121 lines
5.2 KiB
Matlab
121 lines
5.2 KiB
Matlab
%% ===== BEC-Droplets-Stripes Settings =====
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% Specify data location to run analysis on
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dataSources = {
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struct('sequence', 'TwoDGas', ...
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'date', '2025/06/23', ...
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'runs', [300]) % 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.FullODImagesFolder = 'E:/Data - Experiment/FullODImages/202506';
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options.measurementName = 'DropletsToStripes';
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scriptFullPath = mfilename('fullpath');
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options.saveDirectory = fileparts(scriptFullPath);
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% Camera / imaging settings
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options.cam = 4; % 1 - ODT_1_Axis_Camera; 2 - ODT_2_Axis_Camera; 3 - Horizontal_Axis_Camera;, 4 - Vertical_Axis_Camera;
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options.angle = 0; % angle by which image will be rotated
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options.center = [1410, 2030];
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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 = 24.6;
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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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% Flags
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options.skipUnshuffling = false;
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options.skipNormalization = false;
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options.skipFringeRemoval = true;
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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.skipFullODImagesFolderUse = false;
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options.skipSaveData = false;
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options.skipSaveFigures = true;
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options.skipSaveProcessedOD = true;
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options.skipLivePlot = true;
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options.showProgressBar = true;
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% Extras
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options.font = 'Bahnschrift';
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switch options.measurementName
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case 'BECToDroplets'
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options.scan_parameter = 'rot_mag_field';
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options.flipSortOrder = true;
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options.scanParameterUnits = 'gauss';
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options.titleString = 'BEC to Droplets';
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case 'BECToStripes'
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options.scan_parameter = 'rot_mag_field';
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options.flipSortOrder = true;
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options.scanParameterUnits = 'gauss';
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options.titleString = 'BEC to Stripes';
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case 'DropletsToStripes'
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options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
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options.flipSortOrder = false;
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options.scanParameterUnits = 'degrees';
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options.titleString = 'Droplets to Stripes';
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case 'StripesToDroplets'
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options.scan_parameter = 'ps_rot_mag_fin_pol_angle';
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options.flipSortOrder = false;
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options.scanParameterUnits = 'degrees';
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options.titleString = 'Stripes to Droplets';
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end
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%% ===== Collect Images and Launch Viewer =====
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[options.selectedPath, options.folderPath] = Helper.selectDataSourcePath(dataSources, options);
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[od_imgs, scan_parameter_values, scan_reference_values, file_list] = Helper.collectODImages(options);
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%% Minimal pipeline: preprocess + detect patches + extract shapes
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% ---------- user-tunable parameters ----------
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params.backgroundDiskFraction = 1/8; % Fraction of image size used for morphological opening
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params.boundingBoxPadding = 12; % Padding around detected cloud
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params.dogGaussianSmallSigma = 1.2; % Sigma for small Gaussian in Difference-of-Gaussians
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params.dogGaussianLargeSigma = 3.8; % Sigma for large Gaussian in Difference-of-Gaussians
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params.minPeakProminence = 0.02; % Threshold for DoG response
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params.minPeakFraction = 0.80; % Fraction of max DoG response to reject weak patches
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params.minimumPatchArea = 100; % Minimum area (pixels) for detected patches to be kept
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params.shapeMinArea = 20; % Minimum shape area
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params.shapeCloseRadius = 3; % Morphological closing radius (fills holes)
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params.shapeFillHoles = false; % Ensures shapes are solid regions
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params.intensityThreshFraction = 0.45; % Fraction of max intensity to keep
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params.edgeSigma = 1.0; % Gaussian smoothing for Canny
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params.edgeThresholdLow = 0.25; % Low Canny threshold fraction
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params.edgeThresholdHigh = 0.55; % High Canny threshold fraction
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params.pixelSize = 5.86e-6; % Physical pixel size (meters/pixel)
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params.magnification = 23.94; % Magnification factor of imaging system
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% --------------------------------------------
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Analyzer.runInteractiveFeatureDetectorGUI(od_imgs, scan_parameter_values, file_list, options, params)
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