1 |
function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize) |
2 |
|
3 |
% Function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize) |
4 |
% |
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% INPUTS |
6 |
% fpat string containing the file pattern |
7 |
% vars structure array of variable names |
8 |
% |
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% fout output file pattern (DEF: "all.%05d.nc") |
10 |
% fsize max output file size (DEF: 2.0e+9 = +/-2GB) |
11 |
% |
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% OUTPUTS |
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% nt number of usable tiles found |
14 |
% 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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|
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|
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%===== Argument checking and defaults ===== |
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|
35 |
if nargin < 2 |
36 |
disp('Error: there must be at least 2 arguments!'); |
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return |
38 |
end |
39 |
|
40 |
if nargin < 3 |
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fout = 'all.%05d.nc'; |
42 |
end |
43 |
if nargin < 4 |
44 |
fsize = 2.0e+9; |
45 |
end |
46 |
|
47 |
|
48 |
%===== Find and open all the matching files ===== |
49 |
|
50 |
nt = 0; |
51 |
nf = 0; |
52 |
all_ncf = struct([]); |
53 |
|
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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; |
59 |
while frdone == 0 |
60 |
|
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it = it + 1; |
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fnm = sprintf(fpat,it); |
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% disp(fnm); |
64 |
|
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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; |
72 |
end |
73 |
|
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% Open the NetCDF file |
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fnc = netcdf(fnm, 'nowrite'); |
76 |
if length(fnc) == 0 |
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continue; |
78 |
end |
79 |
|
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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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|
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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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all_ncf(n).Nx = fnc.Nx(1); |
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all_ncf(n).Ny = fnc.Ny(1); |
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all_ncf(n).Z = fnc.Z(1); |
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|
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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); |
108 |
end |
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|
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clear fnc |
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end |
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|
113 |
|
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%===== Do some basic sanity checks ===== |
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|
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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 )); |
126 |
end |
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|
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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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|
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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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| (prod(double([all_ncf.sNy] == all_ncf(1).sNy)) ~= 1) |
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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'); |
139 |
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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|
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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 |
153 |
end |
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|
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|
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%===== Get the dims/vars associations ===== |
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|
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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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|
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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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|
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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}; |
198 |
ncv = tncf{myname}; |
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len = length(ncv); |
200 |
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.']; |
203 |
disp(sprintf(warns,myname,all_ncf(itile).name)); |
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continue |
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end |
206 |
tmpdims = dim(ncv); |
207 |
for inm = 1:length(tmpdims) |
208 |
if mydim_names{inm} ~= name(tmpdims{inm}) |
209 |
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' ... |
212 |
' so it will be ignored.']; |
213 |
disp(sprintf(warns,myname)); |
214 |
ierr = 1; |
215 |
break |
216 |
end |
217 |
mydim_sizes{inm} = max([ tmpdims{inm}(:) mydim_sizes{inm} ]); |
218 |
end |
219 |
|
220 |
end |
221 |
|
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if ierr == 0 |
223 |
% check: does the variable have a "horizontal" component |
224 |
has_horiz = 0; |
225 |
horiz_names = { 'X' 'Y' 'Xp1' 'Yp1' }; |
226 |
for id = 1:length(mydim_names) |
227 |
if length([intersect(horiz_names,mydim_names{id})]) > 0 |
228 |
has_horiz = 1; |
229 |
end |
230 |
end |
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% disp([ ' ' myname ' ' sprintf('%d',has_horiz) ]); |
232 |
|
233 |
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; |
239 |
myvars(imy).has_horiz = has_horiz; |
240 |
|
241 |
% this is necessary to make it work with Matlab 6.5 |
242 |
if isempty([mydims.names]) |
243 |
addl = mydim_names; |
244 |
else |
245 |
addl = setdiff(mydim_names,[mydims.names]); |
246 |
end |
247 |
for iaddl = 1:length(addl) |
248 |
np1 = length(mydims) + 1; |
249 |
mydims(np1).names = addl(iaddl); |
250 |
mydims(np1).lens = mydim_sizes(find(strcmp(addl(iaddl),mydim_names))); |
251 |
end |
252 |
|
253 |
end |
254 |
end |
255 |
|
256 |
% For exch == 2, we need to add a "face" dimension |
257 |
if all_ncf(1).exch == 2 |
258 |
np1 = length(mydims) + 1; |
259 |
mydims(np1).names = { 'iface' }; |
260 |
mydims(np1).lens = { length(unique([all_ncf.exch2_myFace])) }; |
261 |
end |
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|
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% myvars.name |
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% myvars.dim_names |
265 |
% myvars.dim_sizes |
266 |
% myvars(2).dim_names |
267 |
% myvars(2).dim_names(4) |
268 |
|
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% mydims |
270 |
% length(mydims) |
271 |
% [ mydims.names ] |
272 |
% [ mydims.lens ] |
273 |
|
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|
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%===== Assemble! ===== |
276 |
|
277 |
|
278 |
if all_ncf(1).exch == 1 |
279 |
|
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% exch "1": |
281 |
|
282 |
% $$$ bi_max = max([all_ncf.bi]); |
283 |
% $$$ bj_max = max([all_ncf.bj]); |
284 |
% $$$ Xmax = bi_max * all_ncf(1).sNx; |
285 |
% $$$ Ymax = bj_max * all_ncf(1).sNy; |
286 |
Xmax = all_ncf(1).Nx; |
287 |
Ymax = all_ncf(1).Ny; |
288 |
% at this point I have to make some assumptions about the domain |
289 |
% decomposition |
290 |
bi_max = Xmax/all_ncf(1).sNx; |
291 |
bj_max = Ymax/all_ncf(1).sNy; |
292 |
itile = 0; |
293 |
for bj=1:bj_max |
294 |
for bi=1:bi_max |
295 |
itile = itile+1; |
296 |
all_ncf(itile).bi=bi; |
297 |
all_ncf(itile).bj=bj; |
298 |
end |
299 |
end |
300 |
|
301 |
horzdim = struct('names',{},'lens',{}); |
302 |
horzdim(1).names = { 'X' }; horzdim(1).lens = { Xmax }; |
303 |
horzdim(2).names = {'Xp1'}; horzdim(2).lens = { Xmax + 1 }; |
304 |
horzdim(3).names = { 'Y' }; horzdim(3).lens = { Ymax }; |
305 |
horzdim(4).names = {'Yp1'}; horzdim(4).lens = { Ymax + 1 }; |
306 |
horzdim(5).names = { 'T' }; horzdim(5).lens = { 0 }; |
307 |
|
308 |
iseq = 0; |
309 |
foutnm = sprintf(fout, iseq); |
310 |
fonc = netcdf(foutnm,'clobber'); % Should append-or-create! |
311 |
|
312 |
for idim = 1:length(mydims) |
313 |
dname = mydims(idim).names{1}; |
314 |
ind = find(strcmp(dname,[horzdim.names])); |
315 |
if length(ind) ~= 0 |
316 |
dlen = horzdim(ind).lens{1}; |
317 |
else |
318 |
dlen = mydims(idim).lens{1}; |
319 |
end |
320 |
comm = sprintf('fonc(''%s'') = %d;',dname,dlen); |
321 |
eval(comm); |
322 |
end |
323 |
|
324 |
for ivar = 1:length(myvars) |
325 |
comm = sprintf('fonc{''%s''} = nc%s( ',myvars(ivar).name,myvars(ivar).type); |
326 |
id = 1; |
327 |
comm = [ comm sprintf('''%s''',myvars(ivar).dim_names{id}) ]; |
328 |
for id = 2:length(myvars(ivar).dim_names) |
329 |
comm = [ comm sprintf(',''%s''',myvars(ivar).dim_names{id}) ]; |
330 |
end |
331 |
comm = [ comm ' );' ]; |
332 |
eval(comm); |
333 |
for iat = 1:length(myvars(ivar).atts.names) |
334 |
comm = sprintf( ... |
335 |
'fonc{''%s''}.%s = nc%s( myvars(ivar).atts.data{iat} );', ... |
336 |
myvars(ivar).name, ... |
337 |
myvars(ivar).atts.names{iat}, ... |
338 |
myvars(ivar).atts.types{iat} ); |
339 |
eval(comm); |
340 |
end |
341 |
end |
342 |
|
343 |
% for itime = 1:Tmax |
344 |
|
345 |
% Here is where we need to check the output file size and start |
346 |
% another file in the sequence, if necessary. |
347 |
|
348 |
for ivar = 1:length(myvars) |
349 |
disp(sprintf(' Copying variable: %s',myvars(ivar).name)) |
350 |
for itile = 1:length(all_ncf) |
351 |
|
352 |
if (myvars(ivar).has_horiz == 1) | (itile == 1) |
353 |
|
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 |
if (dname(1) == 'Y') & (myvars(ivar).has_horiz == 1) |
435 |
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 |
if (myvars(ivar).has_horiz == 1) | (itile == 1) |
459 |
|
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 |
|