added Auger-Meitner plots and interactive NEXAFS
This commit is contained in:
bartels-rausch committed
1 parent
5a65fa13c4
commit
aac4e834c3
1 file changed
+267
-22
+267
-22
@@ -28,11 +28,11 @@ function hdl = nappPlot(DataTable,varargin)
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defaultTableVariable = 'image';
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expectedTableVariable = {'image','imageRoh','spectrum_countsPerSecond','spectrum_counts','spectrum_countsNorm'};
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defaultMode = 'AllInOne';
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expectedMode = {'AllInOne','OneEach','iterations'};
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expectedMode = {'AllInOne','OneEach','iterations','AugerMeitner','interactive'};
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defaultFigureMode = 'screen';
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expectedFigureMode = {'screen','powerpoint','word'};
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defaultEnergyScale = 'kinetic';
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expectedEnergyScale = {'kinetic','binding','xRay'};
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expectedEnergyScale = {'kinetic','binding','xRay','sweeps'};
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defaultTableSelection = true(size(DataTable,1),1);
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defaultPlotStep = 1;
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@@ -49,8 +49,11 @@ addParameter(p,'figureMode',defaultFigureMode,...
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addParameter(p,'energyScale',defaultEnergyScale,...
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@(x) any(validatestring(x,expectedEnergyScale)));
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addParameter(p,'plotStep',defaultPlotStep);
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addParameter(p,'AugerMeitnerEnergies',@isnumeric)
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parse(p,DataTable,varargin{:});
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if ~all(cell2mat(cellfun(@size,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable),'UniformOutput',false)),'all')
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disp('The table variable appears to be empty. I quit now')
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error('The table variable appears to be empty.')
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@@ -88,32 +91,182 @@ elseif contains(p.Results.figureMode,'word')
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end
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if matches(p.Results.mode,'AugerMeitner')
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
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if size(p.Results.AugerMeitnerEnergies) >= 7
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tmp_color = colormap(parula(size(p.Results.AugerMeitnerEnergies,2)));
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else
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tmp_color = colormap(lines(size(p.Results.AugerMeitnerEnergies,2)));
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end
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% Create axes
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hold(gca,'on');
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for ij = 1:size(p.Results.AugerMeitnerEnergies,2)
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% find x-ray energy in data
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tmpXrayEnergy = find(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii} >= p.Results.AugerMeitnerEnergies(ij),1);
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hplot= plot( p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,tmpXrayEnergy));
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hplot.LineWidth = lw;
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hold on
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end
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xlabel('Auger-Meitner electron energy [eV]')
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hYLabel = ylabel('Counts per dwell time');
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legend(string(p.Results.AugerMeitnerEnergies))
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if matches(p.Results.tableVariable,'image')
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end
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end
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end
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if matches(p.Results.tableVariable,'image') && matches(p.Results.mode,'interactive')
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',[20 100 1000 800]);
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tld = tiledlayout(2,2);
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tld.TileSpacing = 'compact';
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tld.Padding = 'compact';
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% image
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ax1= nexttile;
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img_handle = image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',ax1,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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box(gca,'on');
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set( gca, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(gca, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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hdl.Pointer = 'crosshair';
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ij= 1;
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ik=1;
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% Auger-Meitner
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ax2 = nexttile;
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hplot= plot(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij), p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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hplot.LineWidth = lw;
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hold on
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ylabel('A-M e energy [eV]')
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xlabel('Counts per dwell time');
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ax2.YDir = 'reverse';
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box(ax2,'on');
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set( ax2, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(ax2, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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% NEXAFS
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ax3 = nexttile;
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hplot2= plot( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(ik,:));
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hplot2.LineWidth = lw;
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hold on
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xlabel('xray energy [eV]')
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hYLabel = ylabel('Counts per dwell time');
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box(ax3,'on');
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set( ax3, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(ax3, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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if ~matches(p.Results.figureMode,'word')
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title(tld,p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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% % NOW set up datacursor - after all axes are created
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dcm = datacursormode(hdl);
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set(dcm, 'UpdateFcn', {@updatePlots, p.Results, ii, ax2, ax3, hplot, hplot2});
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set(dcm, 'Enable', 'on');
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set(dcm, 'SnapToDataVertex', 'off'); % Allows smooth mouse tracking
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set(dcm, 'DisplayStyle', 'window'); % or 'datatip' for tooltip style
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% Enable continuous update on mouse move
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set(hdl, 'WindowButtonMotionFcn', {@mouseMoveFcn, dcm, p.Results, ii, ax2, ax3, hplot, hplot2, ax1});
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end
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end
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end
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if matches(p.Results.tableVariable,'image') && ~matches(p.Results.mode,'AugerMeitner') && ~matches(p.Results.mode,'interactive')
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
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% Create axes
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hold(gca,'on');
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% Try to plot image with x and y
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try
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% interpolate, to have equal x spacing for image plot
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Xq = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1):0.1:p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end);
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Vq = interp2(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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image(Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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Vq,'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
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ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
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hXLabel = xlabel('Photon energy [eV]');
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hYLabel = ylabel('Auger energy [eV]');
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% if this does not work, plot without scaling (just with row and column numbers)
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catch
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if matches(p.Results.energyScale,'sweep')
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image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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@@ -121,8 +274,33 @@ if matches(p.Results.tableVariable,'image')
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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end
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else
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% Try to plot image with x and y
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try
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% interpolate, to have equal x spacing for image plot
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Xq = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1):0.1:p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end);
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Vq = interp2(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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image(Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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Vq,'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
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ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
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hXLabel = xlabel('Photon energy [eV]');
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hYLabel = ylabel('Auger energy [eV]');
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% if this does not work, plot without scaling (just with row and column numbers)
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catch
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image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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end
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end
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box(gca,'on');
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if ~matches(p.Results.figureMode,'word')
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title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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@@ -404,7 +582,7 @@ if contains(p.Results.tableVariable,'spectrum')
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if contains(p.Results.mode,'AllInOne')
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% generate colormap
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hdl = figure('Name','AllInOneSpectrum','units', unt,'Position',pos);
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if size(p.Results.DataTable(p.Results.tableSelection,:),1) >= 7
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tmp_color = colormap(parula(size(p.Results.DataTable(p.Results.tableSelection,:),1)));
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@@ -435,7 +613,7 @@ if contains(p.Results.tableVariable,'spectrum')
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end
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hXLabel= xlabel('Binding energy [eV]');
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elseif contains(p.Results.energyScale,'xRay')
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hold(gca,'on');
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hold(gca,'on');
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
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hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},...
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@@ -553,5 +731,72 @@ if contains(p.Results.mode,'iterations')
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end
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end
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end
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% Nested callback function
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% function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
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% pos = get(event_obj, 'Position');
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% ij = round(pos(1));
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% ik = round(pos(2));
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%
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% set(hplot2, 'XData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(:,ij));
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% title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
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%
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% set(hplot3, 'YData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(ik,:));
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% title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
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%
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% % Create custom datatip text showing coordinates
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% txt = {sprintf('X index: %d', ij), ...
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% sprintf('Y index: %d', ik), ...
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% sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
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% end
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function mouseMoveFcn(~, ~, dcm, pResults, ii, ax2, ax3, hplot2, hplot3, ax1)
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% Check if mouse is over the image axes
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if gca == ax1
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% Get current mouse position
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cp = get(ax1, 'CurrentPoint');
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ij = round(cp(1, 1)); % X index
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ik = round(cp(1, 2)); % Y index
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% Get the data matrix
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dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
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% Ensure indices are within bounds
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[nRows, nCols] = size(dataMatrix);
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if ij >= 1 && ij <= nCols && ik >= 1 && ik <= nRows
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% Update plots
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set(hplot2, 'XData', dataMatrix(:, ij));
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title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
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set(hplot3, 'YData', dataMatrix(ik, :));
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title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
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end
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end
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end
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% Datatip callback - shows info
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function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
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try
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pos = get(event_obj, 'Position');
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ij = round(pos(1));
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ik = round(pos(2));
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dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
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[nRows, nCols] = size(dataMatrix);
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ij = max(1, min(ij, nCols));
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ik = max(1, min(ik, nRows));
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txt = {sprintf('X: %d', ij), ...
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sprintf('Y: %d', ik), ...
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sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
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catch
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pos = get(event_obj, 'Position');
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txt = {sprintf('X: %.1f', pos(1)), ...
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sprintf('Y: %.1f', pos(2))};
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end
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end
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end
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