Addes a model for gas and condensed 2p spectra (2 doublets). Small improvements and bug fixes
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@@ -577,7 +577,7 @@ expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','spe
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defaultMode = 'widthPosition';
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expectedMode = {'unconstrained','widthPosition','position','width','widthPositionShirley', ...
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'positionShirley','widthShirley','unconstrainedAndWidthPosition','gasAndTwoAcidBasePairs',...
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'widthPositionAreaRatio','widthPositionAmineAreaRatio','TwoSpinOrbitDoublet','TwoSpinOrbitDoubletPseudoVoigtShirley'};
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'widthPositionAreaRatio','widthPositionAmineAreaRatio','TwoSpinOrbitDoublet','TwoSpinOrbitDoubletPseudoVoigtShirley','GasAndSurfaceSpinOrbitDoublet'};
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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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@@ -1771,6 +1771,54 @@ for iuz = 1
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initialParameterVector = [initialParameterVector, 0, 0];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, -Inf, -Inf];
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upperBoundsParameterVector = [upperBoundsParameterVector, Inf, Inf];
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elseif matches(p.Results.mode,'GasAndSurfaceSpinOrbitDoublet')
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%% GasAndSurfaceSpinOrbitDoublet
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modelDefinitionFunction = @(currentParameterVector,energyValues)...
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gaussPeak(energyValues, currentParameterVector(1),currentParameterVector(2), currentParameterVector(3)) ... % Gauss peak 1
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+ gaussPeak(energyValues, currentParameterVector(1)*FitParameter.peakArea(1,2), currentParameterVector(2), currentParameterVector(3)+FitParameter.peakPos(1,2))... % Gauss peak 2
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+ gaussPeak(energyValues, currentParameterVector(4),currentParameterVector(5), currentParameterVector(6))... % Gauss peak 3
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+ gaussPeak(energyValues, currentParameterVector(4)*FitParameter.peakArea(1,4),currentParameterVector(5),currentParameterVector(6)+FitParameter.peakPos(1,4)) ... % Gauss peak 4
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+ linearBackground(energyValues,currentParameterVector(7), currentParameterVector(8));
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initialParameterVector = [];
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lowerBoundsParameterVector = [];
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upperBoundsParameterVector = [];
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% #1: Area 1
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initialParameterVector = [initialParameterVector, FitParameter.peakArea(1, 1)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakAreaLowerBound(1, 1)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakAreaUpperBound(1, 1)];
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% #2: Width 1+2
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initialParameterVector = [initialParameterVector, FitParameter.peakWidth(1, 1)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakWidthLowerBound(1, 1)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakWidthUpperBound(1, 1)];
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% #3: Pos 1
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initialParameterVector = [initialParameterVector, FitParameter.peakPos(1, 1)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakPosLowerBound(1, 1)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakPosUpperBound(1, 1)];
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% #4: Area 3
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initialParameterVector = [initialParameterVector, FitParameter.peakArea(1, 3)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakAreaLowerBound(1, 3)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakAreaUpperBound(1, 3)];
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% #5: Width 3+4
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initialParameterVector = [initialParameterVector, FitParameter.peakWidth(1, 2)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakWidthLowerBound(1, 1)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakWidthUpperBound(1, 1)];
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% #6 Pos 3
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initialParameterVector = [initialParameterVector, FitParameter.peakPos(1, 3)];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, FitParameter.peakPosLowerBound(1, 3)];
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upperBoundsParameterVector = [upperBoundsParameterVector, FitParameter.peakPosUpperBound(1, 3)];
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% #7 & #8 Background: slope, intercept
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initialParameterVector = [initialParameterVector, 0, 0];
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lowerBoundsParameterVector = [lowerBoundsParameterVector, -Inf, -Inf];
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upperBoundsParameterVector = [upperBoundsParameterVector, Inf, Inf];
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elseif matches(p.Results.mode,'TwoSpinOrbitDoubletPseudoVoigtShirley')
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%% TwoSpinOrbitDoubletPseudoVoigtShirley
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@@ -2543,7 +2591,7 @@ for iii= 1
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pos3 = currentParameterVector(3)+currentParameterVector(5);
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area4 = currentParameterVector(4)*FitParameter.peakArea(1,2);
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width4 = currentParameterVector(2);
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pos4 = currentParameterVector(3)+currentParameterVector(5)++FitParameter.peakPos(1,2);
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pos4 = currentParameterVector(3)+currentParameterVector(5)+FitParameter.peakPos(1,2);
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slope = currentParameterVector(6);
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intercept = currentParameterVector(7);
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@@ -2555,6 +2603,34 @@ for iii= 1
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% Background
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resultsBkgrd = [slope, intercept];
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elseif matches(p.Results.mode, 'GasAndSurfaceSpinOrbitDoublet')
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%% GasAndSurfaceSpinOrbitDoublet
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% ===== GAUSSIAN + LINEAR =====
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% Extract parameters
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area1 = currentParameterVector(1);
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width1 = currentParameterVector(2);
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pos1 = currentParameterVector(3);
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area2 = currentParameterVector(1)*FitParameter.peakArea(1,2);
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width2 = currentParameterVector(2);
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pos2 = currentParameterVector(3)+FitParameter.peakPos(1,2);
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area3 = currentParameterVector(4);
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width3 = currentParameterVector(5);
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pos3 = currentParameterVector(6);
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area4 = currentParameterVector(4)*FitParameter.peakArea(1,4);
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width4 = currentParameterVector(5);
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pos4 = currentParameterVector(6)+FitParameter.peakPos(1,4);
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slope = currentParameterVector(7);
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intercept = currentParameterVector(8);
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% Results: areas, positions, FWHM
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resultsPeakArea = [area1, area2, area3, area4];
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resultsPeakPos = [pos1, pos2, pos3, pos4];
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resultsPeakFWHM = [width1, width2, width3, width4];
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% Background
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resultsBkgrd = [slope, intercept];
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elseif matches(p.Results.mode, 'TwoSpinOrbitDoubletPseudoVoigtShirley')
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%% TwoSpinOrbitDoubletPseudoVoigtShirley
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% ===== PSEUDO-VOIGT + SHIRLEY =====
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@@ -2571,7 +2647,7 @@ for iii= 1
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pos3 = currentParameterVector(3)+currentParameterVector(5);
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area4 = currentParameterVector(4)*FitParameter.peakArea(1,2);
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width4 = currentParameterVector(2);
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pos4 = currentParameterVector(3)+currentParameterVector(5)++FitParameter.peakPos(1,2);
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pos4 = currentParameterVector(3)+currentParameterVector(5)+FitParameter.peakPos(1,2);
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% Results: areas, positions, FWHM
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resultsPeakArea = [area1, area2, area3, area4];
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@@ -2797,14 +2873,20 @@ end
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%% Print Results
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if matches(p.Results.showFigures,'on')
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disp(DataTable(p.Results.tableSelection,["name","peakPosition","peakArea","peakFWHM"]))
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disp(DataTable(p.Results.tableSelection,["name","peakPosition"]))
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disp(DataTable(p.Results.tableSelection,["name","peakArea"]))
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disp(DataTable(p.Results.tableSelection,["name","peakFWHM"]))
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disp(DataTable(p.Results.tableSelection,["name","peakBackground"]))
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try
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disp(DataTable(p.Results.tableSelection,["name","peakEta",]))
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if ~isnan(DataTable(p.Results.tableSelection,:).peakEta(1))
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disp(DataTable(p.Results.tableSelection,["name","peakEta",]))
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end
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catch
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end
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try
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disp(DataTable(p.Results.tableSelection,["name","peakShirleyK"]))
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if ~isnan(DataTable(p.Results.tableSelection,:).peakShirleyK(1))
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disp(DataTable(p.Results.tableSelection,["name","peakShirleyK"]))
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end
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catch
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end
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