Added Gauss Peak Fitting to XPS shift determination. First implementation for positionWidth contrained fit. Not yet documented. Not yet fully tested. WIP
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@@ -1,6 +1,6 @@
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function DataTable = nappDetermineShiftXps(DataTable,varargin)
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function DataTable = nappDetermineShiftXps(DataTable, varargin)
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%nappDetermineShiftXps determines the relative shift of each sequence
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%iteration in images or the absolute shift of spectra to a binding energy reference
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%iteration in images or the absolute shift of spectra to a binding energy reference
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%
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% FileList = nappDetermineShiftXps(FileList,eKinStart,eKinEnd,'tableSelection',tmpDataSelection,...
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% 'showFigures','off','tableVariable','spectrum_countsPerSecond','binEnReference',535);
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@@ -9,12 +9,12 @@ function DataTable = nappDetermineShiftXps(DataTable,varargin)
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% 'showFigures','on','tableVariable','image');
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%
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% *input*
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% FileList: data table
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% FileList: data table
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% eKinStart (optional): smallest value of energy range to use for
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% peak fitting. Peak fitting is used to get position of peak
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% eKinEnd (optional): largest value of energy energy range to use for
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% peak fitting. Peak fitting is used to get position of peak
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% tableSelection (optional): logical array to filter data table
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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), => absolute binding energy shift will be determined or
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% ,'image','imageRoh'=> relative kinetic energy shift will be determined.
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@@ -25,22 +25,19 @@ function DataTable = nappDetermineShiftXps(DataTable,varargin)
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% minPeakHeight: findpeak parameter, default 0.1
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% movMeanWindow: findpeak parameter, default 1
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% showFigures, on(default): show fit in figure, off do not show fit in figure
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%
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%
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%
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% *output*
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% new table variable kineticEnergyShift for images
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% new table variable kineticEnergyShift for images
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% new table variable bindingEnergyShift for spectra
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%
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%
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% *ToDo*
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%
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% FIXME: make use of O1s fit more general => use nappFitGaussXps.m function
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% FIXME: Do not use peakfind for image fit => use nappFitGaussXps.m function
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%
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% November 2023: Use nappFitGaussXps.m function to find peak position
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%
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% See also nappnappAlignImages.m nappBindingEnergyXps nappFitGaussXps.m nappCopyShift.m
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defaultKinEnReference = 1;
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defaultKinEnReference = 1;
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defaultTableVariable = 'spectrum_countsPerSecond';
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expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','image','imageRoh'};
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defaultTableSelection = true(size(DataTable,1));
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@@ -49,6 +46,10 @@ defaultMinPeakHeight = 0.1;
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defaultMovMeanWindow = 1;
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defaultShowFigures = 'off';
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expectedShowFigures = {'on','off'};
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defaultMode = 'gaussFit';
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expectedMode = {'gaussFit','findPeak'};
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defaultFitMode = 'widthPosition';
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expectedFitMode = {'unconstrained','widthPosition','position','width','unconstrainedAndWidthPosition'};
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%%
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@@ -58,6 +59,7 @@ p = inputParser;
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addRequired(p,'DataTable',@istable);
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addOptional(p,'eKinStart',@isnumeric)
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addOptional(p,'eKinEnd',@isnumeric)
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addParameter(p,'FitParameter',@isstruct);
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addParameter(p,'binEnReference',@isnumeric)
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addParameter(p,'kinEnReference',defaultKinEnReference,@isnumeric)
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addParameter(p,'tableSelection',defaultTableSelection,@islogical);
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@@ -68,8 +70,11 @@ addParameter(p,'tableVariable',defaultTableVariable,...
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@(x) any(validatestring(x,expectedTableVariable)));
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addParameter(p,'showFigures',defaultShowFigures,...
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@(x) any(validatestring(x,expectedShowFigures)));
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addParameter(p,'mode',defaultMode, @(x) any(validatestring(x,expectedMode)));
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addParameter(p,'fitMode',defaultFitMode, @(x) any(validatestring(x,expectedFitMode)));
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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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@@ -131,7 +136,7 @@ if matches(p.Results.tableVariable,'image')
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warning('There is something wrong with the eKinStart and/or eKinEnd parameters');
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disp('There is something wrong with the eKinStart and/or eKinEnd parameters');
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end
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for ij = 1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)
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[B,x1,y1] = GaussFitOnePeak([p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(start:stop)',...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop,ij)]);
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@@ -162,14 +167,14 @@ if matches(p.Results.tableVariable,'image')
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h = plot(x1,yData_pk2+bkgrd);
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h.LineWidth=1.5;
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h.Color = PsiFarbe.gelb;
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legend OFF
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xlabel('Kinetic Energy [eV]');
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ylabel('PE intensity [-]');
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grid on
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% List results in table
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disp('Results');
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disp(' ' );
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disp(cell2table({sprintf('%.1f',B(3)),...
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@@ -181,8 +186,8 @@ if matches(p.Results.tableVariable,'image')
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end
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end
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%%
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DataTable(p.Results.tableSelection,:).kineticEnergyShift{ii} = tmp_1-tmp_1(p.Results.kinEnReference);
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clearvars tmp_1
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fh = findobj( 'Type', 'Figure', 'Name', 'Gauss Multi Fit ');
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@@ -193,7 +198,7 @@ if matches(p.Results.tableVariable,'image')
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elseif matches(p.Results.tableVariable,'imageRoh')
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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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%%
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try
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if isnumeric(p.Results.eKinStart) && isempty(DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii})
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@@ -225,7 +230,7 @@ elseif matches(p.Results.tableVariable,'imageRoh')
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[B,x1,y1] = GaussFitOnePeak([DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii}(start:stop)',...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop,ij)]);
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end
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tmp_1(ij) = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}-B(3);
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% plot result
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if matches(p.Results.showFigures,'on')
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@@ -253,14 +258,14 @@ elseif matches(p.Results.tableVariable,'imageRoh')
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h = plot(x1,yData_pk2+bkgrd);
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h.LineWidth=1.5;
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h.Color = PsiFarbe.gelb;
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legend OFF
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xlabel('Kinetic Energy [eV]');
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ylabel('PE intensity [-]');
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grid on
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% List results in table
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disp('Results');
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disp(' ' );
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disp(cell2table({sprintf('%.1f',B(3)),...
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@@ -272,7 +277,7 @@ elseif matches(p.Results.tableVariable,'imageRoh')
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end
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end
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%%
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DataTable(p.Results.tableSelection,:).kineticEnergyShift{ii} = tmp_1-tmp_1(p.Results.kinEnReference);
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clearvars tmp_1
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fh = findobj( 'Type', 'Figure', 'Name', 'Gauss Multi Fit ');
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@@ -282,43 +287,69 @@ elseif matches(p.Results.tableVariable,'imageRoh')
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end
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else
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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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%%
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try
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if isnumeric(p.Results.eKinStart)
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start = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}...
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>= p.Results.eKinStart,1);
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stop = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}...
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>= p.Results.eKinEnd,1);
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else
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start = 1;
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stop = length(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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if matches(p.Results.mode,'findPeak')
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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%%
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try
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if isnumeric(p.Results.eKinStart)
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start = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}...
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>= p.Results.eKinStart,1);
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stop = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}...
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>= p.Results.eKinEnd,1);
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else
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start = 1;
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stop = length(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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end
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catch
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warning('There is something wrong with the eKinStart and/or eKinEnd parameters');
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disp('There is something wrong with the eKinStart and/or eKinEnd parameters');
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end
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catch
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warning('There is something wrong with the eKinStart and/or eKinEnd parameters');
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disp('There is something wrong with the eKinStart and/or eKinEnd parameters');
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end
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if contains(p.Results.showFigures,'on')
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figure
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findpeaks(movmean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop),...
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if contains(p.Results.showFigures,'on')
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figure
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findpeaks(movmean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop),...
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p.Results.movMeanWindow),...
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p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(start:stop),...
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'MinPeakWidth',p.Results.minPeakWidth,'MinPeakHeight',p.Results.minPeakHeight)
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end
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[pks,locs]=findpeaks(movmean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop),...
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p.Results.movMeanWindow),...
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p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(start:stop),...
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'MinPeakWidth',p.Results.minPeakWidth,'MinPeakHeight',p.Results.minPeakHeight)
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'MinPeakWidth',p.Results.minPeakWidth,'MinPeakHeight',p.Results.minPeakHeight);
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%%
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[~,I] = max(pks);
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tmp_1(ii,1) = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}-locs(I)-p.Results.binEnReference;
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clearvars tmp_2
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end
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[pks,locs]=findpeaks(movmean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(start:stop),...
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p.Results.movMeanWindow),...
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p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(start:stop),...
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'MinPeakWidth',p.Results.minPeakWidth,'MinPeakHeight',p.Results.minPeakHeight);
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DataTable.bindingEnergyShift(p.Results.tableSelection) = tmp_1;
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elseif matches(p.Results.mode,'gaussFit')
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tmpFitResults = nappFitGaussXps(DataTable,p.Results.tableSelection,p.Results.FitParameter,'tableSelection',p.Results.tableSelection,...
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'energyScale','kinetic','mode',p.Results.fitMode,'showFigures','on');
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DataTable.bindingEnergyShift(p.Results.tableSelection) = tmpFitResults(p.Results.tableSelection,:).xRayEkinRange_eV(:,1) - tmpFitResults(p.Results.tableSelection,:).peakPosition(:,1) - repmat(p.Results.binEnReference,size(DataTable.bindingEnergyShift(p.Results.tableSelection)));
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%%
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[~,I] = max(pks);
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tmp_1(ii,1) = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}-locs(I)-p.Results.binEnReference;
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clearvars tmp_2
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end
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DataTable.bindingEnergyShift(p.Results.tableSelection) = tmp_1;
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end
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try
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fh = findobj( 'Type', 'Figure', 'Name', 'Gauss Multi Fit ');
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close(fh)
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catch
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end
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try
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fh = findobj( 'Type', 'Figure', 'Name', 'GlobalSearch');
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close(fh)
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catch
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end
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end
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@@ -329,7 +360,7 @@ function [B,x1,y1] = GaussFitOnePeak(data1)
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% make data slimmer so that background makes sense
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[~,I] = max(y1);
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tmp1 = find(x1>=x1(I)-5,1);
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tmp1 = find(x1>=x1(I)-8,1);
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tmp2 = find(x1>=x1(I)+5,1);
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if isempty(tmp2)
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y1 = y1(tmp1:end);
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@@ -354,20 +385,20 @@ yfcn1 = @(b,x)...
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+ b(4)/(b(5)*sqrt(pi/2))*exp(-2.*((x(:,1)- b(6)).^2/b(5).^2))... % Gauss peak 2: C-OOH, Ac-
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+b(7).*x(:,1)+b(8); % linear background
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B0 = [80000 1.5 x1(I) ...
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10 1.0 x1(I)-4 ...
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0 0];
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B0 = [1e5 1.5 x1(I) ...
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1e5 1.0 x1(I)-4 ...
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1 0];
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% lower bonds
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lb = [1000 0.5 x1(I)-1. ...
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10 1.0 x1(I)-5 ...
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lb = [100 0.5 x1(I)-1. ...
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100 1.0 x1(I)-5 ...
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-Inf -Inf];
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% upper bond
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ub = [Inf 3 x1(I)+1 ...
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10 1.0 x1(I)-3 ...
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Inf 5 x1(I)-1 ...
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Inf Inf];
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+33
-10
@@ -21,7 +21,8 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakWidthLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakPosLowerBond = #1;
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%
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% spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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% % „unconstrained“ mode
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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4];
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@@ -34,10 +35,22 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakWidthLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakPosLowerBond = [#1 #2 #3 #4];
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%
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% spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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% % „ widthPosition“ mode
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% 1.5
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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4 abs#5];
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% tmpFitParameters.peakWidth = [abs#1-#5];
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% tmpFitParameters.peakPos = [abs#1 rel#2 rel#3 rel#4 rel#5];
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%
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% tmpFitParameters.peakAreaUpperBond = [#1 #2 #3 #4 #5];
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% tmpFitParameters.peakWidthUpperBond = abs#1-#5;
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% tmpFitParameters.peakPosUpperBond = #1;
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4 #5];
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% tmpFitParameters.peakWidthLowerBond = abs#1-#5;
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% tmpFitParameters.peakPosLowerBond = #1;
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% % spectrum range
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% tmpFitParameters.backgroundRange = [5 5];
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%
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% % „ width“ mode
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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4];
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@@ -50,7 +63,8 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakWidthLowerBond = #1-#4;
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% tmpFitParameters.peakPosLowerBond = [#1 #2 #3 #4];
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%
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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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% tmpFitParameters.peakArea = [abs#1 abs#2 abs#3 abs#4 abs#5];
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@@ -63,7 +77,8 @@ function DataTable = nappFitGaussXps(DataTable,~,varargin)
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% tmpFitParameters.peakAreaLowerBond = [#1 #2 #3 #4];
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% tmpFitParameters.peakWidthLowerBond = [#1,2,4,5 #3];
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% tmpFitParameters.peakPosLowerBond = [#1 #2 #3 #4];
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%
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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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@@ -209,25 +224,29 @@ elseif matches(p.Results.mode,'widthPosition')
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+ tmpB(4)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1)- (tmpB(3)+p.Results.FitParameter.peakPos(1,2))).^2/tmpB(2).^2))... % Gauss peak 2
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+ tmpB(5)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1)- (tmpB(3)+p.Results.FitParameter.peakPos(1,3))).^2/tmpB(2).^2))... % Gauss peak 3
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+ tmpB(6)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1)- (tmpB(3)+p.Results.FitParameter.peakPos(1,4))).^2/tmpB(2).^2))... % Gauss peak 4
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+tmpB(7).*x(:,1)+tmpB(8); % linear background
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+ tmpB(7)/(tmpB(2)*sqrt(pi/2))*exp(-2.*((x(:,1)- (tmpB(3)+p.Results.FitParameter.peakPos(1,5))).^2/tmpB(2).^2))... % Gauss peak 4
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+tmpB(8).*x(:,1)+tmpB(9); % 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(1,1)... % 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) ... % Gauss peak 3
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p.Results.FitParameter.peakArea(1,4)... % Gauss peak 4
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p.Results.FitParameter.peakArea(1,4)...
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p.Results.FitParameter.peakArea(1,5)...% Gauss peak 5
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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) ... % Gauss peak 2
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p.Results.FitParameter.peakAreaLowerBond(1,3) ... % Gauss peak 3
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p.Results.FitParameter.peakAreaLowerBond(1,4) ... % Gauss peak 4
|
||||
p.Results.FitParameter.peakAreaLowerBond(1,4) ...
|
||||
p.Results.FitParameter.peakAreaLowerBond(1,5) ... % Gauss peak 5
|
||||
0 0]; % linear background
|
||||
% upper bond
|
||||
ub = [p.Results.FitParameter.peakAreaUpperBond(1,1) p.Results.FitParameter.peakWidthUpperBond(1,1) p.Results.FitParameter.peakPosUpperBond(1,1) ... % Gauss peak 1
|
||||
p.Results.FitParameter.peakAreaUpperBond(1,2) ... % Gauss peak 2
|
||||
p.Results.FitParameter.peakAreaUpperBond(1,3) ... % Gauss peak 3
|
||||
p.Results.FitParameter.peakAreaUpperBond(1,4) ... % Gauss peak 4
|
||||
p.Results.FitParameter.peakAreaUpperBond(1,4) ...
|
||||
p.Results.FitParameter.peakAreaUpperBond(1,5) ...% Gauss peak 5
|
||||
Inf Inf]; % linear background
|
||||
elseif matches(p.Results.mode,'width')
|
||||
yfcn1 = @(tmpB,x)...
|
||||
@@ -365,7 +384,8 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
||||
tmpB(4) tmpB(2) tmpB(3)+p.Results.FitParameter.peakPos(1,2)...
|
||||
tmpB(5) tmpB(2) tmpB(3)+p.Results.FitParameter.peakPos(1,3)...
|
||||
tmpB(6) tmpB(2) tmpB(3)+p.Results.FitParameter.peakPos(1,4)...
|
||||
tmpB(7) tmpB(8)...
|
||||
tmpB(8) tmpB(9)...
|
||||
tmpB(7) tmpB(2) tmpB(3)+p.Results.FitParameter.peakPos(1,5)...
|
||||
NaN NaN NaN];
|
||||
elseif matches(p.Results.mode,'width')
|
||||
B = [tmpB(1) tmpB(2) tmpB(3)...
|
||||
@@ -475,6 +495,9 @@ for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
||||
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))] ;
|
||||
resultsPeakArea(ii,:) = [B(1), B(4), B(7), B(10) B(15)] ;
|
||||
% resultsBkgrd(ii,:) = [B(13), B(14)] ;
|
||||
% close the fiting progess window
|
||||
fh = findobj( 'Type', 'Figure', 'Name', 'GlobalSearch');
|
||||
close(fh)
|
||||
end
|
||||
|
||||
|
||||
|
||||
Reference in new issue
Block a user