Commit 1752244e authored by Jay's avatar Jay
Browse files

v1.19.3 

-- Provide working skeleton for hmrR_tCCA.m that shows how to write the help section and extract data from SINRF variables
-- Add methods to AuxClass to be able to extract time and datatimeseries variables
-- Rename SNIRF DataClass method AppendD to the much clearer AppendDataTimeSeries
parent 590e8c93

DataTree/AcquiredData/Snirf/AuxClass.m

+38 −3
Original line number Diff line number Diff line
@@ -16,8 +16,12 @@ classdef AuxClass < FileLoadSaveClass 
            

            obj.timeOffset = 0;

            if nargin==1

                if isa(varargin{1}, 'AuxClass')

                    obj = varargin{1}.copy();

                elseif ischar(varargin{1})

                    obj.filename = varargin{1};

                    obj.Load();

                end

            elseif nargin==3

                obj.dataTimeSeries    = varargin{1};

                obj.time = varargin{2};
@@ -95,8 +99,17 @@ classdef AuxClass < FileLoadSaveClass 
        end

        

        

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

        function SetDataTimeSeries(obj, val)

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

                return;

            end

            obj.dataTimeSeries = val;

        end

        

        

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

        function d = GetData(obj)

        function d = GetDataTimeSeries(obj)

            d = obj.dataTimeSeries;

        end
@@ -107,6 +120,28 @@ classdef AuxClass < FileLoadSaveClass 
        end

        

        

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

        function val = GetTime(obj)

            val = obj.time;

        end

        

        

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

        function Copy(obj, obj2)

            if isempty(obj)

                obj = DataClass();

            end

            if ~isa(obj2, 'DataClass')

                return;

            end

            for ii=1:length(obj2.measurementList)

                obj.measurementList(ii) = obj2.measurementList(ii).copy();      % shallow copy ok because MeasListClass has no handle properties

            end

            obj.dataTimeSeries = obj2.dataTimeSeries;

            obj.time = obj2.time;

        end

        

        

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

        function B = eq(obj, obj2)

            B = false;

DataTree/AcquiredData/Snirf/SnirfClass.m

+1 −9
Original line number Diff line number Diff line
@@ -648,7 +648,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                return;

            end

            for ii=1:length(obj.aux)

                datamat(:,ii) = obj.aux(ii).GetData();

                datamat(:,ii) = obj.aux(ii).GetDataTimeSeries();

            end

        end
@@ -881,14 +881,6 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

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

        function aux = Get_aux(obj)

            aux = [];

            for ii=1:size(obj.aux,2)

                aux(:,ii) = obj.aux(ii).GetData();

            end

        end

        

        

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

        function s = Get_s(obj, iBlk)

FuncRegistry/UserFunctions/hmrG_SubjAvg.m

+2 −2
Original line number Diff line number Diff line
@@ -104,7 +104,7 @@ for iBlk = 1:length(yAvgSubjs{1}) 
                    end

                end

                if iSubj == nSubj                

                    yAvgOut(iBlk).AppendD(yAvg);

                    yAvgOut(iBlk).AppendDataTimeSeries(yAvg);

                end

            end
@@ -154,7 +154,7 @@ for iBlk = 1:length(yAvgSubjs{1}) 
                    end

                end

                if iSubj == nSubj

                    yAvgOut(iBlk).AppendD(yAvg);

                    yAvgOut(iBlk).AppendDataTimeSeries(yAvg);

                end

            end

FuncRegistry/UserFunctions/hmrR_BandpassFilt.m

+10 −3
Original line number Diff line number Diff line
@@ -28,11 +28,18 @@ 
%



function [data2, ylpf] = hmrR_BandpassFilt( data, hpf, lpf )



if isa(data, 'DataClass')

    data2 = DataClass().empty();

elseif isa(data, 'AuxClass')

    data2 = AuxClass().empty();

end

ylpf = [];

for ii=1:length(data)

    if isa(data, 'DataClass')

        data2(ii) = DataClass(data(ii));

    elseif isa(data, 'AuxClass')

        data2(ii) = AuxClass(data(ii));

    end

    y = data2(ii).GetDataTimeSeries();

    fs = data2(ii).GetTime();

FuncRegistry/UserFunctions/hmrR_BlockAvg.m

+6 −9
Original line number Diff line number Diff line
@@ -59,9 +59,6 @@ for kk=1:length(data) 
    

    datatype = data(kk).GetDataTypeLabel();  % Get the input data type

    y = data(kk).GetDataTimeSeries('reshape');    % Get the data vector 

%     if strncmp(datatype{1},'Hb',2)

%         y = reshape(y, size(y,1), 3, size(y,2)/3);

%     end

    t = data(kk).GetTime();    % Get the time vector 

    dt = t(2)-t(1);

    nPre = round(trange(1)/dt);
@@ -129,9 +126,9 @@ for kk=1:length(data) 
            end

            

            % Snirf stuff: set data vectors

            data_avg(kk).AppendD(yavg(:,:,:,iC));

            data_std(kk).AppendD(ystd(:,:,:,iC));

            data_sum2(kk).AppendD(ysum2(:,:,:,iC));

            data_avg(kk).AppendDataTimeSeries(yavg(:,:,:,iC));

            data_std(kk).AppendDataTimeSeries(ystd(:,:,:,iC));

            data_sum2(kk).AppendDataTimeSeries(ysum2(:,:,:,iC));

        elseif strcmp(datatype{1}, 'dOD')

            yTrials(iC).yblk = yblk(:,:,1:nBlk);

            yavg(:,:,iC) = mean(yblk(:,:,1:nBlk),3);
@@ -155,9 +152,9 @@ for kk=1:length(data) 
            end

            

            % Snirf stuff: set data vectors

            data_avg(kk).AppendD(yavg(:,:,iC));

            data_std(kk).AppendD(ystd(:,:,iC));

            data_sum2(kk).AppendD(ysum2(:,:,iC));

            data_avg(kk).AppendDataTimeSeries(yavg(:,:,iC));

            data_std(kk).AppendDataTimeSeries(ystd(:,:,iC));

            data_sum2(kk).AppendDataTimeSeries(ysum2(:,:,iC));

        end

    end

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