Fix tCCA issues related to new BIDS format support (#130) (14305eef) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+12 −2

Original line number	Diff line number	Diff line
		@@ -190,6 +190,13 @@ classdef DataFilesClass < handle
		['nirs/*.', obj.filetype];
		}

		%%%% 10. BIDS-like folder structure without nirs sub-folder
		{
		'sub-*';
		'ses-*';
		['*.', obj.filetype];
		}

		};
		end

		@@ -470,6 +477,9 @@ classdef DataFilesClass < handle
		if o.GetError() < 0
		obj.logger.Write('DataFilesClass.ErrorCheck: FAILED error check - %s will not be added to data set\n', filename);
		errorIdxs = [errorIdxs, ii]; %#ok<AGROW>
		elseif contains(o.GetErrorMsg(), 'WARNING: ''data'' corrupt and unusable')
		obj.logger.Write('DataFilesClass.ErrorCheck: WARNING data is unusable - %s will not be added to data set\n', filename);
		errorIdxs = [errorIdxs, ii]; %#ok<AGROW>
		else
		dataflag = true;
		end

DataTree/AcquiredData/DataFiles/FileClass.m

+556 −556

Original line number	Diff line number	Diff line
		@@ -194,8 +194,8 @@ classdef FileClass < matlab.mixin.Copyable
		% R2.ext ==> [G1, sub_R2, ses_sub_R2, R2]
		% R3.ext ==> [G1, sub_R3, ses_sub_R3, R3]
		if obj.IsFile && length(parts)==1 && length(subparts)==1
		subjName = ['sub_', fname];
		sessName = ['ses_', subjName];
		subjName = ['sub-', fname];
		sessName = ['ses-', subjName];
		runName = obj.name;
		end

		@@ -212,7 +212,7 @@ classdef FileClass < matlab.mixin.Copyable
		% S3_R3.ext ==> [G1, S2, ses_S2_R3, R3]
		if obj.IsFile && length(parts)==1 && length(subparts)==2
		subjName = subparts{1};
		sessName = ['ses_', subjName, '_', fname];
		sessName = ['ses-', subjName, '_', subjName];
		runName = obj.name;
		end

		@@ -261,7 +261,7 @@ classdef FileClass < matlab.mixin.Copyable
		subjName = obj.name;
		elseif obj.IsFile && length(parts)==2
		subjName = parts{1};
		sessName = [subjName, '/ses-', fname];
		sessName = [subjName, '/ses-', subjName];
		runName = obj.name;
		end

DataTree/AcquiredData/Nirs/NirsClass.m

+454 −80

Original line number	Diff line number	Diff line
		@@ -23,6 +23,8 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		% obj = NirsClass()
		% obj = NirsClass(filename);
		% obj = NirsClass(filename, dataStorageScheme);
		% obj = NirsClass(SD);
		% obj = NirsClass(SD, dataStorageScheme);
		%
		%
		% Example 1:
		@@ -57,14 +59,29 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		if nargin==0
		return;
		end
		if nargin==2
		obj.SetDataStorageScheme(varargin{2});
		end

		% Else we have at least 1 input arg
		if isa(varargin{1}, 'NirsClass')
		obj.Copy(varargin{1});
		return;
		elseif isstruct(varargin{1})
		if isfield(varargin{1}, 'd') && isfield(varargin{1}, 'SD')
		obj.CopyStruct(varargin{1})
		elseif isfield(varargin{1}, 'DetPos') && isfield(varargin{1}, 'SrcPos')
		obj.CopyProbe(varargin{1})
		end
		elseif isa(varargin{1}, 'SnirfClass')
		obj.ConvertSnirf(varargin{1});
		end

		if ~ischar(varargin{1}) && nargin==1
		obj.ErrorCheck();
		return
		end

		if nargin==2
		obj.SetDataStorageScheme(varargin{2});
		end

		filename = varargin{1};
		if ~exist('filename','var') \|\| ~exist(filename,'file')
		obj = NirsClass.empty();
		@@ -76,6 +93,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		if strcmpi(obj.GetDataStorageScheme(), 'memory')
		obj.Load(filename);
		end
		obj.ErrorCheck();
		end


		@@ -83,7 +101,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		function Initialize(obj)
		Initialize@AcqDataClass(obj);

		obj.SD = struct([]);
		obj.SD = obj.InitProbe();
		obj.t = [];
		obj.s = [];
		obj.d = [];
		@@ -99,6 +117,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		'''SD'' is invalid.'
		'''aux'' is invalid.'
		'''s'' is invalid.'
		'WARNING: ''data'' corrupt and unusable'
		'error unknown.'
		};

		@@ -162,7 +181,6 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		catch



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

		@@ -186,8 +204,9 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		% ---------------------------------------------------------
		function err = LoadTime(obj, fdata, err)
		if nargin == 1
		fdata.t = load(obj.GetFilename(),'-mat', 't');
		fdata = load(obj.GetFilename(),'-mat', 't');
		err = 0;
		return
		elseif nargin == 2
		err = 0;
		end
		@@ -211,7 +230,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		% ---------------------------------------------------------
		function err = LoadProbeMeasList(obj, fdata, err)
		if isproperty(fdata,'SD')
		obj.SetSD(fdata.SD);
		obj.CopyProbe(fdata.SD);
		if isempty(obj.SD) && err == 0
		err = -4;
		end
		@@ -285,21 +304,136 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


		% ---------------------------------------------------------
		function SaveMat(obj, fname, ~)
		function SaveMat(obj, fname, options)
		if ~exist('fname','var') \|\| isempty(fname)
		fname = '';
		end
		if ~exist('options','var') \|\| isempty(options)
		options = 'normal';
		end
		if isempty(fname)
		fname = obj.GetFilename();
		end

		SD = obj.SD; %#ok<NASGU,PROPLC>
		s = obj.s;
		CondNames = obj.CondNames;
		[str, fields] = obj.Properties2String();
		for ii = 1:length(fields)
		eval( sprintf('%s = obj.%s;', fields{ii}, fields{ii}) );
		end

		if ~ispathvalid(fname)
		p = fileparts(fname);
		if ~isempty(p) && ~ispathvalid(p, 'dir')
		mkdir(p);
		end
		eval( sprintf('save(fname, ''-mat'', %s)', str) );
		elseif optionExists(options, 'normal')
		save(fname, '-mat', '-append', 'SD','s','CondNames');
		elseif optionExists(options, 'overwrite')
		eval( sprintf('save(fname, ''-mat'', %s)', str) );
		end
		end



		% -------------------------------------------------------
		function b = ProbeEqual(obj, obj2)
		b = false;

		fields{1} = propnames(obj.SD);
		fields{2} = propnames(obj2.SD);

		fieldsToExclude = { ...
		'MeasListAct'; ...
		'SrcMap'; ...
		};

		for kk = 1:length(fields)
		for jj = 1:length(fields{kk})
		field = fields{kk}{jj};

		% Skip excluded fields
		if ~isempty(find(strcmp(fieldsToExclude, field))) %#ok<EFIND>
		continue;
		end

		% Now compare field
		if ~isfield(obj.SD,field) \|\| ~isfield(obj2.SD,field)
		return;
		end
		if eval( sprintf('~strcmp(class(obj.SD.%s), class(obj2.SD.%s))', field, field) )
		return;
		end
		if eval( sprintf('length(obj.SD.%s) ~= length(obj2.SD.%s)', field, field) )
		return;
		end
		EPS = 1.0e-10; %#ok<NASGU>
		if eval( sprintf('iscell(obj.SD.%s)', field) )
		N = eval( sprintf('length(obj.SD.%s(:))', field) );
		for ii = 1:N
		if eval( sprintf('length(obj.SD.%s{ii}(:)) ~= length(obj2.SD.%s{ii}(:))', field, field) )
		return;
		end
		if eval( sprintf('~all(obj.SD.%s{ii}(:) == obj2.SD.%s{ii}(:))', field, field) )
		return;
		end
		end
		elseif eval( sprintf('isstruct(obj.SD.%s)', field) )
		if eval( sprintf('~isempty(comp_struct(obj.SD.%s, obj2.SD.%s))', field, field) )
		return;
		end
		else
		if eval( sprintf('~all( (obj.SD.%s(:) - obj2.SD.%s(:)) < EPS )', field, field) )
		return;
		end
		end
		end
		end
		b = true;
		end



		% -------------------------------------------------------
		function B = eq(obj, obj2)
		B = false;

		if length(obj.t) ~= length(obj2.t)
		return;
		end
		if ~all(obj.t == obj2.t)
		return;
		end

		if length(obj.d) ~= length(obj2.d)
		return;
		end
		if ~all(obj.d(:) == obj2.d(:))
		return;
		end

		if ~obj.ProbeEqual(obj2)
		return;
		end

		if length(obj.s) ~= length(obj2.s)
		return;
		end
		if ~all(obj.s(:) == obj2.s(:))
		return;
		end

		if length(obj.aux) ~= length(obj2.aux)
		return;
		end
		if ~all(obj.aux(:) == obj2.aux(:))
		return;
		end

		B = true;
		end



		% ---------------------------------------------------------
		function err = Copy(obj, obj2)
		err=0;
		@@ -444,11 +578,6 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		val = obj.t;
		end

		% ---------------------------------------------------------
		function SetSD(obj, val)
		obj.SD = val;
		end

		% ---------------------------------------------------------
		function val = GetSD(obj)
		val = obj.SD;
		@@ -470,9 +599,24 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end

		% ---------------------------------------------------------
		function val = GetAux(obj)
		function val = GetAux(obj, options)
		if ~exist('options','var')
		options = 'struct';
		end
		if optionExists(options, 'matrix')
		val = obj.aux;
		else
		structtype = struct('name','', 'dataTimeSeries',[]);
		val = struct(structtype([]));
		for ii = 1:size(obj.aux,2)
		val(ii).name = num2str(ii);
		val(ii).time = obj.t;
		val(ii).dataTimeSeries = obj.aux(:,ii);
		end
		end
		end



		% ---------------------------------------------------------
		function SetCondNames(obj, val)
		@@ -509,12 +653,6 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end


		% ---------------------------------------------------------
		function SetSDG(obj, SD)
		obj.SD = SD;
		end


		% ---------------------------------------------------------
		function ml = GetMeasList(obj, iBlk)
		ml = obj.SD.MeasList;
		@@ -629,6 +767,10 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass

		% ----------------------------------------------------------------------------------
		function SD = Get_SD(obj)
		SD = [];
		if ~obj.IsProbeValid()
		return;
		end
		SD = obj.SD;
		end

		@@ -799,6 +941,238 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		nbytes = nbytes + sizeof(obj.CondNames);
		end



		% ----------------------------------------------------------------------------------
		function landmarks = InitLandmarks(obj)
		landmarks = struct('pos',[], 'labels',{{}});
		end


		% ----------------------------------------------------------------------------------
		function SD = InitProbe(obj)
		SD = struct(...
		'Lambda',[], ...
		'SrcPos',[], ...
		'DetPos',[], ...
		'DummyPos',[], ...
		'SrcPos3D',[], ...
		'DetPos3D',[], ...
		'DummyPos3D',[], ...
		'SrcGrommetType',{{}}, ...
		'DetGrommetType',{{}}, ...
		'DummyGrommetType',{{}}, ...
		'SrcGrommetRot',[], ...
		'DetGrommetRot',[], ...
		'DummyGrommetRot',[], ...
		'nDummys',0, ...
		'Landmarks',obj.InitLandmarks(), ...
		'Landmarks2D',obj.InitLandmarks(), ...
		'Landmarks3D',obj.InitLandmarks(), ...
		'MeasList',[], ...
		'MeasListAct',[], ...
		'SpringList',[], ...
		'AnchorList',[], ...
		'SrcMap',[], ...
		'SpatialUnit','', ...
		'xmin',0, ...
		'xmax',0, ...
		'ymin',0, ...
		'ymax',0, ...
		'auxChannels',[] ...
		);
		end



		% ----------------------------------------------------------------------------------
		function b = IsProbeValid(obj)
		b = false;
		if ~isfield(obj.SD, 'SrcPos')
		return;
		end
		if ~isfield(obj.SD, 'DetPos')
		return;
		end
		if ~isfield(obj.SD, 'MeasList')
		return;
		end
		if ~isfield(obj.SD, 'Lambda')
		return;
		end
		if isempty(obj.SD.SrcPos)
		return;
		end
		if isempty(obj.SD.DetPos)
		return;
		end
		if isempty(obj.SD.MeasList)
		return;
		end
		if isempty(obj.SD.Lambda)
		return;
		end
		b = true;
		end



		% ----------------------------------------------------------------------------------
		function b = IsValid(obj)
		b = ~obj.IsEmpty();
		end



		% ----------------------------------------------------------------------------------
		function b = CopyProbe(obj, SD)
		fields = propnames(obj.SD);
		for ii = 1:length(fields)
		if eval( sprintf('isfield(SD, ''%s'')', fields{ii}) )
		eval( sprintf('obj.SD.%s = SD.%s;', fields{ii}, fields{ii}) );
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function b = CopyStruct(obj, s)
		fields = propnames(obj);
		for ii = 1:length(fields)
		if eval( sprintf('isfield(s, ''%s'')', fields{ii}) )
		if strcmp(fields{ii}, 'SD')
		obj.CopyProbe(s.SD);
		else
		eval( sprintf('obj.%s = s.%s;', fields{ii}, fields{ii}) );
		end
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function ConvertSnirfProbe(obj, snirf)
		obj.SD.Lambda = snirf.probe.wavelengths;
		obj.SD.SrcPos = snirf.probe.sourcePos2D;
		obj.SD.DetPos = snirf.probe.detectorPos2D;
		obj.SD.SrcPos3D = snirf.probe.sourcePos3D;
		obj.SD.DetPos3D = snirf.probe.detectorPos3D;
		obj.SD.MeasList = snirf.GetMeasList();
		obj.SD.SpatialUnit = snirf.GetLengthUnit();
		obj.SD.Landmarks.pos = snirf.probe.landmarkPos2D;
		obj.SD.Landmarks2D.pos = snirf.probe.landmarkPos2D;
		obj.SD.Landmarks3D.pos = snirf.probe.landmarkPos3D;
		obj.SD.Landmarks.labels = snirf.probe.landmarkLabels;
		obj.SD.Landmarks2D.labels = snirf.probe.landmarkLabels;
		obj.SD.Landmarks3D.labels = snirf.probe.landmarkLabels;
		end


		% ----------------------------------------------------------------------------------
		function ConvertSnirfData(obj, snirf)
		obj.d = snirf.data(1).dataTimeSeries;
		obj.t = snirf.data(1).time;
		end


		% ----------------------------------------------------------------------------------
		function ConvertSnirfStim(obj, snirf)
		obj.s = zeros(length(obj.t), length(snirf.stim));
		for ii = 1:length(snirf.stim)
		k = round(nearest_point(obj.t, snirf.stim(ii).data(:,1)));
		for jj = 1:length(k)
		if k(jj) == 0
		k(jj) = 1;
		end
		if k(jj) > length(obj.t)
		k(jj) = length(obj.t);
		end
		obj.s(k(jj),ii) = 1;
		end
		obj.CondNames{ii} = snirf.stim(ii).name;
		end
		end


		% ----------------------------------------------------------------------------------
		function ConvertSnirfAux(obj, snirf)
		obj.aux = zeros(length(obj.t), length(snirf.aux));
		for ii = 1:length(snirf.aux)
		obj.aux(:,ii) = snirf.aux(ii).dataTimeSeries;
		end
		end


		% ----------------------------------------------------------------------------------
		function ConvertSnirf(obj, snirf)
		obj.ConvertSnirfProbe(snirf);
		obj.d = snirf.data(1).dataTimeSeries;
		obj.t = snirf.data(1).time;
		obj.ConvertSnirfStim(snirf);
		obj.ConvertSnirfAux(snirf);
		end



		% ----------------------------------------------------------------------------------
		function ErrorCheck(obj)
		if isempty(obj)
		return
		end
		if isempty(obj.SD.SrcGrommetType)
		for ii = 1:size(obj.SD.SrcPos,1)
		obj.SD.SrcGrommetType{ii} = 'none';
		end
		end

		if isempty(obj.SD.DetGrommetType)
		for ii = 1:size(obj.SD.DetPos,1)
		obj.SD.DetGrommetType{ii} = 'none';
		end
		end

		if isempty(obj.SD.DummyGrommetType)
		for ii = 1:size(obj.SD.DummyPos,1)
		obj.SD.DummyGrommetType{ii} = 'none';
		end
		end

		if isempty(obj.SD.SrcGrommetRot)
		for ii = 1:size(obj.SD.SrcPos,1)
		obj.SD.SrcGrommetRot(ii) = 0;
		end
		end

		if isempty(obj.SD.DetGrommetRot)
		for ii = 1:size(obj.SD.DetPos,1)
		obj.SD.DetGrommetRot(ii) = 0;
		end
		end

		if isempty(obj.SD.DummyGrommetRot)
		for ii = 1:size(obj.SD.DummyPos,1)
		obj.SD.DummyGrommetRot(ii) = 0;
		end
		end

		end


		% ----------------------------------------------------------------
		function [str, fields] = Properties2String(obj)
		str = '';
		fields = propnames(obj);
		for ii = 1:length(fields)
		if isempty(str)
		str = sprintf('''%s''', fields{ii});
		else
		str = sprintf('%s, ''%s''', str, fields{ii});
		end
		end
		end


		end

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

DataTree/AcquiredData/Snirf/DataClass.m

+50 −11

Original line number	Diff line number	Diff line
		@@ -52,12 +52,18 @@ classdef DataClass < FileLoadSaveClass
		elseif nargin==1
		if isa(varargin{1}, 'DataClass')
		obj.Copy(varargin{1});
		elseif isa(varargin{1}, 'NirsClass')
		elseif NirsClass(varargin{1}).IsValid()
		obj.dataTimeSeries = varargin{1}.d;
		obj.time = varargin{1}.t;
		for ii = 1:size(varargin{1}.ml,1)
		obj.measurementList(end+1) = MeasListClass(varargin{1}.ml(ii,:));
		end
		elseif NirsClass(varargin{1}).IsProbeValid()
		obj.dataTimeSeries = zeros(2, size(varargin{1}.MeasList,1));
		obj.time = zeros(2,1);
		for ii = 1:size(varargin{1}.MeasList,1)
		obj.measurementList(end+1) = MeasListClass(varargin{1}.MeasList(ii,:));
		end
		elseif isa(varargin{1}, 'char')
		obj.SetFilename(varargin{1});
		obj.Load();
		@@ -130,6 +136,12 @@ classdef DataClass < FileLoadSaveClass
		try
		% Open group
		[gid, fid] = HDF5_GroupOpen(fileobj, location);
		if isstruct(gid)
		if gid.double < 0
		err = -1;
		return
		end
		end

		obj.dataTimeSeries = HDF5_DatasetLoad(gid, 'dataTimeSeries');
		obj.time = HDF5_DatasetLoad(gid, 'time');
		@@ -237,16 +249,35 @@ classdef DataClass < FileLoadSaveClass

		% -------------------------------------------------------
		function b = IsEmpty(obj)
		b = false;
		if isempty(obj)
		b = true;
		if isempty(obj)
		return;
		end
		if isempty(obj.dataTimeSeries) \|\| isempty(obj.time) \|\| isempty(obj.measurementList)
		b = true;
		return;
		end
		if isempty(obj.measurementList)
		return;
		end
		b = false;
		end


		% -------------------------------------------------------
		function b = IsDataValid(obj, iMeas)
		b = false;
		if ~exist('iMeas','var')
		iMeas = 1:length(obj.measurementList);
		end
		if all(isnan(obj.dataTimeSeries(:)))
		return;
		end
		for ii = iMeas
		if any(isnan(obj.dataTimeSeries(:, iMeas)))
		return;
		end
		end
		b = true;
		end


		@@ -257,18 +288,26 @@ classdef DataClass < FileLoadSaveClass
		end
		if ismember('dataTimeSeries',params)
		if obj.IsEmpty()
		err = -1;
		err = -2;
		return;
		end
		if size(obj.dataTimeSeries,1) ~= length(obj.time)
		err = -1;
		err = -3;
		end
		if size(obj.dataTimeSeries,2) ~= length(obj.measurementList)
		err = -1;
		err = -4;
		end
		if all(obj.dataTimeSeries==0)
		err = 5;
		end
		end
		if ismember('time',params)
		if isempty(obj.time)
		err = -1;
		err = -6;
		return;
		end
		if all(obj.time==0)
		err = 7;
		end
		end
		end

DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+25 −13

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