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Coastlines/read_grads.m

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function [data,header]=read_grads(file_name,var_name,varargin)
% [var,header]=read_grads(file_name,var_name) is a function to read
% in binary files using their GrADS descriptor header.
% If var_name is 'all' or non-existent, all variables are read and
% sent to the base-workspace.
% Please check before-hand the data-type (big/little endian), as well
% as the data precision (single/double...), and adjust if necessary
% the header at the beginning of read_grads.m.
% Optionally, you can improve the indications from the header file in
% the sub-function grads_name (hereafter).
%
% Kristof Sturm, sturm@dkrz.de or sturm@lgge.obs.ujf-grenoble.fr, 29.10.02
global l_quiet
n=strmatch('quiet',{varargin{1:2:end}});
if isempty(n)
l_quiet=0;
else
switch lower(varargin{2*(n-1)+2})
case {1,'yes'}
l_quiet=1;
case {0,'no'}
l_quiet=0;
end
end
header=struct('FILENAME',file_name,...
'VARSIZE',{[]},...
'NVAR',0,...
'DATANAME','-',...
'FID',{[]},...
'BINTYPE','-',...
'BINPRECISION','float32',...
'DSET','-',...
'DTYPE',1,...
'INDEX','-',...
'TITLE','-',...
'UNDEF',0,...
'OPTIONS',{[]},...
'XDEF',{[]},...
'YDEF',{[]},...
'ZDEF',{[]},...
'TDEF',{[]},...
'VARS',struct([]),...
'FILEHEADER',0,...
'THEADER',0,...
'XYHEADER',0);
header.XDEF.rev=0;
header.YDEF.rev=0;
header.ZDEF.rev=0;
% [comp,max_size,endian]=computer;
endian='L';
if endian=='L'
header.BINTYPE='ieee-le';
elseif endian=='B'
header.BINTYPE='ieee-be';
end
data=[];
file_name=deblank(file_name);
if exist(file_name,'file')
fid_ctl = fopen(file_name,'r');
% disp(['CTL opened: ',num2str(fid_ctl)])
% [header.FID]=deal([fid_ctl 0]);
header(1).FID{1}=fid_ctl;
if isunix, sep='/';
else
sep='\\';
end
if ~isempty(strfind(file_name,sep))
slash=max(strfind(file_name,sep));
header(1).DIR=file_name(1:slash);
file_name=file_name((slash+1):end);
end
header(1).FILENAME=file_name;
else
error(['Inexistent header file ',file_name])
end
% Enabling read_grads to handle netcdf files.
point=strfind(file_name,'.');
suf=lower(file_name(point(end)+1:end));
if strcmp(suf,'ctl')
% reading the .ctl file :
while ~feof(fid_ctl)
line=fgets(fid_ctl);
if isempty(line(1:end-1)), break, end
% cutting the line into words.
line_gaps=isspace(line);
% removing consecutive blancks.
while line_gaps(1)==1, line_gaps(1)=[]; line(1)=[]; end
if line(1)=='*'
if ~l_quiet
disp(line)
end
else
no_gaps=0;
while ~no_gaps
line_gap2=find(line_gaps);
if any(diff(line_gap2)==1)
dup=1+find(diff(line_gap2)==1);
line_gaps(line_gap2(dup))=[];
line(line_gap2(dup))=[];
else
no_gaps=1;
end
end
entry=line(1:(min(find(line_gaps))-1));
words={''};
for n=1:(sum(line_gaps)-1)
words{n}=line((line_gap2(n)+1):(line_gap2(n+1)-1));
end
header=read_header(entry,words);
% disp(words)
end
end
% Opening the binary file for later reading:
fid_bin = fopen(header.DATANAME,'r', header.BINTYPE );
% disp(['BIN opened: ',num2str(fid_bin)])
[header(1).FID] = {fid_ctl, fid_bin};
fclose(fid_ctl);
nvar=size(header.VARS,1);
header.NVAR=nvar;
if nargin>1 & isempty(var_name)
if ~l_quiet
disp(['Header for ',header.FILENAME,' read.'])
end
fclose(header.FID{2});
return
end
if nargout==0
assignin('caller','header',header)
assignin('caller','vars',vars);
end
if header.DTYPE % Gridded data set
% Computing the size of each variable:
var_size=zeros(nvar,4); % array of the var. size [X,Y,Z,T]
var_size(:,1)=header.XDEF.num;
var_size(:,2)=header.YDEF.num;
var_size(:,3)=cat(1,header.VARS.levs);
var_size(:,4)=header.TDEF.num;
header.VARSIZE={var_size};
if exist('grads_name','file')
[vars,header]=grads_name(header,vars);
end
% reading the bin. file :
if nargin == 1 | strcmp(lower(var_name),'all')
read_data(header);
elseif nargin == 2
t_limits=[1 header.TDEF.num];
ivar=strmatch(var_name,{header.VARS.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
z_limits=[1 header.VARS(ivar).levs];
y_limits=[1 header.YDEF.num];
x_limits=[1 header.XDEF.num];
data=read_var(header,var_name,t_limits,z_limits,y_limits,x_limits);
header.XDEF.vec=header.XDEF.vec(x_limits(1):x_limits(2));
header.XDEF.num=length(header.XDEF.vec);
header.YDEF.vec=header.YDEF.vec(y_limits(1):y_limits(2));
header.YDEF.num=length(header.YDEF.vec);
else
for n=1:2:nargin-2
switch lower(varargin{n})
case {'x'}
x_limits=varargin{n+1};
case {'lon'}
lon_limits=sort(varargin{n+1});
x_limits=interp1(header.XDEF.vec,1:header.XDEF.num,...
lon_limits,'nearest',NaN);
if any(isnan(x_limits))
if ~l_quiet
disp(['The X-limits ',num2str(lon_limits),...
' exceed the data coverage ',...
num2str(header.XDEF.vec([1 end]))])
end
data=[];
return
end
case {'y'}
y_limits=varargin{n+1};
case {'lat'}
lat_limits=sort(varargin{n+1});
y_limits=interp1(header.YDEF.vec,1:header.YDEF.num,...
lat_limits,'nearest',NaN);
if any(isnan(y_limits))
if ~l_quiet
disp(['The Y-limits ',num2str(lat_limits),...
' exceed the data coverage ',...
num2str(header.YDEF.vec([1 end]))])
end
data=[];
return
end
if header.YDEF.rev,
y_limits=header.YDEF.num*ones(size(y_limits))-fliplr(y_limits)+1;
end
case {'t','time'}
t_limits=varargin{n+1};
case {'z','lev'}
z_limits=varargin{n+1};
ivar=strmatch(var_name,{header.VARS.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
if any(z_limits>header.VARS(ivar).levs)
if ~l_quiet
disp(['The variable ',var_name,' has only ',...
header.VARS(ivar).levs,' levels.'])
end
data=[];
return
end
end
end
if ~exist('t_limits','var'), t_limits=[1 header.TDEF.num]; end
if ~exist('z_limits','var')
ivar=strmatch(var_name,{header.VARS.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
z_limits=[1 header.VARS(ivar).levs];
end
if ~exist('y_limits','var')
y_limits=[1 header.YDEF.num];
end
if ~exist('x_limits','var')
x_limits=[1 header.XDEF.num];
end
data=read_var(header,var_name,t_limits,z_limits,y_limits,x_limits);
header.XDEF.vec=header.XDEF.vec(x_limits(1):x_limits(2));
header.XDEF.num=length(header.XDEF.vec);
if header.YDEF.rev,
y_limits=header.YDEF.num*ones(size(y_limits))-fliplr(y_limits)+1;
end
header.YDEF.vec=header.YDEF.vec(y_limits(1):y_limits(2));
header.YDEF.num=length(header.YDEF.vec);
end
% if header.XDEF.rev, header.XDEF.vec=header.XDEF.vec([end:-1:1]); end
% if header.YDEF.rev, header.YDEF.vec=header.YDEF.vec([end:-1:1]); end
% if header.ZDEF.rev, header.ZDEF.vec=header.ZDEF.vec([end:-1:1]); end
else % Station data set
data=read_station(header);
end
fclose(header.FID{2});
elseif strcmp(suf,'nc') % Enabling NetCDF in read_grads, based on snctools
old_dir=pwd;
if isfield(header,'DIR')
cd(header.DIR)
end % if
% Reading the header, conforming to GrADS conventions:
ncheader=nc_info(file_name);
header.FILENAME=ncheader.Filename;
header.DATANAME=ncheader.Filename;
header.NVAR=length(ncheader.DataSet);
fields={{'lon','longitude','x','i'},'XDEF';
{'lat','latitude','y','j'},'YDEF';
{'lev','plev','nv','bnds'},'ZDEF';
{'time','tps','t','l'},'TDEF'};
for idim=1:size(fields,1)
for dim=fields{idim,1}
dim_id=strmatch(dim{1},{ncheader.DataSet.Name},'exact');
if ~isempty(dim_id), break, end
end % for
if isempty(dim_id)
disp(['Dim ',fields{idim,2},' is missing.'])
vec=1;
num=1;
type='LINEAR';
else
num=ncheader.DataSet(dim_id).Size;
vec=nc_varget(file_name,dim{1});
if length(unique(diff(vec)))==1
type='LINEAR';
else
type='LEVELS';
end
if all(diff(vec)<0)
rev=1;
vec=flipud(reshape(vec,[],1));
elseif all(diff(vec)>0)
rev=0;
else
error(['Unsuitable vector ',dim{1}])
end
end % if
DEF=struct('num',num,'vec',vec,'type',type,'rev',rev);
header=setfield(header,fields{idim,2},DEF);
end % for idim
for ivar=1:header.NVAR
header.VARS(ivar).id=ivar;
header.VARS(ivar).name=ncheader.DataSet(ivar).Name;
header.VARS(ivar).size=ones(1,4);
for idim=1:length(ncheader.DataSet(ivar).Dimension)
[dim_id,j]=ind2sub(size(cat(1,fields{:,1})),...
strmatch(ncheader.DataSet(ivar).Dimension(idim),...
cat(1,fields{:,1}),'exact'));
header.VARS(ivar).size(dim_id)=...
getfield(eval(['header.',fields{dim_id,2}]),'num');
end % for
header.VARS(ivar).levs=header.VARS(ivar).size(3);
end % for
header.VARSIZE={cat(1,header.VARS.size)};
if nargin==1 | isempty(var_name) | strcmp(var_name,'all')
data=[];
if exist('old_dir','var')
cd(old_dir)
end
return
end
var_id=strmatch(var_name,{ncheader.DataSet.Name});
if isempty(var_id)
error(['Variable ',var_name,' is not available in ',file_name,...
': ',{ncheader.DataSet.Name}])
end % if
for n=1:2:nargin-2
switch lower(varargin{n})
case {'x'}
x_limits=varargin{n+1};
case {'lon'}
lon_limits=sort(varargin{n+1});
x_limits=interp1(header.XDEF.vec,1:header.XDEF.num,...
lon_limits,'nearest',NaN);
if any(isnan(x_limits))
if ~l_quiet
disp(['The X-limits ',num2str(lon_limits),...
' exceed the data coverage ',...
num2str(header.XDEF.vec([1 end])')])
end
data=[];
return
end
case {'y'}
y_limits=varargin{n+1};
case {'lat'}
lat_limits=sort(varargin{n+1});
y_limits=interp1(header.YDEF.vec,1:header.YDEF.num,...
lat_limits,'nearest',NaN);
if any(isnan(y_limits))
if ~l_quiet
disp(['The Y-limits ',num2str(lat_limits),...
' exceed the data coverage ',...
num2str(header.YDEF.vec([1 end])')])
end
data=[];
return
end
if header.YDEF.rev,
y_limits=header.YDEF.num*ones(size(y_limits))-fliplr(y_limits)+1;
end
case {'t','l','time'}
t_limits=varargin{n+1};
case {'z','k','lev'}
z_limits=varargin{n+1};
ivar=strmatch(var_name,{header.VARS.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
if any(z_limits>header.VARS(ivar).levs)
if ~l_quiet
disp(['The variable ',var_name,' has only ',...
header.VARS(ivar).levs,' levels.'])
end
data=[];
return
end
end % switch
end % for
if ~exist('t_limits','var'), t_limits=[1 header.TDEF.num]; end
if ~exist('z_limits','var')
ivar=strmatch(var_name,{header.VARS.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
z_limits=[1 header.VARS(ivar).levs];
end % if
if ~exist('y_limits','var')
y_limits=[1 header.YDEF.num];
end
if ~exist('x_limits','var')
x_limits=[1 header.XDEF.num];
end
% data=read_var(header,var_name,t_limits,z_limits,y_limits,x_limits);
% Retrieve the corresponding variable:
if all(header.VARS(var_id).size([3 4])==[1 1])
data=nc_varget(file_name,var_name,...
[y_limits(1),x_limits(1)]-1,...
diff(cat(1,y_limits,x_limits),1,2)'+1);
elseif header.VARS(var_id).size(3)==1
data=nc_varget(file_name,var_name,...
[t_limits(1),y_limits(1),x_limits(1)]-1,...
diff(cat(1,t_limits,y_limits,x_limits),1,2)'+1);
elseif header.VARS(var_id).size(4)==1
data=nc_varget(file_name,var_name,...
[z_limits(1),y_limits(1),x_limits(1)]-1,...
diff(cat(1,z_limits,y_limits,x_limits),1,2)'+1);
else
data=nc_varget(file_name,var_name,...
[t_limits(1),z_limits(1),y_limits(1),x_limits(1)]-1,...
diff(cat(1,t_limits,z_limits,y_limits,x_limits),1,2)'+1);
end
header.XDEF.vec=header.XDEF.vec(x_limits(1):x_limits(2));
header.XDEF.num=length(header.XDEF.vec);
if header.YDEF.rev,
y_limits=header.YDEF.num*ones(size(y_limits))-fliplr(y_limits)+1;
end
if diff(y_limits)<0, error('Unsuitable Y limits'), end
header.YDEF.vec=header.YDEF.vec(y_limits(1):y_limits(2));
header.YDEF.num=length(header.YDEF.vec);
header.ZDEF.vec=z_limits(1):z_limits(2);
header.ZDEF.num=diff(z_limits)+1;
header.TDEF.vec=t_limits(1):t_limits(2);
header.TDEF.num=diff(t_limits)+1;
if length(size(data))==2
data=permute(data,[2 1]);
elseif length(size(data))==3 & header.ZDEF.num==1
data=permute(data,[3 2 4 1]);
elseif length(size(data))==3 & header.TDEF.num==1
data=permute(data,[3 2 1]);
elseif length(size(data))==4
data=permute(data,[4 3 2 1]);
end % if
if header.YDEF.rev
data=flipdim(data,2);
end
if exist('old_dir','var')
cd(old_dir)
end
else
disp(['Suffix .',suf,' is not yet enabled.'])
end % if
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
function header=read_header(entry,words)
% sets the header values according to what was read in the .ctl-file.
% cf. GrADS documentation : http://grads.iges.org/grads/gadoc/descriptorfile.html
global l_quiet
header=evalin('caller','header');
fid_ctl=header.FID{1};
grid_fields={'num','type','vec','rev'};
switch upper(entry)
case 'DSET' % Name of the bin. data file.
param=deal(words{1});
if param(1)=='^' & isfield(header,'DIR')
param(1)=[];
param=[header.DIR,param];
elseif param(1)=='^'
param(1)=[];
end
if exist(param,'file')
header.DATANAME=param;
else
error(['Non-existent file ',param])
end
%
case 'DTYPE' % Gridded or station data-file (not used later)
param=lower(words{1});
switch param
case 'grib'
header.DTYPE=1;
case 'station'
header.DTYPE=0;
end
%
case 'STNMAP' % Name of the map file for station data (set in INDEX)
if header.DTYPE
warning([header.FILENAME,' cannot specify STNMAP=',param,' for a gridded data set.'])
end
param=deal(words{1});
if param(1)=='^'
param(1)=[];
end
if exist(param,'file')
header.INDEX=param;
else
error(['Non-existent file ',param])
end
%
case 'INDEX' % Name of the GRIB map file (not used later)
[header.INDEX]=strcat(words{:});
%
case 'TITLE' % Data title (not used later)
line={words{:}};
space=cell(size(line));
[space{:}]=deal(char(32));
line=cat(1,line,space);
line=reshape(line,1,prod(size(line))); % Rearranging the title to keep spaces between words.
header.TITLE=deblank(cat(2,line{:}));
%
case 'UNDEF' % Missing or undefined data value
param=words{1};
if isreal(str2num(param))
header(1).UNDEF=str2num(param);
else
error(['Wrong missing value format : ',param])
end
%
case 'OPTIONS' % Possible options (not all implemented...)
for param=words
param=param{1};
if ~ischar(param), error(['Wrong option format : ',param]), end
switch lower(param)
case 'big_endian'
header.BINTYPE='ieee-be';
case 'cray_32bit_ieee'
header.BINTYPE='cray';
case 'little_endian'
header.BINTYPE='ieee-le';
case 'binprecision'
% Strange syntax to eliminate digits in BINPRECISION
param=words{2}(find(isnan(str2double(cellstr(upper(words{2})')))));
if any(strmatch(param,...
{'uchar','schar','int','uint','float','single','double',...
'real*','integer*','bit','ubit','char','short','ushort', ...
'long','ulong'}))
header.BINPRECISION=words{2};
end
case 'xrev'
header.XDEF.rev=1;
case 'yrev'
header.YDEF.rev=1;
case 'zrev'
header.ZDEF.rev=1;
case 'sequential'
% Structure of the binary file: ([4 bit][XYHEADER bit][XDEF.num
% x YDEF.num x BINPRECISION bit][4 bit]) x NVAR
header.SEQ=1;
otherwise
fprintf('Option %s not yet supported.\n',param);
end
end % for param=words
%
% $$$ Matlab C/Fortran Description
% $$$ 'uchar' 'unsigned char' unsigned character, 8 bits.
% $$$ 'schar' 'signed char' signed character, 8 bits.
% $$$ 'int8' 'integer*1' integer, 8 bits.
% $$$ 'int16' 'integer*2' integer, 16 bits.
% $$$ 'int32' 'integer*4' integer, 32 bits.
% $$$ 'int64' 'integer*8' integer, 64 bits.
% $$$ 'uint8' 'integer*1' unsigned integer, 8 bits.
% $$$ 'uint16' 'integer*2' unsigned integer, 16 bits.
% $$$ 'uint32' 'integer*4' unsigned integer, 32 bits.
% $$$ 'uint64' 'integer*8' unsigned integer, 64 bits.
% $$$ 'single' 'real*4' floating point, 32 bits.
% $$$ 'float32' 'real*4' floating point, 32 bits.
% $$$ 'double' 'real*8' floating point, 64 bits.
% $$$ 'float64' 'real*8' floating point, 64 bits.
case 'XDEF' % Description of the X-axis (longitude usually)
% Checking the number of x-grid coordinates:
if isreal(str2num(words{1}))
words{1}=str2num(words{1});
elseif str2num(words{1})>1
else
error(['Wrong number of x-grid arguments : ', ...
num2str(words{1})])
end
switch upper(words{2})
case 'LINEAR'
vec(1)=str2num(words{3});
vec(2)=str2num(words{4});
vec2=vec(1) + vec(2) * [0:(words{1}-1)];
words{3}=vec2; % KS, 24.11.2003: coord vector in all cases.
case 'LEVELS'
% $$$ try % all on the same line
% $$$ for i=1:words{1}
% $$$ vec(i)=str2num(words{i+2});
% $$$ end
% $$$ words{3}=vec;
% $$$ catch % all levels written column-wise
% $$$ for i=1:words{1}
% $$$ % vec(i)=fscanf(fid_ctl,'%i',1);
% $$$ vec(i)=str2num(fgetl(fid_ctl));
% $$$ end
% $$$ words{3}=vec;
% $$$ end
% vec=str2num([words{3:end}]');
% vec=str2num(cell2mat({words{3:end}}'))';
vec=str2num(strvcat(words{3:end}));
while length(vec) < words{1}
point=ftell(fid_ctl);
read_line=str2num(fgetl(fid_ctl));
if isempty(read_line)
fseek(fid_ctl,point,'bof');
break
else
vec=cat(2,vec,read_line);
end
end
if length(vec)==words{1}
words{3}=vec;
else
error(['Unsuitable number of X-levels : ',num2str(length(vec))])
end
otherwise
error(['Unsuitable x-mapping method : ',words{2}])
end
% if header(1).XDEF.rev, words{3}=fliplr(words{3}); end
[header(1).XDEF]=cell2struct({words{1},words{2},words{3},header(1).XDEF.rev},grid_fields,2);
%
case 'YDEF' % Description of the Y-axis (latitude usually)
% Checking the number of y-grid coordinates:
if isreal(str2num(words{1}))
words{1}=str2num(words{1});
elseif str2num(words{1})>1
else
error(['Wrong number of y-grid arguments : ', ...
num2str(words{1})])
end
switch upper(words{2})
case 'LINEAR'
vec(1)=str2num(words{3});
vec(2)=str2num(words{4});
vec2=vec(1) + vec(2) * [0:(words{1}-1)];
words{3}=vec2;
case 'LEVELS'
% $$$ try % all on the same line
% $$$ for i=1:words{1}
% $$$ vec(i)=str2num(words{i+2});
% $$$ end
% $$$ words{3}=vec;
% $$$ catch % all levels written column-wise
% $$$ for i=1:words{1}
% $$$ % vec(i)=fscanf(fid_ctl,'%i',1);
% $$$ vec(i)=str2num(fgetl(fid_ctl));
% $$$ end
% $$$ words{3}=vec;
% $$$ end
% vec=str2num([words{3:end}]');
% vec=str2num(cell2mat({words{3:end}}'))';
vec=str2num(strvcat(words{3:end}));
while length(vec) < words{1}
point=ftell(fid_ctl);
read_line=str2num(fgetl(fid_ctl));
if isempty(read_line)
fseek(fid_ctl,point,'bof');
break
else
vec=cat(2,vec,read_line);
end
end
if length(vec)==words{1}
words{3}=vec;
else
error(['Unsuitable number of Y-levels : ',num2str(length(vec))])
end
otherwise
error(['Unsuitable y-mapping method : ',words{2}])
end
% if header.YDEF.rev, words{3}=fliplr(words{3}); end
[header(1).YDEF]=cell2struct({words{1},words{2},words{3},header(1).YDEF.rev},grid_fields,2);
%
case 'ZDEF' % Description of the Z-axis
% Checking the number of z-grid coordinates:
if isreal(str2num(words{1}))
words{1}=str2num(words{1});
elseif str2num(words{1})>1
else
error(['Wrong number of z-grid arguments : ', ...
num2str(words{1})])
end
switch upper(words{2})
case 'LINEAR'
vec(1)=str2num(words{3});
vec(2)=str2num(words{4});
vec2=vec(1) + vec(2) * [0:(words{1}-1)];
words{3}=vec2;
case 'LEVELS'
% $$$ try % all on the same line
% $$$ for i=1:str2num(words{1})
% $$$ vec(i)=str2num(words{i+2});
% $$$ end
% $$$ words{3}=vec;
% $$$ catch % all levels written column-wise
% $$$ for i=1:words{1}
% $$$ % vec(i)=fscanf(fid_ctl,'%i',1);
% $$$ vec(i)=str2num(fgetl(fid_ctl));
% $$$ end
% $$$ words{3}=vec;
% $$$ end
% vec=str2num([words{3:end}]');
% vec=str2num(cell2mat({words{3:end}}'))';
vec=str2num(strvcat(words{3:end}));
while length(vec) < words{1}
point=ftell(fid_ctl);
read_line=str2num(fgetl(fid_ctl));
if isempty(read_line)
fseek(fid_ctl,point,'bof');
break
else
vec=cat(2,vec,read_line);
end
end
if length(vec)==words{1}
words{3}=vec;
else
error(['Unsuitable number of Z-levels : ',num2str(length(vec))])
end
otherwise
error(['Unsuitable z-mapping method : ',words{2}])
end
% if header.ZDEF.rev, words{3}=fliplr(words{3}); end
[header(1).ZDEF]=cell2struct({words{1},words{2},words{3},header(1).ZDEF.rev},grid_fields,2);
%
case 'TDEF' % Description of the T-axis
% Checking the number of t-grid coordinates:
if isreal(str2num(words{1}))
words{1}=str2num(words{1});
elseif str2num(words{1})>1
else
error(['Wrong number of t-scale argument : ', ...
num2str(words{1})])
end
if any(upper(words{2})~='LINEAR')
error(['Unsuitable t-mapping method : ',words{2}])
end
param=words{3};
if (param(3)~=':' | param(6)~='Z' | ...
~isreal(str2num(param([1:2 4:5 7:8 12:length(param)]))))
error(['Unsuitable date format : ',param])
else
vec(1)=str2num(param(1:2)); % hour
vec(2)=str2num(param(4:5)); % min
vec(3)=str2num(param(7:8)); % day
switch lower(param(9:11)) % month
case 'jan'
vec(4)=1;
case 'feb'
vec(4)=2;
case 'mar'
vec(4)=3;
case 'apr'
vec(4)=4;
case 'may'
vec(4)=5;
case 'jun'
vec(4)=6;
case 'jul'
vec(4)=7;
case 'aug'
vec(4)=8;
case 'sep'
vec(4)=9;
case 'oct'
vec(4)=10;
case 'nov'
vec(4)=11;
case 'dec'
vec(4)=12;
otherwise
error(['Wrong month format : ',param(9:11)])
end
vec(5)=str2num(param(12:length(param))); % year
if vec(5)<10
vec(5)=vec(5)+2000;
elseif vec(5)<100
vec(5)=vec(5)+1900;
end
% The time-axis is written in the matlab-time format
% (cf. datestr, datevec...):
init_time=datenum(vec(5),vec(4),vec(3),vec(1),vec(2),0);
param=words{4};
if isreal(str2num(param(1:end-2)))
time_increment=str2num(param(1:end-2));
param(1:end-2)=[];
else
error(['Wrong time increment argument : ',param])
end
switch lower(param)
case 'mn'
time_increment=time_increment*datenum(0,0,0,0,1,0);
case 'hr'
time_increment=time_increment*datenum(0,0,0,1,0,0);
case 'dy' % NB: datenum(0,0,1,0,0,0) = 1.
time_increment=time_increment;
case 'mo' % standardised month
time_increment=time_increment*365.25/12;
case 'yr' % standardised year
time_increment=time_increment*365.25;
otherwise
error(['Wrong time increment argument : ',param])
end
% Writing the final time axis:
clear vec
vec(1)=init_time;
vec(2)=time_increment;
[header(1).TDEF]=cell2struct({words{1},words{2},vec,0},grid_fields,2);
end
%
case 'VARS' % Number and size of variables
if isreal(str2num(words{1}))
n_var = str2num(words{1});
else
error(['Wrong variable number argument : ',words{1}])
end
% Reading the variables :
var_format={'id','name','levs','units','descr'};
varl={};
for i=1:n_var
line_var=fgetl(fid_ctl);
n_blank=length(line_var);
line_var=strrep(line_var,' ',' ');
while length(line_var) < n_blank
n_blank=length(line_var);
line_var=strrep(line_var,' ',' ');
end
while isspace(line_var(1)), line_var(1)=[]; end
var_loc={i,'',NaN,'',''};
var_hole=min(find(isspace(line_var)));
var_loc{2}=line_var(1:(var_hole-1));
line_var(1:var_hole)=[];
var_hole=min(find(isspace(line_var)));
var_loc{3}=str2num(line_var(1:(var_hole-1)));
% cf GrADS doc: If levs is 0, the variable does not correspond
% to any vertical level
var_loc{3}=max([var_loc{3},1]);
line_var(1:var_hole)=[];
var_hole=min(find(isspace(line_var)));
var_loc{4}=line_var(1:(var_hole-1));
line_var(1:var_hole)=[];
var_loc{5}=line_var;
varl=cat(1,varl,var_loc);
end
vars=cell2struct(varl,var_format,2);
if ~l_quiet
disp(['Is it the end ? ',fgets(fid_ctl)]);
else
endvars=deblank(fgets(fid_ctl));
if ~strcmpi((endvars),'ENDVARS')
error(['Wrong end of file : ',endvars])
end
end
header(1).VARS=vars;
assignin('caller','vars',vars);
%
case 'FILEHEADER' % n-byte header of binary data, not to be read
[header.FILEHEADER]=str2num(words{1});
%
case 'THEADER' % n-byte header for each T-block, not to be read
[header.THEADER]=str2num(words{1});
%
case 'XYHEADER' % n-byte header for each XY-block, not to be read
[header.XYHEADER]=str2num(words{1});
%
otherwise
error(['Unknown entry : ',entry])
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
function data=read_data(header,var_name)
% data=read_data(header,var_name) is a function, usually called by
% read_grads.m to use the information contained in the header file
% (.ctl) for reading a binary GrADS file.
% If var_name is 'all', all variables are read and sent to the base-
% workspace.
% Kristof Sturm, 29.10.02
global l_quiet
vars=header.VARS;
nvar=header.NVAR;
var_size=header.VARSIZE{:};
if nargin == 1 | strcmp(lower(var_name),'all') % All variables loaded into workspace
data_list={};
% initialising the data matrices :
var_count=zeros(nvar,1);
for ivar=1:nvar
eval([vars(ivar).name,'=NaN*ones(',int2str(header.XDEF.num),',',...
int2str(header.YDEF.num),',',...
int2str(vars(ivar).levs),',',...
int2str(header.TDEF.num),');']);
fprintf('Size of %s : [%s].\n %s[X Y Z T]\n',...
vars(ivar).name,int2str(size(eval(vars(ivar).name))),...
char(32*ones(1,length(vars(ivar).name))));
end
method = 'loop'; % mainly for debugging...
switch method
case 'loop'
frewind(header.FID{2});
% Implementing the sequential option:
if isfield(header,'SEQ') && header.SEQ
fseek(header.FID{2},4,'bof');
end
if header.FILEHEADER
fseek(header.FID{2},header.FILEHEADER,'bof');
% $$$ if isfield(header,'SEQ') && header.SEQ
% $$$ fseek(header.FID{2},8,'cof');
% $$$ end
end
for l=1:header.TDEF.num
if header.THEADER
fseek(header.FID{2},header.THEADER,'cof');
% $$$ if isfield(header,'SEQ') && header.SEQ
% $$$ fseek(header.FID{2},8,'cof');
% $$$ end
end
for ivar=1:nvar
data=eval(vars(ivar).name);
count0=var_count(ivar);
for k=1:vars(ivar).levs
if header.XYHEADER
fseek(header.FID{2},header.XYHEADER,'cof');
end
[data(:,:,k,l) count1]=fread(header.FID{2},[header.XDEF.num header.YDEF.num],header.BINPRECISION);
count0=count0+count1;
if isfield(header,'SEQ') && header.SEQ
fseek(header.FID{2},8,'cof');
end
end % end k-loop
data(data==header.UNDEF)=NaN; % replacing the
% missing/undefined values
% by NaN (not-a-number)
% data(data==header.UNDEF)=0; % replacing the
% missing/undefined values by
% NaN (not-a-number)
% data=sparse(data);
eval([vars(ivar).name,'=data;']);
var_count(ivar)=var_count(ivar)+count0;
% bytes(ivar)=ftell(header.FID{2});
clear data
end % end ivar-loop
end % end l-loop
% Send the relevent variables into the base workspace:
% assignin('base','var_count',var_count);
% assignin('base','bytes',bytes);
for ivar=1:nvar
data=eval(vars(ivar).name);
if header.XDEF.rev, data=flipdim(data,1); end
if header.YDEF.rev, data=flipdim(data,2); end
if header.ZDEF.rev, data=flipdim(data,3); end
assignin('base',vars(ivar).name,data);
end
% % end 'loop'
otherwise
for ivar=1:nvar
data=read_var(header,vars(ivar).name);
assignin('base',vars(ivar).name,data);
data_list=cat(1,data_list,{data});
end
data=[];
assignin('caller','data_list',data_list);
end
else % Individual var. reading
switch var_name
case {vars.name}
fprintf('Variable %s extracted from %s. \n',var_name, ...
header.DATANAME);
data=read_var(header,var_name);
otherwise
error(['Variable ',var_name,' not available in ', ...
header.DATANAME]);
end
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
function data=read_var(header,ivar,t_limits,z_limits,y_limits,x_limits)
% data=read_varseq(header,ivar) reads in 'ivar' from
% 'header.DATANAME' and return it as a 4-D matlab matrix.
% 'ivar' can be the variable''s short name or its number id.
global l_quiet
vars=header.VARS;
nvar=header.NVAR;
var_size=header.VARSIZE{:};
% different behaviour of the f* functions according to the chosen data precision :
switch lower(header.BINPRECISION)
case {'uchar','schar','int8','uint8'}
byte_length=1;
case {'int16','uint16'}
byte_length=2;
case {'float32','single','int32','uint32'}
byte_length=4;
case {'float64','double','int64','uint64'}
byte_length=8;
otherwise
byte_length=1;
end
if isempty(ivar)
if ~l_quiet
disp(['Header for ',header.FILENAME,' read.'])
end
data=[];
return
end
if ischar(ivar)
var_name=ivar;
ivar=strmatch(ivar,{vars.name},'exact');
if isempty(ivar)
if ~l_quiet
disp(['The variable ',var_name,' cannot be found in ',header.DATANAME])
end
data=[];
return
end
clear var_name
end
if ivar==1
byte_ini=0;
else
byte_ini = sum(prod(var_size(1:(ivar-1),1:3),2),1) ;
end
if isfield(header,'SEQ') && header.SEQ
byte_ini=byte_ini+(sum(var_size(1:ivar-1,3))*8+4)/byte_length;
end
if header.FILEHEADER
byte_ini = byte_ini + header.FILEHEADER/byte_length;
% $$$ if isfield(header,'SEQ') && header.SEQ
% $$$ byte_ini=byte_ini+8/byte_length;
% $$$ end
end
if header.THEADER
byte_ini = byte_ini + header.THEADER/byte_length;
% $$$ if isfield(header,'SEQ') && header.SEQ
% $$$ byte_ini=byte_ini+8/byte_length;
% $$$ end
end
if header.XYHEADER
byte_ini=byte_ini+(sum(var_size(1:ivar-1,3))+1)*header.XYHEADER/byte_length;
% $$$ if isfield(header,'SEQ') && header.SEQ
% $$$ byte_ini=byte_ini+(sum(var_size(1:ivar-1,3))+1)*8/byte_length;
% $$$ end
end
block_length = sum(prod(var_size(:,1:3),2),1);
if isfield(header,'SEQ') && header.SEQ
block_length=block_length+sum(var_size(:,3))*8/byte_length;
end
if header.XYHEADER
block_length=block_length+sum(var_size(:,3))*header.XYHEADER/byte_length;
end
if header.THEADER
block_length=block_length+header.THEADER/byte_length;
end
slice_length = header.XDEF.num*header.YDEF.num+header.XYHEADER/byte_length;
if isfield(header,'SEQ') && header.SEQ
slice_length = slice_length + 8/byte_length ;
end
var_length = prod([header.XDEF.num header.YDEF.num diff(z_limits)+1]);
if header.XYHEADER
var_length = var_length + (diff(z_limits)+1)*header.XYHEADER/byte_length;
end
if isfield(header,'SEQ') && header.SEQ
var_length=var_length+(diff(z_limits)+1)*8/byte_length;
end
% disp(byte_ini)
% Selecting the starting time slice :
byte_ini=byte_ini + (t_limits(1)-1)*block_length + (z_limits(1)-1)*slice_length ;
err_stat = fseek(header.FID{2},byte_ini*byte_length,'bof');
if err_stat == -1, ferror(header.FID{2}), end
% data=NaN(diff(x_limits)+1,diff(y_limits)+1,diff(z_limits)+1,diff(t_limits)+1);
data=NaN*ones(diff(x_limits)+1,diff(y_limits)+1,diff(z_limits)+1,diff(t_limits)+1);
% size(data)
count_byte = 0;
count_byte2 = 0;
for l=1:(t_limits(2)-t_limits(1)+1)
file_ind = ftell(header.FID{2});
for k=1:(z_limits(2)-z_limits(1)+1)
if all([x_limits y_limits]==[1 header.XDEF.num 1 header.YDEF.num])
try
[data(:,:,k,l),n]=fread(header.FID{2},[header.XDEF.num header.YDEF.num],header.BINPRECISION);
count_byte=count_byte+n;
catch
warning(['Data read-in interrupted at l=',int2str(l),' and k=',int2str(k)])
break
end
else
% Advance to the j-th row:
fseek(header.FID{2},(y_limits(1)-1)*header.XDEF.num*byte_length,'cof');
for j=1:(diff(y_limits)+1)
fseek(header.FID{2},(x_limits(1)-1)*byte_length,'cof');
[data(:,j,k,l),n]=fread(header.FID{2},diff(x_limits)+1,header.BINPRECISION);
fseek(header.FID{2},(header.XDEF.num-x_limits(2))*byte_length,'cof');
end
fseek(header.FID{2},(header.YDEF.num-y_limits(2))*header.XDEF.num*byte_length,'cof');
end
if isfield(header,'SEQ') && header.SEQ
fseek(header.FID{2},8,'cof');
end
if header.XYHEADER
fseek(header.FID{2},header.XYHEADER,'cof');
end
end
count_byte2=count_byte2+ftell(header.FID{2})-file_ind;
if l < header.TDEF.num
err_stat=fseek(header.FID{2},(block_length-var_length)*byte_length,'cof');
if err_stat == -1, ferror(header.FID{2}), end
end
end
% disp([byte_ini block_length slice_length var_length file_ind/byte_length ftell(header.FID{2})/byte_length])
data(find(data==header.UNDEF))=NaN; % replacing the missing/undefined values by NaN (not-a-number)
if header.XDEF.rev, data=flipdim(data,1); end
if header.YDEF.rev, data=flipdim(data,2); end
if header.ZDEF.rev, data=flipdim(data,3); end
%if count_byte ~= count_byte2/byte_length
% warning(['Number of elements read : ',num2str(count_byte),...
% ' .NEQ. number of bytes advanced in ',header.DATANAME,': ',num2str(count_byte2/byte_length)])
%end
%fprintf('%i bytes were read in %s .\n size(%s) = [%s], i.e. %i elements.\n',...
% count_byte2,header.DATANAME,vars(ivar).name,int2str(size(data)),count_byte);
% count_byte2,header.DATANAME,vars(ivar).name,int2str(size(data)),prod(size(data)));
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
function data=read_station(header)
% This function uses the information read from the GrADS .ctl file
% to read STATION data into the matlab workspace.
% No reference to the .map file is currently made.
% cf. http://grads.iges.org/grads/gradoc/aboutstationdata.html
% Kristof Sturm, 30.X.02
global l_quiet
fid_bin = header.FID{2};
fseek(fid_bin,0,'eof');
eof=ftell(fid_bin);
frewind(fid_bin);
file_end=0;
istat=1;
data_format={'id','name','lat','lon','var'};
data_tot={};
% Reading the header :
while 1
data_loc={0,'',0,0,[]};
boh=ftell(fid_bin);
stid=fscanf(fid_bin,'%8c',1);
lat=fread(fid_bin,1,'float32');
lon=fread(fid_bin,1,'float32');
tim=fread(fid_bin,1,'float32');
nlev=fread(fid_bin,1,'int32');
nflag=fread(fid_bin,1,'int32');
eoh=ftell(fid_bin);
length_h=eoh-boh;
var=NaN(header.NVAR,header.TDEF.num);
% Reading all variables, skipping the headers :
for t=1:header.TDEF.num
var(:,t)=fread(fid_bin,header.NVAR,'float32');
if ftell(fid_bin) < (eof-2*length_h)
file_err=fseek(fid_bin,2*length_h,'cof');
if file_err==-1, ferror(fid_bin), end
else
fprintf('EOF reached for %s.\n\n',header.DATANAME);
file_end=1;
break
end
var(find(var==header.UNDEF))=NaN;
end
if file_end, break, end
% Rewinding for reading the first of the next headers :
file_err=fseek(fid_bin,-length_h,'cof');
if file_err==-1, ferror(fid_bin), end
% saving all relevant informations into the local cell :
[data_loc]={istat,deblank(lower(stid)),lat,lon,var};
data_tot=cat(1,data_tot,data_loc);
istat=istat+1;
end
data=cell2struct(data_tot,data_format,2);
return
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