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Generator fixes #13

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Merged
mdales merged 2 commits into from
May 16, 2025
Merged

Generator fixes #13

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cdd8580
Ignore hidden files when looking for species in generators.
mdales May 16, 2025
d5fee1e
Make generators more defensive from .DS_store
mdales May 16, 2025
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30 changes: 16 additions & 14 deletions utils/aoh_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import argparse
import os
from pathlib import Path

import pandas as pd

Expand All @@ -10,25 +11,24 @@ def aoh_generator(
data_dir: str,
output_csv_path: str
):
taxas = os.listdir(input_dir)
taxa_dirs = Path(input_dir).glob("[!.]*")
data_dir = Path(data_dir)

res = []
for taxa in taxas:
for taxa_dir_path in taxa_dirs:
for scenario in ['current',]:
source = 'historic' if scenario == 'pnv' else 'current'
taxa_path = os.path.join(input_dir, taxa, source)
speciess = os.listdir(taxa_path)
for species in speciess:
if not species.endswith("geojson"):
continue
taxa_path = taxa_dir_path / source
species_paths = taxa_path.glob("*.geojson")
for species_path in species_paths:
res.append([
os.path.join(os.path.join(data_dir, "habitat_layers"), scenario),
os.path.join(data_dir, "elevation", "elevation-max-1k.tif"),
os.path.join(data_dir, "elevation", "elevation-min-1k.tif"),
os.path.join(data_dir, "crosswalk.csv"),
os.path.join(os.path.join(data_dir, "species-info/"), taxa, source, species),
os.path.join(os.path.join(data_dir, "masks", "terrestrial_mask.tif")),
os.path.join(os.path.join(data_dir, "aohs/"), scenario, taxa)
data_dir / "habitat_layers" / scenario,
data_dir / "elevation" / "elevation-max-1k.tif",
data_dir / "elevation" / "elevation-min-1k.tif",
data_dir / "crosswalk.csv",
species_path,
data_dir / "masks" / "terrestrial_mask.tif",
data_dir / "aohs" / scenario / taxa_dir_path.name,
])

df = pd.DataFrame(res, columns=[
Expand All @@ -40,6 +40,8 @@ def aoh_generator(
'--area',
'--output'
])
output_dir, _ = os.path.split(output_csv_path)
os.makedirs(output_dir, exist_ok=True)
df.to_csv(output_csv_path, index=False)


Expand Down
24 changes: 14 additions & 10 deletions utils/threats_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import argparse
import os
from pathlib import Path

import pandas as pd

Expand All @@ -10,29 +11,32 @@ def threats_generator(
data_dir: str,
output_csv_path: str
):
taxas = os.listdir(input_dir)
taxa_dirs = Path(input_dir).glob("[!.]*")
data_dir = Path(data_dir)

res = []
for taxa in taxas:
for taxa_dir_path in taxa_dirs:
for scenario in ['current',]:
source = 'historic' if scenario == 'pnv' else 'current'
taxa_path = os.path.join(input_dir, taxa, source)
species_infos = os.listdir(taxa_path)
for species_info_path in species_infos:
taxon_id, _ = os.path.splitext(species_info_path)
aoh_path = os.path.join(data_dir, "aohs", source, taxa, f"{taxon_id}_all.tif")
if os.path.exists(aoh_path):
taxa_path = taxa_dir_path / source
species_paths = taxa_path.glob("*.geojson")
for species_path in species_paths:
taxon_id = species_path.stem
aoh_path = data_dir / "aohs" / source / taxa_dir_path.name / f"{taxon_id}_all.tif"
if aoh_path.exists():
res.append([
os.path.join(data_dir, "species-info", taxa, source, species_info_path),
species_path,
aoh_path,
os.path.join(data_dir, "threat_rasters", taxa)
data_dir / "threat_rasters" / taxa_dir_path.name,
])

df = pd.DataFrame(res, columns=[
'--speciesdata',
'--aoh',
'--output'
])
output_dir, _ = os.path.split(output_csv_path)
os.makedirs(output_dir, exist_ok=True)
df.to_csv(output_csv_path, index=False)

def main() -> None:
Expand Down