Python bindings for NCO. A fork from Ralf Mueller's cdo-bindings.
pynco - Use Python to access the power of NCO
This package contains the module python nco, which implements a python style access to the NetCDF Operators (NCO). NCO is a command line tool for processing netCDF data. Its main focus is climate data, but it can by used for other purposes too.
This will install all required and optional dependencies and is the quickest and easiest way to a working pynco installation.
conda install -c conda-forge pyncoPlease see the requirements before installing
pip install ncoPlease see the requirements before installing
python setup.py installMandatory
- Platform: Unix or Mac OS (Windows has not bee tested)
- NetCDF Operators (NCO) - Version 4.6.9 or later. We don't test against every NCO version.
- Python 3.6 or 3.7
Recommended
These will allow pynco operations to return numpy arrays
from nco import NcoFor python an instance has to be created first
from nco import Nco
nco = Nco()Now any NCO command (i.e. ncks, ncra, ...) can be called as a method of nco.
-
Required arguments
input- Input netcdf file name, str
-
Optional arguments
output-strorlistof strings representing input netCDF filenames. If not provided and operator returns a file (not an array or stdout text), the method will return a temporary file.debug-boolorint, if less than 0 or True, debug statements will be turned on for NCO and NCOpy (default:False)returnCdf-bool, return a netCDF file handle (default:False)returnArray-str. return a numpy array of variable name (default:'')returnMaArray-str. return a numpy masked array of variable name (default:'')options-list, NCO input options, for exampleoptions=['-7', '-L 1'](default:[])Atted- a wrapper object to be used for ncatted. Atted objects can be included in the options listLimit- a wrapper object for the hyperslab (-d) command line optionRename- a wrapper object for the-d,-a,-v, and-gcommand line options inncrename**kwargs- any kwarg will be passed as a key, value pair to the nco command--{key}={value}. This allows the user to pass any number of long name commands list in the nco help pages.
-
File information:
ncdump_string = nco.ncdump(input=ifile)
-
Operators with user defined regular output files:
nco.ncra(input=ifile, output=ofile)
-
Use temporary output files:
temp_ofile = nco.ncrcat(input=ifile)
-
Set global NCO options:
nco.ncks(input=ifile, output=ofile, options="--netcdf4")
-
Return multi-dimension arrays:
temperatures = nco.ncra(input=ifile, returnArray=True).variables['T'][:] temperatures = nco.ncra(input=ifile, returnCdf=True).variables['T'][:] temperatures = nco.ncra(input=ifile, returnArray='T')
-
Wrapper Objects
The Atted opject is a convienent wrapper object to the
-acommand-line switch in ncatted. The Limit object is a wrapper to the-dcommand-line switch. The Rename is a wrapper for the-a, -v, -d , -gswitches in ncrename.e.g the following are equivalent:
ncatted -a _FillValue,three_dmn,o,d,-9.91e+33 in.nc nco.ncatted(input="in.nc",options=[c.atted("overwrite","_FillValue","three_dmn",-9.91e+33,'d')])
pynco includes a simple tempfile wrapper, which makes life easier. In the
absence of a specified output file, pynco will create a temporary file to allow the results of the task to be returned to the user. For example:
temperatures = nco.ncra(input=ifile, returnArray='T')is equivalent to:
temperatures = nco.ncra(input=ifile, output=tempfile.mktemp(), returnArray='T')
It is sometimes more tidy to define the atted objects in a separate list then add that list the options in the nco call
opt = [
c.Atted("o", "units", "temperature", "Kelvin"),
c.Atted("c", "min", "temperature", 0.16, 'd'),
c.Atted("m", "max", "temperature", 283.01, 'float64'),
c.Atted("c", "bnds", "time", [0.5, 1.5], 'f')
]
nco.ncatted(input="in.nc", options=opt)You can also use keyword arguments in the call so the above options become
opt = [
c.Atted(mode="o", attName="units", varName="temperature", Value="Kelvin", sType="c"),
c.Atted(mode="create", attName="min", varName="temperature", Value=0.16, sType='d' ),
c.Atted(mode="modify", attName="max", varName="temperature", Value=283.01, sType='float64'),
c.Atted(mode="create", attName="bnds", varName="time", Value=[0.5, 1.5], sType='float32')
]
nco.ncatted(input="in.nc", options=opt)Can be a single value or a list (or any python iterable type or a numpy array).
- If sType is not included then the type is inferred from the first value in the list
- If sType is included then any values in the list are not of sType are converted to the sType
You can use the following: f, d, l/i, s, b, ub, us, u, ll, ull
Or their numpy equivalents: float32, float64, int32, int16, byte, ubyte, uint16, uint32, int64, uint64
For a netCDF3 character string use c or char
For netCDF4 string(s) use sng or string
For mode you can use the single character abbreviations as per ncatted: a, c, d, m, n, o or the following words: a)ppend, create, delete, modify, overwrite
The following are equivalent:
nco
ncks -d time,0,8,2 -d time,10 -d lat,-20.0,20.0 -d lon,50.0,350.0 -d lev,,,4pynco
opt = [
c.Limit("time", 0, 8, 2),
c.LimitSingle("time", 10),
c.Limit("lat", -20.0, 20.0),
c.Limit(dmn_name="lon", srt=50.0, end=350.0),
c.Limit(dmn_name="lev", srd=4)
]
nco.ncks(input="in.nc", output="out.nc", options=opt)The following are equivalent:
nco
ncrename -v p,pressure -v t,temperature in.ncpynco
rDict = {
'p': 'pressure',
't': 'temperature'
}
nco.ncrename(input="in.nc", options=[ c.Rename("variable", rDict) ])Also equivalent:
nco
ncrename -d lon,longitude -d lat,latitude -v lon,longitude -v lat,latitude in.ncpynco
rDict = {
'lon': 'longitude',
'lat': 'latitude'
}
nco.ncrename(input="in.nc", options=[ c.Rename("d", rDict), c.Rename("v", rDict) ])Please use the github page to report issues/bugs/features: https://github.com/nco/pynco.
For usage questions, please use Stack Overflow.
pynco makes use of the MIT License, see LICENSE.txt.
- Requires: NCO version 4.6.9 or newer, Python 3.6 or later
- Optional: scipy or Python netCDF4
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