File size: 7,479 Bytes
c7212b2 | 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 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 | """
Materialize the ARC+ATLAS hires/lores 50/25/25 split into the local project
folder with real files (no symlinks).
The default source is the combined split produced earlier at:
../../ARC/ds004884/derivatives/aggregates/t1w_with_masks/
mni_1mm_ants_fixed/_standardized/_resolution_v2/_splits_50_25_25
which contains symlinks into both ARC and ATLAS standardized datasets.
The default destination is:
./data/splits/50_25_25
Usage
-----
python -m data_prep.materialize_split \
--source ../../ARC/.../_splits_50_25_25 \
--dest ./data/splits/50_25_25 \
--metadata ../../ARC/.../_resolution_v2/_resolution_manifest_v2.csv
If your raw data live elsewhere, override the paths with CLI flags.
"""
from __future__ import annotations
import argparse
import shutil
from pathlib import Path
from typing import Iterable
PROJECT_ROOT = Path(__file__).resolve().parents[2]
def _first_existing_path(candidates: list[Path]) -> Path:
for p in candidates:
if p.exists():
return p
return candidates[0]
DEFAULT_SOURCE = _first_existing_path(
[
PROJECT_ROOT.parent
/ "ARC"
/ "ds004884"
/ "derivatives"
/ "aggregates"
/ "t1w_with_masks"
/ "mni_1mm_ants_fixed"
/ "_standardized"
/ "_resolution_v2"
/ "_splits_50_25_25",
Path("/home/rbielski/ARC/ds004884/derivatives/aggregates/t1w_with_masks/mni_1mm_ants_fixed/_standardized/_resolution_v2/_splits_50_25_25"),
]
)
DEFAULT_DEST = PROJECT_ROOT / "data" / "splits" / "50_25_25"
DEFAULT_METADATA = _first_existing_path(
[
PROJECT_ROOT.parent
/ "ARC"
/ "ds004884"
/ "derivatives"
/ "aggregates"
/ "t1w_with_masks"
/ "mni_1mm_ants_fixed"
/ "_standardized"
/ "_resolution_v2"
/ "_resolution_manifest_v2.csv",
Path("/home/rbielski/ARC/ds004884/derivatives/aggregates/t1w_with_masks/mni_1mm_ants_fixed/_standardized/_resolution_v2/_resolution_manifest_v2.csv"),
]
)
class CopyStats:
def __init__(self) -> None:
self.files = 0
self.bytes = 0
self.symlinks_found: list[Path] = []
def add(self, path: Path) -> None:
self.files += 1
try:
self.bytes += path.stat().st_size
except FileNotFoundError:
pass
def copy_tree_following_symlinks(src: Path, dst: Path, stats: CopyStats) -> None:
"""Recursively copy src -> dst, following symlinks to materialize real files."""
for path in src.rglob("*"):
rel = path.relative_to(src)
out = dst / rel
if path.is_dir():
out.mkdir(parents=True, exist_ok=True)
continue
if path.is_symlink():
stats.symlinks_found.append(path)
target = path.resolve()
out.parent.mkdir(parents=True, exist_ok=True)
shutil.copy2(target, out)
stats.add(out)
elif path.is_file():
out.parent.mkdir(parents=True, exist_ok=True)
shutil.copy2(path, out)
stats.add(out)
def write_manifest(dest_root: Path, extra_meta: Iterable[Path]) -> None:
manifest_path = dest_root / "manifest.txt"
lines = ["Dataset materialized into: " + str(dest_root)]
for meta in extra_meta:
if meta and meta.exists():
dest_meta = dest_root / "meta" / meta.name
dest_meta.parent.mkdir(parents=True, exist_ok=True)
shutil.copy2(meta, dest_meta)
lines.append(f"Copied metadata: {dest_meta.relative_to(dest_root)}")
manifest_path.write_text("\n".join(lines))
def rewrite_resolution_manifest(dest_root: Path) -> None:
"""Rewrites resolution_manifest_v2.csv (if present) to use relative paths inside dest_root.
Original manifest paths point to the source standardized tree. For portability we map by
filename into the copied split (train_hires/test_hires/test_lores).
"""
import csv
meta_src = dest_root / "meta" / "_resolution_manifest_v2.csv"
if not meta_src.exists():
return
# Map filename -> relative path inside dest
name_to_rel = {}
for f in dest_root.rglob("*.nii.gz"):
name_to_rel[f.name] = f.relative_to(dest_root)
rows = []
with open(meta_src, newline="") as f:
reader = csv.DictReader(f)
for row in reader:
t1_name = Path(row["t1_path"]).name
msk_name = Path(row["mask_path"]).name
row["t1_path"] = str(dest_root / name_to_rel.get(t1_name, Path(t1_name)))
row["mask_path"] = str(dest_root / name_to_rel.get(msk_name, Path(msk_name)))
rows.append(row)
out_path = dest_root / "meta" / "_resolution_manifest_v2_local.csv"
with open(out_path, "w", newline="") as f:
writer = csv.DictWriter(f, fieldnames=rows[0].keys())
writer.writeheader(); writer.writerows(rows)
# also overwrite the original to avoid absolute paths lingering
meta_src.write_text(out_path.read_text())
print("Rewrote manifest with local paths ->", out_path)
def rewrite_split_csvs(dest_root: Path) -> None:
"""Update train/test CSVs so t1_path/mask_path point inside dest_root."""
import csv
for csv_path in dest_root.glob("*.csv"):
rows = list(csv.DictReader(open(csv_path)))
if not rows:
continue
for r in rows:
t1_name = Path(r["t1_path"]).name
msk_name = Path(r["mask_path"]).name
# infer subfolder based on CSV stem
split_dir = dest_root / csv_path.stem
r["t1_path"] = str((split_dir / "t1" / t1_name))
r["mask_path"] = str((split_dir / "masks" / msk_name))
with open(csv_path, "w", newline="") as f:
w = csv.DictWriter(f, fieldnames=rows[0].keys())
w.writeheader(); w.writerows(rows)
print("Localized paths in", csv_path)
def main():
p = argparse.ArgumentParser(description=__doc__)
p.add_argument("--source", type=Path, default=DEFAULT_SOURCE, help="Split root containing train_hires/test_hires/test_lores")
p.add_argument("--dest", type=Path, default=DEFAULT_DEST, help="Destination root for fully materialized data")
p.add_argument("--metadata", type=Path, default=DEFAULT_METADATA, help="Path to resolution manifest CSV to copy alongside data")
p.add_argument("--overwrite", action="store_true", help="Delete destination before copying")
args = p.parse_args()
if args.overwrite and args.dest.exists():
shutil.rmtree(args.dest)
if not args.source.exists():
raise SystemExit(f"Source split not found: {args.source}")
stats = CopyStats()
copy_tree_following_symlinks(args.source, args.dest, stats)
write_manifest(args.dest, [args.metadata])
rewrite_resolution_manifest(args.dest)
rewrite_split_csvs(args.dest)
print(f"Copied {stats.files} files into {args.dest}")
print(f"Total size ~ {stats.bytes/1e9:.2f} GB")
if stats.symlinks_found:
print(f"Materialized {len(stats.symlinks_found)} symlinks → real files")
# Final sanity: ensure no symlinks in dest
dangling = list(args.dest.rglob("*"))
leftover_links = [p for p in dangling if p.is_symlink()]
if leftover_links:
raise SystemExit(f"Found symlinks in dest (expected none): {leftover_links[:3]} ...")
print("✅ Dataset is fully materialized (no symlinks).")
if __name__ == "__main__":
main()
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