Remove hardcoded buffer distance

deafrica_waterbodies/plugins/ocean_filtering_using_goas.py

@@ -5,67 +5,35 @@
 
 import geopandas as gpd
 import numpy as np
-import skimage.morphology
 import xarray as xr
 from deafrica_tools.spatial import xr_rasterize
 
+from deafrica_waterbodies.plugins.utils import erode_land_sea_mask
+
 # File extensions to recognise as Parquet files.
 PARQUET_EXTENSIONS = {".pq", ".parquet"}
 
-buffer_pixels = 500 / 30
-
-
-def transform_hydrosheds_land_mask(hydrosheds_land_mask: xr.DataArray) -> xr.DataArray:
-    """
-    Function to transform the HydroSHEDs Land Mask into a boolean mask where
-    0/False are ocean pixels and 1/True are land pixels.
-    """
-    # Indicator values: 1 = land, 2 = ocean sink, 3 = inland sink, 255 is no data.
-    boolean_mask = (hydrosheds_land_mask != 255) & (hydrosheds_land_mask != 2)
-
-    return boolean_mask
-
-
-def erode_land_sea_mask(boolean_land_sea_mask: xr.DataArray, buffer_pixels: float) -> xr.DataArray:
-    """
-    Shrink the land in the land/sea mask.
-
-    Parameters
-    ----------
-    boolean_land_sea_mask : xr.DataArray
-        Boolean mask where 0/False are ocean pixels and 1/True are land pixels.
-    buffer_pixels : float
-        Number of pixels to erode the land by.
-
-    Returns
-    -------
-    xr.DataArray
-        Eroded land sea mask where 0/False are ocean pixels and 1/True are land pixels.
-    """
-    eroded_boolean_land_sea_mask = xr.apply_ufunc(
-        skimage.morphology.binary_erosion,
-        boolean_land_sea_mask,
-        skimage.morphology.disk(buffer_pixels),
-    )
-    return eroded_boolean_land_sea_mask
-
 
 def load_land_sea_mask(
     land_sea_mask_fp: str,
     wofs_alltime_summary_ds: xr.DataArray,
+    buffer_dist_m: float = 500,
 ) -> xr.DataArray:
     """
     Load the Marine Regions Global Oceans and Seas v01 from the file path
     provided. Rasterize the vector data to match the loaded datacube WOfS
     All Time Summary data and transform the raster into
     a boolean mask where 0/False are ocean pixels and 1/True are land pixels.
+    Erode the land pixels by the `buffer_dist_m` buffer distance.
 
     Parameters
     ----------
     land_sea_mask_fp : str
         File path to the Marine Regions Global Oceans and Seas v01 vector data.
     wofs_alltime_summary_ds : xr.DataArray
         Loaded datacube WOfS All Time Summary data to match to.
+    buffer_dist_m : float
+            Distance in meters to erode the land by in the land/sea mask.
 
     Returns
     -------
@@ -87,6 +55,6 @@ def load_land_sea_mask(
     boolean_land_sea_mask = np.logical_not(land_sea_mask_ds)
 
     # Erode the land in the land sea mask
-    eroded_boolean_land_sea_mask = erode_land_sea_mask(boolean_land_sea_mask, buffer_pixels)
+    eroded_boolean_land_sea_mask = erode_land_sea_mask(boolean_land_sea_mask, buffer_dist_m)
 
     return eroded_boolean_land_sea_mask

deafrica_waterbodies/plugins/ocean_filtering_using_hydrosheds.py

@@ -1,11 +1,10 @@
 """
 Ocean filtering using HydroSHEDS Land Mask
 """
-import skimage.morphology
 import xarray as xr
 from datacube.testutils.io import rio_slurp_xarray
 
-buffer_pixels = 500 / 30
+from deafrica_waterbodies.plugins.utils import erode_land_sea_mask
 
 
 def transform_hydrosheds_land_mask(hydrosheds_land_mask: xr.DataArray) -> xr.DataArray:
@@ -19,46 +18,25 @@ def transform_hydrosheds_land_mask(hydrosheds_land_mask: xr.DataArray) -> xr.Dat
     return boolean_mask
 
 
-def erode_land_sea_mask(boolean_land_sea_mask: xr.DataArray, buffer_pixels: float) -> xr.DataArray:
-    """
-    Shrink the land in the land/sea mask.
-
-    Parameters
-    ----------
-    boolean_land_sea_mask : xr.DataArray
-        Boolean mask where 0/False are ocean pixels and 1/True are land pixels.
-    buffer_pixels : float
-        Number of pixels to erode the land by.
-
-    Returns
-    -------
-    xr.DataArray
-        Eroded land sea mask where 0/False are ocean pixels and 1/True are land pixels.
-    """
-    eroded_boolean_land_sea_mask = xr.apply_ufunc(
-        skimage.morphology.binary_erosion,
-        boolean_land_sea_mask,
-        skimage.morphology.disk(buffer_pixels),
-    )
-    return eroded_boolean_land_sea_mask
-
-
 def load_land_sea_mask(
     land_sea_mask_fp: str,
     wofs_alltime_summary_ds: xr.DataArray,
+    buffer_dist_m: float = 500,
 ) -> xr.DataArray:
     """
     Load and reproject the HydroSHEDS Land Mask raster from the file path provided to
-    match the loaded datacube WOfS All Time Summary data and transform the raster into
-    a boolean mask where 0/False are ocean pixels and 1/True are land pixels.
+    match the loaded datacube WOfS All Time Summary data. Transform the loaded raster into
+    a boolean mask where 0/False are ocean pixels and 1/True are land pixels and erode the land
+    pixels by the `buffer_dist_m` buffer distance.
 
     Parameters
     ----------
     land_sea_mask_fp : str
         File path to the HydroSHEDS Land Mask raster.
     wofs_alltime_summary_ds : xr.DataArray
         Loaded datacube WOfS All Time Summary data to match to
-
+    buffer_dist_m : float
+            Distance in meters to erode the land by in the land/sea mask.
     Returns
     -------
     xr.DataArray
@@ -74,6 +52,6 @@ def load_land_sea_mask(
     boolean_land_sea_mask = transform_hydrosheds_land_mask(land_sea_mask_ds)
 
     # Erode the land in the land sea mask
-    eroded_boolean_land_sea_mask = erode_land_sea_mask(boolean_land_sea_mask, buffer_pixels)
+    eroded_boolean_land_sea_mask = erode_land_sea_mask(boolean_land_sea_mask, buffer_dist_m)
 
     return eroded_boolean_land_sea_mask

deafrica_waterbodies/plugins/utils.py

@@ -7,6 +7,9 @@
 from pathlib import Path
 from types import ModuleType
 
+import skimage
+import xarray as xr
+
 
 def run_plugin(plugin_path: str | Path) -> ModuleType:
     """Run a Python plugin from a path.
@@ -42,3 +45,29 @@ def validate_plugin(plugin: ModuleType):
     required_functions = ["load_land_sea_mask"]
     for name in required_functions:
         assert hasattr(getattr(plugin, name), "__call__")
+
+
+def erode_land_sea_mask(boolean_land_sea_mask: xr.DataArray, buffer_dist_m: float) -> xr.DataArray:
+    """
+    Shrink the land in the land/sea mask.
+
+    Parameters
+    ----------
+    boolean_land_sea_mask : xr.DataArray
+        Boolean mask where 0/False are ocean pixels and 1/True are land pixels.
+    buffer_dist_m : float
+        Distance in meters to erode the land by in the land/sea mask.
+
+    Returns
+    -------
+    xr.DataArray
+        Eroded land sea mask where 0/False are ocean pixels and 1/True are land pixels.
+    """
+    buffer_pixels = buffer_dist_m / abs(boolean_land_sea_mask.geobox.resolution[0])
+
+    eroded_boolean_land_sea_mask = xr.apply_ufunc(
+        skimage.morphology.binary_erosion,
+        boolean_land_sea_mask,
+        skimage.morphology.disk(buffer_pixels),
+    )
+    return eroded_boolean_land_sea_mask

deafrica_waterbodies/tiling.py

@@ -29,22 +29,20 @@ def check_tile_intersects_polygons(
     tuple
         Tile id if the extent of the geobox of a tile intersects with the polygons.
     """
-    tile_id = tile[0]
-    tile_extent = tile[1].geobox.extent
 
     if polygons_gdf is not None:
         # Reproject the extent of the geobox of a tile to match the polygons.
-        tile_extent = tile_extent.to_crs(polygons_gdf.crs)
+        tile_extent = tile[1].geobox.extent.to_crs(polygons_gdf.crs)
         # Get the shapely geometry of the reprojected extent of the tile's geobox.
         tile_extent_geom = tile_extent.geom
         # Check if the extent intersects with any of the polygons.
         check_intersection = polygons_gdf.geometry.intersects(tile_extent_geom).any()
         if check_intersection:
-            return tile_id
+            return tile[0]
         else:
             return ()
     else:
-        return tile_id
+        return tile[0]
 
 
 def filter_tiles(
@@ -105,8 +103,7 @@ def tile_wofs_ls_summary_alltime(
     # wofs_ls_summary_alltime grid.
 
     # Regular grid.
-    grid = "africa_30"
-    grid, gridspec = parse_gridspec_with_name(grid)
+    grid, gridspec = parse_gridspec_with_name(s="africa_30")
 
     # Multiply the tile size.
     tile_size = tuple(tile_size_factor * elem for elem in gridspec.tile_size)