Commit 0ca282ac authored by jayd1860's avatar jayd1860
Browse files

v1.35.2 

-- Fix not finding .snirf files in Rob Luke's dataset   https://github.com/rob-luke/BIDS-NIRS-Tapping  because the file name pattern does not match any of the available options in DataFilesClass. Updated list of BIDS file name patterns to earch for.
-- Fix some bugs in DataFilesClass file search (change name of isempty method to IsEmpty so that there's no overriding of matlab's built in isempty: this caused DataFilesClass object to be mysteriously empty when executing constructor, also AddParentDirs method assigning incorrect name to FileClass member objects)
parent 758aa4fa

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+39 −9
Original line number Diff line number Diff line
@@ -162,7 +162,26 @@ classdef DataFilesClass < handle 
                ['nirs/sub-*_run-*_nirs.', obj.filetype];

                }

                

                %%%% 6. BIDS-like folder structure without file naming restrictions

                %%%% 6. BIDS #3

                {

                'sub-*';

                ['nirs/sub-*_*_nirs.', obj.filetype];

                }

                

                %%%% 7. BIDS #4 

                {

                '*';

                ['nirs/sub-*_*_nirs.', obj.filetype];

                }

                

                %%%% 8. BIDS folder structure

                {

                'sub-*';

                'ses-*';

                ['nirs/sub-*_run-*_nirs.', obj.filetype];

                }

                                

                %%%% 9. BIDS-like folder structure without file naming restrictions

                {

                'sub-*';

                'ses-*';
@@ -224,10 +243,9 @@ classdef DataFilesClass < handle 


        

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

        function AddParentDirs(obj, dir)

            pathrel = getPathRelative([dir.rootdir, dir.name], obj.rootdir);

        function AddParentDirs(obj, dirname)

            pathrel = getPathRelative([dirname.rootdir, dirname.name], obj.rootdir);

            subdirs = str2cell_fast(pathrel, {'/','\'});

            notUnique = false;

            N = length(subdirs);

            for ii = 1:N-1

                if strcmp(subdirs{ii}, 'nirs')
@@ -237,7 +255,7 @@ classdef DataFilesClass < handle 
                if obj.SearchLookupTable(pathrel2)

                    continue;

                end

                obj.files(end+1) = FileClass(pathrel2);

                obj.files(end+1) = FileClass([obj.rootdir, '/', pathrel2]);

                obj.AddLookupTable(obj.files(end).name)

            end

        end
@@ -305,7 +323,7 @@ classdef DataFilesClass < handle 
            [p2,f2] = fileparts(filesepStandard(obj.files(ii).rootdir,'nameonly:file'));

            [~,f3]  = fileparts(p2);

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

                filetype = 'file';

                filetype = 'file'; %#ok<*PROPLC>

            else

                filetype = 'folder';

            end
@@ -351,7 +369,7 @@ classdef DataFilesClass < handle 
            

        

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

        function b = isempty(obj)

        function b = IsEmpty(obj)

            if isempty(obj.files)

                b = true;

            else
@@ -441,11 +459,23 @@ classdef DataFilesClass < handle 
            obj.logger.Write('DataTreeClass - Data Set Folder Structure:\n');

            for ii = 1:length(obj.files)

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

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

                if ii<10

                    j=3; 

                elseif ii>9 && ii<100

                    j=2;

                else

                    j=3;

                end

                if optionExists(options, 'flat')

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

                else

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

                    if ii<10

                        j=3; 

                    elseif ii>9 && ii<100

                        j=2; 

                    else 

                        j=3; 

                    end

                    if optionExists(options, 'numbered')

                        n = k*stepsize+stepsize+j;

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

DataTree/AcquiredData/DataFiles/FileClass.m

+2 −2
Original line number Diff line number Diff line
@@ -157,7 +157,7 @@ classdef FileClass < matlab.mixin.Copyable 
            

            % Consolidate second to last 'nirs' part with last part   

            if strcmp(parts{end-1}, 'nirs')

                parts{end} = [parts{end-1}, parts{end}];

                parts{end} = [parts{end-1}, '/', parts{end}];

                parts(end-1) = [];

            end

        end
@@ -258,7 +258,7 @@ classdef FileClass < matlab.mixin.Copyable 
                subjName = obj.name;

            elseif obj.IsFile && length(parts)==2

                subjName = parts{1};

                sessName = [subjName '/ses-',parts{end}];

                sessName = [subjName, '/ses-', fname];

                runName  = obj.name;

            end

DataTree/AcquiredData/DataFiles/FindFiles.m

+6 −6
Original line number Diff line number Diff line
@@ -58,12 +58,12 @@ end 
% Check files data set for errors. If there are no valid

% nirs files don't attempt to load them.

files = DataFilesClass();

while files.isempty()

while files.IsEmpty()

    switch fmt

        case {'snirf','.snirf'}

            files = DataFilesClass(dirnameGroup, 'snirf');

            filesSrc = DataFilesClass(dirnameGroup, 'nirs', '', false);

            if ~filesSrc.isempty()

            if ~filesSrc.IsEmpty()

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

                if nfolders==0

                    nfolders = 1;
@@ -77,7 +77,7 @@ while files.isempty() 
            if ~all(found)

                q = GetOptionsForIncompleteDataSet(files, filesSrc);

                if q==2

                    if files.isempty()

                    if files.IsEmpty()

                        files = [];

                    end

                    return;
@@ -87,7 +87,7 @@ while files.isempty() 
            end

        case {'snirfonly'}

            files = DataFilesClass(dirnameGroup, 'snirf');

            if files.isempty()

            if files.IsEmpty()

                files = [];

                return;

            end
@@ -112,7 +112,7 @@ while files.isempty() 
    

    % If no files were found ion the current format then ask user to choose

    % another group folder

    if files.isempty()

    if files.IsEmpty()

        if strcmp(fmt, 'snirfonly')

            files = [];

            return
@@ -144,7 +144,7 @@ end 
function  q = GetOptionsForIncompleteDataSet(files, filesSrc)

if files.config.RegressionTestActive

    q = 1;

elseif  files.isempty()

elseif  files.IsEmpty()

    msg{1} = sprintf('Homer3 did not find any .snirf files in the current folder but did find %d .nirs files. ', filesSrc.nfiles);

    msg{2} = sprintf('Do you want to convert .nirs files to .snirf format and load them?');

    q = MenuBox(msg, {'YES','NO'}, 'center');

DataTree/DataTreeClass.m

+2 −2
Original line number Diff line number Diff line
@@ -174,7 +174,7 @@ classdef DataTreeClass < handle 
            end

            if ~isempty(k)

                dataInit = FindFiles(obj.dirnameGroups{kk}, supportedFormats{k});

                if isempty(dataInit) || dataInit.isempty()

                if isempty(dataInit) || dataInit.IsEmpty()

                    return;

                end

            else
@@ -253,7 +253,7 @@ classdef DataTreeClass < handle 
                    iter = 1;

                    while dataInit.GetError() < 0

                        dataInit = FindFiles(obj.dirnameGroups{kk}, fmt, options);

                        if isempty(dataInit) || dataInit.isempty()

                        if isempty(dataInit) || dataInit.IsEmpty()

                            return;

                        end

                        dataInitPrev(iter) = dataInit;

DataTree/GroupClass.m

+1 −1
Original line number Diff line number Diff line
@@ -307,7 +307,7 @@ classdef GroupClass < TreeNodeClass 
                subj.SetIndexID(obj.iGroup, jj);

                subj.SetPath(obj.path);                      % Inherit root path from group

                obj.subjs(jj) = subj;

                obj.logger.Write(sprintf('   Added subject %s to group %s.\n', obj.subjs(jj).GetName, obj.GetName));

                obj.logger.Write('   Added subject %s to group %s.\n', obj.subjs(jj).GetFileName, obj.GetFileName);

            end

                        

            % Add sess to subj

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