Update hmrR_MotionCorrectSplineSG.m

% SplineSG_Motion_Correction

% SplineSG_Motion_Correction

%

%

% DESCRIPTION:

% DESCRIPTION:

% Perform a cubic spline correction of the motion artifacts identified in

% The function first identifies the baseline shifts and spikes in the signal. The baseline shifts are corrected using

% tIncCh. The algorithm follows the procedure describe by

% a spline interpolation method. The remaining spikes are corrected by Savitzky-Golay filtering, which is a digital smoothing filter

% Scholkmann et al., Physiol. Meas. 31, 649-662 (2010). Set p = -1 to skip

% that substitutes each value of the signal series with a new value obtained by applying a cubic fitting to a subset of adjacent data points.

% this function.

% The length of the subset is defined by the parameter FrameSize_sec.

% The method is described in the following paper.

% Citation: Jahani et al., Neurophotonics, 2018; doi: 10.1117/1.NPh.5.1.015003. 

% 

% 

% INPUTS:

% INPUTS:

% data_d:        SNIRF object containing time course data

% data_d:        SNIRF object containing time course data

% p:             Parameter p used in the spline interpolation. The value

% p:             Parameter p used in the spline interpolation. The value

%                recommended in the literature is 0.99. Use -1 if you want to skip this

%                recommended in the literature is 0.99. Use -1 if you want to skip this

%                motion correction.

%                motion correction.

% FrameSize_sec:

% FrameSize_sec: The step lenght in seconds that a least-squares minimization will be applied using a cubic Savitzky-Golay filter.  

% turnon:        Optional argument to enable/disable this function in a processing stream chain

% turnon:        Optional argument to enable/disable this function in a processing stream chain

%

%

% OUTPUTS:

% OUTPUTS:

%

%

% LOG:

% LOG:

% Sahar Jahani, October 2017

% Sahar Jahani, October 2017

% Added turn on/off option Meryem Nov 2017

function data_d = hmrR_MotionCorrectSplineSG(data_d, mlActAuto, p, FrameSize_sec, turnon)

function data_d = hmrR_MotionCorrectSplineSG(data_d, mlActAuto, p, FrameSize_sec, turnon)