Add conversion between cf and shapely for lines (#460)

jsignell · pre-commit-ci[bot] · dcherian · web-flow · commit 02b1d742a4ed · 2023-12-10T21:34:08.000-07:00
* Add conversion between cf and shapely for lines * Make polygons raise * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Switch to using `linestrings` and `multilinestrings` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add shapely to CF for lines * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use `from_ragged_array` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix mypy * Full test coverage for patch * [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: Deepak Cherian <dcherian@users.noreply.github.com>
diff --git a/cf_xarray/geometry.py b/cf_xarray/geometry.py
@@ -112,10 +112,10 @@ def shapely_to_cf(geometries: xr.DataArray | Sequence, grid_mapping: str | None
     }
     if types.issubset({"Point", "MultiPoint"}):
         ds = points_to_cf(geometries)
-    elif types.issubset({"Polygon", "MultiPolygon"}) or types.issubset(
-        {"LineString", "MultiLineString"}
-    ):
-        raise NotImplementedError("Only point geometries conversion is implemented.")
+    elif types.issubset({"LineString", "MultiLineString"}):
+        ds = lines_to_cf(geometries)
+    elif types.issubset({"Polygon", "MultiPolygon"}):
+        raise NotImplementedError("Polygon geometry conversion is not implemented.")
     else:
         raise ValueError(
             f"Mixed geometry types are not supported in CF-compliant datasets. Got {types}"
@@ -165,8 +165,10 @@ def cf_to_shapely(ds: xr.Dataset):
     geom_type = ds.geometry_container.attrs["geometry_type"]
     if geom_type == "point":
         geometries = cf_to_points(ds)
-    elif geom_type in ["line", "polygon"]:
-        raise NotImplementedError("Only point geometries conversion is implemented.")
+    elif geom_type == "line":
+        geometries = cf_to_lines(ds)
+    elif geom_type == "polygon":
+        raise NotImplementedError("Polygon geometry conversion is not implemented.")
     else:
         raise ValueError(
             f"Valid CF geometry types are 'point', 'line' and 'polygon'. Got {geom_type}"
@@ -295,3 +297,144 @@ def cf_to_points(ds: xr.Dataset):
         j += n
 
     return xr.DataArray(geoms, dims=node_count.dims, coords=node_count.coords)
+
+
+def lines_to_cf(lines: xr.DataArray | Sequence):
+    """Convert an iterable of lines (shapely.geometry.[Multi]Line) into a CF-compliant geometry dataset.
+
+    Parameters
+    ----------
+    lines : sequence of shapely.geometry.Line or MultiLine
+        The sequence of [multi]lines to translate to a CF dataset.
+
+    Returns
+    -------
+    xr.Dataset
+        A Dataset with variables 'x', 'y', 'crd_x', 'crd_y', 'node_count' and 'geometry_container'
+        and optionally 'part_node_count'.
+    """
+    from shapely import to_ragged_array
+
+    if isinstance(lines, xr.DataArray):
+        dim = lines.dims[0]
+        coord = lines[dim] if dim in lines.coords else None
+        lines_ = lines.values
+    else:
+        dim = "index"
+        coord = None
+        lines_ = np.array(lines)
+
+    _, arr, offsets = to_ragged_array(lines_)
+    x = arr[:, 0]
+    y = arr[:, 1]
+
+    node_count = np.diff(offsets[0])
+    if len(offsets) == 1:
+        indices = offsets[0]
+        part_node_count = node_count
+    else:
+        indices = np.take(offsets[0], offsets[1])
+        part_node_count = np.diff(indices)
+
+    geom_coords = arr.take(indices[:-1], 0)
+    crdX = geom_coords[:, 0]
+    crdY = geom_coords[:, 1]
+
+    ds = xr.Dataset(
+        data_vars={
+            "node_count": xr.DataArray(node_count, dims=("segment",)),
+            "part_node_count": xr.DataArray(part_node_count, dims=(dim,)),
+            "geometry_container": xr.DataArray(
+                attrs={
+                    "geometry_type": "line",
+                    "node_count": "node_count",
+                    "part_node_count": "part_node_count",
+                    "node_coordinates": "x y",
+                    "coordinates": "crd_x crd_y",
+                }
+            ),
+        },
+        coords={
+            "x": xr.DataArray(x, dims=("node",), attrs={"axis": "X"}),
+            "y": xr.DataArray(y, dims=("node",), attrs={"axis": "Y"}),
+            "crd_x": xr.DataArray(crdX, dims=(dim,), attrs={"nodes": "x"}),
+            "crd_y": xr.DataArray(crdY, dims=(dim,), attrs={"nodes": "y"}),
+        },
+    )
+
+    if coord is not None:
+        ds = ds.assign_coords({dim: coord})
+
+    # Special case when we have no MultiLines
+    if len(ds.part_node_count) == len(ds.node_count):
+        ds = ds.drop_vars("part_node_count")
+        del ds.geometry_container.attrs["part_node_count"]
+    return ds
+
+
+def cf_to_lines(ds: xr.Dataset):
+    """Convert line geometries stored in a CF-compliant way to shapely lines stored in a single variable.
+
+    Parameters
+    ----------
+    ds : xr.Dataset
+        A dataset with CF-compliant line geometries.
+        Must have a "geometry_container" variable with at least a 'node_coordinates' attribute.
+        Must also have the two 1D variables listed by this attribute.
+
+    Returns
+    -------
+    geometry : xr.DataArray
+        A 1D array of shapely.geometry.[Multi]Line objects.
+        It has the same dimension as the ``part_node_count`` or the coordinates variables, or
+        ``'features'`` if those were not present in ``ds``.
+    """
+    from shapely import GeometryType, from_ragged_array
+
+    # Shorthand for convenience
+    geo = ds.geometry_container.attrs
+
+    # The features dimension name, defaults to the one of 'part_node_count'
+    # or the dimension of the coordinates, if present.
+    feat_dim = None
+    if "coordinates" in geo:
+        xcoord_name, _ = geo["coordinates"].split(" ")
+        (feat_dim,) = ds[xcoord_name].dims
+
+    x_name, y_name = geo["node_coordinates"].split(" ")
+    xy = np.stack([ds[x_name].values, ds[y_name].values], axis=-1)
+
+    node_count_name = geo.get("node_count")
+    part_node_count_name = geo.get("part_node_count")
+    if node_count_name is None:
+        raise ValueError("'node_count' must be provided for line geometries")
+    else:
+        node_count = ds[node_count_name]
+
+    offset1 = np.insert(np.cumsum(node_count.values), 0, 0)
+    lines = from_ragged_array(GeometryType.LINESTRING, xy, offsets=(offset1,))
+
+    if part_node_count_name is None:
+        # No part_node_count means there are no multilines
+        # And if we had no coordinates, then the dimension defaults to "index"
+        feat_dim = feat_dim or "index"
+        part_node_count = xr.DataArray(node_count.values, dims=(feat_dim,))
+        if feat_dim in ds.coords:
+            part_node_count = part_node_count.assign_coords({feat_dim: ds[feat_dim]})
+
+        geoms = lines
+    else:
+        part_node_count = ds[part_node_count_name]
+
+        # get index of offset1 values that are edges for part_node_count
+        offset2 = np.nonzero(
+            np.isin(offset1, np.insert(np.cumsum(part_node_count), 0, 0))
+        )[0]
+        multilines = from_ragged_array(
+            GeometryType.MULTILINESTRING, xy, offsets=(offset1, offset2)
+        )
+
+        # get items from lines or multilines depending on number of segments
+        geoms = np.where(np.diff(offset2) == 1, lines[offset2[:-1]], multilines)
+
+    return xr.DataArray(geoms, dims=part_node_count.dims, coords=part_node_count.coords)
diff --git a/cf_xarray/tests/test_geometry.py b/cf_xarray/tests/test_geometry.py
@@ -49,6 +49,83 @@ def geometry_ds():
     return cf_ds, shp_ds
 
 
+@pytest.fixture
+def geometry_line_ds():
+    from shapely.geometry import LineString, MultiLineString
+
+    # empty/fill workaround to avoid numpy deprecation(warning) due to the array interface of shapely geometries.
+    geoms = np.empty(3, dtype=object)
+    geoms[:] = [
+        MultiLineString([[[0, 0], [1, 2]], [[4, 4], [5, 6]]]),
+        LineString([[0, 0], [1, 0], [1, 1]]),
+        LineString([[1.0, 1.0], [2.0, 2.0], [1.7, 9.5]]),
+    ]
+
+    ds = xr.Dataset()
+    shp_da = xr.DataArray(geoms, dims=("index",), name="geometry")
+
+    cf_ds = ds.assign(
+        x=xr.DataArray(
+            [0, 1, 4, 5, 0, 1, 1, 1.0, 2.0, 1.7], dims=("node",), attrs={"axis": "X"}
+        ),
+        y=xr.DataArray(
+            [0, 2, 4, 6, 0, 0, 1, 1.0, 2.0, 9.5], dims=("node",), attrs={"axis": "Y"}
+        ),
+        part_node_count=xr.DataArray([4, 3, 3], dims=("index",)),
+        node_count=xr.DataArray([2, 2, 3, 3], dims=("segment",)),
+        crd_x=xr.DataArray([0.0, 0.0, 1.0], dims=("index",), attrs={"nodes": "x"}),
+        crd_y=xr.DataArray([0.0, 0.0, 1.0], dims=("index",), attrs={"nodes": "y"}),
+        geometry_container=xr.DataArray(
+            attrs={
+                "geometry_type": "line",
+                "node_count": "node_count",
+                "part_node_count": "part_node_count",
+                "node_coordinates": "x y",
+                "coordinates": "crd_x crd_y",
+            }
+        ),
+    )
+
+    cf_ds = cf_ds.set_coords(["x", "y", "crd_x", "crd_y"])
+
+    return cf_ds, shp_da
+
+
+@pytest.fixture
+def geometry_line_without_multilines_ds():
+    from shapely.geometry import LineString
+
+    # empty/fill workaround to avoid numpy deprecation(warning) due to the array interface of shapely geometries.
+    geoms = np.empty(2, dtype=object)
+    geoms[:] = [
+        LineString([[0, 0], [1, 0], [1, 1]]),
+        LineString([[1.0, 1.0], [2.0, 2.0], [1.7, 9.5]]),
+    ]
+
+    ds = xr.Dataset()
+    shp_da = xr.DataArray(geoms, dims=("index",), name="geometry")
+
+    cf_ds = ds.assign(
+        x=xr.DataArray([0, 1, 1, 1.0, 2.0, 1.7], dims=("node",), attrs={"axis": "X"}),
+        y=xr.DataArray([0, 0, 1, 1.0, 2.0, 9.5], dims=("node",), attrs={"axis": "Y"}),
+        node_count=xr.DataArray([3, 3], dims=("segment",)),
+        crd_x=xr.DataArray([0.0, 1.0], dims=("index",), attrs={"nodes": "x"}),
+        crd_y=xr.DataArray([0.0, 1.0], dims=("index",), attrs={"nodes": "y"}),
+        geometry_container=xr.DataArray(
+            attrs={
+                "geometry_type": "line",
+                "node_count": "node_count",
+                "node_coordinates": "x y",
+                "coordinates": "crd_x crd_y",
+            }
+        ),
+    )
+
+    cf_ds = cf_ds.set_coords(["x", "y", "crd_x", "crd_y"])
+
+    return cf_ds, shp_da
+
+
 @requires_shapely
 def test_shapely_to_cf(geometry_ds):
     from shapely.geometry import Point
@@ -87,12 +164,45 @@ def test_shapely_to_cf(geometry_ds):
     assert set(out.dims) == {"features", "node"}
 
 
+@requires_shapely
+def test_shapely_to_cf_for_lines_as_da(geometry_line_ds):
+    expected, in_da = geometry_line_ds
+
+    actual = cfxr.shapely_to_cf(in_da)
+    xr.testing.assert_identical(actual, expected)
+
+    in_da = in_da.assign_coords(index=["a", "b", "c"])
+    actual = cfxr.shapely_to_cf(in_da)
+    xr.testing.assert_identical(actual, expected.assign_coords(index=["a", "b", "c"]))
+
+
+@requires_shapely
+def test_shapely_to_cf_for_lines_as_sequence(geometry_line_ds):
+    expected, in_da = geometry_line_ds
+    actual = cfxr.shapely_to_cf(in_da.values)
+    xr.testing.assert_identical(actual, expected)
+
+
+@requires_shapely
+def test_shapely_to_cf_for_lines_without_multilines(
+    geometry_line_without_multilines_ds,
+):
+    expected, in_da = geometry_line_without_multilines_ds
+    actual = cfxr.shapely_to_cf(in_da)
+    xr.testing.assert_identical(actual, expected)
+
+
 @requires_shapely
 def test_shapely_to_cf_errors():
-    from shapely.geometry import LineString, Point
+    from shapely.geometry import Point, Polygon
 
-    geoms = [LineString([[1, 2], [2, 3]]), LineString([[2, 3, 4], [4, 3, 2]])]
-    with pytest.raises(NotImplementedError, match="Only point geometries conversion"):
+    geoms = [
+        Polygon([[1, 1], [1, 3], [3, 3], [1, 1]]),
+        Polygon([[1, 1, 4], [1, 3, 4], [3, 3, 3], [1, 1, 4]]),
+    ]
+    with pytest.raises(
+        NotImplementedError, match="Polygon geometry conversion is not implemented"
+    ):
         cfxr.shapely_to_cf(geoms)
 
     geoms.append(Point(1, 2))
@@ -122,16 +232,47 @@ def test_cf_to_shapely(geometry_ds):
 
 
 @requires_shapely
-def test_cf_to_shapely_errors(geometry_ds):
-    in_ds, expected = geometry_ds
-    in_ds.geometry_container.attrs["geometry_type"] = "line"
-    with pytest.raises(NotImplementedError, match="Only point geometries conversion"):
+def test_cf_to_shapely_for_lines(geometry_line_ds):
+    in_ds, expected = geometry_line_ds
+
+    actual = cfxr.cf_to_shapely(in_ds)
+    assert actual.dims == ("index",)
+    xr.testing.assert_identical(actual.drop_vars(["crd_x", "crd_y"]), expected)
+
+
+@requires_shapely
+def test_cf_to_shapely_for_lines_without_multilines(
+    geometry_line_without_multilines_ds,
+):
+    in_ds, expected = geometry_line_without_multilines_ds
+    actual = cfxr.cf_to_shapely(in_ds)
+    assert actual.dims == ("index",)
+    xr.testing.assert_identical(actual, expected)
+
+    in_ds = in_ds.assign_coords(index=["b", "c"])
+    actual = cfxr.cf_to_shapely(in_ds)
+    assert actual.dims == ("index",)
+    xr.testing.assert_identical(
+        actual.drop_vars(["crd_x", "crd_y"]), expected.assign_coords(index=["b", "c"])
+    )
+
+
+@requires_shapely
+def test_cf_to_shapely_errors(geometry_ds, geometry_line_ds):
+    in_ds, _ = geometry_ds
+    in_ds.geometry_container.attrs["geometry_type"] = "polygon"
+    with pytest.raises(NotImplementedError, match="Polygon geometry"):
         cfxr.cf_to_shapely(in_ds)
 
     in_ds.geometry_container.attrs["geometry_type"] = "punkt"
     with pytest.raises(ValueError, match="Valid CF geometry types are "):
         cfxr.cf_to_shapely(in_ds)
 
+    in_ds, _ = geometry_line_ds
+    del in_ds.geometry_container.attrs["node_count"]
+    with pytest.raises(ValueError, match="'node_count' must be provided"):
+        cfxr.cf_to_shapely(in_ds)
+
 
 @requires_shapely
 def test_reshape_unique_geometries(geometry_ds):
diff --git a/pyproject.toml b/pyproject.toml
@@ -140,6 +140,7 @@ module=[
     "pint",
     "matplotlib",
     "pytest",
+    "shapely",
     "shapely.geometry",
     "xarray.core.pycompat",
 ]

Original file line number	Diff line number	Diff line change
`@@ -140,6 +140,7 @@ module=[`
`140`	`140`	`"pint",`
`141`	`141`	`"matplotlib",`
`142`	`142`	`"pytest",`
	`143`	`+ "shapely",`
`143`	`144`	`"shapely.geometry",`
`144`	`145`	`"xarray.core.pycompat",`
`145`	`146`	`]`