Error when creating variable to create a netCDF file

Question

I was able to figure out the lat, lon dimension declaration as indicated in the following code. I think I am close to obtain the netCDF file. But, I get an error.

import numpy as np
import netCDF4
import os

# load the data

path='C:\Users\.spyder2'
os.chdir(path)
# this load the file into a Nx3 array (three columns)
data = np.loadtxt('TRMM_1998_01_0100_newntcl.csv', delimiter=',')


# create a netcdf Data object

with netCDF4.Dataset('TEST_file.nc', mode="w", format='NETCDF4') as ds:
    # some file-level meta-data attributes:
    ds.Conventions = "CF-1.6" 
    ds.title = 'Non TC precipitation'
    ds.institution = 'USU'

    lat = data[:,0] # the first column 
    lon = data[:,1] # the second column 
    precip = data[:,2] # the third column 

    nlat = lat.reshape( (161, 321) )
    nlon = lon.reshape( (161, 321) )

    # time = ds.createDimension('time', 0)
    ds.createDimension('latitude', 161)
    ds.createDimension('longitude', 321)


    precip = ds.createVariable('precip', 'f4', ('latitude', 'longitude'))
    precip[:] = data[:,:]
    ## adds some attributes
    precip.units = 'mm'
    precip.long_name = 'Precipitation'

Error:

Traceback (most recent call last):

  File "<ipython-input-101-483efc7d87e2>", line 42, in <module>
    precip[:] = data[:,:]

  File "netCDF4.pyx", line 3066, in netCDF4.Variable.__setitem__ (netCDF4.c:38720)

  File "netCDF4.pyx", line 3177, in netCDF4.Variable._put (netCDF4.c:39523)

IndexError: size of data array does not conform to slice

I appreciate if you can clarify here a bit or provide me some clues of what's happening to correct it.

Thanks in advance,

N1B4 · Accepted Answer · 2015-03-16 23:03:39Z

2

Creating dimensions is done with no assignment to a variable. Just remove the lat= and lon= when defining dimensions and then you can reference the dimensions while creating a variable.

ds.createDimension('latitude', 161)
ds.createDimension('longitude', 321)

precip = ds.createVariable('precip, 'f4', ('latitude', 'longitude',))

Also, be careful with scoping issues as you re-use lat several times in the script. Best to use unique names when dealing with the actual data, named dimensions, and dimension sizes. I usually do something like lat_arr (for the data), nlat (for dimension size), and lat or latitude for the dimension name.

answered Mar 16, 2015 at 23:03

N1B4

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2 Comments

user3408139 Over a year ago

Thanks. I did the revisions and now I am getting a different error. Please see the code and error above.

N1B4 Over a year ago

precip is 2D, so it needs to be precip[:,:] = data[:,:]

DopplerShift · Accepted Answer · 2015-03-17 18:56:57Z

1

That error "size of data array does not conform to slice" indicates that precip[:] and data[:,:] do not have the same number of items. At that point in the code, it looks like precip should be a variable of size 161x321. You are trying to assign it data[:,:], which looks like all 3 columns of information.

I think what you really want is: precip[:] = data[:,2]

answered Mar 17, 2015 at 18:56

DopplerShift

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Comments

pwi · Accepted Answer · 2020-06-07 13:18:24Z

0

Don't think this is still relevant for op, but I tried the following. I adapted op's code from mine, which I just managed to get to work (python 3.7; jupyter notebook).

...
lon = ds.createVariable('longitude', float, ('longitude',), zlib=True)
lat = ds.createVariable('latittude', float, ('latitude',), zlib=True)
precip = ds.createVariable('precip', float, ('latitude', 'longitude'), zlib=True)

precip[:] = data
lon[:] = lon
lat[:] = lat
...

Make sure your data has the same dimensions (i.e. (161, 321)) as your lat and lon.

answered Jun 7, 2020 at 13:18

pwi

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