% script for automatically evaluating Brillouin data
% copy this file to the folder with the data you want to evaluate and
% adjust the parameters below if necessary

%% path to the files
filelist = dir('**/*.h5');

%% parameter structure
% use this configuration for new calibrations with water + methanol
peakTypes = {'R', 'B', 'B', 'B', 'B', 'R'};
% use this configuration for old calibrations with only water or methanol
% peakTypes = {'R', 'B', 'B', 'R', 'NaN'};

parameters = struct( ...
    'data', struct( ...
        'rotate', -1, ...               % {-1 , 0, 1} rotate the image by k*90 degrees
        'flipud', false, ...            % flip the image up-down
        'fliplr', false, ...            % flip the image left-right
        'setup', 'S2' ...               % The used setup
    ), ...
    'extraction', struct( ...           % parameters for the extraction
        'do', true ...                  % execute extraction?
    ), ...
    'calibration', struct( ...          % parameters for the calibration
        'do', true, ...                 % execute calibration?
        'findPeaks', false, ...         % find the Rayleigh and Brillouin peaks
        'peakProminence', 15, ...       % the minimal prominence of the peaks
        'peakTypes', {peakTypes}, ...   % expected types of peaks
        'correctOffset', false, ...     % correct the calibration offset?
        'extrapolate', true, ...        % extrapolate the calibration?
        'weighted', false ...           % use weighting for calibration calculation?
    ), ...
    'peakSelection', struct( ...        % parameters for the peak selection
        'do', true, ...                 % execute peak selection?
        'unit', 'GHz', ...              % unit to use {'GHz' or 'pix'}
        'valuesRayleigh', [12.0 18.0], ...  % frequency range for Rayleigh peaks
        'valuesBrillouin', [7.5 12.0]  ...  % frequency range for Brillouin peaks
    ), ...
    'evaluation', struct( ...           % parameters for the evaluation
        'do', true, ...                 % execute evaluation?
        'interpRayleigh', true, ...     % interpolate Rayleigh peaks position?
        'minRayleighPeakHeight', 50, ...% minimum height of Rayleigh peaks
        'nrBrillouinPeaks', 2, ...      % [1]   number of Brillouin peaks to fit
        'constraints', struct( ...      % constraints for the Brillouin peak fit
            'sa', struct( ...           % first peak - frequency
                'Lower', 7.65, ...      % [GHz] lower border
                'Upper', 7.85 ...       % [GHz] upper border
            ), ...
            'wa', struct( ...           % first peak - width
                'Lower', 3, ...         % [pix] lower border
                'Upper', Inf ...        % [pix] upper border
            ), ...
            'Ba', struct( ...           % first peak - intensity
                'Lower', 0, ...         % [a.u.] lower border
                'Upper', Inf ...        % [a.u.] upper border
            ), ...
            'sb', struct( ...           % second peak - frequency
                'Lower', 7.85, ...      % [GHz] lower border
                'Upper', 'max' ...      % [GHz] upper border
            ), ...
            'wb', struct( ...           % second peak - width
                'Lower', 3, ...         % [pix] lower border
                'Upper', Inf ...        % [pix] upper border
            ), ...
            'Bb', struct( ...           % second peak - intensity
                'Lower', 0, ...         % [a.u.] lower border
                'Upper', Inf ...        % [a.u.] upper border
            ) ...
        ) ...
    )...
);

BrillouinEvaluation_Auto(filelist, parameters);