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Update full_pipeline.py #78

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16 changes: 14 additions & 2 deletions pipeline/full_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,6 +154,8 @@ def main(
from gene_to_nissl import main as gene_to_nissl_main
from interpolate_gene import main as interpolate_gene_main
from nissl_to_ccfv3 import main as nissl_to_ccfv3_main
import pathlib
from atldld.config import user_cache_dir

output_dir = Path(output_dir)

Expand All @@ -179,9 +181,19 @@ def main(
)

nissl_path = warped_nissl_path


#remove contents of cache directory to prevent it from filling up
folder = pathlib.Path( user_cache_dir())
for filename in pathlib.Path(".").glob("*.jpg"):
filename.unlink()

gene_experiment_dir = output_dir / "download-gene"
gene_experiment_path = gene_experiment_dir / f"{experiment_id}.npy"
if expression:
gene_experiment_path = gene_experiment_dir / f"{experiment_id}-expres\
sion.npy"
else:
gene_experiment_path = gene_experiment_dir / f"{experiment_id}.npy"

if not gene_experiment_path.exists() or force:
logger.info("Downloading Gene Expression...")
download_gene_main(
Expand Down