Merge pull request #23 from quantifyearth/mwd-expand-tests

Add some tests for major parts of AOH calc and habitat processing scripts

Author: mdales

README.md

@@ -63,7 +63,7 @@ To calculate the AoH we need the following information:
 - Habitats: A directory containing a series of GeoTIFFs, one per habitat class, indicating which pixels contain that habitat. Float values indicate partial occupancy.
 - Elevation-max/Elevation-min: Two GeoTIFFs, in which the highest and lowest elevation for that pixel is recorded. Must be in same units as those in the GeoJSON.
 - Crosswalk: A crosswalk table in CSV format that converts between the IUCN habitat classes and names of the habitat raster layers.
-- Area: An optiona raster containing the area of each pixel, which will be multipled with the AoH raster before saving to produce a result in area rahter than pixel occupancy.
+- Area: An optiona raster containing the area of each pixel, which will be multipled with the AoH raster before saving to produce a result in area rather than pixel occupancy.
 - Force habitat: An optional flag that means rather than following the IUCN RLTWG guidelines, whereby if there is zero area in the habitat layer after filtering for species habitat preferneces we should revert to range, this flag will keep the result as zero. This is to allow for evaluation of scenarios that might lead to extinction via land use chnages.
 - Output directory - Two files will be output to this directory: an AoH raster with the format `{id_no}_{seasonal}.tif` and a manifest containing information about the raster `{id_no}_{seasonal}.json`.
 

aohcalc.py

@@ -5,7 +5,7 @@
 import logging
 import sys
 from pathlib import Path
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Optional, Set, Union
 
 # import pyshark # pylint: disable=W0611
 import numpy as np
@@ -89,15 +89,15 @@ def aohcalc(
         manifest["error"] = "Species data missing one or more needed attributes"
         with open(manifest_filename, 'w', encoding="utf-8") as f:
             json.dump(manifest, f)
-        sys.exit()
+        return
 
     habitat_list = crosswalk_habitats(crosswalk_table, raw_habitats)
     if force_habitat and len(habitat_list) == 0:
         logger.error("No habitats found in crosswalk! %s_%s had %s", species_id, seasonality, raw_habitats)
         manifest["error"] = "No habitats found in crosswalk"
         with open(manifest_filename, 'w', encoding="utf-8") as f:
             json.dump(manifest, f)
-        sys.exit()
+        return
 
     ideal_habitat_map_files = [habitat_path / f"lcc_{x}.tif" for x in habitat_list]
     habitat_map_files = [x for x in ideal_habitat_map_files if x.exists()]
@@ -107,7 +107,7 @@ def aohcalc(
         manifest["error"] = "No matching habitat layers found"
         with open(manifest_filename, 'w', encoding="utf-8") as f:
             json.dump(manifest, f)
-        sys.exit()
+        return
 
     habitat_maps = [RasterLayer.layer_from_file(x) for x in habitat_map_files]
 
@@ -118,7 +118,7 @@ def aohcalc(
         min_elevation_map
     )
 
-    area_map = ConstantLayer(1.0)
+    area_map : Union[ConstantLayer, RasterLayer, UniformAreaLayer] = ConstantLayer(1.0)
     if area_path:
         try:
             area_map = UniformAreaLayer.layer_from_file(area_path)

habitat_process.py

@@ -19,7 +19,7 @@
 
 BLOCKSIZE = 512
 
-def enumerate_subset(
+def _enumerate_subset(
     habitat_path: Path,
     offset: int,
 ) -> Set[int]:
@@ -41,7 +41,7 @@ def enumerate_terrain_types(
     blocks = range(0, ysize, BLOCKSIZE)
     logger.info("Enumerating habitat classes in raster...")
     with Pool(processes=int(cpu_count() / 2)) as pool:
-        sets = pool.map(partial(enumerate_subset, habitat_path), blocks)
+        sets = pool.map(partial(_enumerate_subset, habitat_path), blocks)
     superset = set()
     for s in sets:
         superset.update(s)
@@ -51,7 +51,7 @@ def enumerate_terrain_types(
         pass
     return superset
 
-def make_single_type_map(
+def _make_single_type_map(
     habitat_path: Path,
     pixel_scale: Optional[float],
     target_projection: Optional[str],
@@ -135,12 +135,12 @@ def habitat_process(
     if max_copies > 1:
         with Pool(processes=process_count) as pool:
             pool.map(
-                partial(make_single_type_map, habitat_path, pixel_scale, target_projection, output_directory_path),
+                partial(_make_single_type_map, habitat_path, pixel_scale, target_projection, output_directory_path),
                 habitats
             )
     else:
         for habitat in habitats:
-            make_single_type_map(habitat_path, pixel_scale, target_projection, output_directory_path, habitat)
+            _make_single_type_map(habitat_path, pixel_scale, target_projection, output_directory_path, habitat)
 
 def main() -> None:
     parser = argparse.ArgumentParser(description="Downsample habitat map to raster per terrain type.")

requirements.txt

@@ -18,3 +18,4 @@ mypy
 pytest
 types-psutil
 pandas-stubs
+geojson