hmrR_MotionArtifact and hmrR_MotionArtifactByChannel now take previously...

% SYNTAX:

% tInc = hmrR_MotionArtifact(data, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

% tInc = hmrR_MotionArtifact(data, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

%

% UI NAME:

% Motion_Artifacts

% probe:   SNIRF data structure probe, containing probe source/detector geometry

% mlActMan: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% mlActAuto: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% tIncMan: Cell array of vectors corresponding to the number of time bases in data. 

%          tIncMan has been manually excluded. 0-excluded. 1-included. Vector same length as d.

% tMotion: Check for signal change indicative of a motion artifact over

%       with 1's indicating data included and 0's indicate motion artifact

%

% USAGE OPTIONS:

% Motion_Artifacts:  tIncAuto = hmrR_MotionArtifact(dod, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

% Motion_Artifacts:  tIncAuto = hmrR_MotionArtifact(dod, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

%

% PARAMETERS:

% tMotion: 0.5

% JDUBB 3/18/2019 Adapted to SNIRF format

%

%

function tInc = hmrR_MotionArtifact(data, probe, mlActMan, tIncMan, tMotion, tMask, std_thresh, amp_thresh)

function tInc = hmrR_MotionArtifact(data, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, std_thresh, amp_thresh)

% Init output 

tInc = cell(length(data),1);

if isempty(mlActMan)

    mlActMan = cell(length(data),1);

end

if isempty(mlActAuto)

    mlActAuto = cell(length(data),1);

end

for iBlk=1:length(data)

    if isempty(mlActMan{iBlk})

        mlActMan{iBlk} = ones(size(MeasList,1),1);

    end

    MeasListAct = mlActMan{iBlk};        

    if isempty(mlActAuto{iBlk})

        mlActAuto{iBlk} = ones(size(MeasList,1),1);

    end

    MeasListAct = mlActMan{iBlk} & mlActAuto{iBlk};        

    % Calculate the diff of d to to set the threshold if ncssesary

    diff_d = diff(d);

% [tInc,tIncCh] = hmrR_MotionArtifactByChannel(data, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

% [tInc,tIncCh] = hmrR_MotionArtifactByChannel(data, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

%

% UI NAME:   

% Motion_Artifacts_By_Channel

%          tIncMan has been manually excluded. 0-excluded. 1-included. Vector same length as d.

% mlActMan: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% mlActAuto: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% tMotion: Check for signal change indicative of a motion artifact over

%     time range tMotion. Units of seconds.

% tMask: Mark data over +/- tMask seconds around the identified motion 

%       channel basis

%

% USAGE OPTIONS:

% Motion_Artifacts_By_Channel:  [tIncAuto, tIncAutoCh] = hmrR_MotionArtifactByChannel(dod, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

% Motion_Artifacts_By_Channel:  [tIncAuto, tIncAutoCh] = hmrR_MotionArtifactByChannel(dod, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

%

% PARAMETERS:

% tMotion: 0.5

% TO DO:

% Consider tIncMan

function [tInc, tIncCh] = hmrR_MotionArtifactByChannel(data, probe, mlActMan, tIncMan, tMotion, tMask, std_thresh, amp_thresh)

function [tInc, tIncCh] = hmrR_MotionArtifactByChannel(data, probe, mlActMan, mlActAuto, tIncMan, tMotion, tMask, std_thresh, amp_thresh)

tInc   = cell(length(data), 1);

tIncCh = cell(length(data), 1);

if isempty(mlActMan)

    mlActMan = cell(length(data),1);

end

if isempty(mlActAuto)

    mlActAuto = cell(length(data),1);

end

for iBlk=1:length(data)

    if isempty(mlActMan{iBlk})

        mlActMan{iBlk} = ones(size(MeasList,1),1);

    end

    MeasListAct = mlActMan{iBlk};

    if isempty(mlActAuto{iBlk})

        mlActAuto{iBlk} = ones(size(MeasList,1),1);

    end

    MeasListAct = mlActMan{iBlk} & mlActAuto{iBlk};      

    % Calculate the diff of d to to set the threshold if ncssesary

    diff_d = diff(d);