[Bug]: Replace static references to "time" for the time dimension name with self._dim in TemporalAccessor

[tomvothecoder]

What happened?

The TemporalAccessor class has static references to "time" as the name of the time dimension. However, datasets can use different names for a time dimension, such as "time_centered", "T", "time_counter",

Original source:

In looking at Test 3, I see another issue here. The time axis needed for temporal operations is not actually assigned as a dimension. I thought this could be fixed by dropping time_counter and just using time_centered: this would get rid of the multiple time axes which is the issue for Test 1 and 2 and would also be the appropriate coordinate for temporal operations:

import numpy as np, xarray as xr, xcdat as xc
TS_File ='https://thredds-su.ipsl.fr/thredds/dodsC/ipsl_thredds/omamce/TestCases/XCDAT/thetao_CF_1.nc'
ds = xr.open_dataset(TS_File, decode_times=False)
ds['time_counter'] = ds['time_centered']
ds = ds.drop_vars('time_centered')
ds = ds.rename({'time_counter': 'time_centered'})
ds.to_netcdf('test.nc', 'w', 'NETCDF3_CLASSIC')

ds = xc.open_dataset('test.nc')
ds.temporal.group_average('thetao', freq='year', weighted=True)

But this yields a different error:

AttributeError: 'DataArray' object has no attribute 'time'

@tomvothecoder - do you think this is a separate issue in the temporal averaging logic?

Originally posted by @pochedls in #285 (comment)

What did you expect to happen?

Temporal averaging should work regardless of the name of the time dimension.

Minimal Complete Verifiable Example

import numpy as np, xarray as xr, xcdat as xc
TS_File ='https://thredds-su.ipsl.fr/thredds/dodsC/ipsl_thredds/omamce/TestCases/XCDAT/thetao_CF_1.nc'
ds = xr.open_dataset(TS_File, decode_times=False)
ds['time_counter'] = ds['time_centered']
ds = ds.drop_vars('time_centered')
ds = ds.rename({'time_counter': 'time_centered'})
ds.to_netcdf('test.nc', 'w', 'NETCDF3_CLASSIC')

ds = xc.open_dataset('test.nc')
ds.temporal.group_average('thetao', freq='year', weighted=True)

Relevant log output

No response

Anything else we need to know?

This is a simple fix that involves updating "time" references to self._dim.

xcdat/xcdat/temporal.py

Line 149 in 4c51879

self._dim = get_axis_coord(self._dataset, "T").name

Environment

xcdat = v0.3.0

[jypeter]

@tomvothecoder are you detailing somewhere (maybe some place easy to find in the documentation) what will be recognized as a time axis (you mention above such as "time_centered", "T", "time_counter")?

I'm assuming you don't make a difference between upper and lowercase, but maybe you can have a look at what cdms2 considered a time axis. There is an isTime() Axis method on page 48 of cdms5.pdf (one of the documents I provided in #170) that says (with some copy/paste errors in the original doc):

isTime()
Returns true iff the axis is a time axis. ax is a longitude axis if:
• ax.axis==’T’, or
• ax.id[0:4]==’time’, or
• ax.id is in cdms2.axis.time_aliases

Note that page 47 also describes isLevel(), isLatitude() and isLongitude() that may be worth looking at, because some problems with time could be encountered with the other dimensions

As a last resort, the units attribute of an axis could also be used to determine the axis type. And if an axis matches isCircular() (page 49), it has a good chance to be a longitude axis

[jypeter]

Note: see example usage of isTime() in #310 (comment)

[tomvothecoder]

@tomvothecoder are you detailing somewhere (maybe some place easy to find in the documentation) what will be recognized as a time axis (you mention above such as "time_centered", "T", "time_counter")?

We mention how we map to coordinates in the Planned Features section, under "Things we are striving for".

• https://xcdat.readthedocs.io/en/latest/index.html#planned-features

• Robust handling of coordinates and its associated bounds

  • Coordinate variables are retrieved with cf_xarray using either the "axis", "standard_name", or dimension name attribute
  • Bounds are retrieved with cf_xarray using the "bounds" attr
  • Ability to operate on both longitudinal axis orientations, [0, 360) and [-180, 180)

The related function is called .get_axis_coord() that is used internally and also available as a public function.
Here is the function (with the docstring) and the related API documentation.

• API Source Code:

  xcdat/xcdat/axis.py

  Lines 28 to 87 in 4c51879

  	def get_axis_coord(
  	obj: Union[xr.Dataset, xr.DataArray], axis: CFAxisName
  	) -> xr.DataArray:
  	"""Gets the coordinate variable for an axis.
  	This function uses ``cf_xarray`` to try to find the matching coordinate
  	variable by checking the following attributes in order:
  	- ``"axis"``
  	- ``"standard_name"``
  	- Dimension name
  	- Must follow the valid short-hand convention
  	- For example, ``"lat"`` for latitude and ``"lon"`` for longitude
  	Parameters
  	----------
  	obj : Union[xr.Dataset, xr.DataArray]
  	The Dataset or DataArray object.
  	axis : CFAxisName
  	The CF-compliant axis name ("X", "Y", "T", "Z").
  	Returns
  	-------
  	xr.DataArray
  	The coordinate variable.
  	Raises
  	------
  	KeyError
  	If the coordinate variable was not found.
  	Notes
  	-----
  	Refer to [1]_ for a list of CF-compliant ``"axis"`` and ``"standard_name"``
  	attr names that can be interpreted by ``cf_xarray``.
  	References
  	----------
  	.. [1] https://cf-xarray.readthedocs.io/en/latest/coord_axes.html#axes-and-coordinates
  	"""
  	keys = CF_NAME_MAP[axis]
  	coord_var = None
  	for key in keys:
  	try:
  	coord_var = obj.cf[key]
  	break
  	except KeyError:
  	pass
  	if coord_var is None:
  	raise KeyError(
  	f"A coordinate variable for the {axis} axis was not found. Make sure "
  	"the coordinate variable exists and either the (1) 'axis' attr or (2) "
  	"'standard_name' attr is set, or (3) the dimension name follows the "
  	"short-hand convention (e.g.,'lat')."
  	)
  	return coord_var

• API Documentation (using docstring): https://xcdat.readthedocs.io/en/latest/_modules/xcdat/axis.html#get_axis_coord
• Intro to cf_xarray: https://cf-xarray.readthedocs.io/en/latest/howtouse.html
• cf_xarray mapping table for "axis" and "standard_name" attrs: https://cf-xarray.readthedocs.io/en/latest/coord_axes.html