diff --git a/pipeline/full_pipeline.py b/pipeline/full_pipeline.py index bffae7a..fb57125 100644 --- a/pipeline/full_pipeline.py +++ b/pipeline/full_pipeline.py @@ -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) @@ -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(