278 lines
14 KiB
Matlab
278 lines
14 KiB
Matlab
function DataTable = nappBackground(DataTable,varargin)
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%nappBackground determines and subtracts the background from PE or XAS spectra
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%
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% FileList = nappBackground(FileList,energyStart,energyEnd);
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%
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% FileList = nappBackground(FileList,368,370,'tableSelection',tmpDataSelection,'energyScale','kinetic',...
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% 'mode','mean','showFigures','off');
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%
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%
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% *input*
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% FileList: data table
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% energyStart: smallest value of energy range to use for background calculation
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% (can also be binding energy)
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% energyEnd: largest value of energy energy range to use for background calculation
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% (can also be binding energy)
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% tableSelection (optional): logical array to filter data table
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% tableVariable: choose to process either
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% 'spectrum_counts','spectrum_countsPerSecond' (default), or
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% 'spectrum_countsNorm'.
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% mode: mean(default) subtract the mean of the energy range from
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% spectrum; linfit subtract a linear regression through the energy range
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% from spectrum
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% showFigures, on(default): show fit in figure, off do not show fit in
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% figure
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% energyScale: kinetic(default): work with kinetic energy scale; binding
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% works with binding energy scale.
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%
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%
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% *output*
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% The table variable passed to the function as tableVariable
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% parameter will be overwritten with the background subtracted spectrum.
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%
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% The function parameters (mode, energyStart, energyEnd) are written
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% to the table as log.
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% Define conditions and defaults of input
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defaultTableVariable = 'spectrum_countsPerSecond';
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expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','spectrum_countsNorm'};
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defaultMode = 'mean';
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expectedMode = {'mean','linfit','exponential','mean, divide','linfit, divide','exponential, divide'};
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defaultTableSelection = true(size(DataTable,1),1);
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defaultShowFigures = 'on';
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expectedShowFigures = {'on','off'};
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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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addRequired(p,'energyStart',@isnumeric)
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addRequired(p,'energyEnd',@isnumeric)
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addOptional(p,'tableSelection',defaultTableSelection,@islogical);
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addParameter(p,'tableVariable',defaultTableVariable,...
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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,'showFigures',defaultShowFigures,...
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@(x) any(validatestring(x,expectedShowFigures)));
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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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% add empty table variables (if they don't exist)
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existColumn = strcmp('logBackgroundRange',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundRange = NaN(size(DataTable,1),2);
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end
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existColumn = strcmp('logBackgroundMode',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundMode = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
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end
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existColumn = strcmp('logBackgroundDate',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundDate = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
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end
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% add empty variable to table
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existColumn = strcmp('spectrum_countsNorm',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.spectrum_countsNorm = cell(size(DataTable,1),1);
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end
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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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if startsWith(p.Results.mode,'linfit')
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ft = fittype( 'poly1' );
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elseif contains(p.Results.mode,'exponential')
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ft = fittype( 'exp2' );
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end
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if contains(p.Results.energyScale,'kinetic')
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if ~startsWith(p.Results.mode,'mean')
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[xData, yData] = prepareCurveData(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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excludedPoints = excludedata( xData, yData, 'domain',[p.Results.energyStart(1) p.Results.energyEnd(1)] );
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if size(p.Results.energyStart,2) ==2 && size(p.Results.energyEnd,2) ==1
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excludedPointsEins = excludedPoints;
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clearvars excludedPoints
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excludedPointsZwei = excludedata( xData, yData, 'domain',[xData(1) p.Results.energyStart(2)] );
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excludedPoints = excludedPointsEins & excludedPointsZwei;
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elseif size(p.Results.energyStart,2) ==2 && size(p.Results.energyEnd,2) ==2
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excludedPointsEins = excludedPoints;
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clearvars excludedPoints
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excludedPointsZwei = excludedata( xData, yData, 'domain',[xData(1) p.Results.energyStart(2)] );
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excludedPointsDrei = excludedata( xData, yData, 'domain',[p.Results.energyEnd(2) xData(end)] );
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excludedPoints = excludedPointsEins & excludedPointsZwei & excludedPointsDrei;
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end
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opts = fitoptions( 'Method', 'NonlinearLeastSquares','Exclude', ~excludedPoints );
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opts.Display = 'Off';
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% Fit model to data.
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[fitresult, ~] = fit( xData, yData, ft, opts );
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if contains(p.Results.showFigures,'on')
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% Plot fit with data.
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figure( 'Name', 'untitled fit 1' );
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plot( fitresult, xData, yData, ~excludedPoints );
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% legend( h, 'y vs. x', 'Excluded y vs. x', 'untitled fit 1', 'Location', 'NorthEast', 'Interpreter', 'none' );
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% Label axes
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xlabel( 'kinetic energy [eV]', 'Interpreter', 'none' );
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ylabel( 'PE intensity', 'Interpreter', 'none' );
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grid on
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title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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if endsWith(p.Results.mode,'divide')
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tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}./fitresult(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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else
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tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}-fitresult(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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end
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elseif startsWith(p.Results.mode,'mean')
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b_1 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.energyStart,1);
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b_2 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.energyEnd,1);
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if b_2 == 1
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b_2=10;
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end
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b_mean = mean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(b_1:b_2),'omitnan');
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tmp(ii,1) = cellfun(@(x) x-b_mean,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable)(ii),'UniformOutput',false); %#ok<*AGROW>
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end
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elseif contains(p.Results.energyScale,'binding')
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if ~startsWith(p.Results.mode,'mean')
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[xData, yData] = prepareCurveData(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% Set up fittype and options.
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excludedPoints = excludedata( xData, yData, 'domain',[p.Results.energyStart(1) p.Results.energyEnd(1)] );
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if size(p.Results.energyStart,2) ==2 && size(p.Results.energyEnd,2) ==1
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excludedPointsEins = excludedPoints;
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clearvars excludedPoints
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excludedPointsZwei = excludedata( xData, yData, 'domain',[xData(1) p.Results.energyStart(2)] );
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excludedPoints = excludedPointsEins & excludedPointsZwei;
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elseif size(p.Results.energyStart,2) ==2 && size(p.Results.energyEnd,2) ==2
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excludedPointsEins = excludedPoints;
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clearvars excludedPoints
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excludedPointsZwei = excludedata( xData, yData, 'domain',[p.Results.energyStart(2) p.Results.energyEnd(2)] );
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excludedPoints = excludedPointsEins & excludedPointsZwei;
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end
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opts = fitoptions( 'Method', 'NonlinearLeastSquares','Exclude', ~excludedPoints );
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opts.Display = 'Off';
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% Fit model to data.
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[fitresult, ~] = fit( xData, yData, ft, opts );
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if contains(p.Results.showFigures,'on')
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% Plot fit with data.
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figure( 'Name', 'untitled fit 1' );
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plot( fitresult, xData, yData, excludedPoints );
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% legend( h, 'y vs. x', 'Excluded y vs. x', 'untitled fit 1', 'Location', 'NorthEast', 'Interpreter', 'none' );
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% Label axes
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xlabel( 'binding energy [eV]', 'Interpreter', 'none' );
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ylabel( 'PE intensity', 'Interpreter', 'none' );
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grid on
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title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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if endsWith(p.Results.mode,'divide')
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tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}./fitresult(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii});
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else
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tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}-fitresult(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii});
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end
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elseif startsWith(p.Results.mode,'mean')
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b_1 = find(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii} <= p.Results.energyStart,1);
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b_2 = find(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii} <= p.Results.energyEnd,1);
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if b_2 == 1
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b_2=10;
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end
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b_mean = mean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(b_2:b_1),'omitnan');
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tmp(ii,1) = cellfun(@(x) x-b_mean,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable)(ii),'UniformOutput',false);
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end
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elseif contains(p.Results.energyScale,'xRay')
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if contains(p.Results.mode,'linfit') % LINEAR FIT
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% Fit: 'untitled fit 1'.
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% Set up fittype and options.
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ft = fittype( 'poly1' );
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excludedPoints = excludedata( xData, yData, 'domain',[p.Results.energyStart p.Results.energyEnd] );
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fo = fitoptions('Exclude', excludedPoints);
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% Fit model to data.
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[fitresult, ~] = fit( xData, yData, ft, fo );
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if contains(p.Results.showFigures,'on')
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% Plot fit with data.
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figure( 'Name', 'fit pre-edge' );
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plot( fitresult, xData, yData, excludedPoints );
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xlabel('Photon Energy eV')
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ylabel('partial A-M.E.Y.')
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grid on
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title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}-fitresult(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii});
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elseif contains(p.Results.mode,'mean') % mean
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if p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) < p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% MEAN
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b_1 = find(xData >= p.Results.energyStart,1);
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b_2 = find(xData >= p.Results.energyEnd,1);
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b_mean = mean(yData(b_1:b_2));
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elseif p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) > p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% MEAN
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b_1 = find(xData <= p.Results.energyStart,1);
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b_2 = find(xData <= p.Results.energyEnd,1);
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b_mean = mean(yData(b_2:b_1));
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else
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disp('Warning: Issue with NEXAFS data or energies')
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end
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tmp(ii,1) = cellfun(@(x) x-b_mean,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable)(ii),'UniformOutput',false);
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end
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end
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end
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% fill selected rows
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if endsWith(p.Results.mode,'divide')
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DataTable(p.Results.tableSelection,:).spectrum_countsNorm = tmp;
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else
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DataTable(p.Results.tableSelection,:).(p.Results.tableVariable) = tmp;
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end
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% write log to table
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DataTable.logBackgroundMode(p.Results.tableSelection,:) = cellstr(repmat(p.Results.mode,size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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DataTable.logBackgroundRange(p.Results.tableSelection,:) = repmat([p.Results.energyStart(1) p.Results.energyEnd(1)],size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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DataTable.logBackgroundDate(p.Results.tableSelection,:) = cellstr(repmat(datestr(now),size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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end |