101 lines
4.5 KiB
Matlab
101 lines
4.5 KiB
Matlab
function combinedSpectrum = nappCombineSpectra(DataTable,varargin)
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%nappCombineSpectra combines selected PE or NEXAFS spectra into one. Data
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%are intrapolated along x-axis.
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%
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% MgO_C1s_Warm = nappCombineSpectra(FileList,'tableRow',1,...
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% 'tableSelection',tmpDataSelection,'tableVariable',...
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% 'spectrum_countsNorm','EnergyScale','binding','mode','average');
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%
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% *input*
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% FileList: data table
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% tableSelection (optional): logical array to filter data table
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% tableVariable (optional): select source: 'nexafsSpectrum','spectrum_counts','spectrum_countsPerSecond',...
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% 'spectrum_countsNorm','nexafsSpectrumPreBackground','nexafsSpectrumPreNorm',...
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% 'nexafsSpectrumPreGasPhase','nexafsSpectrumPreI0','nexafsSpectrumPreAdvCarb'
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% tableRow (optional): default 1. Defines the row in filtered table (to be
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% processed). The x-axis of that data set will be used for interpolation.
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% mode: mean (default) averages the spectra; sum adds them, subtract not
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% coded yet.
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% energyScale (optional): kinetic (default) or binding energy scale; only relevant
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% for PE spectra, not for NEXAFS
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%
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%
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% *output*
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% a matrix with energy in column 1, counts in column2, and standard
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% deviation in column 3 (only for mean).
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%
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expectedTableVariable = {'nexafsSpectrum','spectrum_counts','spectrum_countsPerSecond',...
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'spectrum_countsNorm','nexafsSpectrumPreBackground','nexafsSpectrumPreNorm',...
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'nexafsSpectrumPreGasPhase','nexafsSpectrumPreI0','nexafsSpectrumPreAdvCarb'};
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defaultTableSelection = true(size(DataTable,1));
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defaultTableRow = 1;
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defaultMode = 'sum';
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expectedMode = {'sum','average','subtract'};
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defaultEnergyScale = 'kinetic';
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expectedEnergyScale = {'kinetic','binding','xRay'};
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% Parse input
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p = inputParser;
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addRequired(p,'DataTable',@istable);
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addParameter(p,'tableSelection',defaultTableSelection,@islogical);
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addParameter(p,'tableRow',defaultTableRow,@isnumeric);
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addParameter(p,'tableVariable',...
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@(x) any(validatestring(x,expectedTableVariable)));
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addParameter(p,'mode',defaultMode,...
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@(x) any(validatestring(x,expectedMode)));
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addParameter(p,'energyScale',defaultEnergyScale,...
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@(x) any(validatestring(x,expectedEnergyScale)));
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parse(p,DataTable,varargin{:});
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% check input (all elements of input variable need to have non-zero size)
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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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end
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if (contains(p.Results.tableVariable,'counts')) && (contains(p.Results.energyScale,'kinetic'))
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tmpX = p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV;
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elseif (contains(p.Results.tableVariable,'counts')) && (contains(p.Results.energyScale,'binding'))
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tmpX = p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV;
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elseif contains(p.Results.tableVariable,'counts') && (contains(p.Results.energyScale,'xRay'))
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tmpX = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV;
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end
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if contains(p.Results.energyScale,'binding')
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tmpStart = min(cellfun(@(x) x(1), tmpX));
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tmpEnd = max(cellfun(@(x) x(end), tmpX));
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tmpStartIndex = find(tmpX{p.Results.tableRow} <= tmpStart,1);
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tmpEndIndex = find(tmpX{p.Results.tableRow} <= tmpEnd,1);
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else
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tmpStart = max(cellfun(@(x) x(1), tmpX));
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tmpEnd = min(cellfun(@(x) x(end), tmpX));
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tmpStartIndex = find(tmpX{p.Results.tableRow} >= tmpStart,1);
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tmpEndIndex = find(tmpX{p.Results.tableRow} >= tmpEnd,1);
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end
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xq = tmpX{p.Results.tableRow}(tmpStartIndex:tmpEndIndex);
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% repeat this for all columns in input.
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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x = tmpX{ii};
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v = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii};
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vq(:,ii) = interp1(x,v,xq);
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end
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combinedSpectrum(:,1) = xq;
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if contains(p.Results.mode,'sum')
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combinedSpectrum(:,2) = sum(vq,2,'omitnan');
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elseif contains(p.Results.mode,'average')
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combinedSpectrum(:,2) = mean(vq,2,'omitnan');
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combinedSpectrum(:,3) = std(vq,0,2,'omitnan');
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elseif contains(p.Results.mode,'subtract')
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disp('Not supported yet') % FIXME: subtraction is not implemented yet.
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end
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end
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