CBT_project/xfr_cbt_native.py

#!/home/xfr/.conda/envs/cbt/bin/python
"""把 PSO 找到的 CBT 螺絲位置（旋轉 0.5mm 標準系）映回原始
（未旋轉、未重取樣）native CT 空間，整支 volume 各 level 的螺絲
（L1-L5 x L/R，最多 10 支）存成單一 label 體積：

    Output_dir/<run_date>/<volume_id>/cbt.nii.gz
    Output_dir/<run_date>/<volume_id>/x-ap.jpg      合成前後(AP) X 光投影视圖
    Output_dir/<run_date>/<volume_id>/x-lat.jpg     合成側位 X 光投影视圖
                                       （只投影脊椎骨 + 螺絲、不含軟組織；
                                      見 render_xray_projections）

label 值：L1L=1 L1R=2 L2L=3 L2R=4 L3L=5 L3R=6 L4L=7 L4R=8 L5L=9 L5R=10
（0 = 背景）。

座標鏈首選：直接用預處理寫檔時記錄在 <vol>/transform.json 的正向鏈
（imaging.transforms.original_to_source：boxes / std_flip_axes / ap_flip /
rotated R、center、start / 原 CT 幾何；純 index 空間、不依賴 standardized
輸出的物理 header）。該鏈為仿射（original index <-> rotated disk index），
螺絲點經仿射逆向 o = M^-1 (s - t) 精確映射——不重新估算任何平面 / 幾何、
不重取樣 native label。

fallback（僅舊世代 volume 沒有 transform.json、或該 level 沒有 rotated
記錄時）：純 index 空間重算 R/center（template 骨頭 mask 的
best_symmetry_plane / best_upper_endplate_plane）、fstart（rotated 檔
origin 反映到 template index 的整數）、bbox2（native label 0.5mm 線性
重取樣 >0.5 的最大 26-連通區域 bbox）：
  rotated disk r -> t = R^T (r + fstart - c) + c
    -> g0 = bbox2s + (wx-1-tx, wy-1-ty, tz)；ap_flip 時 g0y = N05y-1-g0y
    -> native: rint(g0 * 0.5 / sn)
重算結果可能與生成時參數不完全一致：2026-09-09 驗證 liver_100 螺絲柱
in-label 由 93-99%（transform.json）掉到 30-94%（重算）；新世代資料
（transform.json 在）一律走主路徑。

螺絲參數化（rotated 系、0.5mm index）：pos = [z, y, x, az°, alt°, d mm, L mm]；
方向 d_v = (cos az sin alt, sin az sin alt, cos alt)；末端 = p0 + L/0.5 * d_v；
柱半徑 = d/2 mm。

驗證（2026-09-09，transform.json 路徑）：20260909_141448 run —
0001（10/10）、liver_100（10/10）、covid19（L1/L2 六側）螺絲柱體
in-label >= 92%、2-voxel 膨脹 >= 98%。covid19 L3 兩側除外：該 volume 的
L3 旋轉 bone mask 是 4.5k voxel / 5 slice 的退化區域（L4/L5 預處理缺檔、
先前棘突切除），屬資料問題非映射問題（L3 bone 碎片本身逆向 in-label 97.8%）。
"""

import argparse
import json
import logging
import os
import sys

import numpy as np
import SimpleITK as sitk
from tinydb import TinyDB, Query

from config.constant import LABEL_MAP
from imaging.resample import resample_img
from imaging.segmentation import _largest_cc_bbox
from imaging.orientation import best_symmetry_plane, best_upper_endplate_plane
from imaging.transforms import (level_file_path, load_transform,
                                original_to_source, transform_path)
from visualization.res_bone_figure import compute_normalizing_rotation

standardized_dir = '/mnt/1248/open2/cyrou/CBT/Seg/Resample/standardized-xfr-3'
data_root = '/mnt/1220/Public/dataset/Spine/CTSpine1K/data/'
label_root = '/mnt/1220/Public/dataset/Spine/CTSpine1K/label/'
SUBDIRS = {
    'colon': 'conlon',
    'COVID-19': 'COVID-19',
    'HNSCC-3DCT-RT_neck': 'HNSCC-3DCT-RT_neck',
    'liver': 'Liver',
}
Output_dir = '/mnt/1248/open/cyrou/Output'

_PROJ_DIR = os.path.dirname(os.path.abspath(__file__))
LOG_DIR = os.path.join(_PROJ_DIR, 'logs')
SIDE_RESULT_DIR = os.path.join(LOG_DIR, 'side_results')
META_DB = os.path.join(_PROJ_DIR, 'xfr_image_metadata.json')

LEVELS = ('L1', 'L2', 'L3', 'L4', 'L5')
LEVEL_LABEL_VAL = {v: int(k) for k, v in LABEL_MAP.items() if v in LEVELS}  # {'L1': 20, ...}
PROJ_FILENAME = {'ap': 'x-ap.jpg', 'lateral': 'x-lat.jpg'}

logger = logging.getLogger('xfr_cbt_native')


def find_native_paths(volume_id):
    """回傳 (ct_path, label_path, ap_flip)；找不到 native 檔對時 raise。"""
    ap_flip = False
    try:
        meta = TinyDB(META_DB, access_mode='r').table('images') \
            .get(Query().name == volume_id)
        if meta is None:
            logger.warning(f'{volume_id}: not in metadata db; ap_flip defaults to False')
        else:
            ap_flip = bool(meta.get('ap_flip', False))
    except Exception as e:
        logger.warning(f'{volume_id}: metadata db unavailable ({e}); ap_flip defaults to False')
    for sub, lab_sub in SUBDIRS.items():
        ct = f'{data_root}{sub}/{volume_id}.nii.gz'
        lb = f'{label_root}{lab_sub}/{volume_id}_seg.nii.gz'
        if os.path.isfile(ct) and os.path.isfile(lb):
            return ct, lb, ap_flip
    raise FileNotFoundError(f'{volume_id}: no native CT/label pair under {data_root}')


def level_geometry(volume_id, level, lb_img, lb_arr):
    """每 level 的 (R, c, fstart, bbox2s, wx, wy)；與預處理/驗證腳本同定義。"""
    vol_dir = os.path.join(standardized_dir, volume_id)
    # 未旋轉檔：新世代在 crop/ 子資料夾、舊世代在頂層
    smd_img = sitk.ReadImage(level_file_path(vol_dir, level, 'smd_resampled'))
    smd = sitk.GetArrayFromImage(smd_img).astype(np.float32)
    if not (np.isfinite(smd).all() and smd.min() < 0 and smd.max() > 0):
        b = (sitk.GetArrayFromImage(
            sitk.ReadImage(level_file_path(vol_dir, level, 'binary_nn'))) > 0).astype(np.uint8)
    else:
        b = (smd < 0.5).astype(np.uint8)
    sym = best_symmetry_plane(b)
    symp = best_upper_endplate_plane(b)
    R, c = compute_normalizing_rotation(b, sym, symp)
    rot_img = sitk.ReadImage(f'{vol_dir}/rotated/{level}_binary_sdf.nii.gz')
    fstart = np.round(np.array(
        smd_img.TransformPhysicalPointToIndex(rot_img.GetOrigin()))).astype(float)

    lv = LEVEL_LABEL_VAL[level]
    bin_img = sitk.GetImageFromArray((lb_arr == lv).astype(np.uint8))
    bin_img.CopyInformation(lb_img)
    bin_lin = resample_img(sitk.Cast(bin_img, sitk.sitkFloat32))
    m_full = sitk.GetImageFromArray((sitk.GetArrayFromImage(bin_lin) > 0.5).astype(np.uint8))
    m_full.CopyInformation(bin_lin)
    cc = _largest_cc_bbox(m_full)
    if cc is None:
        raise ValueError(f'{volume_id} {level}: empty native level mask (label {lv})')
    _, bbox2 = cc
    wx, wy = smd_img.GetSize()[0], smd_img.GetSize()[1]
    return R, c, fstart, np.array(bbox2[:3], float), wx, wy


def rotated_to_native(r_xyz, geom, N05, sn, ap_flip):
    """r_xyz: (N,3) rotated disk (x,y,z) index -> (N,3) native 連續 index。"""
    R, c, fstart, bbox2s, wx, wy = geom
    t = (np.asarray(r_xyz, float) + fstart - c) @ R + c
    g0 = np.empty_like(t)
    g0[:, 0] = bbox2s[0] + (wx - 1 - t[:, 0])
    g0[:, 1] = bbox2s[1] + (wy - 1 - t[:, 1])
    g0[:, 2] = bbox2s[2] + t[:, 2]
    if ap_flip:
        g0[:, 1] = N05[1] - 1 - g0[:, 1]
    return g0 * (0.5 / sn)


def screw_voxel_xyz(pos):
    """pos = [z, y, x, az°, alt°, d, L]（rotated 系 0.5mm index）。
    回傳柱體內 (x,y,z) float voxel 座標（N,3）。"""
    z, y, x, az, alt, d, L = (float(v) for v in pos[:7])
    azr, altr = np.radians(az), np.radians(alt)
    ca, sa = np.cos(azr), np.sin(azr)
    ct_, st_ = np.cos(altr), np.sin(altr)
    dv = np.array([ca * st_, sa * st_, ct_])
    e1 = np.array([ca * ct_, sa * ct_, -st_])
    e2 = np.array([-sa, ca, 0.0])
    p0 = np.array([x, y, z])
    p1 = p0 + (L / 0.5) * dv
    rad = d / 0.5 + 3.0
    lo = np.floor(np.minimum(p0, p1)) - rad
    hi = np.ceil(np.maximum(p0, p1)) + rad
    xs, ys, zs = np.meshgrid(np.arange(lo[0], hi[0] + 1),
                             np.arange(lo[1], hi[1] + 1),
                             np.arange(lo[2], hi[2] + 1), indexing='xy')
    P = np.stack([xs.ravel(), ys.ravel(), zs.ravel()], 1)
    dP = P - p0
    xr, yr, zr = dP @ e1, dP @ e2, dP @ dv
    rrad = d  # (d/2 mm 半徑) / 0.5mm 每 voxel = d 個 voxel
    m = (xr ** 2 + yr ** 2 <= rrad ** 2) & (zr >= 0) & (zr <= L / 0.5)
    return P[m]


def write_volume_cbt(volume_id, run_id, output_root=Output_dir, date=None):
    """把一個 volume 的 side_results 螺絲全部映回 native 空間寫 cbt.nii.gz。
    回傳 (path, n_screws)；該 run 無此 volume 時回傳 (None, 0)。"""
    date = date or run_id[:8]
    side_vol_dir = os.path.join(SIDE_RESULT_DIR, run_id, volume_id)
    if not os.path.isdir(side_vol_dir):
        logger.warning(f'{volume_id}: no side results under {side_vol_dir}; cbt skipped')
        return None, 0
    if not any(os.path.isfile(os.path.join(side_vol_dir, f'{l}_{s}.json'))
               for l in LEVELS for s in ('L', 'R')):
        logger.warning(f'{volume_id}: no <level>_<side>.json in {side_vol_dir}; cbt skipped')
        return None, 0

    ct_path, lb_path, ap_flip = find_native_paths(volume_id)
    ct = sitk.ReadImage(ct_path)
    n_xyz = np.array(ct.GetSize(), int)               # (x,y,z)
    n_zyx = n_xyz[::-1].copy()                        # 輸出 (z,y,x)
    sn = np.array(ct.GetSpacing(), float)
    N05 = np.maximum(1, np.ceil(n_xyz.astype(float) * sn / 0.5 - 1e-6).astype(int))

    # 主路徑：transform.json 記錄的正向鏈（仿射），逆向 o = M^-1 (s - t)
    meta = None
    try:
        meta = load_transform(os.path.join(standardized_dir, volume_id))
    except FileNotFoundError:
        logger.warning(f'{volume_id}: no transform.json '
                       f'({transform_path(os.path.join(standardized_dir, volume_id))}); '
                       f'全部 level 退回重算路徑（近似）')
    if meta is not None and not np.array_equal(
            np.asarray(meta['original']['size'], int), n_xyz):
        logger.warning(f'{volume_id}: transform.json original size '
                       f'{meta["original"]["size"]} != CT {list(n_xyz)}; '
                       f'忽略 transform.json，退回重算路徑')
        meta = None

    out_arr = np.zeros(n_zyx, np.uint8)
    lb_img = lb_arr = None          # fallback 才需要讀 native label
    geom_cache = {}                 # fallback：每 level 的 (R, c, fstart, bbox2s, wx, wy)
    aff_cache = {}                  # 主路徑：每 level 的 (M^-1, t)
    n_screws, skipped = 0, []
    n_tf = n_fb = 0
    for li, level in enumerate(LEVELS):
        for side in ('L', 'R'):
            jp = os.path.join(side_vol_dir, f'{level}_{side}.json')
            if not os.path.isfile(jp):
                continue
            pos = json.load(open(jp))['position']
            try:
                cyl = screw_voxel_xyz(pos)
                lv = meta['levels'].get(level) if meta is not None else None
                if lv is not None and 'rotated' in lv:
                    if level not in aff_cache:
                        M, t = original_to_source(meta, level, 'rotated')
                        aff_cache[level] = (np.linalg.inv(M), t)
                    Mi, t = aff_cache[level]
                    nat = (cyl - t) @ Mi.T            # (N,3) 原 CT 連續 index
                    n_tf += 1
                else:
                    if lb_arr is None:
                        lb_img = sitk.ReadImage(lb_path)
                        lb_arr = sitk.GetArrayFromImage(lb_img)
                    if level not in geom_cache:
                        geom_cache[level] = level_geometry(volume_id, level, lb_img, lb_arr)
                    nat = rotated_to_native(cyl, geom_cache[level], N05, sn, ap_flip)
                    n_fb += 1
                ni = np.rint(nat).astype(int)
                valid = (ni >= 0).all(1) & (ni < n_xyz).all(1)
                idx = ni[valid]
                if idx.shape[0] == 0:
                    raise ValueError('all screw voxels out of original CT bounds')
                val = li * 2 + 1 + (1 if side == 'R' else 0)
                out_arr[idx[:, 2], idx[:, 1], idx[:, 0]] = val
                n_screws += 1
            except Exception as e:
                logger.error(f'{volume_id} {level}_{side}: {e}')
                skipped.append(f'{level}_{side} ({e})')

    if n_screws == 0:
        raise ValueError(f'{volume_id}: no screw could be written (skipped: {skipped or "none read"})')
    out_dir = os.path.join(output_root, date, volume_id)
    os.makedirs(out_dir, exist_ok=True)
    out_img = sitk.GetImageFromArray(out_arr)
    out_img.CopyInformation(ct)
    out_path = os.path.join(out_dir, 'cbt.nii.gz')
    sitk.WriteImage(out_img, out_path)
    if skipped:
        logger.warning(f'{volume_id}: failed sides: {", ".join(skipped)}')
    logger.info(f'{volume_id}: {n_screws}/10 screws -> {out_path} '
                f'(transform.json={n_tf}, re-est={n_fb}, ap_flip={ap_flip})')

    # 收尾：原 CT + 螺絲 -> 合成 AP / Lateral X 光投影视圖 (x-ap.jpg / x-lat.jpg)
    try:
        render_xray_projections(out_path, ct_path, out_dir)
    except Exception as e:
        logger.warning(f'{volume_id}: X-ray projection render failed: {e}')
    return out_path, n_screws


def render_xray_projections(cbt_path, ct_path, out_dir,
                            views=('ap', 'lateral'), margin_mm=50.0):
    """原 CT + cbt.nii.gz（native 同一 grid 的螺絲 label）-> 合成「只有骨頭」X 光投影视圖。

    只投影脊椎骨 + 螺絲，不含軟組織：
      - spine mask：native 分割 label（1-24 = C1..L5，見 config.constant.LABEL_MAP）；
        label 缺 / grid 不符時退回 HU 300-3000 閾值。
      - 骨 μ = clip(HU, 0, 2000)/400（松質骨~0.2-1、皮質/終板~2-5）。
      - 螺絲 voxel μ = 60（金屬等效，最亮白）。
    投影视圖 = 沿中心射線 μ 的線積分（AP 沿 y、Lateral 沿 x）；裁到螺絲 bbox 外
    margin_mm 的 spine 區域；骨用 percentile(1,99) 獨立視窗，螺絲再疊加裁白。
    方向：SimpleITK LPS（x→右、y→後、z→上）；AP 頂=上、病人右在畫面左（R 標記）；
    Lateral 頂=上、前位在左、後位在右（A/P 標記）。
    spacing 各軸不等時先重取樣到 min(spacing) 各向同性格，維持投影 aspect ratio。
    輸出 x-ap.jpg / x-lat.jpg，回傳 {view: jpg_path}。"""
    import matplotlib
    matplotlib.use('Agg')
    import matplotlib.pyplot as plt

    vid = os.path.basename(os.path.normpath(out_dir))
    ct = sitk.ReadImage(ct_path)
    cbt = sitk.ReadImage(cbt_path)
    if ct.GetSize() != cbt.GetSize():
        raise ValueError(f'cbt/CT grid 尺寸不符 {cbt.GetSize()} vs {ct.GetSize()}')
    sp = np.array(ct.GetSpacing(), float)                       # (x,y,z)
    native_size = ct.GetSize()
    # spacing 各軸不等：先重取樣 CT/螺絲（與後面的分割 label）到
    # min(spacing) 的各向同性格，維持投影视圖正確的 aspect ratio
    min_sp = float(sp.min())
    isosp = isosize = None
    if not np.allclose(sp, min_sp):
        isosp = [min_sp, min_sp, min_sp]
        isosize = [max(1, int(round(s * v / min_sp))) for s, v in zip(sp, ct.GetSize())]
        o, d = ct.GetOrigin(), ct.GetDirection()
        ct = sitk.Resample(sitk.Cast(ct, sitk.sitkFloat32), isosize, sitk.Transform(),
                           sitk.sitkLinear, o, isosp, d, 0.0)
        cbt = sitk.Resample(cbt, isosize, sitk.Transform(),
                            sitk.sitkNearestNeighbor, o, isosp, d, 0)
    ct_arr = sitk.GetArrayFromImage(ct).astype(np.float32)      # (z,y,x)
    cbt_arr = sitk.GetArrayFromImage(cbt)
    sp = np.array(ct.GetSpacing(), float)

    metal = cbt_arr > 0
    try:
        _, lb_path, _ = find_native_paths(vid)
        lb_img = sitk.ReadImage(lb_path)
        # 比對「重取樣前」的 native grid（label 與原 CT 同格）
        if lb_img.GetSize() != native_size:
            raise ValueError(f'label/CT grid 尺寸不符 {lb_img.GetSize()} vs {native_size}')
        if isosp is not None:
            lb_img = sitk.Resample(lb_img, isosize, sitk.Transform(),
                                   sitk.sitkNearestNeighbor,
                                   ct.GetOrigin(), isosp, ct.GetDirection(), 0)
        lb = sitk.GetArrayFromImage(lb_img)
        spine = (lb >= 1) & (lb <= 24)     # LABEL_MAP: C1..L5 全為脊椎
    except Exception as e:
        logger.warning(f'{vid}: native 分割 label 不可用（{e}）；'
                       f'退回 HU 300-3000 閾值當脊椎骨')
        spine = (ct_arr >= 300) & (ct_arr <= 3000)

    bone_mu = np.where(spine & ~metal, np.clip(ct_arr, 0, 2000) / 400.0, 0.0)
    metal_mu = 60.0 * metal

    z, y, x = np.where(metal)
    if z.size == 0:
        raise ValueError(f'{vid}: cbt 無螺絲 voxel')
    mz, my, mx = (int(margin_mm / s) for s in (sp[2], sp[1], sp[0]))
    zs = slice(max(0, z.min() - mz), min(ct_arr.shape[0], z.max() + mz + 1))
    ys = slice(max(0, y.min() - my), min(ct_arr.shape[1], y.max() + my + 1))
    xs = slice(max(0, x.min() - mx), min(ct_arr.shape[2], x.max() + mx + 1))

    proj = {
        'ap': (bone_mu[zs, :, xs].sum(axis=1), metal_mu[zs, :, xs].sum(axis=1)),    # 沿 y 積分
        'lateral': (bone_mu[zs, ys, :].sum(axis=2), metal_mu[zs, ys, :].sum(axis=2))  # 沿 x 積分
    }
    flip_x = {'ap': True, 'lateral': False}
    markers = {'ap': ('R', 'L'), 'lateral': ('A', 'P')}  # 畫面左=前位(A)、右=後位(P)
    os.makedirs(out_dir, exist_ok=True)
    paths = {}
    for view in views:
        if view not in proj:
            continue
        b, m = proj[view]
        b = b[::-1, ::-1] if flip_x[view] else b[::-1, :]   # 頂=頭端
        m = m[::-1, ::-1] if flip_x[view] else m[::-1, :]
        bnz = b[b > 0]
        if bnz.size:
            lo, hi = np.percentile(bnz, 1), np.percentile(bnz, 99)
            bone = np.clip((b - lo) / (hi - lo + 1e-9), 0, 1) ** 0.7
        else:
            bone = np.zeros_like(b)
        mmax = float(m.max())
        metal_img = (m / (mmax + 1e-9)) ** 0.5 if mmax > 0 else m * 0
        img = np.clip(bone + metal_img, 0, 1)
        ll, rl = markers[view]
        h, w = img.shape
        fig, ax = plt.subplots(figsize=(8.0 * w / h, 8.0), dpi=110)
        ax.imshow(img, cmap='gray', interpolation='nearest')
        ax.set_title(f'{view.upper()} projection (spine + screws) - {vid}',
                     color='white', fontsize=13)
        ax.text(0.01, 0.98, ll, transform=ax.transAxes, color='cyan', fontsize=13,
                va='top', ha='left', fontweight='bold')
        ax.text(0.99, 0.98, rl, transform=ax.transAxes, color='cyan', fontsize=13,
                va='top', ha='right', fontweight='bold')
        ax.axis('off')
        fig.tight_layout(pad=0.5)
        p = os.path.join(out_dir, PROJ_FILENAME[view])
        fig.savefig(p, format='jpg', facecolor='black')
        plt.close(fig)
        paths[view] = p
        logger.info(f'{vid}: {view} projection -> {p}')
    return paths


def main():
    parser = argparse.ArgumentParser(
        description='Write <Output_dir>/<date>/<volume_id>/cbt.nii.gz (screws mapped to native space) '
                    'from a side_results run')
    parser.add_argument('run_id', help='e.g. 20260907_230652')
    parser.add_argument('volumes', nargs='*',
                        help='volume ids (full or trailing digits); default: all in the run')
    parser.add_argument('--date', default=None, help='output date dir (default: run_id[:8])')
    args = parser.parse_args()
    logging.basicConfig(level=logging.INFO,
                        format='%(asctime)s [%(levelname)s] %(name)s: %(message)s',
                        datefmt='%Y-%m-%d %H:%M:%S')
    run_dir = os.path.join(SIDE_RESULT_DIR, args.run_id)
    if not os.path.isdir(run_dir):
        sys.exit(f'side results dir not found: {run_dir}')
    run_vols = sorted(d for d in os.listdir(run_dir) if os.path.isdir(os.path.join(run_dir, d)))
    if args.volumes:
        vols = [v for v in run_vols
                if v in args.volumes or v.rsplit('.', 1)[-1] in args.volumes]
        if not vols:
            sys.exit(f'none of {args.volumes} found in run {args.run_id}')
    else:
        vols = run_vols
    ok, fail = 0, 0
    for vid in vols:
        try:
            write_volume_cbt(vid, args.run_id, date=args.date)
            ok += 1
        except Exception as e:
            fail += 1
            logger.error(f'{vid}: {e}')
    print(f'done: {ok} written, {fail} failed / {len(vols)} volume(s)')


if __name__ == '__main__':
    main()