Commit 4885f3de authored by jayd1860's avatar jayd1860
Browse files

v1.44.0 

-- Fix ordering issue with active/inactive (mlAct) channels in user functions and MainGUI display. Use sources, detectors, wavelength matrix rather than a logical vector.
-- When manually pruning channel only prune at the current wavelength.
-- Implement missing application of active/inactive (mlAct) channels at the higher averaging user functions: hmrE_RunAvg.m, hmrG_SubjAvg.m, hmrS_SessAvg.m
-- Fix incorrect nTrials calculation at the group level
-- Fix PlotProbeGUI/plotProbe.m display issue as a result of fixing the MeasList ordering issue.
parent ea939423

DataTree/AcquiredData/DataFiles/Snirf2Nirs.m

+8 −4
Original line number Diff line number Diff line
@@ -6,16 +6,20 @@ if ~exist('options','var') 
    options = 'sort';

end

rootdir = filesepStandard(rootdir);

files = DataFilesClass(pwd, 'snirf');

files = DataFilesClass(rootdir, 'snirf');

files = files.files;

for ii = 1:length(files)

    fname = filesepStandard([rootdir, files(1).name]);

    if files(ii).IsDir()

        continue

    end

    fname = filesepStandard([files(ii).rootdir, files(ii).name]);    

    s = SnirfClass(fname);

    n = NirsClass(s);

    if optionExists(options, 'sort')

        n.SortData();

    end

    [pname, fname] = filesepStandard(fname);

    fnameNew = [pname, fname, '.nirs'];

    [pname, fname] = fileparts(fname);

    fnameNew = [filesepStandard(pname), fname, '.nirs'];

    fprintf('Converting %s to %s\n', fname, fnameNew)

    n.Save(fnameNew);

end

DataTree/AcquiredData/Nirs/NirsClass.m

+2 −2
Original line number Diff line number Diff line
@@ -134,7 +134,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

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

        function SortData(obj)

            [obj.SD.MeasList, order] = sortrows(obj.SD.MeasList,4);

            [obj.SD.MeasList, order] = sortrows(obj.SD.MeasList);

            obj.d = obj.d(:,order);

            [obj.SD.MeasList, order] = sortrows(obj.SD.MeasList,4);

            obj.d = obj.d(:,order);
@@ -1046,7 +1046,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function b = CopyProbe(obj, SD)            

        function CopyProbe(obj, SD)            

            fields = propnames(obj.SD);

            for ii = 1:length(fields)

                if eval( sprintf('isfield(SD, ''%s'')', fields{ii}) )

DataTree/AcquiredData/Snirf/DataClass.m

+23 −2
Original line number Diff line number Diff line
@@ -386,8 +386,30 @@ classdef DataClass < FileLoadSaveClass 
        

        

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

        function ml = GetMeasurementList(obj)

        function ml = GetMeasurementList(obj, option)

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

                option = '';

            end            

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

            if isempty(option)

            ml = obj.measurementList;

            elseif strcmp(option,'matrix')                

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

                for ii = 1:length(obj.measurementList)

                    k = 0;

                    for jj = 1:length(hbTypes)

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

                            k = jj;

                            break;

                        end

                    end

                    if obj.measurementList(ii).wavelengthIndex > 0

                        ml(ii,:) = [obj.measurementList(ii).sourceIndex, obj.measurementList(ii).detectorIndex, obj.measurementList(ii).dataTypeIndex, obj.measurementList(ii).wavelengthIndex];

                    elseif k > 0

                        ml(ii,:) = [obj.measurementList(ii).sourceIndex, obj.measurementList(ii).detectorIndex, obj.measurementList(ii).dataTypeIndex, k];                        

                    end

                end

            end

        end
@@ -483,7 +505,6 @@ classdef DataClass < FileLoadSaveClass 
                                    iSrcDetPair = find(ml(:,1)==srcs(iS) & ml(:,2)==dets(iD));

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

                                    

                                    

                                    order(kk) = ii;

                                    kk = kk+1;

                                    break;

DataTree/DataTreeClass.m

+6 −2
Original line number Diff line number Diff line
@@ -299,14 +299,18 @@ classdef DataTreeClass < handle 
                banner = '';

            end

            obj.logger.Write('\n');

            if ~isempty(banner)

            	obj.logger.Write('============================================\n');

            end

            if ~isempty(banner)

                obj.logger.Write('%s', banner);

                obj.logger.Write('\n');

                obj.logger.Write('\n');

            end

            obj.groups(1).PrintProcStream();

            if ~isempty(banner)

            	obj.logger.Write('============================================\n');

            end

            obj.logger.Write('\n');

        end

DataTree/ProcStream/ProcResultClass.m

+4 −0
Original line number Diff line number Diff line
@@ -337,6 +337,10 @@ classdef ProcResultClass < handle 
                return;

            end            

            

            if ~ispathvalid([filename, '.mat'], 'file')

                return

            end

            

            % Free memory for this object

            obj.Initialize();

        end

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