Added CLI function for CBA, minor adjustment to path handling in CBA tool

Author: nmaarnio

eis_toolkit/cli.py

@@ -2023,7 +2023,39 @@ def distance_computation_cli(
 
 
 # CBA
-# TODO
+@app.command()
+def cell_based_association_cli(
+    input_vector: INPUT_FILE_OPTION,
+    output_raster: OUTPUT_FILE_OPTION,
+    cell_size: int = typer.Option(),
+    column: Optional[str] = None,
+    subset_target_attribute_values: Optional[List[str]] = None,
+    add_name: Optional[str] = None,
+    add_buffer: Optional[float] = None,
+):
+    """Create a CBA matrix."""
+    from eis_toolkit.vector_processing.cell_based_association import cell_based_association
+
+    typer.echo("Progress: 10%")
+
+    geodataframe = gpd.read_file(input_vector)
+    typer.echo("Progress: 25%")
+
+    cell_based_association(
+        cell_size=cell_size,
+        geodata=[geodataframe],
+        output_path=output_raster,
+        column=column if column is None else [column],
+        subset_target_attribute_values=subset_target_attribute_values
+        if subset_target_attribute_values is None
+        else [subset_target_attribute_values],
+        add_name=add_name if add_name is None else [add_name],
+        add_buffer=add_buffer if add_buffer is None else [add_buffer],
+    )
+
+    typer.echo("Progress: 100%")
+
+    typer.echo(f"Cell based association completed, writing raster to {output_raster}.")
 
 
 # --- PREDICTION ---

eis_toolkit/vector_processing/cell_based_association.py

@@ -1,6 +1,7 @@
 import os
 import warnings
 from numbers import Number
+from os import PathLike
 
 import geopandas as gpd
 import numpy as np
@@ -22,7 +23,7 @@
 def cell_based_association(
     cell_size: int,
     geodata: List[gpd.GeoDataFrame],
-    output_path: str,
+    output_path: Union[str, PathLike],
     column: Optional[List[str]] = None,
     subset_target_attribute_values: Optional[List[Union[None, list, str]]] = None,
     add_name: Optional[List[Union[str, None]]] = None,
@@ -39,7 +40,8 @@ def cell_based_association(
         cell_size: Size of the cells.
         geodata: GeoDataFrame to create the CBA matrix. Additional
             GeoDataFrame(s) can be imputed to add to the CBA matrix.
-        output_path: Name of the saved .tif file.
+        output_path: Name of the saved .tif file. Include file extension (.tif)
+            in the path.
         column: Name of the column of interest. If no attribute is specified,
             then an artificial attribute is created representing the presence
             or absence of the geometries of this file for each cell of the CBA
@@ -528,14 +530,14 @@ def _to_csv(cba: gpd.GeoDataFrame, output_path: str) -> None:
 
 
 @beartype
-def _to_raster(cba: gpd.GeoDataFrame, output_path: str, nan_val: int = -9999) -> None:
+def _to_raster(cba: gpd.GeoDataFrame, output_path: Union[str, PathLike], nan_val: int = -9999) -> None:
     """Intermediate utility.
 
     Saves the object as a raster TIFF file.
 
     Args:
         cba: CBA matrix to save.
-        output_path: Name of the saved file.
+        output_path: Name of the saved file, include file extension (.tif).
         nan_val: values taken by cells with no values in them (outside the study
         area).
 
@@ -579,7 +581,7 @@ def _to_raster(cba: gpd.GeoDataFrame, output_path: str, nan_val: int = -9999) ->
     transform = rasterio.transform.from_bounds(min_x, min_y, max_x, max_y, width=width, height=height)
 
     with rasterio.open(
-        output_path + ".tif",
+        output_path,
         mode="w",
         driver="GTiff",
         height=height,