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netCDF4 variable manipulation

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  netCDF4 variable manipulation Sheldon <shejo284@gmail.com> - 2012-02-20 12:37 -0800
    Re: netCDF4 variable manipulation Dave Angel <d@davea.name> - 2012-02-20 17:52 -0500
    Re: netCDF4 variable manipulation Steven D'Aprano <steve+comp.lang.python@pearwood.info> - 2012-02-20 23:53 +0000
      Re: netCDF4 variable manipulation Sheldon <shejo284@gmail.com> - 2012-02-21 00:29 -0800
        Re: netCDF4 variable manipulation Chris Rebert <clp2@rebertia.com> - 2012-02-21 01:10 -0800

#20635 — netCDF4 variable manipulation

Hi,

I'm trying to read a netCDF4 variable from a file (no problem) and
then scale it before writing over the original variable in the file.

I'm using python 2.7 and the latest netCDF4 module. It's not that I
keep getting an error message but I want to do this without using for
loops and all the manuals seems to be skipping this task as if it is
never done. I'm new to python and coming over from matlab. Does anyone
know how to modify the netCDF4 variable in python and then write it
back without creating a new variable, or using for loops?

Appreciate the help,
/S

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#20636

On 02/20/2012 03:37 PM, Sheldon wrote:
> Hi,
>
> I'm trying to read a netCDF4 variable from a file (no problem) and
> then scale it before writing over the original variable in the file.
>
> I'm using python 2.7 and the latest netCDF4 module. It's not that I
> keep getting an error message but I want to do this without using for
> loops and all the manuals seems to be skipping this task as if it is
> never done. I'm new to python and coming over from matlab. Does anyone
> know how to modify the netCDF4 variable in python and then write it
> back without creating a new variable, or using for loops?
>
> Appreciate the help,
> /S
Are you using netcdf version 4, or is that name just a coincidence?  If 
you're using a 3rd party library, you really should say so, and post a 
link, for those curious.

in any case, if you are, I can't help you.  This is apparently some 
special kind of variable similar to a numpy array.


On the other hand, you may just be asking how to update some bytes in a 
file, in place.  if you read the file in binary mode, then you can use 
seek() to go back the appropriate distance, and simply write it.


-- 

DaveA

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#20637

On Mon, 20 Feb 2012 12:37:22 -0800, Sheldon wrote:

> Hi,
> 
> I'm trying to read a netCDF4 variable from a file (no problem) and then
> scale it before writing over the original variable in the file.
> 
> I'm using python 2.7 and the latest netCDF4 module. It's not that I keep
> getting an error message but I want to do this without using for loops
> and all the manuals seems to be skipping this task as if it is never
> done. I'm new to python and coming over from matlab. Does anyone know
> how to modify the netCDF4 variable in python and then write it back
> without creating a new variable, or using for loops?

There is no such thing as "the netCDF4 variable" in Python -- it is not a 
built-in part of the language, and therefore there is no built-in feature 
for manipulating it.

You are going to have to be more specific about what you want than just 
"how do I modify a variable with for loops?".

My wild guess is that you have some sort of config file which includes a 
field called "netCDF4" and you want to update it in place. We can't tell 
you how to do this without knowing what the config file is -- is it an 
INI file, XML, JSON, YAML, Unix-style rc file, a binary pickle, or 
something else?


-- 
Steven

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#20660

On Feb 21, 12:53 am, Steven D'Aprano <steve
+comp.lang.pyt...@pearwood.info> wrote:
> On Mon, 20 Feb 2012 12:37:22 -0800, Sheldon wrote:
> > Hi,
>
> > I'm trying to read a netCDF4 variable from a file (no problem) and then
> > scale it before writing over the original variable in the file.
>
> > I'm using python 2.7 and the latest netCDF4 module. It's not that I keep
> > getting an error message but I want to do this without using for loops
> > and all the manuals seems to be skipping this task as if it is never
> > done. I'm new to python and coming over from matlab. Does anyone know
> > how to modify the netCDF4 variable in python and then write it back
> > without creating a new variable, or using for loops?
>
> There is no such thing as "the netCDF4 variable" in Python -- it is not a
> built-in part of the language, and therefore there is no built-in feature
> for manipulating it.
>
> You are going to have to be more specific about what you want than just
> "how do I modify a variable with for loops?".
>
> My wild guess is that you have some sort of config file which includes a
> field called "netCDF4" and you want to update it in place. We can't tell
> you how to do this without knowing what the config file is -- is it an
> INI file, XML, JSON, YAML, Unix-style rc file, a binary pickle, or
> something else?
>
> --
> Steven

Hi,

My apologies. I didn't realize this module was not popular. I'm using
the python module "netCDF4"
that I installed using PIP. This module gives me the ability to read
and write netcdf4 files.
The module is an interface to the netcdf4.1.3 and HDF51.8.8 libraries.
What I'm trying to do is open an existing netcdf file, extract an
variable, modify the variable, and then
write it again to the file - effectively replacing the old variable.

rgrp = netCDF4.Dataset('ODIN_NWP_2001_01_01_00.NC','r+')
pv = rgrp.groups['Data_3D'].variables['PV']

print pv
<type 'netCDF4.Variable'>
float32 PV(u'level', u'lat', u'lon')
    longname: Potential Vorticity
    _FillValue: -999.0
    units: K m**2 kg**-1 s**-1
    code: 60
    scale_factor: 1.0
    add_offset: 0.0
path = /Data_3D
unlimited dimensions = ()
current size = (60, 181, 360)

As you can see, pv is described here as a netCDF4.Variable. I'm trying
to modify this pv and then write it back to the file
but the manual is vague on this part. I tried this:

pv = pv*2
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call
last)
----> 1 pv = pv*2
TypeError: unsupported operand type(s) for *: 'netCDF4.Variable' and
'int'

I'm unsure how this is suppose to work.

/S

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#20661

On Tue, Feb 21, 2012 at 12:29 AM, Sheldon <shejo284@gmail.com> wrote:
> On Feb 21, 12:53 am, Steven D'Aprano <steve
> +comp.lang.pyt...@pearwood.info> wrote:
>> On Mon, 20 Feb 2012 12:37:22 -0800, Sheldon wrote:
>> > Hi,
>>
>> > I'm trying to read a netCDF4 variable from a file (no problem) and then
>> > scale it before writing over the original variable in the file.
>>
>> > I'm using python 2.7 and the latest netCDF4 module. It's not that I keep
>> > getting an error message but I want to do this without using for loops
>> > and all the manuals seems to be skipping this task as if it is never
>> > done. I'm new to python and coming over from matlab. Does anyone know
>> > how to modify the netCDF4 variable in python and then write it back
>> > without creating a new variable, or using for loops?
<snip>
> My apologies. I didn't realize this module was not popular. I'm using
> the python module "netCDF4"
> that I installed using PIP. This module gives me the ability to read
> and write netcdf4 files.
> The module is an interface to the netcdf4.1.3 and HDF51.8.8 libraries.
> What I'm trying to do is open an existing netcdf file, extract an
> variable, modify the variable, and then
> write it again to the file - effectively replacing the old variable.
>
> rgrp = netCDF4.Dataset('ODIN_NWP_2001_01_01_00.NC','r+')
> pv = rgrp.groups['Data_3D'].variables['PV']
>
> print pv
> <type 'netCDF4.Variable'>
> float32 PV(u'level', u'lat', u'lon')
>    longname: Potential Vorticity
>    _FillValue: -999.0
>    units: K m**2 kg**-1 s**-1
>    code: 60
>    scale_factor: 1.0
>    add_offset: 0.0
> path = /Data_3D
> unlimited dimensions = ()
> current size = (60, 181, 360)
>
> As you can see, pv is described here as a netCDF4.Variable. I'm trying
> to modify this pv and then write it back to the file
> but the manual is vague on this part. I tried this:
>
> pv = pv*2
> ---------------------------------------------------------------------------
> TypeError                                 Traceback (most recent call
> last)
> ----> 1 pv = pv*2
> TypeError: unsupported operand type(s) for *: 'netCDF4.Variable' and
> 'int'
>
> I'm unsure how this is suppose to work.

The API docs suggest that Variables don't support any arithmetic
operations, just slicing and attribute manipulation. They seem to
interoperate with numpy arrays though, so presumably you could avoid
explicit looping by loading the Variable's contents into a numpy
array, doing your calculations on that, and then assigning the
resulting numpy array back into a slice of the Variable.

Cheers,
Chris

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