Added Example Matlab script with most common during beamtime processing

2025-12-05 15:35:30 +01:00
1 parent 53dd8c6080
commit bbfab45787
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+%% How do I ....
+clc;clear all;close all
+load FileList.mat
+
+%% ... quick-and-dirty normalize
+%
+% Normalize counts per second to a reference intensity? You need to plot the
+% two spectra and use the cursor to read the intensities from the figures.
+% Then change the spectra intensities directly in the table as shown here:
+%
+% Do not save the FileList. This way you can reload it from the MAT file to
+% start fresh.
+close all;clc
+tmpDataSelection =  matches(FileList.name,"0146146_Cl2p_850eV.ibw");
+FileList = nappGenerateSpectra(FileList,tmpDataSelection);
+nappPlot(FileList,tmpDataSelection,'tableVariable','spectrum_countsPerSecond','mode','OneEach');
+xlim([647 652])
+FileList(tmpDataSelection,:).spectrum_countsPerSecond{:} = FileList(tmpDataSelection,:).spectrum_countsPerSecond{:} .* 22335./39687;
+nappPlot(FileList,tmpDataSelection,'tableVariable','spectrum_countsPerSecond','mode','OneEach');
+xlim([647 652])
+ylabel("counts [norm to Al]")
+legend
+distFig
+
+%% ... quick-and-dirty shift spectra
+%
+% If you do not want to generate the binding-energy scale using the
+% nappMATLAB function.
+close all;clc
+% Select your data based on the filename
+tmpDataSelection = startsWith(FileList.name, "0191191_O1s_VB_525eV");
+% List the selected files in the command window
+disp(FileList(tmpDataSelection,{'name','lastModifiedDatestr','scientaPassEnergy_eV'}))
+% Generate spectra
+FileList = nappGenerateSpectra(FileList,tmpDataSelection);
+% Plot in kinetic-energy mode
+nappPlot(FileList,tmpDataSelection,'tableVariable','spectrum_countsPerSecond','mode','AllInOne','energyScale','kinetic');
+% Apply the shift to kinetic energy manually and plot
+FileList(tmpDataSelection,:).scientaEkin_eV{:} = FileList(tmpDataSelection,:).scientaEkin_eV{:}-20;
+nappPlot(FileList,tmpDataSelection,'tableVariable','spectrum_countsPerSecond','mode','AllInOne','energyScale','kinetic');
+distFig
+
+%% ... remove a sweep (sequence iteration) from data
+close all; clc
+% Remove sweep 3:
+tmpDataSelection = contains(FileList.name,'0146146_Al2p_850eV.ibw');
+nappPlot(FileList,tmpDataSelection,'tableVariable','image')
+FileList(tmpDataSelection,:).image{:}(:,3)=[];
+nappPlot(FileList,tmpDataSelection,'tableVariable','image')
+distFig
+
+%% ... remove several sweeps
+close all; clc
+tmpDataSelection = contains(FileList.name,'0146146_Al2p_850eV.ibw');
+% Remove sweeps 5–9
+nappPlot(FileList,tmpDataSelection,'tableVariable','image')
+FileList(tmpDataSelection,:).image{:}(:,5:9)=[];
+nappPlot(FileList,tmpDataSelection,'tableVariable','image')
+distFig
+
+%% ... correct beamline offset
+% This will correct 1.6 eV on the X-ray energies, which is particularly
+% important for NEXAFS data. One can also do this on selected data only.
+FileList.xRayEkin_eV = cellfun(@(x) x+1.6,FileList.xRayEkin_eV,'UniformOutput',false);
+
+%% ... on-the-fly shift data in a figure
+tmpDataSelection =  month(FileList.lastModifiedDatenum) == 11 ...
+    & year(FileList.lastModifiedDatenum) == 2025 ...
+    & ~contains(FileList.sample,"(bad data)") ...
+    & contains(FileList.name,"O_Kedge_Resonant") ...
+    & contains(FileList.name,"0025");
+nappPlot(FileList,tmpDataSelection,'tableVariable','image','mode','AugerMeitner','AugerMeitnerEnergies',[525,545,550]);
+hax = gca;
+hax.XDir = 'reverse';
+xlabel('Auger-Meitner binding energy [eV]');
+% Shift data (same works in Y direction)
+dataObjs = findobj(gcf,'-property','YData');
+dataObjs(1).XData = dataObjs(1).XData -10;
+dataObjs(2).XData = dataObjs(2).XData +10;
+dataObjs(3).XData = dataObjs(3).XData +20;
+
+%% ... on-the-fly smooth data in a figure
+clc;close all
+tmpDataSelection =  month(FileList.lastModifiedDatenum) == 11 ...
+    & year(FileList.lastModifiedDatenum) == 2025 ...
+    & ~contains(FileList.sample,"(bad data)") ...
+    & contains(FileList.name,"O_Kedge_Resonant") ...
+    & contains(FileList.name,"0025");
+nappPlot(FileList,tmpDataSelection,'tableVariable','image','mode','AugerMeitner','AugerMeitnerEnergies',[525,545,550]);
+hax = gca;
+hax.XDir = 'reverse';
+xlabel('Auger-Meitner binding energy [eV]');
+dataObjs = findobj(gcf,'-property','YData');
+y = dataObjs(1).YData;
+dataObjs(1).YData = smoothdata(y ,'sgolay',10);
+y = dataObjs(2).YData;
+dataObjs(2).YData = smoothdata(y ,'sgolay',10);
+y = dataObjs(3).YData;
+dataObjs(3).YData = smoothdata(y ,'sgolay',10);
+
+%% ... on-the-fly remove data from a figure
+clc;close all
+tmpDataSelection =  month(FileList.lastModifiedDatenum) == 11 ...
+    & year(FileList.lastModifiedDatenum) == 2025 ...
+    & ~contains(FileList.sample,"(bad data)") ...
+    & contains(FileList.name,"O_Kedge_Resonant") ...
+    & contains(FileList.name,"0025");
+nappPlot(FileList,tmpDataSelection,'tableVariable','image','mode','AugerMeitner','AugerMeitnerEnergies',[525,545,550]);
+hax = gca;
+hax.XDir = 'reverse';
+xlabel('Auger-Meitner binding energy [eV]');
+
+dataObjs = findobj(gcf,'-property','YData');
+delete(dataObjs(1))
+legend('545','550');
+
+%% ... on-the-fly change colors in a figure
+clc;close all
+tmpDataSelection =  month(FileList.lastModifiedDatenum) == 11 ...
+    & year(FileList.lastModifiedDatenum) == 2025 ...
+    & ~contains(FileList.sample,"(bad data)") ...
+    & contains(FileList.name,"O_Kedge_Resonant") ...
+    & contains(FileList.name,"0025");
+nappPlot(FileList,tmpDataSelection,'tableVariable','image','mode','AugerMeitner','AugerMeitnerEnergies',[525,545,550]);
+hax = gca;
+hax.XDir = 'reverse';
+xlabel('Auger-Meitner binding energy [eV]');
+
+dataObjs = findobj(gcf,'-property','YData');
+dataObjs(2).Color = [184 184 185]/255;
+dataObjs(3).Color = [58 162 190]/255;