v1.32.3 (293f98d2) · Commits · github_fork / Homer3

DataTree/GroupClass.m

+5 −30

Original line number	Diff line number	Diff line
		@@ -276,28 +276,6 @@ classdef GroupClass < TreeNodeClass



		% ----------------------------------------------------------------------------------
		function SetPath(obj, dirname)
		obj.path = dirname;

		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = obj.path;
		end


		% ----------------------------------------------------------------------------------
		function SetPathOutput(obj, dirname)
		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = dirname;
		end


		% ----------------------------------------------------------------------------------
		function Add(obj, subj, run)
		[~,f,e] = fileparts(subj.GetName());
		@@ -319,6 +297,7 @@ classdef GroupClass < TreeNodeClass
		if jj==0
		jj = length(obj.subjs)+1;
		subj.SetIndexID(obj.iGroup, jj);
		subj.SetPath(obj.path); % Inherit root path from group
		obj.subjs(jj) = subj;
		obj.logger.Write(sprintf(' Added subject %s to group %s.\n', obj.subjs(jj).GetName, obj.GetName));
		end
		@@ -486,11 +465,7 @@ classdef GroupClass < TreeNodeClass
		obj.LoadVars(s(iSubj), tHRF_common);
		end

		% Make variables in this group available to processing stream input
		obj.procStream.input.LoadVars(obj.outputVars);

		% Calculate processing stream
		obj.procStream.Calc(obj.GetOutputFilename());
		Calc@TreeNodeClass(obj);

		if obj.DEBUG
		obj.logger.Write(sprintf('Completed processing stream for group %d\n', obj.iGroup));
		@@ -508,11 +483,11 @@ classdef GroupClass < TreeNodeClass

		% ----------------------------------------------------------------------------------
		function Print(obj, indent)
		obj.logger.Write(sprintf('\n'));
		if ~exist('indent', 'var')
		indent = 0;
		end
		obj.logger.Write(sprintf('%s%s, output file: %s\n', blanks(indent), obj.name, obj.procStream.output.SetFilename(obj.GetOutputFilename())));
		% obj.procStream.Print(indent);
		Print@TreeNodeClass(obj, indent);
		for ii = 1:length(obj.subjs)
		obj.subjs(ii).Print(indent);
		end

DataTree/ProcStream/ProcResultClass.m

+1 −1

Original line number	Diff line number	Diff line
		@@ -170,7 +170,7 @@ classdef ProcResultClass < handle
		return;
		end
		[pname, fname] = fileparts(filename);
		options = 'nameonly';
		options = 'nameonly:dir';
		if ispathvalid(fname)
		% Case 1: Flat group dir structure
		if ispathvalid([filename, '.mat'])

DataTree/RunClass.m

+9 −16

Original line number	Diff line number	Diff line
		@@ -26,13 +26,12 @@ classdef RunClass < TreeNodeClass
		obj.name = '';
		return;
		end
		dirname = './';
		if isa(varargin{1}, 'RunClass')
		obj.Copy(varargin{1});
		return;
		elseif isa(varargin{1}, 'FileClass')
		dirname = varargin{1}.pathfull;
		[~, ~, obj.name] = varargin{1}.ExtractNames();
		obj.path = varargin{1}.GetFilesPath(); % Fix wrong root path
		elseif ischar(varargin{1}) && strcmp(varargin{1},'copy')
		return;
		elseif ischar(varargin{1})
		@@ -135,10 +134,10 @@ classdef RunClass < TreeNodeClass
		end

		% Unload derived data
		obj.procStream.FreeMemory(obj.GetOutputFilename());
		obj.procStream.FreeMemory([obj.path, obj.GetOutputFilename()]);

		% Unload acquired data
		obj.acquired.FreeMemory(obj.GetFilename());
		obj.acquired.FreeMemory([obj.path, obj.GetFilename()]);
		end


		@@ -301,16 +300,11 @@ classdef RunClass < TreeNodeClass
		args = obj.procStream.GetInputArgs();

		% b) Find these variables in this run
		vars = [];
		for ii = 1:length(args)
		eval( sprintf('vars.%s = obj.GetVar(args{ii});', args{ii}) );
		eval( sprintf('obj.outputVars.%s = obj.GetVar(args{ii});', args{ii}) );
		end

		% c) Load the needed variables to proc stream input
		obj.procStream.input.LoadVars(vars);

		% Calculate processing stream
		obj.procStream.Calc(obj.GetOutputFilename());
		Calc@TreeNodeClass(obj);

		if obj.DEBUG
		obj.logger.Write(sprintf('Completed processing stream for group %d, subject %d, run %d\n', obj.iGroup, obj.iSubj, obj.iRun));
		@@ -324,10 +318,9 @@ classdef RunClass < TreeNodeClass
		if ~exist('indent', 'var')
		indent = 4;
		else
		indent = indent+2;
		indent = indent+4;
		end
		obj.logger.Write(sprintf('%s%s, output file: %s\n', blanks(indent), obj.name, obj.procStream.output.SetFilename(obj.GetOutputFilename())));
		% obj.procStream.Print(indent);
		Print@TreeNodeClass(obj, indent);
		end

		end % Public methods
		@@ -866,7 +859,7 @@ classdef RunClass < TreeNodeClass
		% ----------------------------------------------------------------------------------
		function b = HaveOutput(obj)
		b1 = ~obj.procStream.output.IsEmpty();
		fname = obj.procStream.output.SetFilename(obj.GetOutputFilename());
		fname = obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename()]);
		b2 = false;
		if ispathvalid(fname)
		r = load(fname);

DataTree/SubjClass.m

+6 −12

Original line number	Diff line number	Diff line
		@@ -184,6 +184,7 @@ classdef SubjClass < TreeNodeClass
		if jj==0
		jj = length(obj.runs)+1;
		run.SetIndexID(obj.iGroup, obj.iSubj, jj);
		run.SetPath(obj.path); % Inherit root path from subject
		obj.runs(jj) = run;
		obj.logger.Write(sprintf(' Added run %s to subject %s.\n', obj.runs(jj).GetFileName, obj.GetName));
		end
		@@ -333,12 +334,7 @@ classdef SubjClass < TreeNodeClass
		obj.LoadVars(r(iRun), tHRF_common);
		end


		% Make variables in this subject available to processing stream input
		obj.procStream.input.LoadVars(obj.outputVars);

		% Calculate processing stream
		obj.procStream.Calc(obj.GetOutputFilename());
		Calc@TreeNodeClass(obj);

		if obj.DEBUG
		fprintf('Completed processing stream for group %d, subject %d\n', obj.iGroup, obj.iSubj);
		@@ -349,7 +345,6 @@ classdef SubjClass < TreeNodeClass
		if ~isempty(obj.updateParentGui)
		obj.updateParentGui('DataTreeClass', [obj.iGroup, obj.iSubj, obj.iRun]);
		end
		pause(.5);

		end

		@@ -357,12 +352,11 @@ classdef SubjClass < TreeNodeClass
		% ----------------------------------------------------------------------------------
		function Print(obj, indent)
		if ~exist('indent', 'var')
		indent = 2;
		indent = 4;
		else
		indent = indent+2;
		indent = indent+4;
		end
		obj.logger.Write(sprintf('%s%s, output file: %s\n', blanks(indent), obj.name, obj.procStream.output.SetFilename(obj.GetOutputFilename())));
		% obj.procStream.Print(indent);
		Print@TreeNodeClass(obj, indent);
		for ii=1:length(obj.runs)
		obj.runs(ii).Print(indent);
		end

DataTree/TreeNodeClass.m

+50 −10

Original line number	Diff line number	Diff line
		@@ -143,16 +143,18 @@ classdef TreeNodeClass < handle
		% obj2 to obj
		% ----------------------------------------------------------------------------------
		function Copy(obj, obj2, conditional)
		if ~isempty(obj2.procStream)
		obj.procStream.Copy(obj2.procStream, obj.GetOutputFilename);
		end
		if nargin==2 \|\| strcmp(conditional, 'unconditional')
		obj.name = obj2.name;
		obj.path = obj2.path;
		obj.outputDirname = obj2.outputDirname;
		obj.type = obj2.type;
		obj.iGroup = obj2.iGroup;
		obj.iSubj = obj2.iSubj;
		obj.iRun = obj2.iRun;
		end
		if ~isempty(obj2.procStream)
		obj.procStream.Copy(obj2.procStream, [obj.path, obj.GetOutputFilename()]);
		end
		end


		@@ -202,6 +204,28 @@ classdef TreeNodeClass < handle
		end


		% ----------------------------------------------------------------------------------
		function SetPath(obj, dirname)
		obj.path = dirname;

		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = obj.path;
		end


		% ----------------------------------------------------------------------------------
		function SetPathOutput(obj, dirname)
		% In case there's not enough disk space in the current
		% group folder, we have a alternative path that can be
		% set independently for saving group results. By default
		% it is set to root group folder.
		obj.pathOutputAlt = dirname;
		end


		% ----------------------------------------------------------------------------------
		function SetProcFlag(obj)
		if obj.procStream.output.IsEmpty()
		@@ -651,6 +675,16 @@ classdef TreeNodeClass < handle
		end


		% ----------------------------------------------------------------------------------
		function Calc(obj)
		% Make variables in this subject available to processing stream input
		obj.procStream.input.LoadVars(obj.outputVars);

		% Calculate processing stream
		obj.procStream.Calc([obj.path, obj.GetOutputFilename()]);
		end


		% ----------------------------------------------------------------------------------
		function FreeMemory(obj)
		if isempty(obj)
		@@ -701,8 +735,8 @@ classdef TreeNodeClass < handle
		if ~exist('options','var')
		options = '';
		end
		filename = obj.SaveMemorySpace(obj.name);
		if isempty(filename)
		filename0 = obj.SaveMemorySpace(obj.name);
		if isempty(filename0)
		return;
		end
		if optionExists(options, 'legacy')
		@@ -710,7 +744,7 @@ classdef TreeNodeClass < handle
		else
		outputDirname = obj.outputDirname;
		end
		[p, f] = fileparts([outputDirname, filename]);
		[p, f] = fileparts([outputDirname, filename0]);
		filename = [filesepStandard(p, 'nameonly:dir'), f];
		end

		@@ -782,7 +816,13 @@ classdef TreeNodeClass < handle
		% ------------------------------------------------------------
		function val = GetError(obj)
		val = obj.err;
		end



		% ------------------------------------------------------------
		function Print(obj, indent)
		obj.logger.Write(sprintf('%s%s\n', blanks(indent), [obj.path, obj.procStream.output.SetFilename(obj.GetOutputFilename())] ));
		end


		@@ -792,8 +832,8 @@ classdef TreeNodeClass < handle
		if ~ispathvalid([obj.path, obj.outputDirname])
		mkdir([obj.path, obj.outputDirname])
		end
		src = obj.procStream.output.SetFilename(obj.GetOutputFilename('legacy'));
		dst = obj.procStream.output.SetFilename(obj.GetOutputFilename());
		src = obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename('legacy')]);
		dst = obj.procStream.output.SetFilename([obj.path, obj.GetOutputFilename()]);
		if ispathvalid(src)
		if ~pathscompare(src, dst)
		obj.logger.Write(sprintf('Moving %s to %s\n', src, dst));

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