Commit fbecb31f authored by jayd1860's avatar jayd1860
Browse files

v1.42.2 

-- Fix error when loading snirf with corrupt stim data. Added error checking to flag bad stim data. Then add file with bad stim data and discard bad stims while displaying warning.
-- Improve warning reporting for files that were allowed to load but with warnings.
-- Fix matlab error in backward compatability code when derived output folder is same as root group folder
parent 2cde4dea

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+13 −7
Original line number Diff line number Diff line
@@ -472,28 +472,34 @@ classdef DataFilesClass < handle 
                if obj.files(ii).isdir

                    continue;

                end

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

                filename = obj.files(ii).name;

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

                if  o.GetError() < 0

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

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

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

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

                    obj.logger.Write('DataFilesClass.ErrorCheck:   WARNING data is unusable - %s will not be added to data set\n', filename);

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

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

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

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

                    obj.logger.Write('DataFilesClass.ErrorCheck:   WARNING data is unusable - %s will not be added to data set\n', filename);

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

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

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

                elseif ~isempty(o.GetErrorMsg())

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

                    dataflag = true;

                else

                    dataflag = true;

                end

                if ~isempty(o.GetErrorMsg())

                    obj.files(ii).SetError(o.GetErrorMsg());

                end

                hwait = waitbar_improved(ii/length(obj.files), hwait, msg);

            end

            

            if dataflag==false

                obj.files = FileClass.empty();

            else

                for jj = 1:length(errorIdxs)

                    obj.filesErr(end+1) = obj.files(errorIdxs(jj)).copy;

                    obj.filesErr(end).SetError('Invalid Data Format');

                end

            	obj.files(errorIdxs) = [];

                obj.nfiles = obj.nfiles - length(errorIdxs);

DataTree/AcquiredData/DataFiles/FileClass.m

+7 −10
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ classdef FileClass < matlab.mixin.Copyable 
        rootdir

        err

        logger

        errmsgs

        errmsg

    end

    

    methods
@@ -38,9 +38,9 @@ classdef FileClass < matlab.mixin.Copyable 
            obj.filename   = '';

            obj.map2group  = struct('iGroup',0, 'iSubj',0, 'iSess',0, 'iRun',0);

            obj.rootdir    = '';

            obj.err        = -1;          % Assume file is not loadable

            obj.errmsg     = '';          % Assume file is not loadable

            obj.logger     = InitLogger(logger);            

            obj.errmsgs    = {'Invalid Data Format','Invalid File Name'};

            obj.errmsg    = '';

            

            

            if nargin==0
@@ -538,22 +538,19 @@ classdef FileClass < matlab.mixin.Copyable 
        

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

        function err = GetError(obj)

            err = obj.err;

            err = ~isempty(obj.errmsg);

        end

        

        

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

        function err = SetError(obj, err)

            if ischar(err)

                err = find(strcmp(obj.errmsgs, err));

            end

            obj.err = err;

        function SetError(obj, errmsg)

            obj.errmsg = errmsg;

        end

        

        

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

        function msg = GetErrorMsg(obj)

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

            msg = obj.errmsg;

        end

        

    end

DataTree/AcquiredData/Snirf/SnirfClass.m

+19 −7
Original line number Diff line number Diff line
@@ -269,12 +269,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            obj.errmsgs = {

                'MATLAB could not load the file.'

                '''formatVersion'' is invalid.'

                '''metaDataTags'' is invalid.'

                '''data'' is invalid.'

                '''stim'' is invalid and could not be loaded'

                '''probe'' is invalid.'

                '''aux'' is invalid and could not be loaded'

                'WARNING: ''data'' corrupt and unusable'

                '''metaDataTags'' field is invalid.'

                '''data'' field is invalid.'

                '''stim'' field has corrupt data. Some or all stims could not be loaded'

                '''probe'' field is invalid.'

                '''aux'' field is invalid and could not be loaded'

                'WARNING: ''data'' field corrupt and unusable'

                };

        end
@@ -450,6 +450,18 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                    obj.stim(ii).delete();

                    obj.stim(ii) = [];

                    break;

                else

                    for kk = 1:ii-1

                        if strcmp(obj.stim(kk).name, obj.stim(ii).name)

                            obj.stim(ii).delete();

                            obj.stim(ii) = [];

                            err = err-6;

                            break

                        end

                    end

                    if err ~= 0

                        break;

                    end

                end

                ii=ii+1;

            end

DataTree/AcquiredData/Snirf/StimClass.m

+9 −7
Original line number Diff line number Diff line
@@ -268,12 +268,14 @@ classdef StimClass < FileLoadSaveClass 
            err = 0;

            

            % According to SNIRF spec, stim data is invalid if it has > 0 AND < 3 columns

            if isempty(obj.data)

                return;

            if isempty(obj.name)

                err = -3;

            end

            if ~isempty(obj.data) && size(obj.data,2)<3

                err = err-4;

                if size(obj.data, 2) ~= length(obj.dataLabels)

                    err = err-5;

                end

            if size(obj.data, 2)<3

                err = -2;

                return;

            end

        end

DataTree/DataTreeClass.m

+46 −1
Original line number Diff line number Diff line
@@ -11,6 +11,8 @@ classdef DataTreeClass < handle 
        logger

        warningflag

        dataStorageScheme

        warnings

        errorStats

    end
@@ -32,7 +34,8 @@ classdef DataTreeClass < handle 
            obj.currElem            = TreeNodeClass().empty();

            obj.reg                 = RegistriesClass().empty();

            obj.dirnameGroups       = {};

            

            obj.warnings            = '';

            obj.errorStats        = [0,0,0];

            

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

            % Parse args
@@ -494,6 +497,30 @@ classdef DataTreeClass < handle 
        

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

        function ErrorCheckLoadedFiles(obj)

            maxWarningsDisplay = 25;

            for iF = 1:length(obj.files)

                if ~isempty(obj.files(iF).GetErrorMsg())

                    if obj.errorStats(2) > maxWarningsDisplay

                        continue

                    end

                    if isempty(obj.warnings)

                        obj.warnings = sprintf('%s:   %s\n\n', obj.files(iF).name, obj.files(iF).GetErrorMsg());

                    elseif obj.errorStats(2) < maxWarningsDisplay-1

                        obj.warnings = sprintf('%s%s:   %s\n\n', obj.warnings, obj.files(iF).name, obj.files(iF).GetErrorMsg());

                    elseif obj.errorStats(2) == maxWarningsDisplay-1

                        obj.warnings = sprintf('%s  . . . Reached maximum number of warnings to display\n\n', obj.warnings);                        

                    end

                    if obj.files(iF).IsFile()

                        obj.errorStats(2) = obj.errorStats(2)+1;

                    end

                else

                    if obj.files(iF).IsFile()

                        obj.errorStats(1) = obj.errorStats(1)+1;

                    end

                end

            end

            obj.errorStats(3) = length(obj.filesErr);



            if isempty(obj.filesErr)

                return

            end
@@ -506,6 +533,24 @@ classdef DataTreeClass < handle 
        end

        

        

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

        function w = GetWarningsReport(obj)

            [nFileSuccess, nFilesWarning, nFilesFailed] = obj.GetErrorStats();

            if ~isempty(obj.warnings)

                obj.warnings = sprintf('The following %d files were loaded with warnings:\n=========================================\n%s', nFilesWarning, obj.warnings);

            end

            w = obj.warnings;

        end

        

        

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

        function [nFileSuccess, nFilesWarning, nFilesFailed] = GetErrorStats(obj)

            nFileSuccess = obj.errorStats(1);

            nFilesWarning = obj.errorStats(2);

            nFilesFailed = obj.errorStats(3);

        end

        

        

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

        function list = DepthFirstTraversalList(obj)

            list = {};

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