distinguish between high-level and low-level routines
This commit is contained in:
Michael Stumpf
parent
c62cf45452
commit
226dbf38ff
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@ -1,134 +0,0 @@
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function [q] = read_field_complete_ucf(file,field,varargin)
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% [data] = read_field_complete_ucf(file,field,varargin)
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% Reads a specific field from all processor chunks.
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% Input
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% file file to be read
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% field field to be read
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% {'u','v','w','p','s1','s2',...}
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% or integer with dataset index (not in tar-mode)
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% ? step index of step to be read (default: 1)
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% ? verbosity verbose output? (default: 0)
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% ? debug debug output? (default: 0)
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% ? tarmode read from tar-file? (default: 0)
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% Output
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% data partial field with dim(nxl+2*ighost,nyl+2*ighost,nzl+2*ighost)
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% Parse optional input arguments
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par = inputParser;
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addParamValue(par,'timestep',1,@isnumeric);
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addParamValue(par,'verbosity',0,@isnumeric);
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addParamValue(par,'debug',0,@isnumeric);
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addParamValue(par,'tarmode',0,@isnumeric);
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parse(par,varargin{:});
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istep = par.Results.timestep;
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% Parse field
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if ischar(field)
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switch field(1)
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case 'u'; ifield=1; fbase='uvwp';
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case 'v'; ifield=2; fbase='uvwp';
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case 'w'; ifield=3; fbase='uvwp';
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case 'p'; ifield=4; fbase='uvwp';
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case 's'; ifield=str2double(field(2:end)); fbase='scal';
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end
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elseif isnumeric(field)
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if par.Results.tarmode
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error('field cannot be numeric, if tar-mode is used.');
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end
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ifield=field; fbase='';
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else
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error('field must either be numeric or string.');
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end
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% Open first file
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obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
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if par.Results.tarmode
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fname = sprintf('%s.%05d',fbase,0);
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obj.opentar(file.pointer(fname));
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else
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[fdir,fbase,fext] = fileparts(file);
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fname = sprintf('%s/%s.%05d',fdir,fbase,0);
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obj.open(fname);
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end
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if ~obj.validateType('field')
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error('read error: no field data.');
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end
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% Read raw data
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[data,params] = obj.readSet(istep,ifield);
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params = cast(params,'double');
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ighost = params(1);
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ib = params(2);
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jb = params(3);
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kb = params(4);
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nxl = params(5);
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nyl = params(6);
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nzl = params(7);
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nx = params(8);
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ny = params(9);
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nz = params(10);
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data = reshape(data,nxl+2*ighost,nyl+2*ighost,nzl+2*ighost);
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if ighost
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data = data(2:end-1,2:end-1,2:end-1);
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end
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% Create global array and assign chunk
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q = zeros(nx,ny,nz,class(data));
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q(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1) = data;
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% Close the first file
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obj.close();
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% Now loop consecutively through files
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ifile = 1;
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if par.Results.tarmode
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loopCondition = @(x) file.isSubfile(x);
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fname = sprintf('%s.%05d',fbase,ifile);
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else
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loopCondition = @(x) exist(x,'file');
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fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
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end
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while loopCondition(fname)
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% Open file
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obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
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if par.Results.tarmode
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obj.opentar(file.pointer(fname));
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else
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obj.open(fname);
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end
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if ~obj.validateType('field')
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error('read error: no field data.');
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end
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% Read raw data
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[data,params] = obj.readSet(istep,ifield);
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params = cast(params,'double');
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ighost = params(1);
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ib = params(2);
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jb = params(3);
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kb = params(4);
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nxl = params(5);
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nyl = params(6);
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nzl = params(7);
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data = reshape(data,nxl+2*ighost,nyl+2*ighost,nzl+2*ighost);
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if ighost
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data = data(2:end-1,2:end-1,2:end-1);
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end
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% Assign chunk
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q(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1) = data;
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% Close the first file
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obj.close();
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% Move on to next file
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ifile = ifile+1;
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if par.Results.tarmode
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fname = sprintf('%s.%05d',fbase,ifile);
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else
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fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
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end
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end
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end
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@ -0,0 +1,61 @@
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function [q,x,y,z] = read_field_complete_ucfmf(fdir,iseq,field,varargin)
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% [q,x,y,z] = read_field_complete_ucfmf(file,field,varargin)
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% Reads a specific field from all processor chunks.(Multi-file tar version)
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% Input
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% fdir directory with files
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% iseq sequence index
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% field field to be read
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% {'u','v','w','p','s1','s2',...}
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% ? step index of step to be read (default: 1)
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% ? verbosity verbose output? (default: 0)
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% ? debug debug output? (default: 0)
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% Output
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% q complete field
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% x,y,z corresponding grid
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% Parse optional input arguments
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par = inputParser;
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addParamValue(par,'step',1,@isnumeric);
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addParamValue(par,'verbosity',0,@isnumeric);
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addParamValue(par,'debug',0,@isnumeric);
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parse(par,varargin{:});
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istep = par.Results.timestep;
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% Parse field
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if ischar(field)
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switch field(1)
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case 'u'; ifield=1; fbase='uvwp'; cmesh='u';
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case 'v'; ifield=2; fbase='uvwp'; cmesh='v';
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case 'w'; ifield=3; fbase='uvwp'; cmesh='w';
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case 'p'; ifield=4; fbase='uvwp'; cmesh='p';
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case 's'; ifield=str2double(field(2:end)); fbase='scal'; cmesh='p';
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otherwise; error('Invalid field: %s',field);
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end
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% Read parameters
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fparam = sprintf('%s/parameters_%04d.asc',fdir,iseq);
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params = read_parameters_ucf(fparam,'tarmode',0);
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% Construct an array with final mesh size
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nx = params.mesh.(sprintf('nx%s',cmesh));
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ny = params.mesh.(sprintf('ny%s',cmesh));
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nz = params.mesh.(sprintf('nz%s',cmesh));
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q = zeros(nx,ny,nz);
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% Read grid
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fgrid = sprintf('%s/grid_%04d.bin',fdir,iseq);
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[x.u,y.u,z.u,x.v,y.v,z.v,x.w,y.w,z.w,x.p,y.p,z.p] = read_grid_ucf(fgrid,'tarmode',0);
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x = x.(cmesh);
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y = y.(cmesh);
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z = z.(cmesh);
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% Get number of processors
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nprocs = params.parallel.nprocs;
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% Now read chunk by chunk
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for iproc=0:nprocs-1
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fq = sprintf('%s/%s_%04d.%05d',fpath,iseq,iproc);
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[data,ib,jb,kb,nxl,nyl,nzl] = read_field_chunk_ucf(fq,ifield,'tarmode',0,'ghost',0,'step',istep);
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q(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1) = data;
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end
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end
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@ -0,0 +1,63 @@
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function [q,x,y,z] = read_field_complete_ucftar(file,field,varargin)
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% [q,x,y,z] = read_field_complete_ucftar(file,field,varargin)
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% Reads a specific field from all processor chunks.(UCF tar version)
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% Input
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% file name of tar-file to be read
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% field field to be read
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% {'u','v','w','p','s1','s2',...}
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% ? step index of step to be read (default: 1)
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% ? verbosity verbose output? (default: 0)
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% ? debug debug output? (default: 0)
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% Output
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% q complete field
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% x,y,z corresponding grid
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% Parse optional input arguments
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par = inputParser;
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addParamValue(par,'step',1,@isnumeric);
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addParamValue(par,'verbosity',0,@isnumeric);
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addParamValue(par,'debug',0,@isnumeric);
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parse(par,varargin{:});
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istep = par.Results.timestep;
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% Parse field
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switch field(1)
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case 'u'; cmesh = 'u';
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case 'v'; cmesh = 'v';
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case 'w'; cmesh = 'w';
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case 'p'; cmesh = 'p';
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case 's'; cmesh = 'p';
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otherwise; error('Invalid field: %s',field);
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end
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% Open tar file
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htar = ustar();
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htar.open(file);
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% Read parameters
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params = read_parameters_ucf(htar,'tarmode',1);
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% Construct an array with final mesh size
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nx = params.mesh.(sprintf('nx%s',cmesh));
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ny = params.mesh.(sprintf('ny%s',cmesh));
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nz = params.mesh.(sprintf('nz%s',cmesh));
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q = zeros(nx,ny,nz);
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% Read grid
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[x.u,y.u,z.u,x.v,y.v,z.v,x.w,y.w,z.w,x.p,y.p,z.p] = read_grid_ucf(htar,'tarmode',1);
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x = x.(cmesh);
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y = y.(cmesh);
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z = z.(cmesh);
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% Get number of processors
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nprocs = params.parallel.nprocs;
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% Now read chunk by chunk
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for iproc=0:nprocs-1
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[data,ib,jb,kb,nxl,nyl,nzl] = read_field_chunk_ucf(htar,field,'tarmode',1,'rank',iproc,'ghost',0,'step',istep);
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q(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1) = data;
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end
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% Close tar file
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htar.close();
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end
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