Index: /issm/trunk/src/m/utils/Miscellaneous/netcdf.m
===================================================================
--- /issm/trunk/src/m/utils/Miscellaneous/netcdf.m	(revision 3135)
+++ /issm/trunk/src/m/utils/Miscellaneous/netcdf.m	(revision 3135)
@@ -0,0 +1,136 @@
+function S = netcdf(File,varargin)
+% Function to read NetCDF files
+%   S = netcdf(File)
+% Input Arguments
+%   File = NetCDF file to read
+% Optional Input Arguments:
+%   'Var',Var - Read data for VarArray(Var), default [1:length(S.VarArray)]
+%   'Rec',Rec - Read data for Record(Rec), default [1:S.NumRecs]
+% Output Arguments:
+%   S    = Structure of NetCDF data organised as per NetCDF definition
+% Notes:
+%   Only version 1, classic 32bit, NetCDF files are supported. By default
+% data are extracted into the S.VarArray().Data field for all variables.
+% To read the header only call S = netcdf(File,'Var',[]);
+%
+% SEE ALSO
+% ---------------------------------------------------------------------------
+S = [];
+
+try
+   if exist(File,'file') fp = fopen(File,'r','b');
+   else fp = []; error('File not found'); end
+   if fp == -1   error('Unable to open file'); end
+
+% Read header
+   Magic = fread(fp,4,'uint8=>char');
+   if strcmp(Magic(1:3),'CDF') error('Not a NetCDF file'); end
+   if uint8(Magic(4))~=1       error('Version not supported'); end
+   S.NumRecs  = fread(fp,1,'uint32=>uint32');
+   S.DimArray = DimArray(fp);
+   S.AttArray = AttArray(fp);
+   S.VarArray = VarArray(fp);
+
+% Setup indexing to arrays and records
+   Var = ones(1,length(S.VarArray));
+   Rec = ones(1,S.NumRecs);
+   for i = 1:2:length(varargin)
+      if     strcmp(upper(varargin{i}),'VAR') Var=Var*0; Var(varargin{i+1})=1;
+      elseif strcmp(upper(varargin{i}),'REC') Rec=Rec*0; Rec(varargin{i+1})=1;
+      else error('Optional input argument not recognised'); end
+   end
+   if sum(Var)==0 fclose(fp); return; end
+
+% Read non-record variables
+   Dim = double(cat(2,S.DimArray.Dim));
+   ID  = double(cat(2,S.VarArray.Type));
+
+   for i = 1:length(S.VarArray)
+      D = Dim(S.VarArray(i).DimID+1); N = prod(D); RecID{i}=find(D==0);
+      if isempty(RecID{i})
+         if length(D)==0 D = [1,1]; N = 1; elseif length(D)==1 D=[D,1]; end
+         if Var(i)
+            S.VarArray(i).Data = ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D);
+            fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8');
+         else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
+      else S.VarArray(i).Data = []; end
+   end
+
+% Read record variables
+   for k = 1:S.NumRecs
+      for i = 1:length(S.VarArray)
+         if ~isempty(RecID{i})
+            D = Dim(S.VarArray(i).DimID+1); D(RecID{i}) = 1; N = prod(D);
+            if length(D)==1 D=[D,1]; end
+            if Var(i) & Rec(k)
+               S.VarArray(i).Data = cat(RecID{i},S.VarArray(i).Data,...
+                  ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D));
+               if N > 1 fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8'); end
+            else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
+         end
+      end
+   end
+
+   fclose(fp);
+catch
+   Err = lasterror; fprintf('%s\n',Err.message);
+   if ~isempty(fp) && fp ~= -1 fclose(fp); end
+end
+
+% ---------------------------------------------------------------------------------------
+% Utility functions
+
+function S = Size(ID)
+% Size of NetCDF data type, ID, in bytes
+   S = subsref([1,1,2,4,4,8],struct('type','()','subs',{{ID}}));
+
+function T = Type(ID)
+% Matlab string for CDF data type, ID
+   T = subsref({'int8','char','int16','int32','single','double'},...
+               struct('type','{}','subs',{{ID}}));
+
+function N = Pad(Num,ID)
+% Number of elements to read after padding to 4 bytes for type ID
+   N = (double(Num) + mod(4-double(Num)*Size(ID),4)/Size(ID)).*(Num~=0);
+
+function S = String(fp)
+% Read a CDF string; Size,[String,[Padding]]
+   S = fread(fp,Pad(fread(fp,1,'uint32=>uint32'),1),'uint8=>char').';
+
+function A = ReOrder(A,S)
+% Rearrange CDF array A to size S with matlab ordering
+   A = permute(reshape(A,fliplr(S)),fliplr(1:length(S)));
+
+function S = DimArray(fp)
+% Read DimArray into structure
+   if fread(fp,1,'uint32=>uint32') == 10 % NC_DIMENSION
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str = String(fp);
+         S(i).Dim = fread(fp,1,'uint32=>uint32');
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end
+
+function S = AttArray(fp)
+% Read AttArray into structure
+   if fread(fp,1,'uint32=>uint32') == 12 % NC_ATTRIBUTE
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str = String(fp);
+         ID       = fread(fp,1,'uint32=>uint32');
+         Num      = fread(fp,1,'uint32=>uint32');
+         S(i).Val = fread(fp,Pad(Num,ID),[Type(ID),'=>',Type(ID)]).';
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end
+
+function S = VarArray(fp)
+% Read VarArray into structure
+   if fread(fp,1,'uint32=>uint32') == 11 % NC_VARIABLE
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str      = String(fp);
+         Num           = double(fread(fp,1,'uint32=>uint32'));
+         S(i).DimID    = double(fread(fp,Num,'uint32=>uint32'));
+         S(i).AttArray = AttArray(fp);
+         S(i).Type     = fread(fp,1,'uint32=>uint32');
+         S(i).VSize    = fread(fp,1,'uint32=>uint32');
+         S(i).Begin    = fread(fp,1,'uint32=>uint32'); % Classic 32 bit format only
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end