.github/workflows/python-package.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -36,7 +36,7 @@ jobs: @@
               python -m pip install -r requirements.txt
           - name: Lint with pylint
             run: |
-              python3 -m pylint utils prepare_layers prepare_species
+              python3 -m pylint utils prepare_layers prepare_species threats
           - name: Tests
             run: |
               python3 -m pytest ./tests

prepare_species/extract_species_data_psql.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,5 +1,6 @@
  
    import argparse

    import importlib

    import json

    import logging

    import math

    import os

    @@ -38,10 +39,24 @@
  
        "scientific_name",

        "family_name",

        "class_name",

        "threats",

        "category",

        "category_weight",

        "geometry"

    ]

    # From Muir et al: For each species, a global STAR threat abatement (START) score

    # is defined. This varies from zero for species of Least Concern to 100

    # for Near Threatened, 200 for Vulnerable, 300 for Endangered and

    # 400 for Critically Endangered species (using established weighting

    # ratios7,8)

    CATEGORY_WEIGHTS = {

        'NT': 100,

        'VU': 200,

        'EN': 300,

        'CR': 400,

    }

    MAIN_STATEMENT = """

    SELECT

        assessments.sis_taxon_id as id_no,

    @@ -84,10 +99,12 @@
  
    THREATS_STATEMENT = """

    SELECT

        supplementary_fields->>'scope' AS scope,

        supplementary_fields->>'severity' AS severity

        threat_lookup.code,

        assessment_threats.supplementary_fields->>'scope' AS scope,

        assessment_threats.supplementary_fields->>'severity' AS severity

    FROM

        assessment_threats

        LEFT JOIN threat_lookup ON assessment_threats.threat_id = threat_lookup.id

    WHERE

        assessment_id = %s

        AND (supplementary_fields->>'timing' is NULL OR supplementary_fields->>'timing' <> 'Past, Unlikely to Return')

    @@ -225,7 +242,7 @@ def process_systems(
  
    ]

    DEFAULT_SEVERITY = "slow, significant declines"

    # Taken from Muir et al 2021, indexed by SCOPE and then SEVERITY

    # Taken from Muir et al 2021 Supplementary Table 2, indexed by SCOPE and then SEVERITY

    THREAT_WEIGHTING_TABLE = [

        [63, 24, 10, 1, 0, 10],

        [52, 18,  9, 0, 0,  9],

    @@ -236,18 +253,19 @@ def process_threats(
  
        threat_data: List,

        report: SpeciesReport,

    ) -> bool:

        total = 0

        for scope, severity in threat_data:

        cleaned_threats = []

        for code, scope, severity in threat_data:

            if scope is None or scope.lower() == "unknown":

                scope = DEFAULT_SCOPE

            if severity is None or severity.lower() == "unknown":

                severity = DEFAULT_SEVERITY

            scope_index = SCOPES.index(scope.lower())

            severity_index = SEVERITIES.index(severity.lower())

            score = THREAT_WEIGHTING_TABLE[scope_index][severity_index]

            total += score

        report.has_threats = total != 0

        return total != 0

            if score > 0:

                cleaned_threats.append((code, score))

        report.has_threats = len(cleaned_threats) > 0

        return cleaned_threats

    def process_habitats(

        habitats_data: List[List[str]],

    @@ -329,7 +347,6 @@ def process_row(
  
            presence += (4,)

            report.possibly_extinct = True # pylint: disable=W0201

        cursor.execute(SYSTEMS_STATEMENT, (assessment_id,))

        systems_data = cursor.fetchall()

        try:

    @@ -340,8 +357,8 @@ def process_row(
  
        cursor.execute(THREATS_STATEMENT, (assessment_id,))

        raw_threats = cursor.fetchall()

        threatened = process_threats(raw_threats, report)

        if not threatened:

        threats = process_threats(raw_threats, report)

        if len(threats) == 0:

            return report

        cursor.execute(HABITATS_STATEMENT, (assessment_id,))

    @@ -370,7 +387,9 @@ def process_row(
  
                scientific_name,

                family_name,

                class_name,

                json.dumps(threats),

                category,

                CATEGORY_WEIGHTS[category],

                geometry

              ]],

            columns=COLUMNS,

tests/test_species_filter.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -105,7 +105,7 @@ def test_empty_threat_list():
  
    def test_no_serious_threats():

        threats_data = [

            ("Minority (<50%)", "No decline"),

            ("3.5", "Minority (<50%)", "No decline"),

        ]

        report = SpeciesReport(1, 2, "name")

        res = process_threats(threats_data, report)

    @@ -114,19 +114,19 @@ def test_no_serious_threats():
  
    def test_serious_threats():

        threats_data = [

            ("Whole (>90%)", "Very rapid declines"),

            ("3.4", "Whole (>90%)", "Very rapid declines"),

        ]

        report = SpeciesReport(1, 2, "name")

        res = process_threats(threats_data, report)

        assert res

        assert res == [("3.4", 63)]

        assert report.has_threats

    def test_mixed_threats():

        threats_data = [

            ("Whole (>90%)", "Very rapid declines"),

            ("Minority (<50%)", "No decline"),

            ("3.4", "Whole (>90%)", "Very rapid declines"),

            ("3.5", "Minority (<50%)", "No decline"),

        ]

        report = SpeciesReport(1, 2, "name")

        res = process_threats(threats_data, report)

        assert res

        assert res == [("3.4", 63)]

        assert report.has_threats

threats/threat_processing.py

-Original file line number
+Diff line change
@@ -0,0 +1,83 @@
+    import argparse
+    import json
+    import os
+    import sys
+    import geopandas as gpd
+    from pyogrio.errors import DataSourceError
+    from yirgacheffe.layers import RasterLayer
+    def threat_processing_per_species(
+        species_data_path: str,
+        aoh_path: str,
+        output_directory_path: str,
+    ) -> None:
+        try:
+            data = gpd.read_file(species_data_path)
+        except DataSourceError:
+            sys.exit(f"Failed to read {species_data_path}")
+        with RasterLayer.layer_from_file(aoh_path) as aoh:
+            os.makedirs(output_directory_path, exist_ok=True)
+            taxon_id = data.id_no[0]
+            category_weight = int(data.category_weight[0])
+            threat_data = json.loads(data.threats[0])
+            try:
+                aoh_base, _ = os.path.splitext(aoh_path)
+                aoh_data_path = aoh_base + ".json"
+                with open(aoh_data_path, "r", encoding="UTF-8") as f:
+                    aoh_data = json.load(f)
+                aoh_total = aoh_data["aoh_total"]
+            except (FileNotFoundError, KeyError):
+                aoh_total = aoh.sum()
+            proportional_aoh_per_pixel = aoh / aoh_total
+            weighted_species = proportional_aoh_per_pixel * category_weight
+            total_threat_weight = sum(x[1] for x in threat_data)
+            for threat_id, weight in threat_data:
+                proportional_threat_weight = weight  / total_threat_weight
+                per_threat_per_species_score = weighted_species * proportional_threat_weight
+                threat_dir_path = os.path.join(output_directory_path, str(threat_id))
+                os.makedirs(threat_dir_path, exist_ok=True)
+                output_path = os.path.join(threat_dir_path, f"{taxon_id}.tif")
+                with RasterLayer.empty_raster_layer_like(aoh, filename=output_path) as result:
+                    per_threat_per_species_score.save(result)
+    def main() -> None:
+        parser = argparse.ArgumentParser(description="Calculate per species threat layers")
+        parser.add_argument(
+            '--speciesdata',
+            type=str,
+            help="Single species/seasonality geojson.",
+            required=True,
+            dest="species_data_path"
+        )
+        parser.add_argument(
+            '--aoh',
+            type=str,
+            help="AoH raster  of speices.",
+            required=True,
+            dest="aoh_path"
+        )
+        parser.add_argument(
+            '--output',
+            type=str,
+            help='Directory where per species/threat layers are stored',
+            required=True,
+            dest='output_directory_path',
+        )
+        args = parser.parse_args()
+        threat_processing_per_species(
+            args.species_data_path,
+            args.aoh_path,
+            args.output_directory_path,
+        )
+    if __name__ == "__main__":
+        main()

Calculate STAR scores #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged

mdales merged 3 commits into main from mwd-star-scores

Mar 26, 2025

-Original file line number
+Diff line change
@@ Expand Up / @@ -36,7 +36,7 @@ jobs: @@
               python -m pip install -r requirements.txt
           - name: Lint with pylint
             run: |
-              python3 -m pylint utils prepare_layers prepare_species
+              python3 -m pylint utils prepare_layers prepare_species threats
           - name: Tests
             run: |
               python3 -m pytest ./tests

-Original file line number
+Diff line change
@@ -0,0 +1,83 @@
+    import argparse
+    import json
+    import os
+    import sys
+    import geopandas as gpd
+    from pyogrio.errors import DataSourceError
+    from yirgacheffe.layers import RasterLayer
+    def threat_processing_per_species(
+        species_data_path: str,
+        aoh_path: str,
+        output_directory_path: str,
+    ) -> None:
+        try:
+            data = gpd.read_file(species_data_path)
+        except DataSourceError:
+            sys.exit(f"Failed to read {species_data_path}")
+        with RasterLayer.layer_from_file(aoh_path) as aoh:
+            os.makedirs(output_directory_path, exist_ok=True)
+            taxon_id = data.id_no[0]
+            category_weight = int(data.category_weight[0])
+            threat_data = json.loads(data.threats[0])
+            try:
+                aoh_base, _ = os.path.splitext(aoh_path)
+                aoh_data_path = aoh_base + ".json"
+                with open(aoh_data_path, "r", encoding="UTF-8") as f:
+                    aoh_data = json.load(f)
+                aoh_total = aoh_data["aoh_total"]
+            except (FileNotFoundError, KeyError):
+                aoh_total = aoh.sum()
+            proportional_aoh_per_pixel = aoh / aoh_total
+            weighted_species = proportional_aoh_per_pixel * category_weight
+            total_threat_weight = sum(x[1] for x in threat_data)
+            for threat_id, weight in threat_data:
+                proportional_threat_weight = weight  / total_threat_weight
+                per_threat_per_species_score = weighted_species * proportional_threat_weight
+                threat_dir_path = os.path.join(output_directory_path, str(threat_id))
+                os.makedirs(threat_dir_path, exist_ok=True)
+                output_path = os.path.join(threat_dir_path, f"{taxon_id}.tif")
+                with RasterLayer.empty_raster_layer_like(aoh, filename=output_path) as result:
+                    per_threat_per_species_score.save(result)
+    def main() -> None:
+        parser = argparse.ArgumentParser(description="Calculate per species threat layers")
+        parser.add_argument(
+            '--speciesdata',
+            type=str,
+            help="Single species/seasonality geojson.",
+            required=True,
+            dest="species_data_path"
+        )
+        parser.add_argument(
+            '--aoh',
+            type=str,
+            help="AoH raster  of speices.",
+            required=True,
+            dest="aoh_path"
+        )
+        parser.add_argument(
+            '--output',
+            type=str,
+            help='Directory where per species/threat layers are stored',
+            required=True,
+            dest='output_directory_path',
+        )
+        args = parser.parse_args()
+        threat_processing_per_species(
+            args.species_data_path,
+            args.aoh_path,
+            args.output_directory_path,
+        )
+    if __name__ == "__main__":
+        main()

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Calculate STAR scores #6

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Uh oh!