ecom_jslice

ECOM_JSLICE:  returns a vertical slice along j=jindex, ECOM file

 The variable must be 4D.

 USAGE:
 >> [u,x,z] = ecom_jslice(cdf,var,time,jindex,[irange])
        u = the selected variable
        x = distance in *km* (assuming x units in netCDF file are in meters)
        z = depth in m
        jindex = j index along which slice is taken
        irange = imin and imax indices along slice (optional).  If this
           argument is not supplied the default takes all the I indices
           except for the first and last, which are always "land" cells.

 see also ISLICE, KSLICE, ZSLICE, ZSLICEUV, KSLICEUV

0001 function [u,x,z] = ecom_jslice(cdf,var,time,jindex,irange)
0002 %ECOM_JSLICE:  returns a vertical slice along j=jindex, ECOM file
0003 %
0004 % The variable must be 4D.
0005 %
0006 % USAGE:
0007 % >> [u,x,z] = ecom_jslice(cdf,var,time,jindex,[irange])
0008 %        u = the selected variable
0009 %        x = distance in *km* (assuming x units in netCDF file are in meters)
0010 %        z = depth in m
0011 %        jindex = j index along which slice is taken
0012 %        irange = imin and imax indices along slice (optional).  If this
0013 %           argument is not supplied the default takes all the I indices
0014 %           except for the first and last, which are always "land" cells.
0015 %
0016 % see also ISLICE, KSLICE, ZSLICE, ZSLICEUV, KSLICEUV
0017 %
0018 if (nargin <4) ,
0019   help jslice; return
0020 end
0021 mexcdf('setopts',0);
0022 ncid=mexcdf('open',cdf,'nowrite');
0023 if(ncid==-1),
0024   disp(['file ' cdf ' not found'])
0025   return
0026 end
0027 [name, nx]=mexcdf('diminq',ncid,'xpos');
0028 [name, nz]=mexcdf('diminq',ncid,'zpos');
0029 if(exist('irange')),
0030   irange(1)=max(1,irange(1));
0031   irange(2)=min(nx-1,irange(2));
0032   istart=irange(1)-1;
0033   icount=irange(2)-irange(1)+1;
0034 else
0035   istart=1
0036   icount=nx-2;
0037 end
0038   u=mexcdf('varget',ncid,var,[(time-1) 0 (jindex-1) istart],...
0039        [1 nz-1 1 icount],1);
0040 if nargout>1,
0041   d=mexcdf('varget',ncid,'depth',[(jindex-1) istart],[1 icount],1);
0042   ind=find(d==-99999.);
0043   d(ind)=d(ind)*nan;
0044   u(ind,:)=u(ind,:)*NaN;
0045   sigma=mexcdf('varget',ncid,'sigma',0,nz,1);
0046 % assume we are slicing a variable defined at
0047 % at the center of the sigma level (t,s,u,v,km)
0048   sigma=0.5*(sigma(1:nz-1)+sigma(2:nz));
0049   h1=mexcdf('varget',ncid,'h1',[(jindex-1) istart],[1 icount],1);
0050   x=cumsum(h1)/1000.;
0051   x=x*ones(1,nz-1);
0052   z=d*(sigma');
0053   ind=find(isnan(z));
0054   z(ind)=zeros(size(ind));
0055 end
0056 mexcdf('close',ncid);