Unverified Commit b000659a authored by jayd1860's avatar jayd1860 Committed by GitHub
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v1.35.11 - Clearly display in MainGUI and DataTree the data files that were... 

v1.35.11 - Clearly display in MainGUI and DataTree the data files that were NOT loaded because of errors (#128)

* v1.35.8

-- Clearly display in MainGUI and DataTree the data files that were NOT loaded because of errors and more clearly display in the logging the ones that were loaded and the ones. In MainGUI display data files NOT loaded in separate listbox window with red font. Clicking on any one of the error files displays error that kept it from loading.

-- Replace version number display for shared libraries with last revision date/time.

-- Improve and clean up code in syncSubmodules tool:
   a) Use last revision date/time instead of version number to sync shared libs.
   b) Warn user of uncommitted changes when syncing files in syncSubmodules.m
   c) Do a general code clean up

* v1.35.9

-- Get rid of version numbers and version files from shared libraries. Instead generate last rev date on the fly and display that (this only applies to git repos, for unzipped code just display lib name).

* v1.35.10

-- Fix error loading SNIRF aux.name field in AuxClass because of changes to MATLAB's HDF5 library. (It seems for string there is no need to transpose the data.)

* v1.35.11

-- Fix minor display issue on MAC where the file search window does NOT display title showing the purpose of the window ("Load Processing Options File"). Use alternative file search GUI (only on MAC) which displays Window title and allows user to select *.cfg file.
parent 247a02c7

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+48 −5
Original line number Original line Diff line number Diff line
@@ -2,6 +2,7 @@ classdef DataFilesClass < handle 
    

    

    properties

    properties

        files;

        files;

        filesErr;

        filetype;

        filetype;

        dirFormats;

        dirFormats;

        err;

        err;
@@ -21,6 +22,7 @@ classdef DataFilesClass < handle 
        % ----------------------------------------------------

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

        function obj = DataFilesClass(varargin)            

        function obj = DataFilesClass(varargin)            

            obj.files = FileClass.empty();

            obj.files = FileClass.empty();

            obj.filesErr = FileClass.empty();

            obj.filetype = '';

            obj.filetype = '';

            obj.rootdir = pwd;

            obj.rootdir = pwd;

            obj.nfiles = 0;

            obj.nfiles = 0;
@@ -116,15 +118,15 @@ classdef DataFilesClass < handle 
                obj.InitLookupTable();

                obj.InitLookupTable();

                obj.FindDataSet(ii);

                obj.FindDataSet(ii);

                

                

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

                % its data

                obj.ErrorCheck();

                obj.ErrorCheck();

                if ~isempty(obj.files)

                if ~isempty(obj.files)

                    break

                    break

                end

                end

            end

            end

            

            

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

            obj.ErrorCheckFinal();

            % its data

            obj.ErrorCheckName();

        end

        end
@@ -290,6 +292,41 @@ classdef DataFilesClass < handle 
        

        

        

        

        

        

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

        function ErrorCheckFinal(obj)

            obj.ErrorCheckName();

            

            % Find all acquisition files in group folder

            fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype]);

            

            % Make alist of all files excluded from current data set  

            for ii = 1:length(fileNames)

                filefound = false;

                

                for jj = 1:length(obj.files)

                    if pathscompare(fileNames{ii}, [obj.rootdir, obj.files(jj).name])

                        filefound = true;

                        break;

                    end

                end

                

                for jj = 1:length(obj.filesErr)

                    if pathscompare(fileNames{ii}, [obj.rootdir, obj.filesErr(jj).name])

                        filefound = true;

                        break;

                    end

                end

                

                if ~filefound

                    obj.filesErr(end+1) = FileClass(fileNames{ii});

                    obj.filesErr(end).SetError('Invalid File Name');

                end

            end

        

        end

        

        

        

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

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

        function answer = AskToFixNameConflicts(obj, ii)

        function answer = AskToFixNameConflicts(obj, ii)

            global cfg

            global cfg
@@ -426,7 +463,7 @@ classdef DataFilesClass < handle 
                filename = [obj.files(ii).rootdir, obj.files(ii).name];

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

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

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

                if o.GetError()<0

                if o.GetError()<0

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

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

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

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

                else

                else

                    dataflag = true;

                    dataflag = true;
@@ -435,7 +472,12 @@ classdef DataFilesClass < handle 
            if dataflag==false

            if dataflag==false

                obj.files = FileClass.empty();

                obj.files = FileClass.empty();

            else

            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.files(errorIdxs) = [];

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

            end

            end

        end

        end
@@ -518,5 +560,6 @@ classdef DataFilesClass < handle 
            b = obj.lookupTable(string2hash(str, n));

            b = obj.lookupTable(string2hash(str, n));

        end

        end

        

        

        

    end

    end

end
 
end

DataTree/AcquiredData/DataFiles/FileClass.m

+18 −1
Original line number Original line Diff line number Diff line
@@ -19,6 +19,7 @@ classdef FileClass < matlab.mixin.Copyable 
        rootdir

        rootdir

        err

        err

        logger

        logger

        errmsgs

    end

    end

    

    

    methods

    methods
@@ -39,6 +40,8 @@ classdef FileClass < matlab.mixin.Copyable 
            obj.rootdir    = '';

            obj.rootdir    = '';

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

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

            obj.logger     = InitLogger(logger);            

            obj.logger     = InitLogger(logger);            

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

            

            

            

            if nargin==0

            if nargin==0

                return;

                return;
@@ -535,6 +538,20 @@ classdef FileClass < matlab.mixin.Copyable 
        end

        end

        

        

        

        

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

        function err = SetError(obj, err)

            if ischar(err)

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

            end

            obj.err = err;

        end

        

        

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

        function msg = GetErrorMsg(obj)

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

        end

        

    end

    end

  

  

end
 
end
 
 No newline at end of file

DataTree/AcquiredData/DataFiles/FindFiles.m

+0 −3
Original line number Original line Diff line number Diff line
@@ -68,7 +68,6 @@ while files.IsEmpty() 
                if nfolders==0

                if nfolders==0

                    nfolders = 1;

                    nfolders = 1;

                end

                end

                fprintf('FindFiles: Found %d .nirs data files in %d folders\n', filesSrc.nfiles, nfolders);

            end

            end

            

            

            % Search for source acquisition files in .nirs format which have not

            % Search for source acquisition files in .nirs format which have not
@@ -134,8 +133,6 @@ while files.IsEmpty() 
        cd(dirnameGroup)

        cd(dirnameGroup)

    end

    end

    

    

    fprintf('FindFiles: Found %d %s data files in %d folders\n', files.nfiles, fmt, length(files.files)-files.nfiles);

    

end

end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_Transpose.m

+2 −2
Original line number Original line Diff line number Diff line
@@ -9,8 +9,8 @@ end 
% with the file format's storage order.

% with the file format's storage order.

if ~isrow(val) && ~iscolumn(val)            % Matrices

if ~isrow(val) && ~iscolumn(val)            % Matrices

    val = permute(val, ndims(val):-1:1);

    val = permute(val, ndims(val):-1:1);

elseif ischar(val)                          % 1D char strings 

% elseif ischar(val)                          % 1D char strings 

    val = permute(val, ndims(val):-1:1);

%     val = permute(val, ndims(val):-1:1);

elseif ~isempty(findstr('multidim', options))   % Force multi-dimensional even if vector

elseif ~isempty(findstr('multidim', options))   % Force multi-dimensional even if vector

    val = permute(val, ndims(val):-1:1);

    val = permute(val, ndims(val):-1:1);

elseif ~isempty(findstr('2D', options))         % Force 2D even if vector

elseif ~isempty(findstr('2D', options))         % Force 2D even if vector

DataTree/DataTreeClass.m

+29 −37
Original line number Original line Diff line number Diff line
@@ -261,15 +261,9 @@ classdef DataTreeClass < handle 
                        iter = iter+1;

                        iter = iter+1;

                    end                    

                    end                    

                    obj.files = dataInit.files;

                    obj.files = dataInit.files;

                    obj.filesErr = dataInit.filesErr;





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

                    obj.PrintDatasetFormat(dataInit);



                    % Print file and folder numbers stats

                    nfolders = length(dataInit.files)-dataInit.nfiles;

                    if nfolders==0

                        nfolders = 1;

                    end

                    obj.logger.Write('DataTreeClass.FindAndLoadGroups: Found %d data files in %d folders\n', dataInit.nfiles, nfolders);

                    

                    

                    % Now load group files to data tree

                    % Now load group files to data tree

                    obj.LoadGroup(iGroupNew, procStreamCfgFile, options);

                    obj.LoadGroup(iGroupNew, procStreamCfgFile, options);
@@ -449,7 +443,7 @@ classdef DataTreeClass < handle 
                group.SetIndexID(jj);

                group.SetIndexID(jj);

                obj.groups(jj) = group;

                obj.groups(jj) = group;

                obj.groups(jj).SetPath(obj.dirnameGroups{jj})

                obj.groups(jj).SetPath(obj.dirnameGroups{jj})

                obj.logger.Write('Added group %s to dataTree.\n', obj.groups(jj).GetName);

                obj.logger.Write('Added group  "%s"  to dataTree.\n', obj.groups(jj).GetName);

            end

            end





            % Add subj, sess and run to group

            % Add subj, sess and run to group
@@ -459,12 +453,15 @@ classdef DataTreeClass < handle 
        

        

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

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

        function ErrorCheckLoadedFiles(obj)

        function ErrorCheckLoadedFiles(obj)

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

            if isempty(obj.filesErr)

                if ~obj.files(iF).Loadable() && obj.files(iF).IsFile()

                return

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

                    obj.files(iF) = [];

            end

            end

            obj.logger.Write('\n')

            obj.logger.Write('DataTreeClass.ErrorCheckLoadedFiles:   WARNING - The following files in this data set were NOT loaded:\n')

            for iF = 1:length(obj.filesErr)

                obj.logger.Write('   %s\n', obj.filesErr(iF).name)

            end

            end

            obj.logger.Write('\n')

        end

        end
@@ -679,29 +676,24 @@ classdef DataTreeClass < handle 
        end

        end





        

        

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

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

        function PrintFolderStructure(obj, options)

        function PrintDatasetFormat(obj, dataInit)

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

            

                options = '';

            % Print file and folder numbers stats

            nfolders = length(dataInit.files)-dataInit.nfiles;

            if nfolders==0

                nfolders = 1;

            end

            end

            stepsize = 3;

            numFilesMsg = sprintf('with %d data files in %d folders\n', dataInit.nfiles, nfolders);

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

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

            obj.logger.Write('DataTreeClass - Data Set Folder Structure:\n');

            if dataInit.nfiles == 0

            for ii = 1:length(obj.files)

                obj.logger.Write('DataTreeClass.FindAndLoadGroups:   Did not find any data0 files %s.\n', numFilesMsg);

                k = length(find(obj.files(ii).name=='/'));   

            elseif dataInit.dirFormats.type > 3 && dataInit.dirFormats.type < 9

                if ii<10, j=3; elseif ii>9 && ii<100, j=2; else j=3; end %#ok<*SEPEX>

                obj.logger.Write('DataTreeClass.FindAndLoadGroups:   Found BIDS data set %s.\n', numFilesMsg);

                if optionExists(options, 'flat')

            elseif dataInit.dirFormats.type < 4

                    obj.logger.Write('%d.%s%s\n', ii, blanks(j), obj.files(ii).name);

                obj.logger.Write('DataTreeClass.FindAndLoadGroups:   Found non-standard format set %s.\n', numFilesMsg);

                else

            elseif dataInit.dirFormats.type > 8

                    if ii<10, j=3; elseif ii>9 && ii<100, j=2; else j=3; end

                obj.logger.Write('DataTreeClass.FindAndLoadGroups:   Found non-standard but BIDS-like data set %s.\n', numFilesMsg);

                    if optionExists(options, 'numbered')

                        n = k*stepsize+stepsize+j;

                        obj.logger.Write('%d.%s%s\n', ii, blanks(n), obj.files(ii).filename);

                    else

                        n = k*stepsize+stepsize;

                        obj.logger.Write('%s%s\n', blanks(n), obj.files(ii).filename);

                    end

                end

            end

            end

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

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

        end

        end

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