Commit 447caaba authored by jayd1860's avatar jayd1860
Browse files

v1.80.1 

-- If no data files were found in group folder because all the potential ones had errors display all the files not loaded in the error files listbox instead of displaying completely empty GUI.

* DataTree, v1.15.1
-- Avoid loading snirf files from derived data folder such as derivatives/homer.
-- Error check measurement list in DataClass. Make sure that for source/detector pair the number of channels is equal to number of data types that is number of wavelengths or for derived data number of Hb types * number of conditions.

* Utils, v1.7.1
-- Avoid loading snirf files from derived data folder such as derivatives/homer. Extend excluded folders in findTypeFiles.m to check for files in derived folder
parent 72e3a8d6

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+25 −3
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ classdef DataFilesClass < handle 
    

    properties (Access = private)

        lookupTable

        excludedFolders

    end

    

    methods
@@ -38,6 +39,7 @@ classdef DataFilesClass < handle 
            

            obj.logger = logger;

            obj.lookupTable = [];

            obj.excludedFolders = {};

            

            skipconfigfile = false;

            askToFixNameConflicts = [];
@@ -74,7 +76,7 @@ classdef DataFilesClass < handle 
            obj.rootdir = filesepStandard(obj.rootdir,'full');           

            

            % Configuration parameters

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

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

            if skipconfigfile==false

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

                if strcmp(str,'true')
@@ -96,6 +98,18 @@ classdef DataFilesClass < handle 
                obj.config.SuppressErrorChecking = true;                

            end

            

            [p, f] = fileparts(cfg.GetValue('Output Folder Name'));

            if isempty(p)

                obj.config.DerivedDataDir = f;

            else

                obj.config.DerivedDataDir = p;

            end

            obj.excludedFolders = {...

                [obj.rootdir, obj.config.DerivedDataDir];

                [obj.rootdir, 'fw'];

                [obj.rootdir, 'imagerecon'];

                [obj.rootdir, 'anatomical'];

                };

            if nargin==0

                return;

            end
@@ -222,6 +236,14 @@ classdef DataFilesClass < handle 
                return

            end

            parentdir = filesepStandard(parentdir);

            

            % Check if folder is excluded, if yes don't search there

            for ii = 1:length(obj.excludedFolders)

                if includes(parentdir, obj.excludedFolders{ii})

                    return;

                end

            end

            

            pattern = obj.dirFormats.choices{iFormat}{iPattern};

            

            dirs = mydir([parentdir, pattern], obj.rootdir);
@@ -307,7 +329,7 @@ classdef DataFilesClass < handle 
            obj.ErrorCheckName();

            

            % Find all acquisition files in group folder

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

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

            

            % Make a list of all files excluded from current data set  

            for ii = 1:length(fileNames)

DataTree/AcquiredData/Snirf/DataClass.m

+23 −0
Original line number Diff line number Diff line
@@ -289,6 +289,8 @@ classdef DataClass < FileLoadSaveClass 
            if ~exist('params','var')

                params = propnames(obj);

            end

            

            % Check dataTimeSeries

            if ismember('dataTimeSeries',params)

                if obj.IsEmpty()

                    err = -2;
@@ -304,6 +306,8 @@ classdef DataClass < FileLoadSaveClass 
                    err = 5;

                end

            end

            

            % Check time 

            if ismember('time',params)

                if isempty(obj.time)

                    err = -6;
@@ -313,6 +317,25 @@ classdef DataClass < FileLoadSaveClass 
                    err = 7;

                end

            end

            

            % Check measurement list

            if ismember('measurementList',params)

                ml = sortrows(obj.GetMeasurementList('matrix'));

                nDatatypes = length(unique(ml(:,4))) * length(unique(ml(:,3)));

                i = 1;

                while i <= size(ml,1)

                    k = find(ml(:,1)==ml(i,1) & ml(:,2)==ml(i,2));

                    if length(k) < nDatatypes

                        err = -7;

                    elseif length(k) > nDatatypes

                        err = -8;

                    end

                    if err < 0

                        break

                    end

                    i = i+length(k);

                end

            end

        end

        

    end

DataTree/DataTreeClass.m

+3 −0
Original line number Diff line number Diff line
@@ -267,6 +267,8 @@ classdef DataTreeClass < handle 
                    while dataInit.GetError() < 0

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

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

                            obj.filesErr = dataInit.filesErr;

                            ErrorCheckLoadedFiles(obj);

                            return;

                        end

                        dataInitPrev(iter) = dataInit;
@@ -374,6 +376,7 @@ classdef DataTreeClass < handle 
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

            obj.AcqData2Group(iGroup);

            if isempty(obj.groups)

                obj.ErrorCheckLoadedFiles();

                return

            end

DataTree/Version.txt

+1 −1
Original line number Diff line number Diff line 
1.15.0
 
 No newline at end of file
 
1.15.1
 
 No newline at end of file

MainGUI/MainGUI.m

+32 −8
Original line number Diff line number Diff line
@@ -84,13 +84,17 @@ function MainGUI_EnableDisableGUI(handles, val) 
   

% Processing element panel

set(handles.listboxGroupTree, 'enable', val);

if strcmp(get(handles.listboxFilesErr, 'visible'), 'on')

    set(handles.listboxFilesErr, 'enable','on');

else

    set(handles.listboxFilesErr, 'enable',val);

end

set(handles.pushbuttonHideErrors, 'enable',val);

set(handles.radiobuttonProcTypeGroup, 'enable', val);

set(handles.radiobuttonProcTypeSubj, 'enable', val);

set(handles.radiobuttonProcTypeSess, 'enable', val);

set(handles.radiobuttonProcTypeRun, 'enable', val);

set(handles.textStatus, 'enable', val);

set(handles.textStatus, 'enable','on');



% Data plot panel

set(handles.textPanLeftRight, 'enable', val);
@@ -153,12 +157,17 @@ function MainGUI_EnableDisablePlotEditMode(handles, val) 


% Processing element panel

set(handles.listboxGroupTree, 'enable', val);

if strcmp(get(handles.listboxFilesErr, 'visible'), 'on')

    set(handles.listboxFilesErr, 'enable','on');

else

    set(handles.listboxFilesErr, 'enable',val);

end

set(handles.textStatus, 'enable','on');

set(handles.pushbuttonHideErrors, 'enable',val);

set(handles.radiobuttonProcTypeGroup, 'enable', val);

set(handles.radiobuttonProcTypeSubj, 'enable', val);

set(handles.radiobuttonProcTypeSess, 'enable', val);

set(handles.radiobuttonProcTypeRun, 'enable', val);

set(handles.textStatus, 'enable', val);



% Control

set(handles.pushbuttonCalcProcStream, 'enable', val);
@@ -246,6 +255,7 @@ maingui.childguis(6) = ChildGuiClass('configSettingsGUI'); 
% Load date files into group tree object

maingui.dataTree = LoadDataTree(maingui.groupDirs, maingui.format, procStreamFile);

if maingui.dataTree.IsEmpty()

    DisplayGroupTree(handles);

    return;

end

if ~isempty(maingui.unitTest)
@@ -379,13 +389,16 @@ maingui.listboxGroupTreeParams = struct('listMaps',struct('names',{{}}, 'idxs', 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Determine the best view for the data files 

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

[viewSetting, views] = SetView(handles, nSubjs, nSess, nRuns);

[viewSetting, ~] = SetView(handles, nSubjs, nSess, nRuns);



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

% Set listbox used for displaying valid data

% Get the GUI listboxGroupTree setting 

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

listboxGroup = {};

if viewSetting <= length(maingui.listboxGroupTreeParams.listMaps)

    listboxGroup = maingui.listboxGroupTreeParams.listMaps(viewSetting).names;

end



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

% Set listbox used for displaying files that did not load correctly
@@ -417,8 +430,16 @@ if ~isempty(handles) 
    if nFilesFailed > 0 || nFilesWarning > 0

        set(handles.textStatus, 'foregroundcolor',maingui.errcolor);

        if nFilesFailed > 0

            set(handles.listboxFilesErr, 'visible','on', 'value',1, 'string',listboxFilesErr)

            set(handles.listboxFilesErr, 'visible','on', 'enable','on','value',1, 'string',listboxFilesErr)

            set(handles.pushbuttonHideErrors, 'visible','on');

            if nFileSuccess==0

                set(handles.pushbuttonHideErrors, 'visible','off');

                p1 = get(handles.listboxGroupTree, 'position');

                p2 = get(handles.listboxFilesErr, 'position');

                offset_y = p1(4)/2;

                set(handles.listboxGroupTree, 'position',[p1(1), p1(2)+offset_y, p1(3), offset_y])

                set(handles.listboxFilesErr, 'position',[p2(1), p2(2), p2(3), p2(4)+offset_y])

            end

        else

            set(handles.listboxFilesErr, 'visible','off');

            set(handles.pushbuttonHideErrors, 'visible','off');
@@ -436,6 +457,9 @@ if ~isempty(handles) 
        set(handles.listboxGroupTree, 'position', [pos1(1) pos2(2) pos1(3) .98-pos2(2)]);

    end

end

if nFileSuccess==0

    return

end



% Select initial data tree processing element in the 'Current Processing Element' panel

idx = [1,1,1,1];

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