------------------
|
||||
|
||||
Plotter.plotAverageSpectra(scan_parameter_values, ...
|
||||
spectral_analysis_results, ...
|
||||
'ScanParameterName', scan_parameter, ...
|
||||
'FigNum', 7, ...
|
||||
'ColormapPS', Colormaps.coolwarm(), ...
|
||||
'Font', 'Bahnschrift', ...
|
||||
'SaveFileName', 'avgSpectra.fig', ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'SkipSaveFigures', options.skipSaveFigures);
|
||||
|
||||
%% ------------------ 7. Compare quantities ------------------
|
||||
% Load Droplets → Stripes data
|
||||
Data = load(dtsFile, ...
|
||||
'unique_scan_parameter_values', ...
|
||||
'mean_max_g2_values', ...
|
||||
'std_error_g2_values');
|
||||
dts_scan_parameter_values = Data.unique_scan_parameter_values;
|
||||
dts_mean_mg2 = Data.mean_max_g2_values;
|
||||
dts_stderr_mg2 = Data.std_error_g2_values;
|
||||
|
||||
% Load Stripes → Droplets data
|
||||
Data = load(stdFile, ...
|
||||
'unique_scan_parameter_values', ...
|
||||
'mean_max_g2_values', ...
|
||||
'std_error_g2_values');
|
||||
std_scan_parameter_values = Data.unique_scan_parameter_values;
|
||||
std_mean_mg2 = Data.mean_max_g2_values;
|
||||
std_stderr_mg2 = Data.std_error_g2_values;
|
||||
|
||||
% Prepare cell arrays for multiple datasets
|
||||
scanValsCell = {dts_scan_parameter_values, std_scan_parameter_values};
|
||||
meanValsCell = {dts_mean_mg2, std_mean_mg2};
|
||||
stderrValsCell = {dts_stderr_mg2, std_stderr_mg2};
|
||||
|
||||
% Compare datasets
|
||||
compareMultipleDatasets(scanValsCell, meanValsCell, stderrValsCell, ...
|
||||
'FigNum', 8, ...
|
||||
'FontName', 'Bahnschrift', ...
|
||||
'MarkerSize', 6, ...
|
||||
'LineWidth', 1.5, ...
|
||||
'CapSize', 5, ...
|
||||
'YLim', [0 1], ...
|
||||
'Labels', {'Droplets → Stripes', 'Stripes → Droplets'}, ...
|
||||
'Title', 'AngularCorrelation_Comparison', ...
|
||||
'XLabel', 'B (G)', ...
|
||||
'YLabel', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
|
||||
'SkipSaveFigures', options.skipSaveFigures, ...
|
||||
'SaveDirectory', [options.saveDirectory '/Results'], ...
|
||||
'SaveFileName', 'AngularCorrelation_Comparison.fig');
|
||||
|
||||
%% ------------------ 8. Heatmaps ------------------
|
||||
|
||||
BFields = [2.35, 2.15, 2.0, 1.85, 1.7, 1.55, 1.4, 1.35];
|
||||
|
||||
% Heatmap of mean_max_g2_values
|
||||
Plotter.plotHeatmap(compiled_results, options.scan_groups, BFields, 'mean_max_g2_values', ...
|
||||
'Colormap', @sky, ...
|
||||
'CLim', [0 1], ...
|
||||
'XLabel', '\alpha (degrees)', ...
|
||||
'YLabel', 'BField (G)', ...
|
||||
'Title', '$\mathrm{max}[g^{(2)}_{[50,70]}(\delta\theta)]$', ...
|
||||
'FigNum', 9, ...
|
||||
'SaveFileName', 'Heatmap_MaxG2.fig', ...
|
||||
'SaveDirectory', options.resultsDir);
|
||||
|
||||
% Heatmap of radial_spectral_contrast
|
||||
Plotter.plotHeatmap(compiled_results, options.scan_groups, BFields, 'radial_spectral_contrast', ...
|
||||
'Colormap', @sky, ...
|
||||
'CLim', [0 0.008], ...
|
||||
'XLabel', '\alpha (degrees)', ...
|
||||
'YLabel', 'BField (G)', ...
|
||||
'Title', 'Radial Spectral Contrast', ...
|
||||
'FigNum', 10, ...
|
||||
'SaveFileName', 'Heatmap_RadialSpectralContrast.fig', ...
|
||||
'SaveDirectory', options.resultsDir);
|
||||
%}
|
||||
116
Data-Analyzer/+Scripts/BECToStripesToDroplets/plotImages.m
Normal file
116
Data-Analyzer/+Scripts/BECToStripesToDroplets/plotImages.m
Normal file
@ -0,0 +1,116 @@
|
||||
%% ===== BEC-Droplets-Stripes Settings =====
|
||||
|
||||
% Specify data location to run analysis on
|
||||
dataSources = {
|
||||
struct('sequence', 'StructuralPhaseTransition', ...
|
||||
'date', '2025/08/18', ...
|
||||
'runs', [12]) % specify run numbers as a string in "" or just as a numeric value
|
||||
};
|
||||
|
||||
options = struct();
|
||||
|
||||
% File / paths
|
||||
options.baseDataFolder = '//DyLabNAS/Data';
|
||||
options.measurementName = 'StripesToDroplets';
|
||||
scriptFullPath = mfilename('fullpath');
|
||||
options.saveDirectory = fileparts(scriptFullPath);
|
||||
|
||||
% Camera / imaging
|
||||
options.cam = 5;
|
||||
options.angle = 0;
|
||||
options.center = [1420, 2050];
|
||||
options.span = [200, 200];
|
||||
options.fraction = [0.1, 0.1];
|
||||
options.pixel_size = 5.86e-6; % in meters
|
||||
options.magnification = 24.6;
|
||||
options.removeFringes = false;
|
||||
options.ImagingMode = 'HighIntensity';
|
||||
options.PulseDuration = 5e-6; % in s
|
||||
|
||||
% Fourier analysis settings
|
||||
options.theta_min = deg2rad(0);
|
||||
options.theta_max = deg2rad(180);
|
||||
options.N_radial_bins = 500;
|
||||
options.Radial_Sigma = 2;
|
||||
options.Radial_WindowSize = 5; % odd number
|
||||
|
||||
options.k_min = 1.2771; % μm⁻¹
|
||||
options.k_max = 2.5541; % μm⁻¹
|
||||
options.N_angular_bins = 180;
|
||||
options.Angular_Threshold = 75;
|
||||
options.Angular_Sigma = 2;
|
||||
options.Angular_WindowSize = 5;
|
||||
options.zoom_size = 50;
|
||||
|
||||
% Scan parameter
|
||||
options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
|
||||
|
||||
switch options.measurementName
|
||||
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 = true;
|
||||
options.skipPreprocessing = true;
|
||||
options.skipMasking = true;
|
||||
options.skipIntensityThresholding = true;
|
||||
options.skipBinarization = true;
|
||||
options.skipSaveFigures = true;
|
||||
options.skipLivePlot = false;
|
||||
options.showProgressBar = true;
|
||||
|
||||
% Extras
|
||||
options.font = 'Bahnschrift';
|
||||
|
||||
%% ===== Build Paths from Data Sources =====
|
||||
|
||||
allPaths = {}; % initialize
|
||||
|
||||
for i = 1:length(dataSources)
|
||||
ds = dataSources{i};
|
||||
|
||||
% Split the date string into year/month/day
|
||||
dateParts = strsplit(ds.date, '/');
|
||||
|
||||
for run = ds.runs
|
||||
runStr = sprintf('%04d', run); % 4-digit run number
|
||||
fullPath = fullfile(options.baseDataFolder, ds.sequence, dateParts{:}, runStr);
|
||||
|
||||
if isfolder(fullPath) % only include valid directories
|
||||
allPaths{end+1} = fullPath;
|
||||
else
|
||||
warning('Path does not exist: %s', fullPath);
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% Let user select a single path
|
||||
set(0,'DefaultUicontrolFontSize',10); % increase default font size
|
||||
[selectedIndex, tf] = listdlg('PromptString','Select a path to analyze:', ...
|
||||
'SelectionMode','single', ...
|
||||
'ListString', allPaths, ...
|
||||
'ListSize',[400, 300]); % width x height in pixels
|
||||
if tf
|
||||
options.folderPath = fullfile(allPaths{selectedIndex}); % ✅ store in options
|
||||
fprintf('Path set to selection: %s\n', options.folderPath);
|
||||
else
|
||||
error('No path selected. Aborting.');
|
||||
end
|
||||
|
||||
%% ===== Collect Images and Launch Viewer =====
|
||||
|
||||
[od_imgs, scan_parameter_values, file_list] = Helper.collectODImages(options);
|
||||
|
||||
Analyzer.runInteractiveODImageViewer(od_imgs, scan_parameter_values, file_list, options);
|
||||
@ -0,0 +1,78 @@
|
||||
%% ===== BEC-Droplets-Stripes Settings =====
|
||||
|
||||
% Specify data location to run analysis on
|
||||
dataSources = {
|
||||
struct('sequence', 'StructuralPhaseTransition', ...
|
||||
'date', '2025/08/16', ...
|
||||
'runs', [8]) % specify run numbers as a string in "" or just as a numeric value
|
||||
};
|
||||
|
||||
options = struct();
|
||||
|
||||
% File / paths
|
||||
options.baseDataFolder = '//DyLabNAS/Data';
|
||||
options.measurementName = 'DropletsToStripes';
|
||||
scriptFullPath = mfilename('fullpath');
|
||||
options.saveDirectory = fileparts(scriptFullPath);
|
||||
|
||||
% Camera / imaging
|
||||
options.cam = 5;
|
||||
options.angle = 0;
|
||||
options.center = [1420, 2050];
|
||||
options.span = [200, 200];
|
||||
options.fraction = [0.1, 0.1];
|
||||
options.pixel_size = 5.86e-6; % in meters
|
||||
options.magnification = 24.6;
|
||||
options.removeFringes = false;
|
||||
options.ImagingMode = 'HighIntensity';
|
||||
options.PulseDuration = 5e-6; % in s
|
||||
|
||||
% Fourier analysis settings
|
||||
options.theta_min = deg2rad(0);
|
||||
options.theta_max = deg2rad(180);
|
||||
options.N_radial_bins = 500;
|
||||
options.Radial_Sigma = 2;
|
||||
options.Radial_WindowSize = 5; % odd number
|
||||
|
||||
options.k_min = 1.2771; % μm⁻¹
|
||||
options.k_max = 2.5541; % μm⁻¹
|
||||
options.N_angular_bins = 180;
|
||||
options.Angular_Threshold = 75;
|
||||
options.Angular_Sigma = 2;
|
||||
options.Angular_WindowSize = 5;
|
||||
options.zoom_size = 50;
|
||||
|
||||
% Scan parameter
|
||||
options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
|
||||
|
||||
switch options.measurementName
|
||||
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.skipSaveFigures = 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