| 1 |
edhill |
1.1 |
function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize) |
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% Function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize) |
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% |
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% INPUTS |
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% fpat string containing the file pattern |
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mlosch |
1.3 |
% vars structure array of variable names |
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edhill |
1.1 |
% |
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% fout output file pattern (DEF: "all.%05d.nc") |
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% fsize max output file size (DEF: 2.0e+9 = +/-2GB) |
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% |
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% OUTPUTS |
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% nt number of usable tiles found |
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% nf number of output files written |
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% |
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% This function "assembles" MNC output. It finds all the per-tile |
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% NetCDF files that match the input pattern, does some basic "sanity" |
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% tests to determine whether the files have compatible sizes, and |
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% then assembles all of the requested data (all of the variables) |
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% into one or more "global" NetCDF files. The global files have |
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% the following dimension conventions: |
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% |
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% "exch 1": all values are within a global horizontal grid |
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% and indicies are (X,Y,Z,T) |
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% |
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% "exch 2": all values are within one of up to six "faces" |
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% of a global cube with indicies (Xf,Yf,F,Z,T) |
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% |
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% where "X,Y.Z,T" are global space/time indicies, "Xf,Yf" are local |
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% per-face spatial indicies, and "F" is a face index. |
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%===== Argument checking and defaults ===== |
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if nargin < 2 |
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disp('Error: there must be at least 2 arguments!'); |
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return |
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end |
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if nargin < 3 |
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fout = 'all.%05d.nc'; |
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end |
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if nargin < 4 |
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fsize = 2.0e+9; |
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end |
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%===== Find and open all the matching files ===== |
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nt = 0; |
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nf = 0; |
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all_ncf = struct([]); |
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% Find all of the files |
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exch2_msg = 0; |
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tmax = 200; |
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frdone = 0; |
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it = 0; |
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while frdone == 0 |
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it = it + 1; |
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fnm = sprintf(fpat,it); |
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% disp(fnm); |
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% Check that the file exists |
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fid = fopen(fnm, 'r'); |
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if fid < 0 |
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if it >= tmax |
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frdone = 1; |
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end |
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continue; |
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end |
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% Open the NetCDF file |
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fnc = netcdf(fnm, 'nowrite'); |
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if length(fnc) == 0 |
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continue; |
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end |
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% Check for exch1/exch2 grid |
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exch = 1; |
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exch2_myFace = fnc.exch2_myFace(:); |
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if length(exch2_myFace) ~= 0 |
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exch = 2; |
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if exch2_msg == 0 |
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exch2_msg = 1; |
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disp(' Grid type appears to be: "exch2"'); |
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end |
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end |
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n = length(all_ncf) + 1; |
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all_ncf(n).name = fnm; |
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all_ncf(n).nc = {fnc}; |
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all_ncf(n).exch = exch; |
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all_ncf(n).tile_number = fnc.tile_number(1); |
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all_ncf(n).bi = fnc.bi(1); |
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all_ncf(n).bj = fnc.bj(1); |
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all_ncf(n).sNx = fnc.sNx(1); |
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all_ncf(n).sNy = fnc.sNy(1); |
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mlosch |
1.2 |
all_ncf(n).Nx = fnc.Nx(1); |
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all_ncf(n).Ny = fnc.Ny(1); |
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edhill |
1.1 |
all_ncf(n).Z = fnc.Z(1); |
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if exch == 2 |
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all_ncf(n).exch2_myFace = exch2_myFace; |
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all_ncf(n).exch2_tbasex = fnc.exch2_tbasex(1); |
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all_ncf(n).exch2_tbasey = fnc.exch2_tbasex(1); |
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end |
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clear fnc |
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end |
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%===== Do some basic sanity checks ===== |
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% check for number of files/tiles found |
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if length(all_ncf) == 0 |
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disp('Error: no tiles found--no need to do any assembly!'); |
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return |
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elseif length(all_ncf) == 1 |
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disp('Error: one tile found--no need to do any assembly!'); |
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return |
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else |
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disp(sprintf(' Found %d files matching the pattern: "%s"', ... |
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length(all_ncf), fpat )); |
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end |
| 127 |
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| 128 |
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% check for consistent "exch" version |
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if prod(double([all_ncf.exch] == all_ncf(1).exch)) ~= 1 |
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disp('Error: not all the "exch" types of the files match.'); |
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return; |
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end |
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% check for consistent sNx,sNy |
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if (prod(double([all_ncf.sNx] == all_ncf(1).sNx)) ~= 1) ... |
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mlosch |
1.2 |
| (prod(double([all_ncf.sNy] == all_ncf(1).sNy)) ~= 1) |
| 137 |
edhill |
1.1 |
disp('Error: the "sNx,sNy" values for all the tiles are not'); |
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disp(' uniform. Future versions of this function will be'); |
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disp(' able to handle non-uniform grid sizes but this'); |
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disp(' feature is not yet implemented.'); |
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return; |
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end |
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% check for redundant tiles and "time series" output |
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if length(all_ncf) ~= length(unique([all_ncf.tile_number])) |
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disp('Error: redundant tiles were found. Please check that'); |
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disp(' the file pattern does not specify output spanning'); |
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disp(' multiple model runs or even multiple time series'); |
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disp(' within a single model run. For multi-time-series'); |
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disp(' data sets, EACH "LEVEL" IN THE OUTPUT SERIES MUST'); |
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disp(' BE ASSEMBLED SEPARATERLY.'); |
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return |
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end |
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%===== Get the dims/vars associations ===== |
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mydims = struct('names', {}, 'lens', {}); |
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myvars = struct([]); |
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clear tncf; |
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for ivar = 1:length(vars) |
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mydim_names = {}; |
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mydim_sizes = {}; |
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myatt.names = {}; |
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myatt.types = {}; |
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myatt.data = {}; |
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myname = vars(ivar).name; |
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disp([' Looking for variable: ' myname]); |
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itile = 1; |
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tncf = all_ncf(itile).nc{1}; |
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ncv = tncf{myname}; |
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len = length(ncv); |
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if length(ncv) == 0 |
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warns = [' Warning: variable "%s" is not defined in "%s"\n' ... |
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' so it will be ignored.']; |
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disp(sprintf(warns,myname,all_ncf(itile).name)); |
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continue |
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end |
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mytype = datatype(ncv); |
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tmpdims = dim(ncv); |
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for inm = 1:length(tmpdims) |
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mydim_names{inm} = name(tmpdims{inm}); |
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mydim_sizes{inm} = tmpdims{inm}(:); |
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end |
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for iat = 1:length(att(ncv)) |
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aaa = att(ncv); |
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myatt.names(iat) = { name(aaa{iat}) }; |
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myatt.types(iat) = { datatype(aaa{iat}) }; |
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aab = aaa{iat}; |
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myatt.data(iat) = { aab(:) }; |
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end |
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% confirm: vars have same dim names across all files |
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ierr = 0; |
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for itile = 2:length(all_ncf) |
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tncf = all_ncf(itile).nc{1}; |
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ncv = tncf{myname}; |
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len = length(ncv); |
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if length(ncv) == 0 |
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warns = [' Warning: variable "%s" is not defined in "%s"\n' ... |
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' so it will be ignored.']; |
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disp(sprintf(warns,myname,all_ncf(itile).name)); |
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continue |
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end |
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tmpdims = dim(ncv); |
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for inm = 1:length(tmpdims) |
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if mydim_names{inm} ~= name(tmpdims{inm}) |
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warns = ... |
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[' Warning: variable "%s" is not CONSISTENTLY defined.\n' ... |
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' It has different dimensions in different files so\n' ... |
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' so it will be ignored.']; |
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disp(sprintf(warns,myname)); |
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ierr = 1; |
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break |
| 216 |
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end |
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mydim_sizes{inm} = max([ tmpdims{inm}(:) mydim_sizes{inm} ]); |
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end |
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end |
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if ierr == 0 |
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% check: does the variable have a "horizontal" component |
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has_horiz = 0; |
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horiz_names = { 'X' 'Y' 'Xp1' 'Yp1' }; |
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for id = 1:length(mydim_names) |
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if length([intersect(horiz_names,mydim_names{id})]) > 0 |
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has_horiz = 1; |
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end |
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end |
| 231 |
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% disp([ ' ' myname ' ' sprintf('%d',has_horiz) ]); |
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imy = length(myvars) + 1; |
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myvars(imy).name = myname; |
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myvars(imy).type = mytype; |
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myvars(imy).dim_names = mydim_names; |
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myvars(imy).dim_sizes = mydim_sizes; |
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myvars(imy).atts = myatt; |
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myvars(imy).has_horiz = has_horiz; |
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mlosch |
1.4 |
% this is necessary to make it work with Matlab 6.5 |
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if isempty([mydims.names]) |
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addl = mydim_names; |
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else |
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addl = setdiff(mydim_names,[mydims.names]); |
| 246 |
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end |
| 247 |
edhill |
1.1 |
for iaddl = 1:length(addl) |
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np1 = length(mydims) + 1; |
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mydims(np1).names = addl(iaddl); |
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mydims(np1).lens = mydim_sizes(find(strcmp(addl(iaddl),mydim_names))); |
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end |
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end |
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end |
| 255 |
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| 256 |
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% For exch == 2, we need to add a "face" dimension |
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if all_ncf(1).exch == 2 |
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np1 = length(mydims) + 1; |
| 259 |
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mydims(np1).names = { 'iface' }; |
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mydims(np1).lens = { length(unique([all_ncf.exch2_myFace])) }; |
| 261 |
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end |
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% myvars.name |
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% myvars.dim_names |
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% myvars.dim_sizes |
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% myvars(2).dim_names |
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% myvars(2).dim_names(4) |
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% mydims |
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% length(mydims) |
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% [ mydims.names ] |
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% [ mydims.lens ] |
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%===== Assemble! ===== |
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if all_ncf(1).exch == 1 |
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| 280 |
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% exch "1": |
| 281 |
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| 282 |
mlosch |
1.2 |
% $$$ bi_max = max([all_ncf.bi]); |
| 283 |
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% $$$ bj_max = max([all_ncf.bj]); |
| 284 |
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% $$$ Xmax = bi_max * all_ncf(1).sNx; |
| 285 |
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% $$$ Ymax = bj_max * all_ncf(1).sNy; |
| 286 |
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Xmax = all_ncf(1).Nx; |
| 287 |
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Ymax = all_ncf(1).Ny; |
| 288 |
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% at this point I have to make some assumptions about the domain |
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% decomposition |
| 290 |
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bi_max = Xmax/all_ncf(1).sNx; |
| 291 |
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bj_max = Ymax/all_ncf(1).sNy; |
| 292 |
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itile = 0; |
| 293 |
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for bj=1:bj_max |
| 294 |
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for bi=1:bi_max |
| 295 |
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itile = itile+1; |
| 296 |
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all_ncf(itile).bi=bi; |
| 297 |
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all_ncf(itile).bj=bj; |
| 298 |
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end |
| 299 |
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end |
| 300 |
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| 301 |
edhill |
1.1 |
horzdim = struct('names',{},'lens',{}); |
| 302 |
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horzdim(1).names = { 'X' }; horzdim(1).lens = { Xmax }; |
| 303 |
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horzdim(2).names = {'Xp1'}; horzdim(2).lens = { Xmax + 1 }; |
| 304 |
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horzdim(3).names = { 'Y' }; horzdim(3).lens = { Ymax }; |
| 305 |
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horzdim(4).names = {'Yp1'}; horzdim(4).lens = { Ymax + 1 }; |
| 306 |
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horzdim(5).names = { 'T' }; horzdim(5).lens = { 0 }; |
| 307 |
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| 308 |
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iseq = 0; |
| 309 |
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foutnm = sprintf(fout, iseq); |
| 310 |
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fonc = netcdf(foutnm,'clobber'); % Should append-or-create! |
| 311 |
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| 312 |
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for idim = 1:length(mydims) |
| 313 |
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dname = mydims(idim).names{1}; |
| 314 |
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ind = find(strcmp(dname,[horzdim.names])); |
| 315 |
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if length(ind) ~= 0 |
| 316 |
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dlen = horzdim(ind).lens{1}; |
| 317 |
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else |
| 318 |
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dlen = mydims(idim).lens{1}; |
| 319 |
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end |
| 320 |
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comm = sprintf('fonc(''%s'') = %d;',dname,dlen); |
| 321 |
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eval(comm); |
| 322 |
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end |
| 323 |
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| 324 |
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for ivar = 1:length(myvars) |
| 325 |
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comm = sprintf('fonc{''%s''} = nc%s( ',myvars(ivar).name,myvars(ivar).type); |
| 326 |
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id = 1; |
| 327 |
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comm = [ comm sprintf('''%s''',myvars(ivar).dim_names{id}) ]; |
| 328 |
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for id = 2:length(myvars(ivar).dim_names) |
| 329 |
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comm = [ comm sprintf(',''%s''',myvars(ivar).dim_names{id}) ]; |
| 330 |
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end |
| 331 |
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comm = [ comm ' );' ]; |
| 332 |
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eval(comm); |
| 333 |
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for iat = 1:length(myvars(ivar).atts.names) |
| 334 |
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comm = sprintf( ... |
| 335 |
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'fonc{''%s''}.%s = nc%s( myvars(ivar).atts.data{iat} );', ... |
| 336 |
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myvars(ivar).name, ... |
| 337 |
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myvars(ivar).atts.names{iat}, ... |
| 338 |
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myvars(ivar).atts.types{iat} ); |
| 339 |
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eval(comm); |
| 340 |
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end |
| 341 |
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end |
| 342 |
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| 343 |
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% for itime = 1:Tmax |
| 344 |
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| 345 |
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% Here is where we need to check the output file size and start |
| 346 |
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% another file in the sequence, if necessary. |
| 347 |
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| 348 |
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for ivar = 1:length(myvars) |
| 349 |
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disp(sprintf(' Copying variable: %s',myvars(ivar).name)) |
| 350 |
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for itile = 1:length(all_ncf) |
| 351 |
|
|
|
| 352 |
mlosch |
1.2 |
if (myvars(ivar).has_horiz == 1) | (itile == 1) |
| 353 |
edhill |
1.1 |
|
| 354 |
|
|
clear nct; |
| 355 |
|
|
nct = all_ncf(itile).nc{1}; |
| 356 |
|
|
ox_off = (all_ncf(itile).bi - 1)*all_ncf(itile).sNx; |
| 357 |
|
|
oy_off = (all_ncf(itile).bj - 1)*all_ncf(itile).sNy; |
| 358 |
|
|
diml_in = ''; |
| 359 |
|
|
diml_out = ''; |
| 360 |
|
|
for jj = 1:length(myvars(ivar).dim_names) |
| 361 |
|
|
doff = 1; |
| 362 |
|
|
if jj > 1 |
| 363 |
|
|
diml_in = sprintf('%s,',diml_in); |
| 364 |
|
|
diml_out = sprintf('%s,',diml_out); |
| 365 |
|
|
end |
| 366 |
|
|
dlen = myvars(ivar).dim_sizes{jj}; |
| 367 |
|
|
diml_in = sprintf('%s%s',diml_in, ':'); |
| 368 |
|
|
fchar = myvars(ivar).dim_names{jj}(1); |
| 369 |
|
|
% disp([' fchar = ' fchar ' ' myvars(ivar).dim_names{jj}]); |
| 370 |
|
|
if strcmp(myvars(ivar).dim_names{jj}(1),'X') == 1 |
| 371 |
|
|
doff = ox_off + doff; |
| 372 |
|
|
dlen = ox_off + dlen; |
| 373 |
|
|
end |
| 374 |
|
|
if strcmp(myvars(ivar).dim_names{jj}(1),'Y') == 1 |
| 375 |
|
|
doff = oy_off + doff; |
| 376 |
|
|
dlen = oy_off + dlen; |
| 377 |
|
|
end |
| 378 |
|
|
diml_out = sprintf('%s%d%s%d',diml_out,doff,':',dlen); |
| 379 |
|
|
end |
| 380 |
|
|
|
| 381 |
|
|
comm = sprintf( ... |
| 382 |
|
|
'fonc{''%s''}(%s) = nct{''%s''}(%s);', ... |
| 383 |
|
|
myvars(ivar).name, diml_out, myvars(ivar).name, diml_in ); |
| 384 |
|
|
% disp([ ' comm: ' comm ]); |
| 385 |
|
|
eval(comm); |
| 386 |
|
|
|
| 387 |
|
|
end |
| 388 |
|
|
|
| 389 |
|
|
end |
| 390 |
|
|
end |
| 391 |
|
|
% end |
| 392 |
|
|
|
| 393 |
|
|
fonc = close(fonc); |
| 394 |
|
|
|
| 395 |
|
|
elseif all_ncf(1).exch == 2 |
| 396 |
|
|
|
| 397 |
|
|
% exch "2": |
| 398 |
|
|
Xmax = 0; |
| 399 |
|
|
Ymax = 0; |
| 400 |
|
|
for ii = 1:length(all_ncf) |
| 401 |
|
|
Xmax = max(Xmax, (all_ncf(ii).exch2_tbasex + all_ncf(ii).sNx)); |
| 402 |
|
|
Ymax = max(Ymax, (all_ncf(ii).exch2_tbasey + all_ncf(ii).sNy)); |
| 403 |
|
|
end |
| 404 |
|
|
|
| 405 |
|
|
horzdim = struct('names',{},'lens',{}); |
| 406 |
|
|
horzdim(1).names = { 'X' }; horzdim(1).lens = { Xmax }; |
| 407 |
|
|
horzdim(2).names = {'Xp1'}; horzdim(2).lens = { Xmax + 1 }; |
| 408 |
|
|
horzdim(3).names = { 'Y' }; horzdim(3).lens = { Ymax }; |
| 409 |
|
|
horzdim(4).names = {'Yp1'}; horzdim(4).lens = { Ymax + 1 }; |
| 410 |
|
|
horzdim(5).names = { 'T' }; horzdim(5).lens = { 0 }; |
| 411 |
|
|
|
| 412 |
|
|
iseq = 0; |
| 413 |
|
|
foutnm = sprintf(fout, iseq); |
| 414 |
|
|
fonc = netcdf(foutnm,'clobber'); % Should append-or-create! |
| 415 |
|
|
|
| 416 |
|
|
for idim = 1:length(mydims) |
| 417 |
|
|
dname = mydims(idim).names{1}; |
| 418 |
|
|
ind = find(strcmp(dname,[horzdim.names])); |
| 419 |
|
|
if length(ind) ~= 0 |
| 420 |
|
|
dlen = horzdim(ind).lens{1}; |
| 421 |
|
|
else |
| 422 |
|
|
dlen = mydims(idim).lens{1}; |
| 423 |
|
|
end |
| 424 |
|
|
comm = sprintf('fonc(''%s'') = %d;',dname,dlen); |
| 425 |
|
|
eval(comm); |
| 426 |
|
|
end |
| 427 |
|
|
|
| 428 |
|
|
for ivar = 1:length(myvars) |
| 429 |
|
|
comm = sprintf('fonc{''%s''} = nc%s( ',myvars(ivar).name,myvars(ivar).type); |
| 430 |
|
|
id = 1; |
| 431 |
|
|
comm = [ comm sprintf('''%s''',myvars(ivar).dim_names{id}) ]; |
| 432 |
|
|
for id = 2:length(myvars(ivar).dim_names) |
| 433 |
|
|
dname = myvars(ivar).dim_names{id}; |
| 434 |
mlosch |
1.2 |
if (dname(1) == 'Y') & (myvars(ivar).has_horiz == 1) |
| 435 |
edhill |
1.1 |
comm = [ comm sprintf(',''%s''','iface') ]; |
| 436 |
|
|
end |
| 437 |
|
|
comm = [ comm sprintf(',''%s''',dname) ]; |
| 438 |
|
|
end |
| 439 |
|
|
comm = [ comm ' );' ]; |
| 440 |
|
|
eval(comm); |
| 441 |
|
|
for iat = 1:length(myvars(ivar).atts.names) |
| 442 |
|
|
comm = sprintf( ... |
| 443 |
|
|
'fonc{''%s''}.%s = nc%s( myvars(ivar).atts.data{iat} );', ... |
| 444 |
|
|
myvars(ivar).name, ... |
| 445 |
|
|
myvars(ivar).atts.names{iat}, ... |
| 446 |
|
|
myvars(ivar).atts.types{iat} ); |
| 447 |
|
|
eval(comm); |
| 448 |
|
|
end |
| 449 |
|
|
end |
| 450 |
|
|
|
| 451 |
|
|
% Here is where we need to check the output file size and start |
| 452 |
|
|
% another file in the sequence, if necessary. |
| 453 |
|
|
|
| 454 |
|
|
for ivar = 1:length(myvars) |
| 455 |
|
|
disp(sprintf(' Copying variable: %s',myvars(ivar).name)) |
| 456 |
|
|
for itile = 1:length(all_ncf) |
| 457 |
|
|
|
| 458 |
mlosch |
1.2 |
if (myvars(ivar).has_horiz == 1) | (itile == 1) |
| 459 |
edhill |
1.1 |
|
| 460 |
|
|
clear nct; |
| 461 |
|
|
nct = all_ncf(itile).nc{1}; |
| 462 |
|
|
ox_off = all_ncf(itile).exch2_tbasex; |
| 463 |
|
|
oy_off = all_ncf(itile).exch2_tbasey; |
| 464 |
|
|
diml_tin = ''; |
| 465 |
|
|
diml_res = ''; |
| 466 |
|
|
diml_in = ''; |
| 467 |
|
|
diml_out = ''; |
| 468 |
|
|
if length(myvars(ivar).dim_names) < 2 |
| 469 |
|
|
comm = sprintf( ... |
| 470 |
|
|
'fonc{''%s''}(%s%d) = nct{''%s''}(:);', ... |
| 471 |
|
|
myvars(ivar).name, '1:', myvars(ivar).dim_sizes{1}, ... |
| 472 |
|
|
myvars(ivar).name ); |
| 473 |
|
|
% disp([ ' ' comm ]); |
| 474 |
|
|
eval(comm); |
| 475 |
|
|
else |
| 476 |
|
|
for jj = 1:length(myvars(ivar).dim_names) |
| 477 |
|
|
doff = 1; |
| 478 |
|
|
if jj > 1 |
| 479 |
|
|
diml_tin = sprintf('%s,',diml_tin); |
| 480 |
|
|
diml_res = sprintf('%s,',diml_res); |
| 481 |
|
|
diml_in = sprintf('%s,',diml_in); |
| 482 |
|
|
diml_out = sprintf('%s,',diml_out); |
| 483 |
|
|
end |
| 484 |
|
|
dnam = myvars(ivar).dim_names{jj}; |
| 485 |
|
|
dlen = myvars(ivar).dim_sizes{jj}; |
| 486 |
|
|
dlenr = dlen; |
| 487 |
|
|
fchar = myvars(ivar).dim_names{jj}(1); |
| 488 |
|
|
% disp([' fchar = ' fchar ' ' myvars(ivar).dim_names{jj}]); |
| 489 |
|
|
if strcmp(dnam(1),'X') == 1 |
| 490 |
|
|
doff = ox_off + doff; |
| 491 |
|
|
dlen = ox_off + dlen; |
| 492 |
|
|
end |
| 493 |
|
|
if strcmp(dnam(1),'Y') == 1 |
| 494 |
|
|
diml_res = sprintf('%s%s',diml_res, '[],'); |
| 495 |
|
|
diml_in = sprintf('%s%s',diml_in, ':,'); |
| 496 |
|
|
diml_out = sprintf('%s%d%s',diml_out,all_ncf(itile).exch2_myFace,','); |
| 497 |
|
|
doff = oy_off + doff; |
| 498 |
|
|
dlen = oy_off + dlen; |
| 499 |
|
|
end |
| 500 |
|
|
diml_tin = sprintf('%s%s',diml_tin, ':'); |
| 501 |
|
|
diml_res = sprintf('%s%d',diml_res, dlenr); |
| 502 |
|
|
diml_in = sprintf('%s%s',diml_in, ':'); |
| 503 |
|
|
diml_out = sprintf('%s%d%s%d',diml_out,doff,':',dlen); |
| 504 |
|
|
end |
| 505 |
|
|
|
| 506 |
|
|
comm = sprintf( ... |
| 507 |
|
|
'tmp = reshape(nct{''%s''}(%s), %s); fonc{''%s''}(%s) = tmp(%s);', ... |
| 508 |
|
|
myvars(ivar).name, diml_tin, diml_res, myvars(ivar).name, ... |
| 509 |
|
|
diml_out, diml_in ); |
| 510 |
|
|
% disp([ ' ' comm ]); |
| 511 |
|
|
eval(comm); |
| 512 |
|
|
end |
| 513 |
|
|
|
| 514 |
|
|
end |
| 515 |
|
|
|
| 516 |
|
|
end |
| 517 |
|
|
end |
| 518 |
|
|
% end |
| 519 |
|
|
|
| 520 |
|
|
fonc = close(fonc); |
| 521 |
|
|
|
| 522 |
|
|
end |
| 523 |
|
|
|
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