v1.22.7 (ba286356) · Commits · github_fork / Homer3

AppSettings.cfg

+2 −2

Original line number	Diff line number	Diff line
		@@ -15,12 +15,12 @@ SNIRF
		On

		% Last Checked For Update
		30-Jun-2020 10:48:25
		07-Jul-2020 13:07:06

		% Check For Updates
		on

		% Data Storage Scheme
		disk
		file

		% END

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+4 −2

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable
		fileformat;
		supportedFomats;
		err;
		options;
		end


		@@ -19,6 +20,7 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable
		'hdf5', {{'hdf','.hdf','hdf5','.hdf5','hf5','.hf5','h5','.h5'}} ...
		);
		obj.err = 0;
		obj.options = 'memory';
		end


		@@ -39,7 +41,7 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable
		switch(lower(format))
		case obj.supportedFomats.matlab
		if ismethod(obj, 'LoadMat')
		obj.err = obj.LoadMat(filename);
		obj.err = obj.LoadMat(filename, params);
		end
		case obj.supportedFomats.hdf5
		if ismethod(obj, 'LoadHdf5')

DataTree/AcquiredData/Nirs/NirsClass.m

+69 −13

Original line number	Diff line number	Diff line
		@@ -17,11 +17,12 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		methods

		% ---------------------------------------------------------
		function obj = NirsClass(arg)
		function obj = NirsClass(varargin)
		%
		% Syntax:
		% obj = NirsClass()
		% obj = NirsClass(filename);
		% obj = NirsClass(filename, options);
		%
		%
		% Example 1:
		@@ -56,18 +57,26 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		if nargin==0
		return;
		end
		if nargin==2
		obj.options = varargin{2};
		end

		if isa(arg, 'NirsClass')
		obj.Copy(arg);
		if isa(varargin{1}, 'NirsClass')
		obj.Copy(varargin{1});
		return;
		end
		filename = arg;
		filename = varargin{1};
		if ~exist('filename','var') \|\| ~exist(filename,'file')
		obj = NirsClass.empty();
		return;
		end
		obj.filename = filename;

		% Conditional loading of snirf file data
		if strcmpi(obj.options, 'memory')
		obj.Load(filename);
		end
		end


		% -------------------------------------------------------
		@@ -90,7 +99,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


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

		% Arg 1
		@@ -147,16 +156,54 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


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

		% Do some error checking
		if ~isempty(fname)
		obj.filename = fname;
		else
		fname = obj.filename;
		end
		if exist(fname, 'file') ~= 2
		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');
		end


		if isproperty(fdata,'s')
		obj.s = fdata.s;
		else
		obj.s = [];
		end
		if isproperty(fdata,'CondNames')
		obj.CondNames = fdata.CondNames;
		else
		@@ -202,8 +249,16 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end



		% -------------------------------------------------------
		function objnew = CopyMutable(obj, options)
		function objnew = CopyMutable(obj, ~)

		% 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.options, 'file')
		obj.LoadStims(obj.filename);
		end

		% Generate new instance of NirsClass
		objnew = NirsClass();

		@@ -214,6 +269,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end



		% ---------------------------------------------------------
		function nTrials = InitCondNames(obj)
		if isempty(obj.CondNames)

DataTree/AcquiredData/Snirf/SnirfClass.m

+129 −68

Original line number	Diff line number	Diff line
		@@ -25,7 +25,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		% Syntax:
		% obj = SnirfClass()
		% obj = SnirfClass(filename);
		% obj = SnirfClass(nirs);
		% obj = SnirfClass(filename, nirsdatanum);
		% obj = SnirfClass(filename, nirsdatanum, options);
		% obj = SnirfClass(filename, options);
		% obj = SnirfClass(dotnirs);
		% obj = SnirfClass(dotnirs, numdatabllocks);
		% obj = SnirfClass(data, stim);
		% obj = SnirfClass(data, stim, probe);
		% obj = SnirfClass(data, stim, probe, aux);
		@@ -34,7 +38,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		%
		% Also for debugging/simulation of time bases
		%
		% obj = SnirfClass(nirs, tfactors);
		% obj = SnirfClass(dotnirs, tfactors);
		%
		% Example 1:
		%
		@@ -69,99 +73,150 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% Set class properties NOT part of the SNIRF format
		obj.fileformat = 'hdf5';
		obj.nirsdatanum = 1;
		obj.location = '/nirs';
		obj.nirsdatanum = 1;

		% See if we're loading .nirs data format
		if nargin>4
		d = varargin{1};
		t = varargin{2}(:);
		SD = varargin{3};
		aux = varargin{4};
		s = varargin{5};
		end
		if nargin>5
		CondNames = varargin{6};
		end

		% TBD: Need to find better way of parsing arguments. It gets complicated
		% because of all the variations of calling this class constructor but
		% there should be a simpler way to do this
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Between 1 and 4 arguments covers the following syntax variants
		%
		% obj = SnirfClass(filename);
		% obj = SnirfClass(filename, nirsdatanum);
		% obj = SnirfClass(filename, nirsdatanum, options);
		% obj = SnirfClass(filename, options);
		% obj = SnirfClass(dotnirs);
		% obj = SnirfClass(dotnirs, numdatabllocks);
		% obj = SnirfClass(data, stim);
		% obj = SnirfClass(data, stim, probe);
		% obj = SnirfClass(data, stim, probe, aux);
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		if nargin>0 && nargin<5

		if nargin==1 \|\| (nargin==2 && isa(varargin{2}, 'double'))
		% obj = SnirfClass(filename);
		if isa(varargin{1}, 'SnirfClass')
		obj.Copy(varargin{1});
		return;
		end

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% obj = SnirfClass(filename, nirsdatanum);
		% obj = SnirfClass(filename, nirsdatanum, options);
		% obj = SnirfClass(filename, options);
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		if ischar(varargin{1})
		obj.filename = varargin{1};
		if nargin==2
		if nargin>1
		% obj = SnirfClass(filename, nirsdatanum);
		if isnumeric(varargin{2})
		obj.nirsdatanum = varargin{2};

		% obj = SnirfClass(filename, nirsdatanum, options);
		if nargin>2
		obj.options = varargin{3};
		end

		% obj = SnirfClass(filename, options);
		elseif ischar(varargin{2})
		obj.options = varargin{2};

		end
		end

		% Conditional loading of snirf file data
		if strcmpi(obj.options, 'memory')
		obj.Load(varargin{1});
		end


		% The basic 5 of a .nirs format in a struct
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% obj = SnirfClass(dotnirs);
		% obj = SnirfClass(dotnirs, numdatabllocks);
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		elseif isstruct(varargin{1}) \|\| isa(varargin{1}, 'NirsClass')

		% obj = SnirfClass(dotnirs);
		tfactors = 1; % Debug simulation parameter

		% obj = SnirfClass(dotnirs, numdatabllocks);
		if nargin==2
		tfactors = varargin{2};
		end
		nirs = varargin{1};
		obj.GenSimulatedTimeBases(nirs, tfactors);
		dotnirs = varargin{1};
		obj.GenSimulatedTimeBases(dotnirs, tfactors);
		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

		for ii=1:size(nirs.s,2)
		if isfield(nirs, 'CondNames')
		obj.stim(ii) = StimClass(nirs.s(:,ii), nirs.t(:), nirs.CondNames{ii});
		for ii=1:size(dotnirs.s,2)
		if isfield(dotnirs, 'CondNames')
		obj.stim(ii) = StimClass(dotnirs.s(:,ii), dotnirs.t(:), dotnirs.CondNames{ii});
		else
		obj.stim(ii) = StimClass(nirs.s(:,ii), nirs.t(:), num2str(ii));
		obj.stim(ii) = StimClass(dotnirs.s(:,ii), dotnirs.t(:), num2str(ii));
		end
		end
		obj.probe = ProbeClass(nirs.SD);
		for ii=1:size(nirs.aux,2)
		obj.aux(ii) = AuxClass(nirs.aux(:,ii), nirs.t(:), sprintf('aux%d',ii));
		obj.probe = ProbeClass(dotnirs.SD);
		for ii=1:size(dotnirs.aux,2)
		obj.aux(ii) = AuxClass(dotnirs.aux(:,ii), dotnirs.t(:), sprintf('aux%d',ii));
		end

		% Add metadatatags
		obj.metaDataTags = MetaDataTagsClass();

		end
		elseif nargin>1 && nargin<5
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% obj = SnirfClass(data, stim);
		% obj = SnirfClass(data, stim, probe);
		% obj = SnirfClass(data, stim, probe, aux);
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		elseif isa(varargin{1}, 'DataClass')

		% obj = SnirfClass(data, stim);
		data = varargin{1};
		obj.SetData(data);
		stim = varargin{2};
		obj.SetStim(stim);

		% obj = SnirfClass(data, stim, probe);
		if nargin>2
		probe = varargin{3};
		obj.SetSd(probe);
		end

		% obj = SnirfClass(data, stim, probe, aux);
		if nargin>3
		aux = varargin{4};
		obj.SetAux(aux);
		end

		% The basic 5 of a .nirs format as separate args
		elseif nargin==5
		obj.data(1) = DataClass(d, t(:), SD.MeasList);
		for ii=1:size(s,2)
		obj.stim(ii) = StimClass(s(:,ii), t(:), num2str(ii));
		end
		obj.probe = ProbeClass(SD);
		for ii=1:size(aux,2)
		obj.aux(ii) = AuxClass(aux, t(:), sprintf('aux%d',ii));
		end

		% Add metadatatags
		obj.metaDataTags = MetaDataTagsClass();
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Between 5 and 6 arguments covers the following syntax variants
		%
		% obj = SnirfClass(d, t, SD, aux, s);
		% obj = SnirfClass(d, t, SD, aux, s, CondNames);
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		elseif nargin>4

		% obj = SnirfClass(d, t, SD, aux, s);
		d = varargin{1};
		t = varargin{2}(:);
		SD = varargin{3};
		aux = varargin{4};
		s = varargin{5};
		CondNames = {};

		% obj = SnirfClass(d, t, SD, aux, s, CondNames);
		if nargin>5
		CondNames = varargin{6};
		end

		% The basic 5 of a .nirs format plus condition names
		elseif nargin==6
		obj.data(1) = DataClass(d, t(:), SD.MeasList);
		for ii=1:size(s,2)
		obj.stim(ii) = StimClass(s(:,ii), t(:), CondNames{ii});
		if nargin==5
		condition = num2str(ii);
		else
		condition = CondNames{ii};
		end
		obj.stim(ii) = StimClass(s(:,ii), t(:), condition);
		end
		obj.probe = ProbeClass(SD);
		for ii=1:size(aux,2)
		@@ -210,6 +265,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		options = '';
		end

		% 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.options, 'file')
		obj.LoadStim(obj.filename);
		end

		% Generate new instance of SnirfClass
		objnew = SnirfClass();

		@@ -364,7 +425,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass


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

		% Arg 1

DataTree/DataTreeClass.m

+72 −70

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