File size: 6,118 Bytes
08764e9 | 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 | """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"
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