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FVCOM
fvcom-toolbox
Commits
53a259b1
Commit
53a259b1
authored
Oct 16, 2012
by
Pierre Cazenave
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Remove some old versions of the code to load the FVCOM model outputs
parent
5c643930
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utilities/read_netCDF_FVCOM_in_progress.m
utilities/read_netCDF_FVCOM_in_progress.m
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-289
utilities/read_netCDF_FVCOM_old.m
utilities/read_netCDF_FVCOM_old.m
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utilities/read_netCDF_FVCOM_in_progress.m
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utilities/read_netCDF_FVCOM_old.m
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5c643930
function
[
varargout
]
=
read_netCDF_FVCOM
(
varargin
)
% funtion to read underway NetCDF files from discovery
% possible intputs are
% all_data = 0 single file or 1 for multiple files
% directory where the data is stored
% files = cell array of filenames or if single string then a search pattern
% i.e. *position-4000.gps
% varnames in cell array of variables to extract i.e. lat, lon, time
% they need to be exact matches of variables contained in the netcdf file
% The options could be (but depend on your model output:
% Itime, Itime2, Times, h, iint, kh, km, kq, l, lat, latc, lon, lonc,
% nprocs, nv, partition, q2, q2l, salinity, siglay, siglay_DT,
% siglay_shift_DT, siglev, siglev_DT, temp, time, u, ua, v, va, wet_cells,
% wet_cells_prev_ext, wet_cells_prev_int, wet_nodes, wet_nodes_prev_int, x,
% xc, y, yc, zeta,
% possible attributes for each variable are:
% nc{'measureTS'} = ncdouble('time'); %% 2983 elements.
% nc{'measureTS'}.element_name = ncchar(''measure time'');
% nc{'measureTS'}.cardinalitymin = nclong(1);
% nc{'measureTS'}.cardinalitymax = nclong(1);
% nc{'measureTS'}.comment = ncchar(''time of measure as determined by the GPS'');
% nc{'measureTS'}.long_name = ncchar(''measure timestamp'');
% nc{'measureTS'}.units = ncchar(''day since 1899-12-30T00:00:00 UTC'');
% nc{'measureTS'}.shortunits = ncchar(''days'');
% nc{'measureTS'}.positive = ncchar(''up'');
% nc{'measureTS'}.C_format = ncchar(''%14.7f'');
% nc{'measureTS'}.axis = ncchar(''T'');
% nc{'measureTS'}.measuretimedata = ncchar(''measureTS'');
% nc{'measureTS'}.valid_max = ncdouble(100000);
% nc{'measureTS'}.valid_min = ncdouble(30000);
% nc{'measureTS'}.precision = nclong(12);
% nc{'measureTS'}.scale = nclong(7);
% nc{'measureTS'}.FillValue_ = ncdouble(0);
% nc{'measureTS'}.missing_value = ncdouble(0);
% nc{'measureTS'}.scale_factor = ncdouble(1);
% nc{'measureTS'}.add_offset = ncdouble(0);
% nc{'measureTS'}.element_version = ncchar(''1.0'');
% nc{'measureTS'}.valid_range = ncchar(''30000.000000,100000.000000'');
netcdfpath
addpath
D
:\
Research
\
Models
\
UMASSDvisit
\
matlab
;
%%
CD
=
pwd
;
disp
([
'Using date conversion of +678942 to go from FVCOM time to matlab time'
])
time_offset
=
678942
;
params_opts
=
{
'time'
,
'data_dir'
,
'files'
,
'nzopt'
,
'trnsopt'
,
'varnames'
,
'trns_idx'
,
'nz_idx'
}
disp
([
'Default values are ...'
])
var_in_list
=
{
'all_data'
,
'netfile_dir'
,
'files'
,
'nz'
,
'trnsxy'
,
'varnames'
,
'trns_idx'
,
'nz_idx'
};
all_data
=
1
;
netfile_dir
=
'D:\research\Data\ICON\underway\netcdf'
;
files
=
'*.nc'
;
nz
=
0
;
nz_idx
=-
1
;
trnsxy
=
0
;
trns_idx
=-
1
;
varnames
=
{
'time'
,
'lat'
,
'lon'
,
'h'
,};
for
aa
=
1
:
2
:
nargin
res
=
strmatch
(
varargin
(
aa
),
params_opts
)
if
~
isempty
(
res
),
eval
([
var_in_list
{
res
},
' = varargin{aa+1};'
])
disp
([
params_opts
{
res
}])
end
% eval([var_in_list{aa},' = varargin{aa};'])
end
if
nz
==
0
nz_idx
=-
1
;
end
if
trnsxy
==
0
;
trns_idx
=-
1
;
end
nvarnames
=
length
(
varnames
);
for
nn
=
1
:
nvarnames
data
{
nn
}
=
[];
end
%%
cd
(
netfile_dir
)
filen
=
dir
(
files
);
for
ff
=
1
:
length
(
filen
)
file_netcdf
{
ff
}
=
filen
(
ff
)
.
name
;
end
% filen(1).name = files;
% file_netcdf{1} = files;
% Extract time range for all available files
files_to_read
=
[];
times
=
[];
for
ff
=
1
:
length
(
filen
)
nc
=
netcdf
(
file_netcdf
{
ff
},
'nowrite'
);
gatts
=
att
(
nc
);
% this are the general file attributes
vars
=
var
(
nc
);
for
ii
=
1
:
length
(
vars
)
output
=
name
(
vars
{
ii
});
to_show
{
ii
}
=
output
;
switch
output
case
'Itime'
[
start_d
(
1
),
end_d
(
1
)]
=
deal
(
vars
{
ii
}(
1
)
+
time_offset
,
vars
{
ii
}(
end
)
+
time_offset
)
[
start_d
(
2
),
end_d
(
2
)]
=
deal
(
vars
{
ii
+
1
}(
1
),
vars
{
ii
+
1
}(
end
))
var_time
{
ff
}
=
(
vars
{
ii
}(:)
+
time_offset
)
+
(
vars
{
ii
+
1
}(:)
.
/(
24
*
600
*
6000
));
end
end
start_date
=
sum
(
start_d
.*
[
1
1
/(
24
*
60
*
60
)]);
end_date
=
sum
(
end_d
.*
[
1
1
/(
24
*
60
*
60
)]);
disp
([
'Start and end of file, '
,
datestr
(
start_date
),
' '
,
datestr
(
end_date
)])
files_to_read
(
ff
)
=
ff
;
times
(
ff
,:)
=
[
start_date
,
end_date
];
close
(
nc
)
end
disp
([
'Possible variables to extract are: '
])
for
ii
=
1
:
length
(
to_show
)
fprintf
(
'%s, '
,
to_show
{
ii
})
end
if
(
length
(
all_data
)
==
2
)
req_st
=
datenum
(
all_data
{
1
},
'dd/mm/yy HH:MM:SS'
);
req_end
=
datenum
(
all_data
{
2
},
'dd/mm/yy HH:MM:SS'
);
files_to_read
(:)
=
NaN
;
sel1
=
find
(
req_st
>
times
(:,
1
)
&
req_st
<
times
(:,
2
));
sel2
=
find
(
req_end
>
times
(:,
1
)
&
req_end
<
times
(:,
2
));
sel
=
[
sel1
,
sel2
];
sel
(
find
(
~
diff
(
sel
)))
=
[];
files_to_read
(
sel
)
=
1
;
if
(
req_end
>
times
(
end
,
2
));
files_to_read
(
end
)
=
1
;
end
end
file_netcdf
(
isnan
(
files_to_read
))
=
[];
var_time
(
isnan
(
files_to_read
))
=
[];
time_idx
=
find
(
req_st
<=
var_time
{
1
}
&
var_time
{
1
}
<=
req_end
);
clear
vars
for
ff
=
1
:
length
(
file_netcdf
)
cdfid
=
ncmex
(
'OPEN'
,
file_netcdf
{
ff
},
'NOWRITE'
)
if
cdfid
==-
1
disp
([
'NetCDF file '
,
file_netcdf
{
ff
},
' not found'
])
return
else
disp
([
'NetCDF file '
,
file_netcdf
{
ff
},
' opened successfully.'
])
end
[
ndims
,
nvars
,
natts
,
recdim
,
status
]
=
ncmex
(
'INQUIRE'
,
cdfid
);
nombre
=
{};
dim
=
{};
for
aa
=
1
:
nvars
[
nombre
{
aa
},
datatype
,
ndims
(
aa
),
dim
{
aa
},
natts
,
status
]
=
ncmex
(
'VARINQ'
,
cdfid
,
aa
-
1
);
end
for
aa
=
1
:
length
(
varnames
)
TF
=
strcmpi
(
varnames
{
aa
},
nombre
);
varidx
(
aa
)
=
find
(
TF
)
-
1
;
TF
=
sum
(
TF
);
dimens
=
ndims
(
aa
);
if
TF
;
disp
([
'Variable '
,
varnames
{
aa
},
' found in file'
])
else
disp
([
'Variable '
,
varnames
{
aa
},
' NOT found in file Stopping. Check variable names.'
])
ncmex
(
'CLOSE'
,
cdfid
)
return
end
[
dud
,
dud
,
dimens
,
vardims
,
dud
,
status
]
=
ncmex
(
'varinq'
,
cdfid
,
varidx
(
aa
));
switch
dimens
case
1
x_dimid
=
vardims
(
dimens
)
[
dud
,
x_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
x_dimid
);
eval
([
'['
,
varnames
{
aa
},
', status] = ncmex(
''
VARGET
''
, cdfid, varidx(aa), [0], [-1],
''
autoscale
''
);'
])
case
2
z_dimid
=
vardims
(
dimens
-
1
)
x_dimid
=
vardims
(
dimens
)
[
dud
,
z_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
z_dimid
);
[
dud
,
x_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
x_dimid
);
eval
([
'['
,
varnames
{
aa
},
', status] = ncmex(
''
VARGET
''
, cdfid, varidx(aa), [0 0], [-1 -1],
''
autoscale
''
);'
])
case
3
z_dimid
=
vardims
(
dimens
-
1
)
x_dimid
=
vardims
(
dimens
)
t_dimid
=
vardims
(
dimens
-
2
)
[
dud
,
z_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
z_dimid
);
[
dud
,
x_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
x_dimid
);
[
dud
,
t_length
,
status
]
=
ncmex
(
'diminq'
,
cdfid
,
t_dimid
);
eval
([
'['
,
varnames
{
aa
},
', status] = ncmex(
''
VARGET
''
, cdfid, varidx(aa), [time_idx(1)-1 nz 0], [length(time_idx) length(nz_idx)*sign(nz_idx(1)) -1],
''
autoscale
''
);'
])
if
trnsxy
eval
([
varnames
{
aa
},
' = squeeze('
,
varnames
{
aa
},
'(trns_idx, : ,:));'
])
end
end
eval
([
'data(aa) = {[data{aa};'
,
varnames
{
aa
},
']};'
])
eval
([
'clear '
,
varnames
{
aa
}])
end
ncmex
(
'CLOSE'
,
cdfid
)
end
cd
(
CD
)
varargout
{
1
}
=
data
;
ncmex
(
'CLOSE'
,
cdfid
)
return
%
% pcolor(zero_to_nan(squeeze(value(:,:,1,1)))'),colorbar
%
%
% ncmex('CLOSE',cdfid)
%
% [value, status] = ncmex('VARGET', cdfid, varid, [0 0 0], [londimid latdimid depdimid])
% [value, status] = ncmex('VARGET', cdfid, varid, [0 0 0], [-1 -1 -1])
%
%
% status = ncmex('VARPUT1', cdfid, varid, coords, value, autoscale)
% [value, status] = ncmex('VARGET1', cdfid, varid, coords, autoscale)
% status = ncmex('VARPUT', cdfid, varid, start, count, value, autoscale)
% [value, status] = ncmex('VARGET', cdfid, varid, start, count, autoscale)
% status = ncmex('VARPUTG', cdfid, varid, start, count, stride, [], value, autoscale)
% [value, status] = ncmex('VARGETG', cdfid, varid, start, count, stride, [], autoscale)
% status = ncmex('VARRENAME', cdfid, varid, 'name')
%
% status = ncmex('ATTPUT', cdfid, varid, 'name', datatype, len, value)
% [datatype, len, status] = ncmex('ATTINQ', cdfid, varid, 'name')
% [value, status] = ncmex('ATTGET', cdfid, varid, 'name')
% status = ncmex('ATTCOPY', incdf, invar, 'name', outcdf, outvar)
% ['name', status] = ncmex('ATTNAME', cdfid, varid, attnum)
% status = ncmex('ATTRENAME', cdfid, varid, 'name', 'newname')
% status = ncmex('ATTDEL', cdfid, varid, 'name')
%
% status = ncmex('RECPUT', cdfid, recnum, [data], autoscale, recdim)
% [[data], status] = ncmex('RECGET', cdfid, recnum, autoscale, recdim)
% [[recvarids], [recsizes], status] = ncmex('RECINQ', cdfid, recdim)
%
% len = ncmex('TYPELEN', datatype)
% old_fillmode = ncmex('SETFILL', cdfid, fillmode)
%
% old_ncopts = ncmex('SETOPTS', ncopts)
% ncerr = ncmex('ERR')
% code = ncmex('PARAMETER', 'NC_...')
%
% Notes:
% 1. The rcode is always zero.
% 2. The dimid can be number or name.
% 3. The varid can be number or name.
% 4. The attname can be name or number.
% 5. The operation and parameter names are not case-sensitive.
% 6. The cmode defaults to 'NC_NOCLOBBER'.
% 7. The mode defaults to 'NC_NOWRITE'.
% 8. The value -1 determines length automatically.
% 9. The operation names can prepend 'nc'.
% 10. The parameter names can drop 'NC_' prefix.
% 11. Dimensions: Matlab (i, j, ...) <==> [..., j, i] NetCDF.
% 12. Indices and identifiers are zero-based.
% 13. One-dimensional arrays are returned as column-vectors.
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