function hdl = nappPlot(DataTable,varargin)
%NAPPLOT Plot photoelectron spectra and NEXAFS images from a data table.
%   hdl = NAPPLOT(DataTable) creates figures for all rows in DataTable
%   using the default visualization options and returns the handle(s) to
%   the generated figure(s).
%
%   hdl = NAPPLOT(DataTable, tableSelection) restricts plotting to rows for
%   which tableSelection is true. The length of tableSelection must
%   match the height of DataTable.
%
%   hdl = NAPPLOT(DataTable, tableSelection, Name, Value) additionally
%   customizes the data source, energy axis, layout mode, and figure
%   formatting using Name-Value arguments.
%
%   NAPPLOT is a general-purpose visualization routine for spectroscopy
%   experiments that can display:
%     - NEXAFS images (h5)
%     - time-resolved XPS/Auger maps (ibw)
%     - 1D spectra from previously generated table variables
%     - interactive NEXAFS + Auger-Meitner views
%
%   Required input
%   --------------
%   DataTable
%       Table that contains spectroscopy data and metadata.
%       Depending on the chosen tableVariable and energyScale, the
%       following variables are typically used:
%         - name                  : file name (string/char), used to
%                                   distinguish '.h5', '.ibw', '.xy'
%         - image                 : processed 2D image (cell of numeric)
%         - imageRoh              : raw 2D image (cell of numeric)
%         - spectrum_counts       : 1D spectrum (in arbitrary counts
%         - spectrum_countsPerSecond
%                                 : 1D spectrum (normalized to counts per second)
%         - spectrum_countsNorm   : 1D normalized spectrum
%         - scientaEkin_eV        : kinetic energy axis (cell of numeric)
%         - bindingEnergy_eV      : binding energy axis (cell of numeric)
%         - xRayEkin_eV           : photon energy axis (cell of numeric)
%         - scientaEkinRange_eV   : [emin emax] for plotting
%         - xRayEkinRange_eV      : [emin emax] for plotting
%         - lastModifiedDatestr   : acquisition or file time stamp
%         - sample                : (optional) sample name for titles
%
%   Optional positional input
%   -------------------------
%   tableSelection
%       Logical vector selecting rows of DataTable to plot.
%       Default: all rows true
%
%   Name-Value arguments
%   --------------------
%   'tableVariable'
%       Name of the variable in DataTable to plot.
%       Type   : char or string
%       Values : 'image'                 (default)
%                'imageRoh'
%                'spectrum_countsPerSecond'
%                'spectrum_counts'
%                'spectrum_countsNorm'
%
%   'energyScale'
%       Energy axis used for plotting
%       Type   : char or string
%       Values : 'kinetic'  (default)  - use scientaEkin_eV
%                'binding'            - use bindingEnergy_eV
%                'xRay'               - use xRayEkin_eV
%                'sweeps'             - use column/iteration index
%
%   'mode'
%       Layout and plotting mode
%       Type   : char or string
%       Values : 'AllInOne'   (default)
%                  - Plot all selected 1D spectra in a single axes
%                    (overlaid).
%                'OneEach'
%                  - One figure per single spectrum or image.
%                'iterations'
%                  - Plot multiple iterations from a 2D stack in different
%                    colors to show time/sequence evolution.
%                'AugerMeitner'
%                  - Extract and plot Auger-Meitner spectra at specified
%                    photon energies for NEXAFS maps ('.h5').
%                'interactive'
%                  - Interactive layout for NEXAFS images with linked
%                    Auger-Meitner and NEXAFS line cuts controlled by
%                    mouse / data cursor callbacks.
%
%   'figureMode'
%       Overall figure formatting, size, and font presets.
%       Type   : char or string
%       Values : 'screen'     (default)
%                  - Standard display window in pixels, moderate fonts.
%                'powerpoint'
%                  - Larger window and fonts optimized for slides.
%                'word'
%                  - Compact figure in centimeters for documents.
%
%   'plotStep'
%       Step size in iteration index for 'iterations' mode.
%       Type   : positive numeric scalar
%       Default: 1  (plot every iteration)
%
%   'AugerMeitnerEnergies'
%       Photon energies (in eV) for 'AugerMeitner' mode
%       At each value, the function extracts one column from the image and
%       plots the corresponding Auger-Meitner electron spectrum.
%       Type   : numeric vector
%
%   Output
%   ------
%   hdl
%       Handle or array of handles to the generated figure(s)
%       For 'AllInOne' this is a single figure. For 'OneEach',
%       'iterations', 'AugerMeitner', and 'interactive', hdl may contain
%       one handle per processed row.
%
%   Notes
%   -----
%   - The function checks that the chosen tableVariable is non-empty for
%     all selected rows and throws an error otherwise.
%   - File type is inferred from the 'name' variable to distinguish h5,
%     ibw, and xy-type data
%   - Axis labels, limits, and titles are adapted automatically based on
%     energyScale, tableVariable, and available metadata (sample name,
%     time stamp)
%   - In 'interactive' mode, datacursor and mouse motion callbacks update
%     linked line plots for Auger-Meitner and NEXAFS traces.
%% TODO
%
% TODO: Add averaging in image and in iteration plot
% TODO: Make code nicer (NEXAFS plotting)

% Define conditions and defaults of input
defaultTableVariable        = 'image';
expectedTableVariable       = {'image','imageRoh','spectrum_countsPerSecond','spectrum_counts','spectrum_countsNorm'};
defaultMode                 = 'AllInOne';
expectedMode                = {'AllInOne','OneEach','iterations','AugerMeitner','interactive'};
defaultFigureMode           = 'screen';
expectedFigureMode          = {'screen','powerpoint','word'};
defaultEnergyScale          = 'kinetic';
expectedEnergyScale         = {'kinetic','binding','xRay','sweeps'};
defaultTableSelection       = true(size(DataTable,1),1);
defaultPlotStep             = 1;

% Parse input
p = inputParser;
addRequired(p,'DataTable',@istable);
addOptional(p,'tableSelection',defaultTableSelection,@islogical);
addParameter(p,'tableVariable',defaultTableVariable,...
    @(x) any(validatestring(x,expectedTableVariable)));
addParameter(p,'mode',defaultMode,...
    @(x) any(validatestring(x,expectedMode)));
addParameter(p,'figureMode',defaultFigureMode,...
    @(x) any(validatestring(x,expectedFigureMode)));
addParameter(p,'energyScale',defaultEnergyScale,...
    @(x) any(validatestring(x,expectedEnergyScale)));
addParameter(p,'plotStep',defaultPlotStep);
addParameter(p,'AugerMeitnerEnergies',@isnumeric)

parse(p,DataTable,varargin{:});


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


% make figure, with options for output.
if contains(p.Results.figureMode ,'screen') % standard
    alw         = get(groot,'DefaultAxesLineWidth');
    fsz         = get(groot,'DefaultAxesFontSize');
    lw          = 2; %get(groot,'DefaultLineLineWidth');
    fnt         = get(groot,'DefaultAxesFontName');
    loc         = 'northeastoutside';
    unt         = 'pixels';
    pos         = [20 100 800 500];

elseif contains(p.Results.figureMode,'powerpoint')
    alw         = 2;
    fsz         = 26;
    lw          = 4;
    fnt         = 'Helvetica Neue';
    loc         = 'northeastoutside';
    unt         = 'pixels';
    pos         = [300 200 1280 720];

elseif contains(p.Results.figureMode,'word')
    alw         = 0.75;
    fsz         = 10;
    lw          = 0.5;
    fnt         = 'Helvetica Neue';
    loc         = 'southoutside';
    unt         = 'centimeters';
    pos         = [8 10 8 10];

end


if matches(p.Results.mode,'AugerMeitner')
    for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
        if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')

            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
            if size(p.Results.AugerMeitnerEnergies) >= 7
                tmp_color = colormap(parula(size(p.Results.AugerMeitnerEnergies,2)));
            else
                tmp_color = colormap(lines(size(p.Results.AugerMeitnerEnergies,2)));
            end

            % Create axes
            hold(gca,'on');


            for ij = 1:size(p.Results.AugerMeitnerEnergies,2)
                % find x-ray energy in data
                tmpXrayEnergy = find(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii} >=  p.Results.AugerMeitnerEnergies(ij),1);
                hplot= plot( p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}, ...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,tmpXrayEnergy));
                hplot.LineWidth = lw;
                hold on
            end
            xlabel('Auger-Meitner electron energy [eV]')
            hYLabel = ylabel('Counts per dwell time');
            legend(string(p.Results.AugerMeitnerEnergies))




        end
    end
end

if matches(p.Results.tableVariable,'image') && matches(p.Results.mode,'interactive')
    for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
        if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.


            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',[20 100 1000 800]);
            tld  = tiledlayout(2,2);
            tld.TileSpacing = 'compact';
            tld.Padding = 'compact';

            % image
            ax1= nexttile;
           


            img_handle = image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',ax1,'CDataMapping','scaled');
            axis(gca,'ij');
            set(gca,'Layer','top');
            ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
            xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
            hXLabel = xlabel('# Photon energy, column number');
            hYLabel = ylabel('# Auger energy, column number');

            box(gca,'on');

            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
            hdl.Pointer = 'crosshair';

            ij= 1;
            ik=1; 
            % Auger-Meitner
            ax2 = nexttile;




            hplot= plot(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij), p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
            hplot.LineWidth = lw;
            hold on

            ylabel('A-M e energy [eV]')
            xlabel('Counts per dwell time');

          
            ax2.YDir = 'reverse';


            box(ax2,'on');

            set( ax2, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , fsz          );

            set(ax2, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );

            % NEXAFS
            ax3 = nexttile;




            hplot2= plot( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
                p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(ik,:));
            hplot2.LineWidth = lw;
            hold on

            xlabel('xray energy [eV]')
            hYLabel = ylabel('Counts per dwell time');

            box(ax3,'on');

            set( ax3, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , fsz          );

            set(ax3, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );

            if ~matches(p.Results.figureMode,'word')
                title(tld,p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
            end

    %         % NOW set up datacursor - after all axes are created
    dcm = datacursormode(hdl);
    set(dcm, 'UpdateFcn', {@updatePlots, p.Results, ii, ax2, ax3, hplot, hplot2});
    set(dcm, 'Enable', 'on');
    set(dcm, 'SnapToDataVertex', 'off');  % Allows smooth mouse tracking
    set(dcm, 'DisplayStyle', 'window');    % or 'datatip' for tooltip style

% Enable continuous update on mouse move
set(hdl, 'WindowButtonMotionFcn', {@mouseMoveFcn, dcm, p.Results, ii, ax2, ax3, hplot, hplot2, ax1});
        end
    end
end

if matches(p.Results.tableVariable,'image') && ~matches(p.Results.mode,'AugerMeitner') && ~matches(p.Results.mode,'interactive')
    for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
        if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.
            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

            % Create axes
            hold(gca,'on');
            if matches(p.Results.energyScale,'sweep')
                image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
                xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                hXLabel = xlabel('# Photon energy, column number');
                hYLabel = ylabel('# Auger energy, column number');
            else
                % Try to plot image with x and y
                try
                    % interpolate, to have equal x spacing for image plot
                    Xq = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1):0.1:p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end);
                    Vq = interp2(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
                    image(Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                        Vq,'Parent',gca,'CDataMapping','scaled');
                    axis(gca,'ij');
                    set(gca,'Layer','top');
                    xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
                    ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
                    hXLabel = xlabel('Photon energy [eV]');
                    hYLabel = ylabel('Auger energy [eV]');
                    % if this does not work, plot without scaling (just with row and column numbers)
                catch
                    image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
                    axis(gca,'ij');
                    set(gca,'Layer','top');
                    ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
                    xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                    hXLabel = xlabel('# Photon energy, column number');
                    hYLabel = ylabel('# Auger energy, column number');
                end

            end
            box(gca,'on');
            if ~matches(p.Results.figureMode,'word')
                title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
            end
            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
        elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')

            if contains(p.Results.energyScale,'kinetic')
                hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

                % Create axes
                hold(gca,'on');
                image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                    1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
                    'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                if size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2) >= 2 
                    ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                end
                xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(end)]);
                hXLabel = xlabel('Electron energy [eV]');
                hYLabel = ylabel('Sequence iteration');
            elseif contains(p.Results.energyScale,'binding')
                hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

                % Create axes
                hold(gca,'on');
                image(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
                    1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
                    'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                % xlim([p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,2)]);
                hXLabel = xlabel('Binding energy [eV]');
                hYLabel = ylabel('Sequence iteration');
            end
            box(gca,'on');
            existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
            if ~matches(p.Results.figureMode,'word')
                if ~any(existColumn)
                    title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
                else
                    title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii}  p.Results.DataTable(p.Results.tableSelection,:).sample{ii}  p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
                end
            end
            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
        end
    end
end
if matches(p.Results.tableVariable,'imageRoh')
    for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
        if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.
            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

            % Create axes
            hold(gca,'on');
            % Try to plot image with x and y
            try
                image(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
                ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
                hXLabel = xlabel('Photon energy [eV]');
                hYLabel = ylabel('Auger energy [eV]');
                % if this does not work, plot without scaling (just with row and column numbers)
            catch
                image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
                xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                hXLabel = xlabel('# Photon energy, column number');
                hYLabel = ylabel('# Auger energy, column number');
            end

            box(gca,'on');
            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
        elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')

            if contains(p.Results.energyScale,'kinetic')
                hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

                % Create axes
                hold(gca,'on');
                existColumn = strcmp('scientaEkinRoh_eV',DataTable.Properties.VariableNames);
                if any(existColumn)
                    image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii},...
                        1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
                        'Parent',gca,'CDataMapping','scaled');
                    xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii}(end)]);

                else
                    image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                        1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
                        'Parent',gca,'CDataMapping','scaled');
                    xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(end)]);

                end
                axis(gca,'ij');
                set(gca,'Layer','top');
                ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                hXLabel = xlabel('Electron energy [eV]');
                hYLabel = ylabel('Sequence iteration');
            elseif contains(p.Results.energyScale,'binding')
                hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

                % Create axes
                hold(gca,'on');
                image(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
                    1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
                    'Parent',gca,'CDataMapping','scaled');
                axis(gca,'ij');
                set(gca,'Layer','top');
                ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
                % xlim([p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,2)]);
                hXLabel = xlabel('Binding energy [eV]');
                hYLabel = ylabel('Sequence iteration');

            end
            box(gca,'on');

            existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
            if ~matches(p.Results.figureMode,'word')
                if ~any(existColumn)
                    title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
                else
                    title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii}  p.Results.DataTable(p.Results.tableSelection,:).sample{ii}  p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
                end
            end
            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
        end
    end
end


if contains(p.Results.tableVariable,'spectrum')
    if contains(p.Results.mode,'OneEach')
        for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);

            % Create axes
            hold(gca,'on');
            if (contains(p.Results.energyScale,'kinetic') && (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')))
                hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}');
                hplot.LineWidth = lw;
                hXLabel = xlabel('Electron kinetic energy [eV]');
                xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);

            elseif (contains(p.Results.energyScale,'binding') && (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw')|| endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')))
                hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}');
                hplot.LineWidth = lw;
                hXLabel= xlabel('Binding energy [eV]');
                xlim([min(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii}) max(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii})]);

            elseif (contains(p.Results.energyScale,'xRay') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5'))
                hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},...
                    p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
                hplot.LineWidth = lw;
                hXLabel = xlabel('Photon Energy eV');
                xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,2)]);

            end
            if contains(p.Results.tableVariable,'Norm')
                hYLabel = ylabel('Counts [arb. unit]');
            elseif contains(p.Results.energyScale,'xRay')
                hYLabel = ylabel('partial A-M.E.Y.');
            else
                hYLabel = ylabel('Counts per second');
            end


            box(gca,'on');
            existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
            if ~matches(p.Results.figureMode,'word')
                if ~any(existColumn)
                    title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
                else
                    try
                        title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii}  p.Results.DataTable(p.Results.tableSelection,:).sample{ii}  p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
                    catch
                        title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii}  p.Results.DataTable(p.Results.tableSelection,:).sample{ii}}] ,'Interpreter','none')
                    end
                end
            end

            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );

        end
    end

    if contains(p.Results.mode,'AllInOne')
        % generate colormap

        hdl = figure('Name','AllInOneSpectrum','units', unt,'Position',pos);
        if size(p.Results.DataTable(p.Results.tableSelection,:),1) >= 7
            tmp_color = colormap(parula(size(p.Results.DataTable(p.Results.tableSelection,:),1)));
        else
            tmp_color = colormap(lines(size(p.Results.DataTable(p.Results.tableSelection,:),1)));
        end
        if contains(p.Results.energyScale,'kinetic')
            % axes('Parent',gcf,'XDir','reverse')
            hold(gca,'on');
            for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
                if (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy'))
                    hplot =  plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}','DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
                    hplot.LineWidth = lw;
                end
            end
            hXLabel = xlabel('Electron kinetic energy [eV]');
        elseif contains(p.Results.energyScale,'binding')
            axes('Parent',gcf,'XDir','reverse')
            hold(gca,'on');

            for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
                if (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy'))
                    hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}','DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
                    hplot.LineWidth = lw;
                end
            end
            hXLabel= xlabel('Binding energy [eV]');
        elseif contains(p.Results.energyScale,'xRay')
            hold(gca,'on');
            for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
                if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
                    hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},...
                        'DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
                    hplot.LineWidth = lw;
                end
            end
            hXLabel = xlabel('Photon Energy eV');
        end
        if contains(p.Results.tableVariable,'Norm')
            hYLabel = ylabel('Counts [arb. unit]');
        elseif contains(p.Results.energyScale,'xRay')
            hYLabel = ylabel('partial A-M.E.Y.');
        else
            hYLabel = ylabel('Counts per second');
        end


        box(gca,'on');
        if ~matches(p.Results.figureMode,'word')
            title('PE Spectra','Interpreter','none')
            hlegend = legend(p.Results.DataTable(p.Results.tableSelection,:).name{:});
            hlegend.FontSize = fsz;
            hlegend.Interpreter = 'none';
            hlegend.Location = loc;
            set(legend, 'Interpreter','none')
        end
        set( gca, ...
            'FontName'   , fnt,'FontSize'   , fsz );
        set([hXLabel, hYLabel], ...
            'FontName'   , fnt);
        set([hXLabel, hYLabel]  , ...
            'FontSize'   , 1.2*fsz          );

        set(gca, ...
            'Box'         , 'off'     , ...
            'TickDir'     , 'out'     , ...
            'TickLength'  , [.02 .02] , ...
            'XMinorTick'  , 'on'      , ...
            'YMinorTick'  , 'off'      , ...
            'XGrid'       , 'on'      , ...
            'XColor'      , [0 0 0], ...
            'YColor'      , [0 0 0], ...
            'LineWidth'   , alw         );



    end


end
if contains(p.Results.mode,'iterations')
    % generate colormap

    for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
        if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')

            hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
            if size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2) >= 7
                tmp_color = colormap(parula(size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)));
            else
                tmp_color = colormap(lines(size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)));
            end

            % Create axes
            hold(gca,'on');

            if contains(p.Results.energyScale,'kinetic')
                for ij = 1:p.Results.plotStep:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)
                    hplot= plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}',...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij),'Color',tmp_color(ij,:));
                    hplot.LineWidth = lw;
                    hold on
                end
                xlabel('Electron kinetic energy [eV]')
            elseif contains(p.Results.energyScale,'binding')
                %axes('Parent',gcf,'XDir','reverse')

                for ij = 1:p.Results.plotStep:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)
                    hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii}',...
                        p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij),'Color',tmp_color(ii,:));
                    hplot.LineWidth = lw;
                end
                hXLabel = xlabel('Binding energy [eV]');
            end
            if contains(p.Results.tableVariable,'Norm')
                hYLabel = ylabel('Counts [arb. unit]');
            else
                hYLabel = ylabel('Counts per second');
            end


            box(gca,'on');
            if ~matches(p.Results.figureMode,'word')
                title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii}  p.Results.DataTable(p.Results.tableSelection,:).sample{ii}  p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
            end
            set( gca, ...
                'FontName'   , fnt,'FontSize'   , fsz );
            set([hXLabel, hYLabel], ...
                'FontName'   , fnt);
            set([hXLabel, hYLabel]  , ...
                'FontSize'   , 1.2*fsz          );

            set(gca, ...
                'Box'         , 'off'     , ...
                'TickDir'     , 'out'     , ...
                'TickLength'  , [.02 .02] , ...
                'XMinorTick'  , 'on'      , ...
                'YMinorTick'  , 'off'      , ...
                'XGrid'       , 'on'      , ...
                'XColor'      , [0 0 0], ...
                'YColor'      , [0 0 0], ...
                'LineWidth'   , alw         );
        end
    end
end




% Nested callback function
    % function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
    %     pos = get(event_obj, 'Position');
    %     ij = round(pos(1));
    %     ik = round(pos(2));
    % 
    %     set(hplot2, 'XData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(:,ij));
    %     title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
    % 
    %     set(hplot3, 'YData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(ik,:));
    %     title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
    % 
    %     % Create custom datatip text showing coordinates
    %     txt = {sprintf('X index: %d', ij), ...
    %            sprintf('Y index: %d', ik), ...
    %            sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
    % end


function mouseMoveFcn(~, ~, dcm, pResults, ii, ax2, ax3, hplot2, hplot3, ax1)
    % Check if mouse is over the image axes
    if gca == ax1
        % Get current mouse position
        cp = get(ax1, 'CurrentPoint');
        ij = round(cp(1, 1));  % X index
        ik = round(cp(1, 2));  % Y index
        
        % Get the data matrix
        dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
        
        % Ensure indices are within bounds
        [nRows, nCols] = size(dataMatrix);
        if ij >= 1 && ij <= nCols && ik >= 1 && ik <= nRows
            % Update plots
            set(hplot2, 'XData', dataMatrix(:, ij));
            title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
            
            set(hplot3, 'YData', dataMatrix(ik, :));
            title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
        end
    end
end

% Datatip callback - shows info
function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
    try
        pos = get(event_obj, 'Position');
        ij = round(pos(1));
        ik = round(pos(2));
        
        dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
        [nRows, nCols] = size(dataMatrix);
        ij = max(1, min(ij, nCols));
        ik = max(1, min(ik, nRows));
        
        txt = {sprintf('X: %d', ij), ...
               sprintf('Y: %d', ik), ...
               sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
    catch
        pos = get(event_obj, 'Position');
        txt = {sprintf('X: %.1f', pos(1)), ...
               sprintf('Y: %.1f', pos(2))};
    end
end
end