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ec-jrc / lisflood-lisvap

Lisflood OS (LISVAP)
https://ec-jrc.github.io/lisflood-lisvap/
European Union Public License 1.2
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AttributeError writing NetCDF _FillValue attribute of spatial dimension variables #17

Closed emiliano-gelati closed 5 years ago

emiliano-gelati commented 5 years ago

Using input NetCDF files created via xarray.Dataset.to_netcdf, which creates a "_FillValue" attribute for all variables (including those corresponding to the spatial dimensions x,y/lon,lat) causes an error when writing the attributes of the spatial dimensions of output NetCDF files: NetCDF4 does not allow setting the "_FillValue" attribute after the variable has been created. See the bold lines in the Traceback at the bottom.

I propose a bug-fix (59a8407637c8791af6fc330af157459ac08088ec) to skip creating the "_FillValue" attribute for spatial dimensions. In addition, a loop over the spatial dimensions replaces 4 nearly identical code blocks.

I could not find any way to prevent xarray.Dataset.to_netcdf from setting the "_FillValue" attribute.

Traceback (most recent call last): File "lisvap/lisvap1.py", line 122, in sys.exit(main()) File "lisvap/lisvap1.py", line 118, in main lisvapexe(lissettings) File "lisvap/lisvap1.py", line 70, in lisvapexe dynfmw.run() File "/opt/pcraster-4.1.0_x86-64/python/pcraster/framework/dynamicFramework.py", line 65, in run self._runDynamic() File "/opt/pcraster-4.1.0_x86-64/python/pcraster/framework/frameworkBase.py", line 362, in _runDynamic self._userModel().dynamic() File "/home/gelatem/BMI_lisflood/lisvap/src/lisvap/lisvapdynamic.py", line 358, in dynamic self.output_module.dynamic() File "/home/gelatem/BMI_lisflood/lisvap/src/lisvap/utils/output.py", line 153, in dynamic self.settings.report_maps_all[maps].unit, 'f4', self.var.calendar_date) File "/home/gelatem/BMI_lisflood/lisvap/src/lisvap/utils/writers.py", line 49, in writenet setattr(latitude, i, metadata_ncdf['lat'][i]) File "netCDF4/_netCDF4.pyx", line 3869, in netCDF4._netCDF4.Variable.setattr AttributeError: _FillValue attribute must be set when variable is created (using fill_value keyword to createVariable)

domeniconappo commented 5 years ago

@emiliano-gelati

Hi Emiliano, Any update on this? should we merge that commit into master and close this issue?

emiliano-gelati commented 5 years ago

@domeniconappo Hi Domenico, Yes, if changes look OK to you, please proceed with merging. Thank you, Emiliano

domeniconappo commented 5 years ago

super! I'm doing some tests and will merge if no problems come up

domeniconappo commented 5 years ago

merged. Thanks!