Create shared code and submodule references to DataTree and Utils (#74) (9e882182) · Commits · github_fork / Homer3

.gitmodules

0 → 100644

+8 −0

Original line number	Diff line number	Diff line
		[submodule "Utils/Shared"]
		path = Utils/Shared
		url = https://github.com/jayd1860/Utils
		branch = development
		[submodule "DataTree"]
		path = DataTree
		url = https://github.com/jayd1860/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 @ 06abb78a

Original line number	Diff line number	Diff line
		Subproject commit 06abb78afc8905e1862c9913078716048ad1ff38

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 = protected)
		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

DataTree/AcquiredData/DataFiles/DataFilesClass.m

deleted100755 → 0

+0 −316

Original line number	Diff line number	Diff line
		classdef DataFilesClass < handle

		properties
		files;
		type;
		err;
		errmsg;
		pathnm;
		config;
		nfiles;
		end

		methods

		% ----------------------------------------------------
		function obj = DataFilesClass(varargin)
		obj.type = '';
		obj.pathnm = pwd;
		obj.nfiles = 0;
		obj.err = -1;
		obj.errmsg = {};

		skipconfigfile = false;
		askToFixNameConflicts = [];

		if nargin==0
		return
		end
		if nargin==1
		obj.pathnm = varargin{1};
		end
		if nargin==2
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		end
		if nargin==3
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		if strcmp(varargin{3}, 'standalone')
		skipconfigfile = true;
		end
		end
		if nargin==4
		obj.pathnm = varargin{1};
		obj.type = varargin{2};
		if strcmp(varargin{3}, 'standalone')
		skipconfigfile = true;
		end
		askToFixNameConflicts = varargin{4};
		end

		if obj.type(1)=='.'
		obj.type(1)='';
		end
		obj.pathnm = filesepStandard(obj.pathnm,'full');

		% Configuration parameters
		obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);
		cfg = ConfigFileClass();
		if skipconfigfile==false
		str = cfg.GetValue('Regression Test Active');
		if strcmp(str,'true')
		obj.config.RegressionTestActive=true;
		else
		obj.config.RegressionTestActive=false;
		end
		else
		obj.config.RegressionTestActive=false;
		end
		if ~isempty(askToFixNameConflicts)
		obj.config.AskToFixNameConflicts = askToFixNameConflicts;
		elseif strcmp(cfg.GetValue('Fix File Name Conflicts'), sprintf('don''t ask again'))
		obj.config.AskToFixNameConflicts = 0;
		end

		if nargin==0
		return;
		end

		obj.err = 0;
		obj.files = mydir(obj.pathnm);
		GetDataSet(obj);
		end


		% -----------------------------------------------------------------------------------
		function GetDataSet(obj)
		if exist(obj.pathnm, 'dir')~=7
		error('Invalid subject folder: ''%s''', obj.pathnm);
		end
		obj.findDataSet(obj.type);
		obj.ErrorCheckName();
		end


		% ----------------------------------------------------
		function findDataSet(obj, type)
		obj.files = mydir([obj.pathnm, '/*.', type]);

		% Remove any files that cannot pass the basic test of loading
		% its data
		obj.ErrorCheck(type);

		if isempty( obj.files )
		% If there are no data files in current dir, don't give up yet - check
		% the subdirs for data files.
		dirs = mydir(obj.pathnm);
		for ii = 1:length(dirs)
		if dirs(ii).isdir && ...
		~strcmp(dirs(ii).name,'.') && ...
		~strcmp(dirs(ii).name,'..') && ...
		~strcmp(dirs(ii).name,'hide')
		dirs(ii).idx = length(obj.files)+1;
		foos = mydir([obj.pathnm, dirs(ii).name, '/*.', type]);
		nfoos = length(foos);
		if nfoos>0
		for jj = 1:nfoos
		foos(jj).subjdir = dirs(ii).name;
		foos(jj).subjdiridx = dirs(ii).idx;
		foos(jj).idx = dirs(ii).idx+jj;
		foos(jj).filename = foos(jj).name;
		foos(jj).name = [dirs(ii).name, '/', foos(jj).name];
		foos(jj).map2group = struct('iGroup',0, 'iSubj',0, 'iRun',0);
		foos(jj).pathfull = dirs(ii).pathfull;
		if ~foos(jj).isdir
		obj.nfiles = obj.nfiles+1;
		end
		end

		% Add file from current subdir to files struct
		if isempty(obj.files)
		obj.files = dirs(ii);
		else
		obj.files(end+1) = dirs(ii);
		end
		obj.files(end+1:end+nfoos) = foos;
		end
		end
		end
		else
		for ii = 1:length(obj.files)
		obj.files(ii).pathfull = obj.pathnm;
		end
		obj.nfiles = obj.nfiles+length(obj.files);
		end
		end



		% ----------------------------------------------------
		function getDataFile(obj, filename)
		obj.files = mydir(filename);
		end



		% ----------------------------------------------------
		function ErrorCheckName(obj)
		for ii = length(obj.files):-1:1
		if obj.files(ii).ErrorCheckName()<0
		q = obj.AskToFixNameConflicts(ii);
		if q == 1
		obj.files(ii).FixNameConflict();
		else
		obj.files(ii).NameConflictFixed();
		end
		end
		if obj.files(ii).GetError()<0
		obj.err = -1;
		end
		end
		end



		% --------------------------------------------------------------------------
		function answer = AskToFixNameConflicts(obj, ii)
		answer = 0;
		if obj.config.AskToFixNameConflicts == 0
		obj.files(ii).NameConflictFixed();
		return
		end
		q = MenuBox(obj.GetErrorMsg(ii), {'YES','NO'},[],[],'askEveryTimeOptions');
		if q(1) == 0
		return;
		end
		if length(q)>1 && q(2) == 1
		cfg = ConfigFileClass();
		cfg.SetValue('Fix File Name Conflicts', sprintf('don''t ask again'));
		cfg.Save()
		obj.config.AskToFixNameConflicts = 0;
		end
		if q(1)==2
		obj.files(ii).NameConflictFixed();
		end
		answer = q(1);
		end



		% -----------------------------------------------------
		function errmsg = GetErrorMsg(obj, ii)
		p1 = fileparts(obj.files(ii).GetName());
		[p2,f2] = fileparts(filesepStandard(obj.files(ii).pathfull,'nameonly:file'));
		[~,f3] = fileparts(p2);
		if isfile_private(obj.files(ii).GetName())
		filetype = 'file';
		else
		filetype = 'folder';
		end
		containingFolder = '';
		if obj.files(ii).GetError() == -1
		containingFolder = p1;
		end
		if obj.files(ii).GetError() == -2
		containingFolder = f2;
		end
		if obj.files(ii).GetError() == -3
		containingFolder = f3;
		end
		msg{1} = sprintf('WARNING: The current %s (%s) has the same name as the folder (%s) containing it. ', filetype, obj.files(ii).GetName(), containingFolder);
		msg{2} = sprintf('All %ss should have a different name than the folder containing them, otherwise ', ['F',filetype(2:end)]);
		msg{3} = sprintf('it may cause incorrect results in processing. Do you want to rename this %s?', filetype);
		errmsg = [msg{:}];
		end



		% -------------------------------------------------------
		function pushbuttonLoadDataset_Callback(~, hObject)
		hp = get(hObject,'parent');
		hc = get(hp,'children');
		for ii=1:length(hc)

		if strcmp(get(hc(ii),'tag'),'pushbuttonLoad')
		hButtnLoad = hc(ii);
		elseif strcmp(get(hc(ii),'tag'),'pushbuttonSelectAnother')
		hButtnSelectAnother = hc(ii);
		end

		end

		if hObject==hButtnLoad
		delete(hButtnSelectAnother);
		elseif hObject==hButtnSelectAnother
		delete(hButtnLoad);
		end
		delete(hp);
		end


		% ----------------------------------------------------------
		function b = isempty(obj)
		if isempty(obj.files)
		b = true;
		else
		b = false;
		end
		end



		% ----------------------------------------------------------
		function found = ConvertedFrom(obj, src)
		found = zeros(length(src.files), 1);
		for ii = 1:length(src.files)
		if src.files(ii).isdir
		found(ii) = -1;
		continue;
		end
		[ps, fs] = fileparts(src.files(ii).name);
		for jj = 1:length(obj.files)
		[pd, fd] = fileparts(obj.files(jj).name);
		if strcmp(filesepStandard([ps,'/',fs], 'nameonly'), filesepStandard([pd,'/',fd], 'nameonly'))
		found(ii) = 1;
		break;
		else
		dbgpt = 1;
		end
		end
		end
		end



		% ----------------------------------------------------------
		function ErrorCheck(obj, type)
		errorIdxs = [];

		% Assume constructor name follows from name of data format type
		constructor = sprintf('%sClass', [upper(type(1)), type(2:end)]);

		% Make sure function by that name exists; otherwise no way to
		% use it to check loadability
		if isempty(which(constructor))
		return;
		end

		% Try to create object of data type and load data into it
		for ii = 1:length(obj.files)
		eval(sprintf('o = %s(obj.files(ii).name);', constructor));
		if o.GetError()<0
		errorIdxs = [errorIdxs, ii];
		end
		end
		obj.files(errorIdxs) = [];
		end


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

		end
		end

Admin message