v1.51.0 (bb59bc7e) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/DataClass.m

+259 −89

Original line number	Diff line number	Diff line
		@@ -464,64 +464,142 @@ classdef DataClass < FileLoadSaveClass


		% ---------------------------------------------------------
		function [d, order] = GetDataTimeSeries(obj, options)
		function [d, t, ml, order] = GetDataTimeSeries(obj, options)
		%
		% SYNTAX:
		% d = GetDataTimeSeries(obj)
		% [d, t] = GetDataTimeSeries(obj)
		% [d, t, ml] = GetDataTimeSeries(obj)
		% [d, t, ml, order] = GetDataTimeSeries(obj)
		% d = GetDataTimeSeries(obj, options)
		% [d, t] = GetDataTimeSeries(obj, options)
		% [d, t, ml] = GetDataTimeSeries(obj, options)
		% [d, t, ml, order] = GetDataTimeSeries(obj, options)
		%
		% DESCRIPTION:
		% If no argument is supplied, or if option='', then dataTimeSeries and accompanying
		% measurementList is returned as is, as it exists in the SNIRF object.
		%
		% If option is supplied then we have the following option values possible values which can be
		% mixed and matched. The options are combined in one string argument with colon ':'.
		%
		% 'reshape' - dataTimeSeries will be sorted, reshaped and reordered with the following dimensions:
		%
		% [ dataTimePoints, sdPairIndex, dataType, condition ]
		%
		% and all dimensions sorted in ascending order. The slowest dimensions to change will be
		% from right-to-left. That is, sdPairIndex, dataType, condition. The rows of measurement list, ml,
		% will follow this order in linear form. That is, the order of ml will index the columns
		% of d squeezed into 2 dimensions d(:,:)
		%
		% 'matrix' - dataTimeSeries will not be modified but ml will be returned as a 2D matrix instead of a
		% MeasListClass structure. It's rows will have the same order as the structure elements.
		%
		% 'datatype' - used in combination with reshape. dataTimeSeries will be reshaped as above but the
		% slowest dimensions to change will be reversed from left-to-right, that is,
		% condition, dataType, sdPair:
		%
		% 'linear' - Reordering as shown above with reshape and datatype, but d will be squeezed into 2D
		% array
		%
		% EXAMPLES:
		%
		% %%%% dod is a DataClass object containing optical density data, with 4 sources, 8 detectors, 9 sd pairs, and 2 wavelengths.
		% %%%% dc is a DataClass object containing concentration data, with 4 sources, 8 detectors, 9 sd pairs, and 3 Hb data types: hbo, hbr, and hbt.
		%
		%
		% % Example 1: Return OD dataTimeSeries, time and measurementList unchanged.
		% [d, t, ml, order] = dod.GetDataTimeSeries();
		%
		%
		% % Example 2: Return OD dataTimeSeries, and time unchanged and measurementList (ml) as a 2D matrix. Channel order is unchanged.
		% [d, t, ml, order] = dod.GetDataTimeSeries('matrix');
		%
		%
		% % Example 3: Return concentration dataTimeSeries as a 3D array (d), and measurementList (ml) as a 2D array. Channel order is sorted,
		% with slowest dimension to change being Hb type.
		% [d, t, ml, order] = dc.GetDataTimeSeries('matrix:reshape');
		%
		%
		% % Example 4: Return concentration dataTimeSeries as a 3D array (d), and measurementList (ml) as a 2D array. Channel order is sorted,
		% with slowest dimension to change being sdPair.
		% [d, t, ml, order] = dc.GetDataTimeSeries('matrix:reshape:datatype');
		%
		%
		% % Example 5: Return concentration dataTimeSeries as a 2D array (d), and measurementList (ml) as a 2D array. Channel order is sorted,
		% with slowest dimension to change being sdPair (ie. same channel as Example 4).
		% [d, t, ml, order] = dc.GetDataTimeSeries('matrix:reshape:datatype:linear');
		%
		%
		%
		d = [];
		t = [];
		ml = [];
		order = [];

		if ~exist('options','var') \|\| isempty(options)
		options = '';
		end
		if isempty(obj.dataTimeSeries)
		if isempty(obj)
		return;
		end
		if ~strcmp(options, 'reshape')
		d = obj.dataTimeSeries;
		return
		if isempty(obj.dataTimeSeries)
		return;
		end

		dataTypeLabels = {};
		srcs = zeros(0,1);
		dets = zeros(0,1);
		conditions = [];
		wavelengths = [];
		hh=1; jj=1; kk=1; ll=1; mm=1;
		for ii = 1:length(obj.measurementList)
		if ~ismember(obj.measurementList(ii).dataTypeLabel, dataTypeLabels) && ~isempty(obj.measurementList(ii).dataTypeLabel)
		dataTypeLabels{hh} = obj.measurementList(ii).dataTypeLabel; %#ok<*AGROW>
		hh=hh+1;
		reshapeOption = '';
		if contains(options, 'reshape')
		reshapeOption = 'reshape';
		end
		if isempty(find(srcs == obj.measurementList(ii).GetSourceIndex()))
		srcs(jj) = obj.measurementList(ii).GetSourceIndex();
		jj=jj+1;
		dimSlow = 'sdpair';
		if contains(lower(options), 'condition')
		dimSlow = 'condition';
		elseif contains(lower(options), 'datatype')
		dimSlow = 'datatype';
		elseif contains(lower(options), 'wavelength')
		dimSlow = 'datatype';
		elseif contains(lower(options), 'hbtype')
		dimSlow = 'datatype';
		end
		if isempty(find(dets == obj.measurementList(ii).GetDetectorIndex())) %#ok<*EFIND>
		dets(kk) = obj.measurementList(ii).GetDetectorIndex();
		kk=kk+1;
		end
		if ~ismember(obj.measurementList(ii).GetCondition(), conditions) && obj.measurementList(ii).GetCondition() > 0
		conditions(ll) = obj.measurementList(ii).GetCondition();
		ll=ll+1;
		end
		if ~ismember(obj.measurementList(ii).GetWavelengthIndex(), wavelengths) && obj.measurementList(ii).GetWavelengthIndex()>0
		wavelengths(mm) = obj.measurementList(ii).GetWavelengthIndex();
		mm=mm+1;
		matrixOption = '';
		if contains(options, 'matrix')
		matrixOption = 'matrix';
		end

		t = obj.time;
		if ~strcmp(reshapeOption, 'reshape')
		d = obj.dataTimeSeries;
		ml = obj.GetMeasurementList(matrixOption);
		order = 1:size(d,2);
		return
		end

		% Sort all the dimension data
		srcs = sort(srcs);
		dets = sort(dets);
		wavelengths = sort(wavelengths);
		hbTypes = sort(dataTypeLabels);
		conditions = sort(conditions);
		measurementListFull = obj.GetMeasurementList('matrix');
		measurementListSDpairs = obj.GetMeasListSrcDetPairs('reshape');

		% Sort all the dimension data
		srcs = sort(unique(measurementListFull(:,1)));
		dets = sort(unique(measurementListFull(:,2)));
		conditions = sort(unique(measurementListFull(:,3)));
		dataTypes = sort(unique(measurementListFull(:,4)));

		if obj.measurementList(1).wavelengthIndex > 0
		wavelengths = dataTypes;
		hbTypes = [];
		else
		wavelengths = [];
		hbTypes = dataTypes;
		end
		if conditions == 0
		conditions = [];
		end
		nWavelengths = length(wavelengths);
		nDataTypeLabels = length(hbTypes);
		nCond = length(conditions);

		measurementListFull = obj.GetMeasurementList('matrix');
		measurementListSDpairs = obj.GetMeasListSrcDetPairs('reshape');

		kk = 1;
		if strcmp(dimSlow, 'sdpair')

		if nWavelengths > 0 && nCond == 0

		for iS = 1:length(srcs)
		@@ -599,6 +677,98 @@ classdef DataClass < FileLoadSaveClass
		end
		end

		elseif strcmp(dimSlow, 'condition') \|\| strcmp(dimSlow, 'datatype')

		if nWavelengths > 0 && nCond == 0

		for iWl = 1:nWavelengths
		for iS = 1:length(srcs)
		for iD = 1:length(dets)

		k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==wavelengths(iWl));
		if ~isempty(k)
		iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
		d(:, iWl, iSDPair) = obj.dataTimeSeries(:,k); %#ok<*FNDSB>
		order(kk) = k;
		kk = kk+1;
		end

		end
		end
		end

		elseif nWavelengths > 0 && nCond > 0

		for iCond = 1:nCond
		for iWl = 1:nWavelengths
		for iS = 1:length(srcs)
		for iD = 1:length(dets)

		k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond & measurementListFull(:,4)==wavelengths(iWl));
		if ~isempty(k)
		iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
		d(:, iWl, iSDPair, iCond) = obj.dataTimeSeries(:,k);
		order(kk) = k;
		kk = kk+1;
		end

		end
		end
		end
		end

		elseif nDataTypeLabels > 0 && nCond == 0

		for iHbType = 1:length(hbTypes)
		for iS = 1:length(srcs)
		for iD = 1:length(dets)

		k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==iHbType);
		if ~isempty(k)
		iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
		d(:, iHbType, iSDPair) = obj.dataTimeSeries(:,k);
		order(kk) = k;
		kk = kk+1;
		end

		end
		end
		end

		elseif nDataTypeLabels > 0 && nCond > 0

		for iCond = 1:nCond
		for iHbType = 1:length(hbTypes)
		for iS = 1:length(srcs)
		for iD = 1:length(dets)

		k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond & measurementListFull(:,4)==iHbType);
		if ~isempty(k)
		iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
		d(:, iHbType, iSDPair, iCond) = obj.dataTimeSeries(:,k);
		order(kk) = k;
		kk = kk+1;
		end

		end
		end
		end
		end
		end

		end

		ml = measurementListFull(order,:);

		if contains(options, 'linear')
		d = d(:,:);
		end
		if ~contains(options, 'matrix')
		ml = obj.measurementList;
		ml(order) = ml;
		end


		d = simulateDataError(d);
		end

DataTree/AcquiredData/Snirf/SnirfClass.m

+5 −3

Original line number	Diff line number	Diff line
		@@ -1011,8 +1011,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass


		% ---------------------------------------------------------
		function datamat = GetDataTimeSeries(obj, options, iBlk)
		datamat = [];
		function [d, t, ml] = GetDataTimeSeries(obj, options, iBlk)
		d = [];
		t = [];
		ml = [];
		if ~exist('options','var')
		options = '';
		end
		@@ -1022,7 +1024,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if iBlk>length(obj.data)
		return;
		end
		datamat = obj.data(iBlk).GetDataTimeSeries(options);
		[d, t, ml] = obj.data(iBlk).GetDataTimeSeries(options);
		end

DataTree/ProcStream/ProcStreamClass.m

+14 −2

Original line number	Diff line number	Diff line
		@@ -120,6 +120,7 @@ classdef ProcStreamClass < handle
		function B = isequal(obj, obj2)
		B = false;
		if isa(obj2, 'ProcStreamClass')
		% Compare in both direction obj -> obj2 AND obj2 -> obj
		for ii = 1:length(obj.fcalls)
		if ii>length(obj2.fcalls)
		return
		@@ -128,6 +129,14 @@ classdef ProcStreamClass < handle
		return;
		end
		end
		for ii = 1:length(obj2.fcalls)
		if ii>length(obj.fcalls)
		return
		end
		if obj.fcalls(ii) ~= obj2.fcalls(ii)
		return;
		end
		end
		elseif isstruct(obj2)
		if ~isproperty(obj2, 'procFunc')
		return;
		@@ -153,6 +162,8 @@ classdef ProcStreamClass < handle
		if length(obj.fcalls) ~= length(obj2.procFunc.funcName)
		return;
		end

		% Compare in both direction obj -> obj2 AND obj2 -> obj
		for ii = 1:length(obj.fcalls)
		obj3.funcName = obj2.procFunc.funcName{ii};
		obj3.funcNameUI = obj2.procFunc.funcNameUI{ii};
		@@ -492,6 +503,7 @@ classdef ProcStreamClass < handle
		end



		% ----------------------------------------------------------------------------------
		function sargin = ParseInputParams(obj, iFcall)
		sargin = '';

DataTree/RunClass.m

+5 −5

Original line number	Diff line number	Diff line
		@@ -399,16 +399,16 @@ classdef RunClass < TreeNodeClass


		% ----------------------------------------------------------------------------------
		function d = GetRawData(obj, iBlk)
		function [d, t, ml] = GetRawData(obj, iBlk)
		if nargin<2
		iBlk = 1;
		end
		d = obj.acquired.GetDataTimeSeries('', iBlk);
		[d, t, ml] = obj.acquired.GetDataTimeSeries('', iBlk);
		end


		% ----------------------------------------------------------------------------------
		function d = GetDataTimeSeries(obj, options, iBlk)
		function [d, t, ml] = GetDataTimeSeries(obj, options, iBlk)
		if ~exist('options','var')
		options = '';
		end
		@@ -416,9 +416,9 @@ classdef RunClass < TreeNodeClass
		iBlk = 1;
		end
		if isempty(options) \|\| strcmp(options, 'reshape')
		d = obj.acquired.GetDataTimeSeries(options, iBlk);
		[d, t, ml] = obj.acquired.GetDataTimeSeries(options, iBlk);
		else
		d = obj.GetDataTimeSeries@TreeNodeClass(options, iBlk);
		[d, t, ml] = obj.GetDataTimeSeries@TreeNodeClass(options, iBlk);
		end
		end

DataTree/SubjClass.m

+4 −1

Original line number	Diff line number	Diff line
		@@ -305,7 +305,10 @@ classdef SubjClass < TreeNodeClass
		if isempty(obj.inputVars.nTrialsSess)
		obj.inputVars.nTrialsSess = obj.sess(iSess).procStream.output.GetVar('nTrials');
		else
		obj.inputVars.nTrialsSess = obj.inputVars.nTrialsSess + obj.sess(iSess).procStream.output.GetVar('nTrials');
		nTrialsSess = obj.sess(iSess).procStream.output.GetVar('nTrials');
		for iBlk = 1:length(obj.inputVars.nTrialsSess)
		obj.inputVars.nTrialsSess{iBlk} = obj.inputVars.nTrialsSess{iBlk} + nTrialsSess{iBlk};
		end
		end
		if ~isempty(obj.sess(iSess).procStream.output.GetVar('misc'))
		if isfield(obj.sess(iSess).procStream.output.misc, 'stim') == 1

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