| |
| """Import a DRMHB ZIP or directory with full ground truth (no features).""" |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| from pathlib import Path |
|
|
| from drmhb_workflow import create_base, positive_int |
| from vibframe_anndata import validate_streamed_h5ad |
|
|
|
|
| def parse_args() -> argparse.Namespace: |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("vibframe", type=Path) |
| parser.add_argument("output", type=Path) |
| parser.add_argument("--block-size-mib", type=positive_int, default=8) |
| parser.add_argument("--dtype", choices=("float32", "float64"), default="float32") |
| parser.add_argument( |
| "--ground-truth-scope", choices=("all", "snapshot", "none"), default="all" |
| ) |
| parser.add_argument( |
| "--without-ground-truth", action="store_true", help="Alias for scope=none" |
| ) |
| parser.add_argument("--max-sidecar-mib", type=positive_int, default=512) |
| parser.add_argument("--overwrite", action="store_true") |
| return parser.parse_args() |
|
|
|
|
| def main() -> None: |
| args = parse_args() |
| scope = "none" if args.without_ground_truth else args.ground_truth_scope |
| output = create_base( |
| args.vibframe, |
| args.output, |
| scope=scope, |
| dtype=args.dtype, |
| block_size_mib=args.block_size_mib, |
| max_sidecar_mib=args.max_sidecar_mib, |
| overwrite=args.overwrite, |
| ) |
| print(f"Created: {output}") |
| for key, value in validate_streamed_h5ad(output).items(): |
| print(f"{key}: {value}") |
| print( |
| f"File size: {output.stat().st_size / 1024**3:.3f} GiB; ground truth scope: {scope}" |
| ) |
| print("Evaluation is outside X/obs. block-size-mib is not a total RAM limit.") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
