Merge in removal of submodule references and replacement with copies of the...

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classdef AcqDataClass < matlab.mixin.Copyable

    properties (Access = private)

        logger

    end

    properties (Access = protected)

        errmsgs

    end

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % These methods must be implemented in any derived class

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    methods(Abstract)

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

        objnew    = GetFormatVersion(obj, options);

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

        val       = GetFormatVersionString(obj);

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

        t         = GetTime(obj, iBlk)

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

        datamat   = GetDataTimeSeries(obj, options, iBlk)

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

        SD        = GetSDG(obj,option)

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

        srcpos    = GetSrcPos(obj,option)

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

        detpos    = GetDetPos(obj,option)

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

        ml        = GetMeasList(obj, iBlk)

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

        wls       = GetWls(obj)

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

        SetStims_MatInput(obj, s, t, CondNames)

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

        s         = GetStims(obj, t)

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

        CondNames = GetConditions(obj)

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

        SetConditions(obj, CondNames)

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

        aux       = GetAuxiliary(obj)

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

        SetStimDuration(obj, icond, duration);

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

        duration = GetStimDuration(obj, icond);

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

        n = GetDataBlocksNum(obj);

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

        [iDataBlks, ich] = GetDataBlocksIdxs(obj, ich);

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

        objnew = CopyMutable(obj, options);

    end

    methods

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

        function Initialize(obj)

            global logger

            obj.logger = InitLogger(logger);

        end

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

        function err = Error(obj)

            err = obj.GetError();

        end

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

        function msg = GetErrorMsg(obj)

            msg = '';

            if isempty(obj)

                msg = 'AcqDataClass object is empty';

                return;

            end

            if isempty(obj.errmsgs)

                return;

            end

            if ~obj.GetError()

                return;

            end

            msg = obj.errmsgs{abs(obj.GetError())};

        end

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

        function FreeMemory(obj, filename)

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

                filename = '';

            end

            if isempty(filename)

                return;

            end            

            obj.Initialize();

        end

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

        function bbox = GetSdgBbox(obj)

            bbox = [];

            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];

            if isempty(optpos)

                return

            end

            xmax = max(optpos(:,1));

            ymax = max(optpos(:,2));

            xmin = min(optpos(:,1));

            ymin = min(optpos(:,2));

            width = xmax-xmin;

            height = ymax-ymin;

            if width==0

                width = 1;

            end

            if height==0

                height = 1;

            end

            px = width * 0.05; 

            py = height * 0.05; 

            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];

        end

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

        function varval = GetVar(obj, varname)

            if ismethod(obj,['Get_', varname])

                varval = eval( sprintf('obj.Get_%s()', varname) );

            elseif ismethod(obj,['Get', varname])

                varval = eval( sprintf('obj.Get%s()', varname) );

            elseif isproperty(obj, varname)

                varval = eval( sprintf('obj.%s', varname) );

            else

                varval = [];

            end

            % If varval is a class object with an IsEmpty() method and length of varval is one or 

            % less, then use it determine whether it's valid. If not, return empty as if it were 

            % really empty. This is useful when we want to copy only part of an object to save on space. 

            % For instance to reconstruct nirs style 's' variable from a SNIRF stim object we need the t 

            % property from a SNIRF data container, but we only need that one property not the whole thing

            % so we initilize only the t property. We don't want this partially initialized data object 

            % to be found (by GetVar) and used directly in the proc stream processing, we only want to use 

            % indirectly to retrieve s from stim. So we do this check to see if it's valid. It won't be 

            % since it's only partially initialized.

            if isa(varval, 'handle') && ismethod(varval,'IsEmpty')

                if length(varval)==1 && varval(1).IsEmpty()

                    varval = [];

                end

            end

        end

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

        function t = GetTimeCombined(obj)

            % Function combines the time vectors for all data blocks into one time vectors. 

            t = obj.GetTime(1);

            tStart = t(1);

            tEnd   = t(end);

            tStep  = mean(diff(t));

            nBlks = obj.GetDataBlocksNum();

            for iBlk=2:nBlks

                t = obj.GetTime(iBlk);

                if t(1) < tStart

                    tStart = t(1);

                end

                if t(end) > tEnd

                    tEnd = t(end);

                end

                if mean(diff(t)) < tStep

                    tStep = mean(diff(t));

                end

            end

            t = tStart:tStep:tEnd;            

        end

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

        function data = GetStimData(~, ~)

            data = [];

        end

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

        function val = GetStimDataLabels(~, ~)

            val = {};

        end

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

        function b = equal(obj, obj2)

            b = true;

            if isempty(obj.GetFilename)

                return;

            end

            if isempty(obj2.GetFilename)

                return;

            end

            [~, fname1, ext1] = fileparts(obj.GetFilename);

            [~, fname2, ext2] = fileparts(obj2.GetFilename);            

            if ~strcmpi([fname1, ext1], [fname2, ext2])

                b = false;

            end

        end

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

        function status = Mismatch(obj, obj2)

            status = 0;

            msg = {};

            if ~exist('obj2','var')

                return;

            end

            if ~obj.equal(obj2)

                [~, fname, ext] = fileparts(obj.GetFilename);

                msg{1} = sprintf('WARNING: The acquisition file "%s" does not match the derived data in this group folder. ', [fname, ext]);

                msg{2} = sprintf('Are you sure this acquisition file belongs in this group folder?');

                obj.logger.Write([msg{:}])

            end

        end

    end

end

classdef DataFilesClass < handle

    properties

        files;

        type;

        err;

        errmsg;

        pathnm;

        config;

        nfiles;

        logger

    end

    methods

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

        function obj = DataFilesClass(varargin)            

            obj.type = '';

            obj.pathnm = pwd;

            obj.nfiles = 0;

            obj.err = -1;

            obj.errmsg = {};

            global logger

            global cfg

            logger = InitLogger(logger);

            cfg    = InitConfig(cfg);

            obj.logger = logger;

            skipconfigfile = false;

            askToFixNameConflicts = [];

            if nargin==0

                return

            end            

            if nargin==1

                obj.pathnm = varargin{1};

            end            

            if nargin==2

                obj.pathnm = varargin{1};

                obj.type = varargin{2};

            end

            if nargin==3

                obj.pathnm = varargin{1};

                obj.type = varargin{2};

                if strcmp(varargin{3}, 'standalone')

                    skipconfigfile = true;

                end

            end            

            if nargin==4

                obj.pathnm = varargin{1};

                obj.type = varargin{2};

                if strcmp(varargin{3}, 'standalone')

                    skipconfigfile = true;

                end

                askToFixNameConflicts = varargin{4};

            end

            if obj.type(1)=='.'

                obj.type(1)='';

            end

            obj.pathnm = filesepStandard(obj.pathnm,'full');

            % Configuration parameters

            obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);

            if skipconfigfile==false

                str = cfg.GetValue('Regression Test Active');

                if strcmp(str,'true')

                    obj.config.RegressionTestActive=true;

                else

                    obj.config.RegressionTestActive=false;

                end

            else

                obj.config.RegressionTestActive=false;

            end

            obj.config.SuppressErrorChecking = false;

            if ~isempty(askToFixNameConflicts)

                obj.config.AskToFixNameConflicts = askToFixNameConflicts;

            elseif strcmp(cfg.GetValue('Fix File Name Conflicts'), sprintf('don''t ask again'))

                obj.config.AskToFixNameConflicts = 0;

            end

            if ~obj.config.AskToFixNameConflicts

                obj.config.SuppressErrorChecking = true;                

            end

            if nargin==0

                return;

            end

            obj.err = 0;

            obj.files = mydir(obj.pathnm);

            GetDataSet(obj);

        end

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

        function GetDataSet(obj)

            if exist(obj.pathnm, 'dir')~=7

                error('Invalid subject folder: ''%s''', obj.pathnm);

            end

            obj.findDataSet(obj.type);

            % Remove any files that cannot pass the basic test of loading

            % its data

            obj.ErrorCheck(obj.type);

            obj.ErrorCheckName();

        end

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

        function findDataSet(obj, type)

            obj.files = mydir([obj.pathnm, '/*.', type]);

            % Remove any files that cannot pass the basic test of loading

            % its data

            obj.ErrorCheck(type);

            if isempty( obj.files )                

                % If there are no data files in current dir, don't give up yet - check

                % the subdirs for data files.

                dirs = mydir(obj.pathnm);

                for ii = 1:length(dirs)

                    if dirs(ii).isdir && ...

                            ~strcmp(dirs(ii).name,'.') && ...

                            ~strcmp(dirs(ii).name,'..') && ...

                            ~strcmp(dirs(ii).name,'hide')

                        dirs(ii).idx = length(obj.files)+1;

                        foos = mydir([obj.pathnm, dirs(ii).name, '/*.', type]);

                        nfoos = length(foos);

                        if nfoos>0

                            for jj = 1:nfoos

                                foos(jj).subjdir      = dirs(ii).name;

                                foos(jj).subjdiridx   = dirs(ii).idx;

                                foos(jj).idx          = dirs(ii).idx+jj;

                                foos(jj).filename     = foos(jj).name;

                                foos(jj).name         = [dirs(ii).name, '/', foos(jj).name];

                                foos(jj).map2group    = struct('iGroup',0, 'iSubj',0, 'iRun',0);

                                foos(jj).pathfull     = dirs(ii).pathfull;

                                if ~foos(jj).isdir

                                    obj.nfiles = obj.nfiles+1;

                                end

                            end

                            % Add file from current subdir to files struct

                            if isempty(obj.files)

                                obj.files = dirs(ii);

                            else

                                obj.files(end+1) = dirs(ii);

                            end

                            obj.files(end+1:end+nfoos) = foos;                                                        

                        end

                    end

                end

            else

                for ii = 1:length(obj.files)

                    obj.files(ii).pathfull = obj.pathnm;

                end

                obj.nfiles = obj.nfiles+length(obj.files);

            end

        end

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

        function getDataFile(obj, filename)

            obj.files = mydir(filename);

        end

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

        function ErrorCheckName(obj)

            for ii = length(obj.files):-1:1

                if obj.files(ii).ErrorCheckName()<0

                    q = obj.AskToFixNameConflicts(ii);                    

                    if q == 1

                        obj.files(ii).FixNameConflict();

                    else

                        obj.files(ii).NameConflictFixed();

                    end

                end

                if obj.files(ii).GetError()<0

                    obj.err = -1;

                end

            end

        end

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

        function answer = AskToFixNameConflicts(obj, ii)

            global cfg

            ConfigFileClass

            answer = 0;

            if obj.config.AskToFixNameConflicts == 0

                obj.files(ii).NameConflictFixed();

                return

            end

            q = MenuBox(obj.GetErrorMsg(ii), {'YES','NO'},[],[],'askEveryTimeOptions');

            if q(1) == 0

                return;

            end

            if length(q)>1 && q(2) == 1

                cfg.SetValue('Fix File Name Conflicts', sprintf('don''t ask again'));

                cfg.Save()

                obj.config.AskToFixNameConflicts = 0;

            end

            if q(1)==2

                obj.files(ii).NameConflictFixed();

            end

            answer = q(1);

        end

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

        function errmsg = GetErrorMsg(obj, ii)

            p1      = fileparts(obj.files(ii).GetName());

            [p2,f2] = fileparts(filesepStandard(obj.files(ii).pathfull,'nameonly:file'));

            [~,f3]  = fileparts(p2);

            if isfile_private(obj.files(ii).GetName())

                filetype = 'file';

            else

                filetype = 'folder';

            end

            containingFolder = '';

            if obj.files(ii).GetError() == -1

                containingFolder = p1;

            end

            if obj.files(ii).GetError() == -2

                containingFolder = f2;

            end

            if obj.files(ii).GetError() == -3

                containingFolder = f3;

            end

            msg{1} = sprintf('WARNING: The current %s (%s) has the same name as the folder (%s) containing it. ', filetype, obj.files(ii).GetName(), containingFolder);

            msg{2} = sprintf('All %ss should have a different name than the folder containing them, otherwise ', ['F',filetype(2:end)]);

            msg{3} = sprintf('it may cause incorrect results in processing. Do you want to rename this %s?', filetype);

            errmsg = [msg{:}];            

        end

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

        function pushbuttonLoadDataset_Callback(~, hObject)

            hp = get(hObject,'parent');

            hc = get(hp,'children');

            for ii=1:length(hc)

                if strcmp(get(hc(ii),'tag'),'pushbuttonLoad')

                    hButtnLoad = hc(ii);

                elseif strcmp(get(hc(ii),'tag'),'pushbuttonSelectAnother')

                    hButtnSelectAnother = hc(ii);

                end

            end

            if hObject==hButtnLoad

                delete(hButtnSelectAnother);

            elseif hObject==hButtnSelectAnother

                delete(hButtnLoad);

            end

            delete(hp);

        end

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

        function b = isempty(obj)

            if isempty(obj.files)

                b = true;

            else

                b = false;

            end

        end

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

        function found = ConvertedFrom(obj, src)

            found = zeros(length(src.files), 1);

            for ii = 1:length(src.files)

                if src.files(ii).isdir

                    found(ii) = -1;

                    continue;

                end

                [ps, fs] = fileparts(src.files(ii).name);

                for jj = 1:length(obj.files)

                    [pd, fd] = fileparts(obj.files(jj).name);

                    if strcmp(filesepStandard([ps,'/',fs], 'nameonly'), filesepStandard([pd,'/',fd], 'nameonly'))

                        found(ii) = 1;

                        break;

                    end

                end

            end

        end

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

        function ErrorCheck(obj, type)

            errorIdxs = [];

            if isempty(obj.files)

                return

            end

            % Assume constructor name follows from name of data format type

            constructor = sprintf('%sClass', [upper(type(1)), type(2:end)]);

            % Make sure function by that name exists; otherwise no way to

            % use it to check loadability

            if isempty(which(constructor))

                return;

            end

            % Try to create object of data type and load data into it

            dataflag = false;

            for ii = 1:length(obj.files)

                if obj.files(ii).isdir

                    continue;

                end

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

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

                if o.GetError()<0

                    obj.logger.Write('FAILED error check:   %s will not be added to data set\n', filename);

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

                else

                    dataflag = true;

                end

            end

            if dataflag==false

                obj.files = FileClass.empty();

            else

            	obj.files(errorIdxs) = [];

            end

        end

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

        function err = GetError(obj)

            err = -1;

            if isempty(obj)

                return;

            end

            err = obj.err;

        end

    end

end

function DeleteDataFiles(varargin)

% Syntax:

%

%   DeleteDataFiles()

%   DeleteDataFiles(dirname)

%   DeleteDataFiles(dirname, datafiles0)

%   DeleteDataFiles(dirname, format)

%   DeleteDataFiles(dirname, datafiles0, options)

%   DeleteDataFiles(dirname, format, options)

%

% Description:

%   

%   Delete all .<format extension> files in group folder. DeleteDataFiles will find all 

%   .<format extension> data acquisition files in the group folder. If dirname is not supplied it'll 

%   treat the current working directory as the group folder. 

%

% Examples:

%

%   1. Delete all .snirf files in the Homer3 Examples directory

%

%       DeleteDataFiles('C:\jdubb\workspaces\Homer3\DataTree\AcquiredData\Snirf\Examples', '.snirf')

%