Merge v1.72.0: Fix for ar_glm_final.m stepwise error in GLM and fix for... (448762b7) · Commits · github_fork / Homer3

DataTree/AcquiredData/Nirs/NirsClass.m

+115 −3

Original line number	Diff line number	Diff line
		@@ -388,7 +388,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		return;
		end
		else
		if eval( sprintf('~all( (obj.SD.%s(:) - obj2.SD.%s(:)) < EPS )', field, field) )
		if eval( sprintf('~all( abs(obj.SD.%s(:) - obj2.SD.%s(:)) < EPS )', field, field) )
		return;
		end
		end
		@@ -1033,6 +1033,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end



		% ----------------------------------------------------------------------------------
		function SD = InitProbe(obj)
		SD = struct(...
		@@ -1049,7 +1050,6 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		'SrcGrommetRot',[], ...
		'DetGrommetRot',[], ...
		'DummyGrommetRot',[], ...
		'nDummys',0, ...
		'Landmarks',obj.InitLandmarks(), ...
		'Landmarks2D',obj.InitLandmarks(), ...
		'Landmarks3D',obj.InitLandmarks(), ...
		@@ -1069,6 +1069,59 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass



		% ----------------------------------------------------------------------------------
		function SetProbeSpatialUnit(obj, spatialUnitNew)
		scaling = 1;
		if strcmpi(spatialUnitNew,'mm')
		if strcmpi(obj.SD.SpatialUnit,'cm')
		scaling = 10;
		end
		elseif strcmpi(spatialUnitNew,'cm')
		if strcmpi(obj.SD.SpatialUnit,'mm')
		scaling = 1/10;
		end
		else
		spatialUnitNew = '';
		end
		obj.SD.SpatialUnit = spatialUnitNew;
		obj.SD.SrcPos = obj.SD.SrcPos * scaling;
		obj.SD.DetPos = obj.SD.DetPos * scaling;
		obj.SD.DummyPos = obj.SD.DummyPos * scaling;
		if size(obj.SD.SpringList,2)==3
		lst = find(obj.SD.SpringList(:,3)~=-1);
		obj.SD.SpringList(lst,3) = obj.SD.SpringList(lst,3) * scaling;
		end
		obj.SD.Landmarks.pos = obj.SD.Landmarks.pos * scaling;
		obj.SD.Landmarks3D.pos = obj.SD.Landmarks3D.pos * scaling;
		obj.SD.Landmarks2D.pos = obj.SD.Landmarks2D.pos * scaling;
		end



		% ----------------------------------------------------------------------------------
		function FixProbeSpatialUnit(obj)
		if isempty(obj.SD.SpatialUnit)
		q = MenuBox('Spatial units not provided in probe data. Please specify spatial units of the optode coordinates?', ...
		{'mm','cm',sprintf('do not know')});
		if q==1
		obj.SD.SpatialUnit = 'mm';
		elseif q==2
		obj.SD.SpatialUnit = 'cm';
		elseif q==3
		obj.SD.SpatialUnit = '';
		end
		end
		if ~strcmpi(obj.SD.SpatialUnit,'mm')
		q = MenuBox(sprintf('This probe uses ''%s'' units for probe coordinates. We recommend converting to ''mm'' units, to be consistent with Homer. Do you want to convert probe coordinates from %s to mm?', ...
		obj.SD.SpatialUnit), {'YES','NO'}, 'upperleft');
		if q==1
		obj.SetProbeSpatialUnit('mm')
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function b = IsProbeValid(obj)
		b = false;
		@@ -1113,11 +1166,70 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		fields = propnames(obj.SD);
		for ii = 1:length(fields)
		if eval( sprintf('isfield(SD, ''%s'')', fields{ii}) )
		if eval( sprintf('strcmp(class(obj.SD.%s), class(SD.%s))', fields{ii}, fields{ii}) )
		eval( sprintf('obj.SD.%s = SD.%s;', fields{ii}, fields{ii}) );
		elseif eval( sprintf('isnumeric(obj.SD.%s) && iscell(SD.%s)', fields{ii}, fields{ii}) )
		if eval( sprintf('~isempty(SD.%s)', fields{ii}) )
		eval( sprintf('obj.SD.%s = cell2array(SD.%s);', fields{ii}, fields{ii}) );
		end
		elseif eval( sprintf('isscalar(obj.SD.%s) && isscalar(SD.%s)', fields{ii}, fields{ii}) )
		eval( sprintf('obj.SD.%s = SD.%s;', fields{ii}, fields{ii}) );
		end
		end
		end

		% Fill in any fields that don't conform to standard SD data structure

		% SrcGrommetType
		d1 = size(obj.SD.SrcPos,1) - length(obj.SD.SrcGrommetType);
		if d1 > 0
		obj.SD.SrcGrommetType(end+1:end+d1) = repmat({'none'}, d1, 1);
		end

		% SrcGrommetRot
		d2 = size(obj.SD.SrcPos,1) - length(obj.SD.SrcGrommetRot);
		if d2 > 0
		obj.SD.SrcGrommetRot(end+1:end+d2) = zeros(d2,1);
		end

		% DetGrommetType
		d1 = size(obj.SD.DetPos,1) - length(obj.SD.DetGrommetType);
		if d1 > 0
		obj.SD.DetGrommetType(end+1:end+d1) = repmat({'none'}, d1, 1);
		end

		% DetGrommetRot
		d2 = size(obj.SD.DetPos,1) - length(obj.SD.DetGrommetRot);
		if d2 > 0
		obj.SD.DetGrommetRot(end+1:end+d2) = zeros(d2,1);
		end

		% DummyGrommetType
		d1 = size(obj.SD.DummyPos,1) - length(obj.SD.DummyGrommetType);
		if d1 > 0
		obj.SD.DummyGrommetType(end+1:end+d1) = repmat({'none'}, d1, 1);
		end

		% DummyGrommetRot
		d2 = size(obj.SD.DummyPos,1) - length(obj.SD.DummyGrommetRot);
		if d2 > 0
		obj.SD.DummyGrommetRot(end+1:end+d2) = zeros(d2,1);
		end

		% MesListAct
		if size(obj.SD.MeasListAct,1) < size(obj.SD.MeasList,1)
		d = size(obj.SD.MeasListAct,1) - size(obj.SD.MeasList,1);
		if d < 0
		obj.SD.MeasListAct(end+1:end+abs(d)) = ones(abs(d),1);
		elseif d>1
		obj.SD.MeasListAct(end-d:end) = [];
		end
		end

		end




		% -------------------------------------------------------
		function CopyStim(obj, obj2)
		@@ -1127,7 +1239,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


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

DataTree/AcquiredData/Snirf/DataClass.m

+3 −0

Original line number	Diff line number	Diff line
		@@ -771,6 +771,9 @@ classdef DataClass < FileLoadSaveClass
		ml = obj.measurementList;
		ml(order) = ml;
		end
		if contains(options, 'reshape')
		ml = measurementListSDpairs;
		end

		obj.SimulateErrors(d);
		end

DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+5 −5

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ classdef MetaDataTagsClass < FileLoadSaveClass
		obj.tags.LengthUnit = 'mm';
		obj.tags.TimeUnit = 'unknown';
		obj.tags.FrequencyUnit = 'unknown';
		obj.tags.AppName = 'snirf-homer3';
		obj.tags.AppName = 'homer3-DataTree';

		if nargin==1 && ~isempty(varargin{1})
		obj.SetFilename(varargin{1});

DataTree/AcquiredData/Snirf/ProbeClass.m

+28 −14

Original line number	Diff line number	Diff line
		@@ -20,6 +20,10 @@ classdef ProbeClass < FileLoadSaveClass
		landmarkLabels
		end

		properties (Access = private)
		scaling
		end



		methods
		@@ -28,11 +32,13 @@ classdef ProbeClass < FileLoadSaveClass
		function obj = ProbeClass(varargin)
		% Set class properties not part of the SNIRF format
		obj.SetFileFormat('hdf5');
		obj.scaling = 1;

		% Set SNIRF fomat properties
		if nargin>0
		if isstruct(varargin{1})
		SD = varargin{1};
		n = NirsClass(varargin{1});
		SD = n.SD;
		obj.wavelengths = SD.Lambda;
		obj.wavelengthsEmission = [];
		if isfield(SD,'SrcPos2D') & ~isempty(SD.SrcPos2D)
		@@ -250,18 +256,16 @@ classdef ProbeClass < FileLoadSaveClass
		end

		% Arg3
		scaling = 1;
		if exist('LengthUnit','var')
		if strcmpi(LengthUnit,'m')
		scaling = 1000;
		elseif strcmpi(LengthUnit,'cm')
		scaling = 10;
		% Figure out the scaling factor to multiple by to get the coorinates to be in mm units
		if strcmpi(LengthUnit,'m') % meter units
		obj.scaling = 100;
		elseif strcmpi(LengthUnit,'cm') % centimeter units
		obj.scaling = 10;
		end
		end




		% Error checking
		if ~isempty(fileobj) && ischar(fileobj)
		obj.SetFilename(fileobj);
		@@ -280,12 +284,12 @@ classdef ProbeClass < FileLoadSaveClass
		% Load datasets
		obj.wavelengths = HDF5_DatasetLoad(gid, 'wavelengths');
		obj.wavelengthsEmission = HDF5_DatasetLoad(gid, 'wavelengthsEmission');
		obj.sourcePos2D = HDF5_DatasetLoad(gid, 'sourcePos2D', [], '2D')*scaling;
		obj.detectorPos2D = HDF5_DatasetLoad(gid, 'detectorPos2D', [], '2D')*scaling;
		obj.landmarkPos2D = HDF5_DatasetLoad(gid, 'landmarkPos2D', [], '2D')*scaling;
		obj.sourcePos3D = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '3D')*scaling;
		obj.detectorPos3D = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '3D')*scaling;
		obj.landmarkPos3D = HDF5_DatasetLoad(gid, 'landmarkPos3D', [], '2D')*scaling;
		obj.sourcePos2D = HDF5_DatasetLoad(gid, 'sourcePos2D', [], '2D') * obj.scaling;
		obj.detectorPos2D = HDF5_DatasetLoad(gid, 'detectorPos2D', [], '2D') * obj.scaling;
		obj.landmarkPos2D = HDF5_DatasetLoad(gid, 'landmarkPos2D', [], '2D') * obj.scaling;
		obj.sourcePos3D = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '3D') * obj.scaling;
		obj.detectorPos3D = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '3D') * obj.scaling;
		obj.landmarkPos3D = HDF5_DatasetLoad(gid, 'landmarkPos3D', [], '2D') * obj.scaling;
		obj.frequencies = HDF5_DatasetLoad(gid, 'frequencies');
		obj.timeDelays = HDF5_DatasetLoad(gid, 'timeDelays');
		obj.timeDelayWidths = HDF5_DatasetLoad(gid, 'timeDelayWidths');
		@@ -350,6 +354,16 @@ classdef ProbeClass < FileLoadSaveClass
		H5F.close(fid);
		end

		% Multiple all coordinates by reciprocal of scaling factor when saving to get the
		% coordinates back to original.
		obj.sourcePos2D = obj.sourcePos2D / obj.scaling;
		obj.detectorPos2D = obj.detectorPos2D / obj.scaling;
		obj.landmarkPos2D = obj.landmarkPos2D / obj.scaling;
		obj.sourcePos3D = obj.sourcePos3D / obj.scaling;
		obj.detectorPos3D = obj.detectorPos3D / obj.scaling;
		obj.landmarkPos3D = obj.landmarkPos3D / obj.scaling;

		% Now save
		hdf5write_safe(fileobj, [location, '/wavelengths'], obj.wavelengths, 'array');
		hdf5write_safe(fileobj, [location, '/wavelengthsEmission'], obj.wavelengthsEmission, 'array');
		hdf5write_safe(fileobj, [location, '/sourcePos2D'], obj.sourcePos2D, 'array');

DataTree/AcquiredData/Snirf/SnirfClass.m

+0 −1

Original line number	Diff line number	Diff line
		@@ -516,7 +516,6 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		LengthUnit = obj.metaDataTags.Get('LengthUnit');
		obj.probe = ProbeClass();
		err = obj.probe.LoadHdf5(fileobj, [obj.location, '/probe'], LengthUnit);
		obj.metaDataTags.Set('LengthUnit','mm');

		% This is a required field. If it's empty means the whole snirf object is bad
		if isempty(obj.probe)

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