Commit 5bfcf19d authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.31.13 

-- Added backward compatibility to data tree for dealing with old format Homer3 derived data which was saved directly under group folder previously. Asks user if they want to move it to new folder if new format data does not exist.
-- Improve data tree algorithm for determining save file name. Added method GetOutputFilename vs GetFilename to distinguish between derived and acquired data
-- Fix some issues with Export data and make it's output save to same folders as regular derived data. Fix also data Reset method
-- Improvements in utility functions.
-- Sync AppSettings.cfg with AtlasViewer they should be the same
parent eba57454

AppSettings.cfg

+4 −4
Original line number Diff line number Diff line
@@ -24,15 +24,15 @@ files 
No



% Group Data Loading Warnings # don't ask again, ask every time

ask every time

don't ask again



% Stim Edit GUI Save Warnings # don't ask again, ask every time

don't ask again



% Output Folder Name

% Output Folder Name # 

homerOutput



% Output File Name

% Output File Name # 

groupResults.mat



% END

DataTree/DataTreeClass.m

+1 −1
Original line number Diff line number Diff line
@@ -555,7 +555,7 @@ classdef DataTreeClass < handle 
            

            t_local = tic;

            for ii = 1:length(obj.groups)

                obj.logger.Write(sprintf('Saving group %d in %s\n', ii, [obj.groups(ii).pathOutputAlt, obj.groups(ii).GetOutputFilename()]));

                obj.logger.Write(sprintf('Saving group %d in %s\n', ii, [obj.groups(ii).pathOutputAlt, obj.groups(ii).GetFilename()]));

                obj.groups(ii).Save(hwait);

            end

            obj.logger.Write(sprintf('Completed saving processing results for all groups in %0.3f seconds.\n', toc(t_local)));

DataTree/GroupClass.m

+70 −24
Original line number Diff line number Diff line
@@ -114,7 +114,7 @@ classdef GroupClass < TreeNodeClass 
        

        

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

        function filename = GetOutputFilename(obj)

        function filename = GetFilename(obj)

            filename = obj.outputFilename;

        end
@@ -482,7 +482,7 @@ classdef GroupClass < TreeNodeClass 
            obj.procStream.input.LoadVars(obj.outputVars);



            % Calculate processing stream

            obj.procStream.Calc(obj.GetFilename);

            obj.procStream.Calc(obj.GetOutputFilename());



            if obj.DEBUG

                obj.logger.Write(sprintf('Completed processing stream for group %d\n', obj.iGroup));
@@ -587,7 +587,7 @@ classdef GroupClass < TreeNodeClass 
            if isempty(obj)

                return;

            end

            err1 = obj.procStream.Load(obj.GetFilename);

            err1 = obj.procStream.Load(obj.GetOutputFilename());

            err2 = obj.subjs(1).LoadSubBranch();

            if err1==0 && err2==0

                err = 0;
@@ -672,7 +672,7 @@ classdef GroupClass < TreeNodeClass 
                obj.logger.Write(sprintf('Auto-saving processing results ...\n'), obj.logger.ProgressBar(), hwait);

            end

            

            group = GroupClass(obj); %#ok<NASGU>

            group = GroupClass(obj);

            try 

                obj.CreateOutputDir();

                save([obj.pathOutputAlt, obj.outputDirname, obj.outputFilename], 'group');
@@ -735,7 +735,7 @@ classdef GroupClass < TreeNodeClass 
                iBlk = 1;

            end

            

            obj.procStream.ExportHRF(obj.name, obj.CondNames, iBlk);

            obj.procStream.ExportHRF(obj.GetOutputFilename, obj.CondNames, iBlk);

            if strcmp(procElemSelect, 'all')

                for ii=1:length(obj.subjs)

                    obj.subjs(ii).ExportHRF('all', iBlk);
@@ -949,13 +949,26 @@ classdef GroupClass < TreeNodeClass 
            end

        end



        

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

        function r = ListOutputFilenames(obj, options)

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

                options = '';

            end

            r = obj.GetOutputFilename(options);

            fprintf('%s %s\n', obj.path, r);

            for ii = 1:length(obj.subjs)

                obj.subjs(ii).ListOutputFilenames(options);

            end

        end        



    end

    

    

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

    % Private methods

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

    methods (Access = private)

    methods (Access = public)

        

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

        % Check whether subject k'th subject from this group exists in group G and return
@@ -1001,25 +1014,58 @@ classdef GroupClass < TreeNodeClass 
        

        

        

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

        function b = HaveOutput(obj)

            b = false;

            for ii = 1:length(obj.subjs)

                b = obj.subjs(ii).HaveOutput();

                if b

                    break;

                end

            end

        end

        

        

                

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

        function BackwardCompatability(obj)

%             if ispathvalid([obj.path, 'groupResults.mat'])

%                 q = MenuBox('Detected derived data in this group folder in the old format. Do you want to save it in the new format?',{'Yes','No'});

%                 if q==1

%                     if ~ispathvalid([obj.path, obj.outputDirname])

%                         mkdir([obj.path, obj.outputDirname])

%                     end

%                     movefile('groupResults.mat', [obj.path, obj.outputDirname, obj.outputFilename])

%                     files = dir('*.mat');

%                     for ii = 1:length(files)

%                         movefile(files(ii).name, [obj.path, obj.outputDirname]);

%                     end

%                 else

%                     obj.outputDirname = '';

%                 end

%             end

            if ispathvalid([obj.path, 'groupResults.mat'])

                g = load([obj.path, 'groupResults.mat']);

                

                % Do not try to restore old data older than Homer3

                if isempty(g)

                    return;

                end

                if ~isproperty(g,'group')

                    return;

                end

                if ~isa(g.group, 'GroupClass')

                    return;

                end

                

                % Do not try to restore old data if there is already data

                % in the new format

                if obj.HaveOutput()

                    return;

                end

                

                msg = sprintf('Detected derived data in an old Homer3 format.');

                obj.logger.Write(sprintf('Backward Compatability: %s\n', msg));

                

                % If we're here it means that old format homer3 data exists

                % AND NO new homer3 format data exists

                q = MenuBox(sprintf('%s. Do you want to save it in the new format?', msg),{'Yes','No'});

                if q==1

                    obj.BackwardCompatability@TreeNodeClass();

                    for ii = 1:length(obj.subjs)

                        obj.subjs(ii).BackwardCompatability();

                    end

                    

                    obj.logger.Write(sprintf('Moving %s to %s\n', 'groupResults.mat', [obj.path, obj.outputDirname, obj.outputFilename]));

                    movefile('groupResults.mat', [obj.path, obj.outputDirname, obj.outputFilename])

                end

            end

        end

            

    end  % Private methods

DataTree/ProcStream/ProcResultClass.m

+18 −35
Original line number Diff line number Diff line
@@ -161,44 +161,27 @@ classdef ProcResultClass < handle 
    methods

        

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

        function SetFilename(obj, filename)

        function filename = SetFilename(obj, filename)            

            if nargin==1

                filename = '';

                return;

            end                

            if isempty(filename)

                return;

            end

            [pname, fname, ext] = fileparts(filename);

            

            % Set the containing folder name 

            if isempty(ext)

                % Filename argument names folder

                                

                rootdir = '';

                if ispathvalid(pname)

                    rootdir = [filesepStandard(pname), filesepStandard(fname, 'nameonly')];

                elseif ispathvalid(filename)

                    rootdir = filesepStandard(filename);

                end

                

                % Set the containing folder name 

                if ispathvalid(['./', rootdir])

                    rootdir = ['./', rootdir];

                elseif ispathvalid(['../', rootdir])

                    rootdir = ['../', rootdir];                    

                end                

                if ispathvalid([rootdir, fname, '.mat'], 'file')

                    pname = rootdir;

                ext = '.mat';

                if ispathvalid([filesepStandard(pname), fname], 'dir')

                    pname = [filesepStandard(pname), fname];

                elseif ispathvalid([filesepStandard(['../', pname]), fname], 'dir')

                    pname = [filesepStandard(['../', pname]), fname];

                elseif ispathvalid(filesepStandard(['../', pname]), 'dir')

                    pname = filesepStandard(['../', pname]);

                end

                pname = filesepStandard(pname);

                

            elseif ispathvalid(pname)

                if ispathvalid(['./', filesepStandard(pname)])

                    pname = ['./', filesepStandard(pname)];

                else

                    pname = [filesepStandard(pname)];

            end



            end

            

            obj.filename = [pname, fname, '.mat'];

            filename = [filesepStandard(pname, 'nameonly:dir'), fname, ext];

            obj.filename = filename;

        end
@@ -212,7 +195,7 @@ classdef ProcResultClass < handle 
                options = 'keepinmemory';

            end

            

            obj.SetFilename(filename)

            obj.SetFilename(filename);

            

            output = obj;

            props = propnames(vars);
@@ -262,7 +245,7 @@ classdef ProcResultClass < handle 
        % ----------------------------------------------------------------------------------

        function err = Load(obj, filename)

            err = 0;

            obj.SetFilename(filename)

            obj.SetFilename(filename);

            if isempty(obj.filename)

                return;

            end
@@ -316,7 +299,7 @@ classdef ProcResultClass < handle 
        function Reset(obj, filename)

            obj.Initialize();



            obj.SetFilename(filename)

            obj.SetFilename(filename);

            if isempty(obj.filename)

                return;

            end
@@ -686,7 +669,7 @@ classdef ProcResultClass < handle 
            if ~exist('filename', 'var')

                filename = '';

            end            

            obj.SetFilename(filename)

            obj.SetFilename(filename);

            

            % If file name is set and exists then load data from file

            if ~isempty(filename) && exist(obj.filename, 'file')

DataTree/ProcStream/ProcStreamClass.m

+2 −2
Original line number Diff line number Diff line
@@ -247,7 +247,7 @@ classdef ProcStreamClass < handle 
                end

                

                % Parse obj.input parameters

                [sargin, p, sarginVal] = obj.ParseInputParams(iFcall);

                [sargin, p, sarginVal] = obj.ParseInputParams(iFcall); %#ok<ASGLU>

                

                % Parse obj.input output arguments

                sargout = obj.ParseOutputArgs(iFcall);
@@ -282,7 +282,7 @@ classdef ProcStreamClass < handle 
                lst = [0, lst, length(foos)+1]; %#ok<*AGROW>

                for ii=1:length(lst)-1

                    foo2 = foos(lst(ii)+1:lst(ii+1)-1);

                    lst2 = strmatch( foo2, paramOut, 'exact' );

                    lst2 = strmatch( foo2, paramOut, 'exact' ); %#ok<MATCH3>

                    idx = strfind(foo2,'foo');

                    if isempty(lst2) && (isempty(idx) || idx>1) && ~isempty(foo2)

                        paramOut{end+1} = foo2;

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