plotStack.m

function plotStack(job,varargin)
%% Function description:
% This function plots a series of maps, figures, graphs, and tables for
% detailed child variant analysis within a single parent grain as follows:
% - By manually supplying a *parentGrainId*, or
% - Using the [grainClick] function and interactively choosing a grain of
% interest.
%
%% Syntax:
%  plotStack(job)
%
%% Input:
%  job          - @parentGrainreconstructor
%  pGrainId     - parent grain Id using the argument 'parentGrainId'
%  direction    - @vector3d
%
%% Options:
%  grains       - plot grain data instead of EBSD data
%  noScalebar   - Remove scalebar from maps
%  noFrame      - Remove frame around maps


if ~isempty(varargin) && any(strcmpi(varargin,'parentGrainId'))
    pGrainId = varargin{find(strcmpi('parentGrainId',varargin)==1)+1};
    if ~isnumeric(pGrainId)
        error('Argument ''parentGrainId'' must be numeric.');
        return;
    end
else
    error('Argument ''parentGrainId'' not specified.');
    return;
end

%% check if the plotStack function was called from grainClick or not
if ~any(strcmpi(varargin,'grainClick2plotStack')) % if not...
    % ...close all other open figures
    allfigh = findall(0,'type','figure');
    % allfigh = findall(groot,'type','figure');
    for ii = 1:numel(allfigh)
        try
            close(ii); % delete figures
            % clf(allfigh(ii)); % clear figures
        catch
            % do nothing
        end
    end
end


%% Define the primary vector of interest
vector = getClass(varargin,'vector3d',vector3d.X);

%% Define the parent grain
pGrain = job.parentGrains(job.parentGrains.id == pGrainId);
pEBSD = job.ebsd(pGrain);
pEBSD = pEBSD(job.csParent);
% Define the parent grain IPF notation
ipfKeyParent = ipfHSVKey(job.csParent);
ipfKeyParent.inversePoleFigureDirection = vector;
% Define the parent PDF
hParent = Miller(0,0,1,job.csParent,'hkl');

%% Define the child grain(s)
clusterGrains = job.grainsPrior(job.mergeId == pGrainId);
cGrains = clusterGrains(job.csChild);
cEBSD = job.ebsdPrior(job.ebsdPrior.id2ind(pEBSD.id));
cEBSD = cEBSD(job.csChild);
% Define the child grain(s) IPF notation
ipfKeyChild = ipfHSVKey(job.csChild);
ipfKeyChild.inversePoleFigureDirection = vector;
% Define the child PDF
hChild = Miller(0,0,1,job.csChild,'hkl');

%% Define the maximum number of variants and packets for the p2c OR
maxVariants = length(job.p2c.variants);
maxPackets = max(job.packetId);
maxBain = max(job.bainId);

%% Define the text output format as Latex
setInterp2Latex

%% Define the window settings for a set of docked figures
% % Ref: https://au.mathworks.com/matlabcentral/answers/157355-grouping-figures-separately-into-windows-and-tabs
warning off
desktop = com.mathworks.mde.desk.MLDesktop.getInstance;
% % Define a unique group name for the dock using the function name
% % and the system timestamp
dockGroupName = ['plotStack_',char(datetime('now','Format','yyyyMMdd_HHmmSS'))];
desktop.setGroupDocked(dockGroupName,0);
bakWarn = warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');



%% Plot the parent phase map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plot(pGrain);
else
    plot(pEBSD);
end
hold all
[~,mP] = plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
set(figH,'Name','Map: Parent phase + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end

if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the child phase map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plot(cGrains);
else
    plot(cEBSD);
end
hold all
plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0.5 0.5 0.5]);
[~,mP] = plot(cGrains.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);

hold off
set(figH,'Name','Map: Child phase + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the parent IPF map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    cbsParent = ipfKeyParent.orientation2color(pGrain.meanOrientation);
    plot(pGrain,cbsParent);
else
    cbsParent = ipfKeyParent.orientation2color(pEBSD.orientations);
    plot(pEBSD,cbsParent);
end
hold all
[~,mP] = plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
set(figH,'Name','Map: Parent grain IPF_x + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the child IPF map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    cbsChild = ipfKeyChild.orientation2color(cGrains.meanOrientation);
    plot(cGrains,cbsChild);
else
    cbsChild = ipfKeyChild.orientation2color(cEBSD.orientations);
    plot(cEBSD,cbsChild);
end
hold all
plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0.5 0.5 0.5]);
[~,mP] = plot(cGrains.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
set(figH,'Name','Map: Child grain IPF_x + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the child variants map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plot(cGrains(~isnan(cGrains.variantId)),cGrains.variantId(~isnan(cGrains.variantId)));
else
    [vId,pId,bId] = calcVariantId(pGrain.meanOrientation,cEBSD.orientations,job.p2c, ...
        'variantMap', job.variantMap);
    plot(cEBSD,vId);
end

hold all
plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0.5 0.5 0.5]);
[~,mP] = plot(cGrains.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(jet(maxVariants));
caxis([1 maxVariants]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxVariants],...
    'YTickLabel',num2str([1:1:maxVariants]'), 'YLim', [1 maxVariants],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','Map: Child grain(s) variant Id(s) + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the child crystallographic packets map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if isnan(maxPackets)
    maxPackets = max(pId);
end
if check_option(varargin,'grains')
    plot(cGrains(~isnan(cGrains.packetId)),cGrains.packetId(~isnan(cGrains.packetId)));
else
    plot(cEBSD,pId);
end
hold all
plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0.5 0.5 0.5]);
[~,mP] = plot(cGrains.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(viridis);
caxis([1 maxPackets]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxPackets],...
    'YTickLabel',num2str([1:1:maxPackets]'), 'YLim', [1 maxPackets],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','Map: Child grain(s) crystallographic packet Id(s) + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the child Bain group map
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if isnan(maxBain)
    maxBain = max(bId);
end
if check_option(varargin,'grains')
    plot(cGrains(~isnan(cGrains.bainId)),cGrains.bainId(~isnan(cGrains.bainId)));
else
    plot(cEBSD,bId);
end
hold all
plot(pGrain.boundary,...
    'lineWidth',1,'lineColor',[0.5 0.5 0.5]);
[~,mP] = plot(cGrains.boundary,...
    'lineWidth',1,'lineColor',[0 0 0]);
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(flipud(hot));
caxis([1 maxBain]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxBain],...
    'YTickLabel',num2str([1:1:maxBain]'), 'YLim', [1 maxBain],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','Map: Child grain(s) Bain group Id(s) + GBs','NumberTitle','on');
if check_option(varargin,'noScalebar'), mP.micronBar.visible = 'off'; end
if check_option(varargin,'noFrame')
    mP.ax.Box = 'off'; mP.ax.YAxis.Visible = 'off'; mP.ax.XAxis.Visible = 'off';
end
drawnow;


%% Plot the parent orientation PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plotPDF(pGrain.meanOrientation,...
        hParent,...
        'equal','antipodal',...
        'MarkerSize',10,'MarkerFaceColor',[1 1 1],...
        'lineWidth',1,'MarkerEdgeColor',job.csParent.color);
else
    plotPDF(pEBSD.orientations,...
        hParent,...
        'equal','antipodal',...
        'MarkerSize',10,'MarkerFaceColor',[1 1 1],...
        'lineWidth',1,'MarkerEdgeColor',job.csParent.color);
end
hold off
set(figH,'Name','PDF: Parent grain orientation','NumberTitle','on');
drawnow;


%% Plot the mean parent orientation PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plotPDF(pGrain.meanOrientation,hParent,'markersize',12,'markerfacecolor' ,'k');
set(figH,'Name','PDF: Mean parent grain orientation','NumberTitle','on');
drawnow;


%% Plot the child IPF PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    cbsChild = ipfKeyChild.orientation2color(cGrains.meanOrientation);
    plotPDF(cGrains.meanOrientation,...
        cbsChild,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',5,'MarkerEdgeColor','k');

else
    cbsChild = ipfKeyChild.orientation2color(cEBSD.orientations);
    plotPDF(cEBSD.orientations,...
        cbsChild,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',3,'MarkerEdgeColor','k');
end
set(figH,'Name','PDF: Child grain(s) IPF_x','NumberTitle','on');
drawnow;


%% Plot the child variants PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plotPDF(cGrains.meanOrientation,...
        cGrains.variantId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotPDF(cEBSD.orientations,...
        vId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',3,'MarkerEdgeColor','k');
end
% Define the maximum number of color levels and plot the colorbar
colormap(jet(maxVariants));
caxis([1 maxVariants]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxVariants],...
    'YTickLabel',num2str([1:1:maxVariants]'), 'YLim', [1 maxVariants],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','PDF: Child grain(s) variant Id(s)','NumberTitle','on');
drawnow;


%% Plot the ideal child variants PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plotPDF_variants(job,pGrain.meanOrientation,hChild);
set(figH,'Name','PDF: Child grain(s) IDEAL variant Id(s)','NumberTitle','on');
drawnow;


%% Plot the child crystallographic packets PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plotPDF(cGrains.meanOrientation,...
        cGrains.packetId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotPDF(cEBSD.orientations,...
        pId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',3,'MarkerEdgeColor','k');
end
% Define the maximum number of color levels and plot the colorbar
colormap(viridis);
caxis([1 maxPackets]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxPackets],...
    'YTickLabel',num2str([1:1:maxPackets]'), 'YLim', [1 maxPackets],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','PDF: Child grain(s) crystallographic packet Id(s)','NumberTitle','on');
drawnow;


%% Plot the ideal child crystallographic packets PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plotPDF_packets(job,pGrain.meanOrientation,hChild);
set(figH,'Name','PDF: Child grain(s) IDEAL crystallographic packet Id(s)','NumberTitle','on');
drawnow;


%% Plot the child Bain group PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
if check_option(varargin,'grains')
    plotPDF(cGrains.meanOrientation,...
        cGrains.bainId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotPDF(cEBSD.orientations,...
        bId,...
        hChild,...
        'equal','antipodal','points','all',...
        'MarkerSize',3,'MarkerEdgeColor','k');
end
% Define the maximum number of color levels and plot the colorbar
colormap(flipud(hot));
caxis([1 maxBain]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxBain],...
    'YTickLabel',num2str([1:1:maxBain]'), 'YLim', [1 maxBain],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','PDF: Child grain(s) Bain group Id(s)','NumberTitle','on');
drawnow;


%% Plot the ideal child Bain group PDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plotPDF_bain(job,pGrain.meanOrientation,hChild);
set(figH,'Name','PDF: Child grain(s) IDEAL Bain group Id(s)','NumberTitle','on');
drawnow;


%% Plot the child variant IPDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plot(ipfKeyChild)
hold all
if check_option(varargin,'grains')
    plotIPDF(cGrains.meanOrientation,...
        cGrains.variantId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotIPDF(cEBSD.orientations,...
        vId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',3,'MarkerEdgeColor','k');
end
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(jet(maxVariants));
caxis([1 maxVariants]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxVariants],...
    'YTickLabel',num2str([1:1:maxVariants]'), 'YLim', [1 maxVariants],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','IPDF: Child grain(s) variant Id(s)','NumberTitle','on');
drawnow;


%% Plot the child crystallographic packets IPDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plot(ipfKeyChild)
hold all
if check_option(varargin,'grains')
    plotIPDF(cGrains.meanOrientation,...
        cGrains.packetId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotIPDF(cEBSD.orientations,...
        pId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',3,'MarkerEdgeColor','k');
end
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(viridis);
caxis([1 maxPackets]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxPackets],...
    'YTickLabel',num2str([1:1:maxPackets]'), 'YLim', [1 maxPackets],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','IPDF: Child grain(s) crystallographic packet Id(s)','NumberTitle','on');
drawnow;


%% Plot the child Bain group IPDF
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
plot(ipfKeyChild)
hold all
if check_option(varargin,'grains')
    plotIPDF(cGrains.meanOrientation,...
        cGrains.bainId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',5,'MarkerEdgeColor','k');
else
    plotIPDF(cEBSD.orientations,...
        bId,...
        ipfKeyChild.inversePoleFigureDirection,...
        hChild,'MarkerSize',3,'MarkerEdgeColor','k');
end
hold off
% Define the maximum number of color levels and plot the colorbar
colormap(flipud(hot));
caxis([1 maxBain]);
colorbar('location','eastOutSide','lineWidth',1.25,'tickLength', 0.01,...
    'YTick', [1:1:maxBain],...
    'YTickLabel',num2str([1:1:maxBain]'), 'YLim', [1 maxBain],...
    'TickLabelInterpreter','latex','FontName','Helvetica','FontSize',14,'FontWeight','bold');
set(figH,'Name','IPDF: Child grain(s) Bain group Id(s)','NumberTitle','on');
drawnow;


%% Plot the weighted area variants Id frequency histogram
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
class_range = 1:1:maxVariants;
if check_option(varargin,'grains')
    [~,abs_counts] = histwc(cGrains.variantId,cGrains.area,maxVariants);
else
    abs_counts = histc(vId,class_range);
end
norm_counts = abs_counts./sum(abs_counts);
h = bar(class_range,norm_counts,'hist');
h.FaceColor =[162 20 47]./255;
set(gca,'FontSize',14);
set(gca,'xlim',[class_range(1)-0.5 class_range(end)+0.5]);
set(gca,'XTick',class_range);
xlabel('\bf Variant Id','FontSize',14);
% xlabel('Variant Id','FontSize',14,'FontWeight','bold');
if size(class_range,2)>1; class_range = class_range'; end
if size(abs_counts,2)>1; abs_counts = abs_counts'; end
if size(norm_counts,2)>1; norm_counts = norm_counts'; end
if check_option(varargin,'grains')
    ylabel('\bf Weighted area relative frequency [$\bf f_w$(g)]','FontSize',14);
    %     ylabel('Weighted area relative frequency ({\itf_w}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Weighted area variant Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': variantId weighted area histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'variantId','wtAreaCounts'})
    table(class_range,norm_counts,'VariableNames',{'variantId','wtAreaFreq'})
else
    ylabel('\bf Relative frequency [$\bf f$(g)]','FontSize',14);
    %     ylabel('Relative frequency ({\itf}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Relative frequency variant Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': variantId histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'variantId','Counts'})
    table(class_range,norm_counts,'VariableNames',{'variantId','Freq'})
end
drawnow;


%% Plot the weighted area crystallographic packets Id frequency histogram
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
class_range = 1:1:maxPackets;
if check_option(varargin,'grains')
    [~,abs_counts] = histwc(cGrains.packetId,cGrains.area,maxPackets);
else
    abs_counts = histc(pId,class_range);
end
norm_counts = abs_counts./sum(abs_counts);
h = bar(class_range,norm_counts,'hist');
h.FaceColor =[162 20 47]./255;
set(gca,'FontSize',14);
set(gca,'xlim',[class_range(1)-0.5 class_range(end)+0.5]);
set(gca,'XTick',class_range);
xlabel('\bf Crystallographic packet Id','FontSize',14);
% xlabel('Crystallographic packet Id','FontSize',14,'FontWeight','bold');
if size(class_range,2)>1; class_range = class_range'; end
if size(abs_counts,2)>1; abs_counts = abs_counts'; end
if size(norm_counts,2)>1; norm_counts = norm_counts'; end
if check_option(varargin,'grains')
    ylabel('\bf Weighted area relative frequency [$\bf f_w$(g)]','FontSize',14);
    %     ylabel('Weighted area relative frequency ({\itf_w}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Weighted area crystallographic packet Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': packetId weighted area histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'packetId','wtAreaCounts'})
    table(class_range,norm_counts,'VariableNames',{'packetId','wtAreaFreq'})
else
    ylabel('\bf Relative frequency [$\bf f$(g)]','FontSize',14);
    %     ylabel('Relative frequency ({\itf}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Relative frequency crystallographic packet Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': packetId histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'packetId','Counts'})
    table(class_range,norm_counts,'VariableNames',{'packetId','Freq'})
end
drawnow;


%% Plot the weighted area Bain group Id frequency histogram
drawnow;
figH = gobjects(1);
figH = figure('WindowStyle','docked');
set(get(handle(figH),'javaframe'),'GroupName',dockGroupName);
drawnow;
class_range = 1:1:maxBain;
if check_option(varargin,'grains')
    [~,abs_counts] = histwc(cGrains.bainId,cGrains.area,maxBain);
else
    abs_counts = histc(bId,class_range);
end
norm_counts = abs_counts./sum(abs_counts);
h = bar(class_range,norm_counts,'hist');
h.FaceColor =[162 20 47]./255;
set(gca,'FontSize',14);
set(gca,'xlim',[class_range(1)-0.5 class_range(end)+0.5]);
set(gca,'XTick',class_range);
xlabel('\bf Bain group Id','FontSize',14);
% xlabel('Bain group Id','FontSize',14,'FontWeight','bold');
if size(class_range,2)>1; class_range = class_range'; end
if size(abs_counts,2)>1; abs_counts = abs_counts'; end
if size(norm_counts,2)>1; norm_counts = norm_counts'; end
if check_option(varargin,'grains')
    ylabel('\bf Weighted area relative frequency [$\bf f_w$(g)]','FontSize',14);
    %     ylabel('Weighted area relative frequency ({\itf_w}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Weighted area Bain group Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': bainId weighted area histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'bainId','wtAreaCounts'})
    table(class_range,norm_counts,'VariableNames',{'bainId','wtAreaFreq'})
else
    ylabel('\bf Relative frequency [$\bf f$(g)]','FontSize',14);
    %     ylabel('Relative frequency ({\itf}(g))','FontSize',14,'FontWeight','bold');
    set(figH,'Name','Histogram: Relative frequency Bain group Ids','NumberTitle','on');
    % % Output histogram data in a table
    screenPrint('Step',['Figure ',num2str(figH.Number),': bainId histogram']);
    %     table(class_range,abs_counts,'VariableNames',{'bainId','Counts'})
    table(class_range,norm_counts,'VariableNames',{'bainId','Freq'})
end
drawnow;


%% Place first tabbed figure on top and return
warning on
% allfigh = findall(0,'type','figure');
% if length(allfigh) > 1
%     figure(length(allfigh)-15);
% else
%     figure(1);
% end
% recheck if the plotStack function was called from grainClick or not
if ~any(strcmpi(varargin,'grainClick2plotStack')) % if not...
    figure(1);
else
    figure(2);
end
warning(bakWarn);
pause(1); % reduce rendering errors
return
end


%% Compute weighted histogram
function [vinterval,histw] = histwc(val,wt,nbins)
% HISTWC  Weighted histogram count given number of bins
%
% This function generates a vector of cumulative weights for data
% histogram. Equal number of bins will be considered using minimum and
% maximum values of the data. Weights will be summed in the given bin.
%
% Usage: [vinterval,histw] = histwc(val, wt, nbins)
%
% Arguments:
%       val    - values as a vector
%       wt     - weights as a vector
%       nbins  - number of bins
%
% Returns:
%       histw     - weighted histogram
%       vinterval - intervals used
%
%
%
% See also: HISTC, HISTWCV
% Author: mehmet.suzen
% BSD License
% July 2013
minV  = 1; %min(val)
maxV  = nbins; %max(val)
delta = (maxV-minV)/nbins;
vinterval = linspace(minV, maxV, nbins)-delta/2.0;
histw = zeros(nbins, 1);
for ii=1:length(val)
    idx = find(vinterval < val(ii),1,'last');
    if ~isempty(idx)
        histw(idx) = histw(idx) + wt(ii);
    end
end
end