Merging development into master for upcoming release (#82) (bfdf8ac5) · Commits · github_fork / Homer3

.gitignore

0 → 100644

+4 −0

Original line number	Diff line number	Diff line
		*.log
		LastCheckForUpdates.dat
		FuncRegistry/UserFunctions/Registry.mat
		*.snirf

.gitmodules

0 → 100644

+8 −0

Original line number	Diff line number	Diff line
		[submodule "Utils/Shared"]
		path = Utils/Shared
		url = https://github.com/BUNPC/Utils
		branch = development
		[submodule "DataTree"]
		path = DataTree
		url = https://github.com/BUNPC/DataTree
		branch = development

AppSettings.cfg

+0 −31

Original line number	Diff line number	Diff line

		% Processing Stream Config File #
		processOpt_default.cfg

		% Regression Test Active # true, false
		false

		% Include Archived User Functions # Yes, No
		No

		% Default Processing Stream Style # SNIRF, NIRS
		SNIRF

		% Logging # On, Off
		On

		% Check For Updates # on, off
		on

		% Data Storage Scheme # files, memory
		files

		% Auto Save Acquisition Files # No, Yes
		No

		% Group Data Loading Warnings # don't ask again, ask every time
		don't ask again

		% Stim Edit GUI Save Warnings # don't ask again, ask every time
		don't ask again

		% Output Folder Name #
		homerOutput

		% Output File Name #
		groupResults.mat

		% Fix File Name Conflicts # don't ask again, ask every time
		ask every time

		% END

DataTree @ 25e07119

Original line number	Diff line number	Diff line
		Subproject commit 25e07119db1607bd4d5d7ae440dbde310e1dd6a6

DataTree/AcquiredData/AcqDataClass.m

deleted100644 → 0

+0 −255

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

		properties (Access = private)
		logger
		end
		properties (Access = public)
		errmsgs
		end

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% These methods must be implemented in any derived class
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		methods(Abstract)

		% ---------------------------------------------------------
		objnew = GetFormatVersion(obj, options);

		% ---------------------------------------------------------
		val = GetFormatVersionString(obj);

		% ---------------------------------------------------------
		t = GetTime(obj, iBlk)

		% ---------------------------------------------------------
		datamat = GetDataTimeSeries(obj, options, iBlk)

		% ---------------------------------------------------------
		SD = GetSDG(obj,option)

		% ---------------------------------------------------------
		srcpos = GetSrcPos(obj,option)

		% ---------------------------------------------------------
		detpos = GetDetPos(obj,option)

		% ---------------------------------------------------------
		ml = GetMeasList(obj, iBlk)


		% ---------------------------------------------------------
		wls = GetWls(obj)

		% ---------------------------------------------------------
		SetStims_MatInput(obj, s, t, CondNames)

		% ---------------------------------------------------------
		s = GetStims(obj, t)

		% ---------------------------------------------------------
		CondNames = GetConditions(obj)


		% ---------------------------------------------------------
		SetConditions(obj, CondNames)

		% ---------------------------------------------------------
		aux = GetAuxiliary(obj)

		% ---------------------------------------------------------
		SetStimDuration(obj, icond, duration);

		% ---------------------------------------------------------
		duration = GetStimDuration(obj, icond);

		% ---------------------------------------------------------
		n = GetDataBlocksNum(obj);

		% ---------------------------------------------------------
		[iDataBlks, ich] = GetDataBlocksIdxs(obj, ich);

		% ---------------------------------------------------------
		objnew = CopyMutable(obj, options);

		end


		methods

		% -------------------------------------------------------
		function Initialize(obj)
		global logger
		obj.logger = InitLogger(logger);
		end


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


		% ---------------------------------------------------------
		function msg = GetErrorMsg(obj)
		msg = '';
		if isempty(obj)
		msg = 'AcqDataClass object is empty';
		return;
		end
		if isempty(obj.errmsgs)
		return;
		end
		if ~obj.GetError()
		return;
		end
		msg = obj.errmsgs{abs(obj.GetError())};
		end


		% -------------------------------------------------------
		function FreeMemory(obj, filename)
		if ~exist('filename','var')
		filename = '';
		end
		if isempty(filename)
		return;
		end
		obj.Initialize();
		end


		% ---------------------------------------------------------
		function bbox = GetSdgBbox(obj)
		bbox = [];

		optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];
		if isempty(optpos)
		return
		end

		xmax = max(optpos(:,1));
		ymax = max(optpos(:,2));

		xmin = min(optpos(:,1));
		ymin = min(optpos(:,2));

		width = xmax-xmin;
		height = ymax-ymin;

		if width==0
		width = 1;
		end
		if height==0
		height = 1;
		end

		px = width * 0.05;
		py = height * 0.05;

		bbox = [xmin-px, xmax+px, ymin-py, ymax+py];
		end


		% ----------------------------------------------------------------------------------
		function varval = GetVar(obj, varname)
		if ismethod(obj,['Get_', varname])
		varval = eval( sprintf('obj.Get_%s()', varname) );
		elseif ismethod(obj,['Get', varname])
		varval = eval( sprintf('obj.Get%s()', varname) );
		elseif isproperty(obj, varname)
		varval = eval( sprintf('obj.%s', varname) );
		else
		varval = [];
		end

		% If varval is a class object with an IsEmpty() method and length of varval is one or
		% less, then use it determine whether it's valid. If not, return empty as if it were
		% really empty. This is useful when we want to copy only part of an object to save on space.
		% For instance to reconstruct nirs style 's' variable from a SNIRF stim object we need the t
		% property from a SNIRF data container, but we only need that one property not the whole thing
		% so we initilize only the t property. We don't want this partially initialized data object
		% to be found (by GetVar) and used directly in the proc stream processing, we only want to use
		% indirectly to retrieve s from stim. So we do this check to see if it's valid. It won't be
		% since it's only partially initialized.
		if isa(varval, 'handle') && ismethod(varval,'IsEmpty')
		if length(varval)==1 && varval(1).IsEmpty()
		varval = [];
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function t = GetTimeCombined(obj)
		% Function combines the time vectors for all data blocks into one time vectors.
		t = obj.GetTime(1);
		tStart = t(1);
		tEnd = t(end);
		tStep = mean(diff(t));

		nBlks = obj.GetDataBlocksNum();
		for iBlk=2:nBlks
		t = obj.GetTime(iBlk);
		if t(1) < tStart
		tStart = t(1);
		end
		if t(end) > tEnd
		tEnd = t(end);
		end
		if mean(diff(t)) < tStep
		tStep = mean(diff(t));
		end
		end
		t = tStart:tStep:tEnd;
		end


		% ----------------------------------------------------------------------------------
		function data = GetStimData(~, ~)
		data = [];
		end


		% ----------------------------------------------------------------------------------
		function val = GetStimDataLabels(~, ~)
		val = {};
		end


		% ----------------------------------------------------------------------------------
		function b = equal(obj, obj2)
		b = true;
		if isempty(obj.GetFilename)
		return;
		end
		if isempty(obj2.GetFilename)
		return;
		end
		[~, fname1, ext1] = fileparts(obj.GetFilename);
		[~, fname2, ext2] = fileparts(obj2.GetFilename);
		if ~strcmpi([fname1, ext1], [fname2, ext2])
		b = false;
		end
		end


		% ----------------------------------------------------------------------------------
		function status = Mismatch(obj, obj2)
		status = 0;
		msg = {};
		if ~exist('obj2','var')
		return;
		end
		if ~obj.equal(obj2)
		[~, fname, ext] = fileparts(obj.GetFilename);
		msg{1} = sprintf('WARNING: The acquisition file "%s" does not match the derived data in this group folder. ', [fname, ext]);
		msg{2} = sprintf('Are you sure this acquisition file belongs in this group folder?');
		obj.logger.Write([msg{:}])
		end
		end



		end

		end

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