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

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
>>
>>
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>>
>>
>>
>> --
>> Sasha
>>
>>
>>
>>
>> --
>> Sasha
>>
>>
>>
>>
>> --
>> Sasha
>
>
>
>
> --
> Sasha

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Received on Mon Nov 18 16:19:00 2013