Optimize ffill, bfill with dask when limit is specified (#9771)

* Reduce the number of tasks when the limit parameter is set on the push function

* Reduce the number of tasks when the limit parameter is set on the push function, and incorporate the method parameter for the cumreduction on the push method

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update xarray/core/dask_array_ops.py

Co-authored-by: Deepak Cherian <[email protected]>

* Use last instead of creating a custom function, and add a keepdims parameter for the last and first to make it compatible with the blelloch method

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove the keepdims on the last and first method and use the nanlast method directly, they already have the parameter

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Include the optimization of ffill and bfill on the whats-new.rst

* Use map_overlap when the n is smaller than all the chunks

* Avoid creating a numpy array to check if all the chunks are bigger than N on the push method

* Updating the whats-new.rst

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Patrick Hoefler <[email protected]>
Co-authored-by: Deepak Cherian <[email protected]>

Author: 4 people

doc/whats-new.rst

@@ -29,6 +29,10 @@ New Features
 - Support lazy grouping by dask arrays, and allow specifying ordered groups with ``UniqueGrouper(labels=["a", "b", "c"])``
   (:issue:`2852`, :issue:`757`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
+- Optimize ffill, bfill with dask when limit is specified
+  (:pull:`9771`).
+  By `Joseph Nowak <https://github.com/josephnowak>`_, and
+  `Patrick Hoefler <https://github.com/phofl>`.
 - Allow wrapping ``np.ndarray`` subclasses, e.g. ``astropy.units.Quantity`` (:issue:`9704`, :pull:`9760`).
   By `Sam Levang <https://github.com/slevang>`_ and `Tien Vo <https://github.com/tien-vo>`_.
 - Optimize :py:meth:`DataArray.polyfit` and :py:meth:`Dataset.polyfit` with dask, when used with

xarray/core/dask_array_ops.py

@@ -75,41 +75,71 @@ def least_squares(lhs, rhs, rcond=None, skipna=False):
     return coeffs, residuals
 
 
-def push(array, n, axis):
+def push(array, n, axis, method="blelloch"):
     """
     Dask-aware bottleneck.push
     """
     import dask.array as da
     import numpy as np
 
     from xarray.core.duck_array_ops import _push
+    from xarray.core.nputils import nanlast
+
+    if n is not None and all(n <= size for size in array.chunks[axis]):
+        return array.map_overlap(_push, depth={axis: (n, 0)}, n=n, axis=axis)
+
+    # TODO: Replace all this function
+    #  once https://github.com/pydata/xarray/issues/9229 being implemented
 
     def _fill_with_last_one(a, b):
-        # cumreduction apply the push func over all the blocks first so, the only missing part is filling
-        # the missing values using the last data of the previous chunk
-        return np.where(~np.isnan(b), b, a)
+        # cumreduction apply the push func over all the blocks first so,
+        # the only missing part is filling the missing values using the
+        # last data of the previous chunk
+        return np.where(np.isnan(b), a, b)
 
-    if n is not None and 0 < n < array.shape[axis] - 1:
-        arange = da.broadcast_to(
-            da.arange(
-                array.shape[axis], chunks=array.chunks[axis], dtype=array.dtype
-            ).reshape(
-                tuple(size if i == axis else 1 for i, size in enumerate(array.shape))
-            ),
-            array.shape,
-            array.chunks,
-        )
-        valid_arange = da.where(da.notnull(array), arange, np.nan)
-        valid_limits = (arange - push(valid_arange, None, axis)) <= n
-        # omit the forward fill that violate the limit
-        return da.where(valid_limits, push(array, None, axis), np.nan)
-
-    # The method parameter makes that the tests for python 3.7 fails.
-    return da.reductions.cumreduction(
-        func=_push,
+    def _dtype_push(a, axis, dtype=None):
+        # Not sure why the blelloch algorithm force to receive a dtype
+        return _push(a, axis=axis)
+
+    pushed_array = da.reductions.cumreduction(
+        func=_dtype_push,
         binop=_fill_with_last_one,
         ident=np.nan,
         x=array,
         axis=axis,
         dtype=array.dtype,
+        method=method,
+        preop=nanlast,
     )
+
+    if n is not None and 0 < n < array.shape[axis] - 1:
+
+        def _reset_cumsum(a, axis, dtype=None):
+            cumsum = np.cumsum(a, axis=axis)
+            reset_points = np.maximum.accumulate(np.where(a == 0, cumsum, 0), axis=axis)
+            return cumsum - reset_points
+
+        def _last_reset_cumsum(a, axis, keepdims=None):
+            # Take the last cumulative sum taking into account the reset
+            # This is useful for blelloch method
+            return np.take(_reset_cumsum(a, axis=axis), axis=axis, indices=[-1])
+
+        def _combine_reset_cumsum(a, b):
+            # It is going to sum the previous result until the first
+            # non nan value
+            bitmask = np.cumprod(b != 0, axis=axis)
+            return np.where(bitmask, b + a, b)
+
+        valid_positions = da.reductions.cumreduction(
+            func=_reset_cumsum,
+            binop=_combine_reset_cumsum,
+            ident=0,
+            x=da.isnan(array, dtype=int),
+            axis=axis,
+            dtype=int,
+            method=method,
+            preop=_last_reset_cumsum,
+        )
+        pushed_array = da.where(valid_positions <= n, pushed_array, np.nan)
+
+    return pushed_array

xarray/core/duck_array_ops.py

@@ -716,6 +716,7 @@ def first(values, axis, skipna=None):
             return chunked_nanfirst(values, axis)
         else:
             return nputils.nanfirst(values, axis)
+
     return take(values, 0, axis=axis)
 
 
@@ -729,6 +730,7 @@ def last(values, axis, skipna=None):
             return chunked_nanlast(values, axis)
         else:
             return nputils.nanlast(values, axis)
+
     return take(values, -1, axis=axis)
 
 
@@ -769,14 +771,14 @@ def _push(array, n: int | None = None, axis: int = -1):
     return bn.push(array, limit, axis)
 
 
-def push(array, n, axis):
+def push(array, n, axis, method="blelloch"):
     if not OPTIONS["use_bottleneck"] and not OPTIONS["use_numbagg"]:
         raise RuntimeError(
             "ffill & bfill requires bottleneck or numbagg to be enabled."
             " Call `xr.set_options(use_bottleneck=True)` or `xr.set_options(use_numbagg=True)` to enable one."
         )
     if is_duck_dask_array(array):
-        return dask_array_ops.push(array, n, axis)
+        return dask_array_ops.push(array, n, axis, method=method)
     else:
         return _push(array, n, axis)
 

xarray/tests/test_duck_array_ops.py

@@ -1008,7 +1008,8 @@ def test_least_squares(use_dask, skipna):
 
 @requires_dask
 @requires_bottleneck
-def test_push_dask():
+@pytest.mark.parametrize("method", ["sequential", "blelloch"])
+def test_push_dask(method):
     import bottleneck
     import dask.array
 
@@ -1018,13 +1019,18 @@ def test_push_dask():
         expected = bottleneck.push(array, axis=0, n=n)
         for c in range(1, 11):
             with raise_if_dask_computes():
-                actual = push(dask.array.from_array(array, chunks=c), axis=0, n=n)
+                actual = push(
+                    dask.array.from_array(array, chunks=c), axis=0, n=n, method=method
+                )
             np.testing.assert_equal(actual, expected)
 
         # some chunks of size-1 with NaN
         with raise_if_dask_computes():
             actual = push(
-                dask.array.from_array(array, chunks=(1, 2, 3, 2, 2, 1, 1)), axis=0, n=n
+                dask.array.from_array(array, chunks=(1, 2, 3, 2, 2, 1, 1)),
+                axis=0,
+                n=n,
+                method=method,
             )
         np.testing.assert_equal(actual, expected)