#1621 optional decode timedelta

doc/whats-new.rst

@@ -60,6 +60,12 @@ New Features
   feature requires cftime version 1.1.0 or greater.  By
   `Spencer Clark <https://github.com/spencerkclark>`_.
 
+- Add keyword ``decode_timedelta`` to :py:func:`xarray.open_dataset`,
+  (:py:func:`xarray.open_dataarray`, :py:func:`xarray.open_dataarray`,
+  :py:func:`xarray.decode_cf`) that allows to disable/enable the decoding of timedeltas
+  independently of time decoding (:issue:`1621`)
+  `Aureliana Barghini <https://github.com/aurghs>`
+
 Bug fixes
 ~~~~~~~~~
 - ``ValueError`` is raised when ``fill_value`` is not a scalar in :py:meth:`full_like`. (:issue`3977`)

xarray/backends/api.py

@@ -303,6 +303,7 @@ def open_dataset(
     drop_variables=None,
     backend_kwargs=None,
     use_cftime=None,
+    decode_timedelta=None,
 ):
     """Open and decode a dataset from a file or file-like object.
 
@@ -383,6 +384,11 @@ def open_dataset(
         represented using ``np.datetime64[ns]`` objects.  If False, always
         decode times to ``np.datetime64[ns]`` objects; if this is not possible
         raise an error.
+    decode_timedelta : bool, optional
+        If True, decode variables and coordinates with time units in
+        {'days', 'hours', 'minutes', 'seconds', 'milliseconds', 'microseconds'}
+        into timedelta objects. If False, leave them encoded as numbers.
+        If None (default), assume the same value of decode_time.
 
     Returns
     -------
@@ -435,6 +441,7 @@ def open_dataset(
         decode_times = False
         concat_characters = False
         decode_coords = False
+        decode_timedelta = False
 
     if cache is None:
         cache = chunks is None
@@ -451,6 +458,7 @@ def maybe_decode_store(store, lock=False):
             decode_coords=decode_coords,
             drop_variables=drop_variables,
             use_cftime=use_cftime,
+            decode_timedelta=decode_timedelta,
         )
 
         _protect_dataset_variables_inplace(ds, cache)
@@ -477,6 +485,7 @@ def maybe_decode_store(store, lock=False):
                 chunks,
                 drop_variables,
                 use_cftime,
+                decode_timedelta,
             )
             name_prefix = "open_dataset-%s" % token
             ds2 = ds.chunk(chunks, name_prefix=name_prefix, token=token)
@@ -561,6 +570,7 @@ def open_dataarray(
     drop_variables=None,
     backend_kwargs=None,
     use_cftime=None,
+    decode_timedelta=None,
 ):
     """Open an DataArray from a file or file-like object containing a single
     data variable.
@@ -640,6 +650,11 @@ def open_dataarray(
         represented using ``np.datetime64[ns]`` objects.  If False, always
         decode times to ``np.datetime64[ns]`` objects; if this is not possible
         raise an error.
+    decode_timedelta : bool, optional
+        If True, decode variables and coordinates with time units in
+        {'days', 'hours', 'minutes', 'seconds', 'milliseconds', 'microseconds'}
+        into timedelta objects. If False, leave them encoded as numbers.
+        If None (default), assume the same value of decode_time.
 
     Notes
     -----
@@ -671,6 +686,7 @@ def open_dataarray(
         drop_variables=drop_variables,
         backend_kwargs=backend_kwargs,
         use_cftime=use_cftime,
+        decode_timedelta=decode_timedelta,
     )
 
     if len(dataset.data_vars) != 1:

xarray/backends/zarr.py

@@ -496,6 +496,7 @@ def open_zarr(
     drop_variables=None,
     consolidated=False,
     overwrite_encoded_chunks=False,
+    decode_timedelta=None,
     **kwargs,
 ):
     """Load and decode a dataset from a Zarr store.
@@ -555,6 +556,11 @@ def open_zarr(
     consolidated : bool, optional
         Whether to open the store using zarr's consolidated metadata
         capability. Only works for stores that have already been consolidated.
+    decode_timedelta : bool, optional
+        If True, decode variables and coordinates with time units in
+        {'days', 'hours', 'minutes', 'seconds', 'milliseconds', 'microseconds'}
+        into timedelta objects. If False, leave them encoded as numbers.
+        If None (default), assume the same value of decode_time.
 
     Returns
     -------
@@ -605,6 +611,7 @@ def open_zarr(
         decode_times = False
         concat_characters = False
         decode_coords = False
+        decode_timedelta = False
 
     def maybe_decode_store(store, lock=False):
         ds = conventions.decode_cf(
@@ -614,6 +621,7 @@ def maybe_decode_store(store, lock=False):
             concat_characters=concat_characters,
             decode_coords=decode_coords,
             drop_variables=drop_variables,
+            decode_timedelta=decode_timedelta,
         )
 
         # TODO: this is where we would apply caching

xarray/conventions.py

@@ -266,6 +266,7 @@ def decode_cf_variable(
     decode_endianness=True,
     stack_char_dim=True,
     use_cftime=None,
+    decode_timedelta=None,
 ):
     """
     Decodes a variable which may hold CF encoded information.
@@ -315,6 +316,9 @@ def decode_cf_variable(
     var = as_variable(var)
     original_dtype = var.dtype
 
+    if decode_timedelta is None:
+        decode_timedelta = decode_times
+
     if concat_characters:
         if stack_char_dim:
             var = strings.CharacterArrayCoder().decode(var, name=name)
@@ -328,12 +332,10 @@ def decode_cf_variable(
         ]:
             var = coder.decode(var, name=name)
 
+    if decode_timedelta:
+        var = times.CFTimedeltaCoder().decode(var, name=name)
     if decode_times:
-        for coder in [
-            times.CFTimedeltaCoder(),
-            times.CFDatetimeCoder(use_cftime=use_cftime),
-        ]:
-            var = coder.decode(var, name=name)
+        var = times.CFDatetimeCoder(use_cftime=use_cftime).decode(var, name=name)
 
     dimensions, data, attributes, encoding = variables.unpack_for_decoding(var)
     # TODO(shoyer): convert everything below to use coders
@@ -442,6 +444,7 @@ def decode_cf_variables(
     decode_coords=True,
     drop_variables=None,
     use_cftime=None,
+    decode_timedelta=None,
 ):
     """
     Decode several CF encoded variables.
@@ -492,6 +495,7 @@ def stackable(dim):
             decode_times=decode_times,
             stack_char_dim=stack_char_dim,
             use_cftime=use_cftime,
+            decode_timedelta=decode_timedelta,
         )
         if decode_coords:
             var_attrs = new_vars[k].attrs
@@ -518,6 +522,7 @@ def decode_cf(
     decode_coords=True,
     drop_variables=None,
     use_cftime=None,
+    decode_timedelta=None,
 ):
     """Decode the given Dataset or Datastore according to CF conventions into
     a new Dataset.
@@ -552,6 +557,11 @@ def decode_cf(
         represented using ``np.datetime64[ns]`` objects.  If False, always
         decode times to ``np.datetime64[ns]`` objects; if this is not possible
         raise an error.
+    decode_timedelta : bool, optional
+        If True, decode variables and coordinates with time units in
+        {'days', 'hours', 'minutes', 'seconds', 'milliseconds', 'microseconds'}
+        into timedelta objects. If False, leave them encoded as numbers.
+        If None (default), assume the same value of decode_time.
 
     Returns
     -------
@@ -583,6 +593,7 @@ def decode_cf(
         decode_coords,
         drop_variables=drop_variables,
         use_cftime=use_cftime,
+        decode_timedelta=decode_timedelta,
     )
     ds = Dataset(vars, attrs=attrs)
     ds = ds.set_coords(coord_names.union(extra_coords).intersection(vars))

xarray/tests/test_conventions.py

@@ -311,6 +311,41 @@ def test_decode_dask_times(self):
             conventions.decode_cf(original).chunk(),
         )
 
+    def test_decode_cf_time_kwargs(self):
+        ds = Dataset.from_dict(
+            {
+                "coords": {
+                    "timedelta": {
+                        "data": np.array([1, 2, 3], dtype="int64"),
+                        "dims": "timedelta",
+                        "attrs": {"units": "days"},
+                    },
+                    "time": {
+                        "data": np.array([1, 2, 3], dtype="int64"),
+                        "dims": "time",
+                        "attrs": {"units": "days since 2000-01-01"},
+                    },
+                },
+                "dims": {"time": 3, "timedelta": 3},
+                "data_vars": {
+                    "a": {"dims": ("time", "timedelta"), "data": np.ones((3, 3))},
+                },
+            }
+        )
+
+        dsc = conventions.decode_cf(ds)
+        assert dsc.timedelta.dtype == np.dtype("m8[ns]")
+        assert dsc.time.dtype == np.dtype("M8[ns]")
+        dsc = conventions.decode_cf(ds, decode_times=False)
+        assert dsc.timedelta.dtype == np.dtype("int64")
+        assert dsc.time.dtype == np.dtype("int64")
+        dsc = conventions.decode_cf(ds, decode_times=True, decode_timedelta=False)
+        assert dsc.timedelta.dtype == np.dtype("int64")
+        assert dsc.time.dtype == np.dtype("M8[ns]")
+        dsc = conventions.decode_cf(ds, decode_times=False, decode_timedelta=True)
+        assert dsc.timedelta.dtype == np.dtype("m8[ns]")
+        assert dsc.time.dtype == np.dtype("int64")
+
 
 class CFEncodedInMemoryStore(WritableCFDataStore, InMemoryDataStore):
     def encode_variable(self, var):