Added more options to exclude data in background fit and made the call to nappFitGAussXps more consitent
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bartels-rausch committed
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+29
-19
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@@ -109,8 +109,9 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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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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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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@@ -121,7 +122,7 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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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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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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+25
-16
@@ -199,7 +199,7 @@ if matches(p.Results.mode,'position')
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p.Results.FitParameter.peakAreaLowerBond(1,2) p.Results.FitParameter.peakWidthLowerBond(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) p.Results.FitParameter.peakWidthLowerBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) p.Results.FitParameter.peakWidthLowerBond(1,4) ... % Gauss peak 4
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0 0]; % linear background
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-Inf 0]; % linear background
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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(1,1) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaUpperBond(1,2) p.Results.FitParameter.peakWidthUpperBond(1,2) ... % Gauss peak 2
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@@ -225,7 +225,7 @@ elseif matches(p.Results.mode,'unconstrained')
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p.Results.FitParameter.peakAreaLowerBond(1,2) p.Results.FitParameter.peakWidthLowerBond(1,2) p.Results.FitParameter.peakPosLowerBond(1,2)... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) p.Results.FitParameter.peakWidthLowerBond(1,3) p.Results.FitParameter.peakPosLowerBond(1,3)... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) p.Results.FitParameter.peakWidthLowerBond(1,4) p.Results.FitParameter.peakPosLowerBond(1,4)... % Gauss peak 4
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0 0]; % linear background
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-Inf 0]; % linear background
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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(1,1) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaUpperBond(1,2) p.Results.FitParameter.peakWidthUpperBond(1,2) p.Results.FitParameter.peakPosUpperBond(1,2)... % Gauss peak 2
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@@ -254,7 +254,7 @@ elseif matches(p.Results.mode,'widthPosition')
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p.Results.FitParameter.peakAreaLowerBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) ...
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p.Results.FitParameter.peakAreaLowerBond(1,5) ... % Gauss peak 5
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0 0]; % linear background
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-Inf -Inf]; % linear background
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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(1,1) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaUpperBond(1,2) ... % Gauss peak 2
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@@ -278,15 +278,15 @@ elseif matches(p.Results.mode,'width')
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0 0]; % linear background
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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(1,1) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaLowerBond(1,2) p.Results.FitParameter.peakWidthLowerBond(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) p.Results.FitParameter.peakWidthLowerBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) p.Results.FitParameter.peakWidthLowerBond(1,4) ... % Gauss peak 4
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0 0]; % linear background
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p.Results.FitParameter.peakAreaLowerBond(1,2) p.Results.FitParameter.peakPos(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) p.Results.FitParameter.peakPos(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) p.Results.FitParameter.peakPos(1,4) ... % Gauss peak 4
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-Inf -Inf]; % linear background
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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(1,1) ... % Gauss peak 1
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p.Results.FitParameter.peakAreaUpperBond(1,2) p.Results.FitParameter.peakWidthUpperBond(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaUpperBond(1,3) p.Results.FitParameter.peakWidthUpperBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaUpperBond(1,4) p.Results.FitParameter.peakWidthUpperBond(1,4) ... % Gauss peak 4
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p.Results.FitParameter.peakAreaUpperBond(1,2) p.Results.FitParameter.peakPos(1,2) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaUpperBond(1,3) p.Results.FitParameter.peakPos(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaUpperBond(1,4) p.Results.FitParameter.peakPos(1,4) ... % Gauss peak 4
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Inf Inf]; % linear background
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elseif matches(p.Results.mode,'unconstrainedAndWidthPosition') % Novum, also the distance between peaks is a fit parameter. [Gauss = area/(width*sqrt(pi/2)) * exp(-2*(x-position)^2/width^2)]
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@@ -312,7 +312,7 @@ elseif matches(p.Results.mode,'unconstrainedAndWidthPosition') % Novum, also the
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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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0 0 ... % linear background
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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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@@ -340,7 +340,7 @@ elseif matches(p.Results.mode,'unconstrainedAndWidthPosition') % Novum, also the
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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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0 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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@@ -440,9 +440,9 @@ for ii = 1:size(DataTable(p.Results.tableSelection,:),1)
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elseif matches(p.Results.mode,'width')
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B = [tmpB(1) tmpB(2) tmpB(3)...
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tmpB(4) tmpB(2) tmpB(5)...
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tmpB(6) tmpB(2) tmpB(8)...
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tmpB(9) tmpB(2) tmpB(10)...
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tmpB(11) tmpB(12)...
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tmpB(6) tmpB(2) tmpB(7)...
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tmpB(8) tmpB(2) tmpB(9)...
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tmpB(10) tmpB(11)...
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NaN NaN NaN];
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elseif matches(p.Results.mode,'unconstrainedAndWidthPosition')
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B = [tmpB(1) tmpB(2) tmpB(3)+tmpB(14)...
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@@ -585,7 +585,7 @@ for ii = 1:size(DataTable(p.Results.tableSelection,:),1)
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resultsPeakPos(ii,:) = [B(3), B(6), B(9), B(12), B(16)] ; %#ok<*AGROW>
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resultsPeakFWHW(ii,:) = [B(2).*sqrt(log(4)), B(5).*sqrt(log(4)), B(8).*sqrt(log(4)), B(11).*sqrt(log(4)), B(17).*sqrt(log(4))] ;
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resultsPeakArea(ii,:) = [B(1), B(4), B(7), B(10) B(15)] ;
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% resultsBkgrd(ii,:) = [B(13), B(14)] ;
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resultsBkgrd(ii,:) = [B(13), B(14)] ;
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% close the fiting progess window
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fh = findobj( 'Type', 'Figure', 'Name', 'GlobalSearch');
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close(fh)
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@@ -606,11 +606,16 @@ try
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if ~any(existColumn)
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DataTable.peakFWHM = NaN(size(DataTable,1),size(resultsPeakFWHW,2));
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end
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existColumn = strcmp('peakBackground',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.peakBackground = NaN(size(DataTable,1),size(resultsBkgrd,2));
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end
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%if contains(p.Results.energyScale,'binding')
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DataTable(p.Results.tableSelection,:).peakPosition = resultsPeakPos(:,:);
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%end
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DataTable(p.Results.tableSelection,:).peakFWHM = resultsPeakFWHW(:,:);
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DataTable(p.Results.tableSelection,:).peakArea = resultsPeakArea(:,:);
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DataTable(p.Results.tableSelection,:).peakBackground = resultsBkgrd(:,:);
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catch
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disp('Could not write results to table. Writing only 4 entries')
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existColumn = strcmp('peakPosition',DataTable.Properties.VariableNames);
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@@ -625,6 +630,10 @@ catch
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if ~any(existColumn)
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DataTable.peakFWHM = NaN(size(DataTable,1),size(resultsPeakFWHW,2));
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end
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existColumn = strcmp('peakBackground',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.peakBackground = NaN(size(DataTable,1),size(resultsPeakFWHW,2));
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end
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%if contains(p.Results.energyScale,'binding')
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DataTable(p.Results.tableSelection,:).peakPosition = resultsPeakPos(:,1:4);
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%end
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