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Added exponential fit. Added divide by background to normalise intensity.

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bartels-rausch committed 2023-11-16 07:17:37 +01:00
1 parent 4ad9ccbd35
commit 8b55810fc6
1 file changed
+55 -11
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beamtime/nappBackground.m
+55 -11
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@@ -1,4 +1,4 @@
function DataTable = nappBackground(DataTable,varargin)
function DataTable = nappBackground(DataTable,varargin)
%nappBackground determines and subtracts the background from PE or XAS spectra
%
% FileList = nappBackground(FileList,energyStart,energyEnd);
@@ -39,7 +39,7 @@
defaultTableVariable = 'spectrum_countsPerSecond';
expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','spectrum_countsNorm'};
defaultMode = 'mean';
expectedMode = {'mean','linfit'};
expectedMode = {'mean','linfit','exponential','mean, divide','linfit, divide','exponential, divide'};
defaultTableSelection = true(size(DataTable,1),1);
defaultShowFigures = 'on';
expectedShowFigures = {'on','off'};
@@ -81,16 +81,56 @@ existColumn = strcmp('logBackgroundDate',DataTable.Properties.VariableNames);
if ~any(existColumn)
DataTable.logBackgroundDate = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
end
% add empty variable to table
existColumn = strcmp('spectrum_countsNorm',DataTable.Properties.VariableNames);
if ~any(existColumn)
DataTable.spectrum_countsNorm = cell(size(DataTable,1),1);
end
% repeat this for all columns in input.
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
if contains(p.Results.energyScale,'kinetic')
% LINEAR FIT
if contains(p.Results.mode,'linfit')
if startsWith(p.Results.mode,'linfit')
disp('linfit not yet supported')
% MEAN
else
% declining background
elseif contains(p.Results.mode,'exponential')
[xData, yData] = prepareCurveData(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
% Set up fittype and options.
ft = fittype( 'exp2' );
excludedPoints = excludedata( xData, yData, 'domain',[p.Results.energyStart(1) p.Results.energyEnd(1)] );
if size(p.Results.energyStart,2) ==2 && size(p.Results.energyEnd,2) ==1
excludedPointsEins = excludedPoints;
clearvars excludedPoints
excludedPointsZwei = excludedata( xData, yData, 'domain',[xData(1) p.Results.energyStart(2)] );
excludedPoints = excludedPointsEins & excludedPointsZwei;
end
opts = fitoptions( 'Method', 'NonlinearLeastSquares','Exclude', ~excludedPoints );
opts.Display = 'Off';
% Fit model to data.
[fitresult, ~] = fit( xData, yData, ft, opts );
if contains(p.Results.showFigures,'on')
% Plot fit with data.
figure( 'Name', 'untitled fit 1' );
plot( fitresult, xData, yData, excludedPoints );
% legend( h, 'y vs. x', 'Excluded y vs. x', 'untitled fit 1', 'Location', 'NorthEast', 'Interpreter', 'none' );
% Label axes
xlabel( 'kinetic energy [eV]', 'Interpreter', 'none' );
ylabel( 'PE intensity', 'Interpreter', 'none' );
grid on
title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
end
if endsWith(p.Results.mode,'divide')
tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}./fitresult(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
else
tmp{ii,1} = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}-fitresult(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii});
end
elseif startsWith(p.Results.mode,'mean')
b_1 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.energyStart,1);
b_2 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.energyEnd,1);
@@ -150,7 +190,7 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
% prepare Data
[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
% MEAN
b_1 = find(xData >= p.Results.energyStart,1);
b_2 = find(xData >= p.Results.energyEnd,1);
@@ -159,7 +199,7 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
elseif p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) > p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
% prepare Data
[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
% MEAN
b_1 = find(xData <= p.Results.energyStart,1);
b_2 = find(xData <= p.Results.energyEnd,1);
@@ -170,18 +210,22 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
end
tmp(ii,1) = cellfun(@(x) x-b_mean,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable)(ii),'UniformOutput',false);
tmp(ii,1) = cellfun(@(x) x-b_mean,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable)(ii),'UniformOutput',false);
end
end
end
% fill selected rows
DataTable(p.Results.tableSelection,:).(p.Results.tableVariable) = tmp;
if endsWith(p.Results.mode,'divide')
DataTable(p.Results.tableSelection,:).spectrum_countsNorm = tmp;
else
DataTable(p.Results.tableSelection,:).(p.Results.tableVariable) = tmp;
end
% write log to table
DataTable.logBackgroundMode(p.Results.tableSelection,:) = cellstr(repmat(p.Results.mode,size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
DataTable.logBackgroundRange(p.Results.tableSelection,:) = repmat([p.Results.energyStart p.Results.energyEnd],size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
DataTable.logBackgroundRange(p.Results.tableSelection,:) = repmat([p.Results.energyStart(1) p.Results.energyEnd],size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
DataTable.logBackgroundDate(p.Results.tableSelection,:) = cellstr(repmat(datestr(now),size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
end