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CSL_Feeding_Detector.m

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+%CSL_Feeding_Detector
+%
+%   Detects prey capture by California sea lions using the surge- and
+%   heave-axis acceleration (from 3-axis acceleration data), as validated
+%   by Cole et al. (in Review)
+%
+%   INPUT PARAMETERS:
+%       A: (required) 3-axis acceleration data from a head-mounted
+%           accelerometer, organized in 3 columns as [sway surge heave].
+%           Be sure acceleration data are in units 'g' (1g = 9.81 m
+%           s^-2). Surge-axis acceleration data must be sampled (or
+%           arranged) such that positive values indicate forward (direction
+%           of swimming) acceleration, and negative values indicate
+%           backward acceleration. 
+%       rateS: (required) tag sampling rate, in Hz
+%       rateA: (optional) desired analysis rate (Hz), if different than
+%           rateS. 
+%       time: (optional) timestamps corresponding to A. Required IF
+%           plotting prey capture against depth or if using a depth threshold
+%       depth: (OPTIONAL) depth vector; add if a plot of feeding events
+%           overlain on a depth profile is desired
+%       rateD: (OPTIONAL; Mandatory if plotting depth) depth sampling rate.
+%       depth_time: (OPTIONAL) timestamps corresponding to optional depth
+%           vector; essential if depth sampling rate differs from that of
+%           acceleration data
+%       depth_threshold: (OPTIONAL) depth in meters (positive values); if
+%           depth_threshold is used, only detected feeding events
+%           deeper than the threshold will appear in plots and outputs. 
+%
+%   OUTPUTS:
+%       Summary: summary statistics describing each detected feeding
+%           event. Arranged as:
+%               Column 1: Event #
+%               Column 2: Detected event Duration
+%               Column 3: Maximum value of smoothed heave-axis Jerk
+%               Column 4: Maximum (negative) value of dynamic surge-axis deceleration
+%               Column 5: Integral of smoothed heave-axis Jerk (area under
+%                        heave-Jerk curve in detected zone)
+%               Column 6: Integral of |dynamic surge-axis values| in
+%                         detected zone
+%               Column 7: timestamp of onset of event
+%
+%       Event_Data: relevent data for each event, all in one big matrix
+%               Column 1: Feeding Event #
+%               Column 2: Feeding Event Data timestamps
+%               Column 3: smoothed heave-axis Jerk data
+%               Column 4: filtered (~dynamic) surge-axis acceleration data
+%
+%       Plots: Fig. 1: Surge-axis filtered acceleration (top) and
+%                       Heave-axis smoothed Jerk (bottom), for visual
+%                       inspection of acceleration signals
+%              Fig. 2: (if depth is added as an input): detected prey capture events plotted on depth profile 
+%
+
+%------------------------------------------------------------------------------------------------------------
+% DEFINE PARAMETERS HERE:
+%    It's important that the variable names do not change, as they are
+%    inputed into a function
+
+A = [acc(:,1) acc(:,2) acc(:,3)];  % [sway surge heave]
+rateS = 50;
+rateA = 50;                             % if rateA not specified, set rateA = [];
+time = t;         % if time not specified, set time = [];
+depth = depth;               % if depth not added, set depth = [];
+rateD = 1;                             % depth sampling rate in Hz. if rateD not specified, set rateD = [];
+depth_time = ptime;    % if depth_time not specified, set depth_time = [];
+depth_threshold = 5;                    % if depth_threshold not specified, set = [];
+
+% Now Run Script!
+%-------------------------------------------------------------------------------------------------------------
+
+% -----------------------------------------------------------------------------------------------------------------
+
+%--------------------------------------------------------------------------------------------------------------------
+%internal function: CSL_Feeding
+[Summary,Event_Data] = CSL_Feeding(A,rateS,rateA,time,depth,rateD,depth_time,depth_threshold);