v1.40.0 (cec54469) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/DataClass.m

+171 −48

Original line number	Diff line number	Diff line
		@@ -168,7 +168,7 @@ classdef DataClass < FileLoadSaveClass

		% Close group
		HDF5_GroupClose(fileobj, gid, fid);
		catch ME
		catch
		err = -1;
		end

		@@ -212,7 +212,7 @@ classdef DataClass < FileLoadSaveClass

		% Close group
		HDF5_GroupClose(fileobj, gid, fid);
		catch ME
		catch
		err = -1;
		end

		@@ -333,7 +333,10 @@ classdef DataClass < FileLoadSaveClass


		% ---------------------------------------------------------
		function ml = GetMeasList(obj)
		function ml = GetMeasList(obj, options)
		if ~exist('options', 'var')
		options = '';
		end
		% Preallocate for speed
		ml = ones(length(obj.measurementList), 4);

		@@ -355,22 +358,35 @@ classdef DataClass < FileLoadSaveClass

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

		% Sort according to wavelength
		ml = sortrows(ml,4);
		if strcmp(options, 'reshape')
		ml = sortrows(ml);
		end
		end



		% ---------------------------------------------------------
		function ml = GetMeasListSrcDetPairs(obj)
		function ml = GetMeasListSrcDetPairs(obj, options)
		if ~exist('options', 'var')
		options = '';
		end
		ml = zeros(0, 2);
		jj=1;
		for ii=1:length(obj.measurementList)
		if isempty(find(ml(:,1)==obj.measurementList(ii).GetSourceIndex() & ml(:,2)==obj.measurementList(ii).GetDetectorIndex()))
		ml(jj,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex()];
		if isempty(find(ml(:,1) == obj.measurementList(ii).sourceIndex & ml(:,2) == obj.measurementList(ii).detectorIndex))
		ml(jj,:) = [obj.measurementList(ii).sourceIndex, obj.measurementList(ii).detectorIndex];
		jj=jj+1;
		end
		end
		if strcmp(options, 'reshape')
		ml = sortrows(ml);
		end
		end


		% ---------------------------------------------------------
		function ml = GetMeasurementList(obj)
		ml = obj.measurementList;
		end


		@@ -400,9 +416,11 @@ classdef DataClass < FileLoadSaveClass
		end



		% ---------------------------------------------------------
		function d = GetDataTimeSeries(obj, options)
		function [d, order] = GetDataTimeSeries(obj, options)
		d = [];
		order = [];
		if ~exist('options','var') \|\| isempty(options)
		options = '';
		end
		@@ -414,51 +432,155 @@ classdef DataClass < FileLoadSaveClass
		return
		end

		% Get information for each ch in d matrix
		dataTypeLabels = {};
		srcDetPairs = zeros(0,2);
		srcs = zeros(0,2);
		dets = zeros(0,2);
		conditions = [];
		wavelengths = [];
		hh=1; jj=1; kk=1; ll=1;
		hh=1; jj=1; kk=1; ll=1; mm=1;
		for ii = 1:length(obj.measurementList)
		if ~ismember(obj.measurementList(ii).GetDataTypeLabel(), dataTypeLabels)
		dataTypeLabels{hh} = obj.measurementList(ii).GetDataTypeLabel();
		if ~ismember(obj.measurementList(ii).dataTypeLabel, dataTypeLabels) && ~isempty(obj.measurementList(ii).dataTypeLabel)
		dataTypeLabels{hh} = obj.measurementList(ii).dataTypeLabel; %#ok<*AGROW>
		hh=hh+1;
		end
		if isempty(find(srcDetPairs(:,1)==obj.measurementList(ii).GetSourceIndex() & srcDetPairs(:,2)==obj.measurementList(ii).GetDetectorIndex()))
		srcDetPairs(jj,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex()];
		if isempty(find(srcs == obj.measurementList(ii).GetSourceIndex()))
		srcs(jj) = obj.measurementList(ii).GetSourceIndex();
		jj=jj+1;
		end
		if ~ismember(obj.measurementList(ii).GetCondition(), conditions)
		conditions(kk) = obj.measurementList(ii).GetCondition();
		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).GetWavelengthIndex(), wavelengths)
		wavelengths(ll) = obj.measurementList(ii).GetWavelengthIndex();
		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;
		end
		end

		hbTypes = {'hbo','hbr','hbt'};
		nWavelengths = length(wavelengths);
		nDataTypeLabels = length(dataTypeLabels);
		nCond = length(conditions);
		ml = obj.GetMeasListSrcDetPairs('reshape');

		kk = 1;
		if nWavelengths > 0 && nCond == 0

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

		for ii = 1:length(obj.measurementList)
		if obj.measurementList(ii).sourceIndex == iS && ...
		obj.measurementList(ii).detectorIndex == iD && ...
		obj.measurementList(ii).wavelengthIndex == iWl

		iSrcDetPair = find(ml(:,1)==iS & ml(:,2)==iD);
		d(:, iWl, iSrcDetPair) = obj.dataTimeSeries(:,ii); %#ok<*FNDSB>


		order(kk) = ii;
		kk = kk+1;
		break;

		end

		end
		end
		end
		end

		elseif nWavelengths > 0 && nCond > 0

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

		for ii = 1:length(obj.measurementList)
		if obj.measurementList(ii).sourceIndex == iS && ...
		obj.measurementList(ii).detectorIndex == iD && ...
		obj.measurementList(ii).wavelengthIndex == iWl && ...
		obj.measurementList(ii).dataTypeIndex == iCond

		iSrcDetPair = find(ml(:,1)==iS & ml(:,2)==iD);
		d(:, iWl, iSrcDetPair, iCond) = obj.dataTimeSeries(:,ii);

		order(kk) = ii;
		kk = kk+1;
		break;

		end
		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)

		for ii = 1:length(obj.measurementList)
		if obj.measurementList(ii).sourceIndex == iS && ...
		obj.measurementList(ii).detectorIndex == iD && ...
		~isempty(strfind(lower(obj.measurementList(ii).dataTypeLabel), hbTypes{iHbType}))

		iSrcDetPair = find(ml(:,1)==iS & ml(:,2)==iD);
		d(:, iHbType, iSrcDetPair) = obj.dataTimeSeries(:,ii);

		order(kk) = ii;
		kk = kk+1;
		break;

		end

		end

		end
		end
		dim1 = length(obj.dataTimeSeries(:,1));
		if all(wavelengths(:)~=0) && all(conditions(:)==0)
		dim2 = length(wavelengths(:)) * size(srcDetPairs,1);
		dim3 = 1;
		dim4 = 1;
		elseif all(wavelengths(:)~=0) && all(conditions(:)~=0)
		dim2 = length(wavelengths(:)) * size(srcDetPairs,1);
		dim3 = length(conditions(:));
		dim4 = 1;
		elseif all(wavelengths(:)==0) && all(conditions(:)==0)
		dim2 = length(dataTypeLabels);
		dim3 = size(srcDetPairs,1);
		dim4 = 1;
		elseif all(wavelengths(:)==0) && all(conditions(:)~=0)
		dim2 = length(dataTypeLabels);
		dim3 = size(srcDetPairs,1);
		dim4 = length(conditions(:));
		end
		d = reshape(obj.dataTimeSeries, dim1, dim2, dim3, dim4);

		elseif nDataTypeLabels > 0 && nCond > 0

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

		for ii = 1:length(obj.measurementList)
		if obj.measurementList(ii).sourceIndex == iS && ...
		obj.measurementList(ii).detectorIndex == iD && ...
		~isempty(strfind(lower(obj.measurementList(ii).dataTypeLabel), hbTypes{iHbType})) && ...
		obj.measurementList(ii).dataTypeIndex == iCond

		iSrcDetPair = find(ml(:,1)==iS & ml(:,2)==iD);
		d(:, iHbType, iSrcDetPair, iCond) = obj.dataTimeSeries(:,ii);

		order(kk) = ii;
		kk = kk+1;
		break;

		end
		end

		end
		end
		end
		end

		end

		end



		% ---------------------------------------------------------
		function SetDataTimeSeries(obj, val)
		@@ -469,6 +591,7 @@ classdef DataClass < FileLoadSaveClass
		end



		% ---------------------------------------------------------
		function SetTime(obj, val, datacheck)
		if ~exist('val','var')

DataTree/AcquiredData/Snirf/SnirfClass.m

+16 −0

Original line number	Diff line number	Diff line
		@@ -979,6 +979,22 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end


		% ---------------------------------------------------------
		function ml = GetMeasurementList(obj, iBlk)
		ml = [];
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		if iBlk>length(obj.data)
		return;
		end
		for ii = 1:length(iBlk)
		ml = [ml; obj.data(ii).measurementList];
		end
		end



		% ---------------------------------------------------------
		function datamat = GetDataTimeSeries(obj, options, iBlk)
		datamat = [];

DataTree/ProcStream/ProcStreamClass.m

+77 −0

Original line number	Diff line number	Diff line
		@@ -1422,6 +1422,83 @@ classdef ProcStreamClass < handle
		end


		% ---------------------------------------------------------
		function ml = GetMeasurementList(obj, options, iBlk)
		ml = [];
		if ~exist('options','var')
		options = 'conc';
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		for ii = 1:length(iBlk)
		switch(lower(options))
		case 'od'
		if ii <= length(obj.output.dod)
		ml = [ml; obj.output.dod(ii).measurementList];
		end
		case {'conc','hb','hbo','hbr','hbt'}
		if ii <= length(obj.output.dc)
		ml = [ml; obj.output.dc(ii).measurementList];
		end
		case {'od hrf','od_hrf'}
		if ii <= length(obj.output.dodAvg)
		ml = [ml; obj.output.dodAvg(ii).measurementList];
		end
		case {'hb hrf','conc hrf','hb_hrf','conc_hrf'}
		if ii <= length(obj.output.dcAvg)
		ml = [ml; obj.output.dcAvg(ii).measurementList];
		end
		end
		end
		end



		% ---------------------------------------------------------
		function t = GetTHRF(obj, iBlk)
		t = [];
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		t = obj.output.tHRF;
		end



		% ---------------------------------------------------------
		function dataTimeSeries = GetDataTimeSeries(obj, options, iBlk)
		dataTimeSeries = [];
		if ~exist('options','var')
		options = 'conc';
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		for ii = 1:length(iBlk)
		switch(lower(options))
		case 'od'
		if ii <= length(obj.output.dod)
		dataTimeSeries = [dataTimeSeries, obj.output.dod(ii).dataTimeSeries];
		end
		case {'conc','hb','hbo','hbr','hbt'}
		if ii <= length(obj.output.dc)
		dataTimeSeries = [dataTimeSeries; obj.output.dc(ii).dataTimeSeries];
		end
		case {'od hrf','od_hrf'}
		if ii <= length(obj.output.dodAvg)
		dataTimeSeries = [dataTimeSeries; obj.output.dodAvg(ii).dataTimeSeries];
		end
		case {'hb hrf','conc hrf','hb_hrf','conc_hrf'}
		if ii <= length(obj.output.dcAvg)
		dataTimeSeries = [dataTimeSeries; obj.output.dcAvg(ii).dataTimeSeries];
		end
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function SetTincMan(obj, val, iBlk)
		if ~exist('iBlk','var')

DataTree/RunClass.m

+18 −8

Original line number	Diff line number	Diff line
		classdef RunClass < TreeNodeClass

		properties % (Access = private)
		acquired;
		end

		methods

		% ----------------------------------------------------------------------------------
		@@ -396,7 +392,11 @@ classdef RunClass < TreeNodeClass
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		if isempty(options) \|\| strcmp(options, 'reshape')
		d = obj.acquired.GetDataTimeSeries(options, iBlk);
		else
		d = obj.GetDataTimeSeries@TreeNodeClass(options, iBlk);
		end
		end


		@@ -447,11 +447,16 @@ classdef RunClass < TreeNodeClass
		obj.procStream.input.SetMeasListVis(ones(size(ch, 1), 1));
		end



		% ----------------------------------------------------------------------------------
		function ch = GetMeasList(obj, iBlk)
		function ch = GetMeasList(obj, options, iBlk)
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk=1;
		end
		if ~exist('options','var')
		options = '';
		end

		ch = struct('MeasList',[], 'MeasListVis',[], 'MeasListActMan',[], 'MeasListActAuto',[]);

		@@ -466,6 +471,11 @@ classdef RunClass < TreeNodeClass
		ch.MeasListActAuto = ones(size(ch.MeasList,1),1);
		end
		ch.MeasListAct = bitand(ch.MeasListActMan, ch.MeasListActMan);
		if strcmp(options,'reshape')
		[ch.MeasList, order] = sortrows(ch.MeasList);
		ch.MeasListActMan = ch.MeasListActMan(order);
		ch.MeasListActAuto = ch.MeasListActAuto(order);
		end
		end

DataTree/TreeNodeClass.m

+83 −12

Original line number	Diff line number	Diff line
		@@ -9,6 +9,7 @@ classdef TreeNodeClass < handle
		iRun;
		iFile;
		children;
		acquired;
		procStream;
		err;
		CondNames;
		@@ -47,6 +48,7 @@ classdef TreeNodeClass < handle

		obj.type = '';
		obj.procStream = ProcStreamClass();
		obj.acquired = [];
		obj.err = 0;
		obj.CondNames = {};
		obj.path = filesepStandard(pwd);
		@@ -559,12 +561,81 @@ classdef TreeNodeClass < handle
		end


		% ----------------------------------------------------------------------------------
		function ch = GetMeasList(obj, iBlk)
		% ---------------------------------------------------------
		function ml = GetMeasurementList(obj, options, iBlk)
		ml = [];
		if ~exist('options','var')
		options = 'RAW';
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		for ii = 1:length(iBlk)
		switch(lower(options))
		case 'raw'
		if isempty(obj.acquired)
		continue
		end
		ml = [ml; obj.acquired.GetMeasurementList(ii)]; %#ok<*AGROW>
		case 'od'
		ml = [ml; obj.procStream.GetMeasurementList('od',ii)];
		case {'conc','hb','hbo','hbr','hbt'}
		ml = [ml; obj.procStream.GetMeasurementList('conc',ii)];
		case {'od hrf','od_hrf'}
		ml = [ml; obj.procStream.GetMeasurementList('od hrf',ii)];
		case {'hb hrf','conc hrf','hb_hrf','conc_hrf'}
		ml = [ml; obj.procStream.GetMeasurementList('conc hrf',ii)];
		end
		end
		end



		% ---------------------------------------------------------
		function [d, t] = GetDataTimeSeries(obj, options, iBlk)
		d = [];
		t = [];
		if ~exist('options','var')
		options = 'RAW';
		end
		if ~exist('iBlk','var') \|\| isempty(iBlk)
		iBlk = 1;
		end
		for ii = 1:length(iBlk)
		switch(lower(options))
		case 'raw'
		if isempty(obj.acquired)
		continue
		end
		d = [d, obj.acquired.GetDataTimeSeries(ii)]; %#ok<*AGROW>
		t = [t; obj.GetTime(ii)];
		case 'od'
		d = [d, obj.procStream.GetDataTimeSeries('od',ii)];
		t = [t; obj.GetTime(ii)];
		case {'conc','hb','hbo','hbr','hbt'}
		d = [d, obj.procStream.GetDataTimeSeries('conc',ii)];
		t = [t; obj.GetTime(ii)];
		case {'od hrf','od_hrf'}
		d = [d, obj.procStream.GetDataTimeSeries('od hrf',ii)];
		t = [t; obj.procStream.GetTHRF(ii)];
		case {'hb hrf','conc hrf','hb_hrf','conc_hrf'}
		d = [d, obj.procStream.GetDataTimeSeries('conc hrf',ii)];
		t = [t; obj.procStream.GetTHRF(ii)];
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function ch = GetMeasList(obj, options, iBlk)
		ch = [];
		if ~exist('options','var')
		options = '';
		end
		if ~exist('iBlk','var')
		iBlk = 1;
		end
		for ii = 1:length(obj.children)
		if isempty(ch)
		ch = obj.children(ii).GetMeasList(iBlk);
		@@ -578,9 +649,15 @@ classdef TreeNodeClass < handle
		end
		end
		end
		if strcmp(options,'reshape')
		[ch.MeasList, order] = sortrows(ch.MeasList);
		ch.MeasListActMan = ch.MeasListActMan(order);
		ch.MeasListActAuto = ch.MeasListActAuto(order);
		end
		end



		% ----------------------------------------------------------------------------------
		function SetMeasListVis(obj, chVis, iBlk)
		if ~exist('chVis','var')
		@@ -773,12 +850,6 @@ classdef TreeNodeClass < handle
		end


		% ----------------------------------------------------------------------------------
		function d = GetDataTimeSeries(~, ~, ~)
		d = [];
		end


		% ----------------------------------------------------------------------------------
		function t = GetTime(~, ~)
		t = [];
		@@ -895,7 +966,7 @@ classdef TreeNodeClass < handle
		procStreamFunctionsExportFilenames = findTypeFiles([obj.path, obj.outputDirname], fmt);
		for ii = 1:length(procStreamFunctionsExportFilenames)
		[~, fname, ext] = fileparts(procStreamFunctionsExportFilenames{ii});
		fname = [fname, ext]; %#ok<AGROW>
		fname = [fname, ext];
		if ~strcmp(fname(end-length(suffix)+1 : end), suffix)
		continue;
		end

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