Merge pull request #10 from jayd1860/master (f932d68d) · Commits · github_fork / Homer3

AppSettings.cfg

+4 −1

Original line number	Diff line number	Diff line
		@@ -15,9 +15,12 @@ SNIRF
		On

		% Last Checked For Update
		12-Mar-1998 17:03:23
		30-Jun-2020 10:48:25

		% Check For Updates
		on

		% Data Storage Scheme
		disk

		% END

DataTree/AcquiredData/AcqDataClass.m

+32 −8

Original line number	Diff line number	Diff line
		@@ -69,6 +69,30 @@ classdef AcqDataClass < matlab.mixin.Copyable

		methods

		% -------------------------------------------------------
		function b = Error(obj)
		if obj.err<0
		b = true;
		elseif obj.err==0
		b = false;
		else
		b = true;
		end
		end


		% -------------------------------------------------------
		function FreeMemory(obj, filename)
		if ~exist('filename','var')
		filename = '';
		end
		if isempty(filename)
		return;
		end
		obj.Initialize();
		end


		% ---------------------------------------------------------
		function bbox = GetSdgBbox(obj)
		optpos = [obj.GetSrcPos(); obj.GetDetPos()];

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+2 −2

Original line number	Diff line number	Diff line
		@@ -39,11 +39,11 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable
		switch(lower(format))
		case obj.supportedFomats.matlab
		if ismethod(obj, 'LoadMat')
		obj.LoadMat(filename);
		obj.err = obj.LoadMat(filename);
		end
		case obj.supportedFomats.hdf5
		if ismethod(obj, 'LoadHdf5')
		obj.LoadHdf5(filename, params);
		obj.err = obj.LoadHdf5(filename, params);
		end
		end
		end

DataTree/AcquiredData/Nirs/NirsClass.m

+48 −11

Original line number	Diff line number	Diff line
		@@ -46,12 +46,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		%

		% Initialize Nirs public properties
		obj.SD = struct([]);
		obj.t = [];
		obj.s = [];
		obj.d = [];
		obj.aux = [];
		obj.CondNames = {};
		obj.Initialize();

		% Set base class properties not part of NIRS format
		obj.filename = '';
		@@ -75,6 +70,17 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end


		% -------------------------------------------------------
		function Initialize(obj)
		obj.SD = struct([]);
		obj.t = [];
		obj.s = [];
		obj.d = [];
		obj.aux = [];
		obj.CondNames = {};
		end


		% ---------------------------------------------------------
		function SortStims(obj)
		[~,idx] = sort(obj.CondNames);
		@@ -98,36 +104,67 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		else
		fname = obj.filename;
		end
		if isempty(fname)
		if exist(fname, 'file') ~= 2
		err = -1;
		return;
		end

		% Don't reload if not empty
		if ~obj.IsEmpty()
		return;
		end

		warning('off', 'MATLAB:load:variableNotFound');
		fdata = load(fname,'-mat', 'SD','t','d','s','aux','CondNames');

		% Mandatory fields
		if isproperty(fdata,'d')
		obj.d = fdata.d;
		if isempty(obj.d)
		err = -2;
		end
		else
		err = -2;
		end
		if isproperty(fdata,'t')
		obj.t = fdata.t;
		if ~isempty(obj.t)
		obj.errmargin = min(diff(obj.t))/10;
		else
		err = -3;
		end
		else
		err = -3;
		end
		if isproperty(fdata,'SD')
		obj.SetSD(fdata.SD);
		if isempty(obj.SD)
		err = -4;
		end
		else
		err = -4;
		end


		% Optional fields
		if isproperty(fdata,'s')
		obj.s = fdata.s;
		else
		obj.s = [];
		end
		if isproperty(fdata,'aux')
		obj.aux = fdata.aux;
		else
		obj.aux = [];
		end
		if isproperty(fdata,'CondNames')
		obj.CondNames = fdata.CondNames;
		else
		obj.InitCondNames();
		end
		if ~isempty(obj.t)
		obj.errmargin = min(diff(obj.t))/10;
		end

		% Always sort stimulus conditions and associated stims
		% to have a predictable order for display
		obj.SortStims();
		end

DataTree/AcquiredData/Snirf/DataClass.m

+8 −2

Original line number	Diff line number	Diff line
		@@ -221,7 +221,10 @@ classdef DataClass < FileLoadSaveClass

		% ---------------------------------------------------------
		function ml = GetMeasList(obj)
		ml = [];
		% Preallocate for speed
		ml = ones(length(obj.measurementList), 4);

		% Convert obj.measurementList to matrix
		for ii = 1:length(obj.measurementList)
		% If this data contains block average then only get the measurements for first condition. That will
		% contain all the measurement channels
		@@ -230,6 +233,9 @@ classdef DataClass < FileLoadSaveClass
		end
		ml(ii,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex(), 1, obj.measurementList(ii).GetWavelengthIndex()];
		end

		% Remove any unused allocated rows that were pre-allocated
		ml(ii+1:end,:) = [];
		end

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