Commit c118c689 authored by jayd1860's avatar jayd1860
Browse files

v1.48.1 

-- Fix typo in hmrR_MotionCorrectWavelet.m causing matlab-generated exception
-- More fixes in user functions hmrR_MotionArtifactByChannel.m and hmrR_MotionCorrectCbsi.m of inactive channels mlAct
-- Added another performance enhancer in DataClass.GetDataTimeSeries() to speed up retrieval of measurement list and thus data time series. Added cache for measurement list matrix to avoid recalculating it.
parent ab0fe489

DataTree/AcquiredData/Snirf/DataClass.m

+16 −2
Original line number Diff line number Diff line
@@ -6,6 +6,9 @@ classdef DataClass < FileLoadSaveClass 
        measurementList

    end

    

    properties

        cache

    end

    

    methods
@@ -46,6 +49,7 @@ classdef DataClass < FileLoadSaveClass 
            

            % Set SNIRF fomat properties

            obj.measurementList = MeasListClass().empty();

            obj.cache = struct('measurementListMatrix',[]);

            

            if nargin==0

                return;
@@ -387,13 +391,20 @@ classdef DataClass < FileLoadSaveClass 
        

        % ---------------------------------------------------------

        function ml = GetMeasurementList(obj, option)

            ml = [];

            if ~exist('option','var')

                option = '';

            end            

            hbTypes         = {'hbo','hbr','hbt'};

            if isempty(option)

                ml = obj.measurementList;

            elseif strcmp(option,'matrix')                

            elseif strncmp(option,'matrix',length('matrix'))

                if ~isempty(obj.cache) && ~isempty(obj.cache.measurementListMatrix)

                    if strcmp(option,'matrix')

                        ml = obj.cache.measurementListMatrix;

                        return

                    end

                end

                ml = zeros(length(obj.measurementList),4);

                for ii = 1:length(obj.measurementList)

                    k = 0;
@@ -409,6 +420,9 @@ classdef DataClass < FileLoadSaveClass 
                        ml(ii,:) = [obj.measurementList(ii).sourceIndex, obj.measurementList(ii).detectorIndex, obj.measurementList(ii).dataTypeIndex, k];                        

                    end

                end

                

                % Cache the results to avoid recalculating 

                obj.cache.measurementListMatrix = ml;

            end

        end

FuncRegistry/UserFunctions/hmrR_MotionArtifactByChannel.m

+5 −10
Original line number Diff line number Diff line
@@ -94,7 +94,7 @@ for iBlk = 1:length(data) 
    d           = data(iBlk).GetDataTimeSeries();

    fs          = data(iBlk).GetTime();

    MeasList    = data(iBlk).GetMeasList();

    Lambda      = probe.GetWls();

    nDataTypes  = unique(MeasList(:,4));

    

    if length(fs)~=1

        fs = 1/(fs(2)-fs(1));
@@ -103,7 +103,6 @@ for iBlk = 1:length(data) 
    if isempty(tIncMan{iBlk})

        tIncMan{iBlk} = ones(size(d,1),1);

    end    

    

    tInc{iBlk}   = ones(size(d,1),1);

    tIncCh{iBlk} = ones(size(d,1), size(MeasList,1));
@@ -111,17 +110,13 @@ for iBlk = 1:length(data) 
    mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, MeasList);

    MeasListAct = mlActMan{iBlk}(:,3) & mlActAuto{iBlk}(:,3);

    

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

       

    % set artifact buffer for tMask seconds on each side of spike

    art_buffer = round(tMask*fs); % time in seconds times sample rate

    

    % get list of active channels

    %lstAct = find(MeasListAct==1);

    lstAct = zeros(size(MeasList,1),1);

    nLambda = length(Lambda);

    lst1 = find(MeasList(:,4)==1);

    for ii = 1:nLambda

    for ii = 1:nDataTypes

        for jj = 1:length(lst1)

            lst(jj) = find(MeasList(:,1)==MeasList(lst1(jj),1) & ...

                           MeasList(:,2)==MeasList(lst1(jj),2) & ...

FuncRegistry/UserFunctions/hmrR_MotionCorrectCbsi.m

+7 −12
Original line number Diff line number Diff line
@@ -51,14 +51,9 @@ for iBlk=1:length(data_dc) 
    dc = data_dc(iBlk).GetDataTimeSeries('reshape');

    ml = data_dc(iBlk).GetMeasListSrcDetPairs('reshape');

        

    dc = reshape(dc, size(dc,1), 3, size(dc,2)/3);

    mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, ml);

    lstAct          = mlAct_Matrix2IndexList(mlActAuto{iBlk}, ml);

    

    if isempty(mlActAuto{iBlk})

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

    end    

    mlAct = mlActAuto{iBlk};



    lstAct = find(mlAct(1:size(ml,1))==1);

    dcCbsi = dc;

    

    for ii = 1:length(lstAct)

FuncRegistry/UserFunctions/hmrR_MotionCorrectWavelet.m

+4 −4
Original line number Diff line number Diff line
@@ -62,11 +62,11 @@ if isempty(mlActAuto) 
    mlActAuto = cell(length(data_dod),1);

end



for kk=1:length(data_dod)

for iBlk = 1:length(data_dod)



    dod         = data_dod(kk).GetDataTimeSeries();

    dod         = data_dod(iBlk).GetDataTimeSeries();

    dodWavelet  = dod;

    MeasList    = data_dod(kk).GetMeasList();   

    MeasList    = data_dod(iBlk).GetMeasList();   

    

    mlActMan{iBlk} = mlAct_Initialize(mlActMan{iBlk}, MeasList);

    mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, MeasList);
@@ -109,7 +109,7 @@ for kk=1:length(data_dod) 
        

        dodWavelet(:,idx_ch) = ARSignal(1:length(dod));

    end

    data_dod(kk).SetDataTimeSeries(dodWavelet);

    data_dod(iBlk).SetDataTimeSeries(dodWavelet);

    

end

Version.txt

+1 −1
Original line number Diff line number Diff line 
1.48.0

1.48.1

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