TreeNodeClass.m

classdef TreeNodeClass < handle
    
    properties % (Access = private)
        name;
        type;
        iGroup;
        iSubj;
        iSess;
        iRun;
        iFile;
        children;
        acquired;
        procStream;
        err;
        CondNames;
        updateParentGui;
    end
    
    properties
        inputVars
        DEBUG
        path
        logger
        pathOutputAlt        
        outputDirname
        cfg
        chVis
        hFig
    end
    
    methods        
        
        % ---------------------------------------------------------------------------------
        function obj = TreeNodeClass(arg)
            global logger
            global cfg

            logger                  = InitLogger(logger, 'TreeNodeClass');
            cfg                     = InitConfig(cfg);

            obj.logger              = logger;
            obj.cfg                 = cfg;

            obj.DEBUG = 0;
            
            obj.name = '';
            
            obj.iGroup = 0;
            obj.iSubj = 0;
            obj.iSess = 0;
            obj.iRun = 0;
            
            obj.type = '';
            obj.procStream = ProcStreamClass();
            obj.acquired = [];
            obj.err = 0;
            obj.CondNames = {};
            obj.path = filesepStandard(pwd);            
            
            obj.outputDirname = filesepStandard(obj.cfg.GetValue('Output Folder Name'), 'nameonly:dir');

            obj.InitParentAppFunc();
            obj.children = [];
            obj.hFig = [-1; -1];
            
            % If this constructor is called from this class' copy method,
            % then we want to exit before we obliterate the persistent
            % variables (only one copy of which is shared across all objects 
            % of this class, like a static var in C++). 
            % 
            % Essentially if a copy arg is passed this constructor
            % is used as a copy constructor (to borrow C++ terminology)
            %
            if nargin==1
                if iscell(arg) && ~isempty(arg) 
                    arg = arg{1};
                end
                if ischar(arg) && strcmp(arg,'copy')
                    return;
                end
            end
            obj.CondColTbl('init');
            obj.GroupDataLoadWarnings();            
        end
        
    end
    
    
    methods
        
        % ---------------------------------------------------------------------------------
        function err = LoadProcStreamConfigFile(obj, filename)
            err = obj.procStream.LoadConfigFile(filename, class(obj));
        end        
        
                
        % ---------------------------------------------------------------------------------
        function SaveProcStreamConfigFile(obj, filename)
            obj.procStream.SaveConfigFile(filename, class(obj));
        end        
                
        
        % ---------------------------------------------------------------------------------
        function CreateProcStreamDefault(obj)
            obj.procStream.CreateDefault()
        end
        
        
        % ---------------------------------------------------------------------------------
        function procStream = GetProcStreamDefault(obj)
            procStream = obj.procStream.GetDefault(class(obj));
        end 
       
    end
    
    
    methods
        
        % ----------------------------------------------------------------------------------
        % Override == operator: 
        % ----------------------------------------------------------------------------------
        function B = eq(obj1, obj2)
            B = equivalent(obj1, obj2);
        end

        
        % ----------------------------------------------------------------------------------
        % Override ~= operator
        % ----------------------------------------------------------------------------------
        function B = ne(obj1, obj2)
            B = ~equivalent(obj1, obj2);
        end
        
        
        % ----------------------------------------------------------------------------------
        % Copy function to do deep copy
        % ----------------------------------------------------------------------------------
        function objnew = copy(obj)
            switch(class(obj))
                case 'RunClass'
                    objnew = RunClass('copy');
                case 'SessClass'
                    objnew = SessClass('copy');
                case 'SubjClass'
                    objnew = SubjClass('copy');
                case 'GroupClass'
                    objnew = GroupClass('copy');
                case ''
            end
            objnew.name = obj.name;
            objnew.type = obj.type;
            objnew.err = obj.err;
            objnew.CondNames = obj.CondNames;
            objnew.procStream.Copy(obj.procStream, obj.GetOutputFilename);
        end
        
               
        % ----------------------------------------------------------------------------------
        % Copy processing params (procInut and procResult) from
        % obj2 to obj
        % ----------------------------------------------------------------------------------
        function Copy(obj, obj2, conditional)
            if nargin==2 || strcmp(conditional, 'unconditional')
                obj.name = obj2.name;
                obj.path = obj2.path;
                obj.outputDirname = obj2.outputDirname;
                obj.type = obj2.type;
                obj.iGroup = obj2.iGroup;
                obj.iSubj = obj2.iSubj;
                obj.iSess = obj2.iSess;
                obj.iRun = obj2.iRun;
                obj.CondNames = obj2.CondNames;
                switch(class(obj2.children))
                    case 'SubjClass'
                        obj.children = obj.subjs;
                    case 'SessClass'
                        obj.children = obj.sess;
                    case 'RunClass'                        
                        obj.children = obj.runs;
                end
            end
            if ~isempty(obj2.procStream)
                [pathname, filename] = fileparts([obj.path, obj.GetOutputFilename()]);                
                
                % Recreate the same relative dir structure under derived output
                % folder as exists directly under the group folder
                if ispathvalid([filesepStandard(obj.path), obj.name], 'dir')
                    pathname = [filesepStandard(pathname), filename];
                end
                obj.procStream.SaveInitOutput(pathname, filename);
                obj.procStream.Copy(obj2.procStream, [obj.path, obj.GetOutputFilename()]);
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function Reset(obj)
            global cfg
            obj.procStream.output.Reset([obj.path, obj.GetOutputFilename()]);
            delete([obj.path, obj.GetOutputFilename(), '*.txt']);
            delete([obj.path, 'tCCAfilter_*.txt'])
            v = '';
            if ~isempty(cfg)
                v = cfg.GetValue('Include Archived User Functions');
            end
            if strcmpi(v, 'yes')
                delete([obj.path, '*_events.tsv'])
            end                
        end
        
        
        % ----------------------------------------------------------------------------------
        % 
        % ----------------------------------------------------------------------------------
        function options_s = parseSaveOptions(~, options)
            options_s = struct('derived',false, 'acquired',false);
            C = str2cell(options, {':',',','+',' '});
            
            for ii=1:length(C)
                if isproperty(options_s, C{ii})
                    eval( sprintf('options_s.%s = true;', C{ii}) );
                end
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function InitParentAppFunc(obj)
            global maingui
            if isfield(maingui, 'Update')
                obj.updateParentGui = maingui.Update;
            end
        end
        

        % ----------------------------------------------------------------------------------
        function SetIndexID(obj, iGroup, iSubj, iSess, iRun)
            if nargin>1
                obj.iGroup = iGroup;
            end            
            if nargin>2
                obj.iSubj = iSubj;
            end
            if nargin>3
                obj.iSess = iSess;
            end
            if nargin>4
                obj.iRun = iRun;
            end
        end
        
        
        % ----------------------------------------------------------
        function idx = FindProcElem(obj, name)
            idx = [];
            if strcmp(name, obj.GetName())
                idx = obj.GetIndexID();
                return;
            end
            if strcmp(name, obj.GetFilename())
                idx = obj.GetIndexID();
                return;
            end
            for ii = 1:length(obj.children)
                if strcmp(name, obj.children(ii).GetName())
                    idx = obj.children(ii).GetIndexID();
                    return;
                end
                if strcmp(name, obj.children(ii).GetFilename())
                    idx = obj.children(ii).GetIndexID();
                    return;
                end
                idx = obj.children(ii).FindProcElem(name);
                if ~isempty(idx)
                    return;
                end
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function SetPath(obj, dirname)
            obj.path = dirname;
            
            % In case there's not enough disk space in the current
            % group folder, we have a alternative path that can be 
            % set independently for saving group results. By default 
            % it is set to root group folder. 
            obj.pathOutputAlt = obj.path;
        end
        
        
        % ----------------------------------------------------------------------------------
        function SetPathOutput(obj, dirname)
            % In case there's not enough disk space in the current
            % group folder, we have a alternative path that can be 
            % set independently for saving group results. By default 
            % it is set to root group folder. 
            obj.pathOutputAlt = dirname;
        end
        
        
        % ----------------------------------------------------------------------------------
        function SetProcFlag(obj)
            if obj.procStream.output.IsEmpty()
                return;
            end
            if isa(obj, 'GroupClass')
                obj.GroupsProcFlags(obj.iGroup, 1);
            elseif isa(obj, 'SubjClass')
                obj.SubjsProcFlags(obj.iGroup, obj.iSubj, 1);
            elseif isa(obj, 'SessClass')
                obj.SubjsProcFlags(obj.iGroup, obj.iSubj, obj.iSess, 1);
            elseif isa(obj, 'RunClass')
                obj.RunsProcFlags(obj.iGroup, obj.iSubj, obj.iSess, obj.iRun, 1);
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function idx = GetIndexID(obj)
            idx = [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun];
        end
        
        
        % ----------------------------------------------------------------------------------
        function b = IsGroup(obj)
            if strcmp('group', obj.type)
                b = true;
            else
                b = false;
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function b = IsSubj(obj)
            if strcmp('subj', obj.type)
                b = true;
            else
                b = false;
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function b = IsSess(obj)
            if strcmp('sess', obj.type)
                b = true;
            else
                b = false;
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function b = IsRun(obj)
            if strcmp('run', obj.type)
                b = true;
            else
                b = false;
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function b = IsSame(obj, iGroup, iSubj, iSess, iRun)
            b = false;
            if isempty(obj)
                return;
            end
            if iGroup==obj.iGroup && iSubj==obj.iSubj && iSess==obj.iSess && iRun==obj.iRun
                b = true;
            end                
        end
                
    end
        
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Methods for setting/getting TreeNode procStream output
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    methods
               
        % ----------------------------------------------------------------------------------
        function t = GetTHRF(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            t = obj.procStream.output.GetTHRF(iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function d = GetRawData(~)            
            d = [];
        end
        
        
        % ----------------------------------------------------------------------------------
        function dod = GetDod(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dod = obj.procStream.output.GetDataTimeCourse('dod',iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dc = GetDc(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dc = obj.procStream.output.GetDataTimeCourse('dc',iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dodAvg = GetDodAvg(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                icond = 1:length(obj.GetConditions());
            elseif ischar(condition)
                icond = obj.GetConditionIdx(condition);
            else
                icond = condition;
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dodAvg = obj.procStream.output.GetDodAvg('dodAvg', icond, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dcAvg = GetDcAvg(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                icond = 1:length(obj.GetConditions());
            elseif ischar(condition)
                icond = obj.GetConditionIdx(condition);
            else
                icond = condition;
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dcAvg = obj.procStream.output.GetDcAvg('dcAvg', icond, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dodAvgStd = GetDodAvgStd(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                condition = 1:length(obj.GetConditions());
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dodAvgStd = obj.procStream.output.GetDodAvg('dodAvgStd', condition, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dcAvgStd = GetDcAvgStd(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                condition = 1:length(obj.GetConditions());
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dcAvgStd = obj.procStream.output.GetDcAvg('dcAvgStd', condition, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dodSum2 = GetDodSum2(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                condition = 1:length(obj.GetConditions());
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dodSum2 = obj.procStream.output.GetDodSum2('dodSum2', condition, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function dcSum2 = GetDcSum2(obj, condition, iBlk)
            if ~exist('condition','var') || isempty(condition)
                condition = 1:length(obj.GetConditions());
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk=1;
            end
            dcSum2 = obj.procStream.output.GetDcSum2('dcSum2', condition, iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function nTrials = GetNtrials(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            nTrials = obj.procStream.output.GetNtrials(iBlk);
        end
        
        
        % ----------------------------------------------------------------------------------
        function pValues = GetPvalues(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = [];
            end
            pValues = obj.procStream.output.GetVar('pValues');
            if ~isempty(iBlk) && iBlk<=length(pValues)
                pValues = pValues{iBlk};
            end
        end
        
    end
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Methods for retrieving TreeNode params
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    methods
        
        % ----------------------------------------------------------------------------------
        function s = GetStims(~, ~)
            s = [];
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function ReloadStim(obj)
            % 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
            for ii = 1:length(obj.children)
                obj.children(ii).ReloadStim();
            end            
            pause(.5);
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function fnameTsv = GetStimTsvFilename(obj)
            fnameTsv = [];
            if isempty(obj.acquired)
                return;
            end
            fnameTsv = obj.acquired.GetStimTsvFilename();
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function EditStim(obj, waitForInput)
            if ~exist('waitForInput','var')
                waitForInput = 0;
            end
            if isempty(obj.acquired)
                MenuBox(sprintf('%s level processing does not have stims. Please select a run to edit stim marks\n', [upper(obj.type(1)), obj.type(2:end)]));
                return;
            end
            filenameData = [obj.path, obj.GetFilename()];
            
            % From data file name get events TSV file and load in matlab editor
            filenameEvents = obj.GetStimTsvFilename();
            if ~ispathvalid(filenameEvents)
                obj.logger.Write('Events TSV file for %s doesn''t exist.\n', filenameData);
                obj.ExportStim();
            end
            obj.logger.Write('Editing %s\n', filenameEvents);
            
            % Edit commands
            if ~isdeployed()
                edit(filenameEvents);
                editorTabs = matlab.desktop.editor.getAll;
                
                % Search for editor tab containing loaded file and make it active
                for ii = 1:length(editorTabs)
                    if pathscompare(editorTabs(ii).Filename, filenameEvents)
                        break
                    end
                end
                editorTab = editorTabs(ii);
                editorTab.makeActive;
                if waitForInput
                    MenuBox('Please edit TSV stim file and save it, then click the ''OK'' button.');
                end
            else
                if ispc()
                    cmd = sprintf('start notepad %s', filenameEvents);
                    obj.logger.Write('cmd:  "%s"', cmd);
                    system(cmd);
                elseif ismac()
                    cmd = sprintf('open -a TextEdit %s', filenameEvents);
                    obj.logger.Write('cmd:  "%s"', cmd);
                    system(cmd);                    
                    if waitForInput
                        MenuBox(sprintf('The events file associated with the current processing element is\n%s\n Open the file in a text editor to modify stim marks', filenameEvents));
                    end
                end
            end
        end
        
        
        
        % --------------------------------------------------------------
        function CopyStimAcquired(obj)
            obj.procStream.CopyStims(obj.acquired);
        end
               
        
        
        % ----------------------------------------------------------------------------------
        function CondNames = GetConditions(obj)
            CondNames = obj.CondNames;
        end

        
        
        % ----------------------------------------------------------------------------------
        function RenameCondition(obj, oldname, newname)
            % Function to rename a condition. Important to remeber that changing the
            % condition involves 2 distinct well defined steps:
            %   a) For the current element change the name of the specified (old)
            %      condition for ONLY for ALL the acquired data elements under the
            %      currElem, be it session, subj, or group . In this step we DO NOT TOUCH
            %      the condition names of the session, subject or group .
            %   b) Rebuild condition names and tables of all the tree nodes group, subjects
            %      and sessions same as if you were loading during Homer3 startup from the
            %      acquired data.
            %
            if ~exist('oldname','var') || ~ischar(oldname)
                return;
            end
            if ~exist('newname','var')  || ~ischar(newname)
                return;
            end            
            newname = obj.ErrCheckNewCondName(newname);
            if obj.err ~= 0
                return;
            end
            for ii = 1:length(obj.children)
                obj.children(ii).RenameCondition(oldname, newname);
            end
        end
        
                
                
        % ----------------------------------------------------------------------------------
        function idx = GetConditionIdx(obj, CondName)
            C = obj.GetConditions();
            idx = find(strcmp(C, CondName));
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function SD = GetSDG(obj, option)            
            if exist('option','var')
                SD = obj.runs(1).GetSDG(option);
            else
                SD = obj.runs(1).GetSDG();
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function srcpos = GetSrcPos(obj, options)
            srcpos = [];
            if exist('options','var')
                options = '';
            end
            if isempty(obj.children)
                return;
            end
            srcpos = obj.children(1).GetSrcPos(options);
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function detpos = GetDetPos(obj, options)
            detpos = [];
            if exist('options','var')
                options = '';
            end
            if isempty(obj.children)
                return;
            end
            detpos = obj.children(1).GetDetPos(options);
        end
        
        
        
        % ---------------------------------------------------------
        function ml = GetMeasurementList(obj, matrixMode, iBlk, dataType)
            if ~exist('matrixMode','var')
                matrixMode = '';
            end
            if ~exist('dataType','var')
                dataType = 'raw';
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            switch(lower(dataType))
                case 'raw'
                    if isempty(obj.acquired)
                        ml = obj.children(1).GetMeasurementList(matrixMode, iBlk); %#ok<*AGROW>
                    else
                        ml = obj.acquired.GetMeasurementList(matrixMode, iBlk); %#ok<*AGROW>
                    end
                otherwise
                    ml = obj.procStream.GetMeasurementList(matrixMode, iBlk, dataType);
            end
        end
        
        
        
        % ---------------------------------------------------------
        function [d, t, ml] = GetData(obj, datatype, iBlk)
            d = [];
            t = [];
            ml = [];
            datatypes = obj.procStream.GetDataTypes();
            if ~exist('datatype','var')
                datatype = 'raw';
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            switch(lower(datatype))
                case datatypes.RAW
                    if isempty(obj.acquired)
                        return
                    end
                    [d, t] = obj.acquired.GetData(); %#ok<*AGROW>
                    ml = obj.acquired.GetMeasurementList('matrix',iBlk);
                case datatypes.OPTICAL_DENSITY
                    [d, t] = obj.procStream.GetData('od');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od');
                case datatypes.CONCENTRATION
                    [d, t] = obj.procStream.GetData('conc');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc');
                case datatypes.HRF_OPTICAL_DENSITY
                    [d, t] = obj.procStream.GetData('od hrf');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od hrf');
                case datatypes.HRF_OPTICAL_DENSITY_STD
                    [d, t] = obj.procStream.GetData('od hrf std');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od hrf std');
                case datatypes.HRF_CONCENTRATION
                    [d, t] = obj.procStream.GetData('conc hrf');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc hrf');
                case datatypes.HRF_CONCENTRATION_STD
                    [d, t] = obj.procStream.GetData('conc hrf std');
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc hrf std');
            end
        end
        
        

        % ---------------------------------------------------------
        function [d, t, ml] = GetDataTimeSeries(obj, datatype, iBlk)
            d = [];
            t = [];
            ml = [];
            datatypes = obj.procStream.GetDataTypes();
            if ~exist('datatype','var')
                datatype = 'RAW';
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            switch(lower(datatype))
                case datatypes.RAW
                    if isempty(obj.acquired)
                        return
                    end
                    [d, t] = obj.acquired.GetDataTimeSeries(iBlk); %#ok<*AGROW>
                    ml = obj.acquired.GetMeasurementList('matrix',iBlk);
                case datatypes.OPTICAL_DENSITY
                    [d, t] = obj.procStream.GetDataTimeSeries('od',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od');
                case datatypes.CONCENTRATION
                    [d, t] = obj.procStream.GetDataTimeSeries('conc',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc');
                case datatypes.HRF_OPTICAL_DENSITY
                    [d, t] = obj.procStream.GetDataTimeSeries('od hrf',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od hrf');
                case datatypes.HRF_OPTICAL_DENSITY_STD
                    [d, t] = obj.procStream.GetDataTimeSeries('od hrf std',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'od hrf std');
                case datatypes.HRF_CONCENTRATION
                    [d, t] = obj.procStream.GetDataTimeSeries('conc hrf',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc hrf');
                case datatypes.HRF_CONCENTRATION_STD
                    [d, t] = obj.procStream.GetDataTimeSeries('conc hrf std',iBlk);
                    ml = obj.procStream.GetMeasurementList('matrix',iBlk,'conc hrf std');
            end
        end
        
        

        % -----------------------------------------------------------------------
        function [md2d, md3d] = GetChannelsMeanDistance(obj)
            md2d = [];
            md3d = [];
            if isempty(obj.acquired)
                return;
            end
            [md2d, md3d] = obj.acquired.GetChannelsMeanDistance();
        end
        
                
        
        % ----------------------------------------------------------------------------------
        function ch = GetMeasList(obj, options, iBlk)
            if ~exist('options','var')
                options = '';
            end
            if ~exist('iBlk','var')
                iBlk = 1;
            end
                        
            % The following code is for calculating and displaying pruned channels
            % (mlActAuto) in higher processing levels: Group, Subject, and Session
            % It works well to for identifying inactive channels BUT is
            % very slow the higher the level (thus is slowest when displaying group probe) 
            % So for now commenting out until it can be optimized. In other
            % words we set mlAct display at the Group, Subject, and Session to all
            % active for now, until it can be optimized. NOTE: this will NOT have an effect on
            % processing as mlActAuto is only used at the run level
            % processing. Channel pruning at the higher level is a natural consequence 
            % of inactive run channels being set to NaN and so on up the processing chain
            % jdubb, 08/17/2022
            if 0
                
                for ii = 1:length(obj.children) %#ok<UNRCH>
                    if isempty(ch)
                        ch = obj.children(ii).GetMeasList(iBlk);
                    else
                        temp = obj.children(ii).GetMeasList(iBlk);
                        if length(ch.MeasListActMan) == length(temp.MeasListActMan)
                            ch.MeasListActMan = ch.MeasListActMan | temp.MeasListActMan;
                        end
                        if length(ch.MeasListActAuto) == length(temp.MeasListActAuto)
                            ch.MeasListActAuto = ch.MeasListActAuto | temp.MeasListActAuto;
                        end
                    end
                end
                
            else
                
                ch = obj.children(1).GetMeasList(iBlk);
	            if strcmp(options,'reshape')
                    ch.MeasList = sortrows(ch.MeasList);
	            end
                ch.MeasListActMan(:,3) = 1;
                ch.MeasListActAuto(:,3) = 1;
                
            end
        end

        
        
        % ----------------------------------------------------------------------------------
        function mlAct = GetActiveChannels(obj)
            mlAct = [];
            for ii = 1:length(obj.children)
                m = obj.children(1).GetActiveChannels();
                if isempty(m)
                    continue;
                end
                if isempty(mlAct)
                    mlAct = m;
                else
                    mlAct(:,3) = mlAct(:,3) | m(:,3);                    
                end
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function SetMeasListActMan(obj, ml)
            if ~exist('ml','var')
                ml = [];
            end
            obj.procStream.input.SetMeasListActMan(ml);
        end

        
        
        % ----------------------------------------------------------------------------------
        function SetMeasListVis(obj, sdpair, iBlk)
            if ~exist('sdpair','var')
                sdpair = [];
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            if ~isempty(obj.children)
                ch = obj.children(1).GetMeasList(iBlk);
            else
                ch = obj.GetMeasList(iBlk);
            end
            if isempty(sdpair)
                idxs = find(ch.MeasList(:,4)==1);
                obj.chVis = [ch.MeasList(idxs,1:2), ones(size(idxs,1),1)];
            else
                k = find(obj.chVis(:,1) == sdpair(1,1) & obj.chVis(:,2) == sdpair(1,2));
                if ~isempty(k)
                    if obj.chVis(k,3) == 0
                        obj.chVis(k,3) = 1;
                    else
                        obj.chVis(k,3) = 0;
                    end
                end
            end
         end
                
        
        % ----------------------------------------------------------------------------------
        function chVis = GetMeasListVis(obj, iBlk)
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            if isempty(obj.chVis)
                if ~isempty(obj.children)
                    ch = obj.children(1).GetMeasList(iBlk);
                else
                    ch = obj.GetMeasList(iBlk);
                end
                idxs = find(ch.MeasList(:,4)==1);
                obj.chVis = [ch.MeasList(idxs,1:2), ones(size(idxs,1),1)];
            end
            chVis = obj.chVis;
        end
                
        
        % ----------------------------------------------------------------------------------
        function varval = GetVar(obj, varname)
            varval = [];
            if isproperty(obj, varname)
                varval = eval( sprintf('obj.%s', varname) );
            end
            if isempty(varval)
                varval = obj.procStream.GetVar(varname);
            end
        end
        
               
        % ----------------------------------------------------------------------------------
        function AddStims(~, ~, ~)
            return;
        end        
        
        
        % ----------------------------------------------------------------------------------
        function DeleteStims(~, ~)
            return;
        end
        
        
        % ----------------------------------------------------------------------------------
        function ToggleStims(~, ~)
            return;
        end
        
        
        % ----------------------------------------------------------------------------------
        function SetStimDuration(~, ~, ~)
            return;
        end
    
        
        % ----------------------------------------------------------------------------------
        function duration = GetStimDuration(~, ~)
            duration = [];            
        end
        
        
        % ----------------------------------------------------------------------------------
        function data = GetStimData(~, ~)
            data = [];
        end
        
        
        % ----------------------------------------------------------------------------------
        function val = GetStimDataLabels(~, ~)
            val = {};
        end
                        
        
        % ----------------------------------------------------------------------------------
        function newname = ErrCheckNewCondName(obj, newname)
            msg1 = sprintf('Condition name ''%s'' already exists. New name must be unique. Do you want to choose another name?', newname);
            while ismember(newname, obj.CondNames)                
                q = MenuBox(msg1, {'YES','NO'});
                if q==2
                    obj.err = -1;
                    return;
                end
                newname = inputdlg({'New Condition Name'}, 'New Condition Name');
                if isempty(newname) || isempty(newname{1})
                    obj.err = 1;
                    return;
                end
                newname = newname{1};
            end
            msg2 = sprintf('Condition name is not valid. New name must be character string. Do you want to choose another name?');
            while ~ischar(newname)                
                q = MenuBox(msg2, {'YES','NO'});
                if q==2
                    obj.err = -1;
                    return;
                end
                newname = inputdlg({'New Condition Name'}, 'New Condition Name');
                if isempty(newname) || isempty(newname{1})
                    obj.err = 1;
                    return;
                end
                newname = newname{1};
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function err = GetErrStatus(obj)
            err = obj.err;
            
            % Reset error status
            obj.err = 0;
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function y = reshape_y(obj, y, MeasList)
            yold = y;
            lst1 = find(MeasList(:,4)==1);
            Lambda = obj.GetWls();

            if ndims(y)==2 %#ok<*ISMAT>
                y = zeros(size(yold,1),length(lst1),length(Lambda));
            elseif ndims(y)==3
                y = zeros(size(yold,1),length(lst1),length(Lambda),size(yold,3));
            end
            
            for iML = 1:length(lst1)
                for iLambda = 1:length(Lambda)
                    idx = find(MeasList(:,1)==MeasList(lst1(iML),1) & ...
                               MeasList(:,2)==MeasList(lst1(iML),2) & ...
                               MeasList(:,4)==iLambda );
                    if ndims(yold)==2
                        y(:,iML,iLambda) = yold(:,idx);
                    elseif ndims(yold)==3
                        y(:,iML,iLambda,:) = yold(:,idx,:);
                    end
                end
            end            
        end
        
        
        % ----------------------------------------------------------------------------------
        function name = GetName(obj)
            name = '';
            if isempty(obj)
                return;
            end
            name = obj.name;
        end
        
        
        % ----------------------------------------------------------------------------------
        function SetName(obj, name)
            if isempty(obj)
                return;
            end
            obj.name = name;
        end
        
        
        % ----------------------------------------------------------------------------------
        function name = GetFileName(obj)
            name = '';
            if isempty(obj)
                return;
            end
            [~, fname, ext] = fileparts(obj.name);
            name = [fname, ext];
        end
        
        
        % ----------------------------------------------------------------------------------
        function t = GetTime(~, ~)
            t = [];
        end

        
        % ----------------------------------------------------------------------------------
        function aux = GetAux(~)
            aux = [];
        end

        
        % ----------------------------------------------------------------------------------
        function t = GetAuxiliaryTime(~, ~)
            t = [];
        end

        
        % ----------------------------------------------------------------------------------
        function t = GetTimeCombined(~)
            t = [];
        end
        
        
        % ----------------------------------------------------------------------------------
        function t = GetTincAuto(~, ~)
            t = [];
        end
        
        
        % ----------------------------------------------------------------------------------
        function t = GetTincAutoCh(~, ~)
            t = [];
        end
        
        
        % ----------------------------------------------------------------------------------
        function t = GetTincMan(~, ~)
            t = [];
        end

        
        % ----------------------------------------------------------------------------------
        function SetTincMan(~, ~, ~, ~)
            
        end
               
    end
        
    
    methods
        
        % ----------------------------------------------------------------------------------
        function err = Load(obj)
            err = -1;
            if isempty(obj)
                return
            end
            err = obj.LoadSubBranch(); %#ok<*MCNPN>
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function Calc(obj)                        
            % Make variables in this subject available to processing stream input
            obj.procStream.input.LoadVars(obj.inputVars);

            % Calculate processing stream
            fcalls = obj.procStream.Calc([obj.path, obj.GetOutputFilename()]); %#ok<NASGU>

            % Clean up folder of .error files
            if exist([pwd, '/.error'],'file')
                try
                    delete([pwd, '/.error'])
                catch
                end
            end

        end
        
        
         % ----------------------------------------------------------------------------------
         function stim = GetStim(obj)
             stim = [];
             if ~isempty(obj.children)
                 return;
             end
             stim = obj.procStream.GetStim();
         end
         
         
         
         % ----------------------------------------------------------------------------------
         function ExportDerivedData(obj, procElemSelect, hwait)
             global logger
             if ~exist('hwait','var')
                 hwait = [];
             end

             flag = false;
             if ~ishandles(hwait)
                 hwait = waitbar_improved(0, 'Exporting Derived Data ... Please Wait');
                 flag = 1;
                 pause(1);
             end

             obj.Load();
             s = SnirfClass();
             s.probe = obj.GetProbe();
             s.data(1) = obj.GetData('conc hrf');
             [pname, fname] = fileparts(obj.GetOutputFilename());
             filename = [obj.path, filesepStandard(pname), fname, '.snirf'];
             logger.Write('Exporting derived data %s', filename);

             [~, fname, ext] = fileparts(filename);
             waitbar_improved(0, hwait, sprintf('Exporting %s ...', [fname, ext]));
             s.Save(filename);

             % If all under it selected
             if strcmp(procElemSelect, 'all')
                 for ii = 1:length(obj.children)
                     obj.children(ii).ExportDerivedData(procElemSelect, hwait);
                 end
             end

             if flag
                 close(hwait)
             end
         end
        
    end
        
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Data Plotting mthods
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    methods
        
        % ----------------------------------------------------------------------------------
        function iChs = SdPairIdxs2vectorIdxs(obj, datatype, sdPairs, iBlk)
            iChs = [];
            datatypes = obj.procStream.GetDataTypes();
            if ~exist('datatype','var')
                datatype = 'conc hrf';
            end
            if ~exist('sdPairs','var')
                sdPairs = [1,1,0,1];
            end            
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            
            % Error Checking
            if size(sdPairs, 2)>1 && size(sdPairs, 2)~=4
                fprintf('ERROR: invalid sdPair. sdPair has to be a Nx4 2D array\n');
                return;
            end
            
            
            % If sdPairs argument is a column vector then we are done because channels are 
            % already specified in the output format i.e., as single number indices. 
            if size(sdPairs, 2)==1
                iChs = sdPairs;
                return;
            end            
                        
            switch(lower(datatype))
                case datatypes.RAW
                    if isempty(obj.acquired)
                        return
                    end
                    ml = obj.acquired.GetMeasurementList('matrix', iBlk);
                case datatypes.OPTICAL_DENSITY
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od');
                case datatypes.CONCENTRATION
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc');
                case datatypes.HRF_OPTICAL_DENSITY
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od hrf');
                case datatypes.HRF_OPTICAL_DENSITY_STD
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od hrf std');
                case datatypes.HRF_CONCENTRATION
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc hrf');
                case datatypes.HRF_CONCENTRATION_STD
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc hrf std');
            end
            
            % Error checking
            if isempty(ml)
                return
            end
            
            for ii = 1:size(sdPairs,1)
                k = find(ml(:,1)==sdPairs(ii,1)  &  ml(:,2)==sdPairs(ii,2)  &  ml(:,3)==sdPairs(ii,3)  &  ml(:,4)==sdPairs(ii,4));
                if isempty(k)
                    continue;
                end
                iChs(ii,1) = k;
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function sdPairs = VectorIdxs2SdPairIdxs(obj, datatype, iChs, iBlk)
            %
            % Syntax:
            %   iChs = TreeNodeClass.VectorIdxs2SdPairIdxs(obj, datatype, iChs , ml)
            %
            % Description:
            %   Given a set of channels specified by a column vetor of channel idxs, convert to a 2d array 
            %   channel idxs where each row representing a single channel is a tuple: 
            %   [source idx, detector idx, condition idx, datatype idx]
            % 
            % Example:
            %   % Convert concentration HRF source detectror pair [2,3] to single number indices
            %   cd(<dataset_root_path>)
            %   dataTree = DataTreeClass();
            %   dataTree.currElem.Calc();
            %   sdPairs = dataTree.currElem.SdPairIdxs2vectorIdxs('hrf conc',[34; 35; 36])
            %
            sdPairs = [];
            datatypes = obj.procStream.GetDataTypes();
            if ~exist('datatype','var') || isempty(datatype)
                datatype = 'raw';
            end
            if ~exist('iChs','var')
                iChs = 1;
            end            
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            
            % If sdPairs argument is not a column vector then we are done;  because the 
            % channels are already specified in the output format i.e., as a 2d array. 
            if size(iChs, 2)>1
                sdPairs = iChs;
                return;
            end
            
            switch(lower(datatype))
                case datatypes.RAW
                    if isempty(obj.acquired)
                        return
                    end
                    ml = obj.acquired.GetMeasurementList('matrix', iBlk);
                case datatypes.OPTICAL_DENSITY
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od');
                case datatypes.CONCENTRATION
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc');
                case datatypes.HRF_OPTICAL_DENSITY
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od hrf');
                case datatypes.HRF_OPTICAL_DENSITY_STD
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'od hrf std');
                case datatypes.HRF_CONCENTRATION
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc hrf');
                case datatypes.HRF_CONCENTRATION_STD
                    ml = obj.procStream.GetMeasurementList('matrix', iBlk, 'conc hrf std');
            end
            
            % Remove any invalid indices
            iChs(iChs==0) = [];
            iChs(iChs>size(ml,1)) = [];
            
            sdPairs = ml(iChs,:);
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function hAxes = GenerateStandaloneAxes(obj, datatype, iChs)
            k = find(obj.hFig(1,:)==-1);
            obj.hFig(1,k(1)) = figure;
            hAxes = gca;
            plotname = sprintf('"%s" (%s);   %s data ;   channels idxs: [%s]', obj.GetName(), num2str([obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]), ...
                               datatype, num2str(iChs'));
            namesize = uint32(length(plotname)/3);
            set(obj.hFig(1,k(1)), 'units','characters');
            p1 = get(obj.hFig(1,k(1)), 'position');
            set(obj.hFig(1,k(1)), 'name',plotname, 'menubar','none', 'NumberTitle','off', 'position',[p1(1)/2, p1(2), p1(3)+namesize, p1(4)]);
            obj.hFig(:,k(1)+1) = -1;
        end
           
        
            
        % ----------------------------------------------------------------------------------
        function hAxes = DisplayProbe(obj, chSelect, chSelectColors, hAxes)
            % Parse args
            if ~exist('chSelect','var')
                chSelect = [];
            end
            if ~exist('chSelectColors','var')                
                chSelectColors = repmat([1.0, 0.5, 0.2], size(chSelect,1),1);
            end
            if ~exist('hAxes','var')
                hAxes = [];
            end
            
            % If chSelect is in the form of a column vector rather than sd pairs
            % then convert to sd pairs
            chSelect = obj.VectorIdxs2SdPairIdxs('', chSelect);            
            
            freememoryflag = false;
            if ~isempty(obj.acquired) && obj.acquired.IsEmpty()
                obj.acquired.Load();
                freememoryflag = true;
            end
            
            % Set up the axes
            bbox = obj.GetSdgBbox();
            if isempty(hAxes)
                k = find(obj.hFig(2,:)==-1);
                
                % See if there's a data plot associated with this probe display
                % If there is get its name and use it to name this figure
                plotname = '';
                if ishandle(obj.hFig(1,k(1)))
                    plotname = get(obj.hFig(1,k(1)), 'name');
                end
                obj.hFig(2,k(1)) = figure('menubar','none', 'NumberTitle','off', 'name',plotname);
                hAxes = gca;
            end
            axis(hAxes, [bbox(1), bbox(2), bbox(3), bbox(4)]);
            gridsize = get(hAxes, {'xlim', 'ylim', 'zlim'});
            if ismac() || islinux()
                fs = 18;
            else
                fs = 11;
            end

            % Get probe paramaters
            probe = obj.GetProbe();
            srcpos = probe.sourcePos2D;
            detpos = probe.detectorPos2D;
            ml = obj.GetMeasurementList('matrix');
            lstSDPairs = find(ml(:,4)==1);
            
            % Draw all channels
            for ii = 1:length(lstSDPairs)
                hCh(ii) = line2(srcpos(ml(lstSDPairs(ii),1),:), detpos(ml(lstSDPairs(ii),2),:), [], gridsize, hAxes);
                col = [1.00 1.00 1.00] * 0.85;
                if ~isempty(chSelect)
                    k = find(chSelect(:,1)==ml(lstSDPairs(ii),1) & chSelect(:,2)==ml(lstSDPairs(ii),2));
                    if ~isempty(k)
                        col = chSelectColors(k(1),:);
                    end
                end
                set(hCh(ii), 'color',col, 'linewidth',2, 'linestyle','-', 'userdata',ml(lstSDPairs(ii),1:2));
            end
            
            % ADD SOURCE AND DETECTOR LABELS
            for iSrc = 1:size(srcpos,1)
                if ~isempty(find(ml(:,1)==iSrc)) %#ok<*EFIND>
                    hSD(iSrc) = text( srcpos(iSrc,1), srcpos(iSrc,2), sprintf('%d', iSrc), 'fontsize',fs, 'fontweight','bold', 'color','r' );
                    set(hSD(iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
                end
            end
            for iDet = 1:size(detpos,1)
                if ~isempty(find(ml(:,2)==iDet))
                    hSD(iDet+iSrc) = text( detpos(iDet,1), detpos(iDet,2), sprintf('%d', iDet), 'fontsize',fs, 'fontweight','bold', 'color','b' );
                    set(hSD(iDet+iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
                end
            end
            
            if freememoryflag
                obj.acquired.FreeMemory();
            end            
        end        
        
        

        % ----------------------------------------------------------------------------------
        function [hfig, iChs] = Plot(obj, datatype, sdPairs, iBlk, hAxes)
            %
            % SYNTAX:
            %   TreeNodeClass.Plot(datatype, iChs, iBlk, hAxes)
            % 
            %
            % DESCRIPTION:
            %   Plot data from channels specified by 2d array where each row spoecifying a single channel
            %   contains indices [source, detector, condition, wavelength]. In addtion to the data, this method 
            %   plots any existing stims, and the probe associated with the SNIRF object from which the data 
            %   was taken. NOTE: the args iBlk and hAxes can be ommitted and will default to 1 and current 
            %   axes respectively.
            %
            %
            % INPUT:
            %   datatype -  Type of data to plot. It will be accessed either from the acquired field of the 
            %               TreeNodeClass object or derived field (ie., procStream.output) of the 
            %               TreeNodeClass object. Here's the list of possible string values for this argument
            %
            %       raw data:                 'raw' | 'raw data' | 'intensity'
            %       optical density:          'od'}
            %       concentration:            'conc' | 'hb' | 'hbo' | 'hbr' | 'hbt'
            %       hrf concentration:        'hrf conc' | 'hrf_conc' | 'hb hrf' | 'conc hrf' | 'hb_hrf' | 'conc_hrf'
            %       hrf optical density:      'hrf od' | 'hrf_od' | 'od hrf' | 'od_hrf'}} |  ...
            %       hrf concentration std:    'hrf conc std' | 'hrf_conc_std' | 'hb hrf std' | 'conc hrf std' | 'hb_hrf_std' | 'conc_hrf_std'
            %       hrf optical density std:  'hrf od std' | 'hrf_od_std' | 'od hrf std' | 'od_hrf_std'
            %       
            %   sdPairs - 2d array of channel indices where each row represents a channel consisting of the indices 
            %             [source, detector, condition, datatype]
            %
            %   iBlk - Optional argument (defaults = 1). In theory SNIRF data field is an array of data blocks. This argunment selects the 
            %          data block from which the plot data is taken.
            %   
            %   hAxes - Optional argument (default is current axes or gca()), specifying the axes handle of the axes in which to plot the data.
            %
            %
            % EXAMPLES:
            %
            %   % 1. Load data set into dataTree and plot all wavelengths of the raw data for the source/detector pair [2,3] 
            %   %    of the current element
            %   cd(<dataset_root_folder>);
            %   dataTree = DataTreeClass();
            %   dataTree.currElem.Plot('raw', [2,3,0,1; 2,3,0,2])
            %
            %   % 2. Calculate and plot concentration HRF data (HbR), for condition 5, source/detector pair [2,3], 
            %   %    of the current element
            %   dataTree.currElem.Calc();
            %   dataTree.currElem.Plot('hrf conc', [2,3,2,5])
            %
            %   % 3. Calculate and plot concentration HRF data (HbR and HbT), for condition 1, source/detector pair [2,3], 
            %   %    of group 1
            %   dataTree.groups(1).Calc();
            %   dataTree.groups(1).Plot('hrf conc', [2,3,1,2; 2,3,1,3])
            %
            %   % 4. Calculate and plot All concentration HRF data (HbO, HbR and HbT), for condition 4, source/detector pair [2,3], 
            %   %    of group 1
            %   dataTree.groups(1).Calc();
            %   dataTree.groups(1).Plot('hrf conc', [2,3,4,1; 2,3,4,2; 2,3,4,3])
            %
            %   % 5. Calculate and plot All concentration HRF data (HbO), for condition 4, source/detector pairs 
            %   %    [3,5] and [4,7], of group 1
            %   dataTree.groups(1).Calc();
            %   dataTree.groups(1).Plot('hrf conc', [3,5,4,1; 4,7,4,1])
            %
            %
            
            d = [];
            t = [];
            datatypes = obj.procStream.GetDataTypes();
            hfig = [];

            % Parse input args
            if ~exist('datatype','var')
                datatype = 'conc hrf';
            end
            if ~exist('sdPairs','var')
                sdPairs = [1,1,0,1];
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            if ~exist('hAxes','var')
                hAxes = [];
            end

            % Remove zombie figure handles
            if all(~ishandle(obj.hFig(:)))
                obj.hFig = [-1; -1];
            end

            
            % Convert channels in the form of a list of sd pairs to a column vector of indices into the measurement list
            iChs = obj.SdPairIdxs2vectorIdxs(datatype, sdPairs, iBlk);
            
            
            % Extract SNIRF parameters for plotting:  probe, data, time, measuremntList and stim
            stim = [];
            switch(lower(datatype))
                case datatypes.RAW
                    if isempty(obj.acquired)
                        return
                    end
                    [d, t, ml] = obj.acquired.GetDataTimeSeries('matrix', iBlk);
                    if ~isempty(obj.procStream.input.acquired)
                        stim = obj.procStream.input.acquired.stim;
                    end
                case datatypes.OPTICAL_DENSITY
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('od',iBlk);
                    if ~isempty(obj.procStream.input.acquired)
                        stim = obj.procStream.input.acquired.stim;
                    end
                case datatypes.CONCENTRATION
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('conc',iBlk);
                    if ~isempty(obj.procStream.input.acquired)
                        stim = obj.procStream.input.acquired.stim;
                    end
                case datatypes.HRF_OPTICAL_DENSITY
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('od hrf',iBlk);
                case datatypes.HRF_OPTICAL_DENSITY_STD
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('od hrf std',iBlk);
                case datatypes.HRF_CONCENTRATION
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('conc hrf',iBlk);
                case datatypes.HRF_CONCENTRATION_STD
                    [d, t, ml] = obj.procStream.GetDataTimeSeries('conc hrf std',iBlk);
            end
            
            % If there's no data to plot then exit
            if isempty(d)
                fprintf('No data to plot\n');
                return;
            end
            
            
            % Set up standalone figure with axes for plotting data, if axes handle was not passed down from caller 
            % in the last arg. There will be a separate figure displaying the probe associated with this data plot. 
            % a few lines down in DisplayProbe.
            if isempty(hAxes)
                hAxes = obj.GenerateStandaloneAxes(datatype, iChs);
            end
            
            
            % Plot data
            hold on
            chSelect = [];
            for ii = 1:length(iChs)
                hdata(ii) = plot(hAxes, t, d(:,iChs(ii)), 'linewidth',2);
                chSelect(ii,:) = [ml(iChs(ii),1), ml(iChs(ii),2), ml(iChs(ii),3), ml(iChs(ii),4), get(hdata(ii), 'color')]; 
            end
            set(hAxes, 'xlim', [t(1), t(end)]);

            
            % Plot stim
            if ~isempty(stim)
                hCond = [];
                iCond = [];
                kk = 1;
                ylim = get(hAxes, 'ylim');
                d = (1e-4)*(ylim(2)-ylim(1));
                yrange = [ylim(1)+d, ylim(2)-d];
                CondColTbl = obj.CondColTbl();
                for jj = 1:length(stim)
                    h = [];
                    for ii = 1:size(stim(jj).data,1)
                        h = plot(hAxes, stim(jj).data(ii,1)*[1,1], yrange, 'color',CondColTbl(jj,:));
                    end
                    if ~isempty(h)
                        hCond(kk) = h; 
                        iCond(kk) = jj;
                        kk = kk+1;                    
                    end
                end
                [iCond, k] = sort(iCond);
                CondNames = obj.CondNames;
                if ishandles(hCond)
                    legend(hAxes, hCond(k), CondNames(iCond));
                end
            end
            
            
            % Display probe in separate figure
            if isempty(chSelect)
                fprintf('ERROR: no valid channels were selelcted');
                obj.DisplayProbe();
            else
                obj.DisplayProbe(chSelect(:,1:2), chSelect(:,5:7));
            end
            
            
            % Wrap up before exiting
            drawnow;
            pause(.1);
            hfig = obj.hFig;
            hold off
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function ClosePlots(obj, option)
            if ~exist('option','var')
                option = '';
            end
            if strcmp(option, 'all')
                for kk = 1:length(obj.children)
                    obj.children(kk).ClosePlots('all');
                end
            end

            % Data plots            
            for ii = 1:length(obj.hFig(1,:))
                if ishandles(obj.hFig(1,ii))
                    close(obj.hFig(1,ii))
                    obj.hFig(1,ii) = -1;
                end
            end
            
            % Probe plots
            for ii = 1:length(obj.hFig(2,:))
                if ishandles(obj.hFig(2,ii))
                    close(obj.hFig(2,ii))
                    obj.hFig(2,ii) = -1;
                end
            end
            
            if all(~ishandle(obj.hFig(:)))
                obj.hFig = [-1; -1];
            end
        end
        
    end
       
    
   
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Export mthods
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    methods        

        % ----------------------------------------------------------------------------------
        function ExportProcStreamFunctions(obj)
            if ispathvalid([obj.path, obj.outputDirname, 'ProcStreamFunctionsSummary.txt'])
                try
                    delete([obj.path, obj.outputDirname, 'ProcStreamFunctionsSummary.txt'])
                catch
                end
            end
            if strcmpi(obj.cfg.GetValue('Export Processing Stream Functions'), 'no')
                return
            end
            obj.ExportProcStreamFunctionsSummary();
        end

        
        
        % ----------------------------------------------------------------------------------
        function ExportProcStreamFunctionsSummary(obj)
            fmt = '.json';
            suffix = ['_processing',fmt];
            
            fid = fopen([obj.path, obj.outputDirname, 'ProcStreamFunctionsSummary.txt'], 'w');
            fprintf(fid, 'Application Name :   %s, (v%s)\n', getNamespace(), getVernum(getNamespace()));
            fprintf(fid, 'Date/Time        :   %s\n\n\n\n', char(datetime(datetime, 'Format','MMMM d, yyyy,   HH:mm:ss')));                        
            procStreamFunctionsExportFilenames = findTypeFiles([obj.path, obj.outputDirname], fmt);            
            for ii = 1:length(procStreamFunctionsExportFilenames)
                [~, fname, ext] = fileparts(procStreamFunctionsExportFilenames{ii});
                fname = [fname, ext];
                if ~strcmp(fname(end-length(suffix)+1 : end), suffix)
                    continue;
                end
                k = strfind(procStreamFunctionsExportFilenames{ii}, obj.outputDirname);
                iS = k+length(obj.outputDirname);
                iE = length(procStreamFunctionsExportFilenames{ii}) - length(suffix);
                fname = procStreamFunctionsExportFilenames{ii}(iS : iE);
                objtype = lower(class(obj.procStream.input.acquired));
                j = strfind(objtype, 'class');
                acqtype = lower(objtype(1:j-1));
                ext = ['.', acqtype];
                if ~ispathvalid([obj.path, fname, ext])
                    ext = '';
                end
                
                fprintf(fid, '%s\n', uint32('-') + uint32(zeros(1, length([fname, ext])+2)));
                fprintf(fid, '%s :\n', [fname, ext]);
                fprintf(fid, '%s\n', uint32('-') + uint32(zeros(1, length([fname, ext])+2)));
                txt = loadjson(procStreamFunctionsExportFilenames{ii});
                
                % Backwards compatability
                if isfield(txt.Processing,'FunctionCalls')
                    fcalls = txt.Processing.FunctionCalls;
                elseif isfield(txt.Processing,'FunctionsCalls')
                    fcalls = txt.Processing.FunctionsCalls;
                end
                for kk = 1:length(fcalls)
                    fprintf(fid, '%s\n', fcalls{kk});
                end
                fprintf(fid, '\n\n');
            end
            fclose(fid);
        end
        
        
                
        % ----------------------------------------------------------------------------------
        function ExportStim(obj, options)
            global cfg
            if ~exist('options','var')
                options = '';
                if strcmpi(cfg.GetValue('Load Stim from TSV file'), 'no')
                    options = 'regenerate';
                end
            end
            for ii = 1:length(obj.children)
                obj.children(ii).ExportStim(options);
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function DeleteExportStim(obj)
            for ii = 1:length(obj.children)
                obj.children(ii).DeleteExportStim();
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function FreeMemory(obj)
            if isempty(obj)
                return
            end
            obj.FreeMemorySubBranch();
            obj.procStream.FreeMemory(obj.GetOutputFilename);
        end
        

        % ----------------------------------------------------------------------------------
        function ExportHRF(obj, procElemSelect, iBlk)
            if ~exist('procElemSelect','var') || isempty(procElemSelect)
                q = MenuBox('Export only current element OR current element and all current element''s data ?', ...
                            {'Current data element only','Current element and all it''s data','Cancel'});
                if q==1
                    procElemSelect  = 'current';
                elseif q==2
                    procElemSelect  = 'all';
                else
                    return
                end
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end

            if strcmp(procElemSelect, 'all')
                for ii = 1:length(obj.children)
                    obj.children(ii).ExportHRF('all', iBlk);
                end
            end            
            obj.logger.Write('Exporting  %s', [obj.path, obj.GetOutputFilename()]);

            % 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 derived data and export it
            obj.procStream.Load([obj.path, obj.GetOutputFilename()]);
            if ~obj.DEBUG
                obj.procStream.ExportHRF([obj.path, obj.GetOutputFilename()], obj.CondNames, iBlk);
            end
            pause(.5);
        end
    
        
        % ----------------------------------------------------------------------------------
        function ExportMeanHRF(obj, procElemSelect, trange, iBlk)
            if ~exist('procElemSelect','var') || isempty(procElemSelect)
                q = MenuBox('Export only current element OR current element and all current element''s data ?', ...
                            {'Current data element only','Current element and all it''s data','Cancel'});
                if q==1
                    procElemSelect  = 'current';
                elseif q==2
                    procElemSelect  = 'all';
                else
                    return
                end
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end

            if strcmp(procElemSelect, 'all')
                for ii = 1:length(obj.children)
                    obj.children(ii).ExportMeanHRF(procElemSelect, trange, iBlk);
                end
            end            
            obj.logger.Write('Exporting HRF mean %s', [obj.path, obj.GetOutputFilename()]);

            % 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 derived data and export it
            obj.procStream.Load([obj.path, obj.GetOutputFilename()]);
            if ~obj.DEBUG
                obj.procStream.ExportMeanHRF([obj.path, obj.GetOutputFilename()], obj.CondNames, trange, iBlk);
            end
            pause(.5);
        end
    
        
        
        % ----------------------------------------------------------------------------------
        function filename = ExportHRF_GetFilename(obj)
            filename = obj.procStream.ExportHRF_GetFilename([obj.path, obj.GetOutputFilename()]);
        end
    
        
        
        % ----------------------------------------------------------------------------------
        function tblcells = ExportMeanHRF_Alt(obj, procElemSelect, trange, iBlk)
            tblcells = [];
            if isempty(obj.children)
                return
            end
            if ~exist('trange','var') || isempty(trange)
                trange = [];
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            
            
            %%%%% First export child data if user asked  
            nChild = length(obj.children);            
            if strcmp(procElemSelect, 'all')
                for iChild = 1:nChild
                    obj.children(iChild).ExportMeanHRF(procElemSelect, trange, iBlk);
                end
            end

            
            %%%%% Now export parent data 
            obj.logger.Write('Exporting HRF mean %s', [obj.path, obj.GetOutputFilename()]);

            nCh   = obj.procStream.GetNumChForOneCondition(iBlk);
            nCond = length(obj.CondNames);

            % Determine table dimensions            
            nHdrRows = 3;               % Blank line + name of columns
            nHdrCols = 2;               % Condition name + subject name
            nDataRows = nChild*nCond;    
            nDataCols = nCh;                 % Number of channels for one condition (for example, if data type is Hb Conc: (HbO + HbR + HbT) * num of SD pairs)
            nTblRows = nDataRows + nHdrRows;
            nTblCols = nDataCols + nHdrCols;
            cellwidthCond = max(length('Condition'), obj.CondNameSizeMax());
            cellwidthChild = max(length(sprintf('%s Name', obj.GetChildTypeLabel())), obj.NameSizeMax());
            
            % Initialize 2D array of TableCell objects with the above row * column dimensions            
            tblcells = repmat(TableCell(), nTblRows, nTblCols);
            
            % Header row: Condition, Subject Name, HbO,1,1, HbR,1,1, HbT,1,1, ...
            tblcells(2,1) = TableCell('Condition', cellwidthCond);
            tblcells(2,2) = TableCell(sprintf('%s Name',  obj.GetChildTypeLabel()), cellwidthChild);
            [tblcells(2,3:end), cellwidthData] = obj.procStream.GenerateTableCellsHeader_MeanHRF(iBlk);
            
            % Generate data rows
            for iChild = 1:nChild
                rowIdxStart = ((iChild-1)*nCond)+1 + nHdrRows;
                rowIdxEnd   = rowIdxStart + nCond - 1;
                
                c = obj.children(iChild).GenerateTableCellsHeader_MeanHRF(cellwidthCond, cellwidthChild);
                if isempty(c)
                    continue
                end
                tblcells(rowIdxStart:rowIdxEnd, 1:2) = c;
                
                c = obj.children(iChild).GenerateTableCells_MeanHRF(trange, cellwidthData, iBlk);
                if isempty(c)
                    continue
                end
                tblcells(rowIdxStart:rowIdxEnd, 3:nTblCols) = c;
            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
            
            % Create ExportTable initialized with the filled in 2D TableCell array. 
            % ExportTable object is what actually does the exporting to a file.
            obj.procStream.ExportMeanHRF_Alt([obj.path, obj.GetOutputFilename()], tblcells);
            pause(.5);
        end
                        
        
        
        % ----------------------------------------------------------------------------------
        function tblcells = GenerateTableCellsHeader_MeanHRF(obj, widthCond, widthChild)
            tblcells = repmat(TableCell(), length(obj.CondNames), 2);
            for iCond = 1:length(obj.CondNames)
                % First 2 columns contain condition name and group, subject or session name
                tblcells(iCond, 1) = TableCell(obj.CondNames{iCond}, widthCond);
                tblcells(iCond, 2) = TableCell(obj.name, widthChild);
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function tblcells = GenerateTableCells_MeanHRF(obj, trange, width, iBlk)
            if ~exist('trange','var') || isempty(trange)
                trange = [0,0];
            end
            if ~exist('width','var') || isempty(width)
                width = 12;
            end
            if ~exist('iBlk','var') || isempty(iBlk)
                iBlk = 1;
            end
            obj.Load();
            tblcells = obj.procStream.GenerateTableCells_MeanHRF_Alt(obj.name, obj.CondNames, trange, width, iBlk);
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function n = CondNameSizeMax(obj)
            n = 0;
            if isempty(obj.CondNames)
                return;
            end
            for ii = 1:length(obj.CondNames)
                if length(obj.CondNames{ii}) > n
                    n = length(obj.CondNames{ii});
                end
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function n = NameSizeMax(obj)
            n = 0;
            if isempty(obj.children)
                return;
            end
            for ii = 1:length(obj.children)
                if length(obj.children(ii).name) > n
                    n = length(obj.children(ii).name);
                end
            end
        end
        
        
        
        % ----------------------------------------------------------------------------------
        function ApplyParamEditToAll(obj, iFcall, iParam, val)
            % Figure out which level we are: group, subj, sess, or run
            if obj.iSubj==0 && obj.iSess==0 && obj.iRun==0
                for ii = 1:length(obj.subjs)
                    obj.subjs(ii).procStream.EditParam(iFcall, iParam, val);
                end
             elseif obj.iSubj>0 && obj.iSess>0 && obj.iRun==0
                for ii = 1:length(obj.subjs)
                    for jj = 1:length(obj.subjs(ii).sess)
                        obj.subjs(ii).sess(jj).procStream.EditParam(iFcall, iParam, val);
                    end
                end
            elseif obj.iSubj>0 && obj.iSess>0 && obj.iRun>0
                for ii = 1:length(obj.subjs)
                    for jj = 1:length(obj.subjs(ii).sess)
                        for kk = 1:length(obj.subjs(ii).sess(jj).runs)
                            obj.subjs(ii).sess(jj).runs(kk).procStream.EditParam(iFcall, iParam, val);
                        end
                    end
                end
            end
        end
        


        % ----------------------------------------------------------------------------------
        function typelabel = GetChildTypeLabel(obj)
            typelabel = '';
            if isempty(obj)
                return;
            end
            if isempty(obj.children)
                return;
            end
            temp = class(obj.children(1));
            k = strfind(temp, 'Class');
            typelabel = temp(1:k-1);            
        end        
        
        
        
        % ----------------------------------------------------------------------------------
        function b = HaveOutput(obj)
            b = false;
            for ii = 1:length(obj.children)
                b = obj.children(ii).HaveOutput();
                if b
                    break;
                end
            end
        end
        
        
                
        % ----------------------------------------------------------------------------------
        function nbytes = MemoryRequired(obj)
            if isempty(obj)
                return;
            end            
            nbytes = obj.procStream.MemoryRequired();
        end
        
        
        % ----------------------------------------------------------------------------------
        function filename = GetOutputFilename(obj, options)
            filename = '';
            if isempty(obj)
                return;
            end
            if ~exist('options','var')
                options = '';
            end
            filename0 = obj.SaveMemorySpace(obj.name);
            if isempty(filename0)
                return;
            end
            if optionExists(options, 'legacy')
                outputDirname = ''; %#ok<*PROPLC>
            else
                outputDirname = obj.outputDirname;
            end
            [p, f] = fileparts([outputDirname, filename0]);
            filename = [filesepStandard(p, 'nameonly:dir'), f];            
        end
        
        
        % ----------------------------------------------------------------------------------
        function filename = GetFilename(obj)
            filename = '';
            if isempty(obj)
                return;
            end
            filename = obj.SaveMemorySpace(obj.name);
            if isempty(filename)
                return;
            end
        end
        
        
        % ----------------------------------------------------------------------------------
        function status = Mismatch(obj, obj2)
            status = 0;
            if exist('obj2','var')                
                if obj == obj2
                    return
                end
            end
            status = 1;
                        
            configFileOptions =  MenuBox('', {}, [], [], 'dontAskAgainOptions');
            choices = { ...
                sprintf('Continue Loading'); ...
                sprintf('Quit Loading'); ...
            };
        
            if exist('obj2','var')
                msg{1} = sprintf('WARNING: Saved processing data for %s "%s" does not match this group folder. ', obj.type, obj.name);
                msg{2} = sprintf('Are you sure this saved data belongs to this group folder?');
            else
                msg{1} = sprintf('WARNING: The %s "%s" does not match the saved group data. ', obj.type, obj.name);
                msg{2} = sprintf('Are you sure the saved data belongs to this group folder?');
            end
            obj.logger.Write([msg{:}])
            if strcmp(obj.GroupDataLoadWarnings, configFileOptions{1})
                return;
            end
            selection = MenuBox(msg, choices, [], [], 'dontAskAgainOptions');
            if length(selection)<2
                selection(2)=0;
            end
            
            % Find out if config value does not equal current selection. If
            % not then reset config value
            if selection(2)>0
                if ~strcmp(obj.GroupDataLoadWarnings, configFileOptions{selection(2)})
                    % Overwrite config value
                    obj.cfg.SetValue('Group Data Loading Warnings', configFileOptions{selection(2)});
                    obj.cfg.Save();
                    obj.GroupDataLoadWarnings()
                end
            end
                        
        end
        
        
        % ------------------------------------------------------------
        function val = GetError(obj)
            val = obj.err;            
        end

        
        
        % ------------------------------------------------------------
        function msg = GetErrorMsg(obj)
            msg = '';
            if isempty(obj.acquired)
                return;
            end
            msg = obj.acquired.GetErrorMsg();
        end

        
        
        % ------------------------------------------------------------
        function Print(obj, indent)
            obj.logger.Write('%s%s\n', blanks(indent), obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename()]) );
        end

        
        
        % ----------------------------------------------------------------------------------
        function BackwardCompatability(obj)
            if ~ispathvalid([obj.path, obj.outputDirname])
                mkdir([obj.path, obj.outputDirname])
            end
            src = obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename('legacy')]);
            dst = obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename()]);
            if ispathvalid(src)
                if ~pathscompare(src, dst)
                    obj.logger.Write(sprintf('Moving %s to %s\n', src, dst));
                    rootpath = fileparts(dst);
                    try
                        if ~ispathvalid(rootpath)
                            mkdir(rootpath)
                        end
                    	movefile(src, dst);
                    catch
                        obj.logger.Write(sprintf('ERROR: Failed to to move old output to new format\n'));
                    end
                end
            end
        end
        
        
        
        % -------------------------------------------------------
        function Rename(obj, namenew)
            [pnameAcquiredNew, fnameAcquiredNew] = fileparts(namenew);
            [pnameAcquired, fnameAcquired, ext] = fileparts(obj.name);            
            filenameOutput = obj.GetOutputFilename();
            [pnameDerived, fnameDerived] = fileparts(filenameOutput);
            
            pnameAcquired = filesepStandard(pnameAcquired);
            pnameAcquiredNew = filesepStandard(pnameAcquiredNew, 'nameonly:dir');
            pnameDerived = filesepStandard(pnameDerived);
            
            obj.logger.Write(sprintf('Renaming %s to %s', obj.name, namenew));

            if ispathvalid([pnameAcquired, fnameAcquired, ext])
                obj.logger.Write(sprintf('  Moving %s to %s', [pnameAcquired, fnameAcquired, ext], [pnameAcquiredNew, fnameAcquiredNew, ext]));
                %movefile([filenameOutput, ext], [pnameAcquired, namenew, ext]);
            end
            
            
            % Dewrived data
            if ispathvalid([pnameDerived, fnameDerived, '.mat'])
                obj.logger.Write(sprintf('  Moving %s to %s', [pnameDerived, fnameDerived, '.mat'], [pnameAcquiredNew, namenew, '.mat']));
                %movefile([filenameOutput, '.mat'], [pnameDerived, namenew, '.mat']);
            elseif ispathvalid([pnameDerived, fnameDerived, '/', fnameDerived, '.mat'])
                obj.logger.Write(sprintf('  Moving %s to %s', [pnameDerived, fnameDerived, '/', fnameDerived, '.mat'], ...
                    [pnameDerived, fnameDerived, '/', namenew, '.mat']));
                obj.logger.Write(sprintf('  Moving %s to %s', [pnameDerived, fnameDerived], ...
                    [pnameAcquiredNew, namenew]));
                %movefile([filenameOutput, '.mat'], [pnameDerived, namenew, '.mat']);
            end
            
            if ispathvalid([pnameDerived, fnameDerived])
                obj.logger.Write(sprintf('  Moving %s to %s', [pnameDerived, fnameDerived], [pnameDerived, fnameNew]));
                %movefile([filenameOutput, ext], [pnameDerived, namenew, ext]);
            end
%             obj.name = [filesepStandard(pnameNew), fnameNew, ext];
        end
        
        
    end

    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Static class methods implementing runs, subjs, groups processing 
    % flags for quickly calculating required memory and color table
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    methods (Static)
                
        % ----------------------------------------------------------------------------------
        function out = CondColTbl(arg)
            persistent tbl;
            if nargin==0
                out = tbl;
                return;
            end
            if ~strcmp(arg,'init')
                return
            end
            tbl = distinguishable_colors(128);
        end
   
        
        
        % --------------------------------------------------------------------------------
        function out = SaveMemorySpace(arg)
            persistent v;
            out = [];
                        
            % If first time we call SaveMemorySpace is with a filename argument, that is arg is a char string 
            % rather than a numeric, then we want to set v to true to make sure not to load everything into memory 
            % by default. Later in the Homer3 initalization if we detect our data set is small, we can reverse that 
            % and set the SaveMemorySpace to false to improve responce time. 
            if isempty(v)
                v = true;
            end
            
            if islogical(arg) || isnumeric(arg)
                v = arg;
                out = v;
            elseif ischar(arg)                
                if v
                    out = arg;
                else
                    out = '';
                end
            end
        end
   
                
        % --------------------------------------------------------------------------------
        function out = GroupDataLoadWarnings()
            global cfg
            
            persistent v;
            if ~exist('arg','var')
                v = cfg.GetValue('Group Data Loading Warnings');
            elseif exist('arg','var')
                v = arg;
            end
            out = v;
        end
        
    end
    
end