v1.31.4 (d7a78333) · Commits · github_fork / Homer3

AppSettings.cfg

+6 −0

Original line number	Diff line number	Diff line
		@@ -29,4 +29,10 @@ ask every time
		% Stim Edit GUI Save Warnings # don't ask again, ask every time
		don't ask again

		% Output Folder Name
		homerOutput

		% Output File Name
		groupResults.mat

		% END

DataTree/DataTreeClass.m

+10 −8

Original line number	Diff line number	Diff line
		@@ -13,6 +13,9 @@ classdef DataTreeClass < handle
		dataStorageScheme
		end




		methods

		% ---------------------------------------------------------------
		@@ -368,7 +371,11 @@ classdef DataTreeClass < handle
		runCurr = RunClass().empty();
		end
		end
		obj.logger.Write(sprintf('\nLoaded acquisition data in %0.1f seconds\n\n', toc));
		obj.logger.Write(sprintf('\n'));
		obj.logger.Write(sprintf('Loaded group %s acquisition data in %0.1f seconds\n', obj.groups(iG).name, toc));
		obj.logger.Write(sprintf(' Derived data output folder : %s%s\n', obj.groups(iG).path, obj.groups(iG).outputDirname));
		obj.logger.Write(sprintf(' Derived data output file : %s\n\n', obj.groups(iG).outputFilename));

		end


		@@ -392,11 +399,6 @@ classdef DataTreeClass < handle
		group.SetIndexID(jj);
		obj.groups(jj) = group;
		obj.groups(jj).SetPath(obj.dirnameGroups{jj})

		% In case there's not enough disk space in the current
		% group folder, we have a separate path for saving group
		% results
		obj.groups(jj).SetPathOutput(obj.dirnameGroups{jj})
		obj.logger.Write(sprintf('Added group %s to dataTree.\n', obj.groups(jj).GetName));
		end

		@@ -553,10 +555,10 @@ 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).pathOutput, 'groupResults.mat']));
		obj.logger.Write(sprintf('Saving group %d in %s\n', ii, [obj.groups(ii).pathOutputAlt, obj.groups(ii).GetOutputFilename()]));
		obj.groups(ii).Save(hwait);
		end
		obj.logger.Write(sprintf('Completed saving groupResults.mat for all groups in %0.3f seconds.\n', toc(t_local)));
		obj.logger.Write(sprintf('Completed saving processing results for all groups in %0.3f seconds.\n', toc(t_local)));
		end

DataTree/GroupClass.m

+76 −16

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@ classdef GroupClass < TreeNodeClass
		end

		properties % (Access = private)
		pathOutput
		outputFilename
		end


		@@ -29,6 +29,11 @@ classdef GroupClass < TreeNodeClass
		obj.type = 'group';
		obj.subjs = SubjClass().empty;

		obj.outputFilename = obj.cfg.GetValue('Output File Name');
		if isempty(obj.outputFilename)
		obj.outputFilename = 'groupResults.mat';
		end

		if nargin==0
		return;
		end
		@@ -108,6 +113,12 @@ classdef GroupClass < TreeNodeClass
		end


		% ----------------------------------------------------------------------------------
		function filename = GetOutputFilename(obj)
		filename = obj.outputFilename;
		end


		% ----------------------------------------------------------------------------------
		function InitVersionStrFull(obj)
		if isempty(obj.version)
		@@ -268,12 +279,22 @@ classdef GroupClass < TreeNodeClass
		% ----------------------------------------------------------------------------------
		function SetPath(obj, dirname)
		obj.path = dirname;

		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = obj.path;
		end


		% ----------------------------------------------------------------------------------
		function SetPathOutput(obj, dirname)
		obj.pathOutput = dirname;
		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = dirname;
		end


		@@ -324,7 +345,7 @@ classdef GroupClass < TreeNodeClass
		% Find out if we need to ask user for processing options
		% config file to initialize procStream.fcalls at the
		% run, subject or group level. First try to find the proc
		% input at each level from the save results groupresults.mat
		% input at each level from the saved derived data.
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		g = obj;
		s = obj.subjs(1);
		@@ -498,8 +519,8 @@ classdef GroupClass < TreeNodeClass
		if ~exist('option','var')
		option = 'down';
		end
		if exist([obj.path, 'groupResults.mat'],'file')
		delete([obj.path, 'groupResults.mat']);
		if exist([obj.path, obj.outputDirname, obj.outputFilename],'file')
		delete([obj.path, obj.outputDirname, obj.outputFilename]);
		end
		if strcmp(option, 'down')
		for jj=1:length(obj.subjs)
		@@ -584,11 +605,13 @@ classdef GroupClass < TreeNodeClass
		return;
		end

		obj.BackwardCompatability();

		group = [];
		if exist([obj.path, 'groupResults.mat'],'file')
		g = load([obj.path, 'groupResults.mat']);
		if ispathvalid([obj.path, obj.outputDirname, obj.outputFilename],'file')
		g = load([obj.path, obj.outputDirname, obj.outputFilename]);

		% Do some basic error checks on groupResults contents
		% Do some basic error checks on saved derived data contents
		if isproperty(g, 'group') && isa(g.group, 'GroupClass')
		if isproperty(g.group, 'version')
		if ismethod(g.group, 'GetVersion')
		@@ -602,7 +625,7 @@ classdef GroupClass < TreeNodeClass
		% Copy saved group to current group if versions are compatible. obj.CompareVersions==0
		% means the versions of the saved group and current one are equal.
		if ~isempty(group) && obj.CompareVersions(group)<=0
		% Do a conditional copy of group from groupResults file. Conditional copy copies ONLY
		% Do a conditional copy of group from saved processing output file. Conditional copy copies ONLY
		% derived data, that is, only from procStream but NOT acqruired. We do not want to
		% overwrite the real acquired data loaded from acquisition files
		hwait = waitbar(0,'Loading group');
		@@ -610,9 +633,10 @@ classdef GroupClass < TreeNodeClass
		close(hwait);
		else
		group = obj; %#ok<NASGU>
		if exist([obj.path, 'groupResults.mat'],'file')
		obj.logger.Write(sprintf('Warning: This folder contains old version of groupResults.mat. Will move it to groupResults_old.mat\n'));
		movefile([obj.path, 'groupResults.mat'], './groupResults_old.mat')
		if exist([obj.path, obj.outputDirname, obj.outputFilename],'file')
		obj.logger.Write(sprintf('Warning: This folder contains old version of processing results. Will move it to *_old.mat\n'));
		[~,outputFilename] = fileparts(obj.outputFilename);
		movefile([obj.path, obj.outputDirname, obj.outputFilename], [obj.path, obj.outputDirname, outputFilename, '_old.mat'])
		end
		obj.Save();
		end
		@@ -627,15 +651,16 @@ classdef GroupClass < TreeNodeClass
		hwait = [];
		end

		obj.logger.Write(sprintf('Saving processed data in %s\n', [obj.path, 'groupResults.mat']));
		obj.logger.Write(sprintf('Saving processed data in %s\n', [obj.path, obj.outputDirname, obj.outputFilename]));

		if ishandle(hwait)
		obj.logger.Write(sprintf('Auto-saving processing results ...\n'), obj.logger.ProgressBar(), hwait);
		end

		group = GroupClass(obj); %#ok<NASGU>
		group = GroupClass(obj);
		try
		save([obj.pathOutput, 'groupResults.mat'], 'group');
		obj.CreateOutputDir();
		save([obj.pathOutputAlt, obj.outputDirname, obj.outputFilename], 'group');
		catch ME
		MessageBox(ME.message);
		obj.logger.Write(ME.message);
		@@ -644,6 +669,19 @@ classdef GroupClass < TreeNodeClass



		% ----------------------------------------------------------------------------------
		function CreateOutputDir(obj)
		if ispathvalid([obj.pathOutputAlt, obj.outputDirname])
		return;
		end
		mkdir([obj.pathOutputAlt, obj.outputDirname]);
		for ii = 1:length(obj.subjs)
		obj.subjs(ii).CreateOutputDir();
		end
		end



		% ----------------------------------------------------------------------------------
		function SaveAcquiredData(obj)
		for ii = 1:length(obj.subjs)
		@@ -946,6 +984,28 @@ classdef GroupClass < TreeNodeClass
		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
		end


		end % Private methods

		end % classdef GroupClass < TreeNodeClass

DataTree/ProcStream/ProcResultClass.m

+48 −24

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@ classdef ProcResultClass < handle

		properties (Access=private)
		filename
		logger
		end


		@@ -25,6 +26,10 @@ classdef ProcResultClass < handle

		% ---------------------------------------------------------------------------
		function obj = ProcResultClass()
		global logger

		obj.logger = InitLogger(logger);

		obj.Initialize();
		obj.filename = '';
		end
		@@ -160,36 +165,36 @@ classdef ProcResultClass < handle
		if isempty(filename)
		return;
		end
		[pname, fname] = fileparts(filename);
		[pname, fname, ext] = fileparts(filename);

		% Set the containing folder name
		if isempty(pname)
		% See if folder corresponding to saved output exists. If it
		% does then set it to be same as the .mat filename (without
		% the extension)
		rootdir = '';
		if exist(['./', fname], 'dir')==7
		rootdir = fname;
		if isempty(ext)
		% Filename argument names folder

		% Next 3 lines are for backwards compatibility: if the saved output
		% for subject is stored in the group instead of subject folder as was
		% done in previous versions of this code, then move saved file to
		% subject folder
		if exist(['./', fname, '.mat'], 'file')==2
		movefile(['./', fname, '.mat'], ['./', rootdir, '/', fname, '.mat']);
		end
		rootdir = '';
		if ispathvalid(pname)
		rootdir = [filesepStandard(pname), filesepStandard(fname)];
		elseif ispathvalid(filename)
		rootdir = filesepStandard(filename);
		end

		% Set the containing folder name
		if exist(['./', rootdir, '/', fname, '.mat'], 'file')==2
		if ispathvalid(['./', rootdir, fname, '.mat'], 'file')
		pname = ['./', rootdir];
		elseif exist(['../', rootdir, '/', fname, '.mat'], 'file')==2
		elseif ispathvalid(['../', rootdir, fname, '.mat'], 'file')
		pname = ['../', rootdir];
		else
		pname = ['./', rootdir];
		end
		pname = filesepStandard(pname);

		elseif ispathvalid(pname)

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

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

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


		@@ -205,7 +210,7 @@ classdef ProcResultClass < handle

		obj.SetFilename(filename)

		output = obj; %#ok<NASGU>
		output = obj;
		props = propnames(vars);
		for ii=1:length(props)
		if eval( sprintf('isproperty(output, ''%s'');', props{ii}) )
		@@ -221,7 +226,26 @@ classdef ProcResultClass < handle
		return;
		end

		% If saving this data for the first time folder might have to be created under
		% the processd data output folder, depending on the group folder folder structure
		pname = fileparts(obj.filename);
		if ~isempty(pname)
		if ~ispathvalid(pname)
		mkdir(pname)
		end
		end

		try
		obj.logger.Write(sprintf('Saving derived data output: %s', obj.filename));
		save(obj.filename, '-mat', 'output');
		catch
		if ~ispathvalid(obj.filename)
		msg = sprintf('ERROR: Was not able to save processed data - %s not found.', obj.filename);
		MessageBox(msg);
		obj.logger.Write(msg);
		return;
		end
		end

		% Free memory for this object
		if ~isempty(findstr('freememory', options)) %#ok<FSTR>
		@@ -246,7 +270,7 @@ classdef ProcResultClass < handle
		end

		% Error check file
		if ~exist(obj.filename,'file')
		if ~ispathvalid(obj.filename,'file')
		return
		end

		@@ -294,7 +318,7 @@ classdef ProcResultClass < handle
		end

		% Check that data file associated with this processing element exists
		if exist(obj.filename,'file')
		if ispathvalid(obj.filename, 'file')
		% Delete file containing the actual datas
		delete(obj.filename);
		end
		@@ -302,7 +326,7 @@ classdef ProcResultClass < handle

		% Check that exported data file associated with this processing element exists
		[pname, fname] = fileparts(obj.filename);
		if exist([pname, '/', fname, '_HRF.txt'], 'file')
		if ispathvalid([pname, '/', fname, '_HRF.txt'], 'file')
		delete([pname, '/', fname, '_HRF.txt']);
		end
		end

DataTree/SubjClass.m

+13 −0

Original line number	Diff line number	Diff line
		@@ -233,6 +233,19 @@ classdef SubjClass < TreeNodeClass
		end


		% ----------------------------------------------------------------------------------
		function CreateOutputDir(obj)
		if ispathvalid([obj.pathOutputAlt, obj.outputDirname, obj.name])
		return;
		end
		if ~ispathvalid([obj.pathOutputAlt, obj.name])
		return;
		end
		mkdir([obj.pathOutputAlt, obj.outputDirname, obj.name]);
		end



		% ----------------------------------------------------------------------------------
		function LoadVars(obj, r, tHRF_common)
		% Set common tHRF: make sure size of tHRF, dcAvg and dcAvg is same for

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