v1.29.3, v1.29.2, v1.29.1 (a3e3afb5) · Commits · github_fork / Homer3

DataTree/AcquiredData/AcqDataClass.m

+21 −7

Original line number	Diff line number	Diff line
		@@ -3,6 +3,9 @@ classdef AcqDataClass < matlab.mixin.Copyable
		properties (Access = private)
		logger
		end
		properties (Access = public)
		errmsgs
		end

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% These methods must be implemented in any derived class
		@@ -81,14 +84,25 @@ classdef AcqDataClass < matlab.mixin.Copyable


		% -------------------------------------------------------
		function b = Error(obj)
		if obj.GetError()<0
		b = true;
		elseif obj.GetError()==0
		b = false;
		else
		b = true;
		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

DataTree/AcquiredData/Nirs/NirsClass.m

+140 −72

Original line number	Diff line number	Diff line
		@@ -34,15 +34,15 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		%
		% NirsClass with properties:
		%
		% SD: [1�1 struct]
		% t: [12698�1 double]
		% s: [12698�2 double]
		% d: [12698�18 double]
		% aux: [12698�1 double]
		% SD: [1x1 struct]
		% t: [12698x1 double]
		% s: [12698x2 double]
		% d: [12698x18 double]
		% aux: [12698x1 double]
		% CondNames: {'1' '2'}
		% filename: './s1/neuro_run01.nirs'
		% fileformat: 'mat'
		% supportedFomats: [1�1 struct]
		% supportedFomats: [1x1 struct]
		% err: 0
		%

		@@ -89,6 +89,19 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		obj.d = [];
		obj.aux = [];
		obj.CondNames = {};


		% Initialize non-.nirs variables
		obj.errmsgs = {
		'MATLAB could not load the file.'
		'''d'' is invalid.'
		'''t'' is invalid.'
		'''SD'' is invalid.'
		'''aux'' is invalid.'
		'''s'' is invalid.'
		'error unknown.'
		};

		end


		@@ -101,9 +114,10 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


		% ---------------------------------------------------------
		function err = LoadMat(obj, fname, params)
		function err = LoadMat(obj, fname, ~)
		err = 0;

		try
		% Arg 1
		if ~exist('fname','var') \|\| ~exist(fname,'file')
		fname = '';
		@@ -122,63 +136,99 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass

		% Don't reload if not empty
		if ~obj.IsEmpty()
		err = obj.GetError(); % preserve error state if exiting early
		return;
		end

		warning('off', 'MATLAB:load:variableNotFound');
		fdata = load(fname,'-mat', 'SD','t','d','s','aux','CondNames');

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% NOTE: Optional fields have positive error codes if they are
		% missing, but negative error codes if they're not missing but
		% invalid
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


		% Mandatory fields
		err = obj.LoadRawData(fdata, err);
		err = obj.LoadTime(fdata, err);
		err = obj.LoadProbeMeasList(fdata, err);

		% Optional fields
		err = obj.LoadAux(fdata, err);
		err = obj.LoadStims(fdata, err);

		catch



		end
		warning('on', 'MATLAB:load:variableNotFound');

		end



		% ---------------------------------------------------------
		function err = LoadRawData(obj, fdata, err)
		if isproperty(fdata,'d')
		obj.d = fdata.d;
		if isempty(obj.d)
		if isempty(obj.d) && err == 0
		err = -2;
		end
		else
		elseif err == 0
		err = -2;
		end
		end


		% ---------------------------------------------------------
		function err = LoadTime(obj, fdata, err)
		if isproperty(fdata,'t')
		obj.t = fdata.t;
		if ~isempty(obj.t)
		obj.errmargin = min(diff(obj.t))/10;
		else
		elseif err == 0
		err = -3;
		end
		else
		elseif err == 0
		err = -3;
		end
		if length(fdata.t) ~= size(fdata.d,1) && err == 0
		err = -3;
		end
		end


		% ---------------------------------------------------------
		function err = LoadProbeMeasList(obj, fdata, err)
		if isproperty(fdata,'SD')
		obj.SetSD(fdata.SD);
		if isempty(obj.SD)
		if isempty(obj.SD) && err == 0
		err = -4;
		end
		else
		elseif err == 0
		err = -4;
		end
		end


		% Optional fields
		% ---------------------------------------------------------
		function err = LoadAux(obj, fdata, err)
		if isproperty(fdata,'aux')
		obj.aux = fdata.aux;
		else
		obj.aux = [];
		end
		if obj.LoadStims(fname, fdata)<0
		err = -4;
		elseif err==0
		err = 5;
		end
		end



		% ---------------------------------------------------------
		function err = LoadStims(obj, fname, fdata)
		err = 0;

		if ~exist('fdata','var') \|\| isempty(fdata)
		% Arg 1
		if ~exist('fname','var') \|\| ~exist(fname,'file')
		fname = '';
		end
		function err = LoadStims(obj, fdata, err)
		if ischar(fdata)
		fname = fdata;

		% Do some error checking
		if ~isempty(fname)
		@@ -190,24 +240,32 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		err = -1;
		return;
		end

		% Don't reload if not empty
		if ~obj.IsEmpty()
		return;
		end

		warning('off', 'MATLAB:load:variableNotFound');
		fdata = load(fname,'-mat', 's','CondNames');
		fdata = load(fname,'-mat', 's','CondNames','t');
		end

		if ~isproperty(fdata,'s')
		if err==0
		err = 6;
		end
		return;
		end

		if isproperty(fdata,'s')
		obj.s = fdata.s;
		else
		obj.s = [];
		if size(fdata.s,1) ~= size(fdata.t)
		if err==0
		err = -6;
		end
		return;
		end
		if isproperty(fdata,'CondNames')
		obj.CondNames = fdata.CondNames;
		if size(fdata.s,1) ~= length(fdata.CondNames)
		if err==0
		err = -6;
		end
		return;
		end
		else
		obj.InitCondNames();
		end
		@@ -261,7 +319,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		% If we're working off the snirf file instead of loading everything into memory
		% then we have to load stim here from file before accessing it.
		if strcmpi(obj.GetDataStorageScheme(), 'files')
		obj.LoadStims(obj.GetFilename());
		obj.LoadStims(obj.GetFilename(), 0);
		end

		% Generate new instance of NirsClass
		@@ -534,6 +592,16 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		ich={ich};
		end


		% ---------------------------------------------------------
		function t = GetAuxiliaryTime(obj)
		t = [];
		if isempty(obj.aux)
		return;
		end
		t = obj.t;
		end

		end

DataTree/AcquiredData/Snirf/AuxClass.m

+80 −10

Original line number	Diff line number	Diff line
		@@ -7,6 +7,11 @@ classdef AuxClass < FileLoadSaveClass
		timeOffset
		end

		% Properties not part of the SNIRF spec. These parameters aren't loaded or saved to files
		properties (Access = private)
		debuglevel
		end

		methods

		% -------------------------------------------------------
		@@ -14,6 +19,8 @@ classdef AuxClass < FileLoadSaveClass
		% Set class properties not part of the SNIRF format
		obj.SetFileFormat('hdf5');

		obj.debuglevel = DebugLevel('none');

		obj.timeOffset = 0;
		if nargin==1
		if isa(varargin{1}, 'AuxClass')
		@@ -31,13 +38,11 @@ classdef AuxClass < FileLoadSaveClass
		obj.dataTimeSeries = [];
		obj.time = [];
		end

		end


		% -------------------------------------------------------
		function err = LoadHdf5(obj, fileobj, location)
		err = 0;

		% Arg 1
		if ~exist('fileobj','var') \|\| (ischar(fileobj) && ~exist(fileobj,'file'))
		@@ -51,7 +56,7 @@ classdef AuxClass < FileLoadSaveClass
		location = ['/',location];
		end

		% Error checking
		% Error checking for file existence
		if ~isempty(fileobj) && ischar(fileobj)
		obj.SetFilename(fileobj);
		elseif isempty(fileobj)
		@@ -66,8 +71,10 @@ classdef AuxClass < FileLoadSaveClass
		try
		% Open group
		[gid, fid] = HDF5_GroupOpen(fileobj, location);
		if gid<0
		err = -1;

		% Absence of optional aux field raises error > 0
		if gid.double < 0
		err = 1;
		return;
		end

		@@ -76,10 +83,20 @@ classdef AuxClass < FileLoadSaveClass
		obj.time = HDF5_DatasetLoad(gid, 'time');
		obj.timeOffset = HDF5_DatasetLoad(gid, 'timeOffset');

		err = obj.ErrorCheck();

		% Close group
		HDF5_GroupClose(fileobj, gid, fid);

		catch
		err = -2;

		if gid.double > 0
		% If optional aux field exists BUT is in some way invalid it raises error < 0
		err = -6;
		else
		err = 1;
		end

		end
		end

		@@ -103,6 +120,10 @@ classdef AuxClass < FileLoadSaveClass
		H5F.close(fid);
		end

		if obj.debuglevel.Get() == obj.debuglevel.SimulateBadData()
		obj.SimulateBadData();
		end

		hdf5write_safe(fileobj, [location, '/name'], obj.name);
		hdf5write_safe(fileobj, [location, '/dataTimeSeries'], obj.dataTimeSeries);
		hdf5write_safe(fileobj, [location, '/time'], obj.time);
		@@ -182,6 +203,55 @@ classdef AuxClass < FileLoadSaveClass
		end


		% ----------------------------------------------------------------------------------
		function b = IsEmpty(obj)
		b = true;
		if isempty(obj)
		return
		end
		if isempty(obj.name)
		return
		end
		if isempty(obj.dataTimeSeries)
		return
		end
		if isempty(obj.time)
		return
		end
		if length(obj.dataTimeSeries) ~= length(obj.time)
		return
		end
		b = false;
		end


		% ----------------------------------------------------------------------------------
		function err = ErrorCheck(obj)
		err = 0;
		if isempty(obj.name)
		err = -1;
		return
		end
		if isempty(obj.dataTimeSeries)
		err = -2;
		return
		end
		if isempty(obj.time)
		err = -3;
		return
		end
		if length(obj.dataTimeSeries) ~= length(obj.time)
		err = -4;
		return
		end
		end


		% ----------------------------------------------------------------------------------
		function SimulateBadData(obj)
		obj.dataTimeSeries(end,:) = [];
		end

		end

		end

DataTree/AcquiredData/Snirf/SnirfClass.m

+91 −45

Original line number	Diff line number	Diff line
		@@ -143,10 +143,16 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end
		dotnirs = varargin{1};
		obj.GenSimulatedTimeBases(dotnirs, tfactors);

		% Required fields
		for ii=1:length(tfactors)
		obj.data(ii) = DataClass(obj.nirs_tb(ii).d, obj.nirs_tb(ii).t(:), obj.nirs_tb(ii).SD.MeasList);
		end
		obj.probe = ProbeClass(dotnirs.SD);


		% Optional fields
		if isfield(dotnirs,'s')
		for ii=1:size(dotnirs.s,2)
		if isfield(dotnirs, 'CondNames')
		obj.stim(ii) = StimClass(dotnirs.s(:,ii), dotnirs.t(:), dotnirs.CondNames{ii});
		@@ -154,14 +160,18 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		obj.stim(ii) = StimClass(dotnirs.s(:,ii), dotnirs.t(:), num2str(ii));
		end
		end
		obj.probe = ProbeClass(dotnirs.SD);
		end
		if isfield(dotnirs,'aux')
		for ii=1:size(dotnirs.aux,2)
		obj.aux(ii) = AuxClass(dotnirs.aux(:,ii), dotnirs.t(:), sprintf('aux%d',ii));
		end
		end

		% Add metadatatags
		% Add required field metadatatags that has no .nirs
		% equivalent
		obj.metaDataTags = MetaDataTagsClass();


		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% obj = SnirfClass(data, stim);
		% obj = SnirfClass(data, stim, probe);
		@@ -244,7 +254,17 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		obj.probe = ProbeClass().empty();
		obj.aux = AuxClass().empty();

		% Initialize non-SNIRF variables
		obj.stim0 = StimClass().empty();
		obj.errmsgs = {
		'MATLAB could not load the file.'
		'''formatVersion'' is invalid.'
		'''metaDataTags'' is invalid.'
		'''data'' is invalid.'
		'''stim'' is invalid and could not be loaded'
		'''probe'' is invalid.'
		'''aux'' is invalid and could not be loaded'
		};
		end


		@@ -397,12 +417,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if ii > length(obj.stim)
		obj.stim(ii) = StimClass;
		end
		if obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/stim', num2str(ii)]) < 0
		err = obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/stim', num2str(ii)]);
		if err ~= 0
		obj.stim(ii).delete();
		obj.stim(ii) = [];
		if ii==1
		err = 1; % Absence of optional field raises error > 0
		end
		break;
		end
		ii=ii+1;
		@@ -415,7 +433,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if ii > length(obj.stim0)
		obj.stim0(ii) = StimClass;
		end
		if obj.stim0(ii).LoadHdf5(fileobj, [obj.location, '/stim0', num2str(ii)]) < 0
		if obj.stim0(ii).LoadHdf5(fileobj, [obj.location, '/stim0', num2str(ii)]) ~= 0
		obj.stim0(ii).delete();
		obj.stim0(ii) = [];
		break;
		@@ -443,12 +461,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if ii > length(obj.aux)
		obj.aux(ii) = AuxClass;
		end
		if obj.aux(ii).LoadHdf5(fileobj, [obj.location, '/aux', num2str(ii)]) < 0
		err = obj.aux(ii).LoadHdf5(fileobj, [obj.location, '/aux', num2str(ii)]);
		if err ~= 0
		obj.aux(ii).delete();
		obj.aux(ii) = [];
		if ii==1
		err = 1; % Error code for no optional field is > 0
		end
		break;
		end
		ii=ii+1;
		@@ -479,6 +495,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% Don't reload if not empty
		if ~obj.IsEmpty()
		err = obj.GetError(); % preserve error state if exiting early
		return;
		end

		@@ -491,38 +508,53 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		[obj.gid, obj.fid] = HDF5_GroupOpen(fileobj, '/');


		if obj.SetLocation() < 0 & err == 0
		if obj.SetLocation() < 0 && err == 0
		err = -1;
		end

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% NOTE: Optional fields have positive error codes if they are
		% missing, but negative error codes if they're not missing but
		% invalid
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

		%%%% Load formatVersion
		if obj.LoadFormatVersion() < 0 & err == 0
		if obj.LoadFormatVersion() < 0 && err == 0
		err = -2;
		end

		%%%% Load metaDataTags
		if obj.LoadMetaDataTags(obj.fid) < 0 & err == 0
		err = -3;
		if obj.LoadMetaDataTags(obj.fid) < 0 && err == 0
		% Here a positive return value means that invalid data meta tags
		% should NOT be a show stopper if we can help it, if the reste of the data
		% is valid. So just let user know they're invalid with a warning.
		err = 3;
		end

		%%%% Load data
		if obj.LoadData(obj.fid) < 0 & err == 0
		if obj.LoadData(obj.fid) < 0 && err == 0
		err = -4;
		end

		%%%% Load stim
		if obj.LoadStim(obj.fid) < 0 & err == 0
		err = -5;
		if obj.LoadStim(obj.fid) < 0 && err == 0
		% Optional field: even if invalid we still want to be
		% able to work with the rest of the data. Only log
		% warning
		err = 5;
		end

		%%%% Load probe
		if obj.LoadProbe(obj.fid) < 0 & err == 0
		if obj.LoadProbe(obj.fid) < 0 && err == 0
		err = -6;
		end

		%%%% Load aux. This is an optional field
		if obj.LoadAux(obj.fid) < 0 & err == 0
		err = -7;
		if obj.LoadAux(obj.fid) < 0 && err == 0
		% Optional field: even if invalid we still want to be
		% able to work with the rest of the data. Only log
		% warning
		err = 7;
		end

		% Close group
		@@ -795,6 +827,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end
		B = true;
		end

		end


		@@ -936,6 +969,19 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end


		% ---------------------------------------------------------
		function t = GetAuxiliaryTime(obj)
		t = [];
		if isempty(obj.aux)
		return;
		end
		if obj.aux(1).IsEmpty()
		return;
		end
		t = obj.aux(1).GetTime();
		end


		% ---------------------------------------------------------
		function ml = GetMeasList(obj, iBlk)
		ml = [];

DataTree/AcquiredData/Snirf/StimClass.m

+57 −11

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