Xarray percentile - support non-dask input and percentiles in a new

libs/algo/odc/algo/__init__.py

@@ -62,6 +62,8 @@
 
 from ._tiff import save_cog
 
+from ._percentile import xr_quantile
+
 __all__ = (
     "apply_numexpr",
     "safe_div",
@@ -106,4 +108,5 @@
     "colorize",
     "xr_reproject",
     "save_cog",
+    "xr_quantile",
 )

libs/algo/odc/algo/_percentile.py

@@ -4,6 +4,7 @@
 import numpy as np
 from ._masking import keep_good_np
 from dask.base import tokenize
+import dask
 from functools import partial
 
 
@@ -34,9 +35,9 @@ def np_percentile(xx, percentile, nodata):
     return keep_good_np(xx, (valid_counts >= 3), nodata)
 
 
-def xr_percentile(
+def xr_quantile_bands(
     src: xr.Dataset,
-    percentiles: Sequence,
+    quantiles: Sequence,
     nodata,
 ) -> xr.Dataset:
 
@@ -49,7 +50,7 @@ def xr_percentile(
         float or integer with `nodata` values to indicate gaps in data.
         `nodata` must be the largest or smallest values in the dataset or NaN.
 
-    :param percentiles: A sequence of percentiles in the [0.0, 1.0] range
+    :param percentiles: A sequence of quantiles in the [0.0, 1.0] range
 
     :param nodata: The `nodata` value
     """
@@ -58,21 +59,81 @@ def xr_percentile(
     for band, xx in src.data_vars.items():
 
         xx_data = xx.data
-        if len(xx.chunks[0]) > 1:
-            xx_data = xx_data.rechunk({0: -1})
+
+        if dask.is_dask_collection(xx_data):
+            if len(xx.chunks[0]) > 1:
+                xx_data = xx_data.rechunk({0: -1})
 
-        tk = tokenize(xx_data, percentiles, nodata)
-        for percentile in percentiles:
-            name = f"{band}_pc_{int(100 * percentile)}"
-            yy = da.map_blocks(
-                partial(np_percentile, percentile=percentile, nodata=nodata), 
-                xx_data, 
-                drop_axis=0, 
-                meta=np.array([], dtype=xx.dtype),
-                name=f"{name}-{tk}",
-            )
-
+        tk = tokenize(xx_data, quantiles, nodata)
+        for quantile in quantiles:
+            name = f"{band}_pc_{int(100 * quantile)}"
+            if dask.is_dask_collection(xx_data):
+                yy = da.map_blocks(
+                    partial(np_percentile, percentile=quantile, nodata=nodata), 
+                    xx_data, 
+                    drop_axis=0, 
+                    meta=np.array([], dtype=xx.dtype),
+                    name=f"{name}-{tk}",
+                )
+            else:
+                yy = np_percentile(xx_data, percentile=quantile, nodata=nodata)
             data_vars[name] = (xx.dims[1:], yy)
 
     coords = dict((dim, src.coords[dim]) for dim in xx.dims[1:])
+    return xr.Dataset(data_vars=data_vars, coords=coords, attrs=src.attrs)
+
+
+def xr_quantile(
+    src: xr.Dataset,
+    quantiles: Sequence,
+    nodata,
+) -> xr.Dataset:
+
+    """
+    Calculates the percentiles of the input data along the time dimension.
+
+    This approach is approximately 700x faster than the `numpy` and `xarray` nanpercentile functions.
+
+    :param src: xr.Dataset, bands can be either
+        float or integer with `nodata` values to indicate gaps in data.
+        `nodata` must be the largest or smallest values in the dataset or NaN.
+
+    :param percentiles: A sequence of quantiles in the [0.0, 1.0] range
+
+    :param nodata: The `nodata` value
+    """
+
+    data_vars = {}
+    for band, xx in src.data_vars.items():
+
+        xx_data = xx.data
+        out_dims = ('quantile',) + xx.dims[1:]
+
+        if dask.is_dask_collection(xx_data):
+            if len(xx.chunks[0]) > 1:
+                xx_data = xx_data.rechunk({0: -1})
+
+        tk = tokenize(xx_data, quantiles, nodata)
+        data = []
+        for quantile in quantiles:
+            name = f"{band}_pc_{int(100 * quantile)}"
+            if dask.is_dask_collection(xx_data):
+                yy = da.map_blocks(
+                    partial(np_percentile, percentile=quantile, nodata=nodata), 
+                    xx_data, 
+                    drop_axis=0, 
+                    meta=np.array([], dtype=xx.dtype),
+                    name=f"{name}-{tk}",
+                )
+            else:
+                yy = np_percentile(xx_data, percentile=quantile, nodata=nodata)
+            data.append(yy)
+
+        if dask.is_dask_collection(yy):
+            data_vars[band] = (out_dims, da.stack(data, axis=0))
+        else:
+            data_vars[band] = (out_dims, np.stack(data, axis=0))
+
+    coords = dict((dim, src.coords[dim]) for dim in xx.dims[1:])
+    coords['quantile'] = np.array(quantiles)
     return xr.Dataset(data_vars=data_vars, coords=coords, attrs=src.attrs)

libs/algo/tests/test_percentile.py

@@ -1,4 +1,4 @@
-from odc.algo._percentile import np_percentile, xr_percentile
+from odc.algo._percentile import np_percentile, xr_quantile_bands, xr_quantile
 import numpy as np
 import pytest
 import dask.array as da
@@ -55,8 +55,9 @@ def test_np_percentile_bad_data(nodata):
     np.testing.assert_equal(np_percentile(arr, 0.0, nodata), np.array([nodata, 3]))
 
 
-@pytest.mark.parametrize("nodata", [255, 200, np.nan, -1]) #should do -1
-def test_xr_percentile(nodata):
+@pytest.mark.parametrize("nodata", [255, 200, np.nan, -1])
+@pytest.mark.parametrize("use_dask", [False, True])
+def test_xr_quantile_bands(nodata, use_dask):
     band_1 = np.random.randint(0, 100, size=(10, 100, 200)).astype(type(nodata))
     band_2 = np.random.randint(0, 100, size=(10, 100, 200)).astype(type(nodata))
 
@@ -69,8 +70,42 @@ def test_xr_percentile(nodata):
     true_results["band_1_pc_60"] = np_percentile(band_1, 0.6, nodata)
     true_results["band_2_pc_60"] = np_percentile(band_2, 0.6, nodata)
 
-    band_1 = da.from_array(band_1, chunks=(2, 20, 20))
-    band_2 = da.from_array(band_2, chunks=(2, 20, 20))
+    if use_dask:
+        band_1 = da.from_array(band_1, chunks=(2, 20, 20))
+        band_2 = da.from_array(band_2, chunks=(2, 20, 20))
+
+    attrs = {"test": "attrs"}
+    coords = {
+        "x": np.linspace(10, 20, band_1.shape[2]), 
+        "y": np.linspace(0, 5, band_1.shape[1]), 
+        "t": np.linspace(0, 5, band_1.shape[0])
+    }
+
+    data_vars = {"band_1": (("t", "y", "x"), band_1), "band_2": (("t", "y", "x"), band_2)}
+
+    dataset = xr.Dataset(data_vars=data_vars, coords=coords, attrs=attrs)
+    output = xr_quantile_bands(dataset, [0.2, 0.6], nodata).compute()
+
+    for band in output.keys():
+        np.testing.assert_equal(output[band], true_results[band])
+
+
+@pytest.mark.parametrize("nodata", [255, 200, np.nan, -1])
+@pytest.mark.parametrize("use_dask", [False, True])
+def test_xr_quantile(nodata, use_dask):
+    band_1 = np.random.randint(0, 100, size=(10, 100, 200)).astype(type(nodata))
+    band_2 = np.random.randint(0, 100, size=(10, 100, 200)).astype(type(nodata))
+
+    band_1[np.random.random(size=band_1.shape) > 0.5] = nodata
+    band_2[np.random.random(size=band_1.shape) > 0.5] = nodata
+
+    true_results = dict()
+    true_results["band_1"] = np.stack([np_percentile(band_1, 0.2, nodata), np_percentile(band_1, 0.6, nodata)], axis=0)
+    true_results["band_2"] = np.stack([np_percentile(band_2, 0.2, nodata), np_percentile(band_2, 0.6, nodata)], axis=0)
+
+    if use_dask:
+        band_1 = da.from_array(band_1, chunks=(2, 20, 20))
+        band_2 = da.from_array(band_2, chunks=(2, 20, 20))
 
     attrs = {"test": "attrs"}
     coords = {
@@ -82,7 +117,7 @@ def test_xr_percentile(nodata):
     data_vars = {"band_1": (("t", "y", "x"), band_1), "band_2": (("t", "y", "x"), band_2)}
 
     dataset = xr.Dataset(data_vars=data_vars, coords=coords, attrs=attrs)
-    output = xr_percentile(dataset, [0.2, 0.6], nodata).compute()
+    output = xr_quantile(dataset, [0.2, 0.6], nodata).compute()
 
-    for key in output.keys():
-        np.testing.assert_equal(output[key], true_results[key])
+    for band in output.keys():
+        np.testing.assert_equal(output[band], true_results[band])

libs/stats/odc/stats/_fc_percentiles.py

@@ -10,7 +10,7 @@
 from odc.stats.model import Task
 from odc.algo.io import load_with_native_transform
 from odc.algo import keep_good_only
-from odc.algo._percentile import xr_percentile
+from odc.algo._percentile import xr_quantile_bands
 from odc.algo._masking import _xr_fuse, _or_fuser, _first_valid_np, _fuse_or_np, _fuse_and_np
 from .model import StatsPluginInterface
 from . import _plugins
@@ -97,7 +97,7 @@ def reduce(xx: xr.Dataset) -> xr.Dataset:
         xx = xx.drop_vars(["dry", "wet"])
         xx = keep_good_only(xx, mask, nodata=NODATA)
 
-        yy = xr_percentile(xx, [0.1, 0.5, 0.9], nodata=NODATA)
+        yy = xr_quantile_bands(xx, [0.1, 0.5, 0.9], nodata=NODATA)
         is_ever_wet = _or_fuser(wet).squeeze(wet.dims[0], drop=True)
 
         band, *bands = yy.data_vars.keys()