Merge remote-tracking branch 'remotes/origin/development' (571410ee) · Commits · github_fork / Homer3

DataTree/AcquiredData/AcqDataClass.m

+3 −0

Original line number	Diff line number	Diff line
		@@ -49,6 +49,9 @@ classdef AcqDataClass < matlab.mixin.Copyable
		% ---------------------------------------------------------
		s = GetStims(obj, t)

		% ---------------------------------------------------------
		s = GetStim(obj)

		% ---------------------------------------------------------
		CondNames = GetConditions(obj)

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+25 −3

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@ classdef DataFilesClass < handle

		properties (Access = private)
		lookupTable
		excludedFolders
		end

		methods
		@@ -38,6 +39,7 @@ classdef DataFilesClass < handle

		obj.logger = logger;
		obj.lookupTable = [];
		obj.excludedFolders = {};

		skipconfigfile = false;
		askToFixNameConflicts = [];
		@@ -74,7 +76,7 @@ classdef DataFilesClass < handle
		obj.rootdir = filesepStandard(obj.rootdir,'full');

		% Configuration parameters
		obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);
		obj.config = struct('RegressionTestActive','', 'AskToFixNameConflicts',1, 'DerivedDataDir','');
		if skipconfigfile==false
		str = cfg.GetValue('Regression Test Active');
		if strcmp(str,'true')
		@@ -96,6 +98,18 @@ classdef DataFilesClass < handle
		obj.config.SuppressErrorChecking = true;
		end

		[p, f] = fileparts(cfg.GetValue('Output Folder Name'));
		if isempty(p)
		obj.config.DerivedDataDir = f;
		else
		obj.config.DerivedDataDir = p;
		end
		obj.excludedFolders = {...
		[obj.rootdir, obj.config.DerivedDataDir];
		[obj.rootdir, 'fw'];
		[obj.rootdir, 'imagerecon'];
		[obj.rootdir, 'anatomical'];
		};
		if nargin==0
		return;
		end
		@@ -222,6 +236,14 @@ classdef DataFilesClass < handle
		return
		end
		parentdir = filesepStandard(parentdir);

		% Check if folder is excluded, if yes don't search there
		for ii = 1:length(obj.excludedFolders)
		if includes(parentdir, obj.excludedFolders{ii})
		return;
		end
		end

		pattern = obj.dirFormats.choices{iFormat}{iPattern};

		dirs = mydir([parentdir, pattern], obj.rootdir);
		@@ -307,7 +329,7 @@ classdef DataFilesClass < handle
		obj.ErrorCheckName();

		% Find all acquisition files in group folder
		fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype]);
		fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype], obj.excludedFolders);

		% Make a list of all files excluded from current data set
		for ii = 1:length(fileNames)

DataTree/AcquiredData/Nirs/NirsClass.m

+6 −0

Original line number	Diff line number	Diff line
		@@ -770,6 +770,12 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		end


		% ---------------------------------------------------------
		function s = GetStim(obj)
		s = obj.s;
		end


		% ----------------------------------------------------------------------------------
		function SetConditions(obj, CondNames)
		if nargin==1

DataTree/AcquiredData/Snirf/DataClass.m

+23 −0

Original line number	Diff line number	Diff line
		@@ -289,6 +289,8 @@ classdef DataClass < FileLoadSaveClass
		if ~exist('params','var')
		params = propnames(obj);
		end

		% Check dataTimeSeries
		if ismember('dataTimeSeries',params)
		if obj.IsEmpty()
		err = -2;
		@@ -304,6 +306,8 @@ classdef DataClass < FileLoadSaveClass
		err = 5;
		end
		end

		% Check time
		if ismember('time',params)
		if isempty(obj.time)
		err = -6;
		@@ -313,6 +317,25 @@ classdef DataClass < FileLoadSaveClass
		err = 7;
		end
		end

		% Check measurement list
		if ismember('measurementList',params)
		ml = sortrows(obj.GetMeasurementList('matrix'));
		nDatatypes = length(unique(ml(:,4))) * length(unique(ml(:,3)));
		i = 1;
		while i <= size(ml,1)
		k = find(ml(:,1)==ml(i,1) & ml(:,2)==ml(i,2));
		if length(k) < nDatatypes
		err = -7;
		elseif length(k) > nDatatypes
		err = -8;
		end
		if err < 0
		break
		end
		i = i+length(k);
		end
		end
		end

		end

DataTree/AcquiredData/Snirf/SnirfClass.m

+266 −2

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		nirsdatanum
		nirs_tb
		stim0
		hFig
		end

		methods
		@@ -78,6 +79,8 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		obj.SetFileFormat('hdf5');
		obj.location = '/nirs';
		obj.nirsdatanum = 1;
		obj.hFig = [-1; -1];


		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Between 1 and 4 arguments covers the following syntax variants
		@@ -1005,8 +1008,17 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end

		% ---------------------------------------------------------
		function val = GetData(obj)
		val = obj.data;
		function [val, t] = GetData(obj, iBlk)
		val = [];
		t = [];
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		if isempty(obj) \|\| isempty(obj.data)
		return;
		end
		val = obj.data(iBlk);
		t = obj.data(iBlk).time;
		end

		% ---------------------------------------------------------
		@@ -1889,6 +1901,258 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass



		% ----------------------------------------------------------------------------------
		function hAxes = GenerateStandaloneAxes(obj, datatype, iChs)
		k = find(obj.hFig(1,:)==-1);
		obj.hFig(1,k(1)) = figure;
		hAxes = gca;
		plotname = sprintf('"%s"; %s data ; channels idxs: [%s]', obj.GetFilename(), datatype, num2str(iChs'));
		namesize = uint32(length(plotname)/3);
		set(obj.hFig(1,k(1)), 'units','characters');
		p1 = get(obj.hFig(1,k(1)), 'position');
		set(obj.hFig(1,k(1)), 'name',plotname, 'menubar','none', 'NumberTitle','off', 'position',[p1(1)/2, p1(2), p1(3)+namesize, p1(4)]);
		obj.hFig(:,k(1)+1) = -1;
		end



		% ----------------------------------------------------------------------------------
		function Plot(obj, sdPairs, iBlk)
		%
		% SYNTAX:
		% TreeNodeClass.Plot(iChs, iBlk)
		%
		%
		% DESCRIPTION:
		% Plot data from channels specified by 2d array where each row spoecifying a single channel
		% contains indices [source, detector, condition, wavelength]. In addtion to the data, this method
		% plots any existing stims, and the probe associated with the SNIRF object from which the data
		% was taken. NOTE: the args iBlk and hAxes can be ommitted and will default to 1 and current
		% axes respectively.
		%
		%
		% INPUT:
		% sdPairs - 2d array of channel indices where each row represents a channel consisting of the indices
		% [source, detector, condition, datatype]
		%
		% iBlk - Optional argument (defaults = 1). In theory SNIRF data field is an array of data blocks. This argunment selects the
		% data block from which the plot data is taken.
		%
		% hAxes - Optional argument (default is current axes or gca()), specifying the axes handle of the axes in which to plot the data.
		%
		%

		% Parse input args
		if ~exist('sdPairs','var')
		sdPairs = [1,1,0,1];
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end


		% Convert channels in the form of a list of sd pairs to a column vector of indices into the measurement list
		iChs = obj.SdPairIdxs2vectorIdxs(sdPairs, iBlk);


		% Extract SNIRF parameters for plotting: probe, data, time, measuremntList and stim
		d = obj.data(1).dataTimeSeries;
		t = obj.data(1).time;
		ml = obj.data(1).GetMeasurementList('matrix');

		% If there's no data to plot then exit
		if isempty(d)
		fprintf('No data to plot\n');
		return;
		end


		% Set up standalone figure with axes for plotting data, if axes handle was not passed down from caller
		% in the last arg. There will be a separate figure displaying the probe associated with this data plot.
		% a few lines down in DisplayProbe.
		hAxes = obj.GenerateStandaloneAxes('HRF', iChs);

		% Plot data
		hold on
		chSelect = [];
		for ii = 1:length(iChs)
		hdata(ii) = plot(hAxes, t, d(:,iChs(ii)), 'linewidth',2);
		chSelect(ii,:) = [ml(iChs(ii),1), ml(iChs(ii),2), ml(iChs(ii),3), ml(iChs(ii),4), get(hdata(ii), 'color')];
		end
		set(hAxes, 'xlim', [t(1), t(end)]);

		% Display probe in separate figure
		if isempty(chSelect)
		fprintf('ERROR: no valid channels were selelcted\n');
		obj.DisplayProbe();
		else
		obj.DisplayProbe(chSelect(:,1:2), chSelect(:,5:7));
		end


		% Wrap up before exiting
		drawnow;
		pause(.1);
		hold off
		end


		% ----------------------------------------------------------------------------------
		function iChs = SdPairIdxs2vectorIdxs(obj, sdPairs, iBlk)
		iChs = [];
		if ~exist('sdPairs','var')
		sdPairs = [1,1,0,1];
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end

		% Error Checking
		if size(sdPairs, 2)>1 && size(sdPairs, 2)~=4
		fprintf('ERROR: invalid sdPair. sdPair has to be a Nx4 2D array\n');
		return;
		end


		% If sdPairs argument is a column vector then we are done because channels are
		% already specified in the output format i.e., as single number indices.
		if size(sdPairs, 2)==1
		iChs = sdPairs;
		return;
		end

		ml = obj.data(1).GetMeasurementList('matrix', iBlk);

		% Error checking
		if isempty(ml)
		return
		end

		for ii = 1:size(sdPairs,1)
		k = find(ml(:,1)==sdPairs(ii,1) & ml(:,2)==sdPairs(ii,2) & ml(:,3)==sdPairs(ii,3) & ml(:,4)==sdPairs(ii,4));
		if isempty(k)
		continue;
		end
		iChs(ii,1) = k;
		end
		end



		% ----------------------------------------------------------------------------------
		function sdPairs = VectorIdxs2SdPairIdxs(obj, iChs, iBlk)
		if ~exist('iChs','var')
		iChs = 1;
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end

		% If sdPairs argument is not a column vector then we are done; because the
		% channels are already specified in the output format i.e., as a 2d array.
		if size(iChs, 2)>1
		sdPairs = iChs;
		return;
		end

		ml = obj.data(1).GetMeasurementList('matrix', iBlk);

		% Remove any invalid indices
		iChs(iChs==0) = [];
		iChs(iChs>size(ml,1)) = [];

		sdPairs = ml(iChs,:);
		end



		% ----------------------------------------------------------------------------------
		function hAxes = DisplayProbe(obj, chSelect, chSelectColors, hAxes)
		% Parse args
		if ~exist('chSelect','var')
		chSelect = [];
		end
		if ~exist('chSelectColors','var')
		chSelectColors = repmat([1.0, 0.5, 0.2], size(chSelect,1),1);
		end
		if ~exist('hAxes','var')
		hAxes = [];
		end

		% If chSelect is in the form of a column vector rather than sd pairs
		% then convert to sd pairs
		chSelect = obj.VectorIdxs2SdPairIdxs(chSelect);

		freememoryflag = false;
		if ~isempty(obj) && obj.IsEmpty()
		obj.acquired.Load();
		freememoryflag = true;
		end

		% Set up the axes
		bbox = obj.GetSdgBbox();
		if isempty(hAxes)
		k = find(obj.hFig(2,:)==-1);

		% See if there's a data plot associated with this probe display
		% If there is get its name and use it to name this figure
		plotname = '';
		if ishandle(obj.hFig(1,k(1)))
		plotname = get(obj.hFig(1,k(1)), 'name');
		end
		obj.hFig(2,k(1)) = figure('menubar','none', 'NumberTitle','off', 'name',plotname);
		hAxes = gca;
		end

		axis(hAxes, [bbox(1), bbox(2), bbox(3), bbox(4)]);
		gridsize = get(hAxes, {'xlim', 'ylim', 'zlim'});
		if ismac() \|\| islinux()
		fs = 18;
		else
		fs = 11;
		end

		% Get probe paramaters
		probe = obj.GetProbe();
		srcpos = probe.sourcePos2D;
		detpos = probe.detectorPos2D;
		ml = obj.GetMeasurementList('matrix');
		lstSDPairs = find(ml(:,4)==1);

		% Draw all channels
		for ii = 1:length(lstSDPairs)
		hCh(ii) = line2(srcpos(ml(lstSDPairs(ii),1),:), detpos(ml(lstSDPairs(ii),2),:), [], gridsize, hAxes);
		col = [1.00 1.00 1.00] * 0.85;
		if ~isempty(chSelect)
		k = find(chSelect(:,1)==ml(lstSDPairs(ii),1) & chSelect(:,2)==ml(lstSDPairs(ii),2));
		if ~isempty(k)
		col = chSelectColors(k(1),:);
		end
		end
		set(hCh(ii), 'color',col, 'linewidth',2, 'linestyle','-', 'userdata',ml(lstSDPairs(ii),1:2));
		end

		% ADD SOURCE AND DETECTOR LABELS
		for iSrc = 1:size(srcpos,1)
		if ~isempty(find(ml(:,1)==iSrc)) %#ok<*EFIND>
		hSD(iSrc) = text( srcpos(iSrc,1), srcpos(iSrc,2), sprintf('%d', iSrc), 'fontsize',fs, 'fontweight','bold', 'color','r' );
		set(hSD(iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
		end
		end
		for iDet = 1:size(detpos,1)
		if ~isempty(find(ml(:,2)==iDet))
		hSD(iDet+iSrc) = text( detpos(iDet,1), detpos(iDet,2), sprintf('%d', iDet), 'fontsize',fs, 'fontweight','bold', 'color','b' );
		set(hSD(iDet+iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
		end
		end

		if freememoryflag
		obj.FreeMemory();
		end
		end



		end

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