scripts/preprocess_step1_correct_ply.py

#!/usr/bin/env python3
"""
preprocess_step1_correct_ply.py
================================
NEST3D Pre-processing Step 1: PLY correction.

For each sample in <data-dir>/sampleXXX/sampleXXX.ply:
  Fix 1 - Outlier grass removal:
      Keep all tree+nest points.
      Keep only grass within 5m XY of any tree/nest point.
  Fix 2 - Ground plane leveling (samples 015, 061, 063 only):
      RANSAC plane fit on grass -> rotate to horizontal.
  Fix 3 - Z grounding (all samples):
      Subtract 5th percentile of grass Z -> ground becomes ~0.
  Fix 4 - Point budget (all samples):
      If total > 10M: keep ALL nest, keep 1M grass min, downsample tree.

Points labeled 255 (unclassified/ignore) are preserved unchanged throughout
all four fixes -- never removed, downsampled, or reassigned.

Input:  <data-dir>/sampleXXX/sampleXXX.ply
Output: <data-dir>/sampleXXX/sampleXXX_corrected.ply

Labels (CloudCompare):
  0   = grass
  1   = tree
  2   = nest
  255 = unclassified / ignore

Usage:
  python preprocess_step1_correct_ply.py --data-dir /path/to/reconstructions

Author: NEST3D team
"""

import argparse
import numpy as np
import json
from pathlib import Path
from plyfile import PlyData, PlyElement
from sklearn.neighbors import BallTree

# ── Config ────────────────────────────────────────────────────────────────────
GRASS_KEEP_RADIUS_M  = 5.0
MAX_TOTAL_POINTS     = 10_000_000
GRASS_MINIMUM        = 1_000_000
DOWNSAMPLE_SEED      = 42
Z_GROUND_PERCENTILE  = 5

NEST_LABEL = 2
TREE_LABEL = 1

TILT_SAMPLES = {
    "sample015": {"ransac_min_inlier_frac": 0.5},
    "sample061": {"ransac_min_inlier_frac": 0.5},
    "sample063": {"ransac_min_inlier_frac": 0.15},
}
RANSAC_ITERATIONS  = 1000
RANSAC_THRESHOLD_M = 0.08

# ── I/O ───────────────────────────────────────────────────────────────────────
def load_ply(path):
    ply = PlyData.read(str(path))
    v = ply["vertex"]
    xyz      = np.stack([v["x"], v["y"], v["z"]], axis=1).astype(np.float64)
    rgb      = np.stack([v["red"], v["green"], v["blue"]], axis=1)
    lbl      = np.array(v["scalar_Classification"], dtype=np.int32)
    orig_idx = np.array(v["scalar_Original_cloud_index"], dtype=np.int32)
    return xyz, rgb, lbl, orig_idx

def save_ply(path, xyz, rgb, lbl, orig_idx):
    n = len(xyz)
    arr = np.zeros(n, dtype=[
        ("x","f4"),("y","f4"),("z","f4"),
        ("red","u1"),("green","u1"),("blue","u1"),
        ("scalar_Classification","f4"),
        ("scalar_Original_cloud_index","f4"),
    ])
    arr["x"], arr["y"], arr["z"] = xyz[:,0], xyz[:,1], xyz[:,2]
    arr["red"], arr["green"], arr["blue"] = rgb[:,0], rgb[:,1], rgb[:,2]
    arr["scalar_Classification"]       = lbl.astype(np.float32)
    arr["scalar_Original_cloud_index"] = orig_idx.astype(np.float32)
    PlyData([PlyElement.describe(arr,"vertex")], text=False).write(str(path))

# ── Fix 1: Outlier grass removal ──────────────────────────────────────────────
def remove_isolated_grass(xyz, rgb, lbl, orig_idx):
    tree_nest = (lbl==TREE_LABEL)|(lbl==NEST_LABEL)
    grass     = (lbl==0)
    other     = ~(grass|tree_nest)

    if tree_nest.sum()==0 or grass.sum()==0:
        return xyz, rgb, lbl, orig_idx, 0

    bt = BallTree(xyz[tree_nest,:2], metric="euclidean")
    dist,_ = bt.query(xyz[grass,:2], k=1)
    near = dist[:,0] <= GRASS_KEEP_RADIUS_M

    keep = np.zeros(len(xyz), bool)
    keep[tree_nest] = True
    keep[other]     = True
    gi = np.where(grass)[0]
    keep[gi[near]]  = True
    removed = int((~keep).sum())
    return xyz[keep], rgb[keep], lbl[keep], orig_idx[keep], removed

# ── Fix 2: Ground leveling ────────────────────────────────────────────────────
def fit_plane_ransac(pts, min_inlier_frac):
    best_normal, best_d, best_n = None, None, 0
    min_inliers = int(min_inlier_frac * len(pts))
    rng = np.random.default_rng(DOWNSAMPLE_SEED)
    for _ in range(RANSAC_ITERATIONS):
        idx = rng.choice(len(pts), 3, replace=False)
        p0,p1,p2 = pts[idx]
        normal = np.cross(p1-p0, p2-p0)
        nl = np.linalg.norm(normal)
        if nl < 1e-8: continue
        normal /= nl
        d = -normal @ p0
        if normal[2] < 0: normal,d = -normal,-d
        n_in = int((np.abs(pts@normal+d) < RANSAC_THRESHOLD_M).sum())
        if n_in > best_n:
            best_n, best_normal, best_d = n_in, normal.copy(), d
    return best_normal, best_d, best_n >= min_inliers

def rotation_to_up(normal):
    up = np.array([0.,0.,1.])
    normal = normal/np.linalg.norm(normal)
    axis = np.cross(normal, up)
    al = np.linalg.norm(axis)
    if al < 1e-8:
        return np.eye(3) if normal[2]>0 else np.diag([1.,-1.,-1.])
    axis /= al
    angle = np.arccos(np.clip(np.dot(normal,up),-1,1))
    K = np.array([[0,-axis[2],axis[1]],[axis[2],0,-axis[0]],[-axis[1],axis[0],0]])
    return np.eye(3)+np.sin(angle)*K+(1-np.cos(angle))*(K@K)

def level_ground(xyz, lbl, min_inlier_frac):
    grass_pts = xyz[lbl==0]
    if len(grass_pts) < 100:
        return xyz, False
    normal, d, ok = fit_plane_ransac(grass_pts, min_inlier_frac)
    if not ok:
        return xyz, False
    R = rotation_to_up(normal)
    return (R @ xyz.T).T, True

# ── Fix 3: Z grounding ────────────────────────────────────────────────────────
def ground_z(xyz, lbl):
    grass_z = xyz[lbl==0, 2]
    z_ref = np.percentile(grass_z if len(grass_z)>0 else xyz[:,2], Z_GROUND_PERCENTILE)
    xyz = xyz.copy()
    xyz[:,2] -= z_ref
    return xyz, float(z_ref)

# ── Fix 4: Point budget ───────────────────────────────────────────────────────
def apply_budget(xyz, rgb, lbl, orig_idx):
    if len(xyz) <= MAX_TOTAL_POINTS:
        return xyz, rgb, lbl, orig_idx, 0, 0

    nest_mask  = (lbl==NEST_LABEL)
    tree_mask  = (lbl==TREE_LABEL)
    grass_mask = (lbl==0)
    other_mask = ~(nest_mask|tree_mask|grass_mask)

    n_nest  = int(nest_mask.sum())
    n_tree  = int(tree_mask.sum())
    n_grass = int(grass_mask.sum())
    n_other = int(other_mask.sum())

    n_grass_keep = min(GRASS_MINIMUM, n_grass)
    n_tree_keep  = MAX_TOTAL_POINTS - n_nest - n_grass_keep - n_other

    rng = np.random.default_rng(DOWNSAMPLE_SEED)
    keep = np.zeros(len(xyz), bool)
    keep[nest_mask]  = True
    keep[other_mask] = True

    gi = np.where(grass_mask)[0]
    keep[rng.choice(gi, n_grass_keep, replace=False)] = True

    ti = np.where(tree_mask)[0]
    if n_tree_keep > 0:
        n_tree_keep = min(n_tree_keep, n_tree)
        keep[rng.choice(ti, n_tree_keep, replace=False)] = True

    grass_rm = n_grass - n_grass_keep
    tree_rm  = max(0, n_tree - n_tree_keep)
    return xyz[keep], rgb[keep], lbl[keep], orig_idx[keep], grass_rm, tree_rm

# ── Main ──────────────────────────────────────────────────────────────────────
def main():
    parser = argparse.ArgumentParser(description="NEST3D Step 1: PLY correction")
    parser.add_argument(
        "--data-dir", type=Path, default=Path("./reconstructions"),
        help="Path to the reconstructions/ folder containing sampleXXX subfolders (default: ./reconstructions)"
    )
    args = parser.parse_args()
    recon_dir = args.data_dir

    sample_dirs = sorted(recon_dir.glob("sample*"))
    print(f"Found {len(sample_dirs)} samples in {recon_dir}\n")

    log = {}
    for sample_dir in sample_dirs:
        sample_id = sample_dir.name
        in_ply    = sample_dir / f"{sample_id}.ply"
        out_ply   = sample_dir / f"{sample_id}_corrected.ply"

        if not in_ply.exists():
            print(f"[SKIP] {sample_id}: no PLY found")
            continue
        if out_ply.exists():
            print(f"[SKIP] {sample_id}: already corrected")
            continue

        print(f"[PROC] {sample_id}")
        xyz, rgb, lbl, orig_idx = load_ply(in_ply)
        n_before = len(xyz)

        # Fix 1
        print(f"  Fix1 grass outliers ...", end=" ")
        xyz, rgb, lbl, orig_idx, grass_rm = remove_isolated_grass(xyz, rgb, lbl, orig_idx)
        print(f"removed {grass_rm:,}")

        # Fix 2
        if sample_id in TILT_SAMPLES:
            print(f"  Fix2 leveling ...", end=" ")
            cfg = TILT_SAMPLES[sample_id]
            xyz, ok = level_ground(xyz, lbl, cfg["ransac_min_inlier_frac"])
            print("done" if ok else "FAILED")

        # Fix 3
        print(f"  Fix3 Z grounding ...", end=" ")
        xyz, z_ref = ground_z(xyz, lbl)
        print(f"z_ref={z_ref:.3f}m")

        # Fix 4
        print(f"  Fix4 budget ({len(xyz):,} pts) ...", end=" ")
        xyz, rgb, lbl, orig_idx, g_rm, t_rm = apply_budget(xyz, rgb, lbl, orig_idx)
        print(f"grass-{g_rm:,} tree-{t_rm:,} -> {len(xyz):,}")

        save_ply(out_ply, xyz, rgb, lbl, orig_idx)

        log[sample_id] = {
            "n_before": n_before, "n_after": len(xyz),
            "grass_outliers_removed": grass_rm,
            "grass_downsampled": g_rm, "tree_downsampled": t_rm,
            "z_ref": z_ref,
        }
        print(f"  -> saved {out_ply.name}\n")

    log_path = recon_dir / "correction_log.json"
    with open(log_path, "w") as f:
        json.dump(log, f, indent=2)
    print(f"Done! Log saved to {log_path}")

if __name__ == "__main__":
    main()