This page contains solutions for some of the more common problems
encountered with the ncdfCF package and netCDF data.
If you have a problem or are encountering an error and there is no solution to be found on this page, please open an issue.
Can’t assign a value to a CF object
ds <- open_ncdf("my_data.nc")
ds[["time"]]$orientation <- "T"
#> Error in `ds[["time"]]$orientation <- "T"`:
#> ! cannot add bindings to a locked environmentThis is an issue related to how R interprets the code.
ncdfCF is built using the R6 framework and the
ncdfCF classes are thus environments. The sore point is
assigning a value to an indirectly referenced object using the
[[ indexing operator. The solution is then to first take a
reference to the object you’d like to assign a value to:
axT <- ds[["time"]]
axT$orientation <- "T"
axT
#> <Time axis> [0] time
#> Length : 1800 (unlimited)
#> Axis : T
#> Calendar : 360_day
#> Range : 2041-01-01T12:00:00 ... 2045-12-30T12:00:00 (days)
#> Bounds : 2041-01-01 ... 2046-01-01
#>
#> Attributes:
#> ...Axes are not specified properly
Sometimes when you open a netCDF file you find that the axes are incompletely specified. While this may not generate an error or a warning and the data will still be usable, certain operations on the data are not possible, such as automatically orienting the data in a certain way or exporting the data variables to a different format.
(ds <- open_ncdf("~/METEO_DATA_202003120000.NC"))
#> <Dataset> METEO_DATA_202003120000.NC
#> Resource : ~/METEO_DATA_202003120000.NC
#> Format : classic4
#> Collection : Generic netCDF data
#> Conventions: (not indicated)
#> Keep open : FALSE
#>
#> Variables:
#> name long_name units data_type axes
#> lwrc Incoming longwave radiation W m-2 NC_DOUBLE time, northing, easting
#> sdri Incoming direct shortwave radiation... W m-2 NC_DOUBLE time, northing, easting
#> sdfd Incoming diffuse shortwave radiation W m-2 NC_DOUBLE time, northing, easting
#> tais Air temperature at 10 m above ground K NC_DOUBLE time, northing, easting
#> rhus Relative humidity at 10 m above ground % NC_DOUBLE time, northing, easting
#> pail Air pressure Pa NC_DOUBLE time, northing, easting
#> wnsd Wind speed at 10 m above ground m/s NC_DOUBLE time, northing, easting
#> wndd Wind direction at 10 m above ground deg NC_DOUBLE time, northing, easting
#> proi Precipitation mm/hr NC_DOUBLE time, northing, easting
#>
#> Attributes:
#> name type length value
#> title NC_CHAR 108 High-resolution hydrometeorological data for th...
#> summary NC_CHAR 244 This dataset contains high-resolution meteorolo...
#> ...
# Open a data variable
(lwrc <- ds[["lwrc"]])
#> <Variable> lwrc
#> Long name: Incoming longwave radiation
#>
#> Axes:
#> axis name long_name length values unit
#> T time 24 [2020-03-12T00:00:00 ... 2020-03-12T23:00:00] days since 2020-03-12T00:00:00+01:00
#> northing Northing 180 [189950 ... 172050] m
#> easting Easting 185 [776050 ... 794450] m
#>
#> Attributes:
#> name type length value
#> _FillValue NC_DOUBLE 1 -9999
#> standard_name NC_CHAR 32 downwelling_longwave_flux_in_air
#> long_name NC_CHAR 27 Incoming longwave radiation
#> coverage_content_type NC_CHAR 11 modelResult
#> units NC_CHAR 5 W m-2This all looks ok but the northing and
easting axes are not recognised as Y and
X. You can remedy that manually:
ax <- lwrc$axes[["northing"]]
ax$orientation <- "Y"
ax <- lwrc$axes[["easting"]]
ax$orientation <- "X"
lwrc
#> <Variable> lwrc
#> Long name: Incoming longwave radiation
#>
#> Axes:
#> axis name long_name length values unit
#> T time 24 [2020-03-12T00:00:00 ... 2020-03-12T23:00:00] days since 2020-03-12T00:00:00+01:00
#> Y northing Northing 180 [189950 ... 172050] m
#> X easting Easting 185 [776050 ... 794450] m
#>
#> Attributes:
#> name type length value
#> _FillValue NC_DOUBLE 1 -9999
#> standard_name NC_CHAR 32 downwelling_longwave_flux_in_air
#> long_name NC_CHAR 27 Incoming longwave radiation
#> coverage_content_type NC_CHAR 11 modelResult
#> units NC_CHAR 5 W m-2Note that you have to do this only once: all nine data variables
share the same instance of the northing and
easting axes and it is those objects that the
$orientation field applies to.
The above procedure solves the issue for the currently loaded data. If you want to fix the netCDF file permanently, you should open it for writing, set the appropriate attributes and save the edits:
ds <- open_ncdf("~/METEO_DATA_202003120000.NC", write = TRUE)
northing <- ds[["northing"]]
northing$set_attribute("standard_name", "NC_CHAR", "projected_y_coordinate")
northing$set_attribute("axis", "NC_CHAR", "Y")
easting <- ds[["easting"]]
easting$set_attribute("standard_name", "NC_CHAR", "projected_x_coordinate")
easting$set_attribute("axis", "NC_CHAR", "X")
ds$save()