Development sk (#135) (5e0b668f) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/10-5-System_Mastoids_EGI129.csd

0 → 100644

+467 −0

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DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+6 −5

Original line number	Diff line number	Diff line
		@@ -10,7 +10,6 @@ classdef MetaDataTagsClass < FileLoadSaveClass
		function obj = MetaDataTagsClass(varargin)
		% Set class properties not part of the SNIRF format
		obj.SetFileFormat('hdf5');

		obj.tags.SubjectID = 'default';
		obj.tags.MeasurementDate = datestr(now,29);
		obj.tags.MeasurementTime = datestr(now,'hh:mm:ss');
		@@ -175,10 +174,12 @@ classdef MetaDataTagsClass < FileLoadSaveClass


		% ----------------------------------------------------------------------------------
		function Set(obj, name, val) %#ok<INUSL>
		eval(sprintf('obj.tags.%s = %s;', name, val));
		function Set(obj, name, value)
		if ~exist('name', 'var') \|\| ~exist('value', 'var')
		retrun
		end
		eval( sprintf('obj.tags.%s = ''%s'';', name, value) )
		end


		% ----------------------------------------------------------------------------------
		function SetLengthUnit(obj, unit)

DataTree/AcquiredData/Snirf/ProbeClass.m

+123 −20

Original line number	Diff line number	Diff line
		@@ -21,6 +21,7 @@ classdef ProbeClass < FileLoadSaveClass
		end



		methods

		% -------------------------------------------------------
		@@ -122,31 +123,118 @@ classdef ProbeClass < FileLoadSaveClass
		end
		end

		% -------------------------------------------------------------------------------
		function xy = convert_optodepos_to_circlular_2D_pos(obj, pos, T, norm_factor)
		pos = [pos ones(size(pos,1),1)];
		pos_unit_sphere = pos*T;
		pos_unit_sphere_norm = sqrt(sum(pos_unit_sphere.^2,2));
		pos_unit_sphere = pos_unit_sphere./pos_unit_sphere_norm ;

		[azimuth,elevation,r] = cart2sph(pos_unit_sphere(:,1),pos_unit_sphere(:,2),pos_unit_sphere(:,3));
		elevation = pi/2-elevation;
		[x,y] = pol2cart(azimuth,elevation); % get plane coordinates
		xy = [x y];
		xy = xy/norm_factor; % set maximum to unit length
		end


		% ----------------------------------------------
		function isValid = isValidLandmarkLabels(obj)
		isValid = 1;
		refpts_labels = {'T7','T8','Oz','Fpz','Cz','C3','C4','Pz','Fz'};
		for u = 1:length(refpts_labels)
		label = refpts_labels{u};
		idx = ismember(obj.landmarkLabels, label);
		if sum(idx) == 0
		isValid = 0;
		return
		end
		end
		end

		% -------------------------------------------------------
		function Project_3D_to_2D(obj)
		if isempty(obj.landmarkPos2D) \|\| isempty(obj.landmarkPos3D)

		% When 3D landmarks aren't available use crude default 3D-to-2D projection algorithm
		if isempty(obj.sourcePos2D)
		obj.sourcePos2D = project_3D_to_2D(obj.sourcePos3D);
		if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D)
		if isempty(obj.landmarkPos3D) \|\| ~obj.isValidLandmarkLabels()
		optodePos3D = [];
		nSource = 0;
		optodePos3D = [obj.sourcePos3D; obj.detectorPos3D];
		nSource = size(optodePos3D,1);

		optodePos2D = project_3D_to_2D(optodePos3D);
		if ~isempty(optodePos2D)
		if nSource ~= 0
		obj.sourcePos2D = optodePos2D(1:nSource,:);
		end
		if size(optodePos3D,1) > nSource
		obj.detectorPos2D = optodePos2D(nSource+1:end,:);
		end
		if isempty(obj.detectorPos2D)
		obj.detectorPos2D = project_3D_to_2D(obj.detectorPos3D);
		end

		else
		if ~isempty(obj.sourcePos3D) && ~isempty(obj.detectorPos3D)
		[sphere.label, sphere.theta, sphere.phi, sphere.r, sphere.xc, sphere.yc, sphere.zc] = textread('10-5-System_Mastoids_EGI129.csd','%s %f %f %f %f %f %f','commentstyle','c++');
		% ref pt labels used for affine transformation
		refpts_labels = {'T7','T8','Oz','Fpz','Cz','C3','C4','Pz','Fz'};

		% 3D landmarks are available, use ...
		% get positions for refpts_labels from both sphere and probe ref pts
		for u = 1:length(refpts_labels)
		label = refpts_labels{u};

		idx = ismember(obj.landmarkLabels, label);
		if isempty(idx)
		return
		end
		probe_refps_pos(u,:) = obj.landmarkPos3D(idx,:);
		idx = ismember(sphere.label, label);
		sphere_refpts_pos(u,:) = [sphere.xc(idx) sphere.yc(idx) sphere.zc(idx)];
		end

		% get affine transformation
		% probe_refps*T = sphere_refpts
		probe_refps_pos = [probe_refps_pos(:,1:3) ones(size(probe_refps_pos,1),1)];
		T = probe_refps_pos\sphere_refpts_pos;

		% tranform optode positions onto unit sphere.
		% opt_pos = probe.optpos_reg;
		% opt_pos = [opt_pos ones(size(opt_pos,1),1)];
		% sphere_opt_pos = opt_pos*T;
		% sphere_opt_pos_norm = sqrt(sum(sphere_opt_pos.^2,2));
		% sphere_opt_pos = sphere_opt_pos./sphere_opt_pos_norm ;
		%%
		% get 2D circular refpts for current selecetd reference point system
		probe_refpts_idx = ismember(sphere.label, obj.landmarkLabels);

		% refpts_2D.pos = [sphere_xc(probe_refpts_idx) sphere_yc(probe_refpts_idx) sphere_zc(probe_refpts_idx)];
		refpts_2D.label = sphere.label(probe_refpts_idx);
		%%
		refpts_theta = sphere.theta(probe_refpts_idx);
		refpts_phi = 90 - sphere.phi(probe_refpts_idx); % elevation angle from top axis

		refpts_theta = (2 * pi * refpts_theta) / 360; % convert to radians
		refpts_phi = (2 * pi * refpts_phi) / 360;
		[x,y] = pol2cart(refpts_theta, refpts_phi); % get plane coordinates
		xy = [x y];

		%%
		norm_factor = max(max(xy));
		xy = xy/norm_factor; % set maximum to unit length
		refpts_2D.pos = xy;
		obj.landmarkPos2D = refpts_2D.pos;

		%%

		obj.sourcePos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.sourcePos3D, T, norm_factor);
		obj.detectorPos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.detectorPos3D, T, norm_factor);
		end
		end
		end
		end



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

		% Arg 1
		@@ -161,6 +249,19 @@ classdef ProbeClass < FileLoadSaveClass
		location = ['/',location];
		end

		% Arg3
		scaling = 1;
		if exist('LengthUnit','var')
		if strcmpi(LengthUnit,'m')
		scaling = 1000;
		elseif strcmpi(LengthUnit,'cm')
		scaling = 10;
		end
		end




		% Error checking
		if ~isempty(fileobj) && ischar(fileobj)
		obj.SetFilename(fileobj);
		@@ -179,12 +280,12 @@ classdef ProbeClass < FileLoadSaveClass
		% Load datasets
		obj.wavelengths = HDF5_DatasetLoad(gid, 'wavelengths');
		obj.wavelengthsEmission = HDF5_DatasetLoad(gid, 'wavelengthsEmission');
		obj.sourcePos2D = HDF5_DatasetLoad(gid, 'sourcePos2D', [], '2D');
		obj.detectorPos2D = HDF5_DatasetLoad(gid, 'detectorPos2D', [], '2D');
		obj.landmarkPos2D = HDF5_DatasetLoad(gid, 'landmarkPos2D', [], '2D');
		obj.sourcePos3D = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '3D');
		obj.detectorPos3D = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '3D');
		obj.landmarkPos3D = HDF5_DatasetLoad(gid, 'landmarkPos3D', [], '2D');
		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.frequencies = HDF5_DatasetLoad(gid, 'frequencies');
		obj.timeDelays = HDF5_DatasetLoad(gid, 'timeDelays');
		obj.timeDelayWidths = HDF5_DatasetLoad(gid, 'timeDelayWidths');
		@@ -248,6 +349,7 @@ classdef ProbeClass < FileLoadSaveClass
		fid = H5F.create(fileobj, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');
		H5F.close(fid);
		end

		hdf5write_safe(fileobj, [location, '/wavelengths'], obj.wavelengths, 'array');
		hdf5write_safe(fileobj, [location, '/wavelengthsEmission'], obj.wavelengthsEmission, 'array');
		hdf5write_safe(fileobj, [location, '/sourcePos2D'], obj.sourcePos2D, 'array');
		@@ -269,6 +371,7 @@ classdef ProbeClass < FileLoadSaveClass




		% ---------------------------------------------------------
		function wls = GetWls(obj)
		wls = obj.wavelengths;

DataTree/AcquiredData/Snirf/SnirfClass.m

+4 −1

Original line number	Diff line number	Diff line
		@@ -479,8 +479,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% -------------------------------------------------------
		function err = LoadProbe(obj, fileobj, ~)
		% get lenth unit through class method
		LengthUnit = obj.metaDataTags.Get('LengthUnit');
		obj.probe = ProbeClass();
		err = obj.probe.LoadHdf5(fileobj, [obj.location, '/probe']);
		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)

MainGUI/MainGUI.m

+25 −0

Original line number	Diff line number	Diff line
		@@ -822,6 +822,31 @@ function menuItemPlotProbeGUI_Callback(hObject, ~, handles)
		global maingui
		LaunchChildGuiFromMenu('PlotProbeGUI', hObject, GetDatatype(handles), maingui.condition);

		% --------------------------------------------------------------------
		% function menuItemPlotProbe2_Callback(hObject, ~, handles)
		% global maingui

		%%%% It will be in the next release
		% procElem = maingui.dataTree.currElem;
		% % Derived data that we want to save in a Snirf file.
		% % To save in a snirf file we need to create a SnirfClass
		% % object. A SnirfClass object is DataTree's implementation
		% % of the Snirf format.
		% data(1) = procElem.procStream.output.dcAvg;
		% data(2) = procElem.procStream.output.dod;
		%
		% % To complete SnirfClass object arguments we need to supply these
		% % which we get from acquired data of the first run associated with
		% % our procElem.
		% probe = procElem.acquired.probe;
		% stim = procElem.acquired.stim;
		% metaDataTags = procElem.acquired.metaDataTags;
		%
		% obj = SnirfClass(data, stim, probe, metaDataTags);
		%
		% % call PlotProbe2 GUI
		% PlotProbe2(obj);



		% -------------------------------------------------------------------

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