Update 3D to 2D projection (77e61b92) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/ProbeClass.m

+102 −12

Original line number	Diff line number	Diff line
		@@ -122,25 +122,115 @@ 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
		xy = xy/2 + 0.5;
		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)
		if ~isempty(obj.sourcePos3D)
		obj.sourcePos2D = obj.sourcePos3D(:,1:2);
		end
		if isempty(obj.detectorPos2D)
		obj.detectorPos2D = project_3D_to_2D(obj.detectorPos3D);
		if ~isempty(obj.detectorPos3D)
		obj.detectorPos2D = obj.detectorPos3D(:,1:2);
		end

		% if isfield(obj,'DummyPos3D') & ~isempty(obj.DummyPos3D)
		% obj.DummyPos2D = obj.DummyPos3D(:,1:2);
		% end
		else

		% 3D landmarks are available, use ...

		end
		[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'};

		% 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 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
		xy = xy/2 + 0.5; % adjust to range 0-1
		refpts_2D.pos = xy;
		obj.landmarkPos2D = refpts_2D.pos;

		%%
		if ~isempty(obj.sourcePos3D)
		obj.sourcePos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.sourcePos3D, T, norm_factor);
		end
		if ~isempty(obj.detectorPos3D)
		obj.detectorPos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.detectorPos3D, T, norm_factor);
		end
		% if isfield(obj,'DummyPos3D') & ~isempty(obj.DummyPos3D)
		% obj.DummyPos2D = convert_optodepos_to_circlular_2D_pos(obj.DummyPos3D, T, norm_factor);
		% end
		end
		end
		% 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);
		% end
		% if isempty(obj.detectorPos2D)
		% obj.detectorPos2D = project_3D_to_2D(obj.detectorPos3D);
		% end
		%
		% else
		%
		% % 3D landmarks are available, use ...
		%
		% end
		end

MainGUI/MainGUI.fig

−3.28 KiB (96.1 KiB)

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MainGUI/MainGUI.m

+24 −0

Original line number	Diff line number	Diff line
		@@ -826,6 +826,30 @@ function menuItemPlotProbeGUI_Callback(hObject, ~, handles)
		global maingui
		LaunchChildGuiFromMenu('PlotProbeGUI', hObject, GetDatatype(handles), maingui.condition);

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

		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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