merge development branch into SK branch (10d483b2) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+69 −9

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@ classdef DataFilesClass < handle

		properties
		files;
		filesErr;
		filetype;
		dirFormats;
		err;
		@@ -21,6 +22,7 @@ classdef DataFilesClass < handle
		% ----------------------------------------------------
		function obj = DataFilesClass(varargin)
		obj.files = FileClass.empty();
		obj.filesErr = FileClass.empty();
		obj.filetype = '';
		obj.rootdir = pwd;
		obj.nfiles = 0;
		@@ -116,15 +118,15 @@ classdef DataFilesClass < handle
		obj.InitLookupTable();
		obj.FindDataSet(ii);

		% Remove any files that cannot pass the basic test of loading
		% its data
		obj.ErrorCheck();
		if ~isempty(obj.files)
		break
		end
		end

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


		@@ -188,6 +190,13 @@ classdef DataFilesClass < handle
		['nirs/*.', obj.filetype];
		}

		%%%% 10. BIDS-like folder structure without nirs sub-folder
		{
		'sub-*';
		'ses-*';
		['*.', obj.filetype];
		}

		};
		end

		@@ -215,10 +224,13 @@ classdef DataFilesClass < handle
		parentdir = filesepStandard(parentdir);
		pattern = obj.dirFormats.choices{iFormat}{iPattern};

		dirs = mydir([parentdir, pattern]);
		dirs = mydir([parentdir, pattern], obj.rootdir);

		dirnamePrev = '';
		for ii = 1:length(dirs)
		if dirs(ii).IsEmpty()
		continue;
		end
		if dirs(ii).IsFile()
		if strcmp(pattern, '*')
		continue
		@@ -255,7 +267,7 @@ classdef DataFilesClass < handle
		if obj.SearchLookupTable(pathrel2)
		continue;
		end
		obj.files(end+1) = FileClass([obj.rootdir, '/', pathrel2]);
		obj.files(end+1) = FileClass([obj.rootdir, '/', pathrel2], obj.rootdir);
		obj.AddLookupTable(obj.files(end).name)
		end
		end
		@@ -290,6 +302,41 @@ classdef DataFilesClass < handle



		% ----------------------------------------------------
		function ErrorCheckFinal(obj)
		obj.ErrorCheckName();

		% Find all acquisition files in group folder
		fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype]);

		% Make alist of all files excluded from current data set
		for ii = 1:length(fileNames)
		filefound = false;

		for jj = 1:length(obj.files)
		if pathscompare(fileNames{ii}, [obj.rootdir, obj.files(jj).name])
		filefound = true;
		break;
		end
		end

		for jj = 1:length(obj.filesErr)
		if pathscompare(fileNames{ii}, [obj.rootdir, obj.filesErr(jj).name])
		filefound = true;
		break;
		end
		end

		if ~filefound
		obj.filesErr(end+1) = FileClass(fileNames{ii});
		obj.filesErr(end).SetError('Invalid File Name');
		end
		end

		end



		% --------------------------------------------------------------------------
		function answer = AskToFixNameConflicts(obj, ii)
		global cfg
		@@ -418,6 +465,8 @@ classdef DataFilesClass < handle
		end

		% Try to create object of data filetype and load data into it
		msg = 'Please wait while we check group folder for valid data files ...';
		hwait = waitbar_improved(0, msg);
		dataflag = false;
		for ii = 1:length(obj.files)
		if obj.files(ii).isdir
		@@ -426,17 +475,27 @@ classdef DataFilesClass < handle
		filename = [obj.files(ii).rootdir, obj.files(ii).name];
		eval( sprintf('o = %s(filename);', constructor) );
		if o.GetError() < 0
		obj.logger.Write('FAILED error check: %s will not be added to data set\n', filename);
		obj.logger.Write('DataFilesClass.ErrorCheck: FAILED error check - %s will not be added to data set\n', filename);
		errorIdxs = [errorIdxs, ii]; %#ok<AGROW>
		elseif contains(o.GetErrorMsg(), 'WARNING: ''data'' corrupt and unusable')
		obj.logger.Write('DataFilesClass.ErrorCheck: WARNING data is unusable - %s will not be added to data set\n', filename);
		errorIdxs = [errorIdxs, ii]; %#ok<AGROW>
		else
		dataflag = true;
		end
		hwait = waitbar_improved(ii/length(obj.files), hwait, msg);
		end
		if dataflag==false
		obj.files = FileClass.empty();
		else
		for jj = 1:length(errorIdxs)
		obj.filesErr(end+1) = obj.files(errorIdxs(jj)).copy;
		obj.filesErr(end).SetError('Invalid Data Format');
		end
		obj.files(errorIdxs) = [];
		obj.nfiles = obj.nfiles - length(errorIdxs);
		end
		close(hwait);
		end


		@@ -518,5 +577,6 @@ classdef DataFilesClass < handle
		b = obj.lookupTable(string2hash(str, n));
		end


		end
		end

DataTree/AcquiredData/DataFiles/FileClass.m

+560 −539

Original line number	Diff line number	Diff line
		@@ -19,6 +19,7 @@ classdef FileClass < matlab.mixin.Copyable
		rootdir
		err
		logger
		errmsgs
		end

		methods
		@@ -39,6 +40,8 @@ classdef FileClass < matlab.mixin.Copyable
		obj.rootdir = '';
		obj.err = -1; % Assume file is not loadable
		obj.logger = InitLogger(logger);
		obj.errmsgs = {'Invalid Data Format','Invalid File Name'};


		if nargin==0
		return;
		@@ -59,7 +62,7 @@ classdef FileClass < matlab.mixin.Copyable
		else
		file.rootdir = pwd;
		end
		file.rootdir = filesepStandard(file.rootdir);
		file.rootdir = filesepStandard(file.rootdir, 'full');

		obj.Add(file);
		end
		@@ -75,15 +78,15 @@ classdef FileClass < matlab.mixin.Copyable
		end

		if isproperty(obj2, 'folder')
		rootdir = [filesepStandard(obj2.folder), obj2.name]; %#ok<*PROPLC>
		rootpath = [filesepStandard(obj2.folder), obj2.name]; %#ok<*PROPLC>
		else
		rootdir = [filesepStandard(obj2.rootdir), obj2.name];
		rootpath = [filesepStandard(obj2.rootdir), obj2.name];
		end

		obj.idx = obj.idx+1;
		obj.isdir = obj2.isdir;
		obj.filename = obj2.name;
		obj.name = getPathRelative(rootdir, obj2.rootdir);
		obj.name = getPathRelative(rootpath, obj2.rootdir);
		obj.rootdir = obj2.rootdir;
		obj.err = 0; % Set error to NO ERROR
		end
		@@ -116,7 +119,11 @@ classdef FileClass < matlab.mixin.Copyable
		end
		dirname(k) = '*';
		end
		file = dir(dirname);
		temp = dir(dirname);
		if isempty(temp)
		return;
		end
		file = temp(1);
		end


		@@ -191,8 +198,8 @@ classdef FileClass < matlab.mixin.Copyable
		% R2.ext ==> [G1, sub_R2, ses_sub_R2, R2]
		% R3.ext ==> [G1, sub_R3, ses_sub_R3, R3]
		if obj.IsFile && length(parts)==1 && length(subparts)==1
		subjName = ['sub_', fname];
		sessName = ['ses_', subjName];
		subjName = ['sub-', fname];
		sessName = ['ses-', subjName];
		runName = obj.name;
		end

		@@ -209,7 +216,7 @@ classdef FileClass < matlab.mixin.Copyable
		% S3_R3.ext ==> [G1, S2, ses_S2_R3, R3]
		if obj.IsFile && length(parts)==1 && length(subparts)==2
		subjName = subparts{1};
		sessName = ['ses_', subjName, '_', fname];
		sessName = ['ses-', subjName, '_', subjName];
		runName = obj.name;
		end

		@@ -258,7 +265,7 @@ classdef FileClass < matlab.mixin.Copyable
		subjName = obj.name;
		elseif obj.IsFile && length(parts)==2
		subjName = parts{1};
		sessName = [subjName, '/ses-', fname];
		sessName = [subjName, '/ses-', subjName];
		runName = obj.name;
		end

		@@ -535,6 +542,20 @@ classdef FileClass < matlab.mixin.Copyable
		end


		% -----------------------------------------------------
		function err = SetError(obj, err)
		if ischar(err)
		err = find(strcmp(obj.errmsgs, err));
		end
		obj.err = err;
		end


		% -----------------------------------------------------
		function msg = GetErrorMsg(obj)
		msg = obj.errmsgs{abs(obj.err)};
		end

		end

		end
		No newline at end of file

DataTree/AcquiredData/DataFiles/FindFiles.m

+0 −3

Original line number	Diff line number	Diff line
		@@ -68,7 +68,6 @@ while files.IsEmpty()
		if nfolders==0
		nfolders = 1;
		end
		fprintf('FindFiles: Found %d .nirs data files in %d folders\n', filesSrc.nfiles, nfolders);
		end

		% Search for source acquisition files in .nirs format which have not
		@@ -134,8 +133,6 @@ while files.IsEmpty()
		cd(dirnameGroup)
		end

		fprintf('FindFiles: Found %d %s data files in %d folders\n', files.nfiles, fmt, length(files.files)-files.nfiles);

		end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_Transpose.m

+1 −0

Original line number	Diff line number	Diff line
		@@ -18,3 +18,4 @@ elseif iscolumn(val) && ischar(val)
		val = permute(val, ndims(val):-1:1);

		end

DataTree/AcquiredData/DataFiles/mydir.m

+1 −1

Original line number	Diff line number	Diff line
		@@ -77,7 +77,7 @@ if ~exist('pathname','var') \|\| isempty(pathname)
		pathname = pwd;
		end
		if ~exist('pathroot','var') \|\| isempty(pathroot)
		pathroot = pwd;
		pathroot = fileparts(pathname);
		end

		if ispathvalid(pathname, 'dir') && ~includes(pathname, '*')

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