-- Fix bug in SnirfClass .snirf file fomat conversion to NirsClas .nirs. (ea939423) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/Snirf2Nirs.m

0 → 100644

+23 −0

Original line number	Diff line number	Diff line
		function Snirf2Nirs(rootdir, options)
		if ~exist('rootdir','var')
		rootdir = pwd;
		end
		if ~exist('options','var')
		options = 'sort';
		end
		rootdir = filesepStandard(rootdir);
		files = DataFilesClass(pwd, 'snirf');
		for ii = 1:length(files)
		fname = filesepStandard([rootdir, files(1).name]);
		s = SnirfClass(fname);
		n = NirsClass(s);
		if optionExists(options, 'sort')
		n.SortData();
		end
		[pname, fname] = filesepStandard(fname);
		fnameNew = [pname, fname, '.nirs'];
		fprintf('Converting %s to %s\n', fname, fnameNew)
		n.Save(fnameNew);
		end

+22 −10

Original line number	Diff line number	Diff line
		@@ -132,6 +132,15 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end


		% ---------------------------------------------------------
		function SortData(obj)
		[obj.SD.MeasList, order] = sortrows(obj.SD.MeasList,4);
		obj.d = obj.d(:,order);
		[obj.SD.MeasList, order] = sortrows(obj.SD.MeasList,4);
		obj.d = obj.d(:,order);
		end


		% ---------------------------------------------------------
		function err = LoadMat(obj, fname, ~)
		err = 0;
		@@ -469,9 +478,8 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		% Always sort stimulus conditions and associated stims
		% to have a predictable order for display
		objnew.s = obj.s;
		obj.SortStims();

		objnew.CondNames = obj.CondNames;
		objnew.SortStims();
		end


		@@ -1093,15 +1101,19 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		function ConvertSnirfStim(obj, snirf)
		obj.s = zeros(length(obj.t), length(snirf.stim));
		for ii = 1:length(snirf.stim)
		k = round(nearest_point(obj.t, snirf.stim(ii).data(:,1)));
		for jj = 1:length(k)
		if k(jj) == 0
		k(jj) = 1;
		if isempty(snirf.stim(ii).data)
		ik = [];
		else
		[~,ik] = nearest_point(obj.t, snirf.stim(ii).data(:,1));
		end
		for jj = 1:length(ik)
		if ik(jj) == 0
		ik(jj) = 1;
		end
		if k(jj) > length(obj.t)
		k(jj) = length(obj.t);
		if ik(jj) > length(obj.t)
		ik(jj) = length(obj.t);
		end
		obj.s(k(jj),ii) = 1;
		obj.s(ik(jj),ii) = 1;
		end
		obj.CondNames{ii} = snirf.stim(ii).name;
		end

+1 −1

Original line number	Diff line number	Diff line
		@@ -45,7 +45,7 @@ if start
		reg.DeleteSaved();

		SCRAMBLE = true;
		ERROR_ODDS_CONST = generateErrorOddsConstant(5);
		ERROR_ODDS_CONST = generateErrorOddsConstant(0);
		end

		% Clean up after ourselves; delete non-versioned acquisition files and

+1 −1

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ if strcmp(ns, 'AtlasViewerGUI')
		elseif nargin == 5
		[out1] = points_on_line_AtlasViewerGUI(inp1, inp2, inp3, inp4, inp5);
		end
		elseif strcmp(ns, 'Homer3')
		elseif strcmp(ns, 'Homer3') \|\| strcmp(ns, 'DataTreeClass')
		if nargin == 0
		[out1] = points_on_line_Homer3();
		elseif nargin == 1