v1.16.3 (04a8d3ab) · Commits · github_fork / Homer3

DataTree/AcquiredData/Snirf/DataClass.m

+15 −18

Original line number	Diff line number	Diff line
		@@ -213,24 +213,21 @@ classdef DataClass < FileLoadSaveClass


		% ---------------------------------------------------------
		function ml = GetMeasListDod(obj)
		ml = zeros(length(obj.measurementList), 2);
		for ii=1:length(obj.measurementList)
		if obj.measurementList(ii).GetWavelengthIndex()==1
		ml(ii,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex()];
		end
		end
		function idxs = GetMeasurementListIdxs(obj, CondIdxs)
		% Get all the measurementList array idxs matching the
		% conditions in the CondNames argument
		idxs = zeros(1,length(obj.measurementList));
		kk=1;
		for iCh = 1:length(obj.measurementList)
		for iCond = 1:length(CondIdxs)
		if sum(obj.measurementList(iCh).dataTypeIndex == CondIdxs)
		idxs(kk) = iCh;
		kk=kk+1;
		break;
		end


		% ---------------------------------------------------------
		function ml = GetMeasListDc(obj)
		ml = zeros(length(obj.measurementList), 2);
		for ii=1:length(obj.measurementList)
		if obj.measurementList(ii).GetDataTypeLabel()==6
		ml(ii,:) = [obj.measurementList(ii).GetSourceIndex(), obj.measurementList(ii).GetDetectorIndex()];
		end
		end
		idxs(idxs==0) = [];
		end

DataTree/GroupClass.m

+74 −0

Original line number	Diff line number	Diff line
		@@ -625,6 +625,52 @@ classdef GroupClass < TreeNodeClass
		end


		% ----------------------------------------------------------------------------------
		function tblcells = ExportMeanHRF(obj, iBlk)
		if nargin<2
		iBlk = 1;
		end

		nCh = obj.procStream.GetNumChForOneCondition(iBlk);
		nCond = length(obj.CondNames);
		nSubj = length(obj.subjs);

		% Determine table dimensions
		nHdrRows = 3; % Blank line + name of columns
		nHdrCols = 2; % Condition name + subject name
		nDataRows = nSubj*nCond;
		nDataCols = nCh; % Number of channels for one condition (for example, if data type is Hb Conc: (HbO + HbR + HbT) * num of SD pairs)
		nTblRows = nDataRows + nHdrRows;
		nTblCols = nDataCols + nHdrCols;
		cellwidthCond = max(length('Condition'), obj.CondNameSizeMax());
		cellwidthSubj = max(length('Subject Name'), obj.SubjNameSizeMax());

		%%%% Initialize 2D array of TableCell objects with the above row * column dimensions
		tblcells = repmat(TableCell(), nTblRows, nTblCols);

		% Header row: Condition, Subject Name, HbO,1,1, HbR,1,1, HbT,1,1, ...
		tblcells(2,1) = TableCell('Condition', cellwidthCond);
		tblcells(2,2) = TableCell('Subject Name', cellwidthSubj);
		[tblcells(2,3:end), cellwidthData] = obj.procStream.GenerateTableCellsHeader_MeanHRF(iBlk);

		% Generate data rows
		for iSubj = 1:nSubj
		rowIdxStart = ((iSubj-1)*nCond)+1 + nHdrRows;
		rowIdxEnd = rowIdxStart + nCond - 1;

		tblcells(rowIdxStart:rowIdxEnd, 1:2) = obj.subjs(iSubj).GenerateTableCellsHeader_MeanHRF(cellwidthCond, cellwidthSubj);
		tblcells(rowIdxStart:rowIdxEnd, 3:nTblCols) = obj.subjs(iSubj).GenerateTableCells_MeanHRF(cellwidthData, iBlk);
		end

		% Create ExportTable initialized with the filled in 2D TableCell array.
		% ExportTable object is what actually does the exporting to a file.
		tbl = ExportTable(obj.name, 'HRF mean', tblcells);
		tbl.Open()
		tbl.Save();
		tbl.Close();

		end

		end % Public Save/Load methods


		@@ -777,6 +823,34 @@ classdef GroupClass < TreeNodeClass
		end
		end


		% ----------------------------------------------------------------------------------
		function n = CondNameSizeMax(obj)
		n = 0;
		if isempty(obj.CondNames)
		return;
		end
		for ii = 1:length(obj.CondNames)
		if length(obj.CondNames{ii}) > n
		n = length(obj.CondNames{ii});
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function n = SubjNameSizeMax(obj)
		n = 0;
		if isempty(obj.subjs)
		return;
		end
		for ii = 1:length(obj.subjs)
		if length(obj.subjs(ii).name) > n
		n = length(obj.subjs(ii).name);
		end
		end
		end

		end % Private methods

		end % classdef GroupClass < TreeNodeClass

DataTree/ProcStream/ProcResultClass.m

+75 −9

Original line number	Diff line number	Diff line
		@@ -439,7 +439,7 @@ classdef ProcResultClass < handle


		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Export related methods
		%
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		methods

		@@ -507,17 +507,81 @@ classdef ProcResultClass < handle
		end
		end


		% ----------------------------------------------------------------------------------
		function n = GetNumChForOneCondition(obj, iBlk)
		n = [];
		if nargin<2
		iBlk = 1;
		end
		if isa(obj.dcAvg, 'DataClass')
		n = length(obj.dcAvg(iBlk).GetMeasurementListIdxs(1));
		end
		end

		end


		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Export related methods
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		methods

		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_HRF(obj, CondNames, iBlk)
		function [tblcells, maxwidth] = GenerateTableCellsHeader_MeanHRF(obj, iBlk)
		if nargin<5
		iBlk = 1;
		end
		tblcells = TableCell.empty();
		maxwidth = length('HRF HbX,999,999');
		if isa(obj.dcAvg, 'DataClass')
		measList = obj.dcAvg(iBlk).measurementList;
		measListIdxs = obj.dcAvg(iBlk).GetMeasurementListIdxs(1);
		for iCh = measListIdxs
		tblcells(1,iCh) = TableCell(sprintf('%s,%d,%d', measList(iCh).dataTypeLabel, measList(iCh).sourceIndex, measList(iCh).detectorIndex), maxwidth);
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_MeanHRF(obj, name, CondNames, width, iBlk)
		if nargin<4
		width = 12;
		end
		if nargin<5
		iBlk = 1;
		end
		tblcells = TableCell.empty();
		if isa(obj.dcAvg, 'DataClass')
		dataTimeSeries = obj.dcAvg(iBlk).GetDataTimeSeries();

		% Data rows
		for iCond = 1:length(CondNames)
		measListIdxs = obj.dcAvg(iBlk).GetMeasurementListIdxs(iCond);
		for iCh = measListIdxs
		meanData = mean(dataTimeSeries(:,iCh));
		if isnan(meanData)
		cname = 'N/A';
		else
		cname = sprintf('%s%0.5e', blanks(meanData>=0), meanData);
		end
		tblcells(iCond, mod(iCh-1, length(measListIdxs))+1) = TableCell(cname, width);
		end
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_HRF(obj, CondNames, iBlk)
		if nargin<3
		iBlk = 1;
		end
		tblcells = TableCell.empty();
		if isa(obj.dcAvg, 'DataClass')
		dataTimeSeries = obj.dcAvg.GetDataTimeSeries();
		measList = obj.dcAvg.measurementList;
		dataTimeSeries = obj.dcAvg(iBlk).GetDataTimeSeries();
		measList = obj.dcAvg(iBlk).measurementList;

		% Header: stim condition name row
		for iCh = 1:length(measList)
		@@ -540,6 +604,8 @@ classdef ProcResultClass < handle
		tblcells(t+2,iCh) = TableCell(cname, 12);
		end
		end
		else

		end
		end

DataTree/ProcStream/ProcStreamClass.m

+57 −11

Original line number	Diff line number	Diff line
		@@ -339,15 +339,6 @@ classdef ProcStreamClass < handle
		b = obj.output.HaveTimeCourseOutput();
		end


		% ----------------------------------------------------------------------------------
		function ExportHRF(obj, filename, CondNames, iBlk)
		if nargin<3
		iBlk = 1;
		end
		obj.output.ExportHRF(filename, CondNames, iBlk);
		end

		end


		@@ -1289,6 +1280,15 @@ classdef ProcStreamClass < handle
		pValues = obj.output.GetVar('pValues',iBlk);
		end


		% ----------------------------------------------------------------------------------
		function n = GetNumChForOneCondition(obj, iBlk)
		if nargin<2
		iBlk = 1;
		end
		n = obj.output.GetNumChForOneCondition(iBlk);
		end

		end


		@@ -1455,5 +1455,51 @@ classdef ProcStreamClass < handle

		end


		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Export related methods
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		methods

		% ----------------------------------------------------------------------------------
		function [tblcells, maxwidth] = GenerateTableCellsHeader_MeanHRF(obj, iBlk)
		if nargin<2
		iBlk = 1;
		end
		[tblcells, maxwidth] = obj.output.GenerateTableCellsHeader_MeanHRF(iBlk);
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_MeanHRF(obj, name, CondNames, width, iBlk)
		if nargin<4
		width = 12;
		end
		if nargin<5
		iBlk = 1;
		end
		tblcells = obj.output.GenerateTableCells_MeanHRF(name, CondNames, width, iBlk);
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_HRF(obj, CondNames, iBlk)
		if nargin<3
		iBlk = 1;
		end
		tblcells = obj.output.GenerateTableCells_HRF(name, CondNames, iBlk);
		end


		% ----------------------------------------------------------------------------------
		function ExportHRF(obj, filename, CondNames, iBlk)
		if nargin<3
		iBlk = 1;
		end
		obj.output.ExportHRF(filename, CondNames, iBlk);
		end

		end

		end

DataTree/SubjClass.m

+23 −0

Original line number	Diff line number	Diff line
		@@ -425,6 +425,29 @@ classdef SubjClass < TreeNodeClass
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCells_MeanHRF(obj, width, iBlk)
		if nargin<2
		width = 12;
		end
		if nargin<3
		iBlk = 1;
		end
		tblcells = obj.procStream.GenerateTableCells_MeanHRF(obj.name, obj.CondNames, width, iBlk);
		end


		% ----------------------------------------------------------------------------------
		function tblcells = GenerateTableCellsHeader_MeanHRF(obj, widthCond, widthSubj)
		tblcells = repmat(TableCell(), length(obj.CondNames), 2);
		for iCond = 1:length(obj.CondNames)
		% First 2 columns contain condition name and group, subject or run name
		tblcells(iCond, 1) = TableCell(obj.CondNames{iCond}, widthCond);
		tblcells(iCond, 2) = TableCell(obj.name, widthSubj);
		end
		end


		% ----------------------------------------------------------------------------------
		function ExportHRF(obj, options, iBlk)
		if nargin<2 \|\| isempty(options)

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