How to pass complex arguments in netcdf python

Question

I would like to read a netcdf file using python. This file contain a netcdf variable in the double format.

I know that this quantity should be complex and I know that the last argument is always 2 numbers (real and im).

I would like to read the nedcdf variable IN AN EFFICIENT WAY and allocate it to a complex python/numpy variable.

For the moment I have the following INEFFICIENT program that work:

import numpy as N
self.EIG2D = N.zeros((self.nkpt,self.nband,3,self.natom,3,self.natom),dtype=complex)
EIG2Dtmp = root.variables['second_derivative_eigenenergies'][:,:,:,:,:,:,:] #number_of_atoms, 
                                   # number_of_cartesian_directions, number_of_atoms, number_of_cartesian_directions,
                                   # number_of_kpoints, product_mband_nsppol, cplex
for ikpt in N.arange(nkpt):
  for iband in N.arange(nband):
    for icart in N.arange(3):
      for iatom in N.arange(natom):
        for jcart in N.arange(0,3):
          for jatom in N.arange(natom):
            self.EIG2D[ikpt,iband,icart,iatom,jcart,jatom] = complex(EIG2Dtmp[iatom,icart,jatom,jcart,ikpt,iband,0],\
                                                                     EIG2Dtmp[iatom,icart,jatom,jcart,ikpt,iband,1])

How to make this more efficient ?

Thank you in advance,

Samuel.

Look into the netCDF4-python module. Are you looping over every index of the EIG2Dtmp array? If so, you can just do self.EIG2D = root.variables[:] rather than looping through everything. — Spencer Hill
– Spencer Hill, Commented May 29, 2014 at 14:59
I'm not. There are 7 arguments to EIG2Dtmp and 6 to self.EIG2D. The missing one beeing simply the real and im part. — sponce
– sponce, Commented May 29, 2014 at 15:04
I see. The accepted answer to this question seems to be exactly what you need. — Spencer Hill
– Spencer Hill, Commented May 29, 2014 at 17:31
It is worth looking at the rest of the answers to that question. Depending on the array ordering, a simple "complex view" on the same array may suffice, as described in another answer (I unfortunately do not know how to link to a specific answer) — eickenberg
– eickenberg, Commented May 29, 2014 at 18:33
@Spencer Hill: It seems to work: numpy.vectorize(complex)(Data[...,0], Data[...,1]). The only issue for me is that I also need to change the ordering A[a,b,c] ==> A[c,b,a] but I should probably made a new thread for that I guess. Thanks a lot ! — sponce
– sponce, Commented May 29, 2014 at 21:18

Community · Accepted Answer · 2017-05-23 12:04:04Z

2

Thanks to Spencer Hill, the solution for me was

self.EIG2D = numpy.vectorize(complex)(EIG2Dtmp[...,0], EIG2Dtmp[...,1])

You can also refer to Numpy: Creating a complex array from 2 real ones?

edited May 23, 2017 at 12:04

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answered May 31, 2014 at 10:00

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