Merge pull request #66 from BUNPC/development (cc591fe5) · Commits · github_fork / Homer3

AppSettings.cfg

+11 −2

Original line number	Diff line number	Diff line
		@@ -24,9 +24,18 @@ 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 #
		homerOutput

		% Output File Name #
		groupResults.mat

		% Fix File Name Conflicts # don't ask again, ask every time
		ask every time

		% END

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+126 −20

Original line number	Diff line number	Diff line
		@@ -16,31 +16,48 @@ classdef DataFilesClass < handle
		function obj = DataFilesClass(varargin)
		obj.type = '';
		obj.pathnm = pwd;
		skipconfigfile = false;
		obj.nfiles = 0;
		obj.err = -1;
		obj.errmsg = {};

		skipconfigfile = false;
		askToFixNameConflicts = [];

		if nargin>0
		if nargin==0
		return
		end
		if nargin==1
		obj.pathnm = varargin{1};
		end
		obj.pathnm = filesepStandard(obj.pathnm,'full');

		if nargin>1
		if nargin==2
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		if obj.type(1)=='.'
		obj.type(1)='';
		end
		if nargin==3
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		if strcmp(varargin{3}, 'standalone')
		skipconfigfile = true;
		end
		obj.errmsg = {};

		if nargin>2
		end
		if nargin==4
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		if strcmp(varargin{3}, 'standalone')
		skipconfigfile = true;
		end
		askToFixNameConflicts = varargin{4};
		end

		obj.config = struct('RegressionTestActive','');
		if skipconfigfile==false
		if obj.type(1)=='.'
		obj.type(1)='';
		end
		obj.pathnm = filesepStandard(obj.pathnm,'full');

		% Configuration parameters
		obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);
		cfg = ConfigFileClass();
		if skipconfigfile==false
		str = cfg.GetValue('Regression Test Active');
		if strcmp(str,'true')
		obj.config.RegressionTestActive=true;
		@@ -50,11 +67,17 @@ classdef DataFilesClass < handle
		else
		obj.config.RegressionTestActive=false;
		end
		if ~isempty(askToFixNameConflicts)
		obj.config.AskToFixNameConflicts = askToFixNameConflicts;
		elseif strcmp(cfg.GetValue('Fix File Name Conflicts'), sprintf('don''t ask again'))
		obj.config.AskToFixNameConflicts = 0;
		end

		if nargin==0
		return;
		end

		obj.err = 0;
		obj.files = mydir(obj.pathnm);
		GetDataSet(obj);
		end
		@@ -63,9 +86,10 @@ classdef DataFilesClass < handle
		% -----------------------------------------------------------------------------------
		function GetDataSet(obj)
		if exist(obj.pathnm, 'dir')~=7
		error(sprintf('Invalid subject folder: ''%s''', obj.pathnm));
		error('Invalid subject folder: ''%s''', obj.pathnm);
		end
		obj.findDataSet(obj.type);
		obj.ErrorCheckName();
		end


		@@ -117,6 +141,7 @@ classdef DataFilesClass < handle
		end



		% ----------------------------------------------------
		function getDataFile(obj, filename)
		obj.files = mydir(filename);
		@@ -124,8 +149,80 @@ classdef DataFilesClass < handle



		% ----------------------------------------------------
		function ErrorCheckName(obj)
		for ii = length(obj.files):-1:1
		if obj.files(ii).ErrorCheckName()<0
		q = obj.AskToFixNameConflicts(ii);
		if q == 1
		obj.files(ii).FixNameConflict();
		else
		obj.files(ii).NameConflictFixed();
		end
		end
		if obj.files(ii).GetError()<0
		obj.err = -1;
		end
		end
		end



		% --------------------------------------------------------------------------
		function answer = AskToFixNameConflicts(obj, ii)
		answer = 0;
		if obj.config.AskToFixNameConflicts == 0
		obj.files(ii).NameConflictFixed();
		return
		end
		q = MenuBox(obj.GetErrorMsg(ii), {'YES','NO'},[],[],'askEveryTimeOptions');
		if q(1) == 0
		return;
		end
		if length(q)>1 && q(2) == 1
		cfg = ConfigFileClass();
		cfg.SetValue('Fix File Name Conflicts', sprintf('don''t ask again'));
		cfg.Save()
		obj.config.AskToFixNameConflicts = 0;
		end
		if q(1)==2
		obj.files(ii).NameConflictFixed();
		end
		answer = q(1);
		end



		% -----------------------------------------------------
		function errmsg = GetErrorMsg(obj, ii)
		p1 = fileparts(obj.files(ii).GetName());
		[p2,f2] = fileparts(filesepStandard(obj.files(ii).pathfull,'nameonly:file'));
		[~,f3] = fileparts(p2);
		if isfile_private(obj.files(ii).GetName())
		filetype = 'file';
		else
		filetype = 'folder';
		end
		containingFolder = '';
		if obj.files(ii).GetError() == -1
		containingFolder = p1;
		end
		if obj.files(ii).GetError() == -2
		containingFolder = f2;
		end
		if obj.files(ii).GetError() == -3
		containingFolder = f3;
		end
		msg{1} = sprintf('WARNING: The current %s (%s) has the same name as the folder (%s) containing it. ', filetype, obj.files(ii).GetName(), containingFolder);
		msg{2} = sprintf('All %ss should have a different name than the folder containing them, otherwise ', ['F',filetype(2:end)]);
		msg{3} = sprintf('it may cause incorrect results in processing. Do you want to rename this %s?', filetype);
		errmsg = [msg{:}];
		end



		% -------------------------------------------------------
		function pushbuttonLoadDataset_Callback(obj, hObject)
		function pushbuttonLoadDataset_Callback(~, hObject)
		hp = get(hObject,'parent');
		hc = get(hp,'children');
		for ii=1:length(hc)
		@@ -172,10 +269,19 @@ classdef DataFilesClass < handle
		if strcmp(filesepStandard([ps,'/',fs], 'nameonly'), filesepStandard([pd,'/',fd], 'nameonly'))
		found(ii) = 1;
		break;
		else
		dbgpt = 1;
		end
		end
		end
		end



		% ----------------------------------------------------------
		function err = GetError(obj)
		err = obj.err;
		end

		end
		end

DataTree/AcquiredData/DataFiles/FileClass.m

+110 −3

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ classdef FileClass < matlab.mixin.Copyable
		datenum

		% FileClass specific properties
		namePrev
		idx
		subjdir
		subjdiridx
		@@ -19,11 +20,13 @@ classdef FileClass < matlab.mixin.Copyable
		map2group
		pathfull
		err
		logger
		end

		methods

		function obj = FileClass(varargin)
		global logger

		obj.name = '';
		obj.date = '';
		@@ -31,6 +34,7 @@ classdef FileClass < matlab.mixin.Copyable
		obj.isdir = 0;
		obj.datenum = 0;

		obj.namePrev = '';
		obj.idx = 0;
		obj.subjdir = '';
		obj.subjdiridx = 0;
		@@ -38,6 +42,7 @@ classdef FileClass < matlab.mixin.Copyable
		obj.map2group = struct('iSubj',0,'iRun',0);
		obj.pathfull = '';
		obj.err = -1; % Assume file is not loadable
		obj.logger = InitLogger(logger);

		if nargin==0
		return;
		@@ -87,7 +92,7 @@ classdef FileClass < matlab.mixin.Copyable


		% -----------------------------------------------------------
		function file_struct = Dirname2Struct(obj, dirnameFull)
		function file_struct = Dirname2Struct(~, dirnameFull)
		file_struct = [];
		[~, dirname] = fileparts(dirnameFull);
		dirs = dir([dirnameFull, '/..']);
		@@ -211,6 +216,108 @@ classdef FileClass < matlab.mixin.Copyable
		end


		% ----------------------------------------------------
		function err = ErrorCheckName(obj)
		a = obj.name;
		[p1,f1] = fileparts(obj.name);
		[p2,f2] = fileparts(filesepStandard(obj.pathfull,'nameonly:file'));
		[~,f3] = fileparts(p2);
		if strcmp(f1, p1)
		obj.err = -1;
		end
		if strcmp(f1, f2)
		obj.err = -2;
		end
		if strcmp(f1, f3)
		obj.err = -3;
		end
		err = obj.err;
		end



		% ----------------------------------------------------
		function FixNameConflict(obj)
		if obj.err == 0
		return
		end
		keeptrying = true;
		while keeptrying
		[p,f,e] = fileparts(obj.name);
		suggestedRenaming = obj.SuggestRenaming(f,e);
		[rootpath, newname] = SaveFileGUI(suggestedRenaming, p, '', 'rename');
		newnameFull = [rootpath, newname];
		if isempty(newnameFull)
		% Means user chnaged mind and canceled. So we call it fixed
		obj.NameConflictFixed()
		return;
		end
		if strcmp(newname, [f,e])
		q = MenuBox('ERROR: The file name has not been renamed. Do you want to try again?', {'YES','NO'});
		if q==1
		continue;
		else
		return;
		end
		end
		if pathscompare(obj.name, newnameFull)
		return;
		end
		if ~isempty(e)
		d = dir([filesepStandard(p),f,'.*']);
		[p2,f2] = fileparts(newnameFull);
		for ii = 1:length(d)
		[~,~,e1] = fileparts(d(ii).name);
		obj.logger.Write(sprintf('FileClass: Renaming %s to %s\n', [filesepStandard(p),f,e1], [filesepStandard(p2),f2,e1]));
		movefile([filesepStandard(p),f,e1], [filesepStandard(p2),f2,e1]);
		end
		else
		obj.logger.Write(sprintf('FileClass: Renaming %s to %s\n', obj.name, newnameFull));
		movefile(obj.name, newnameFull);
		end
		obj.namePrev = obj.name;
		obj.name = [filesepStandard(p), newname];
		keeptrying = false;
		end
		end



		% -----------------------------------------------------------------
		function name = SuggestRenaming(~, fname, ext)
		n = 1;
		base = fname;
		if isempty(ext)
		addon = 's';
		else
		addon = 'r';
		end
		name = sprintf('%s_%s%d%s', base, addon, n, ext);
		while ispathvalid(name)
		n = n+1;
		name = sprintf('%s_%s%d%s', base, addon, n, ext);
		end
		end


		% -----------------------------------------------------
		function NameConflictFixed(obj)
		obj.err = 0;
		end


		% -----------------------------------------------------
		function name = GetName(obj)
		name = obj.name;
		end


		% -----------------------------------------------------
		function err = GetError(obj)
		err = obj.err;
		end


		end

		end
		No newline at end of file

DataTree/AcquiredData/DataFiles/FindFiles.m

+16 −12

Original line number	Diff line number	Diff line
		@@ -62,7 +62,7 @@ while files.isempty()
		switch fmt
		case {'snirf','.snirf'}
		files = DataFilesClass(dirnameGroup, 'snirf');
		filesSrc = DataFilesClass(dirnameGroup, 'nirs');
		filesSrc = DataFilesClass(dirnameGroup, 'nirs', '', false);
		if ~filesSrc.isempty()
		nfolders = length(filesSrc.files)-filesSrc.nfiles;
		if nfolders==0
		@@ -125,6 +125,10 @@ while files.isempty()
		files = DataFilesClass();
		return;
		end

		% Change current folder to new group
		cd(dirnameGroup)

		case {'snirfonly'}
		files = [];
		end

DataTree/AcquiredData/Snirf/DataClass.m

+7 −1

Original line number	Diff line number	Diff line
		@@ -231,7 +231,13 @@ classdef DataClass < FileLoadSaveClass
		if obj.measurementList(ii).GetCondition()>1
		break;
		end
		% Deal with the cases where the measurementList contains
		% wavelengthIndex versus not
		if ~isempty(obj.measurementList(ii).GetWavelengthIndex())
		ml(ii,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex(), 1, obj.measurementList(ii).GetWavelengthIndex()];
		else
		ml(ii,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex(), 1, 1];
		end
		end

		% Remove unused rows that were pre-allocated

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