ucftools/matlab/read_uvwp_complete_ucf.m

function [u,v,w,p] = read_uvwp_complete_ucf(file,varargin)
    % [u,v,w,p] = read_uvwp_complete_ucf(file,varargin)
    % Reads u,v,w,p from all processor chunks and combines them to a single field.
    % Input
    %   file              file to be read
    % Optional input (key/value pair)
    %   timestep          index of timestep to be read (default: 1)
    %   verbosity         verbose output? (default: no)
    %   debug             debug output? (default: no)
    % Output
    %   u,v,w,p           complete fields with dim(nx,ny,nz)

    % Parse optional input arguments
    par = inputParser;
    addOptional(par,'timestep',1,@isnumeric);
    addOptional(par,'verbosity',0,@isnumeric);
    addOptional(par,'debug',0,@isnumeric);
    parse(par,varargin{:});
    istep = par.Results.timestep;

    % Define sets to be read
    sets = {'u','v','w','p'};
    nset = numel(sets);
    
    % Parse filename
    [fdir,fbase,fext] = fileparts(file);
    fname = sprintf('%s/%s.%05d',fdir,fbase,0);
    
    % Open first file
    obj = ucf(fname,'read','verbosity',par.Results.verbosity,'debug',par.Results.debug);
    if ~obj.validateType('field')
      error('read error: no field data.'); 
    end
        
    % Read raw data
    q  = cell(1,nset);
    ib  = cell(1,nset);
    jb  = cell(1,nset);
    kb  = cell(1,nset);
    nxl = cell(1,nset);
    nyl = cell(1,nset);
    nzl = cell(1,nset);
    nx  = cell(1,nset);
    ny  = cell(1,nset);
    nz  = cell(1,nset);
    for iset=1:nset
      [data,params] = obj.readSet(istep,iset);
      params = cast(params,'double');
      ighost   = params(1);
      ib{iset} = params(2);
      jb{iset} = params(3);
      kb{iset} = params(4);
      nxl{iset}= params(5);
      nyl{iset}= params(6);
      nzl{iset}= params(7);
      nx{iset} = params(8);
      ny{iset} = params(9);
      nz{iset} = params(10);
      q{iset}  = reshape(data,nxl{iset}+2*ighost,nyl{iset}+2*ighost,nzl{iset}+2*ighost);
      if ighost
        q{iset} = q{iset}(2:end-1,2:end-1,2:end-1);
      end
    end
    
    % Reassign content from loop and create global arrays
    iset = find(strcmp(sets,'u'));
    u = zeros(nx{iset},ny{iset},nz{iset},class(q{iset}));
    u(ib{iset}:ib{iset}+nxl{iset}-1,...
      jb{iset}:jb{iset}+nyl{iset}-1,...
      kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
      
    iset = find(strcmp(sets,'v'));
    v = zeros(nx{iset},ny{iset},nz{iset},class(q{iset}));
    v(ib{iset}:ib{iset}+nxl{iset}-1,...
      jb{iset}:jb{iset}+nyl{iset}-1,...
      kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
      
    iset = find(strcmp(sets,'w'));
    w = zeros(nx{iset},ny{iset},nz{iset},class(q{iset}));
    w(ib{iset}:ib{iset}+nxl{iset}-1,...
      jb{iset}:jb{iset}+nyl{iset}-1,...
      kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
  
    iset = find(strcmp(sets,'p'));
    p = zeros(nx{iset},ny{iset},nz{iset},class(q{iset}));
    p(ib{iset}:ib{iset}+nxl{iset}-1,...
      jb{iset}:jb{iset}+nyl{iset}-1,...
      kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};

    % Close the first file
    obj.close();

    % Now loop consecutively through files
    ifile = 1;
    fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
    while exist(fname,'file')
      % Open file
      obj = ucf(fname,'read','verbosity',par.Results.verbosity,'debug',par.Results.debug);
      if ~obj.validateType('field')
        error('read error: no field data.'); 
      end
          
      % Read raw data
      q  = cell(1,nset);
      ib  = cell(1,nset);
      jb  = cell(1,nset);
      kb  = cell(1,nset);
      nxl = cell(1,nset);
      nyl = cell(1,nset);
      nzl = cell(1,nset);
      for iset=1:nset
        [data,params] = obj.readSet(istep,iset);
        params = cast(params,'double');
        ighost   = params(1);
        ib{iset} = params(2);
        jb{iset} = params(3);
        kb{iset} = params(4);
        nxl{iset}= params(5);
        nyl{iset}= params(6);
        nzl{iset}= params(7);
        q{iset}  = reshape(data,nxl{iset}+2*ighost,nyl{iset}+2*ighost,nzl{iset}+2*ighost);
        if ighost
          q{iset} = q{iset}(2:end-1,2:end-1,2:end-1);
        end
      end
      
      % Reassign content from loop and create global arrays
      iset = find(strcmp(sets,'u'));
      u(ib{iset}:ib{iset}+nxl{iset}-1,...
        jb{iset}:jb{iset}+nyl{iset}-1,...
        kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
        
      iset = find(strcmp(sets,'v'));
      v(ib{iset}:ib{iset}+nxl{iset}-1,...
        jb{iset}:jb{iset}+nyl{iset}-1,...
        kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
        
      iset = find(strcmp(sets,'w'));
      w(ib{iset}:ib{iset}+nxl{iset}-1,...
        jb{iset}:jb{iset}+nyl{iset}-1,...
        kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
    
      iset = find(strcmp(sets,'p'));
      p(ib{iset}:ib{iset}+nxl{iset}-1,...
        jb{iset}:jb{iset}+nyl{iset}-1,...
        kb{iset}:kb{iset}+nzl{iset}-1) = q{iset};
  
      % Close file
      obj.close();
      
      % Move on to next file
      ifile = ifile+1;
      fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
    end
end