Unverified Commit 6405dbc5 authored by jayd1860's avatar jayd1860 Committed by GitHub
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-- Fix 2 issues with loading Rob Luke's BIDS datasets (#121) 

* 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)

* -- Fix some bugs in unit test logging - and displaying call stack in case of error

* v1.35.3

-- Fix Rob Luke's https://github.com/rob-luke/BIDS-NIRS-Tapping dataset not being loaded correctly probe lacks sourcePos2D and detectorPos2D. It has sourcePos3D and detectorPos3D so we project 3D to 2D if the 2D fields are empty. If landmarks are missing then we use crude default 3D-to-2D projection algorithm. If landmarks are available then we use another algorithm that Sreekanth Kura and David Boas are developing

* -- Change syncSubmodules to not use version numbers any more and rely on dates instead
parent 758aa4fa

DataTree/AcquiredData/DataFiles/DataFilesClass.m

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

                ['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-*';

                'sub-*';

                'ses-*';

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




        

        

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

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

        function AddParentDirs(obj, dir)

        function AddParentDirs(obj, dirname)

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

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

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

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

            notUnique = false;

            N = length(subdirs);

            N = length(subdirs);

            for ii = 1:N-1

            for ii = 1:N-1

                if strcmp(subdirs{ii}, 'nirs')

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

                if obj.SearchLookupTable(pathrel2)

                    continue;

                    continue;

                end

                end

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

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

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

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

            end

            end

        end

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

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

            [~,f3]  = fileparts(p2);

            [~,f3]  = fileparts(p2);

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

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

                filetype = 'file';

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

            else

            else

                filetype = 'folder';

                filetype = 'folder';

            end

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

            

        

        

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

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

        function b = isempty(obj)

        function b = IsEmpty(obj)

            if isempty(obj.files)

            if isempty(obj.files)

                b = true;

                b = true;

            else

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

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

            for ii = 1:length(obj.files)

            for ii = 1:length(obj.files)

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

                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')

                if optionExists(options, 'flat')

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

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

                else

                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')

                    if optionExists(options, 'numbered')

                        n = k*stepsize+stepsize+j;

                        n = k*stepsize+stepsize+j;

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

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

            

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

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

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

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

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

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

                parts(end-1) = [];

                parts(end-1) = [];

            end

            end

        end

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

                subjName = obj.name;

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

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

                subjName = parts{1};

                subjName = parts{1};

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

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

                runName  = obj.name;

                runName  = obj.name;

            end

            end

DataTree/AcquiredData/DataFiles/FindFiles.m

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

% Check files data set for errors. If there are no valid

% nirs files don't attempt to load them.

% nirs files don't attempt to load them.

files = DataFilesClass();

files = DataFilesClass();

while files.isempty()

while files.IsEmpty()

    switch fmt

    switch fmt

        case {'snirf','.snirf'}

        case {'snirf','.snirf'}

            files = DataFilesClass(dirnameGroup, 'snirf');

            files = DataFilesClass(dirnameGroup, 'snirf');

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

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

            if ~filesSrc.isempty()

            if ~filesSrc.IsEmpty()

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

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

                if nfolders==0

                if nfolders==0

                    nfolders = 1;

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

            if ~all(found)

                q = GetOptionsForIncompleteDataSet(files, filesSrc);

                q = GetOptionsForIncompleteDataSet(files, filesSrc);

                if q==2

                if q==2

                    if files.isempty()

                    if files.IsEmpty()

                        files = [];

                        files = [];

                    end

                    end

                    return;

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

            end

        case {'snirfonly'}

        case {'snirfonly'}

            files = DataFilesClass(dirnameGroup, 'snirf');

            files = DataFilesClass(dirnameGroup, 'snirf');

            if files.isempty()

            if files.IsEmpty()

                files = [];

                files = [];

                return;

                return;

            end

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

    

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

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

    % another group folder

    % another group folder

    if files.isempty()

    if files.IsEmpty()

        if strcmp(fmt, 'snirfonly')

        if strcmp(fmt, 'snirfonly')

            files = [];

            files = [];

            return

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

function  q = GetOptionsForIncompleteDataSet(files, filesSrc)

if files.config.RegressionTestActive

if files.config.RegressionTestActive

    q = 1;

    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{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?');

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

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

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

DataTree/AcquiredData/Snirf/ProbeClass.m

+24 −1
Original line number Original line Diff line number Diff line
@@ -124,6 +124,27 @@ classdef ProbeClass < FileLoadSaveClass 




        

        

        

        

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

        function Project_3D_to_2D(obj) 

            if isempty(obj.landmarkPos3D)

                

                % When 3D landmarks aren't available use crude default 3D-to-2D projection algorithm 

                if isempty(obj.sourcePos2D)

                    obj.sourcePos2D = project_3D_to_2D(obj.sourcePos3D);

                end

                if isempty(obj.detectorPos2D)

                    obj.detectorPos2D = project_3D_to_2D(obj.detectorPos3D);

                end

                

            else



                % 3D landmarks are available, use ...



            end

        end



        

        

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

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

        function err = LoadHdf5(obj, fileobj, location)

        function err = LoadHdf5(obj, fileobj, location)

            err = 0;

            err = 0;
@@ -174,6 +195,8 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.detectorLabels            = HDF5_DatasetLoad(gid, 'detectorLabels', obj.detectorLabels);

                obj.detectorLabels            = HDF5_DatasetLoad(gid, 'detectorLabels', obj.detectorLabels);

                obj.landmarkLabels            = HDF5_DatasetLoad(gid, 'landmarkLabels', obj.landmarkLabels);

                obj.landmarkLabels            = HDF5_DatasetLoad(gid, 'landmarkLabels', obj.landmarkLabels);

                

                

                obj.Project_3D_to_2D();

                

                % Close group

                % Close group

                HDF5_GroupClose(fileobj, gid, fid);

                HDF5_GroupClose(fileobj, gid, fid);

DataTree/DataTreeClass.m

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

            end

            if ~isempty(k)

            if ~isempty(k)

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

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

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

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

                    return;

                    return;

                end

                end

            else

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

                    iter = 1;

                    while dataInit.GetError() < 0

                    while dataInit.GetError() < 0

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

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

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

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

                            return;

                            return;

                        end

                        end

                        dataInitPrev(iter) = dataInit;

                        dataInitPrev(iter) = dataInit;

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