Fix LengthUnit error (2443e449) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_Transpose.m

+8 −6

Original line number	Diff line number	Diff line
		@@ -7,12 +7,14 @@ end
		% Matlab stores contiguous muti-dimensional arrays in column-major order.
		% HDF5 stores them in row-major order. We want to transpose the data to agree
		% with the file format's storage order.
		if ~isrow(val) && ~iscolumn(val) % Matrices
		val = permute(val, ndims(val):-1:1);
		elseif ischar(val) % 1D char strings
		val = permute(val, ndims(val):-1:1);
		elseif ~isempty(findstr('multidim', options)) % Force multi-dimensional even if vector
		if (~isrow(val) && ~iscolumn(val)) \|\| ... % Matrices
		~isempty(findstr('multidim', options)) \|\| ... % Force multi-dimensional even if vector
		~isempty(findstr('2D', options)) % Force 2D even if vector

		val = permute(val, ndims(val):-1:1);
		elseif ~isempty(findstr('2D', options)) % Force 2D even if vector

		elseif iscolumn(val) && ischar(val)

		val = permute(val, ndims(val):-1:1);

		end

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

0 → 100644

+467 −0

File added.

Preview size limit exceeded, changes collapsed.

DataTree/AcquiredData/Snirf/ProbeClass.m

+70 −55

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



		methods

		% -------------------------------------------------------
		@@ -145,15 +146,16 @@ classdef ProbeClass < FileLoadSaveClass
		if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D)
		if isempty(obj.landmarkPos3D)
		if ~isempty(obj.sourcePos3D)
		obj.sourcePos2D = obj.sourcePos3D(:,1:2);
		obj.sourcePos2D = project_3D_to_2D(obj.sourcePos3D);
		end
		if ~isempty(obj.detectorPos3D)
		obj.detectorPos2D = obj.detectorPos3D(:,1:2);
		obj.detectorPos2D = project_3D_to_2D(obj.detectorPos3D);
		end
		% if isfield(obj,'DummyPos3D') & ~isempty(obj.DummyPos3D)
		% obj.DummyPos2D = obj.DummyPos3D(:,1:2);
		% 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'};
		@@ -173,7 +175,7 @@ classdef ProbeClass < FileLoadSaveClass

		% get affine transformation
		% probe_refps*T = sphere_refpts
		probe_refps_pos = [probe_refps_pos ones(size(probe_refps_pos,1),1)];
		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.
		@@ -205,10 +207,8 @@ classdef ProbeClass < FileLoadSaveClass
		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)
		@@ -236,7 +236,7 @@ classdef ProbeClass < FileLoadSaveClass


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

		% Arg 1
		@@ -251,6 +251,19 @@ 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);
		@@ -269,12 +282,12 @@ 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');
		@@ -338,6 +351,7 @@ 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');
		@@ -359,6 +373,7 @@ 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
		@@ -464,8 +464,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% -------------------------------------------------------
		function err = LoadProbe(obj, fileobj, ~)
		% get lenth unit through class method
		LengthUnit = obj.metaDataTags.Get('LengthUnit').value;
		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)

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