[Pytables-users] Re: Re: nctoh5 script

[Jeff W. <js...@fa...>]

Francesc:  There was no good reason for using Array instead of EArray 
for rank-1 variables, other than I wasn't sure EArrays were appropriate 
for variables that were not going to be appended to.

Thanks for extending the script!  I noticed one typo (StringAtom was 
used instead of tables.StringAtom).  Also, it doesn't yet work on files 
with netcdf character variables.  I get errors like this:

Traceback (most recent call last):
  File "nctoh5_new.py", line 175, in ?
    overwritefile)
  File "nctoh5_new.py", line 61, in nctoh5
    vardata.append(var[n:n+1])
  File "/sw/lib/python2.3/site-packages/tables/EArray.py", line 196, in 
append
    naarr = convertIntoNA(object, self.atom)
  File "/sw/lib/python2.3/site-packages/tables/utils.py", line 208, in 
convertIntoNA
    shape=arr.shape)
  File 
"/sw/src/root-numarray-py23-1.0-1/sw/lib/python2.3/site-packages/numarray/numarraycore.py", 
line 318, in array
  File 
"/sw/src/root-numarray-py23-1.0-1/sw/lib/python2.3/site-packages/numarray/numarraycore.py", 
line 256, in getTypeObject
  File 
"/sw/src/root-numarray-py23-1.0-1/sw/lib/python2.3/site-packages/numarray/numarraycore.py", 
line 245, in _typeFromTypeAndTypecode
  File 
"/sw/src/root-numarray-py23-1.0-1/sw/lib/python2.3/site-packages/numarray/numerictypes.py", 
line 457, in getType
TypeError: Not a numeric type


If I replace

                vardata.append(var[n:n+1])

with

            if dtype == 'c':
                chararr = numarray.strings.array(var[n].tolist())
                newshape = list(chararr.shape)
                newshape.insert(0,1)
                chararr.setshape(tuple(newshape))
                vardata.append(chararr)
            else:
                vardata.append(var[n:n+1])


it seems to work.  Note that I have to reshape the chararray to have an 
extra singleton dimension or pytables complains that the data being 
appended has the wrong shape.   This is also the reason I had to use 
var[n:n+1] instead of var[n] in the append.  Is there a better way to do 
this?

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/CDC  R/CDC1        Email  : Jef...@no...
325 Broadway                Web    : www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80303-3328 Office : Skaggs Research Cntr 1D-124