Merge branch 'main' of github.com:NCAS-CMS/cf-python

Author: davidhassell

Changelog.rst

@@ -3,6 +3,8 @@ version 3.17.0
 
 **2024-??-??**
 
+* New methods: `cf.Field.pad_missing` and `cf.Data.pad_missing`
+  (https://github.com/NCAS-CMS/cf-python/issues/717)
 * Fix occasional bug when calculating UGRID cell areas when
   non-spatial coordinates span the discrete axis
   (https://github.com/NCAS-CMS/cf-python/issues/721)

cf/aggregate.py

@@ -3920,7 +3920,22 @@ def _sort_indices(m, canonical_axes):
     """
     canonical_axes = [m.id_to_axis[identity] for identity in canonical_axes]
     sort_indices = tuple([m.sort_indices[axis] for axis in canonical_axes])
-    needs_sorting = sort_indices != (slice(None),) * len(sort_indices)
+
+    # Whether or not one or more of the axes needs sorting
+    needs_sorting = False
+    for sort_index in sort_indices:
+        # Note: sort_index can only be a slice object or a numpy array
+        #       (see `_create_hash_and_first_values`)
+        if isinstance(sort_index, slice):
+            if sort_index != slice(None):
+                # sort_index is a slice other than slice(None)
+                needs_sorting = True
+                break
+        elif sort_index.size > 1:
+            # sort_index is an array of 2 or more integers
+            needs_sorting = True
+            break
+
     return sort_indices, needs_sorting
 
 

cf/data/data.py

@@ -2180,6 +2180,109 @@ def mean_of_upper_decile(
 
         return d
 
+    @_inplace_enabled(default=False)
+    def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
+        """Pad an axis with missing data.
+
+        :Parameters:
+
+            axis: `int`
+                Select the axis for which the padding is to be
+                applied.
+
+                *Parameter example:*
+                  Pad second axis: ``axis=1``.
+
+                *Parameter example:*
+                  Pad the last axis: ``axis=-1``.
+
+            {{pad_width: sequence of `int`, optional}}
+
+            {{to_size: `int`, optional}}
+
+            {{inplace: `bool`, optional}}
+
+        :Returns:
+
+            `Data` or `None`
+                The padded data, or `None` if the operation was
+                in-place.
+
+        **Examples**
+
+        >>> d = cf.Data(np.arange(6).reshape(2, 3))
+        >>> print(d.array)
+        [[0 1 2]
+         [3 4 5]]
+        >>> e = d.pad_missing(1, (1, 2))
+        >>> print(e.array)
+        [[-- 0 1 2 -- --]
+         [-- 3 4 5 -- --]]
+        >>> f = e.pad_missing(0, (0, 1))
+        >>> print(f.array)
+        [[--  0  1  2 -- --]
+         [--  3  4  5 -- --]
+         [-- -- -- -- -- --]]
+
+        >>> g = d.pad_missing(1, to_size=5)
+        >>> print(g.array)
+        [[0 1 2 -- --]
+         [3 4 5 -- --]]
+
+        """
+        if not 0 <= axis < self.ndim:
+            raise ValueError(
+                f"'axis' must be a valid dimension position. Got {axis}"
+            )
+
+        if to_size is not None:
+            # Set pad_width from to_size
+            if pad_width is not None:
+                raise ValueError("Can't set both 'pad_width' and 'to_size'")
+
+            pad_width = (0, to_size - self.shape[axis])
+        elif pad_width is None:
+            raise ValueError("Must set either 'pad_width' or 'to_size'")
+
+        pad_width = np.asarray(pad_width)
+        if pad_width.shape != (2,) or not pad_width.dtype.kind == "i":
+            raise ValueError(
+                "'pad_width' must be a sequence of two integers. "
+                f"Got: {pad_width}"
+            )
+
+        pad_width = tuple(pad_width)
+        if any(n < 0 for n in pad_width):
+            if to_size is not None:
+                raise ValueError(
+                    f"'to_size' ({to_size}) must not be smaller than the "
+                    f"original axis size ({self.shape[axis]})"
+                )
+
+            raise ValueError(
+                f"Can't set a negative number of pad values. Got: {pad_width}"
+            )
+
+        d = _inplace_enabled_define_and_cleanup(self)
+
+        dx = d.to_dask_array()
+        mask0 = da.ma.getmaskarray(dx)
+
+        pad = [(0, 0)] * dx.ndim
+        pad[axis] = pad_width
+
+        # Pad the data with zero. This will lose the original mask.
+        dx = da.pad(dx, pad, mode="constant", constant_values=0)
+
+        # Pad the mask with True
+        mask = da.pad(mask0, pad, mode="constant", constant_values=True)
+
+        # Set the mask
+        dx = da.ma.masked_where(mask, dx)
+
+        d._set_dask(dx)
+        return d
+
     @_inplace_enabled(default=False)
     def percentile(
         self,

cf/docstring/docstring.py

@@ -587,6 +587,14 @@
     "{{weights auto: `bool`, optional}}": """auto: `bool`, optional
                 If True then return `False` if weights can't be found,
                 rather than raising an exception.""",
+    # pad_width
+    "{{pad_width: sequence of `int`, optional}}": """pad_width: sequence of `int`, optional
+                Number of values to pad before and after the edges of
+                the axis.""",
+    # to_size
+    "{{to_size: `int`, optional}}": """to_size: `int`, optional
+                Pad the axis after so that the new axis has the given
+                size.""",
     # ----------------------------------------------------------------
     # Method description substitutions (4 levels of indentation)
     # ----------------------------------------------------------------

cf/field.py

@@ -11953,6 +11953,136 @@ def halo(
 
         return f
 
+    @_inplace_enabled(default=False)
+    def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
+        """Pad an axis with missing data.
+
+         The field's data and all metadata constructs that span the
+         axis are padded.
+
+        .. versionadded:: 3.17.0
+
+        :Parameters:
+
+             axis: `str` or `int`
+                 Select the domain axis which is to be padded, defined
+                 by that which would be selected by passing the given
+                 axis description to a call of the field construct's
+                 `domain_axis` method. For example, for a value of
+                 ``'X'``, the domain axis construct returned by
+                 ``f.domain_axis('X')`` is selected.
+
+             {{pad_width: sequence of `int`, optional}}
+
+             {{to_size: `int`, optional}}
+
+             {{inplace: `bool`, optional}}
+
+         :Returns:
+
+             `Field` or `None`
+                 The padded field construct, or `None` if the operation
+                 was in-place.
+
+        **Examples*
+
+        >>> f = cf.example_field(6)
+        >>> print(f)
+        Field: precipitation_amount (ncvar%pr)
+        --------------------------------------
+        Data            : precipitation_amount(cf_role=timeseries_id(2), time(4))
+        Dimension coords: time(4) = [2000-01-16 12:00:00, ..., 2000-04-15 00:00:00] gregorian
+        Auxiliary coords: latitude(cf_role=timeseries_id(2)) = [25.0, 7.0] degrees_north
+                        : longitude(cf_role=timeseries_id(2)) = [10.0, 40.0] degrees_east
+                        : cf_role=timeseries_id(cf_role=timeseries_id(2)) = [x1, y2]
+                        : altitude(cf_role=timeseries_id(2), 3, 4) = [[[1.0, ..., --]]] m
+        Coord references: grid_mapping_name:latitude_longitude
+        >>> print(f.array)
+        [[1. 2. 3. 4.]
+         [5. 6. 7. 8.]]
+        >>> g = f.pad_missing('T', (0, 5))
+        >>> print(g)
+        Field: precipitation_amount (ncvar%pr)
+        --------------------------------------
+        Data            : precipitation_amount(cf_role=timeseries_id(2), time(9))
+        Dimension coords: time(9) = [2000-01-16 12:00:00, ..., --] gregorian
+        Auxiliary coords: latitude(cf_role=timeseries_id(2)) = [25.0, 7.0] degrees_north
+                        : longitude(cf_role=timeseries_id(2)) = [10.0, 40.0] degrees_east
+                        : cf_role=timeseries_id(cf_role=timeseries_id(2)) = [x1, y2]
+                        : altitude(cf_role=timeseries_id(2), 3, 4) = [[[1.0, ..., --]]] m
+        Coord references: grid_mapping_name:latitude_longitude
+        >>> print(g.array)
+        [[1.0 2.0 3.0 4.0 -- -- -- -- --]
+         [5.0 6.0 7.0 8.0 -- -- -- -- --]]
+        >>> h = g.pad_missing('cf_role=timeseries_id', (0, 1))
+        >>> print(h)
+        Field: precipitation_amount (ncvar%pr)
+        --------------------------------------
+        Data            : precipitation_amount(cf_role=timeseries_id(3), time(9))
+        Dimension coords: time(9) = [2000-01-16 12:00:00, ..., --] gregorian
+        Auxiliary coords: latitude(cf_role=timeseries_id(3)) = [25.0, 7.0, --] degrees_north
+                        : longitude(cf_role=timeseries_id(3)) = [10.0, 40.0, --] degrees_east
+                        : cf_role=timeseries_id(cf_role=timeseries_id(3)) = [x1, y2, --]
+                        : altitude(cf_role=timeseries_id(3), 3, 4) = [[[1.0, ..., --]]] m
+        Coord references: grid_mapping_name:latitude_longitude
+        >>> print(h.array)
+        [[1.0 2.0 3.0 4.0 -- -- -- -- --]
+         [5.0 6.0 7.0 8.0 -- -- -- -- --]
+         [ --  --  --  -- -- -- -- -- --]]
+
+        >>> print(f.pad_missing('time', to_size=6))
+        Field: precipitation_amount (ncvar%pr)
+        --------------------------------------
+        Data            : precipitation_amount(cf_role=timeseries_id(2), time(6))
+        Dimension coords: time(6) = [2000-01-16 12:00:00, ..., --] gregorian
+        Auxiliary coords: latitude(cf_role=timeseries_id(2)) = [25.0, 7.0] degrees_north
+                        : longitude(cf_role=timeseries_id(2)) = [10.0, 40.0] degrees_east
+                        : cf_role=timeseries_id(cf_role=timeseries_id(2)) = [x1, y2]
+                        : altitude(cf_role=timeseries_id(2), 3, 4) = [[[1.0, ..., --]]] m
+        Coord references: grid_mapping_name:latitude_longitude
+
+        """
+        f = _inplace_enabled_define_and_cleanup(self)
+
+        try:
+            axis1 = f._parse_axes(axis)
+        except ValueError:
+            raise ValueError(
+                f"Can't pad_missing: Bad axis specification: {axis!r}"
+            )
+
+        if len(axis1) != 1:
+            raise ValueError(
+                f"Can't pad_missing: Bad axis specification: {axis!r}"
+            )
+
+        data_axes = f.get_data_axes()
+        axis = axis1[0]
+        iaxis = data_axes.index(axis)
+
+        # Pad the field
+        super(Field, f).pad_missing(
+            iaxis, pad_width=pad_width, to_size=to_size, inplace=True
+        )
+
+        # Set new domain axis size
+        domain_axis = f.domain_axis(axis)
+        domain_axis.set_size(f.shape[iaxis])
+
+        data_axes = f.constructs.data_axes()
+        for key, construct in f.constructs.filter_by_data(todict=True).items():
+            construct_axes = data_axes[key]
+            if axis not in construct_axes:
+                continue
+
+            # Pad the construct
+            iaxis = construct_axes.index(axis)
+            construct.pad_missing(
+                iaxis, pad_width=pad_width, to_size=to_size, inplace=True
+            )
+
+        return f
+
     def percentile(
         self,
         ranks,

cf/mixin/propertiesdata.py

@@ -1888,6 +1888,38 @@ def minimum(self):
             "ERROR: Can't get the minimum when there is no data array"
         )
 
+    @_inplace_enabled(default=False)
+    def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
+        """Pad an axis with missing data.
+
+        :Parameters:
+
+            axis: `int`
+                Select the axis for which the padding is to be
+                applied.
+
+            {{pad_width: sequence of `int`, optional}}
+
+            {{to_size: `int`, optional}}
+
+            {{inplace: `bool`, optional}}
+
+        :Returns:
+
+            `{{class}}` or `None`
+                The {{class}} with padded data, or `None` if the
+                operation was in-place.
+
+        """
+        return self._apply_data_oper(
+            _inplace_enabled_define_and_cleanup(self),
+            "pad_missing",
+            axis=axis,
+            pad_width=pad_width,
+            to_size=to_size,
+            inplace=inplace,
+        )
+
     def period(self, *value, **config):
         """Return or set the period of the data.
 

cf/mixin/propertiesdatabounds.py

@@ -3874,6 +3874,40 @@ def inspect(self):
         """
         print(cf_inspect(self))  # pragma: no cover
 
+    @_inplace_enabled(default=False)
+    def pad_missing(self, axis, pad_width=None, to_size=None, inplace=False):
+        """Pad an axis with missing data.
+
+        :Parameters:
+
+            axis: `int`
+                Select the axis for which the padding is to be
+                applied.
+
+            {{pad_width: sequence of `int`, optional}}
+
+            {{to_size: `int`, optional}}
+
+            {{inplace: `bool`, optional}}
+
+        :Returns:
+
+            `{{class}}` or `None`
+                The {{class}} with padded data, or `None` if the
+                operation was in-place.
+
+        """
+        return self._apply_superclass_data_oper(
+            _inplace_enabled_define_and_cleanup(self),
+            "pad_missing",
+            bounds=True,
+            interior_ring=True,
+            axis=axis,
+            pad_width=pad_width,
+            to_size=to_size,
+            inplace=inplace,
+        )
+
     def period(self, *value, **config):
         """Return or set the period for cyclic values.