Merge new feature (v1.58.0) to export and load stim to and from BIDS events TSV files. (c187f581) · Commits · github_fork / Homer3

AppSettings.cfg

+2 −0

Original line number	Diff line number	Diff line
		@@ -10,5 +10,7 @@ don't ask again
		% Export HRF Mean Output Style # all child processing elements in one file, one processing element per file
		one processing element per file

		% Load Stim From TSV File # Yes, No
		Yes

		% END

DataTree/AcquiredData/AcqDataClass.m

+112 −0

Original line number	Diff line number	Diff line
		classdef AcqDataClass < matlab.mixin.Copyable

		properties (Access = public)
		bids
		end
		properties (Access = private)
		logger
		end
		@@ -76,6 +79,24 @@ classdef AcqDataClass < matlab.mixin.Copyable

		methods

		% -------------------------------------------------------
		function obj = AcqDataClass(fileobj)
		if nargin == 0
		return
		end
		if iscell(fileobj)
		if ~isempty(fileobj)
		fileobj = fileobj{1};
		end
		end
		if ~ischar(fileobj)
		fileobj = '';
		end
		obj.LoadBids(fileobj);
		end



		% -------------------------------------------------------
		function Initialize(obj)
		global logger
		@@ -83,12 +104,14 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



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



		% ---------------------------------------------------------
		function msg = GetErrorMsg(obj)
		msg = '';
		@@ -106,6 +129,77 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



		% -------------------------------------------------------
		function err = LoadBids(obj, fileobj)
		err = obj.LoadStimOverride(fileobj);
		end



		% -------------------------------------------------------
		function status = LoadStimOverride(obj, fileobj)
		global cfg
		status = false;
		cfg = InitConfig(cfg);
		if strcmpi(cfg.GetValue('Load Stim From TSV File'), 'no')
		return
		end
		obj.bids = struct('stim',{{}});
		if isempty(fileobj)
		return
		end
		[p,f] = fileparts(fileobj);
		if isempty(p)
		p = filesepStandard(pwd);
		end
		k = strfind(f, '_nirs');
		if isempty(k)
		k = length(f)+1;
		end
		fnameTsv = [filesepStandard(p), f(1:k-1), '_events.tsv'];
		file = mydir(fnameTsv);
		if isempty(file)
		return
		end
		obj.bids.stim = readTsv([filesepStandard(p), file(1).name],'numstr2num');
		if isempty(obj.bids.stim)
		return
		end
		s = TsvFile2Snirf(obj.bids.stim);
		obj.stim = s.stim.copy();
		status = true;
		end



		% -------------------------------------------------------
		function err = ReloadStim(obj, fileobj)
		err = 0;
		obj.bids = struct('stim',{{}});
		if isempty(fileobj)
		return
		end
		[p,f] = fileparts(fileobj);
		if isempty(p)
		p = filesepStandard(pwd);
		end
		k = strfind(f, '_nirs');
		if isempty(k)
		k = length(f)+1;
		end
		fnameTsv = [filesepStandard(p), f(1:k-1), '_events.tsv'];
		file = mydir(fnameTsv);
		if isempty(file)
		return
		end
		obj.bids.stim = readTsv([filesepStandard(p), file(1).name],'numstr2num');
		s = TsvFile2Snirf(obj.bids.stim);
		obj.stim = s.stim.copy();
		end



		% -------------------------------------------------------
		function FreeMemory(obj, filename)
		if ~exist('filename','var')
		@@ -118,6 +212,7 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



		% ---------------------------------------------------------
		function bbox = GetSdgBbox(obj)
		bbox = [];
		@@ -150,6 +245,7 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



		% ----------------------------------------------------------------------------------
		function varval = GetVar(obj, varname)
		if ismethod(obj,['Get_', varname])
		@@ -179,6 +275,7 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



		% ----------------------------------------------------------------------------------
		function t = GetTimeCombined(obj)
		% Function combines the time vectors for all data blocks into one time vectors.
		@@ -204,6 +301,7 @@ classdef AcqDataClass < matlab.mixin.Copyable
		end



		% ----------------------------------------------------------------------------------
		function data = GetStimData(~, ~)
		data = [];
		@@ -250,6 +348,20 @@ classdef AcqDataClass < matlab.mixin.Copyable



		% ----------------------------------------------------------------------------------
		function fnameTsv = GetStimTsvFilename(obj)
		fnameTsv = '';
		[pname, fname] = fileparts(obj.GetFilename());
		k = strfind(fname, '_nirs');
		if isempty(k)
		k = length(fname)+1;
		end
		if isempty(fname)
		return;
		end
		fnameTsv = [filesepStandard(pname), fname(1:k-1), '_events.tsv'];
		end

		end

		end

DataTree/AcquiredData/DataFiles/DeleteDataFiles.m

+1 −0

Original line number	Diff line number	Diff line
		@@ -88,6 +88,7 @@ for ii = 1:length(datafiles)
		if strcmp(options, 'delete')
		fprintf('Deleting %s\n', [datafiles(ii).rootdir, '/', datafiles(ii).name]);
		delete([datafiles(ii).rootdir, '/', datafiles(ii).name]);
		delete([datafiles(ii).rootdir, '/*_events.tsv']);
		elseif strcmp(options, 'move')
		fprintf('Moving %s to %s\n', [datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', datafiles(ii).name, '.old']);
		movefile([datafiles(ii).rootdir, '/', datafiles(ii).name], [datafiles(ii).rootdir, '/', datafiles(ii).name, '.old']);

DataTree/AcquiredData/DataFiles/DeleteTsv.m

0 → 100644

+7 −0

Original line number	Diff line number	Diff line
		function DeleteTsv(rootdir)
		if ~exist('rootdir','var')
		rootdir = pwd;
		end
		rootdir = filesepStandard(rootdir);
		Snirf2Tsv(rootdir, 'remove');

DataTree/AcquiredData/DataFiles/Snirf2Tsv.m

0 → 100644

+36 −0

Original line number	Diff line number	Diff line
		function Snirf2Tsv(rootdir, options)
		if ~exist('rootdir','var')
		rootdir = pwd;
		end
		if ~exist('options','var')
		options = pwd;
		end
		rootdir = filesepStandard(rootdir);
		files = DataFilesClass(rootdir, 'snirf');
		files = files.files;
		for ii = 1:length(files)
		if files(ii).IsDir()
		continue
		end
		fname = filesepStandard([files(ii).rootdir, files(ii).name]);
		[pname, fname, ext1] = fileparts(fname);
		k = strfind(fname, '_nirs');
		if isempty(k)
		k = length(fname)+1;
		end
		fnameNew = [filesepStandard(pname), fname(1:k-1), '_events.tsv'];
		src = [filesepStandard(pname), fname, ext1];
		dst = fnameNew;
		if optionExists(options, 'delete') \|\| optionExists(options, 'remove')
		if ispathvalid(dst)
		fprintf('Deleting %s\n', dst);
		delete(dst);
		end
		else
		fprintf('Converting %s to %s\n', src, dst);
		SnirfFile2Tsv(src, dst, 'removeStim');
		end
		end

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