Merge branch 'development' (849792e9) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/ProbeClass.m

+1 −3

Original line number	Diff line number	Diff line
		@@ -157,10 +157,8 @@ classdef ProbeClass < FileLoadSaveClass

		if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D)
		if isempty(obj.landmarkPos3D) \|\| ~obj.isValidLandmarkLabels()
		optodePos3D = [];
		nSource = 0;
		nSource = size(obj.sourcePos3D,1);
		optodePos3D = [obj.sourcePos3D; obj.detectorPos3D];
		nSource = size(optodePos3D,1);

		optodePos2D = project_3D_to_2D(optodePos3D);
		if ~isempty(optodePos2D)

DataTree/AppSettings.cfg

+1 −1

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ No
		don't ask again

		% Output Folder Name #
		homerOutput
		derivatives/homer

		% Output File Name #
		groupResults.mat

DataTree/GroupClass.m

+70 −47

Original line number	Diff line number	Diff line
		@@ -8,6 +8,8 @@ classdef GroupClass < TreeNodeClass

		properties % (Access = private)
		outputFilename
		oldDerivedPaths
		derivedPathBidsCompliant
		end


		@@ -21,6 +23,8 @@ classdef GroupClass < TreeNodeClass
		obj@TreeNodeClass(varargin);

		obj.InitVersion();
		obj.oldDerivedPaths = {obj.path, [obj.path, 'homerOutput']};
		obj.derivedPathBidsCompliant = 'derivatives/homer';

		if nargin<3 \|\| ~strcmp(varargin{3}, 'noprint')
		obj.logger.Write('Current GroupClass version %s\n', obj.GetVersionStr());
		@@ -865,15 +869,6 @@ classdef GroupClass < TreeNodeClass
		end


		% ----------------------------------------------------------------------------------
		function ch = GetMeasList(obj, iBlk)
		if ~exist('iBlk','var')
		iBlk=1;
		end
		ch = obj.subjs(1).GetMeasList(iBlk);
		end


		% ----------------------------------------------------------------------------------
		function wls = GetWls(obj)
		wls = obj.subjs(1).GetWls();
		@@ -1071,10 +1066,12 @@ classdef GroupClass < TreeNodeClass

		% ----------------------------------------------------------------------------------
		function BackwardCompatability(obj)
		if ispathvalid([obj.path, 'groupResults.mat'])
		for jj = 1:length(obj.oldDerivedPaths)
		oldDerivedPath = filesepStandard(obj.oldDerivedPaths{jj});
		if ispathvalid([oldDerivedPath, 'groupResults.mat'])
		try
		g = load([obj.path, 'groupResults.mat']);
		catch ME
		g = load([oldDerivedPath, 'groupResults.mat']);
		catch
		g = [];
		end

		@@ -1095,24 +1092,50 @@ classdef GroupClass < TreeNodeClass
		return;
		end

		msg = sprintf('Detected derived data in an old Homer3 format.');
		oldDerivedPathRel = pathsubtract(oldDerivedPath, obj.path);
		if oldDerivedPathRel(end) == '/' \|\| oldDerivedPathRel(end) == '\'
		oldDerivedPathRel(end) = '';
		end
		msg{1} = sprintf('Detected derived data in older Homer3 folder "%s" ', oldDerivedPathRel);
		if pathscompare(obj.derivedPathBidsCompliant, obj.outputDirname, 'nameonly')
		msg{2} = sprintf('The current derived output folder, "%s", is BIDS compliant. ', ...
		filesepStandard(obj.derivedPathBidsCompliant, 'filesepwide:nameonly'));
		else
		msg{2} = '.';
		end
		msg = [msg{:}];
		obj.logger.Write('Backward Compatability: %s\n', msg);

		% If we're here it means that old format homer3 data exists
		% AND NO new homer3 format data exists
		q = MenuBox(sprintf('%s. Do you want to save it in the new format?', msg),{'Yes','No'});
		q = MenuBox(sprintf('%s Do you want to move %s to the new folder?', msg, oldDerivedPathRel),{'Yes','No'});
		if q==1
		obj.BackwardCompatability@TreeNodeClass();
		for ii = 1:length(obj.subjs)
		obj.subjs(ii).BackwardCompatability();
		if ispathvalid([obj.path, obj.outputDirname])
		try
		rmdir([obj.path, obj.outputDirname], 's')
		catch
		MenuBox(sprintf('ERROR: Could not remove new derived folder'),{'OK'});
		return
		end
		end
		obj.logger.Write('Moving %s to %s\n', oldDerivedPath, [obj.path, obj.outputDirname]);
		movefile(oldDerivedPath, [obj.path, obj.outputDirname])

		obj.logger.Write('Moving %s to %s\n', 'groupResults.mat', [obj.path, obj.outputDirname, obj.outputFilename]);
		movefile('groupResults.mat', [obj.path, obj.outputDirname, obj.outputFilename])
		if ispathvalid([obj.path, obj.outputDirname, obj.outputFilename])
		if ~strcmp(obj.outputFilename, 'groupResults.mat')
		obj.logger.Write('Moving %s to %s\n', [obj.path, obj.outputDirname, 'groupResults.mat'], ...
		[obj.path, obj.outputDirname, obj.outputFilename])
		movefile([obj.path, obj.outputDirname, 'groupResults.mat'], [obj.path, obj.outputDirname, obj.outputFilename])
		end
		end
		end
		break
		end

		end
		end


		end % Private methods

		end % classdef GroupClass < TreeNodeClass

DataTree/ProcStream/ProcInputClass.m

+11 −8

Original line number	Diff line number	Diff line
		@@ -233,11 +233,14 @@ classdef ProcInputClass < handle
		end
		if isempty(obj.mlActMan)
		obj.mlActMan{iBlk} = ml;
		elseif isempty(obj.mlActMan{iBlk})
		obj.mlActMan{iBlk} = ml;
		elseif length(obj.mlActMan{iBlk}) == length(ml)
		obj.mlActMan{iBlk} = ml;
		end
		end


		% ----------------------------------------------------------------------------------
		function ml = GetMeasListVis(obj, iBlk)
		if ~exist('iBlk','var')

DataTree/ProcStream/ProcStreamClass.m

+36 −11

Original line number	Diff line number	Diff line
		@@ -355,6 +355,27 @@ classdef ProcStreamClass < handle
		end


		% ----------------------------------------------------------------------------------
		function mlActMan = CompressMlActMan(obj)
		mlActMan = [];
		if isempty(obj.input.mlActMan)
		return
		end
		mlActMan = compressLogicalArray(obj.input.mlActMan{1});
		end


		% ----------------------------------------------------------------------------------
		function tIncMan = CompresstIncMan(obj)
		tIncMan = [];
		if isempty(obj.input.tIncMan)
		return
		end
		tIncMan = compressLogicalArray(obj.input.tIncMan{1});
		end



		% ----------------------------------------------------------------------------------
		function ExportProcStream(obj, filename, fcalls)
		global logger
		@@ -363,13 +384,17 @@ classdef ProcStreamClass < handle
		return;
		end
		[p,f] = fileparts(temp);
		fname = [filesepStandard(p), f, '_ProcStream.txt'];
		fname = [filesepStandard(p), f, '_processing.json'];
		if obj.ExportProcStreamFunctions()==true
		fid = fopen(fname, 'w');
		logger.Write('Saving processing stream %s:\n', fname);
		for ii = 1:length(fcalls)
		fprintf(fid, '%s\n', fcalls{ii});
		end
		appname = sprintf('%s, (v%s)', getNamespace(), getVernum(getNamespace()));
		dt = sprintf('%s', char(datetime(datetime, 'Format','MMMM d, yyyy, HH:mm:ss')));
		mlActManCompressed = obj.CompressMlActMan();
		tIncManCompressed = obj.CompresstIncMan();
		jsonstruct = struct('ApplicationName',appname, 'DateTime',dt, 'tIncMan',tIncManCompressed, 'mlActMan',mlActManCompressed, 'FunctionsCalls',{fcalls});
		jsonStr = savejson('Processing', jsonstruct);
		fid = fopen(fname, 'w');
		fwrite(fid, jsonStr, 'uint8');
		fclose(fid);
		else
		if ispathvalid(fname)

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