Commit ab0fe489 authored by jayd1860's avatar jayd1860
Browse files

v1.48.0 

-- Fix very slow processing at the group, subject and session levels and slow display. All were caused by the same issue: very inefficient DataClass.GetDataTimeSeries('reshape') method. Changed it's code to be much more efficient.
-- Fix typo in plotProbeAndSetProperties.m causing matlab-generated error
-- Minor improvement to display of location of current processing in MainGUI listboxGroupTree when calculating provcessing stream
parent 150061c6

DataTree/AcquiredData/Snirf/DataClass.m

+27 −57
Original line number Diff line number Diff line
@@ -488,6 +488,7 @@ classdef DataClass < FileLoadSaveClass 
            nWavelengths    = length(wavelengths);

            nDataTypeLabels = length(dataTypeLabels);

            nCond           = length(conditions);

            measurementList = obj.GetMeasurementList('matrix');            

            ml              = obj.GetMeasListSrcDetPairs('reshape');

            

            kk = 1;
@@ -497,24 +498,17 @@ classdef DataClass < FileLoadSaveClass 
                    for iS = 1:length(srcs)

                        for iD = 1:length(dets)

                            

                            for ii = 1:length(obj.measurementList)

                                if obj.measurementList(ii).sourceIndex == srcs(iS) && ...

                                   obj.measurementList(ii).detectorIndex == dets(iD) &&  ...

                                   obj.measurementList(ii).wavelengthIndex == iWl

                                    

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

                            if ~isempty(k)

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

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

                                    

                                    order(kk) = ii;

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

                                order(kk) = k;

                                kk = kk+1;

                                    break;



                            end

                            

                        end

                    end

                end

                end

                

            elseif nWavelengths > 0 && nCond > 0
@@ -523,20 +517,12 @@ classdef DataClass < FileLoadSaveClass 
                        for iD = 1:length(dets)

                            for iCond = 1:nCond

                            

                                for ii = 1:length(obj.measurementList)

                                    if obj.measurementList(ii).sourceIndex == srcs(iS) && ...

                                       obj.measurementList(ii).detectorIndex == dets(iD) &&  ...

                                       obj.measurementList(ii).wavelengthIndex == iWl && ...

                                       obj.measurementList(ii).dataTypeIndex == iCond

                                        

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

                                if ~isempty(k)

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

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

                                        

                                        order(kk) = ii;

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

                                    order(kk) = k;

                                    kk = kk+1;

                                        break;



                                    end

                                end



                            end
@@ -550,20 +536,12 @@ classdef DataClass < FileLoadSaveClass 
                    for iS = 1:length(srcs)

                        for iD = 1:length(dets)

                            

                            for ii = 1:length(obj.measurementList)

                                if obj.measurementList(ii).sourceIndex == srcs(iS) && ...

                                   obj.measurementList(ii).detectorIndex == dets(iD) && ...

                                   ~isempty(strfind(lower(obj.measurementList(ii).dataTypeLabel), hbTypes{iHbType}))



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

                            if ~isempty(k)

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

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



                                    order(kk) = ii;

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

                                order(kk) = k;

                                kk = kk+1;

                                    break;



                                end



                            end

                            

                        end
@@ -577,20 +555,12 @@ classdef DataClass < FileLoadSaveClass 
                        for iD = 1:length(dets)

                            for iCond = 1:nCond



                                for ii = 1:length(obj.measurementList)

                                    if obj.measurementList(ii).sourceIndex == srcs(iS) && ...

                                       obj.measurementList(ii).detectorIndex == dets(iD) &&  ...

                                       ~isempty(strfind(lower(obj.measurementList(ii).dataTypeLabel), hbTypes{iHbType})) && ...

                                       obj.measurementList(ii).dataTypeIndex == iCond

                                        

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

                                if ~isempty(k)

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

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

                                        

                                        order(kk) = ii;

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

                                    order(kk) = k;

                                    kk = kk+1;

                                        break;



                                    end

                                end

                                

                            end

DataTree/GroupClass.m

+5 −6
Original line number Diff line number Diff line
@@ -579,6 +579,10 @@ classdef GroupClass < TreeNodeClass 
                tHRF_common = obj.subjs(iSubj).procStream.output.GeneratetHRFCommon(tHRF_common);

            end

           

            % Update call application GUI using it's generic Update function

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

                        

            % Load all the output valiraibles that might be needed by procStream.Calc() to calculate proc stream for this group

            obj.LoadInputVars(tHRF_common);
@@ -590,11 +594,6 @@ classdef GroupClass < TreeNodeClass 
                obj.logger.Write('\n');

            end

            

            % Update call application GUI using it's generic Update function

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

            

        end

DataTree/SessClass.m

+5 −6
Original line number Diff line number Diff line
@@ -332,6 +332,10 @@ classdef SessClass < TreeNodeClass 
                tHRF_common = obj.runs(iRun).procStream.output.GeneratetHRFCommon(tHRF_common);

            end

            

            % Update call application GUI using it's generic Update function 

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

            

            % Load all the variables that might be needed by procStream.Calc() to calculate proc stream for this session

            obj.LoadInputVars(tHRF_common);
@@ -343,11 +347,6 @@ classdef SessClass < TreeNodeClass 
                fprintf('\n');

            end

                        

            % Update call application GUI using it's generic Update function 

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

            

        end

DataTree/SubjClass.m

+5 −6
Original line number Diff line number Diff line
@@ -363,6 +363,10 @@ classdef SubjClass < TreeNodeClass 
                tHRF_common = obj.sess(iSess).procStream.output.GeneratetHRFCommon(tHRF_common);

            end

            

            % Update call application GUI using it's generic Update function 

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

            

            % Load all the variables that might be needed by procStream.Calc() to calculate proc stream for this subject

            obj.LoadInputVars(tHRF_common);
@@ -374,11 +378,6 @@ classdef SubjClass < TreeNodeClass 
                fprintf('\n');

            end

                        

            % Update call application GUI using it's generic Update function 

            if ~isempty(obj.updateParentGui)

                obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]);

            end

            

        end

PlotProbeGUI/plotProbeAndSetProperties.m

+2 −2
Original line number Diff line number Diff line
@@ -93,8 +93,8 @@ if ~isempty(plotprobe.y{iBlk}) 
    if ~isempty(plotprobe.y{iBlk})

        plotprobe.y{iBlk} = plotprobe.y{iBlk}(:,k);

    end

    if ~isempty(plotprobe.y{iBlk})

        plotprobe.ystd{iBlk} = plotprobe.y{iBlk}(:,k);

    if ~isempty(plotprobe.ystd{iBlk})

        plotprobe.ystd{iBlk} = plotprobe.ystd{iBlk}(:,k);

    end

    if ~isempty(plotprobe.ml{iBlk})

        plotprobe.ml{iBlk} = plotprobe.ml{iBlk}(k,:);

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