Re: PyNIO: Assigning data to 3-d NetCDF variable

Just do it like this, have you tried it? without looping

f_out.variables['hi'].assign_value(Clime_hi)

2013/11/18 Gregory Deemer <gjdeemer@alaska.edu>

> Sasha,
>
> Yep, I pulled the trigger too quickly on the resolution. The file size
> alone is an indicator that 2-D array was only assigned once. It is simply
> overwritten 365 times given the loop that I have set up.
>
>
> On Nov 18, 2013, at 1:53 PM, Oleksandr Huziy wrote:
>
> Are you sure this works, if i understand correctly, here you are assigning
> a 2d array to a 3d var, it should have complained.... Or it is writing all
> the time to the first time slice of the hi variable... check the output
> with ncview for other time steps...
>
> for i in range(0, Clime_hi.shape[0]):
>>>>>> f_out.variables['hi'].assign_value(Clime_hi[i,:,:])
>>>>>>
>>>>> If it is OK, then I am very surprised))
>
> Cheers
> --
> Oleksandr (Sasha)
>
>
>
> 2013/11/18 Gregory Deemer <gjdeemer@alaska.edu>
>
>> Hi Oleksandr,
>>
>> Thank you for your help today, I think we have reached a solution.
>> Declaring the variable as double, and reassigning my _FillValue from
>> np.float32 to np.double to match this new type was the trick. It is a bit
>> puzzling though, as I know the data that was ingested came from a
>> single-precision floating point flat binary file.
>>
>> The logic in my value assignment statement:
>>
>> for i in range(0, Clime_hi.shape[0]):
>>>>>>> f_out.variables['hi'].assign_value(Clime_hi[i,:,:])
>>>>>>>
>>>>>> Was of the correct form and is now functioning.
>>
>> Once again, thank you!
>> Greg
>>
>>
>> O
>> n Nov 18, 2013, at 1:03 PM, Oleksandr Huziy wrote:
>>
>> The ESG site is not letting me in yet))
>> See here: http://www.pyngl.ucar.edu/FAQ/#ReadNetCDF
>> item 23.
>>
>> Cheers
>>
>>
>> 2013/11/18 Gregory Deemer <gjdeemer@alaska.edu>
>>
>>> Hi Oleksandr,
>>>
>>> The double data type did not work out.
>>>
>>> fatal:NetCDF: Not a valid data type or _FillValue type mismatch: error
>>> attempting to write variable (hi) to file
>>>
>>> Perhaps my _FillValue being -9999.0 is causing the type error mismatch?
>>> I have written data to a NetCDF using similar methods, but my _FillValue
>>> was a positive int in those cases.
>>>
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>> - - - - - - - - - -
>>>
>>> Gregory J. Deemer
>>> Graduate Research Assistant
>>> Department of Atmospheric Sciences
>>> University of Alaska Fairbanks
>>> IARC 338K
>>> Office: (907) 474-5430
>>> Cell: (907) 750-1063
>>>
>>>
>>>
>>> On Mon, Nov 18, 2013 at 12:39 PM, Oleksandr Huziy <guziy.sasha@gmail.com
>>> > wrote:
>>>
>>>> Gregory:
>>>>
>>>> I am trying to install nio now. Try to create the variable as double:
>>>>
>>>> # ICE THICKNESS
>>>> f_out.create_variable('hi', 'd', ('time', 'y', 'x'))
>>>>
>>>>
>>>> 2013/11/18 Gregory Deemer <gjdeemer@alaska.edu>
>>>>
>>>>> Oleksandr,
>>>>>
>>>>> Thank you for the quick reply. I attempted the code examples that you
>>>>> suggested and PyNIO came back with errors.
>>>>>
>>>>> f_out.variables['hi'][i,:,:] = Clime_hi[i,:,:]
>>>>>
>>>>> self._obj[xsel] = value
>>>>> NIOError: type or dimensional mismatch writing to variable (hi)
>>>>>
>>>>>
>>>>> f_out.variables['hi'][:] = Clime_hi
>>>>> self._obj[xsel] = value
>>>>> NIOError: type or dimensional mismatch writing to variable (hi)
>>>>>
>>>>> I will try a few other permutations of your suggestion by replacing
>>>>> '=' with .assign_value()
>>>>>
>>>>> Thanks again,
>>>>> Greg
>>>>>
>>>>>
>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>>> - - - - - - - - - - -
>>>>>
>>>>> Gregory J. Deemer
>>>>> Graduate Research Assistant
>>>>> Department of Atmospheric Sciences
>>>>> University of Alaska Fairbanks
>>>>> IARC 338K
>>>>> Office: (907) 474-5430
>>>>> Cell: (907) 750-1063
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Nov 18, 2013 at 12:14 PM, Oleksandr Huziy <
>>>>> guziy.sasha@gmail.com> wrote:
>>>>>
>>>>>> Hi Gregory:
>>>>>>
>>>>>> Does it work like this?
>>>>>>
>>>>>> # Write values to file
>>>>>> for i in range(0, Clime_hi.shape[0]):
>>>>>> f_out.variables['hi'][i,:,:] = Clime_hi[i,:,:]
>>>>>>
>>>>>>
>>>>>> or
>>>>>>
>>>>>> f_out.variables['hi'][:] = Clime_hi
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2013/11/18 Gregory Deemer <gjdeemer@alaska.edu>
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I'm wanting to assign values to a 3-D variable consisting of time,
>>>>>>> y, x. The time dimension is unlimited but is assigned 366 values. I have
>>>>>>> seen some examples of how to approach this problem with other scripting
>>>>>>> languages where a loop is applied to write the 2-D slice per timestep, and
>>>>>>> that is the approach I have taken here, but I am receiving the error
>>>>>>> message:
>>>>>>>
>>>>>>> NIOError: type or dimensional mismatch writing to variable (hi)
>>>>>>>
>>>>>>> For reference, the shapes of pertinent variables in the code
>>>>>>> snippet to follow are:
>>>>>>>
>>>>>>> Clime_hi.shape = (366, 120, 360)
>>>>>>> time_dat.shape = (366,) # values spanning 0 - 365
>>>>>>> lat_datR.shape = (120, 360)
>>>>>>> lon_datR.shape = (120, 360)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> # Create new variable dimensions
>>>>>>> f_out.create_dimension('time', None)
>>>>>>> f_out.create_dimension('y', 120)
>>>>>>> f_out.create_dimension('x', 360)
>>>>>>>
>>>>>>> # TIME
>>>>>>> f_out.create_variable('time', 'd', ('time',))
>>>>>>> # Attributes of time
>>>>>>> setattr(f_out.variables['time'], 'standard_name', 'Valid Time')
>>>>>>> setattr(f_out.variables['time'], 'units', 'hours since 2001-01-01
>>>>>>> 00:00:00')
>>>>>>> setattr(f_out.variables['time'], 'time_origin', '2001-01-01
>>>>>>> 00:00:00')
>>>>>>> setattr(f_out.variables['time'], 'calendar', 'gregorian')
>>>>>>> setattr(f_out.variables['time'], 'axis', 'T')
>>>>>>> # Write values to file
>>>>>>> f_out.variables['time'].assign_value(time_dat)
>>>>>>>
>>>>>>> # LATITUDE
>>>>>>> f_out.create_variable('lat', 'd', ('y','x'))
>>>>>>> # Attributes of latitude
>>>>>>> setattr(f_out.variables['lat'], 'standard_name', 'latitude')
>>>>>>> setattr(f_out.variables['lat'], 'units', 'degrees_north')
>>>>>>> setattr(f_out.variables['lat'], 'axis', 'Y')
>>>>>>> # Write values to file
>>>>>>> f_out.variables['lat'].assign_value(lat_datR)
>>>>>>>
>>>>>>> # LONGITUDE
>>>>>>> f_out.create_variable('lon', 'd', ('y', 'x'))
>>>>>>> # Attributes of longitude
>>>>>>> setattr(f_out.variables['lon'], 'standard_name', 'longitude')
>>>>>>> setattr(f_out.variables['lon'], 'units', 'degrees_east')
>>>>>>> setattr(f_out.variables['lon'], 'axis', 'X')
>>>>>>> # Write values to file
>>>>>>> f_out.variables['lon'].assign_value(lon_datR)
>>>>>>>
>>>>>>> # ICE THICKNESS
>>>>>>> f_out.create_variable('hi', 'f', ('time', 'y', 'x'))
>>>>>>> # Create variable attributes
>>>>>>> setattr(f_out.variables['hi'], 'standard_name', 'sea_ice_thickness')
>>>>>>> setattr(f_out.variables['hi'], 'units', 'm')
>>>>>>> setattr(f_out.variables['hi'], '_FillValue', _FillandMiss)
>>>>>>> setattr(f_out.variables['hi'], 'missing_value', _FillandMiss)
>>>>>>> # Write values to file
>>>>>>> for i in range(0, Clime_hi.shape[0]):
>>>>>>> f_out.variables['hi'].assign_value(Clime_hi[i,:,:])
>>>>>>>
>>>>>>> Again, the error message that I am given once the loop as finished
>>>>>>> its iteration is this:
>>>>>>>
>>>>>>> for i in range(0, Clime_hi.shape[0]):
>>>>>>> NIOError: type or dimensional mismatch writing to variable (hi)
>>>>>>>
>>>>>>> Please let me know if more information is needed to solve this error.
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Greg
>>>>>>>
>>>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>>>>> - - - - - - - - - - - -
>>>>>>>
>>>>>>> Gregory J. Deemer
>>>>>>> Graduate Research Assistant
>>>>>>> Department of Atmospheric Sciences
>>>>>>> University of Alaska Fairbanks
>>>>>>> IARC 338K
>>>>>>> Office: (907) 474-5430
>>>>>>> Cell: (907) 750-1063
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> pyngl-talk mailing list
>>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Sasha
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Sasha
>>>>
>>>
>>>
>>
>>
>> --
>> Sasha
>>
>>
>>
>
>
> --
> Sasha
>
>
>

-- 
Sasha

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Received on Mon Nov 18 16:23:01 2013