Merge pull request #116 from BUNPC/development (f2addb82) · Commits · github_fork / Homer3

.gitmodules

0 → 100644

+6 −0

Original line number	Original line	Diff line number	Diff line
			[submodule "Utils/Shared"]
			path = Utils/Shared
			url = https://github.com/BUNPC/Utils
			[submodule "Group/DataTree"]
			path = DataTree
			url = https://github.com/BUNPC/DataTree

DataTree/.numberfiles

deleted100644 → 0

+0 −1

Original line number	Original line	Diff line number	Diff line
	67
	No newline at end of file

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+210 −71

Original line number	Original line	Diff line number	Diff line
	@@ -2,24 +2,31 @@ classdef DataFilesClass < handle

	properties		properties
	files;		files;
	type;		filetype;
			dirFormats;
	err;		err;
	errmsg;		errmsg;
	pathnm;		rootdir;
	config;		config;
	nfiles;		nfiles;
	logger		logger
	end		end

			properties (Access = private)
			lookupTable
			end

	methods		methods

	% ----------------------------------------------------		% ----------------------------------------------------
	function obj = DataFilesClass(varargin)		function obj = DataFilesClass(varargin)
	obj.type = '';		obj.files = FileClass.empty();
	obj.pathnm = pwd;		obj.filetype = '';
			obj.rootdir = pwd;
	obj.nfiles = 0;		obj.nfiles = 0;
	obj.err = -1;		obj.err = -1;
	obj.errmsg = {};		obj.errmsg = {};
			obj.dirFormats = struct('type',0, 'choices',{{}});

	global logger		global logger
	global cfg		global cfg
	@@ -28,6 +35,7 @@ classdef DataFilesClass < handle
	cfg = InitConfig(cfg);		cfg = InitConfig(cfg);

	obj.logger = logger;		obj.logger = logger;
			obj.lookupTable = [];

	skipconfigfile = false;		skipconfigfile = false;
	askToFixNameConflicts = [];		askToFixNameConflicts = [];
	@@ -36,32 +44,32 @@ classdef DataFilesClass < handle
	return		return
	end		end
	if nargin==1		if nargin==1
	obj.pathnm = varargin{1};		obj.rootdir = varargin{1};
	end		end
	if nargin==2		if nargin==2
	obj.pathnm = varargin{1};		obj.rootdir = varargin{1};
	obj.type = varargin{2};		obj.filetype = varargin{2};
	end		end
	if nargin==3		if nargin==3
	obj.pathnm = varargin{1};		obj.rootdir = varargin{1};
	obj.type = varargin{2};		obj.filetype = varargin{2};
	if strcmp(varargin{3}, 'standalone')		if strcmp(varargin{3}, 'standalone')
	skipconfigfile = true;		skipconfigfile = true;
	end		end
	end		end
	if nargin==4		if nargin==4
	obj.pathnm = varargin{1};		obj.rootdir = varargin{1};
	obj.type = varargin{2};		obj.filetype = varargin{2};
	if strcmp(varargin{3}, 'standalone')		if strcmp(varargin{3}, 'standalone')
	skipconfigfile = true;		skipconfigfile = true;
	end		end
	askToFixNameConflicts = varargin{4};		askToFixNameConflicts = varargin{4};
	end		end

	if obj.type(1)=='.'		if obj.filetype(1) == '.'
	obj.type(1)='';		obj.filetype(1) = '';
	end		end
	obj.pathnm = filesepStandard(obj.pathnm,'full');		obj.rootdir = filesepStandard(obj.rootdir,'full');

	% Configuration parameters		% Configuration parameters
	obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);		obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);
	@@ -91,82 +99,156 @@ classdef DataFilesClass < handle
	end		end

	obj.err = 0;		obj.err = 0;
	obj.files = mydir(obj.pathnm);
	GetDataSet(obj);		obj.InitFolderFromats();
			obj.GetDataSet();
	end		end



	% -----------------------------------------------------------------------------------		% -----------------------------------------------------------------------------------
	function GetDataSet(obj)		function GetDataSet(obj)
	if exist(obj.pathnm, 'dir')~=7		if exist(obj.rootdir, 'dir')~=7
	error('Invalid subject folder: ''%s''', obj.pathnm);		error('Invalid subject folder: ''%s''', obj.rootdir);
			end

			for ii = 1:length(obj.dirFormats.choices)
			obj.InitLookupTable();
			obj.FindDataSet(ii);

			obj.ErrorCheck();
			if ~isempty(obj.files)
			break
			end
	end		end
	obj.findDataSet(obj.type);

	% Remove any files that cannot pass the basic test of loading		% Remove any files that cannot pass the basic test of loading
	% its data		% its data
	obj.ErrorCheck(obj.type);
	obj.ErrorCheckName();		obj.ErrorCheckName();
	end		end



			% -----------------------------------------------------------------------------------
			function InitFolderFromats(obj)
			obj.dirFormats.choices = {

			%%%% 1. Flat #1
			{
			['_run.', obj.filetype];
			}

			%%%% 2. Flat #2
			{
			['*.', obj.filetype];
			}

			%%%% 3. Subjects
			{
			'*';
			['*.', obj.filetype];
			}

			%%%% 4. BIDS #1, sub-<label>[_ses-<label>][_task-<label>][_run-<index>]_nirs.snirf
			{
			'sub-*';
			'ses-*';
			['nirs/sub-_run-_nirs.', obj.filetype];
			}

			%%%% 5. BIDS #2
			{
			'sub-*';
			['nirs/sub-_run-_nirs.', obj.filetype];
			}

			%%%% 6. BIDS-like folder structure without file naming restrictions
			{
			'sub-*';
			'ses-*';
			['nirs/*.', obj.filetype];
			}

			};
			end




	% ----------------------------------------------------		% ----------------------------------------------------
	function findDataSet(obj, type)		function FindDataSet(obj, iFormat, iPattern, parentdir)
	obj.files = mydir([obj.pathnm, '/*.', type]);		if ~exist('iFormat','var')
			iFormat = 1;
			end
			if ~exist('iPattern','var')
			iPattern = 1;
			end
			if ~exist('parentdir','var')
			parentdir = obj.rootdir;
			end

	% Remove any files that cannot pass the basic test of loading		if iFormat > length(obj.dirFormats.choices)
	% its data		return
	obj.ErrorCheck(type);		end
			if iPattern > length(obj.dirFormats.choices{iFormat})
			return
			end
			parentdir = filesepStandard(parentdir);
			pattern = obj.dirFormats.choices{iFormat}{iPattern};

	if isempty( obj.files )		dirs = mydir([parentdir, pattern]);
	% If there are no data files in current dir, don't give up yet - check
	% the subdirs for data files.		dirnamePrev = '';
	dirs = mydir(obj.pathnm);
	for ii = 1:length(dirs)		for ii = 1:length(dirs)
	if dirs(ii).isdir && ...		if dirs(ii).IsFile()
	~strcmp(dirs(ii).name,'.') && ...		if strcmp(pattern, '*')
	~strcmp(dirs(ii).name,'..') && ...		continue
	~strcmp(dirs(ii).name,'hide')		end
	dirs(ii).idx = length(obj.files)+1;		if includes(dirs(ii).name, obj.filetype)
	foos = mydir([obj.pathnm, dirs(ii).name, '/*.', type]);		if ~strcmp(dirs(ii).name, dirnamePrev)
	nfoos = length(foos);		obj.AddParentDirs(dirs(ii));
	if nfoos>0
	for jj = 1:nfoos
	foos(jj).subjdir = dirs(ii).name;
	foos(jj).subjdiridx = dirs(ii).idx;
	foos(jj).idx = dirs(ii).idx+jj;
	foos(jj).filename = foos(jj).name;
	foos(jj).name = [dirs(ii).name, '/', foos(jj).name];
	foos(jj).map2group = struct('iGroup',0, 'iSubj',0, 'iRun',0);
	foos(jj).pathfull = dirs(ii).pathfull;
	if ~foos(jj).isdir
	obj.nfiles = obj.nfiles+1;
	end		end
			obj.AddFile(dirs(ii));
	end		end

	% Add file from current subdir to files struct		if obj.dirFormats.type == 0
	if isempty(obj.files)		obj.dirFormats.type = iFormat;
	obj.files = dirs(ii);
	else
	obj.files(end+1) = dirs(ii);
	end		end
	obj.files(end+1:end+nfoos) = foos;		elseif dirs(ii).IsDir()
			obj.FindDataSet(iFormat, iPattern+1, [parentdir, dirs(ii).filename])
	end		end
			dirnamePrev = dirs(ii).name;
	end		end
	end		end
	else
	for ii = 1:length(obj.files)
	obj.files(ii).pathfull = obj.pathnm;
			% ----------------------------------------------------
			function AddParentDirs(obj, dir)
			pathrel = getPathRelative([dir.rootdir, dir.name], obj.rootdir);
			subdirs = str2cell_fast(pathrel, {'/','\'});
			notUnique = false;
			N = length(subdirs);
			for ii = 1:N-1
			if strcmp(subdirs{ii}, 'nirs')
			continue;
	end		end
	obj.nfiles = obj.nfiles+length(obj.files);		pathrel2 = buildpathfrompathparts(subdirs(1:ii));
			if obj.SearchLookupTable(pathrel2)
			continue;
			end
			obj.files(end+1) = FileClass(pathrel2);
			obj.AddLookupTable(obj.files(end).name)
	end		end
	end		end



	% ----------------------------------------------------		% ----------------------------------------------------
	function getDataFile(obj, filename)		function AddFile(obj, file)
	obj.files = mydir(filename);		obj.files(end+1) = file;
			obj.nfiles = obj.nfiles+1;
			obj.AddLookupTable(obj.files(end).filename)
	end		end


	@@ -220,7 +302,7 @@ classdef DataFilesClass < handle
	% -----------------------------------------------------		% -----------------------------------------------------
	function errmsg = GetErrorMsg(obj, ii)		function errmsg = GetErrorMsg(obj, ii)
	p1 = fileparts(obj.files(ii).GetName());		p1 = fileparts(obj.files(ii).GetName());
	[p2,f2] = fileparts(filesepStandard(obj.files(ii).pathfull,'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';
	@@ -301,7 +383,7 @@ classdef DataFilesClass < handle


	% ----------------------------------------------------------		% ----------------------------------------------------------
	function ErrorCheck(obj, type)		function ErrorCheck(obj)
	errorIdxs = [];		errorIdxs = [];

	if isempty(obj.files)		if isempty(obj.files)
	@@ -309,7 +391,7 @@ classdef DataFilesClass < handle
	end		end

	% Assume constructor name follows from name of data format type		% Assume constructor name follows from name of data format type
	constructor = sprintf('%sClass', [upper(type(1)), type(2:end)]);		constructor = sprintf('%sClass', [upper(obj.filetype(1)), obj.filetype(2:end)]);

	% Make sure function by that name exists; otherwise no way to		% Make sure function by that name exists; otherwise no way to
	% use it to check loadability		% use it to check loadability
	@@ -317,13 +399,13 @@ classdef DataFilesClass < handle
	return;		return;
	end		end

	% Try to create object of data type and load data into it		% Try to create object of data filetype and load data into it
	dataflag = false;		dataflag = false;
	for ii = 1:length(obj.files)		for ii = 1:length(obj.files)
	if obj.files(ii).isdir		if obj.files(ii).isdir
	continue;		continue;
	end		end
	filename = [obj.files(ii).pathfull, obj.files(ii).name];		filename = [obj.files(ii).rootdir, obj.files(ii).name];
	eval( sprintf('o = %s(filename);', constructor) );		eval( sprintf('o = %s(filename);', constructor) );
	if o.GetError()<0		if o.GetError()<0
	obj.logger.Write('FAILED error check: %s will not be added to data set\n', filename);		obj.logger.Write('FAILED error check: %s will not be added to data set\n', filename);
	@@ -349,5 +431,62 @@ classdef DataFilesClass < handle
	err = obj.err;		err = obj.err;
	end		end

			% ----------------------------------------------------------
			function PrintFolderStructure(obj, options)
			if ~exist('options','var')
			options = '';
			end
			stepsize = 3;
			obj.logger.Write('\n');
			obj.logger.Write('DataTreeClass - Data Set Folder Structure:\n');
			for ii = 1:length(obj.files)
			k = length(find(obj.files(ii).name=='/'));
			if ii<10, j=3; elseif ii>9 && ii<100, j=2; else j=3; end
			if optionExists(options, 'flat')
			obj.logger.Write(sprintf('%d.%s%s\n', ii, blanks(j), obj.files(ii).name));
			else
			if ii<10, j=3; elseif ii>9 && ii<100, j=2; else j=3; end
			if optionExists(options, 'numbered')
			n = k*stepsize+stepsize+j;
			obj.logger.Write(sprintf('%d.%s%s\n', ii, blanks(n), obj.files(ii).filename));
			else
			n = k*stepsize+stepsize;
			obj.logger.Write(sprintf('%s%s\n', blanks(n), obj.files(ii).filename));
			end
			end
			end
			obj.logger.Write('\n');
			end

			end



			methods (Access = private)

			% ----------------------------------------------------------
			function InitLookupTable(obj)
			width = 4;
			if isempty(obj.lookupTable)
			obj.lookupTable = int32(zeros((10^width)-1, 1));
			else
			obj.lookupTable(:) = 0;
			end
			end


			% ----------------------------------------------------------
			function AddLookupTable(obj, str)
			n = round(log10(length(obj.lookupTable)));
			obj.lookupTable(string2hash(str, n)) = 1;
			end


			% ----------------------------------------------------------
			function b = SearchLookupTable(obj, str)
			n = round(log10(length(obj.lookupTable)));
			b = obj.lookupTable(string2hash(str, n));
			end

	end		end
	end		end

DataTree/AcquiredData/DataFiles/DeleteDataFiles.m

+6 −6

Original line number	Original line	Diff line number	Diff line
	@@ -86,15 +86,15 @@ for ii=1:length(datafiles)
	continue;		continue;
	end		end
	if strcmp(options, 'delete')		if strcmp(options, 'delete')
	fprintf('Deleting %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name]);		fprintf('Deleting %s\n', [datafiles(ii).rootdir, '/', datafiles(ii).name]);
	delete([datafiles(ii).pathfull, '/', datafiles(ii).name]);		delete([datafiles(ii).rootdir, '/', datafiles(ii).name]);
	elseif strcmp(options, 'move')		elseif strcmp(options, 'move')
	fprintf('Moving %s to %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', datafiles(ii).name, '.old']);		fprintf('Moving %s to %s\n', [datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', datafiles(ii).name, '.old']);
	movefile([datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', datafiles(ii).name, '.old']);		movefile([datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', datafiles(ii).name, '.old']);
	elseif strcmp(options, 'restore')		elseif strcmp(options, 'restore')
	[pname, fname] = fileparts(datafiles(ii).name);		[pname, fname] = fileparts(datafiles(ii).name);
	fprintf('Restoring %s to %s\n', [datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', pname, '/', fname]);		fprintf('Restoring %s to %s\n', [datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', pname, '/', fname]);
	movefile([datafiles(ii).pathfull, '/', datafiles(ii).name], [datafiles(ii).pathfull, '/', pname, '/', fname]);		movefile([datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', pname, '/', fname]);
	end		end
	pause(0.25);		pause(0.25);
	end		end

DataTree/AcquiredData/DataFiles/FileClass.m

+286 −69

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