Xarray: Let's list all the netCDF files that xarray can't open
At the Pangeo developers meetings, I am hearing lots of reports from folks like @dopplershift and @rsignell-usgs about netCDF datasets that xarray can't open.
My expectation is that xarray doesn't have strong requirements on the contents of datasets. (It doesn't "enforce" cf compatibility for example; that's optional.) Anything that can be written to netCDF should be readable by xarray.
I would like to collect examples of places where xarray fails. So far, I am only aware of one:
- Self-referential multidimensional coordinates (#2233). Datasets which contain variables like
siglay(siglay, node). Onlysiglay(siglay)would work.
__Are there other distinct cases?__
Please provide links / sample code of netCDF datasets that xarray can't read. Even better would be short code snippets to create such datasets in python using the netcdf4 interface.
rabernat
All 20 comments
I believe the last one in the notebook below is already fixed and the first two are mentioned above but here is a data point:
http://nbviewer.jupyter.org/gist/ocefpaf/1bf3b86359c459c89d44a81d3129f967
ocefpaf
on 15 Aug 2018
import xarray as xr
xr.open_dataset('http://thredds.ucar.edu/thredds/dodsC/grib/NCEP/GFS/Global_0p5deg/TwoD')
---------------------------------------------------------------------------
MissingDimensionsError Traceback (most recent call last)
<ipython-input-6-e2a87d803d99> in <module>()
----> 1 xr.open_dataset(gfs_cat.datasets[0].access_urls['OPENDAP'])
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs)
344 lock = _default_lock(filename_or_obj, engine)
345 with close_on_error(store):
--> 346 return maybe_decode_store(store, lock)
347 else:
348 if engine is not None and engine != 'scipy':
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/api.py in maybe_decode_store(store, lock)
256 store, mask_and_scale=mask_and_scale, decode_times=decode_times,
257 concat_characters=concat_characters, decode_coords=decode_coords,
--> 258 drop_variables=drop_variables)
259
260 _protect_dataset_variables_inplace(ds, cache)
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables)
428 vars, attrs, concat_characters, mask_and_scale, decode_times,
429 decode_coords, drop_variables=drop_variables)
--> 430 ds = Dataset(vars, attrs=attrs)
431 ds = ds.set_coords(coord_names.union(extra_coords).intersection(vars))
432 ds._file_obj = file_obj
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/dataset.py in __init__(self, data_vars, coords, attrs, compat)
363 coords = {}
364 if data_vars is not None or coords is not None:
--> 365 self._set_init_vars_and_dims(data_vars, coords, compat)
366 if attrs is not None:
367 self.attrs = attrs
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/dataset.py in _set_init_vars_and_dims(self, data_vars, coords, compat)
381
382 variables, coord_names, dims = merge_data_and_coords(
--> 383 data_vars, coords, compat=compat)
384
385 self._variables = variables
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in merge_data_and_coords(data, coords, compat, join)
363 indexes = dict(extract_indexes(coords))
364 return merge_core(objs, compat, join, explicit_coords=explicit_coords,
--> 365 indexes=indexes)
366
367
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in merge_core(objs, compat, join, priority_arg, explicit_coords, indexes)
433 coerced = coerce_pandas_values(objs)
434 aligned = deep_align(coerced, join=join, copy=False, indexes=indexes)
--> 435 expanded = expand_variable_dicts(aligned)
436
437 coord_names, noncoord_names = determine_coords(coerced)
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in expand_variable_dicts(list_of_variable_dicts)
209 var_dicts.append(coords)
210
--> 211 var = as_variable(var, name=name)
212 sanitized_vars[name] = var
213
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/variable.py in as_variable(obj, name)
112 'dimensions %r. xarray disallows such variables because they '
113 'conflict with the coordinates used to label '
--> 114 'dimensions.' % (name, obj.dims))
115 obj = obj.to_index_variable()
116
MissingDimensionsError: 'time' has more than 1-dimension and the same name as one of its dimensions ('reftime', 'time'). xarray disallows such variables because they conflict with the coordinates used to label dimensions.
dopplershift
on 15 Aug 2018
Here's a sample CDL for a file:
netcdf temp {
dimensions:
profile = 1 ;
station = 1 ;
isobaric = 31 ;
station_name_strlen = 10 ;
station_description_strlen = 33 ;
variables:
float isobaric(station, profile, isobaric) ;
isobaric:standard_name = "isobaric" ;
isobaric:long_name = "isobaric" ;
isobaric:units = "Pa" ;
isobaric:positive = "down" ;
isobaric:axis = "Z" ;
float Geopotential_height_isobaric(station, profile, isobaric) ;
Geopotential_height_isobaric:standard_name = "Geopotential_height_isobaric" ;
Geopotential_height_isobaric:long_name = "Geopotential_height_isobaric" ;
Geopotential_height_isobaric:units = "gpm" ;
Geopotential_height_isobaric:coordinates = "time longitude latitude isobaric" ;
char station_name(station, station_name_strlen) ;
station_name:long_name = "station name" ;
station_name:cf_role = "timeseries_id" ;
char station_description(station, station_description_strlen) ;
station_description:long_name = "station description" ;
station_description:standard_name = "platform_name" ;
double latitude(station) ;
latitude:units = "degrees_north" ;
latitude:long_name = "profile latitude" ;
double longitude(station) ;
longitude:units = "degrees_east" ;
longitude:long_name = "profile longitude" ;
double time(station, profile) ;
time:units = "Hour since 2018-08-15T12:00:00Z" ;
time:calendar = "proleptic_gregorian" ;
time:standard_name = "time" ;
time:long_name = "GRIB forecast or observation time" ;
// global attributes:
:Conventions = "CDM-Extended-CF" ;
:history = "Written by CFPointWriter" ;
:title = "Extract Points data from Grid file /data/ldm/pub/native/grid/NCEP/GFS/Global_0p5deg/GFS_Global_0p5deg_20180815_1200.grib2.ncx3#LatLon_361X720-p25S-180p0E" ;
:featureType = "timeSeriesProfile" ;
:time_coverage_start = "2018-08-15T18:00:00Z" ;
:time_coverage_end = "2018-08-15T18:00:00Z" ;
:geospatial_lat_min = 39.9995 ;
:geospatial_lat_max = 40.0005 ;
:geospatial_lon_min = -105.0005 ;
:geospatial_lon_max = -104.9995 ;
}
which gives:
---------------------------------------------------------------------------
MissingDimensionsError Traceback (most recent call last)
<ipython-input-10-d6f8d8651b9f> in <module>()
4 query.add_lonlat().accept('netcdf4')
5 nc = ncss.get_data(query)
----> 6 xr.open_dataset(NetCDF4DataStore(nc))
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs)
352 store = backends.ScipyDataStore(filename_or_obj)
353
--> 354 return maybe_decode_store(store)
355
356
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/api.py in maybe_decode_store(store, lock)
256 store, mask_and_scale=mask_and_scale, decode_times=decode_times,
257 concat_characters=concat_characters, decode_coords=decode_coords,
--> 258 drop_variables=drop_variables)
259
260 _protect_dataset_variables_inplace(ds, cache)
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables)
428 vars, attrs, concat_characters, mask_and_scale, decode_times,
429 decode_coords, drop_variables=drop_variables)
--> 430 ds = Dataset(vars, attrs=attrs)
431 ds = ds.set_coords(coord_names.union(extra_coords).intersection(vars))
432 ds._file_obj = file_obj
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/dataset.py in __init__(self, data_vars, coords, attrs, compat)
363 coords = {}
364 if data_vars is not None or coords is not None:
--> 365 self._set_init_vars_and_dims(data_vars, coords, compat)
366 if attrs is not None:
367 self.attrs = attrs
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/dataset.py in _set_init_vars_and_dims(self, data_vars, coords, compat)
381
382 variables, coord_names, dims = merge_data_and_coords(
--> 383 data_vars, coords, compat=compat)
384
385 self._variables = variables
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in merge_data_and_coords(data, coords, compat, join)
363 indexes = dict(extract_indexes(coords))
364 return merge_core(objs, compat, join, explicit_coords=explicit_coords,
--> 365 indexes=indexes)
366
367
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in merge_core(objs, compat, join, priority_arg, explicit_coords, indexes)
433 coerced = coerce_pandas_values(objs)
434 aligned = deep_align(coerced, join=join, copy=False, indexes=indexes)
--> 435 expanded = expand_variable_dicts(aligned)
436
437 coord_names, noncoord_names = determine_coords(coerced)
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/merge.py in expand_variable_dicts(list_of_variable_dicts)
209 var_dicts.append(coords)
210
--> 211 var = as_variable(var, name=name)
212 sanitized_vars[name] = var
213
~/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/core/variable.py in as_variable(obj, name)
112 'dimensions %r. xarray disallows such variables because they '
113 'conflict with the coordinates used to label '
--> 114 'dimensions.' % (name, obj.dims))
115 obj = obj.to_index_variable()
116
MissingDimensionsError: 'isobaric' has more than 1-dimension and the same name as one of its dimensions ('station', 'profile', 'isobaric'). xarray disallows such variables because they conflict with the coordinates used to label dimensions.
The two examples by @dopplershift are the same problem as in https://github.com/pydata/xarray/issues/2233
fmaussion
on 16 Aug 2018
This is mentioned elsewhere (can't find the issue right now) and may be out of scope for this issue but I'm going to say it anyway: opening a NetCDF file with groups was not as easy as I wanted it to be when first starting out with xarray.
djhoese
on 17 Aug 2018
I found this problem too long ago (see #457). Back then the workaround we implemented is to exclude the offending variable ("siglay" or "isobaric" in the examples above) with the "drop_variables" optional argument. Of course this is not great if you want to actually use the values in the variable you are dropping.
I personally don't like the notion of a "two dimensional coordinate", I find it confusing. However this kind of netCDFs are common, so fully supporting them in xarray would be nice. But I don't know how. Maybe just renaming the variable instead of dropping it with a "rename_variables"? This is the only thing that comes to my mind.
markelg
on 23 Aug 2018
@djhoese - it would be great if you could track down a more specific example of the issue you are referring to.
Excluding this possible problem with groups, my assessment of the feedback above is that, actually, the only problem is #2233: we can't have multidimensional variables that are also their own dimensions. This is a good thing. It means we have a specific problem to fix.
Right now this is ok:
dimensions:
x = 4
y = 3
variables:
int x(x);
int y(y);
float data(y, x)
But this is not
dimensions:
x = 4
y = 3
variables:
int x(x);
float y(y, x);
float data(y, x)
Personally I find this to be an incredibly confusing, recursive use of the concept of "dimensions". For me, dimensions should be orthogonal. In the second example, y is a [non-dimension] coordinate, not a dimension! The actual dimension is implicit, some sort of logical y_index. I wish that CF / netCDF had never chosen to accept this as a valid schema. But I admit that perhaps my internal mental model is too wrapped up with xarray!
So the question is: what can we do about it?
I propose the following general outline:
- Create a new decoding function to effectively "fix" the recursively defined dimension by renaming
y(y, x)into something likey_coordinate(y, x) - Add a new option to
open_datasetcalleddecode_recursive_dimensionwhich defaults toFalse - Raise a more informative error when these types of datasets are encountered which suggests calling
open_datasetwithdecode_recursive_dimension=True
Finally, we might want to raise this upstream with netCDF or CF conventions to try to understand better why this sort of schema is being encouraged.
rabernat
on 6 Sep 2018
@rabernat For the groups NetCDF files I had in mind the NASA L1B data files for the satellite instrument VIIRS onboard Suomi-NPP and NOAA-20 satellites. You can see an example file here.
The summary of the ncdump is:
netcdf VNP02IMG.A2018008.0000.001.2018061001540 {
dimensions:
number_of_scans = 202 ;
number_of_lines = 6464 ;
number_of_pixels = 6400 ;
number_of_LUT_values = 65536 ;
... lots of global attributes ...
group: scan_line_attributes {
variables:
double scan_start_time(number_of_scans) ;
scan_start_time:long_name = "Scan start time (TAI93)" ;
scan_start_time:units = "seconds" ;
scan_start_time:_FillValue = -999.9 ;
scan_start_time:valid_min = 0. ;
scan_start_time:valid_max = 2000000000. ;
... lots of other variables in this group ...
group: observation_data {
variables:
ushort I04(number_of_lines, number_of_pixels) ;
I04:long_name = "I-band 04 earth view radiance" ;
I04:units = "Watts/meter^2/steradian/micrometer" ;
I04:_FillValue = 65535US ;
I04:valid_min = 0US ;
I04:valid_max = 65527US ;
I04:scale_factor = 6.104354e-05f ;
I04:add_offset = 0.0016703f ;
I04:flag_values = 65532US, 65533US, 65534US ;
I04:flag_meanings = "Missing_EV Bowtie_Deleted Cal_Fail" ;
When I first started out with xarray I assumed I would be able to do something like:
import xarray as xr
nc = xr.open_dataset('VNP02IMG.A2018008.0000.001.2018061001540.nc')
band_data = nc['observation_data/I04']
Which I can't do, but can do with the python netcdf4 library:
In [7]: from netCDF4 import Dataset
In [8]: nc = Dataset('VNP02IMG.A2018008.0000.001.2018061001540.nc')
In [9]: nc['observation_data/I04']
Out[9]:
<class 'netCDF4._netCDF4.Variable'>
I understand that I can provide the group keyword to open_dataset but then I have to open the file twice if I want to get the global attributes. So any interface I had set up in my code to pass around one object with all of the file contents won't work. That isn't xarray's fault and shouldn't necessarily be something xarray has to solve, but it is a type of NetCDF4 file that is valid and can't be read "perfectly" with xarray.
djhoese
on 6 Sep 2018
@rabernat While I agree that they're (somewhat) confusing files, I think you're missing two things:
netCDF doesn't enforce naming on dimensions and variables. Full stop. The only naming netCDF will care about is any conflict with an internal reserved name (I'm not sure that those even exist for anything besides attributes.) IMO that's a good thing, but more importantly it's not the netCDF library's job to enforce any of it.
CF is an attribute convention. This also means that the conventions say absolutely nothing about naming of variables and dimensions.
IMO, xarray is being overly pedantic here. XArray states that it adopts the Common Data Model (CDM); netCDF-java and the CDM were the tools used to generate the failing examples above.
dopplershift
on 6 Sep 2018
@dopplershift - thanks for the clarifications! I agree that it's good for netCDF to be as open-ended as possible.
So I guess my quarrel is with the CDM. This is what it says about variables and dimensions:
A Variable is a container for data. It has a DataType, a set of Dimensions that define its array shape, and optionally a set of Attributes. Any shared Dimension it uses must be in the same Group or a parent Group.
A Dimension is used to define the array shape of a Variable. It may be shared among Variables, which provides a simple yet powerful way of associating Variables. When a Dimension is shared, it has a unique name within the Group. If unlimited, a Dimension's length may increase. If variableLength, then the actual length is data dependent, and can only be found by reading the data. A variableLength Dimension cannot be shared or unlimited.
then later
A Variable can have zero or more Coordinate Systems containing one or more CoordinateAxis. A CoordinateAxis can only be part of a Variable's CoordinateSystem if the CoordinateAxis' set of Dimensions is a subset of the Variable's set of Dimensions. This ensures that every data point in the Variable has a corresponding coordinate value for each of the CoordinateAxis in the CoordinateSystem.
A Coordinate System has one or more CoordinateAxis, and zero or more CoordinateTransforms.
A CoordinateAxis is a subtype of Variable, and is optionally classified according to the types in AxisType.
These are the rules which restrict which Variables can be used as Coordinate Axes:
Shared Dimensions: All dimensions used by a Coordinate Axis must be shared with the data variable. When a variable is part of a Structure, the dimensions used by the parent Structure(s) are considered to be part of the nested Variable.
I have a very hard time understanding what all of this means. Can the same variable be a "Dimension" and a "CoordinateAxis" in CDM?
It seems much simpler to me to use the CF approach to describe the physical coordinates of the data using "auxiliary coordinate variables" and to keep the dimensions as purely 1D "coordinate variables".
IMO, xarray is being overly pedantic here.
What would you like xarray to do with these datasets, given the fact that orthogonality of dimensions is central to its data model?
rabernat
on 6 Sep 2018
Perhaps part of the confusion is simply that y has different meanings in different contexts. When used as a dimension (e.g. to "define the array shape of a Variable" in CDM terms), it is indeed 1D. When used as a variable (or "CoordinateAxis"), it is 2D. XArray doesn't have a separate namespace for dimensions and variables.
rabernat
on 6 Sep 2018
Currently, xarray requires that variables with a name matching a dimension are 1D variables along that dimension, e.g.,
for dim in dataset.dims:
if dim in dataset.variables:
assert dataset.variables[dim].dims == (dim,)
I agree that this unnecessarily complicates our data model. There's no particular advantage to this invariant, besides removing the need to check the dimensions of variables used for indexing lookups. I'm sure there are some cases internally where we currently rely on this assumption, but it should be relatively easy to relax.
shoyer
on 6 Sep 2018
It seems like this relaxation is compatible with the refactoring of indexes. Right now, we automatically create 1D indexes for all coordinate variables. The problem with 2D dimensions is that such indexes don't make sense:
data.sel(y=3.14)
But maybe we could turn multi-dimensional coordinate variables into multi-indexes? Or no index at all? In any case, we could still do
data.isel(y=3)
i.e. logical indexing on the dimension axis.
rabernat
on 6 Sep 2018
Or no index at all?
This would be my inclination (for the default behavior). It would mean that you could not longer count on anyways being able to do labeled indexing along each dimension, but in the broader scheme of things I don't think that's a big deal.
shoyer
on 6 Sep 2018
That sounds reasonable to me. I don't necessarily expect all of the xarray goodness to work with those files, but I do expect them to open without error.
dopplershift
on 6 Sep 2018
Just adding that netCDF files produced as output from the GOTM turbulence model cannot be opened by xarray. I believe the reason is self-referential multidimensional coordinates.
nordam
on 30 Nov 2018
@nordam , can you provide an example?
rsignell-usgs
on 30 Nov 2018
Indeed. An example file (1.1 MB) can be found here:
http://folk.ntnu.no/nordam/entrainment.nc
And the error message I get on trying to open this file is:
ValueError: 'z' has more than 1-dimension and the same name as one of its dimensions ('time', 'z', 'lat', 'lon'). xarray disallows such variables because they conflict with the coordinates used to label dimensions.
nordam
on 30 Nov 2018
We are working on fixing this in #2405. That PR (mine) has most of the basic functionality there, but it still needs more testing. Unfortunately, I don't have bandwidth right now to complete the required work.
If anyone here needs this fixed urgently and actually has time to work on it, I encourage you to pick up that PR and try to finish it off. We will be happy to provide help and support along the way.
rabernat
on 30 Nov 2018
Adding another example. While working through the Model Evaluation Tool (MET) tutorial, I created a NetCDF file with the tool, and wasn't able to open the file it created.
MissingDimensionsError: 'lat' has more than 1-dimension and the same name as one of its dimensions ('lat', 'lon'). xarray disallows such variables because they conflict with the coordinates used to label dimensions.
Sounds to me like the same error caused by https://github.com/pydata/xarray/issues/2233
Below is the .nc file contents with ncdump
>>ncdump sample_fcst_24L_2005080800V_12A.nc -h
netcdf sample_fcst_24L_2005080800V_12A {
dimensions:
lat = 129 ;
lon = 185 ;
variables:
float lat(lat, lon) ;
lat:long_name = "latitude" ;
lat:units = "degrees_north" ;
lat:standard_name = "latitude" ;
float lon(lat, lon) ;
lon:long_name = "longitude" ;
lon:units = "degrees_east" ;
lon:standard_name = "longitude" ;
float APCP_12(lat, lon) ;
APCP_12:name = "APCP_12" ;
APCP_12:long_name = "Total precipitation" ;
APCP_12:level = "A12" ;
APCP_12:units = "kg/m^2" ;
APCP_12:_FillValue = -9999.f ;
APCP_12:init_time = "20050807_000000" ;
APCP_12:init_time_ut = "1123372800" ;
APCP_12:valid_time = "20050808_000000" ;
APCP_12:valid_time_ut = "1123459200" ;
APCP_12:accum_time = "120000" ;
APCP_12:accum_time_sec = 43200 ;
// global attributes:
:MET_version = "V8.1.2" ;
:MET_tool = "pcp_combine" ;
:RunCommand = "Sum: 4 files with accumulations of 030000." ;
:Projection = "Lambert Conformal" ;
:hemisphere = "N" ;
:scale_lat_1 = "25.000000" ;
:scale_lat_2 = "25.000000" ;
:lat_pin = "12.190000" ;
:lon_pin = "-133.459000" ;
:x_pin = "0.000000" ;
:y_pin = "0.000000" ;
:lon_orient = "-95.000000" ;
:d_km = "40.635000" ;
:r_km = "6371.200000" ;
:nx = "185" ;
:ny = "129 grid_points" ;
}
blaylockbk
on 30 Jan 2020
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Most helpful comment
Currently, xarray requires that variables with a name matching a dimension are 1D variables along that dimension, e.g.,
I agree that this unnecessarily complicates our data model. There's no particular advantage to this invariant, besides removing the need to check the dimensions of variables used for indexing lookups. I'm sure there are some cases internally where we currently rely on this assumption, but it should be relatively easy to relax.