v1.46.0 (5d3d66e0) · Commits · github_fork / Homer3

PlotProbeGUI/PlotProbeGUI.m

+6 −5

Original line number	Diff line number	Diff line
		@@ -273,7 +273,7 @@ SetTextFilename(handles);
		DisplayData(handles, hObject);

		if ~menuItemSyncBrowsing_Callback(handles.menuItemSyncBrowsing, 'get')
		menuItemSyncBrowsing_Callback(handles.menuItemSyncBrowsing, '', handles);
		menuItemSyncBrowsing_Callback(handles.menuItemSyncBrowsing, '');
		end


		@@ -497,7 +497,7 @@ if length(foo)~=1
		foo = plotprobe.tMarkInt;
		elseif ~isnumeric(foo)
		foo = plotprobe.tMarkInt;
		elseif foo<5 \|\| foo>t(end)
		elseif foo<2 \|\| foo>t(end)
		foo = plotprobe.tMarkInt;
		end
		plotprobe.tMarkInt = foo;
		@@ -698,6 +698,7 @@ nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();
		plotprobe.y = cell(nDataBlks,1);
		plotprobe.t = cell(nDataBlks,1);

		tMarkAmp = str2num(get(handles.editPlotProbeTimeMarkersAmp, 'string'));
		for iBlk = 1:nDataBlks
		if datatype == plotprobe.datatypeVals.OD_HRF
		plotprobe.y{iBlk} = plotprobe.dataTreeHandle.currElem.GetDodAvg(condition, iBlk);
		@@ -706,7 +707,7 @@ for iBlk = 1:nDataBlks
		elseif datatype == plotprobe.datatypeVals.CONC_HRF
		plotprobe.y{iBlk} = plotprobe.dataTreeHandle.currElem.GetDcAvg(condition, iBlk);
		plotprobe.t{iBlk} = plotprobe.dataTreeHandle.currElem.GetTHRF();
		plotprobe.tMarkAmp = plotprobe.tMarkAmp/1e6;
		plotprobe.tMarkAmp = tMarkAmp/1e6;
		plotprobe.tMarkUnits = '(micro-molars)';
		end

PlotProbeGUI/plotProbe.m

+146 −222

Original line number	Diff line number	Diff line
		@@ -14,9 +14,9 @@
		% <DATA TIME POINTS> x <CHANNELS OF ALL WAVELENGTHS>
		%
		% If empty, then the probe is plotted with lines joining sources
		% and detectors in the ch.MeasList with solid line and
		% and detectors in the ml with solid line and
		% dotted line distringuishing active measurements as indicated in
		% ch.MeasListActMan
		% mlActMan
		%
		% t - is the corresponding time vector
		%
		@@ -41,10 +41,7 @@
		% toggle nearest neighbors
		% assuming y is concentration data... need to check dimensions

		function h = plotProbe( y, t, SD, ch, ystd, axFactor, tStep, tAmp, tVis)

		EXPLODE_THRESH = 0.02;
		EXPLODE_VECTOR = [0.02, 0.08];
		function h = plotProbe( y, t, SD, ml, ~, axFactor, tStep, tAmp, tVis)

		h = [];

		@@ -74,8 +71,8 @@ end
		if ~isempty(t)
		if ~exist('tStep','var') \|\| isempty(tStep) \|\| tStep>t(end)
		tStep = t(end);
		elseif tStep<5 && tStep~=0
		tStep = 5;
		elseif tStep<2 && tStep~=0
		tStep = 2;
		end
		end
		if ~exist('tAmp','var') \|\| isempty(tAmp) \|\| tAmp<0
		@@ -86,16 +83,14 @@ end
		if ~exist('SD','var') \|\| isempty(SD)
		return;
		end
		if ~exist('ch','var') \|\| isempty(ch)
		return;
		end


		% This section will give the option to display subsections of the probe
		% based on nearest-neighbor etc distances. If the probe only has one
		% distance, this option is not given
		Distances=((SD.SrcPos(ch.MeasList(:,1),1) - SD.DetPos(ch.MeasList(:,2),1)).^2 +...
		(SD.SrcPos(ch.MeasList(:,1),2) - SD.DetPos(ch.MeasList(:,2),2)).^2 +...
		(SD.SrcPos(ch.MeasList(:,1),3) - SD.DetPos(ch.MeasList(:,2),3)).^2).^0.5;
		Distances = ((SD.SrcPos(ml(:,1),1) - SD.DetPos(ml(:,2),1)).^2 +...
		(SD.SrcPos(ml(:,1),2) - SD.DetPos(ml(:,2),2)).^2 +...
		(SD.SrcPos(ml(:,1),3) - SD.DetPos(ml(:,2),3)).^2).^0.5;
		nearneighborLst = ones(length(Distances),1);
		lstNN = find(nearneighborLst==1);

		@@ -114,7 +109,6 @@ sd2axScl = max(sdWid,sdHgt);
		sPos = sPos / sd2axScl;
		dPos = dPos / sd2axScl; % xlim([min(t) max(t)])


		nAcross = length(unique([sPos(:,1); dPos(:,1)]))+1;
		nUp = length(unique([sPos(:,2); dPos(:,2)]))+1;

		@@ -124,17 +118,12 @@ axHgt = axFactor(2) * 1/nUp;
		axXoff = mean([sPos(:,1);dPos(:,1)])-.5;
		axYoff = mean([sPos(:,2);dPos(:,2)])-.5;

		ml = ch.MeasList;
		mlAct = ones(size(ml,1),1);

		%This is the plotting routine
		try
		% Initialize channel idx for try/catch. Catch uses it
		% to display which channel was being processed when
		% error ocurred.
		idx = 0;

		if ndims(y)==3
		color = [
		1.00 0.00 0.00;
		0.00 0.00 1.00;
		@@ -143,47 +132,24 @@ try
		0.00 1.00 1.00;
		0.50 0.80 0.30
		];
		else
		if SD.Lambda(1)<SD.Lambda(2)
		color=[
		0.00 0.00 1.00;
		1.00 0.00 0.00;
		0.00 1.00 1.00;
		1.00 0.00 1.00;
		0.50 0.80 0.30
		];
		else
		color=[
		1.00 0.00 0.00;
		0.00 0.00 1.00;
		1.00 0.00 1.00;
		0.00 1.00 1.00;
		0.50 0.80 0.30
		];
		end
		end

		% ha = subplot(1,1,1);
		minT = min(t);
		maxT = max(t);

		if ~isempty(y)
		lstW1 = find(ml(:,4)==1);
		lstW2 = find(ml(:,4)==2);
		nCh = length(lstW1);
		nDataTypes = ndims(y);
		nTSteps = round(t(end)/tStep);
		tStep = tStep/(t(2)-t(1));

		% To eliminate displayed data drifting when scaling y up
		% or down offset data to align min/max midpoint with zero.
		[Avg, offset] = offsetData(y,nCh,nDataTypes);
		if ~isempty(y)
		iSrc = ml(1,1);
		iDet = ml(1,2);
		iMeasSDpair = find( (ml(:,1) == iSrc) & (ml(:,2) == iDet) );
		nDataTypes = length(iMeasSDpair);
		nSDpairs = size(ml,1)/nDataTypes;
		iSDpairs = find( ml(:,4) == 1 );

		if ndims(Avg)==3
		minAmp=min(min(min(Avg)));
		maxAmp=max(max(max(Avg)));
		else
		minAmp=min(min(Avg));
		maxAmp=max(max(Avg));
		end
		minAmp = min(min(y));
		maxAmp = max(max(y));

		if length(tAmp)==2
		cmin = tAmp(1);
		@@ -193,59 +159,42 @@ try
		cmax = maxAmp;
		end

		nTSteps = round(t(end)/tStep);
		tStep = tStep/(t(2)-t(1));
		h=zeros(nCh,nDataTypes+nTSteps);
		ls=repmat({''},nCh,1);
		lw=zeros(nCh,nDataTypes+nTSteps);
		lv=repmat({''},nCh,nDataTypes+nTSteps);
		lc=zeros(nCh,nDataTypes+nTSteps,3);
		h = zeros(nSDpairs, nDataTypes);
		ls = repmat({''}, nSDpairs, 1);
		lw = zeros(nSDpairs, nDataTypes);
		lv = repmat({''}, nSDpairs, nDataTypes);
		lc = zeros(nSDpairs, nDataTypes, 3);

		xyas = [];

		for idx=1:length(lstW1)
		try
		for iSD = 1:length(iSDpairs)

		% Record line graphics properties based on the object type
		[lc,lv,lw,ls] = setLineProperties(lc,lv,lw,ls,idx,mlAct,color,nDataTypes,nTSteps);
		% Get all measurements with current source and detector pair
		iSrc = ml(iSDpairs(iSD),1);
		iDet = ml(iSDpairs(iSD),2);
		iSDpairAllMeas = find( (ml(:,1) == iSrc) & (ml(:,2) == iDet) );

		xa = (sPos(ml(lstW1(idx),1),1) + dPos(ml(lstW1(idx),2),1))/2 - axXoff;
		ya = (sPos(ml(lstW1(idx),1),2) + dPos(ml(lstW1(idx),2),2))/2 - axYoff;
		% To eliminate displayed data drifting when scaling y up
		% or down offset data to align min/max midpoint with zero.
		[y, yOffset] = offsetData(y, iSDpairAllMeas);

		for i = 1:size(xyas, 1)
		if sqrt((xyas(i, 1) - xa)^2 + (xyas(i, 2) - ya)^2) < EXPLODE_THRESH
		xa = xa + EXPLODE_VECTOR(1);
		ya = ya + EXPLODE_VECTOR(2);
		end
		end
		for iMeasType = 1:length(iSDpairAllMeas)

		% Record line graphics properties based on the object type
		[lc,lv,lw,ls] = setLineProperties(lc,lv,lw,ls,iMeasType,mlAct,color,nDataTypes,nTSteps);

		xa = ( sPos(ml(iSDpairAllMeas(iMeasType),1), 1) + dPos(ml(iSDpairAllMeas(iMeasType),2), 1) ) / 2 - axXoff;
		ya = ( sPos(ml(iSDpairAllMeas(iMeasType),1), 2) + dPos(ml(iSDpairAllMeas(iMeasType),2), 2) ) / 2 - axYoff;

		xyas = [xyas; [xa, ya]];
		hold on

		xT = xa-axWid/4 + axWid*((t-minT)/(maxT-minT))/2;
		if ndims(Avg)==3
		AvgT = ya-axHgt/4 + axHgt*((Avg(:,:,idx)-cmin)/(cmax-cmin))/2;
		else
		AvgT(:,1) = ya-axHgt/4 + axHgt*((Avg(:,lstW1(idx))-cmin)/(cmax-cmin))/2;
		AvgT(:,2) = ya-axHgt/4 + axHgt*((Avg(:,lstW2(idx))-cmin)/(cmax-cmin))/2;
		end
		AvgT = ya-axHgt/4 + axHgt*((y(:,iSDpairAllMeas(iMeasType))-cmin)/(cmax-cmin))/2;

		hold on
		h(iSD,iMeasType) = plot( xT, AvgT,'color',color(iMeasType,:), 'visible','on', 'linewidth',2);

		if ~isempty(ystd) % Plot error bars if available
		h(idx,1)=errorbar(xT, AvgT(:,1), ystd(:,1), 'color',color(1,:), 'visible',lv{idx,1});
		if size(AvgT,2)>1
		h(idx,2)=errorbar(xT, AvgT(:,2), ystd(:,2), 'color',color(2,:), 'visible',lv{idx,2});
		end
		if size(AvgT,2)>2
		h(idx,3)=errorbar(xT, AvgT(:,3), ystd(:,3), 'color',color(3,:), 'visible',lv{idx,3});
		end
		else % Plot data without error bars
		h(idx,1)=plot( xT, AvgT(:,1),'color',color(1,:), 'visible',lv{idx, 1});
		if size(AvgT,2)>1
		h(idx,2)=plot( xT, AvgT(:,2),'color',color(2,:), 'visible',lv{idx, 2});
		end
		if size(AvgT,2)>2
		h(idx,3)=plot( xT, AvgT(:,3),'color',color(3,:), 'visible',lv{idx, 3});
		end
		end

		% Plot time markers starting with stim onset
		@@ -272,32 +221,30 @@ try
		AvgTmax = ya-axHgt/4 + axHgt*(((cmax-offset(idx))-cmin)/(cmax-cmin))/2;
		AvgTmin = ya-axHgt/4 + axHgt*(((cmin-offset(idx))-cmin)/(cmax-cmin))/2;
		end
		ii = nDataTypes+1;
		yStim = [AvgTmin,AvgTmax];
		kk = nDataTypes+1;
		yMark = [AvgTmin,AvgTmax]-yOffset;
		xT0 = xT(find(t==0));
		xTStep = tStep*(xT(2)-xT(1));
		if strcmp(lv{idx, ii}, 'off')
		if strcmp(lv{iSD(1),kk}, 'off')
		tvis_ch = 'off';
		else
		tvis_ch = tVis;
		end
		for xTi = xT0:xTStep:xT(end)
		xTi = [xTi xTi];
		h(idx,ii) = plot(xTi, yStim, 'color', 'k', 'visible', tvis_ch);
		lw(idx,ii) = 1.0;
		ii=ii+1;
		if ii-ndims(Avg)>nTSteps
		break;
		end
		xTi = [xTi, xTi];
		hTmarks = plot(xTi, yMark, 'color','k', 'visible',tvis_ch);
		h(iSD,kk) = hTmarks;
		lw(iSD,kk) = 1.0;
		kk = kk+1;
		end

		end

		% After plotting all the data, modify lines colors, styles, and width
		for idx=1:length(lstW1)
		for j=1:size(h,2)
		set(h(idx,j),'color',lc(idx,j,:),'linestyle',ls{idx},'linewidth',lw(idx,j));
		end
		catch

		menu(sprintf('plotProbe exited with ERROR while plotting data for channel # %d',iSD),'OK');
		h=[];

		end
		end

		@@ -326,12 +273,6 @@ try
		set(ht,'color',[0 0 1])
		end

		catch

		menu(sprintf('plotProbe exited with ERROR while plotting data for channel # %d',idx),'OK');
		h=[];

		end
		hold off


		@@ -377,49 +318,32 @@ end




		% ------------------------------------------------------
		function [y,ampMp] = offsetData(y,nCh,nDataTypes)

		if nDataTypes==3
		minAmp=squeeze(min(min(y)));
		maxAmp=squeeze(max(max(y)));
		elseif nDataTypes==2
		for idx=1:nCh
		minAmp(idx)=min(min(y(:,[idx idx+nCh])));
		maxAmp(idx)=max(max(y(:,[idx idx+nCh])));
		end
		end
		function [y,ampMp] = offsetData(y, k)
		minAmp = min(min(y(:,k)));
		maxAmp = max(max(y(:,k)));

		% Find amplitude mid-point
		% Find amplitude mid-point and shift data midpoint to zero
		ampDiff = maxAmp - minAmp;
		ampMp = minAmp + ampDiff/2;
		for idx=1:nCh
		% Shift data midpoint to zero
		if nDataTypes==3
		y(:,:,idx) = y(:,:,idx) - ampMp(idx);
		else
		y(:,[idx idx+nCh]) = y(:,[idx idx+nCh]) - ampMp(idx);
		end
		end
		y(:,k) = y(:,k) - ampMp;




		% ------------------------------------------------------
		function b = isProbeDrawn(SD)
		b = false;
		nOpt = size(SD.SrcPos,1)+size(SD.DetPos,1);
		hc = get(gca, 'children');
		nOptDrawn = 0;
		for ii=1:length(hc)
		if strcmpi(hc(ii).Type, 'Text')
		if hc(ii).String(1)=='S' \|\| hc(ii).String(1)=='D'
		nOptDrawn = nOptDrawn+1;
		end
		end
		function [y,ampMp] = offsetData2(y, iSDpairs, nSDpairs, ml)
		nDataTypes = size(y,2) / nSDpairs;
		minAmp = min(y(iSDpairs));
		maxAmp = max(y(iSDpairs));

		% Find amplitude mid-point and shift data midpoint to zero
		ampDiff = maxAmp - minAmp;
		ampMp = minAmp + ampDiff/2;
		for iSD = 1:nSDpairs
		for iDt = 1:nDataTypes
		iSDmeas = find(ml(iSDpairs,4) == iDt);
		y(:,iSDmeas) = y(:,iSDmeas) - ampMp(iSD);
		end
		if nOptDrawn==nOpt
		b = true;
		end

PlotProbeGUI/plotProbeAndSetProperties.m

+7 −5

Original line number	Diff line number	Diff line
		@@ -15,10 +15,8 @@ else
		ystd = [];
		end

		y = plotprobe.y{iBlk};
		ch.MeasList = plotprobe.dataTree.currElem.procStream.output.dcAvg.GetMeasurementList('matrix');
		k = find(ch.MeasList(:,4) == 1);
		ch.MeasList = ch.MeasList(k,:);
		y = plotprobe.dataTree.currElem.procStream.output.dcAvg.GetDataTimeSeries();
		ml = plotprobe.dataTree.currElem.procStream.output.dcAvg.GetMeasurementList('matrix');
		t = plotprobe.t{iBlk};
		tMarkInt = plotprobe.tMarkInt;
		axScl = plotprobe.axScl;
		@@ -26,9 +24,13 @@ tMarkAmp = plotprobe.tMarkAmp;
		tMarkVis = plotprobe.tMarkShow;
		SD = plotprobe.dataTree.currElem.GetSDG('2D');

		k = find(ml(:,3) == plotprobe.condition);
		y = y(:,k);
		ml = ml(k,:);

		data = getappdata(handles.figure, 'data');
		set(handles.textTimeMarkersAmpUnits, 'string',plotprobe.tMarkUnits);
		hData = plotProbe( y, t, SD, ch, ystd, axScl, tMarkInt, tMarkAmp, tMarkVis );
		hData = plotProbe( y, t, SD, ml, ystd, axScl, tMarkInt, tMarkAmp, tMarkVis );
		data{iFig} = hData;
		setappdata(handles.figure, 'data',data);

Version.txt

+1 −1

Original line number	Diff line number	Diff line
		1.45.0
		1.46.0

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