pre/code/assemble.py

"""Assemble a unified label volume (canal = 1..28, tooth body = 29..56) per case.

Some cases (e.g. 21-30) ship with ONLY the canal/pulp annotation; their tooth
labels are supplied separately and dropped into paths.extra_tooth_dir. This module
detects whether a case already has tooth-body labels; if not, it loads the
supplementary tooth label and merges it.

Auto-detected supplementary-tooth schemes:
  * values in 29..56            -> used as tooth-body directly
  * values in 1..28             -> per-tooth instances, mapped to body = id + 28
  * binary {0,1}                -> components matched to the nearest canal centroid
The final volume keeps canal voxels as 1..28 and body voxels as 29..56 (disjoint:
the canal cavity is carved out of the solid tooth), matching the 31-35 scheme.
"""
import os, glob
import numpy as np
from scipy import ndimage as ndi
from .utils import load_nii, numeric_id

_FULL26 = np.ones((3, 3, 3), int)


def find_extra_tooth(case_num, extra_dir):
    """Locate a supplementary tooth-label file for a given case number.

    Matches several common naming conventions. We scan ALL numeric runs in the
    filename and accept one that lies in the valid case range (1..40) and equals
    `case_num`. Example: `0300316ok.nii.gz` -> first runs are 0300316; the
    largest valid sub-run is 30 (leading "030" -> int 30).
    """
    import re
    if not extra_dir or not os.path.isdir(extra_dir):
        return None
    cands = glob.glob(os.path.join(extra_dir, "**", "*.nii.gz"), recursive=True)
    matches = []
    for p in cands:
        base = os.path.basename(p)
        # collect every numeric run AND every plausible 2-3 digit sub-run
        runs = re.findall(r"\d+", base)
        plausible = set()
        for r in runs:
            # full run
            n = int(r)
            if 1 <= n <= 40:
                plausible.add(n)
            # plausible 2-3 digit sub-windows (handles "0300316" -> 30, 300)
            for w in (2, 3):
                for i in range(len(r) - w + 1):
                    n = int(r[i:i + w])
                    if 1 <= n <= 40:
                        plausible.add(n)
        if case_num in plausible:
            matches.append(p)
    if matches:
        # if multiple match (e.g. zzz28.nii.gz and zzz28 (6).nii.gz), pick the largest
        return max(matches, key=lambda p: os.path.getsize(os.path.realpath(p)))
    return None


def _map_tooth_to_body(tooth, canal, ls):
    """Return a body-label volume in 29..56 from an arbitrary tooth annotation."""
    body = np.zeros_like(tooth, dtype=np.int16)
    vals = np.unique(tooth[tooth > 0])
    off = ls["pair_offset"]
    if vals.size == 0:
        return body
    if vals.min() >= ls["body_lo"] and vals.max() <= ls["body_hi"]:
        return tooth.astype(np.int16)                              # already body ids
    if vals.max() <= ls["canal_hi"]:
        m = tooth > 0
        body[m] = tooth[m].astype(np.int16) + off                  # 1..28 -> 29..56
        return body
    if set(vals.tolist()) <= {1}:                                  # binary -> match canals
        lab, n = ndi.label(tooth > 0, structure=_FULL26)
        for k in range(1, n + 1):
            comp = lab == k
            cen = np.array(ndi.center_of_mass(comp))
            # nearest canal instance centroid
            best, bestd = None, 1e18
            for cid in range(ls["canal_lo"], ls["canal_hi"] + 1):
                cm = canal == cid
                if not cm.any():
                    continue
                d = np.linalg.norm(np.array(ndi.center_of_mass(cm)) - cen)
                if d < bestd:
                    bestd, best = d, cid
            if best is not None:
                body[comp] = best + off
        return body
    # fallback: relabel components sequentially into body range
    lab, n = ndi.label(tooth > 0, structure=_FULL26)
    for k in range(1, min(n, ls["n_teeth"]) + 1):
        body[lab == k] = ls["body_lo"] + (k - 1)
    return body


def assemble_label(primary_label, case_num, cfg):
    """Return (label_volume, status). status in
        {'complete', 'extra_override', 'merged', 'canal_only'}.

    Logic:
      1. If `primary_label` already has tooth-body labels (29..56) AND no extra
         file is provided, use it as-is.
      2. If an extra file is provided in `extra_tooth_dir`, inspect it:
            - if it already contains BOTH canal (1..28) and body (29..56) labels
              => it's a complete annotation, OVERRIDE the primary label with it.
            - else (tooth-only / 1..28 / binary) => merge it with the primary canal.
      3. If nothing usable is provided and the primary lacks body labels, signal
         'canal_only' so preprocessing skips the case with a clear warning.
    """
    ls = cfg["label_scheme"]
    has_body = ((primary_label >= ls["body_lo"]) &
                (primary_label <= ls["body_hi"])).any()
    extra_path = find_extra_tooth(case_num, cfg["paths"].get("extra_tooth_dir"))

    # case 1: primary already complete, no extra
    if has_body and extra_path is None:
        return primary_label.astype(np.int16), "complete"

    # case 2: an extra label was provided
    if extra_path is not None:
        extra, _ = load_nii(extra_path)
        extra = np.rint(extra).astype(np.int16)
        ex_has_canal = ((extra >= ls["canal_lo"]) & (extra <= ls["canal_hi"])).any()
        ex_has_body  = ((extra >= ls["body_lo"])  & (extra <= ls["body_hi"])).any()
        if ex_has_canal and ex_has_body:
            return extra, "extra_override"           # complete -> override
        # otherwise treat extra as tooth-only and merge with primary canal
        canal = primary_label.astype(np.int16)
        body = _map_tooth_to_body(extra, canal, ls)
        merged = np.zeros_like(canal, dtype=np.int16)
        merged[body > 0] = body[body > 0]
        cmask = (canal >= ls["canal_lo"]) & (canal <= ls["canal_hi"])
        merged[cmask] = canal[cmask]                  # canal carves cavity
        return merged, "merged"

    # case 3: nothing usable
    return primary_label.astype(np.int16), "canal_only"