Added model with 5 features: acid-base, gas-phase, acid-base. Both acid-base (feature 1,2,4,5) have one fixed and one relative BE. Position and width of gas-phase feature is unconstrained.
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+101
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@@ -66,7 +66,7 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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% % „ unconstrainedAndWidthPosition" mode (novel: rel distance fit parameter)
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% % „unconstrainedAndWidthPosition" mode (novel: rel distance fit parameter)
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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4 abs#5];
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% tmpFitParameters.peakWidth = [abs#1,2,4,5 abs#3];
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% tmpFitParameters.peakPos = [rel#1 abs#2 abs#3 abs#4 abs#5];
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@@ -80,6 +80,21 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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% % „gasAndTwoAcidBasePairs" mode (novel: rel distance fit parameter)
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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4 abs#5];
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% tmpFitParameters.peakWidth = [abs#1,2,4,5 abs#3];
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% tmpFitParameters.peakPos = [rel#1 abs#2 abs#3 rel#4 abs#5]; % rel#4
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% is realative to abs#5, rel#1 is relative to abs#2
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%
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% tmpFitParameters.peakAreaUpperBond = [#1 #2 #3 #4 #5];
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% tmpFitParameters.peakWidthUpperBond = [#1,2,4,5 #3];
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% tmpFitParameters.peakPosUpperBond = [#1 #2 #3 #4 #5];
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4 #5];
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% tmpFitParameters.peakWidthLowerBond = [#1,2,4,5 #3];
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% tmpFitParameters.peakPosLowerBond = [#1 #2 #3 #4 #5];
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% spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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%
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% tableSelection (optional): logical array to filter data table
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% tableVariable (optional): select source: image(default),'imageRoh'
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@@ -108,7 +123,7 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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defaultTableVariable = 'spectrum_countsPerSecond';
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expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','spectrum_countsNorm'};
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defaultMode = 'widthPosition';
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expectedMode = {'unconstrained','widthPosition','position','width','unconstrainedAndWidthPosition'};
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expectedMode = {'unconstrained','widthPosition','position','width','unconstrainedAndWidthPosition','gasAndTwoAcidBasePairs'};
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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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@@ -118,7 +133,7 @@ expectedEnergyScale = {'kinetic','binding'};
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% Parse input
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p = inputParser;
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addRequired(p,'DataTable',@istable); % TODO: allow combinedSpectrum input.
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addRequired(p,'DataTable',@istable);
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addRequired(p,'FitParameter',@isstruct);
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addOptional(p,'tableSelection',defaultTableSelection,@islogical);
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addParameter(p,'tableVariable',defaultTableVariable,...
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@@ -309,6 +324,42 @@ elseif matches(p.Results.mode,'unconstrainedAndWidthPosition') % Novum, also the
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p.Results.FitParameter.peakAreaUpperBond(1,5) p.Results.FitParameter.peakPosUpperBond(1,5) ... % Gauss peak 4
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Inf Inf ... % linear background
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p.Results.FitParameter.peakPosUpperBond(1,1)]; % shift upper bond
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elseif matches(p.Results.mode,'gasAndTwoAcidBasePairs') % Novum, also the distance between peaks is a fit parameter.
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% [Gauss = area/(width*sqrt(pi/2)) * exp(-2*(x-position)^2/width^2)]
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yfcn1 = @(tmpB,x)...
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tmpB(1)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1) - (tmpB(3)+tmpB(14))).^2/tmpB(2).^2)) ... % Gauss peak 1: width and position
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+ tmpB(4)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1) - tmpB(3)).^2/tmpB(2).^2))... % Gauss peak 2: width and position
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+ tmpB(5)/(tmpB(6)*sqrt(pi/2))*exp(-2.*((x(:,1) - tmpB(7)).^2/tmpB(6).^2))... % Gauss peak 3: unconstrained
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+ tmpB(8)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1) - (tmpB(11)+tmpB(9))).^2/tmpB(2).^2))... % Gauss peak 4: width and position
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+ tmpB(10)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1)- tmpB(11)).^2/tmpB(2).^2))... % Gauss peak 5: width and position
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+ tmpB(12).*x(:,1)+tmpB(13); % linear background
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% initial value
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B0= [p.Results.FitParameter.peakArea(1,1) p.Results.FitParameter.peakWidth(1,1) p.Results.FitParameter.peakPos(1,2)... % Gauss peak 1
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p.Results.FitParameter.peakArea(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakArea(1,3) p.Results.FitParameter.peakWidth(1,2) p.Results.FitParameter.peakPos(1,3)... % Gauss peak 3
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p.Results.FitParameter.peakArea(1,4) p.Results.FitParameter.peakPos(1,4)... % Gauss peak 4
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p.Results.FitParameter.peakArea(1,5) p.Results.FitParameter.peakPos(1,5)... % Gauss peak 5
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1 0 ... % linear background
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p.Results.FitParameter.peakPos(1,1)];
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% lower bonds
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lb = [p.Results.FitParameter.peakAreaLowerBond(1,1) p.Results.FitParameter.peakWidthLowerBond(1,1) p.Results.FitParameter.peakPosLowerBond(1,2) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaLowerBond(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) p.Results.FitParameter.peakWidthLowerBond(1,2) p.Results.FitParameter.peakPosLowerBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) p.Results.FitParameter.peakPosLowerBond(1,4) ...
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p.Results.FitParameter.peakAreaLowerBond(1,5) p.Results.FitParameter.peakPosLowerBond(1,5) ...% Gauss peak 4
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-Inf -Inf ... % linear background
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p.Results.FitParameter.peakPosLowerBond(1,1)];
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% upper bond
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ub = [p.Results.FitParameter.peakAreaUpperBond(1,1) p.Results.FitParameter.peakWidthUpperBond(1,1) p.Results.FitParameter.peakPosUpperBond(1,2) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaUpperBond(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaUpperBond(1,3) p.Results.FitParameter.peakWidthUpperBond(1,2) p.Results.FitParameter.peakPosUpperBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaUpperBond(1,4) p.Results.FitParameter.peakPosUpperBond(1,4) ...
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p.Results.FitParameter.peakAreaUpperBond(1,5) p.Results.FitParameter.peakPosUpperBond(1,5) ... % Gauss peak 4
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Inf Inf ... % linear background
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p.Results.FitParameter.peakPosUpperBond(1,1)]; % shift upper bond
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end
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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@@ -401,6 +452,13 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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tmpB(8) tmpB(2) tmpB(9)...
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tmpB(12) tmpB(13) ...
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tmpB(10) tmpB(2) tmpB(11)];
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elseif matches(p.Results.mode,'gasAndTwoAcidBasePairs')
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B = [tmpB(1) tmpB(2) tmpB(3)+tmpB(14)...
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tmpB(4) tmpB(2) tmpB(3)...
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tmpB(5) tmpB(6) tmpB(7)...
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tmpB(8) tmpB(2) tmpB(11)+tmpB(9)...
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tmpB(12) tmpB(13) ...
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tmpB(10) tmpB(2) tmpB(11)];
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end
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% print out result table and result plots based on B. Because B has the
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@@ -414,6 +472,30 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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disp('Fit results')
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disp(p.Results.DataTable(p.Results.tableSelection,:).name{ii});
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disp(' ' );
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if (B(1) <= 1 || B(4) <= 1)
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disp(cell2table({sprintf('%.1f',B(3)),...
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sprintf('%.1f',B(2)*sqrt(log(4))),...
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sprintf('%.1f',B(2)),...
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sprintf('%.3f',B(1));...
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sprintf('%.1f',B(6)),...
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sprintf('%.1f',B(5)*sqrt(log(4))),...
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sprintf('%.1f',B(5)),...
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sprintf('%.3f',B(4));...
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sprintf('%.1f',B(9)),...
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sprintf('%.1f',B(8)*sqrt(log(4))),...
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sprintf('%.1f',B(8)),...
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sprintf('%.3f',B(7));...
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sprintf('%.1f',B(12)),...
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sprintf('%.1f',B(11)*sqrt(log(4))),...
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sprintf('%.1f',B(11)),...
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sprintf('%.3f',B(10)); ...
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sprintf('%.1f',B(17)),...
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sprintf('%.1f',B(16)*sqrt(log(4))),...
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sprintf('%.1f',B(16)),...
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sprintf('%.3f',B(15))},...
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'VariableNames',{'position';'FWHW';'width';'area'},...
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'RowNames',{'peak1','peak2','peak3','peak4','peak5'})); % 'RowNames',{'peak1','peak2','peak3','peak4','peak5'}));
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else
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disp(cell2table({sprintf('%.1f',B(3)),...
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sprintf('%.1f',B(2)*sqrt(log(4))),...
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sprintf('%.1f',B(2)),...
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@@ -436,7 +518,7 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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sprintf('%7.0f',B(15))},...
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'VariableNames',{'position';'FWHW';'width';'area'},...
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'RowNames',{'peak1','peak2','peak3','peak4','peak5'})); % 'RowNames',{'peak1','peak2','peak3','peak4','peak5'}));
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end
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% plot result
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% eliminate NaN in B
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B(isnan(B))=0.01;
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@@ -460,11 +542,11 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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yData_pk4= Gauss(xGaussPlot ,B(10), B(12), B(11));
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yData_pk5= Gauss(xGaussPlot ,B(15), B(17), B(16));
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bkgrd = linear(xGaussPlot,B(13),B(14));
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% plot data
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plot(x1,y1,'.')
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hold on
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% plot fit
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h = plot(xGaussPlot,yData_pk1+yData_pk2+yData_pk3+yData_pk4+yData_pk5+bkgrd);
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hold on
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h.LineWidth=2;
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h.Color = PsiFarbe.dunkelblau;
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% plot each gauss peak
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@@ -484,10 +566,20 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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h.LineWidth=1.5;
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h.Color = PsiFarbe.gelb;
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plot(xGaussPlot, bkgrd);
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set(ax(1),'Xdir','reverse');
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if x1(1)<= x1(end)
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xlabel('Kinetic Energy [eV]');
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else
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set(ax(1),'Xdir','reverse');
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xlabel('Binding Energy [eV]');
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end
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% plot data
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plot(x1,y1,'o',"MarkerFaceColor","white")
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legend OFF
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xlabel('Binding Energy [eV]');
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if matches(p.Results.tableVariable,'spectrum_countsPerSecond')
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ylabel('PE Intensity [counts per second]');
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else
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ylabel('PE intensity [-]');
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end
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grid on
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end
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% Write results to List, we need all fitting results
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