118 lines
4.2 KiB
Matlab
118 lines
4.2 KiB
Matlab
%% ===== 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.baseDataFolder = '//DyLabNAS/Data';
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options.measurementName = 'BECToDroplets';
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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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options.angle = 0;
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options.center = [1420, 2050];
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options.span = [200, 200];
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options.fraction = [0.1, 0.1];
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options.pixel_size = 5.86e-6; % in meters
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options.magnification = 23.94;
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options.removeFringes = false;
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options.ImagingMode = 'HighIntensity';
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options.PulseDuration = 5e-6; % in s
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% Fourier analysis settings
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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
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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;
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% Scan parameter
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options.scan_parameter = 'rot_mag_field';
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switch options.measurementName
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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 = 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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options.skipIntensityThresholding = true;
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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.showProgressBar = true;
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% Extras
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options.font = 'Bahnschrift';
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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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Analyzer.runInteractiveODImageViewer(od_imgs, scan_parameter_values, file_list, options); |