Commit 402d7875 authored by jayd1860's avatar jayd1860
Browse files

v1.50.0 

-- Fix another channel order bug in DataClass.GetDataTimeSeries. order need to match linear order when squeezing dimensions > 1 into 1D. This caused incorrect results to be displayed for concentration HbT after running  hmrR_MotionCorrectCbsi
-- Fix minor display issue in MainGUI.m icorrectly enabling OD and concentration radio buttons even though no results exists.
-- Add diagnostic/debug functions to unit test to generate simulated data time series whose data identifies the channel it originated in.
parent 48ea9bf4

DataTree/AcquiredData/Snirf/DataClass.m

+42 −35
Original line number Diff line number Diff line
@@ -479,8 +479,8 @@ classdef DataClass < FileLoadSaveClass 
            end

                      

            dataTypeLabels = {};

            srcs = zeros(0,2);

            dets = zeros(0,2);

            srcs = zeros(0,1);

            dets = zeros(0,1);

            conditions = [];

            wavelengths = [];

            hh=1; jj=1; kk=1; ll=1; mm=1;
@@ -507,24 +507,31 @@ classdef DataClass < FileLoadSaveClass 
                end

            end

            

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

            % Sort all the dimension data

            srcs            = sort(srcs);

            dets            = sort(dets);

            wavelengths     = sort(wavelengths);

            hbTypes         = sort(dataTypeLabels);            

            conditions      = sort(conditions);

            

            nWavelengths    = length(wavelengths);

            nDataTypeLabels = length(dataTypeLabels);

            nDataTypeLabels = length(hbTypes);

            nCond           = length(conditions);

            measurementList = obj.GetMeasurementList('matrix');            

            ml              = obj.GetMeasListSrcDetPairs('reshape');



            measurementListFull = obj.GetMeasurementList('matrix');

            measurementListSDpairs = obj.GetMeasListSrcDetPairs('reshape');

            

            kk = 1;

            if nWavelengths > 0 && nCond == 0

                

                for iWl = 1:nWavelengths

                for iS = 1:length(srcs)

                    for iD = 1:length(dets)

                        for iWl = 1:nWavelengths

                            

                            k = find(measurementList(:,1)==srcs(iS) & measurementList(:,2)==dets(iD) & measurementList(:,4)==iWl);

                            k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==wavelengths(iWl));

                            if ~isempty(k)

                                iSrcDetPair = find(ml(:,1)==srcs(iS) & ml(:,2)==dets(iD));

                                d(:, iWl, iSrcDetPair) = obj.dataTimeSeries(:,k); %#ok<*FNDSB>

                                iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));

                                d(:, iWl, iSDPair) = obj.dataTimeSeries(:,k); %#ok<*FNDSB>

                                order(kk) = k;

                                kk = kk+1;

                            end
@@ -535,15 +542,15 @@ classdef DataClass < FileLoadSaveClass 
                

            elseif nWavelengths > 0 && nCond > 0 

                

                for iWl = 1:nWavelengths

                for iS = 1:length(srcs)

                    for iD = 1:length(dets)

                        for iWl = 1:nWavelengths

                            for iCond = 1:nCond

                                

                                k = find(measurementList(:,1)==srcs(iS) & measurementList(:,2)==dets(iD) & measurementList(:,3)==iCond &  measurementList(:,4)==iWl);

                                k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==wavelengths(iWl));

                                if ~isempty(k)

                                    iSrcDetPair = find(ml(:,1)==srcs(iS) & ml(:,2)==dets(iD));

                                    d(:, iWl, iSrcDetPair, iCond) = obj.dataTimeSeries(:,k);

                                    iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));

                                    d(:, iWl, iSDPair, iCond) = obj.dataTimeSeries(:,k);

                                    order(kk) = k;

                                    kk = kk+1;

                                end
@@ -555,14 +562,14 @@ classdef DataClass < FileLoadSaveClass 
                

            elseif nDataTypeLabels > 0 && nCond == 0 

                

                for iHbType = 1:length(hbTypes)

                for iS = 1:length(srcs)

                    for iD = 1:length(dets)

                        for iHbType = 1:length(hbTypes)

                            

                            k = find(measurementList(:,1)==srcs(iS) & measurementList(:,2)==dets(iD) & measurementList(:,4)==iHbType);

                            k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==iHbType);

                            if ~isempty(k)

                                iSrcDetPair = find(ml(:,1)==srcs(iS) & ml(:,2)==dets(iD));

                                d(:, iHbType, iSrcDetPair) = obj.dataTimeSeries(:,k);

                                iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));

                                d(:, iHbType, iSDPair) = obj.dataTimeSeries(:,k);

                                order(kk) = k;

                                kk = kk+1;

                            end
@@ -573,15 +580,15 @@ classdef DataClass < FileLoadSaveClass 
                

            elseif nDataTypeLabels > 0 && nCond > 0 

                

                for iHbType = 1:length(hbTypes)

                for iS = 1:length(srcs)

                    for iD = 1:length(dets)

                        for iHbType = 1:length(hbTypes)

                            for iCond = 1:nCond



                                k = find(measurementList(:,1)==srcs(iS) & measurementList(:,2)==dets(iD) & measurementList(:,3)==iCond &  measurementList(:,4)==iHbType);

                                k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==iHbType);

                                if ~isempty(k)

                                    iSrcDetPair = find(ml(:,1)==srcs(iS) & ml(:,2)==dets(iD));

                                    d(:, iHbType, iSrcDetPair, iCond) = obj.dataTimeSeries(:,k);

                                    iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));

                                    d(:, iHbType, iSDPair, iCond) = obj.dataTimeSeries(:,k);

                                    order(kk) = k;

                                    kk = kk+1;

                                end

FuncRegistry/UserFunctions/hmrR_MotionCorrectCbsi.m

+2 −2
Original line number Diff line number Diff line
@@ -48,7 +48,7 @@ if isempty(mlActAuto) 
end



for iBlk = 1:length(data_dc)

    dc = data_dc(iBlk).GetDataTimeSeries('reshape');

    [dc, order] = data_dc(iBlk).GetDataTimeSeries('reshape');

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

        

    mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, ml);
@@ -71,7 +71,7 @@ for iBlk = 1:length(data_dc) 
        dcCbsi(:,2,idx_ch) = -(1/alfa)*dcCbsi(:,1,idx_ch);

        dcCbsi(:,3,idx_ch) = dcCbsi(:,1,idx_ch) + dcCbsi(:,2,idx_ch);

    end

    dcCbsi = reshape(dcCbsi, size(dcCbsi,1), size(dcCbsi,2)*size(dcCbsi,3));    

    dcCbsi(:,order) = dcCbsi(:,:);

    data_dc(iBlk).SetDataTimeSeries(dcCbsi);

end

MainGUI/MainGUI.m

+7 −3
Original line number Diff line number Diff line
@@ -115,13 +115,15 @@ set(handles.textPanDisplay, 'enable', val); 
% Plot type selected panel

set(handles.listboxPlotConc, 'enable', val);

set(handles.listboxPlotWavelength, 'enable', val);



set(handles.radiobuttonPlotRaw, 'enable', val);

set(handles.radiobuttonPlotOD,  'enable', val);

set(handles.radiobuttonPlotConc, 'enable', val);

set(handles.checkboxPlotHRF, 'enable', val);



set(handles.popupmenuAux, 'enable', val);

set(handles.checkboxPlotAux, 'enable', val);

set(handles.popupmenuConditions, 'enable', val);

set(handles.checkboxPlotHRF, 'enable', val);



% Motion artifact panel

set(handles.checkboxShowExcludedTimeManual, 'enable', val);
@@ -252,6 +254,10 @@ InitGuiControls(handles); 


% Display data from currently selected processing element

DisplayGroupTree(handles);



% If data set has no errors enable window gui objects

MainGUI_EnableDisableGUI(handles,'on');



Display(handles, hObject);



% Store Original X and Y Lims for AxesSDG
@@ -269,8 +275,6 @@ set(hObject,'name', title); 
maingui.logger.InitChapters()

maingui.logger.CurrTime(sprintf('MainGUI: Startup time - %0.1f seconds\n', toc(startuptimer)));



% If data set has no errors enable window gui objects

MainGUI_EnableDisableGUI(handles,'on');

UnitTests/generateSimData.m

0 → 100644
+31 −0
Original line number Diff line number Diff line 
function obj = generateSimData(obj)

d = [];

if ischar(obj)

    obj = SnirfClass(obj);

    d = obj.data;

elseif isa(obj, 'SnirfClass')

    d = obj.data;

elseif isa(obj, 'DataClass')

    d = obj;

    obj = SnirfClass(d);

end

ml = d.GetMeasurementList('matrix');

for iBlk = length(d)

    nTpts = size(d(iBlk).dataTimeSeries,1);

    for iM = 1:length(d(iBlk).measurementList)

        data = ml(iM,:);

        stepsize = floor(nTpts / length(data));

        for iDt = 1:length(data)

            y = data(iDt);

            iTptS = (iDt-1) * stepsize + 1;

            iTptE = iTptS + stepsize - 1;            

            if iTptE > nTpts

                iTptE = nTpts;

            end

            d(iBlk).dataTimeSeries(iTptS:iTptE, iM) = y;

        end

    end

end



obj.data = d;

UnitTests/plotDataTimeSeries.m

0 → 100644
+14 −0
Original line number Diff line number Diff line 
function k = plotDataTimeSeries(y, iS, iD, iDt, option)

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

    option = '';

end

ml = y.GetMeasurementList('matrix');

k = find(ml(:,1)==iS & ml(:,2)==iD & ml(:,4)==iDt);

if ishandle(1)

    if ~strcmp(option,'keep') && ~strcmp(option,'keepopen') && ~strcmp(option,'open')

        close(1);

    end

end

figure

plot(y.dataTimeSeries(:,k))

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