Problem reading aggregated data

[cgentemann]

I'm following code here:
https://climate-cms.org/2019/01/18/using-opendap.html

run:
import xarray as xr
aggr_url = "https://thredds.jpl.nasa.gov/thredds/dodsC/OceanTemperature/MUR-JPL-L4-GLOB-v4.1.nc"
data = xr.open_dataset(aggr_url)

returns:
OSError: [Errno -45] NetCDF: Not a valid data type or _FillValue type mismatch: b'https://thredds.jpl.nasa.gov/thredds/dodsC/OceanTemperature/MUR-JPL-L4-GLOB-v4.1.nc'

I tried
data = xr.open_dataset(aggr_url,decode_cf=False)

returns same error as above

suggestions?
thanks, chelle

[yiboj]

Hi Chelle,

I am not familiar with xarray package and you may have to check your xarray installation. But please check the following code which uses popular netCDF package to read the thredds aggregated data:

Code: Select all

import numpy as np
from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/

nc_f = 'https://thredds.jpl.nasa.gov/thredds/dodsC/OceanTemperature/MUR-JPL-L4-GLOB-v4.1.nc'
nc_fid = Dataset(nc_f, 'r')  # Dataset is the class behavior to open the file
                             # and create an instance of the ncCDF4 class

# Extract data from NetCDF file
lats = nc_fid.variables['lat'][:]  # extract/copy the data
lons = nc_fid.variables['lon'][:]
# Close original NetCDF file.
nc_fid.close()


Regards,

PODAAC DE

[cgentemann]

I tried this code and still get the same error.

I ran:

Code: Select all

import numpy as np
from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
nc_f = 'https://thredds.jpl.nasa.gov/thredds/dodsC/OceanTemperature/MUR-JPL-L4-GLOB-v4.1.nc'
nc_fid = Dataset(nc_f, 'r')  # Dataset is the class behavior to open the file
                             # and create an instance of the ncCDF4 class

# Extract data from NetCDF file
lats = nc_fid.variables['lat'][:]  # extract/copy the data
lons = nc_fid.variables['lon'][:]
# Close original NetCDF file.
nc_fid.close()
nc_fid


error:
OSError: [Errno -45] NetCDF: Not a valid data type or _FillValue type mismatch: b'https://thredds.jpl.nasa.gov/thredds/dodsC/OceanTemperature/MUR-JPL-L4-GLOB-v4.1.nc'

[yiboj]

Hi Chelle,

Looks like your netCDF library or netCDF package may have issue, please check your installation.

Regards,

PODAAC DE

[jimp]

Can you give more specifics on the problems with the netcdf library? I'm using python (3.8.3) with netCDF4 (1.5.3) and can read Chelle's URL no problem, but I get the same error she reported when accessing the MODIS aggregation:

Code: Select all

from netCDF4 import Dataset
nc_f = 'https://thredds.jpl.nasa.gov/thredds/dodsC/ncml_aggregation/OceanTemperature/modis/aqua/11um/4km/aggregate__MODIS_AQUA_L3_SST_THERMAL_MONTHLY_4KM_DAYTIME_V2019.0.ncml'
nc_fid = Dataset(nc_f, 'r')


Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "netCDF4/_netCDF4.pyx", line 2321, in netCDF4._netCDF4.Dataset.__init__
File "netCDF4/_netCDF4.pyx", line 1885, in netCDF4._netCDF4._ensure_nc_success
OSError: [Errno -45] NetCDF: Not a valid data type or _FillValue type mismatch: b'https://thredds.jpl.nasa.gov/thredds/dodsC/ncml_aggregation/OceanTemperature/modis/aqua/11um/4km/aggregate__MODIS_AQUA_L3_SST_THERMAL_MONTHLY_4KM_DAYTIME_V2019.0.ncml'

Thanks,

Jim