v1.29.2 (809d37b8) · 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

+63 −9

Original line number	Diff line number	Diff line
		@@ -31,13 +31,11 @@ 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 +49,7 @@ 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 +64,10 @@ 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 +76,20 @@ 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

		@@ -182,6 +192,50 @@ 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


		end

		end

DataTree/AcquiredData/Snirf/SnirfClass.m

+83 −43

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.'
		'''probe'' is invalid.'
		'''aux'' is invalid.'
		};
		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

		@@ -491,37 +508,46 @@ 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
		if obj.LoadStim(obj.fid) < 0 && err == 0
		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
		if obj.LoadAux(obj.fid) < 0 && err == 0
		err = -7;
		end

		@@ -795,6 +821,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end
		B = true;
		end

		end


		@@ -936,6 +963,19 @@ 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

+35 −9

Original line number	Diff line number	Diff line
		@@ -68,7 +68,6 @@ classdef StimClass < FileLoadSaveClass

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

		% Arg 1
		if ~exist('fileobj','var') \|\| (ischar(fileobj) && ~exist(fileobj,'file'))
		@@ -82,7 +81,7 @@ classdef StimClass < FileLoadSaveClass
		location = ['/',location];
		end

		% Error checking
		% Error checking for file existence
		if ~isempty(fileobj) && ischar(fileobj)
		obj.SetFilename(fileobj);
		elseif isempty(fileobj)
		@@ -98,6 +97,12 @@ classdef StimClass < FileLoadSaveClass
		% Open group
		[gid, fid] = HDF5_GroupOpen(fileobj, location);

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

		% Load datasets
		obj.name = HDF5_DatasetLoad(gid, 'name');
		obj.data = HDF5_DatasetLoad(gid, 'data', [], '2D');
		@@ -106,16 +111,22 @@ classdef StimClass < FileLoadSaveClass
		obj.data = [];
		end

		err = obj.ErrorCheck();

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

		catch ME
		obj.updateStates();

		catch

		err = -1;
		return
		if gid.double > 0
		err = -2;
		else
		err = 1;
		end

		end
		obj.updateStates();
		end


		@@ -193,6 +204,8 @@ classdef StimClass < FileLoadSaveClass
		B = true;
		end


		% -------------------------------------------------------
		function updateStates(obj)
		% Generate or regenerate a state list compatible with the data
		% array. Match up existing states with new list of time points
		@@ -217,6 +230,19 @@ classdef StimClass < FileLoadSaveClass
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function err = ErrorCheck(obj)
		err = 0;
		if size(obj.data, 2)<3
		err = -2;
		return;
		end
		end


		end

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