/[MITgcm]/MITgcm_contrib/gael/matlab_class/gcmfaces_IO/process2nctiles.m
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revision 1.2 by gforget, Sat Feb 1 18:19:26 2014 UTC revision 1.9 by gforget, Sun Aug 3 19:49:58 2014 UTC
# Line 1  Line 1 
1  function []=process2nctiles(dirModel,fileModel,fldModel);  function []=process2nctiles(dirModel,fileModel,fldModel,tileSize);
2  %process2nctiles(dirModel);  %process2nctiles(dirModel);
3  %object : convert MITgcm binary output to netcdf files (tiled)  %object : convert MITgcm binary output to netcdf files (tiled)
4  %inputs : dirModel is the MITgcm run directory  %inputs : dirModel is the MITgcm run directory
# Line 9  function []=process2nctiles(dirModel,fil Line 9  function []=process2nctiles(dirModel,fil
9  %           By default : all variables in e.g. 'state_2d_set1*'  %           By default : all variables in e.g. 'state_2d_set1*'
10  %           files will be processed, and writen individually to  %           files will be processed, and writen individually to
11  %           nctiles (tiled netcdf) that will be located in 'nctiles/'  %           nctiles (tiled netcdf) that will be located in 'nctiles/'
12  %         fldModel (optional) can be specifiec as e.g. 'ETAN'  %         fldModel (by default []) can be specified (as e.g. 'ETAN')
13    %            when fldModel is empty, all fields are processed
14    %         tileSize (optional) is e.g. [90 90] (by default tiles=faces)
15  %output : (netcdf files)  %output : (netcdf files)
16    
17  gcmfaces_global;  gcmfaces_global;
18    
19    %listFiles={'state_2d_set1','state_2d_set2','state_3d_set1','state_3d_set2'};
20    %listFiles={'trsp_3d_set1','trsp_3d_set2','trsp_3d_set3'};
21    %for ff=1:length(listFiles); process2nctiles('iter12/',listFiles{ff},[],[90 90]); end;
22    
23    %replace time series with monthly climatology?
24    doClim=0;
25    
26  %directory names  %directory names
27  listDirs={'STATE/','TRSP/'};  listDirs={'STATE/','TRSP/'};
28  filAvailDiag=[dirModel 'available_diagnostics.log'];  filAvailDiag=[dirModel 'available_diagnostics.log'];
29  filReadme=[dirModel 'README'];  filReadme=[dirModel 'README'];
30  dirOut=[dirModel 'nctiles/'];  dirOut=[dirModel 'nctiles_tmp/'];
31  if ~isdir(dirOut); mkdir(dirOut); end;  if ~isdir(dirOut); mkdir(dirOut); end;
32    
33  %seacrh in subdirectories  %search in subdirectories
34  subDir=[];  subDir=[];
35  for ff=1:length(listDirs);  for ff=1:length(listDirs);
36  tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);  tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);
# Line 37  else; Line 46  else;
46  end;  end;
47    
48  %set list of variables to process  %set list of variables to process
49  if ~isempty(who('fldModel'));  if ~isempty(fldModel);
50     if ischar(fldModel); listFlds={fldModel};     if ischar(fldModel); listFlds={fldModel};
51     else; listFlds=fldModel;     else; listFlds=fldModel;
52     end;     end;
# Line 46  else; Line 55  else;
55     listFlds=meta.fldList;     listFlds=meta.fldList;
56  end;  end;
57    
58    %determine map of tile indices (by default tiles=faces)
59    if isempty(whos('tileSize'));
60      tileNo=mygrid.XC;
61      for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
62    else;
63      tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2));
64    end;
65    
66  %now do the actual processing  %now do the actual processing
67  for vv=1:length(listFlds);  for vv=1:length(listFlds);
68  nameDiag=deblank(listFlds{vv})  nameDiag=deblank(listFlds{vv})
# Line 58  if length(irec)~=1; error('field not in Line 75  if length(irec)~=1; error('field not in
75  %read time series  %read time series
76  myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);  myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);
77    
78  %ancilliary fields for netcdf file  %replace time series with monthly climatology
79  tim=[1:size(myDiag{1},3)];  if doClim; myDiag=compClim(myDiag); end;
80  descr=nameDiag;  
81    %set ancilliary time variable
82    nn=length(size(myDiag{1}));
83    nn=size(myDiag{1},nn);
84    %tim=[1:nn];
85    tim=[1992*ones(nn,1) [1:nn]' 15*ones(nn,1)];
86    tim=datenum(tim)-datenum([1992 1 0]);
87    timUnits='days since 1992-1-1 0:0:0';
88    
89    %get time step axis
90    [listTimes]=diags_list_times({[dirModel 'diags/STATE/']},{'state_2d_set1'});
91    
92  %get units and long name from available_diagnostics.log  %get units and long name from available_diagnostics.log
93  [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);  [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
# Line 70  descr=nameDiag; Line 97  descr=nameDiag;
97  disp(rdm');  disp(rdm');
98    
99  %convert to MITgcm format (90x1170 array)  %convert to MITgcm format (90x1170 array)
100  myFile=[dirOut nameDiag];  myFile=[dirOut nameDiag];%first instance is for subdirectory name
101    if ~isdir(myFile); mkdir(myFile); end;
102    myFile=[myFile '/' nameDiag];%second instance is for file name base
103    
104  %get grid params  %get grid params
105  [grid_diag]=set_grid_diag(avail_diag);  [grid_diag]=set_grid_diag(avail_diag);
106    
107    %apply mask, and convert to land mask
108    msk=grid_diag.msk;
109    if length(size(myDiag{1}))==3;
110      msk=repmat(msk,[1 1 size(myDiag{1},3)]);
111    end;
112    for kk=1:size(myDiag{1},4);
113      myDiag(:,:,:,kk)=myDiag(:,:,:,kk).*msk;
114    end;
115    clear msk;
116    %
117    land=isnan(grid_diag.msk);
118    
119    %set 'coord' attribute
120    if avail_diag.nr~=1;
121      coord='lon lat dep tim';
122    else;
123      coord='lon lat tim';
124    end;
125    
126    %replace time series with monthly climatology
127    if doClim;
128      listTimes=listTimes(1:12);
129      timUnits='days since year-1-1 0:0:0';
130      avail_diag.longNameDiag=[avail_diag.longNameDiag ' (climatology) '];
131    end;
132    
133  %create netcdf file using write2nctiles (works only with old matlab, thus far ...)  %create netcdf file using write2nctiles (works only with old matlab, thus far ...)
134  doCreate=1;  doCreate=1;
135  dimOut=write2nctiles(myFile,myDiag,doCreate,...  dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},...
136      {'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...      {'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
137      {'units',avail_diag.units},{'descr',descr},{'rdm',rdm});      {'units',avail_diag.units},{'descr',nameDiag},{'coord',coord},{'rdm',rdm});
   
 %prepare to add fields  
 doCreate=0;  
138    
139  %determine relevant dimensions (note the reverse order)  %determine relevant dimensions
140  for ff=1:mygrid.nFaces;  for ff=1:length(dimlist);
141    dimtim{ff}={dimOut{ff}{1}};    dim.tim{ff}={dimlist{ff}{1}};
142    dim2d{ff}={dimOut{ff}{end-1:end}};    dim.twoD{ff}={dimlist{ff}{end-1:end}};
143    if avail_diag.nr~=1;    if avail_diag.nr~=1;
144      dimmsk{ff}={dimOut{ff}{end-2:end}};      dim.threeD{ff}={dimlist{ff}{end-2:end}};
145      dimdep{ff}={dimOut{ff}{end-2}};      dim.dep{ff}={dimlist{ff}{end-2}};
146    else;    else;
147      dimmsk{ff}=dim2d{ff};      dim.threeD{ff}=dim.twoD{ff};
148      dimdep{ff}=[];      dim.dep{ff}=[];
149    end;    end;
150  end;  end;
151    
152    %prepare to add fields
153    doCreate=0;
154    
155  %now add fields  %now add fields
156  write2nctiles(myFile,tim,doCreate,{'fldName','month'},...  write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},...
157    {'longName','month index starting Jan. 1992'},...    {'fldName','tim'},{'longName','time'},...
158    {'units',''},{'dimIn',dimtim});    {'units',timUnits},{'dimIn',dim.tim});
159  write2nctiles(myFile,grid_diag.lon,doCreate,...  write2nctiles(myFile,listTimes,doCreate,{'tileNo',tileNo},...
160    {'fldName','longitude'},{'units',''},{'dimIn',dim2d});    {'fldName','step'},{'longName','final time step number'},...
161  write2nctiles(myFile,grid_diag.lat,doCreate,...    {'units','1'},{'dimIn',dim.tim});
162    {'fldName','latitude'},{'units',''},{'dimIn',dim2d});  write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
163  write2nctiles(myFile,grid_diag.msk,doCreate,...    {'fldName','lon'},{'units','degrees_east'},{'dimIn',dim.twoD});
164    {'fldName','landmask'},{'units',''},...  write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
165    {'longName','land mask'},{'dimIn',dimmsk});    {'fldName','lat'},{'units','degrees_north'},{'dimIn',dim.twoD});
166  write2nctiles(myFile,grid_diag.RAC,doCreate,...  write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
167    {'fldName','cellarea'},{'units','m^2'},...    {'fldName','land'},{'units','1'},{'longName','land mask'},{'dimIn',dim.threeD});
168    {'longName','grid cell area'},{'dimIn',dim2d});  write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
169      {'fldName','area'},{'units','m^2'},{'longName','grid cell area'},{'dimIn',dim.twoD});
170  if isfield(grid_diag,'dep');  if isfield(grid_diag,'dep');
171      write2nctiles(myFile,grid_diag.dep,doCreate,...      write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
172        {'fldName','depth'},{'units','m'},{'dimIn',dimdep});        {'fldName','dep'},{'units','m'},{'dimIn',dim.dep});
173      write2nctiles(myFile,grid_diag.dz,doCreate,...      write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
174        {'fldName','cellthick'},{'units','m'},{'dimIn',dimdep});        {'fldName','thic'},{'units','m'},{'dimIn',dim.dep});
175  end;  end;
176    
177  end;%for vv=1:length(listFlds);  end;%for vv=1:length(listFlds);
# Line 124  function [meta]=read_meta(fileName); Line 180  function [meta]=read_meta(fileName);
180    
181  %read meta file  %read meta file
182  tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;  tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
183  tmp2=strfind(fileName,'/');  tmp2=strfind(fileName,filesep);
184  if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;  if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
185  tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);  tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
186  while 1;  while 1;
# Line 235  if avail_diag.nr~=1; Line 291  if avail_diag.nr~=1;
291      grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);      grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
292      grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);      grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
293  end;  end;
294    
295    %%replace time series with monthly climatology
296    function [FLD]=compClim(fld);
297    
298    gcmfaces_global;
299    
300    ndim=length(size(fld{1}));
301    nyear=size(fld{1},ndim)/12;
302    
303    if ndim==3; FLD=NaN*fld(:,:,1:12); end;
304    if ndim==4; FLD=NaN*fld(:,:,:,1:12); end;
305    
306    for mm=1:12;
307    if ndim==3; FLD(:,:,mm)=mean(fld(:,:,mm:12:12*nyear),ndim); end;
308    if ndim==4; FLD(:,:,:,mm)=mean(fld(:,:,:,mm:12:12*nyear),ndim); end;
309    end;
310    
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