added tarmode support

matlab/read_parameters_ucf.m

@@ -3,19 +3,27 @@ function [params] = read_parameters_ucf(file,varargin)
   % Reads the entire parameters_XXXX.asc as written by UCF file format
   % into a struct.
   % Input
-  %   file          file name
+  %   file          file name (if tar-mode: ustar handle)
-  % Optional input
+  % ? verbosity     verbose screen output? (default: 0)
-  %   verbosity     verbose screen output? (default: no)
+  % ? tarmode       read from tar-file? (default: 0)
   % Output
   %   params        struct with content of parameters_XXXX.asc
   
   % Parse optional input arguments
   par = inputParser;
   addOptional(par,'verbosity',0,@isnumeric);
+  addOptional(par,'tarmode',0,@isnumeric);
   parse(par,varargin{:});
-
+  % Open file
   obj = ini('verbosity',par.Results.verbosity);
-  obj.open(file);
+  if par.Results.tarmode
+    ptr = file.pointer('parameters.asc');
+    obj.opentar(ptr);
+  else
+    obj.open(file);
+  end
+  % Get parsed content
   params = obj.getContent();
+  % Close file
   obj.close();
 end

matlab/read_particles_ucf.m

@@ -2,16 +2,16 @@ function [pp,col,stime] = read_particles_ucf(file,varargin)
     % [pp,col] = read_particles_ucf(file,varargin)
     % Reads particle data from UCF file
     % Input
-    %   file              file to be read
+    %   file              file name (if tar-mode: ustar handle)
-    % Optional input (key/value pair)
+    % ? step              timestep to be read (default: 0 [all])
-    %   timestep          timestep to be read (default: all)
+    % ? format            MATLAB format (default: 'array')
-    %   format            MATLAB format (default: 'array')
     %                       'array'     plain array with dim(ncol.np,nt)
     %                       'struct'    structure array with short fieldnames
     %                       'paraview'  structure array with H5Part fieldnames
     %                       'cell'      cell array with dim(1,nt) and plain arrays with dim(ncol,np) inside
-    %   verbosity         verbose output? (default: no)
+    % ? verbosity         verbose output? (default: no)
-    %   debug             debug output? (default: no)
+    % ? debug             debug output? (default: no)
+    % ? tarmode       read from tar-file? (default: 0)
     % Output
     %   pp                particle data in specified format
     %   col               container map 'char'->'double' which maps quantity names to column index
@@ -19,17 +19,23 @@ function [pp,col,stime] = read_particles_ucf(file,varargin)
     
     % Parse optional input arguments
     par = inputParser;
-    addOptional(par,'timestep',0,@isnumeric);
+    addOptional(par,'step',0,@isnumeric);
     addOptional(par,'format','array',@ischar);
     addOptional(par,'verbosity',0,@isnumeric);
     addOptional(par,'debug',0,@isnumeric);
+    addOptional(par,'tarmode',0,@isnumeric);
     parse(par,varargin{:});
-    istep     = par.Results.timestep;
+    istep     = par.Results.step;
     mlformat  = par.Results.format;
     
     % Open file
     obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
-    obj.open(file);
+    if par.Results.tarmode
+      ptr = file.pointer('particles.bin');
+      obj.opentar(ptr);
+    else
+      obj.open(file);
+    end
     if ~obj.validateType('particle')
       error('read error: no particle data.'); 
     end

matlab/read_procgrid_ucf.m

@@ -8,10 +8,9 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
     %  ibegp,iendp,jbegp,jendp,kbegp,kendp] = read_procgrid_ucf(file,varargin)
     % Reads processor grids.
     % Input
-    %   file              file to be read
+    %   file              file name (if tar-mode: ustar handle)
-    % Optional input (key/value pair)
+    % ? verbosity         verbose output? (default: 0)
-    %   verbosity         verbose output? (default: no)
+    % ? tarmode           read from tar-file? (default: 0)
-    %
     % Output
     %  ibegu,iendu,jbegu,jendu,kbegu,kendu    processor grid u
     %  ibegv,iendv,jbegv,jendv,kbegv,kendv    processor grid v
@@ -22,6 +21,7 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
     par = inputParser;
     addOptional(par,'verbosity',0,@isnumeric);
     addOptional(par,'debug',0,@isnumeric);
+    addOptional(par,'tarmode',0,@isnumeric);
     parse(par,varargin{:});
     
     % Define sets to be read
@@ -30,7 +30,12 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
     
     % Open file
     obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
-    obj.open(file);
+    if par.Results.tarmode
+      ptr = file.pointer('proc.bin');
+      obj.opentar(ptr);
+    else
+      obj.open(file);
+    end
     
     % Read raw data
     ibeg = cell(1,nset);
@@ -58,34 +63,34 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
     
     % Reassign content from loop
     iset = find(strcmp(sets,'u'));
-    ibegu = ibeg{iset};
+    ibegu = cast(ibeg{iset},'double');
-    iendu = iend{iset};
+    iendu = cast(iend{iset},'double');
-    jbegu = jbeg{iset};
+    jbegu = cast(jbeg{iset},'double');
-    jendu = jend{iset};
+    jendu = cast(jend{iset},'double');
-    kbegu = kbeg{iset};
+    kbegu = cast(kbeg{iset},'double');
-    kendu = kend{iset};
+    kendu = cast(kend{iset},'double');
     
     iset = find(strcmp(sets,'v'));
-    ibegv = ibeg{iset};
+    ibegv = cast(ibeg{iset},'double');
-    iendv = iend{iset};
+    iendv = cast(iend{iset},'double');
-    jbegv = jbeg{iset};
+    jbegv = cast(jbeg{iset},'double');
-    jendv = jend{iset};
+    jendv = cast(jend{iset},'double');
-    kbegv = kbeg{iset};
+    kbegv = cast(kbeg{iset},'double');
-    kendv = kend{iset};
+    kendv = cast(kend{iset},'double');
     
     iset = find(strcmp(sets,'w'));
-    ibegw = ibeg{iset};
+    ibegw = cast(ibeg{iset},'double');
-    iendw = iend{iset};
+    iendw = cast(iend{iset},'double');
-    jbegw = jbeg{iset};
+    jbegw = cast(jbeg{iset},'double');
-    jendw = jend{iset};
+    jendw = cast(jend{iset},'double');
-    kbegw = kbeg{iset};
+    kbegw = cast(kbeg{iset},'double');
-    kendw = kend{iset};
+    kendw = cast(kend{iset},'double');
     
     iset = find(strcmp(sets,'p'));
-    ibegp = ibeg{iset};
+    ibegp = cast(ibeg{iset},'double');
-    iendp = iend{iset};
+    iendp = cast(iend{iset},'double');
-    jbegp = jbeg{iset};
+    jbegp = cast(jbeg{iset},'double');
-    jendp = jend{iset};
+    jendp = cast(jend{iset},'double');
-    kbegp = kbeg{iset};
+    kbegp = cast(kbeg{iset},'double');
-    kendp = kend{iset};
+    kendp = cast(kend{iset},'double');
 end

matlab/read_scal_chunk_ucf.m

@@ -2,12 +2,13 @@ function [s,ib,jb,kb,nxl,nyl,nzl,ighost] = read_scal_chunk_ucf(file,varargin)
     % [s,ib,jb,kb,nxl,nyl,nzl,ighost] = read_scal_chunk_ucf(file,varargin)
     % Reads scalar fields from one processor chunk.
     % Input
-    %   file                file to be read
+    %   file                file name (if tar-mode: ustar handle)
-    % Optional input (key/value pair)
+    % ? step                index of timestep to be read (default: 1)
-    %   timestep            index of timestep to be read (default: 1)
+    % ? ghost               keep ghost cells? (default: 1)
-    %   ghost               keep ghost cells? (default: yes)
+    % ? verbosity           verbose output? (default: 0)
-    %   verbosity           verbose output? (default: no)
+    % ? debug               debug output? (default: 0)
-    %   debug               debug output? (default: no)
+    % ? tarmode             read from tar-file? (default: 0)
+    % ? rank                rank of processor, ignored if not in tarmode (default: 0)
     % Output
     %   s                   partial fields with dim(nxl+2*ighost,nyl+2*ighost,nzl+2*ighost,nscal)
     %   ib,jb,kb,...        global index of first grid point of the partial field w/o ghost cells
@@ -16,17 +17,25 @@ function [s,ib,jb,kb,nxl,nyl,nzl,ighost] = read_scal_chunk_ucf(file,varargin)
 
     % Parse optional input arguments
     par = inputParser;
-    addOptional(par,'timestep',1,@isnumeric);
+    addOptional(par,'step',1,@isnumeric);
     addOptional(par,'ghost',1,@isnumeric);
     addOptional(par,'verbosity',0,@isnumeric);
     addOptional(par,'debug',0,@isnumeric);
+    addOptional(par,'tarmode',0,@isnumeric);
+    addOptional(par,'rank',0,@isnumeric);
     parse(par,varargin{:});
-    istep     = par.Results.timestep;
+    istep     = par.Results.step;
     keepghost = par.Results.ghost;
   
     % Open file
     obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
-    obj.open(file);
+    if par.Results.tarmode
+      subfile = sprintf('scal.%05d',par.Results.rank);
+      obj.opentar(file.pointer(subfile));
+    else
+      obj.open(file);
+    end
+  
     if ~obj.validateType('field')
       error('read error: no field data.'); 
     end

matlab/read_scal_complete_ucf.m

@@ -2,29 +2,34 @@ function [s] = read_scal_complete_ucf(file,varargin)
     % [s] = read_scal_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
+    %   file              file name (if tar-mode: ustar handle)
-    % Optional input (key/value pair)
+    % ? step              index of timestep to be read (default: 1)
-    %   timestep          index of timestep to be read (default: 1)
+    % ? verbosity         verbose output? (default: 0)
-    %   verbosity         verbose output? (default: no)
+    % ? debug             debug output? (default: 0)
-    %   debug             debug output? (default: no)
+    % ? tarmode           read from tar-file? (default: 0)
     % Output
     %   s                 complete scalar fields with dim(nx,ny,nz,nscal)
 
     % Parse optional input arguments
     par = inputParser;
-    addOptional(par,'timestep',1,@isnumeric);
+    addOptional(par,'step',1,@isnumeric);
     addOptional(par,'verbosity',0,@isnumeric);
     addOptional(par,'debug',0,@isnumeric);
+    addOptional(par,'tarmode',0,@isnumeric);
     parse(par,varargin{:});
-    istep = par.Results.timestep;
+    istep = par.Results.step;
-
-    % Parse filename
-    [fdir,fbase,fext] = fileparts(file);
-    fname = sprintf('%s/%s.%05d',fdir,fbase,0);
 
     % Open first file
     obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
-    obj.open(fname);
+    if par.Results.tarmode
+      fname = sprintf('scal.%05d',0);
+      obj.opentar(file.pointer(fname));
+    else
+      [fdir,fbase,fext] = fileparts(file);
+      fname = sprintf('%s/%s.%05d',fdir,fbase,0);
+      obj.open(fname);
+    end
+
     if ~obj.validateType('field')
       error('read error: no field data.');
     end
@@ -62,11 +67,22 @@ function [s] = read_scal_complete_ucf(file,varargin)
 
     % Now loop consecutively through files
     ifile = 1;
-    fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
+    if par.Results.tarmode
-    while exist(fname,'file')
+      loopCondition = @(x) file.isSubfile(x);
+      fname = sprintf('scal.%05d',ifile);
+    else
+      loopCondition = @(x) exist(x,'file');
+      fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
+    end
+    while loopCondition(fname)
       % Open file
       obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
-      obj.open(fname)
+      if par.Results.tarmode
+        obj.opentar(file.pointer(fname));
+      else
+        obj.open(fname);
+      end
+
       if ~obj.validateType('field')
         error('read error: no field data.');
       end
@@ -99,6 +115,10 @@ function [s] = read_scal_complete_ucf(file,varargin)
 
       % Move on to next file
       ifile = ifile+1;
-      fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
+      if par.Results.tarmode
+        fname = sprintf('scal.%05d',ifile);
+      else
+        fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
+      end
     end
 end