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Updates to species richness script #12

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Jan 28, 2025
Merged

Updates to species richness script #12

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13 changes: 6 additions & 7 deletions summaries/species_richness.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import sys
import tempfile
import time
from glob import glob
from pathlib import Path
from multiprocessing import Manager, Process, Queue, cpu_count

from osgeo import gdal
Expand Down Expand Up @@ -86,7 +86,7 @@ def stage_2_worker(
merged_result = temp

if merged_result:
final = RasterLayer.empty_raster_layer_like(merged_result, filename=output_tif)
final = RasterLayer.empty_raster_layer_like(merged_result, filename=output_tif, nodata=0)
merged_result.save(final)

def species_richness(
Expand All @@ -97,14 +97,13 @@ def species_richness(
output_dir, filename = os.path.split(output_path)
os.makedirs(output_dir, exist_ok=True)

aohs = glob("**/*.tif", root_dir=aohs_dir)
print(f"We found {len(aohs)} AoH rasters")
aohs = list(Path(aohs_dir).rglob('*.tif'))
print(f"We found {len(list(aohs))} AoH rasters")

species_rasters = {}
for raster_path in aohs:
speciesid = os.path.basename(raster_path).split('_')[0]
full_path = os.path.join(aohs_dir, raster_path)
species_rasters[speciesid] = species_rasters.get(speciesid, set()).union({full_path})
species_rasters[speciesid] = species_rasters.get(speciesid, set()).union({raster_path})
print(f"Species detected: {len(species_rasters)} ")

with tempfile.TemporaryDirectory() as tempdir:
Expand Down Expand Up @@ -143,7 +142,7 @@ def species_richness(
source_queue
))
single_worker.start()
nextfiles = [os.path.join(tempdir, x) for x in glob("*.tif", root_dir=tempdir)]
nextfiles = Path(tempdir).rglob('*.tif')
for file in nextfiles:
source_queue.put(file)
source_queue.put(None)
Expand Down
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