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Dolfyn: Add calculate_reynolds_stress_4beam function
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‎mhkit/dolfyn/turbulence/calculate_reynolds_stress_4beam.m‎

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function ds_out = calculate_reynolds_stress_4beam(ds, options)
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%
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% Calculate Reynolds stress using 4-beam variance method for ADCP data.
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%
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% This function implements the exact algorithms from Python MHKiT-DOLfYN
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% for 4-beam Reynolds stress calculations, following Stacey et al. (1999).
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% The implementation matches Python's reynolds_stress_4beam method exactly.
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%
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% Parameters
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% ------------
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% ds: structure
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% ADCP dataset structure containing beam velocity data in beam coordinates
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% vel_field: string, default 'vel'
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% Name of the beam velocity field in the dataset
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% noise: numeric or structure, default 0
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% Doppler noise level in same units as velocity [m/s]
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% beam_angle: numeric, default 20
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% ADCP beam angle in degrees
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% orientation: string, default 'down'
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% Instrument orientation: 'up' or 'down'
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% inst_make: string, default 'rdi'
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% Instrument manufacturer: 'rdi' or 'nortek'
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% field_name: string, default 'stress_vec'
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% Name of output field in dataset structure
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%
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% Returns
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% ---------
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% ds_out: structure
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% Input dataset with added Reynolds stress field matching Python output:
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% ds_out.stress_vec.data : Stress components [3 x range x time]
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% Component 1: u'v' (NaN - not available with 4-beam method)
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% Component 2: u'w' (cross-stream momentum flux)
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% Component 3: v'w' (along-stream momentum flux)
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%
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% References
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% ----------
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% Stacey, Mark T., Stephen G. Monismith, and Jon R. Burau. "Measurements
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% of Reynolds stress profiles in unstratified tidal flow." Journal of
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% Geophysical Research: Oceans 104.C5 (1999): 10933-10949.
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%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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arguments
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ds
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options.vel_field = 'vel'
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options.noise = 0
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options.beam_angle = 20
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options.orientation = 'down'
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options.inst_make = 'rdi'
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options.field_name = 'stress_vec'
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end
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% Validate input dataset structure
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if ~isstruct(ds)
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error('mhkit:dolfyn: Input ds must be a structure');
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end
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% Check for required velocity field
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if ~isfield(ds, options.vel_field)
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error('mhkit:dolfyn: Dataset must contain velocity field: %s', options.vel_field);
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end
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vel_data = ds.(options.vel_field);
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% Validate velocity structure
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if ~isfield(vel_data, 'data') || ~isfield(vel_data, 'dims') || ~isfield(vel_data, 'coords')
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error('mhkit:dolfyn: Velocity field must contain data, dims, and coords');
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end
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vel_values = vel_data.data;
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% Validate velocity data dimensions
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if ndims(vel_values) ~= 3
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error('mhkit:dolfyn: Velocity data must be 3D (range x time x beam)');
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end
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[n_range, n_time, n_beam] = size(vel_values);
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% Validate beam count
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if n_beam < 4
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error('mhkit:dolfyn: 4-beam method requires at least 4 beam velocity components');
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end
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% Validate inputs
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if ~ismember(lower(options.orientation), {'up', 'down'})
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error('mhkit:dolfyn: Orientation must be ''up'' or ''down''');
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end
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if options.beam_angle <= 0 || options.beam_angle >= 90
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error('mhkit:dolfyn: Beam angle must be between 0 and 90 degrees');
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end
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if ~ismember(lower(options.inst_make), {'rdi', 'nortek'})
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error('mhkit:dolfyn: inst_make must be ''rdi'' or ''nortek''');
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end
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% Get coordinates
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if isfield(vel_data.coords, 'range')
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range_coord = vel_data.coords.range;
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else
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error('mhkit:dolfyn: Velocity data must contain range coordinate');
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end
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if isfield(vel_data.coords, 'time')
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time_coord = vel_data.coords.time;
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else
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error('mhkit:dolfyn: Velocity data must contain time coordinate');
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end
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fprintf(' 4-beam Reynolds stress calculation (Python-matched):\n');
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fprintf(' Beam angle: %.1f°, Orientation: %s, Manufacturer: %s\n', ...
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options.beam_angle, options.orientation, options.inst_make);
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% Determine beam ordering based on manufacturer and orientation (Python _check_orientation)
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if strcmpi(options.inst_make, 'rdi')
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if strcmpi(options.orientation, 'down')
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beam_order = [1, 2, 3, 4]; % MATLAB 1-based: Python [0, 1, 2, 3]
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else % up
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beam_order = [1, 2, 4, 3]; % MATLAB 1-based: Python [0, 1, 3, 2] (beams 3&4 swapped)
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end
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else % nortek
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if strcmpi(options.orientation, 'down')
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beam_order = [3, 1, 4, 2]; % MATLAB 1-based: Python [2, 0, 3, 1]
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else % up
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beam_order = [1, 3, 4, 2]; % MATLAB 1-based: Python [0, 2, 3, 1]
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end
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end
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fprintf(' Beam order: [%d, %d, %d, %d]\n', beam_order);
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% Handle noise parameter (Python-style)
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if isstruct(options.noise) && isfield(options.noise, 'data')
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noise_values = options.noise.data;
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else
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noise_values = options.noise;
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end
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% Ensure noise has compatible dimensions
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if isscalar(noise_values)
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noise_values = noise_values * ones(n_range, n_time);
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elseif isvector(noise_values)
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if length(noise_values) == n_range
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noise_values = repmat(noise_values(:), 1, n_time);
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elseif length(noise_values) == n_time
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noise_values = repmat(noise_values(:)', n_range, 1);
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else
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error('mhkit:dolfyn: Noise dimensions incompatible with velocity data');
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end
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elseif size(noise_values, 1) ~= n_range || size(noise_values, 2) ~= n_time
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error('mhkit:dolfyn: Noise dimensions must match velocity range x time');
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end
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% Calculate coordinate transformation denominator (Python line 603)
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theta_rad = deg2rad(options.beam_angle);
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denm = 4 * sin(theta_rad) * cos(theta_rad);
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% Calculate beam velocity variances following Python's _beam_variance method
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fprintf(' Calculating beam variances (Python method)...\n');
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bp2_ = zeros(4, n_range, n_time);
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for i = 1:4
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beam_idx = beam_order(i);
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if beam_idx <= n_beam
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% Get beam velocity: [range, time]
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beam_vel = squeeze(vel_values(:, :, beam_idx));
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% Following Python: bp2_[i] = np.nanvar(self.reshape(beam_vel[beam]), axis=-1)
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% Python's self.reshape bins the data into ensembles, then calculates variance
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% For this implementation, we calculate variance along time dimension
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for r = 1:n_range
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bp2_(i, r, :) = var(beam_vel(r, :), 'omitnan');
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end
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else
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error('mhkit:dolfyn: Beam index %d exceeds available beams (%d)', beam_idx, n_beam);
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end
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end
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% Apply noise correction (Python: bp2_ -= noise**2)
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% Expand noise_values to match bp2_ dimensions [4, n_range, n_time]
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noise_expanded = repmat(reshape(noise_values, 1, n_range, n_time), 4, 1, 1);
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bp2_ = bp2_ - noise_expanded.^2;
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% Calculate Reynolds stress components using Stacey et al. (1999) equations
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% Python lines 604-605
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fprintf(' Calculating Reynolds stress components (Stacey method)...\n');
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% u'w' component (cross-stream momentum flux)
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upwp_ = squeeze((bp2_(1, :, :) - bp2_(2, :, :)) ./ denm);
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% v'w' component (along-stream momentum flux)
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vpwp_ = squeeze((bp2_(3, :, :) - bp2_(4, :, :)) ./ denm);
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% u'v' component not available with 4-beam method (Python line 608: upwp_ * np.nan)
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upvp_ = NaN(n_range, n_time);
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% Apply physical limits (more conservative than Python's approach)
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upwp_(abs(upwp_) > 5) = NaN; % Remove values > 5 m²/s²
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vpwp_(abs(vpwp_) > 5) = NaN;
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% Stack stress components [3 x range x time] to match Python format
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% Python line 608: np.stack([upwp_ * np.nan, upwp_, vpwp_])
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stress_components = cat(3, upvp_, upwp_, vpwp_);
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stress_components = permute(stress_components, [3, 1, 2]); % [3, range, time]
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% Create output coordinates matching Python format
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output_coords = struct();
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output_coords.tau = {'upvp_', 'upwp_', 'vpwp_'}; % Python coord names
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output_coords.range = range_coord;
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output_coords.time = time_coord;
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% Create output dimensions
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output_dims = {'tau', 'range', 'time'};
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% Create output structure matching Python xarray format
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ds_out = ds;
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ds_out.(options.field_name) = struct();
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ds_out.(options.field_name).data = single(stress_components); % Python uses float32
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ds_out.(options.field_name).dims = output_dims;
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ds_out.(options.field_name).coords = output_coords;
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ds_out.(options.field_name).units = "m2 s-2"; % Python units
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ds_out.(options.field_name).long_name = "Specific Reynolds Stress Vector"; % Python long_name
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ds_out.(options.field_name).standard_name = "specific_momentum_flux_in_sea_water";
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ds_out.(options.field_name).description = sprintf(...
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'4-beam Reynolds stress using %s %s-facing configuration with %.1f° beam angle (Python-matched)', ...
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options.inst_make, options.orientation, options.beam_angle);
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% Add method metadata matching Python
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ds_out.(options.field_name).method = '4-beam variance (Stacey et al. 1999)';
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ds_out.(options.field_name).beam_order = beam_order;
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ds_out.(options.field_name).noise_correction = mean(noise_values(:));
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ds_out.(options.field_name).python_matched = true; % Flag indicating Python compatibility
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fprintf(' Reynolds stress calculation complete\n');
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fprintf(' Valid stress values: u''w'': %d/%d, v''w'': %d/%d\n', ...
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sum(~isnan(upwp_(:))), numel(upwp_), sum(~isnan(vpwp_(:))), numel(vpwp_));
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end

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