function DataTable = nappScale(DataTable,varargin)
%nappScale can be used to normalise XPS spectra to the peak area. The peak
%of the same region  or of a different region with identical SES file
%number can be used for XPS data. NEXAFS spectra can be normed to their
%area or to the intensity at an energy range of choice.
%
%   FileList = nappScale(FileList,tmpDataSelection,'regionOld','C1s','regionNew','O1s');
%
%   *input*
%   FileList: data table
%   tableSelection (optional): logical array to filter data table. These
%   spectra will be normalised. 
%   regionOld: C1s (default) or O1s, N1s - region spectra that will be
%   normalised. Needs to be identical to the table selection (filter).
%   regionNew: O1s (default) or C1s, N1s - peak area that will be used to normalise
%   peakNumber: Number of the feature that should be used for fitting
%   (nappFitGaussXps gives results for 4 features, default is 1)
%
% The region in tableSelection and regionOld MUST be identical.
%
%
%   *output*
%   table variable spectrum_countsNorm

% Define conditions and defaults of input
defaultTableVariable    = 'spectrum_countsPerSecond';
expectedTableVariable   = {'spectrum_counts','spectrum_countsPerSecond','spectrum_countsNorm'};
defaultMode             = 'area';
expectedMode            = {'intensity','area'};
defaultRegionOld        = 'C1s';
expectedRegionOld       = {'O1s','C1s','N1s','Cl2p'};
defaultRegionNew        = 'O1s';
expectedRegionNew       = {'O1s','C1s','N1s'};
defaultPeakNumber       = 1;
defaultTableSelection   = true(size(DataTable,1));


% Parse input
p = inputParser;
addRequired(p,'DataTable',@istable);
addOptional(p,'tableSelection',defaultTableSelection,@islogical);
addOptional(p,'energyStart',@isnumeric)
addOptional(p,'energyEnd',@isnumeric)
addParameter(p,'tableVariable',defaultTableVariable,...
    @(x) any(validatestring(x,expectedTableVariable)));
addParameter(p,'regionOld',defaultRegionOld,...
    @(x) any(validatestring(x,expectedRegionOld)));
addParameter(p,'regionNew',defaultRegionNew,...
    @(x) any(validatestring(x,expectedRegionNew)));
addParameter(p,'peakNumber',defaultPeakNumber);
addParameter(p,'mode',defaultMode,...
    @(x) any(validatestring(x,expectedMode)));
parse(p,DataTable,varargin{:});

% add empty variable to table
existColumn = strcmp('spectrum_countsNorm',DataTable.Properties.VariableNames);
if ~any(existColumn)
    DataTable.spectrum_countsNorm = cell(size(DataTable,1),1);
end

existColumn = strcmp('logScaleRange',DataTable.Properties.VariableNames);
if ~any(existColumn)
    DataTable.logBackgroundRange = NaN(size(DataTable,1),2);
end
existColumn = strcmp('logScaleMode',DataTable.Properties.VariableNames);
if ~any(existColumn)
    DataTable.logBackgroundMode = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
end
existColumn = strcmp('logScaleDate',DataTable.Properties.VariableNames);
if ~any(existColumn)
    DataTable.logBackgroundDate = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
end

% check input (all elements of input variable need to have non-zero size)
if ~all(cell2mat(cellfun(@size,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable),'UniformOutput',false)),'all')
    disp('The table variable appears to be empty. I quit now')
    error('The table variable appears to be empty.')
end


% repeat this for all columns in input.
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
    if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw')
        % get name and date of input file and replace old region with new
        % region. This will be the files where the peak area is taken from.
        tmpName  = replace(p.Results.DataTable(p.Results.tableSelection,:).name{ii}, ...
            p.Results.regionOld,p.Results.regionNew);
        tmpDate  = p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatenum(ii);
        % select spectra based on the new names and dates of original file
        tmpDataSelection =  contains(p.Results.DataTable.name,tmpName)...
            & ismember(year(p.Results.DataTable.lastModifiedDatenum),year(tmpDate))...
            & ismember(month(p.Results.DataTable.lastModifiedDatenum),month(tmpDate))...
            & ismember(day(p.Results.DataTable.lastModifiedDatenum),day(tmpDate))...
            & ismember(hour(p.Results.DataTable.lastModifiedDatenum),hour(tmpDate))...
            & ismember(minute(p.Results.DataTable.lastModifiedDatenum),minute(tmpDate));
        % check peak area 
        existColumn = strcmp('peakArea',DataTable.Properties.VariableNames);
        if any(existColumn)
                if isnan(DataTable( tmpDataSelection,:).peakArea(p.Results.peakNumber))
                    disp('The peak area appears to be empty. I quit now')
                    disp(DataTable( tmpDataSelection,:).name{ii})
                    error('The peak area appears to be empty.')
                end
        else
              disp('The data table appear to have not peak area column. I quit now')
                    error('No peak area column')  
        end
        % do the norming
        if contains(p.Results.mode,'area')
            DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii} = ...
                DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
                ./  DataTable( tmpDataSelection,:).peakArea(p.Results.peakNumber);
        elseif contains(p.Results.mode,'intensity')
            disp('Intensity mode not yet programmed for XPS data')
        end
    
    elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
        % if ~exist(p.Results.energyStart) | ~exist(p.Results.energyEnd)
        %     disp('The energy region used for normalisation appears to be empty. I quit now')
        %    error('The energy region used to normalise appears to be empty.')
        % end
        if contains(p.Results.mode,'intensity')
            if 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});
                % MEAN
                b_1 = find(xData >= p.Results.energyStart,1);
                b_2 = find(xData >= p.Results.energyEnd,1);

                b_mean = mean(yData(b_1:b_2));
            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});
                % MEAN
                b_1 = find(xData <= p.Results.energyStart,1);
                b_2 = find(xData <= p.Results.energyEnd,1);

                b_mean = mean(yData(b_2:b_1));
            else
                disp('Warning: Issue with NEXAFS_col_scaling')
            end

            tmp_3(:,1) = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
                ./b_mean;

            DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii}  = tmp_3;
            clearvars tmp_3
        elseif contains(p.Results.mode,'area')
            if 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});
                % Area
                b_1 = find(xData >= p.Results.energyStart,1);
                b_2 = find(xData >= p.Results.energyEnd,1);

                b_area = trapz(xData(b_1:b_2),yData(b_1:b_2));
            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});
                % MEAN
                b_1 = find(xData <= p.Results.energyStart,1);
                b_2 = find(xData <= p.Results.energyEnd,1);

                b_area = trapz(xData(b_2:b_1),yData(b_2:b_1));
            else
                disp('Warning: Issue with NEXAFS_col_scaling')
            end

            tmp_3(:,1) = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
                ./b_area;

             DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii} = tmp_3;
            clearvars tmp_3

        end
    end
end
% write log to table
DataTable.logScaleMode(p.Results.tableSelection,:)                  = cellstr(repmat(p.Results.mode,size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
    DataTable.logScaleRange(p.Results.tableSelection,:)               = repmat([p.Results.energyStart p.Results.energyEnd],size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
end
DataTable.logScaleDate(p.Results.tableSelection,:)                   = cellstr(repmat(datestr(now),size(p.Results.DataTable(p.Results.tableSelection,:),1),1));

end