function plotdat = plot_rank_histogram(fname, timeindex, varargin)
%% plot_rank_histogram plots the rank histogram of the observations - segregated by level and variable.
% Part of the observation-space diagnostics routines.
%
% 'obs_diag' produces a netcdf file containing the diagnostics.
% 'obs_diag' condenses the 'obs_seq.final' information into summaries
%            for a few specified regions - on a level-by-level basis.
%
% USAGE: plotdat = plot_rank_histogram(fname, timeindex, [,obstypestring]);
%
% fname         : netcdf file produced by 'obs_diag'
% timeindex     : the index of the timestep of interest
% obstypestring : 'observation type' string. Optional.
%                 Must match something in the 'ObservationTypes' variable.
%                 (ncdump -v ObservationTypes obs_diag_output.nc)
%                 If specified, only this observation type will be plotted.
%                 If not specified, ALL observation types incluced in the
%                 netCDF file will be plotted.
%
% OUTPUT: two files will result for each observation type plotted. One is a
%         postscript file containing a page for each level - all regions.
%         The other file is a simple text file containing summary information
%         about how many obs were assimilated, how many were available, etc.
%         Both filenames contain the observation type as part of the name.
%
% EXAMPLE 1 - plot the rank histogram for ALL observation types, ALL levels
%
% fname     = 'obs_diag_output.nc'; % netcdf file produced by 'obs_diag'
% timeindex = 1;                    % plot the histogram for the first timestep
% plotdat   = plot_rank_histogram(fname, timeindex);
%
%
% EXAMPLE 2 - rank histogram for a particular timestep of radiosonde temperature observations.
%             This requires knowledge that 'RADIOSONDE_TEMPERATURE' is an
%             observation type in the netCDF file.
%
% fname     = 'obs_diag_output.nc'; % netcdf file produced by 'obs_diag'
% timeindex = 3;                    % plot the histogram for the third timestep
% plotdat   = plot_rank_histogram(fname, timeindex, 'RADIOSONDE_TEMPERATURE');
%
%
% EXAMPLE 3 - single rank histogram for all timesteps of radiosonde temperature observations.
%
% fname     = 'obs_diag_output.nc'; % netcdf file produced by 'obs_diag'
% timeindex = -1;                   % use ALL available timesteps
% plotdat   = plot_rank_histogram(fname, timeindex, 'RADIOSONDE_TEMPERATURE');

%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
% provided by UCAR, "as is", without charge, subject to all terms of use at
% http://www.image.ucar.edu/DAReS/DART/DART_download
%
% DART $Id$

if nargin == 2
    nvars = 0;
elseif nargin == 3
    varname = varargin{1};
    nvars = 1;
else
    error('wrong number of arguments ... ')
end

% Make sure the file exists.

if (exist(fname,'file') ~= 2)
    error('file/fname <%s> does not exist',fname)
end

% Make sure the variable exists.

if (nvars > 0)
    fullvarname = BuildFullVarname(varname);
    if ( ~ nc_isvar(fname,fullvarname) )
        error('There is no %s variable in %s', fullvarname, fname)
    end
end

% Harvest plotting info/metadata from netcdf file.

plotdat.fname         = fname;
plotdat.timecenters   = nc_varget(fname,'time');
plotdat.timeedges     = nc_varget(fname,'time_bounds');
plotdat.mlevel        = local_nc_varget(fname,'mlevel');
plotdat.plevel        = local_nc_varget(fname,'plevel');
plotdat.plevel_edges  = local_nc_varget(fname,'plevel_edges');
plotdat.hlevel        = local_nc_varget(fname,'hlevel');
plotdat.hlevel_edges  = local_nc_varget(fname,'hlevel_edges');
plotdat.Nrhbins       = length(nc_varget(fname,'rank_bins'));
plotdat.ncopies       = length(nc_varget(fname,'copy'));
plotdat.nregions      = length(nc_varget(fname,'region'));
plotdat.region_names  = strtrim(nc_varget(fname,'region_names'));

% Matlab does a crazy thing with the strings for 1 region
if (plotdat.nregions == 1 && (size(plotdat.region_names,2) == 1) )
    plotdat.region_names = deblank(plotdat.region_names');
end

dimensionality             = local_nc_attget(fname, nc_global, 'LocationRank');
plotdat.timeseparation     = nc_attget(fname, nc_global, 'bin_separation');
plotdat.timewidth          = nc_attget(fname, nc_global, 'bin_width');
plotdat.biasconv           = nc_attget(fname, nc_global, 'bias_convention');
time_to_skip               = nc_attget(fname, nc_global, 'time_to_skip');
plotdat.outlierstring      = nc_attget(fname, nc_global, 'outliers_in_histogram');
plotdat.QCsusedstring      = nc_attget(fname, nc_global, 'DART_QCs_in_histogram');
plotdat.lonlim1            = nc_attget(fname, nc_global, 'lonlim1');
plotdat.lonlim2            = nc_attget(fname, nc_global, 'lonlim2');
plotdat.latlim1            = local_nc_attget(fname, nc_global, 'latlim1');
plotdat.latlim2            = local_nc_attget(fname, nc_global, 'latlim2');

% Make sure the time index makes sense.

if (timeindex > length(plotdat.timecenters))
    error('There are only %d time indices in the file, you asked for # %d', ...
        length(plotdat.timecenters), timeindex)
end

% Coordinate between time types and dates

calendar     = nc_attget(fname,'time','calendar');
timeunits    = nc_attget(fname,'time','units');
timebase     = sscanf(timeunits,'%*s%*s%d%*c%d%*c%d'); % YYYY MM DD
timeorigin   = datenum(timebase(1),timebase(2),timebase(3));
skip_seconds = time_to_skip(4)*3600 + time_to_skip(5)*60 + time_to_skip(6);
iskip        = time_to_skip(3) + skip_seconds/86400;

% set up a structure with all static plotting components

plotdat.timecenters = plotdat.timecenters + timeorigin;
plotdat.timeedges   = plotdat.timeedges   + timeorigin;
plotdat.Ntimes      = length(plotdat.timecenters);
plotdat.toff        = plotdat.timecenters(1) + iskip;

if ( timeindex < 1 )
    plotdat.timeindex = 1:plotdat.Ntimes;
    plotdat.timespan = sprintf('%s -- %s', datestr(min(plotdat.timeedges(:,1)),21), ...
        datestr(max(plotdat.timeedges(:,2)),21));
else
    plotdat.timeindex = timeindex;
    plotdat.timespan = sprintf('%s -- %s', datestr(plotdat.timeedges(timeindex,1),21), ...
        datestr(plotdat.timeedges(timeindex,2),21));
end

if (nvars == 0)
    [plotdat.allvarnames, plotdat.allvardims] = get_varsNdims(fname);
    [plotdat.varnames,    plotdat.vardims]    = FindTemporalVars(plotdat);
    plotdat.nvars       = length(plotdat.varnames);
else
    plotdat.varnames{1} = varname;
    plotdat.nvars       = nvars;
end

plotdat.Npossindex  = get_copy_index(fname,'Nposs');
plotdat.Nusedindex  = get_copy_index(fname,'Nused');
plotdat.NQC4index   = get_copy_index(fname,'N_DARTqc_4');
plotdat.NQC5index   = get_copy_index(fname,'N_DARTqc_5');
plotdat.NQC6index   = get_copy_index(fname,'N_DARTqc_6');
plotdat.NQC7index   = get_copy_index(fname,'N_DARTqc_7');

figuredata = setfigure();

%----------------------------------------------------------------------
% Loop around (time-copy-level-region) observation types
%----------------------------------------------------------------------
psfname = cell(plotdat.nvars);

for ivar = 1:plotdat.nvars
    
    % create the variable names of interest.
    % netCDF can only support variable names less than 41 chars.
    
    plotdat.myvarname = plotdat.varnames{ivar};
    plotdat.guessvar  = sprintf('%s_guess',plotdat.varnames{ivar});
    
    plotdat.rhistvar = BuildFullVarname(plotdat.varnames{ivar});
    
    [present, ~] = nc_var_exists(fname, plotdat.rhistvar);
    if ( ~ present )
        fprintf('Could not find %s in %s ... skipping\n',plotdat.rhistvar, fname)
        continue
    end
    
    % remove any existing postscript file - will simply append each
    % level as another 'page' in the .ps file.
    
    for iregion = 1:plotdat.nregions
        psfname{iregion} = sprintf('%s_rank_hist_region%d.ps',plotdat.varnames{ivar},iregion);
        fprintf('Removing %s from the current directory.\n',psfname{iregion})
        system(sprintf('rm %s',psfname{iregion}));
    end
    
    % remove any existing log file -
    
    lgfname = sprintf('%s_rank_hist_obscount.txt',plotdat.varnames{ivar});
    fprintf('Removing %s from the current directory.\n',lgfname)
    system(sprintf('rm %s',lgfname));
    logfid = fopen(lgfname,'wt');
    fprintf(logfid,'%s\n',lgfname);
    
    % get appropriate vertical coordinate variable
    
    guessdims = nc_var_dims(fname, plotdat.guessvar);
    rhistdims = nc_var_dims(fname, plotdat.rhistvar);
    
    if ( dimensionality == 1 ) % observations on a unit circle, no level
        plotdat.level = 1;
        plotdat.level_units = [];
    elseif ( strfind(guessdims{3},'surface') > 0 )
        plotdat.level       = 1;
        plotdat.level_units = 'surface';
    elseif ( strfind(guessdims{3},'undef') > 0 )
        plotdat.level       = 1;
        plotdat.level_units = 'undefined';
    else
        plotdat.level       = nc_varget(fname, guessdims{3});
        plotdat.level_units = nc_attget(fname, guessdims{3}, 'units');
    end
    plotdat.nlevels = length(plotdat.level);
    
    % Here is the tricky part. Singleton dimensions are auto-squeezed ...
    % single levels, single regions ...
    
    guess_raw = nc_varget(fname, plotdat.guessvar);
    guess = reshape(guess_raw, plotdat.Ntimes,  plotdat.ncopies, ...
        plotdat.nlevels, plotdat.nregions);
    
    rhist_raw = nc_varget(fname, plotdat.rhistvar);
    rhist = reshape(rhist_raw, plotdat.Ntimes,  plotdat.Nrhbins, ...
        plotdat.nlevels, plotdat.nregions);
    
    % Collapse the time dimension if need be.
    % >@todo TJH FIXME ... this should honor the time_to_skip ...
    
    if ( timeindex < 0 )
        guess             = sum(guess,1);
        rhist             = sum(rhist,1);
        plotdat.timeindex = 1;
    end
    
    % check to see if there is anything to plot
    nposs = sum(guess(plotdat.timeindex,plotdat.Npossindex,:,:)) - ...
        sum(guess(plotdat.timeindex,plotdat.NQC5index ,:,:)) - ...
        sum(guess(plotdat.timeindex,plotdat.NQC6index ,:,:));
    
    if ( sum(nposs(:)) < 1 )
        fprintf('no obs for %s ...  skipping\n', plotdat.varnames{ivar})
        continue
    end
    
    for ilevel = 1:plotdat.nlevels
        
        fprintf(logfid,'\nlevel %d %f %s\n',ilevel,plotdat.level(ilevel),plotdat.level_units);
        
        plotdat.ges_Nqc4  = squeeze(guess(plotdat.timeindex,plotdat.NQC4index  ,ilevel,:));
        fprintf(logfid,'DART QC == 4, prior %d\n',sum(plotdat.ges_Nqc4(:)));
        
        plotdat.ges_Nqc5  = squeeze(guess(plotdat.timeindex,plotdat.NQC5index  ,ilevel,:));
        fprintf(logfid,'DART QC == 5, prior %d\n',sum(plotdat.ges_Nqc5(:)));
        
        plotdat.ges_Nqc6  = squeeze(guess(plotdat.timeindex,plotdat.NQC6index  ,ilevel,:));
        fprintf(logfid,'DART QC == 6, prior %d\n',sum(plotdat.ges_Nqc6(:)));
        
        plotdat.ges_Nqc7  = squeeze(guess(plotdat.timeindex,plotdat.NQC7index  ,ilevel,:));
        fprintf(logfid,'DART QC == 7, prior %d\n',sum(plotdat.ges_Nqc7(:)));
        
        plotdat.ges_Nposs = squeeze(guess(plotdat.timeindex,plotdat.Npossindex, ilevel,:)) ...
            - plotdat.ges_Nqc5 - plotdat.ges_Nqc6;
        fprintf(logfid,'# obs poss,   prior %d\n',sum(plotdat.ges_Nposs(:)));
        
        plotdat.ges_Nused = squeeze(guess(plotdat.timeindex,plotdat.Nusedindex, ilevel,:));
        fprintf(logfid,'# obs used,   prior %d\n',sum(plotdat.ges_Nused(:)));
        
        % plot by region
        
        for iregion = 1:plotdat.nregions
            figure(iregion); clf; orient(figuredata.orientation); wysiwyg
            
            plotdat.region   = iregion;
            plotdat.myregion = deblank(plotdat.region_names(iregion,:));
            if ( isempty(plotdat.level_units) )
                plotdat.title    = plotdat.myvarname;
            else
                plotdat.title    = sprintf('%s @ %d %s',    ...
                    plotdat.myvarname,     ...
                    plotdat.level(ilevel), ...
                    plotdat.level_units);
            end
            
            plotdat.rank_hist = squeeze(rhist(plotdat.timeindex, :, ilevel,iregion));
            
            myplot(plotdat,figuredata);
            
            % create a postscript file
            print(gcf,'-dpsc','-append',psfname{iregion});
            
            % block to go slow and look at each one ...
            % disp('Pausing, hit any key to continue ...')
            % pause
        end
    end
end

%----------------------------------------------------------------------
% 'Helper' functions
%----------------------------------------------------------------------

function myplot(plotdat,figdata)

nobs_poss = plotdat.ges_Nposs(plotdat.region);

% nobs_used = plotdat.ges_Nused(plotdat.region);
nobs_used = sum(plotdat.rank_hist(:));
obsstring = sprintf('%d obs possible, %d obs binned',nobs_poss, nobs_used);

% Determine some quantities for the legend
% Plot

ax1 = subplot('position',figdata.position);
bar(plotdat.rank_hist, 1.0);
set(ax1,'TickDir','out','FontSize',figdata.fontsize,'YGrid','on')

axlims = axis;
axlims = [0 plotdat.Nrhbins+1 0 axlims(4)];
axis(axlims)

h = text(plotdat.Nrhbins/2, 0.9*axlims(4),obsstring);
set(h,'FontSize',figdata.fontsize,'FontWeight','Bold')
set(h,'HorizontalAlignment','center')

if ( strcmp(plotdat.outlierstring,  'TRUE'))
    ylabelstring = 'count - including outlier observations';
else
    ylabelstring = 'count';
end

set(get(gca,'Ylabel'),'String', ylabelstring, ...
    'Interpreter','none','FontSize',figdata.fontsize)
set(get(gca,'Xlabel'),'String', {'Observation Rank (among ensemble members)', plotdat.timespan}, ...
    'Interpreter','none','FontSize',figdata.fontsize)

title({plotdat.myregion, plotdat.title}, ...
    'Interpreter', 'none', 'Fontsize', figdata.fontsize, 'FontWeight', 'bold')

BottomAnnotation(plotdat.fname)


%=====================================================================


function BottomAnnotation(main)
% annotates the directory containing the data being plotted
subplot('position',[0.10 0.01 0.8 0.04])
axis off

fullname = which(main);   % Could be in MatlabPath
if( isempty(fullname) )
    if ( main(1) == '/' )  % must be a absolute pathname
        string1 = sprintf('data file: %s',main);
    else                   % must be a relative pathname
        mydir = pwd;
        string1 = sprintf('data file: %s/%s',mydir,main);
    end
else
    string1 = sprintf('data file: %s',fullname);
end

h = text(0.5, 0.5, string1);
set(h,'HorizontalAlignment','center', ...
    'VerticalAlignment','middle',...
    'Interpreter','none',...
    'FontSize',8)


%=====================================================================


function [y,ydims] = FindTemporalVars(x)
% Returns UNIQUE (i.e. base) temporal variable names
if ( ~(isfield(x,'allvarnames') && isfield(x,'allvardims')))
    error('Doh! no ''allvarnames'' and ''allvardims'' components')
end

j = 0;

for i = 1:length(x.allvarnames)
    indx = strfind(x.allvardims{i},'time');
    if (indx > 0)
        j = j + 1;
        
        basenames{j} = ReturnBase(x.allvarnames{i});
        basedims{j}  = x.allvardims{i};
    end
end

[~,i,j] = unique(basenames);
y     = cell(length(i),1);
ydims = cell(length(i),1);
for k = 1:length(i)
    fprintf('%2d is %s\n',k,basenames{i(k)})
    y{k} = basenames{i(k)};
    ydims{k} = basedims{i(k)};
end


%=====================================================================


function s = ReturnBase(string1)
inds = strfind(string1,'_guess');
if (inds > 0 )
    s = string1(1:inds-1);
end

inds = strfind(string1,'_analy');
if (inds > 0 )
    s = string1(1:inds-1);
end

inds = strfind(string1,'_VPguess');
if (inds > 0 )
    s = string1(1:inds-1);
end

inds = strfind(string1,'_VPanaly');
if (inds > 0 )
    s = string1(1:inds-1);
end


%=====================================================================


function s = BuildFullVarname(varname)
% netCDF restricts the length of a variable name to
% be 40 characters.

rankvar = sprintf('%s_guess_RankHist',varname);
if (length(rankvar) > 40 )
    s = rankvar(1:40);
else
    s = rankvar;
end


%=====================================================================


function figdata = setfigure()
%%
%  figure out a page layout
%  extra space at the bottom for the date/file annotation
%  extra space at the top because the titles have multiple lines

orientation = 'portrait';
fontsize    = 16;
position    = [0.15 0.25 0.7 0.6];
linewidth   = 2.0;

figdata = struct('expcolors',  {{'k','r','g','m','b','c','y'}}, ...
    'expsymbols', {{'o','s','d','p','h','s','*'}}, ...
    'prpolines',  {{'-',':'}}, 'position', position, ...
    'fontsize',fontsize, 'orientation',orientation, ...
    'linewidth',linewidth);


%=====================================================================


function value = local_nc_varget(fname,varname)
%% If the variable exists in the file, return the contents of the variable.
% if the variable does not exist, return empty value instead of error-ing
% out.

[variable_present, varid] = nc_var_exists(fname,varname);
if (variable_present)
    ncid  = netcdf.open(fname,'NOWRITE');
    value = netcdf.getVar(ncid, varid);
    netcdf.close(ncid)
else
    value = [];
end


%=====================================================================


function value = local_nc_attget(fname,varid,varname)
%% If the (global) attribute exists, return the value.
% If it does not, do not throw a hissy-fit.

value = [];
if (varid == nc_global)
    finfo = ncinfo(fname);
    for iatt = 1:length(finfo.Attributes)
        if (strcmp(finfo.Attributes(iatt).Name, deblank(varname)))
            value = finfo.Attributes(iatt).Value;
            return
        end
    end
else
    fprintf('function not supported for local variables, only global atts.\n')
end


% <next few lines under version control, do not edit>
% $URL$
% $Revision$
% $Date$

