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175 lines (157 loc) · 5.72 KB
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import os
import tools
configfile: "/blue/ewhite/everglades/everwatch-workflow/snakemake_config.yml"
# Check if the test environment variable exists
test_env_name = "TEST_ENV"
test_env_set = os.environ.get(test_env_name)
working_dir = "/blue/ewhite/everglades_test" if test_env_set else "/blue/ewhite/everglades"
# Define wildcards for orthomosaics
ORTHOMOSAICS = glob_wildcards(f"{working_dir}/orthomosaics/{{year}}/{{site}}/{{flight}}.tif")
FLIGHTS = ORTHOMOSAICS.flight
SITES = ORTHOMOSAICS.site
YEARS = ORTHOMOSAICS.year
# Extract combinations of SITES and YEARS
site_year_combos = {*zip(SITES, YEARS)}
SITES_SY, YEARS_SY = list(zip(*site_year_combos))
def flights_in_year_site(wildcards):
basepath = f"{working_dir}/predictions"
flights_in_year_site = []
for site, year, flight in zip(SITES, YEARS, FLIGHTS):
flight_path = os.path.join(basepath, year, site, f"{flight}_projected.shp")
# Assuming there is a tools.get_event function
event = tools.get_event(flight_path)
if site == wildcards.site and year == wildcards.year and event[0] == "primary":
flights_in_year_site.append(flight_path)
return flights_in_year_site
rule all:
input:
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/PredictedBirds.zip",
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/nest_detections_processed.zip",
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/forecast_web_updated.txt",
expand(f"{working_dir}/predictions/{{year}}/{{site}}/{{flight}}_projected.shp",
zip, site=SITES, year=YEARS, flight=FLIGHTS),
expand(f"{working_dir}/processed_nests/{{year}}/{{site}}/{{site}}_{{year}}_processed_nests.shp",
zip, site=SITES, year=YEARS),
expand(f"{working_dir}/mapbox/last_uploaded/{{year}}/{{site}}/{{flight}}.mbtiles",
zip, site=SITES, year=YEARS, flight=FLIGHTS)
rule project_mosaics:
input:
orthomosaic=f"{working_dir}/orthomosaics/{{year}}/{{site}}/{{flight}}.tif"
output:
projected=f"{working_dir}/projected_mosaics/{{year}}/{{site}}/{{flight}}_projected.tif",
webmercator=f"{working_dir}/projected_mosaics/webmercator/{{year}}/{{site}}/{{flight}}_projected.tif"
conda: "envs/mbtiles.yml"
threads: 1
resources:
mem_mb=32000,
project_mosaic_slot=1
shell:
"python project_orthos.py {input.orthomosaic}"
rule predict_birds:
input:
projected=f"{working_dir}/projected_mosaics/{{year}}/{{site}}/{{flight}}_projected.tif"
output:
f"{working_dir}/predictions/{{year}}/{{site}}/{{flight}}_projected.shp"
conda: "envs/predict.yml"
threads: 1
resources:
gpu=1,
mem_mb=40000,
predict_birds_slot=1
shell:
"python predict.py {input.projected}"
rule combine_birds_site_year:
input:
flights_in_year_site
output:
f"{working_dir}/predictions/{{year}}/{{site}}/{{site}}_{{year}}_combined.shp"
conda: "envs/everwatch.yml"
threads: 1
resources:
mem_mb=8000
shell:
"python combine_birds_site_year.py {input}"
rule combine_predicted_birds:
input:
expand(f"{working_dir}/predictions/{{year}}/{{site}}/{{site}}_{{year}}_combined.shp",
zip, site=SITES_SY, year=YEARS_SY)
output:
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/PredictedBirds.zip"
conda: "envs/everwatch.yml"
threads: 1
resources:
mem_mb=8000
shell:
"python combine_bird_predictions.py {input}"
rule detect_nests:
input:
f"{working_dir}/predictions/{{year}}/{{site}}/{{site}}_{{year}}_combined.shp"
output:
f"{working_dir}/detected_nests/{{year}}/{{site}}/{{site}}_{{year}}_detected_nests.shp"
conda: "envs/everwatch.yml"
threads: 1
resources:
mem_mb=8000
shell:
"python nest_detection.py {input}"
rule process_nests:
input:
f"{working_dir}/detected_nests/{{year}}/{{site}}/{{site}}_{{year}}_detected_nests.shp"
output:
f"{working_dir}/processed_nests/{{year}}/{{site}}/{{site}}_{{year}}_processed_nests.shp"
conda: "envs/everwatch.yml"
threads: 1
resources:
mem_mb=8000
shell:
"python process_nests.py {input}"
rule combine_nests:
input:
expand(f"{working_dir}/processed_nests/{{year}}/{{site}}/{{site}}_{{year}}_processed_nests.shp",
zip, site=SITES_SY, year=YEARS_SY)
output:
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/nest_detections_processed.zip"
conda: "envs/everwatch.yml"
threads: 1
resources:
mem_mb=8000
shell:
"python combine_nests.py {input}"
rule create_mbtile:
input:
f"{working_dir}/projected_mosaics/webmercator/{{year}}/{{site}}/{{flight}}_projected.tif"
output:
f"{working_dir}/mapbox/{{year}}/{{site}}/{{flight}}.mbtiles"
conda: "envs/mbtiles.yml"
threads: 1
resources:
mem_mb=32000
shell:
"python mbtile.py {input} {config[mapbox-param]}"
rule upload_mapbox:
input:
f"{working_dir}/mapbox/{{year}}/{{site}}/{{flight}}.mbtiles"
output:
f"{working_dir}/mapbox/last_uploaded/{{year}}/{{site}}/{{flight}}.mbtiles"
conda: "envs/mbtiles.yml"
threads: 1
resources:
mem_mb=4000
shell:
"""
python upload_mapbox.py {input}
touch {output}
"""
rule update_everwatch_predictions:
input:
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/PredictedBirds.zip"
output:
f"{working_dir}/everwatch-workflow/App/Zooniverse/data/forecast_web_updated.txt"
threads: 1
resources:
mem_mb=4000
shell:
"""
bash archive_predictions.sh
touch {output}
"""