Commit 54a831e5 authored by jayd1860's avatar jayd1860
Browse files

v1.42.4 

-- Fix bugs found by Meryem in fNIRS 2018 course SS_DEMO_1, Finger_Tapping_*.snirf.

Errors when running processing stream in
1. hmrR_MotionArtifact fixed by getting rid of 'reshape' option to DataTimeSeries()
2. hmrR_OD2Conc.m fixed by getting rid of 'reshape' option to DataTimeSeries()
3. hmrR_GLM.m fixed in DataClass.m by NOT assuming source and detector indices do not skip numbers

-- Just like for hmrR_MotionArtifact.m no need to reshape for hmrR_MotionArtifactByChannel.m since the

-- Better error/warning logging in DataFilesClass.m and FileLoadSaveClass.m
parent 1c45ec6d

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+5 −5
Original line number Diff line number Diff line
@@ -472,19 +472,19 @@ classdef DataFilesClass < handle 
                if obj.files(ii).isdir

                    continue;

                end

                filename = obj.files(ii).name;

                filename = [obj.rootdir, obj.files(ii).name];

                eval( sprintf('o = %s(filename);', constructor) );

                if  o.GetError() < 0

                    obj.logger.Write('DataFilesClass.ErrorCheck - ERROR: In file "%s" %s. File will not be added to data set\n', filename, o.GetErrorMsg());

                    obj.logger.Write('DataFilesClass.ErrorCheck - ERROR: In file "%s" %s. File will not be added to data set\n', obj.files(ii).name, o.GetErrorMsg());

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                elseif  contains(o.GetErrorMsg(), '''data'' field corrupt and unusable')                    

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file "%s" %s. File will not be added to data set\n', filename, o.GetErrorMsg());

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file "%s" %s. File will not be added to data set\n', obj.files(ii).name, o.GetErrorMsg());

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                elseif  contains(o.GetErrorMsg(), '''data'' field is invalid')                    

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file "%s" %s. File will not be added to data set\n', filename, o.GetErrorMsg());

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file "%s" %s. File will not be added to data set\n', obj.files(ii).name, o.GetErrorMsg());

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                elseif ~isempty(o.GetErrorMsg())

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file  "%s"  %s. File will be added anyway.\n', filename, o.GetErrorMsg());

                    obj.logger.Write('DataFilesClass.ErrorCheck - WARNING: In file  "%s"  %s. File will be added anyway.\n', obj.files(ii).name, o.GetErrorMsg());

                    dataflag = true;

                else

                    dataflag = true;

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+0 −1
Original line number Diff line number Diff line
@@ -144,7 +144,6 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable 
        function err = GetError(obj)

            err = [];

            if isempty(obj)

                fprintf('Warning: object is empty.')

                return

            end

            err = obj.err;

DataTree/AcquiredData/Snirf/DataClass.m

+12 −12
Original line number Diff line number Diff line
@@ -476,11 +476,11 @@ classdef DataClass < FileLoadSaveClass 
                        for iD = 1:length(dets)

                            

                            for ii = 1:length(obj.measurementList)

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

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

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

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

                                   obj.measurementList(ii).wavelengthIndex == iWl

                                    

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

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

                                    d(:, iWl, iSrcDetPair) = obj.dataTimeSeries(:,ii); %#ok<*FNDSB>
@@ -503,12 +503,12 @@ classdef DataClass < FileLoadSaveClass 
                            for iCond = 1:nCond

                            

                                for ii = 1:length(obj.measurementList)

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

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

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

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

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

                                       obj.measurementList(ii).dataTypeIndex == iCond

                                        

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

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

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

                                        

                                        order(kk) = ii;
@@ -530,11 +530,11 @@ classdef DataClass < FileLoadSaveClass 
                        for iD = 1:length(dets)

                            

                            for ii = 1:length(obj.measurementList)

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

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

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

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

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



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

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

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



                                    order(kk) = ii;
@@ -557,12 +557,12 @@ classdef DataClass < FileLoadSaveClass 
                            for iCond = 1:nCond

                            

                                for ii = 1:length(obj.measurementList)

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

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

                                    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

                                        

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

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

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

                                        

                                        order(kk) = ii;

FuncRegistry/UserFunctions/hmrR_MotionArtifact.m

+17 −27
Original line number Diff line number Diff line
@@ -92,9 +92,9 @@ end 


for iBlk=1:length(data)



    d           = data(iBlk).GetDataTimeSeries('reshape');

    d           = data(iBlk).GetDataTimeSeries();

    fs          = data(iBlk).GetTime();

    MeasList    = data(iBlk).GetMeasList('reshape');

    MeasList    = data(iBlk).GetMeasList();

    Lambda      = probe.GetWls();

    nWav        = length(Lambda);
@@ -113,20 +113,17 @@ for iBlk=1:length(data) 
    end

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

      

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

    diff_d = diff(d);

    

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

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

    for ii=1:nWav

    for iW = 1:nWav

        for jj = 1:length(lst1)

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

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

                MeasList(:,4)==ii );

                           MeasList(:,4) == iW );

            lstAct(lst(jj)) = MeasListAct(jj);

        end

    end
@@ -142,7 +139,6 @@ for iBlk=1:length(data) 
    end

    

    % find indices with motion artifacts based on std_thresh or amp_thresh

    bad_inds = [];

    mc_thresh = std_diff*std_thresh;

    bad_inds = find( max(max_diff  >  ones(size(max_diff,1),1) * mc_thresh, [], 2) == 1 | ...

                     max(max_diff,[],2) > amp_thresh );
@@ -159,12 +155,6 @@ for iBlk=1:length(data) 
        tIncAuto{iBlk}(1+bad_inds) = 0; % bad inds calculated on diff so add 1        

    end

       

    % calculate the variance due to motion relative to total variance

    lst = find(tIncAuto{iBlk}==0);

    dstd0 = std(d(lst,:),[],1);

    lst = find(tIncAuto{iBlk}==1);

    dstd1 = std(d(lst,:),[],1);

    

end

FuncRegistry/UserFunctions/hmrR_MotionArtifactByChannel.m

+14 −21
Original line number Diff line number Diff line
@@ -91,9 +91,9 @@ end 


for iBlk = 1:length(data)

    

    d           = data(iBlk).GetDataTimeSeries('reshape');

    d           = data(iBlk).GetDataTimeSeries();

    fs          = data(iBlk).GetTime();

    MeasList    = data(iBlk).GetMeasList('reshape');

    MeasList    = data(iBlk).GetMeasList();

    Lambda      = probe.GetWls();

    

    if length(fs)~=1
@@ -116,7 +116,6 @@ for iBlk=1:length(data) 
    MeasListAct = mlActMan{iBlk} & mlActAuto{iBlk};      

        

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

    diff_d = diff(d);

       

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

    art_buffer = round(tMask*fs); % time in seconds times sample rate
@@ -155,7 +154,7 @@ for iBlk=1:length(data) 
        bad_inds = zeros(size(max_diff));

        mc_thresh = std_diff*std_thresh;

        for ii = 1:length(lstActTmp)

            bad_inds(:,ii) = max( [max_diff(:,ii)>mc_thresh(ii) max_diff(:,ii)>amp_thresh], [],2);

            bad_inds(:,ii) = max( [ max_diff(:,ii)>mc_thresh(ii), max_diff(:,ii)>amp_thresh ], [], 2);

        end

        bad_inds = find(max(bad_inds,[],2)==1);
@@ -177,11 +176,5 @@ for iBlk=1:length(data) 
    tInc{iBlk}(find(tIncMan{iBlk}==0)) = 0;

    tIncCh{iBlk}(find(tIncMan{iBlk}==0),:) = 0;

    

    % calculate the variance due to motion relative to total variance

    lst = find(tInc{iBlk}==0);

    dstd0 = std(d(lst,:),[],1);

    lst = find(tInc{iBlk}==1);

    dstd1 = std(d(lst,:),[],1);

    

end

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