#!/usr/bin/env python3 """ slice_n4_run.py --------------- Slice the canonical RGC N4 logistic CSV into 253 roughly equal pieces with small tail overlaps on every interior slice. Design goals ------------ * Stream the source file — never load the full multi-GB CSV into RAM. * Keep every slice self-contained (identical header row). * Prefer cuts that fall on frame boundaries (multiples of 49 data rows) so a 49-core lattice snapshot is never split mid-frame. * Add a configurable overlap (default 1.5 MB ≈ a few thousand frames) at the *start* of every slice except the first, and at the *end* of every slice except the last. This gives contiguous analysis windows a small shared context for ACF / period-3 / order-parameter continuity. * Produce deterministic, numbered output files: n4_slice_000.csv … n4_slice_252.csv Usage ----- python slice_n4_run.py /path/to/logistic_20260606_145947.csv \\ [--outdir ./n4_slices] \\ [--n-slices 253] \\ [--overlap-mb 1.5] \\ [--cores 49] The script only needs read access to the source and write access to the output directory. It prints a progress summary and a final manifest (slice index, byte range, row estimate, file size). """ from __future__ import annotations import argparse import os import sys from pathlib import Path from typing import List, Tuple # --------------------------------------------------------------------------- # Helpers # --------------------------------------------------------------------------- def human(n: float) -> str: """Pretty-print a byte count.""" for unit in ("B", "KB", "MB", "GB", "TB"): if abs(n) < 1024.0: return f"{n:6.1f} {unit}" n /= 1024.0 return f"{n:.1f} PB" def find_frame_aligned_offset( fh, target_byte: int, cores: int, header_len: int, search_window: int = 512 * 1024, ) -> int: """ Return a byte offset >= target_byte that sits on a clean frame boundary (i.e. after a complete set of `cores` data rows). Strategy: jump near the target, read a modest window, count newlines, and advance until (data_rows_seen % cores) == 0. """ file_size = fh.seek(0, os.SEEK_END) if target_byte >= file_size: return file_size # Start a little before the target so we have context start = max(header_len, target_byte - search_window // 4) fh.seek(start) buf = fh.read(search_window) if not buf: return file_size # If we started mid-line, discard the partial first line if start > header_len and buf[0:1] != b"\n": nl = buf.find(b"\n") if nl < 0: return min(file_size, start + len(buf)) buf = buf[nl + 1 :] start += nl + 1 # Walk line-by-line until we are past target_byte *and* on a frame edge pos = start data_rows = 0 for line in buf.splitlines(keepends=True): pos += len(line) data_rows += 1 if pos >= target_byte and (data_rows % cores) == 0: return min(pos, file_size) # Fallback: just return the end of the window (still better than mid-line) return min(pos, file_size) def compute_slice_plan( file_size: int, header_len: int, n_slices: int, overlap_bytes: int, cores: int, fh, ) -> List[Tuple[int, int, int, int]]: """ Return a list of (slice_idx, start_byte, end_byte, pure_end_byte). start_byte – inclusive, may include leading overlap end_byte – exclusive, may include trailing overlap pure_end_byte – the nominal boundary *without* trailing overlap (used so the next slice knows where its leading overlap should begin) """ body_size = file_size - header_len if body_size <= 0: raise ValueError("File contains only a header (or is empty).") nominal_chunk = body_size / n_slices plan = [] # First pass: pure (non-overlapping) boundaries, frame-aligned pure_bounds = [header_len] for i in range(1, n_slices): target = header_len + int(i * nominal_chunk) aligned = find_frame_aligned_offset(fh, target, cores, header_len) pure_bounds.append(aligned) pure_bounds.append(file_size) # Second pass: expand each interior slice by overlap_bytes on both sides for i in range(n_slices): pure_start = pure_bounds[i] pure_end = pure_bounds[i + 1] if i == 0: start = pure_start # no leading overlap on first slice else: # Walk backward from pure_start by ~overlap_bytes, stay frame-aligned target = max(header_len, pure_start - overlap_bytes) start = find_frame_aligned_offset(fh, target, cores, header_len) # Guarantee we do not go past the previous pure boundary in a # way that would create negative-length regions start = min(start, pure_start) if i == n_slices - 1: end = pure_end # no trailing overlap on last slice else: target = min(file_size, pure_end + overlap_bytes) end = find_frame_aligned_offset(fh, target, cores, header_len) plan.append((i, start, end, pure_end)) return plan # --------------------------------------------------------------------------- # Main slicing routine # --------------------------------------------------------------------------- def slice_file( src: Path, outdir: Path, n_slices: int = 253, overlap_mb: float = 1.5, cores: int = 49, bufsize: int = 8 * 1024 * 1024, ) -> None: if not src.is_file(): sys.exit(f"ERROR: source file not found: {src}") outdir.mkdir(parents=True, exist_ok=True) overlap_bytes = int(overlap_mb * 1024 * 1024) file_size = src.stat().st_size print(f"Source : {src}") print(f"Size : {human(file_size)}") print(f"Slices : {n_slices}") print(f"Overlap : {overlap_mb} MB ({human(overlap_bytes)})") print(f"Cores/frame : {cores}") print(f"Output dir : {outdir}") print() with open(src, "rb") as fh: # Read header (first line) header = fh.readline() if not header: sys.exit("ERROR: empty file") header_len = len(header) print(f"Header ({header_len} bytes): {header.decode('utf-8', errors='replace').rstrip()}") print() plan = compute_slice_plan( file_size, header_len, n_slices, overlap_bytes, cores, fh ) manifest = [] for idx, start, end, pure_end in plan: out_path = outdir / f"n4_slice_{idx:03d}.csv" length = end - start # Leading / trailing overlap sizes for the log lead = max(0, pure_end - start) if idx > 0 else 0 # Actually lead = pure_start - start; we approximate via plan pure_start = plan[idx][1] if idx == 0 else plan[idx - 1][3] # Recompute cleanly pure_start_i = header_len if idx == 0 else plan[idx - 1][3] lead_ov = max(0, pure_start_i - start) if idx > 0 else 0 trail_ov = max(0, end - pure_end) if idx < n_slices - 1 else 0 with open(out_path, "wb") as out: out.write(header) # every slice is self-describing fh.seek(start) remaining = length while remaining > 0: chunk = fh.read(min(bufsize, remaining)) if not chunk: break out.write(chunk) remaining -= len(chunk) final_size = out_path.stat().st_size manifest.append( { "idx": idx, "file": out_path.name, "start": start, "end": end, "bytes": final_size, "lead_ov": lead_ov, "trail_ov": trail_ov, } ) print( f" [{idx:03d}] {out_path.name} " f"{human(final_size)} " f"bytes {start:,}–{end:,} " f"lead_ov={human(lead_ov)} trail_ov={human(trail_ov)}" ) # Write a small manifest CSV for later bookkeeping man_path = outdir / "slice_manifest.csv" with open(man_path, "w", encoding="utf-8") as m: m.write("slice_idx,filename,start_byte,end_byte,file_bytes,lead_overlap_bytes,trail_overlap_bytes\n") for row in manifest: m.write( f"{row['idx']},{row['file']},{row['start']},{row['end']}," f"{row['bytes']},{row['lead_ov']},{row['trail_ov']}\n" ) print() print(f"Manifest written to {man_path}") print(f"Done — {n_slices} slices.") # --------------------------------------------------------------------------- # CLI # --------------------------------------------------------------------------- def main() -> None: p = argparse.ArgumentParser( description="Slice canonical RGC N4 logistic CSV into overlapping pieces." ) p.add_argument( "source", type=Path, help="Path to the full logistic_*.csv (canonical N4 run)", ) p.add_argument( "--outdir", type=Path, default=Path("./n4_slices"), help="Directory for the slice files (default: ./n4_slices)", ) p.add_argument( "--n-slices", type=int, default=253, help="Number of slices (default: 253)", ) p.add_argument( "--overlap-mb", type=float, default=1.5, help="Overlap size in MiB at each interior boundary (default: 1.5)", ) p.add_argument( "--cores", type=int, default=49, help="Cores per lattice frame (default: 49)", ) args = p.parse_args() if args.n_slices < 1: sys.exit("--n-slices must be >= 1") if args.overlap_mb < 0: sys.exit("--overlap-mb must be >= 0") slice_file( src=args.source, outdir=args.outdir, n_slices=args.n_slices, overlap_mb=args.overlap_mb, cores=args.cores, ) if __name__ == "__main__": main()