File size: 1,761 Bytes
2ad85cb 881cb3b 2ad85cb 881cb3b 70a5538 2ad85cb 881cb3b 2ad85cb 881cb3b 2ad85cb 881cb3b 70a5538 881cb3b 2ad85cb 881cb3b 2ad85cb 881cb3b 2ad85cb 881cb3b 2ad85cb 881cb3b 70a5538 881cb3b 70a5538 881cb3b 2ad85cb | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | #!/usr/bin/env python3
"""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()
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