Xiao Furen
d167c1f7c7
Introduce a robust coordinate transformation system to manage the relationship between original CT space and rotated/standardized segmentation spaces. This includes a new directory hierarchy to separate unrotated crops from rotated outputs and utility functions for geometric mapping. Key changes: - Implement `imaging/transforms.py` to handle bounding box metadata, affine standardization, and coordinate mapping between spaces. - Restructure dataset output: unrotated segmentation files (binary, SDF, ROI, etc.) are now stored in a `<vol>/crop/` subdirectory to distinguish them from `<vol>/rotated/` aligned versions. - Add `level_file_path` utility to abstract file discovery across legacy (top-level) and new (crop-based) directory structures. - Enhance `seg_bone` to capture and export bounding box metadata (`bbox2`, `nn_bbox`, `bbox_orig`) into `transform.json`. - Implement `xfr_cbt_native.py` for mapping screw positions back to original CT space. - Update preprocessing and visualization scripts to support the new directory layout and transformation metadata. - Improve TinyDB metadata migration logic to prevent accidental corruption of existing database structures.
418 lines
No EOL
20 KiB
Python
418 lines
No EOL
20 KiB
Python
import os
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import numpy as np
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import SimpleITK as sitk
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from imaging.resample import resample_img
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from imaging.affine import standardize_affine
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from imaging.segmentation import seg_bone
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import json
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import glob
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from config.constant import LABEL_MAP
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from imaging.nifti_io import sitk_to_nibabel, nibabel_to_sitk
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from imaging.orientation import anterior_y_side
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from imaging.transforms import (build_volume_meta, img_geom, margined_box,
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save_transform, std_flip_axes_for_direction)
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def flip_y_sitk(img):
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"""index 系 y 軸（array axis 1，前後方向）翻轉：
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只翻數據、spacing/origin/direction 等幾何不變，即整顆體積的前後
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朝向在 index 系翻轉（y 大側 <-> y 小側）。供 supine / prone 個案
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統一前後慣例（前側 = y 大側）用。"""
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arr = np.flip(sitk.GetArrayFromImage(img), axis=1)
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out = sitk.GetImageFromArray(arr)
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out.CopyInformation(img)
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return out
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def load_progress(PROGRESS_FILE):
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if os.path.exists(PROGRESS_FILE):
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with open(PROGRESS_FILE, "r") as f:
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return json.load(f)
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return {}
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def save_progress(progress, PROGRESS_FILE):
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with open(PROGRESS_FILE, "w") as f:
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json.dump(progress, f, indent=2)
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def process_single_image(image_path, label_path, output_dir_base=None, max_z_spacing=None, allowed_levels=None, min_levels=None, metadata_cache=None, crop_subdir=False):
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"""metadata_cache：可選，需提供 get(name) -> dict|None 與
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put(name, dict)。dict 可含 spacing=[x,y,z]、labels=[label id]。
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兩者都在 db 裡時整支跳過判定不需讀影像 / label 檔。
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crop_subdir=True：各 level 的未旋轉輸出（_binary / _smd /
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_smd_resampled / _binary_sdf / _binary_nn / _roi）改写到
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<vol>/crop/ 子資料夾（False＝舊佈局、<vol>/ 頂層）。"""
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file_name = os.path.basename(image_path)
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name = file_name.replace(".nii.gz", "")
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# pixel spacing / labels 優先用 metadata db，避免每次 run 都讀檔
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meta = metadata_cache.get(name) if metadata_cache is not None else None
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image = None
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label = None
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spacing = meta.get("spacing") if meta is not None else None
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existing_labels = meta.get("labels") if meta is not None else None
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if spacing is None:
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image = sitk.ReadImage(image_path)
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spacing = [float(v) for v in image.GetSpacing()]
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if metadata_cache is not None:
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metadata_cache.put(name, {"spacing": spacing})
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# z spacing 過大（低解析度掃描）跳過整支 pipeline
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if max_z_spacing is not None and spacing[2] > max_z_spacing:
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z_spacing = spacing[2]
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print(f"z spacing {z_spacing:.2f} mm > {max_z_spacing} mm, "
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f"skipping pipeline for {name}")
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return {
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"processed_labels": [],
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"missing_labels": [],
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"skipped": True,
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"skip_reason": f"z spacing {z_spacing:.2f} mm > {max_z_spacing} mm"
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}
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if existing_labels is None:
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label = sitk.ReadImage(label_path)
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# 取得現有 label
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lssif = sitk.LabelShapeStatisticsImageFilter()
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lssif.Execute(label)
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existing_labels = [int(v) for v in lssif.GetLabels()] # 例如 [1,2,3,20,21]
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if metadata_cache is not None:
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metadata_cache.put(name, {"labels": existing_labels})
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else:
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print(f"Metadata db hit for {name} (spacing={spacing}, labels={existing_labels})")
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print(f"Existing labels in {os.path.basename(label_path)}: {existing_labels}")
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allowed_label_list = [n for n in existing_labels
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if n in LABEL_MAP and (allowed_levels is None
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or LABEL_MAP[n] in allowed_levels)]
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# 沒有任何符合 allowed levels（如 lumbar）的 label：不建立輸出資料夾、
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# 不做重取樣，整檔跳過（不計入 max_images）
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if not allowed_label_list:
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print(f"No label matches allowed levels {allowed_levels} in {name}, "
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f"skipping (no output folder)")
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return {
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"processed_labels": [],
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"missing_labels": [],
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"skipped": True,
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"skip_reason": f"no label in allowed levels {allowed_levels}"
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}
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# 符合 allowed levels 的 label 少於 min_levels（如 lumbar < 2 層）：
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# 整支 pipeline 跳過，不建立輸出資料夾（不計入 max_images）
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if min_levels is not None and len(allowed_label_list) < min_levels:
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have = ", ".join(f"{n} ({LABEL_MAP[n]})" for n in allowed_label_list)
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print(f"Only {len(allowed_label_list)} allowed-level label(s) [{have}] in {name} "
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f"< {min_levels}, skipping pipeline (no output folder)")
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return {
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"processed_labels": [],
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"missing_labels": [],
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"skipped": True,
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"skip_reason": (f"only {len(allowed_label_list)} label(s) in allowed "
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f"levels < {min_levels}")
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}
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# 進入 pipeline：若上面的 spacing / labels 來自 metadata db，
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# 影像與 label 檔還沒讀，這裡補讀
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if image is None:
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image = sitk.ReadImage(image_path)
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if label is None:
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label = sitk.ReadImage(label_path)
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# LabelStatisticsImageFilter computes statistics (e.g., mean, minimum, maximum, median) of pixel values in an image, segmented by labels in a corresponding label image.
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lsif = sitk.LabelStatisticsImageFilter()
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lsif.Execute(image, label)
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# Assume to have some sitk image (itk_image) and label (itk_label)
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resampled_sitk_img = resample_img(image, out_spacing=[0.5, 0.5, 0.5], is_label=False)
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resampled_sitk_lbl = resample_img(label, out_spacing=[0.5, 0.5, 0.5], is_label=True)
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# 前後（AP）方向判定：本流程最終輸出慣例是前側 = y 大側（後 = y 小側）。
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# 但 prone（伏位）掃描個案經 standardize_affine 後前側落在 y 小側
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# （例：CTSpine1K colon 0003、0075、0460...，全 dataset 約 1%），
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# 不修正時上終板 / 棘突 / 椎體分割與 rotated/ 對齊全部反掉。
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#
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# 判定（對每個 allowed level 的 0.5mm label 個別做、再票決——不能
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# 直接 union 多層：腰椎前凸（lordosis）下各層椎體在 AP 投影會散開，
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# 椎管「空隙」被其它層的骨填掉）：
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# 1) anterior_y_side 回傳工作體積（0.5mm 重取樣、standardize_affine
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# 之前）grid 中椎體塊所在的 y 端（y_min / y_max / None）；
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# 2) standardize_affine（nibabel 端）會在輸出 affine y 分量 < 0 時
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# 再翻一次 y。注意 nibabel affine 與 SimpleITK direction 的 y 分
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# 量符號相反（NIfTI RAS <-> SITK LPS），所以
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# standardize_affine 會翻 y <=> direction[4] > 0；
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# 最終 y 端 = pre_side（若會翻 y 則 y_min<->y_max 互換）；
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# 3) 最終前側會落 y 小側時，現在先對 CT 與 label 做 y 翻轉
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# （純 index 翻轉、幾何不變），與 standardize_affine 的翻轉
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# 組成淨效果，使所有輸出與其它個案同方向。
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# 無法判定 / 投票平手時維持原方向（寧可不翻、不誤翻）。
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# 判定結果存入 metadata db（ap_flip），重跑免重算。
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ap_flip = (meta or {}).get("ap_flip")
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if ap_flip is None:
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# standardize_affine 是否會翻轉 y（nibabel affine[1,1] < 0，
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# 等价於 sitk direction[4] > 0，兩者符號相反）
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std_flips_y = resampled_sitk_img.GetDirection()[4] > 0
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arr_lbl = sitk.GetArrayFromImage(resampled_sitk_lbl)
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votes = []
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for n in allowed_label_list:
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side = anterior_y_side(arr_lbl == n)
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if side is not None:
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votes.append(side)
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n_min = votes.count("y_min")
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n_max = votes.count("y_max")
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if n_min > n_max:
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pre_side = "y_min"
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elif n_max > n_min:
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pre_side = "y_max"
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else:
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pre_side = None
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if pre_side is None:
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ap_flip = False
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print(f"AP orientation undetermined for {name} (votes={votes}); "
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f"proceeding with default orientation (anterior = large y)")
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else:
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final_side = (pre_side if not std_flips_y
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else ("y_min" if pre_side == "y_max" else "y_max"))
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ap_flip = final_side == "y_min"
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print(f"AP orientation for {name}: pre={pre_side} "
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f"(std_flips_y={std_flips_y}) -> final={final_side} "
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f"[votes={votes}], flip={ap_flip}")
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if metadata_cache is not None:
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metadata_cache.put(name, {"ap_flip": bool(ap_flip)})
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if ap_flip:
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# label（原解析度 raw label）也要翻：seg_bone 的主遮罩鏈
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#（_binary / SMD / _binary_sdf）是用 original_label（= label）
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# 算的，不是用 0.5mm resampled label；漏翻時翻轉不生效。
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label = flip_y_sitk(label)
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resampled_sitk_img = flip_y_sitk(resampled_sitk_img)
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resampled_sitk_lbl = flip_y_sitk(resampled_sitk_lbl)
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print(f"AP orientation corrected for {name}: CT and label flipped "
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f"along y; outputs unified to anterior = large y")
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# 建立每個檔案的輸出資料夾
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file_name = os.path.basename(image_path)
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name = file_name.replace(".nii.gz", "")
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output_dir = os.path.join(output_dir_base, name)
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os.makedirs(output_dir, exist_ok=True)
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# 各 level 的未旋轉輸出寫入位置：crop_subdir=True 時在 <vol>/crop/
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# 子資料夾（旋轉版在 <vol>/rotated/，xfr_preprocess 產出）
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if crop_subdir:
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seg_dir = os.path.join(output_dir, 'crop')
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os.makedirs(seg_dir, exist_ok=True)
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else:
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seg_dir = output_dir
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# 存現有 label 到 txt
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txt_path = os.path.join(output_dir, f"{name}_labels.txt")
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with open(txt_path, "w") as f:
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for lab in existing_labels:
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f.write(f"{lab}\t{LABEL_MAP.get(lab, 'Unknown')}\n")
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# 遍歷現有 label 做分割；個別 label 失敗（label_map 缺該 label、
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# 或 seg_bone 報錯）只跳過該 label，不中斷整檔處理
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processed = []
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skipped = []
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level_entries = {} # level name -> transform.json 的 level 條目
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std_flips = None # standardize_affine 實際翻的軸（整卷一致；記錄用）
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for n in existing_labels:
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if n not in LABEL_MAP:
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print(f"Label {n} not found in label_map, skipping this label (file continues).")
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skipped.append(n)
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continue
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if allowed_levels is not None and LABEL_MAP[n] not in allowed_levels:
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print(f"Label {n} ({LABEL_MAP[n]}) not in allowed levels, "
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f"skipping this label (file continues).")
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skipped.append(n)
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continue
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try:
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res = seg_bone(n, name, resampled_sitk_img, resampled_sitk_lbl, seg_dir,
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label_map=LABEL_MAP, original_label=label)
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if res is None:
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print(f"Label {n}: empty after largest-CC extraction, skipping this label.")
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skipped.append(n)
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continue
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(roi_path, binary_path, roi2_path, cortical_path, binary_nn_path,
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binary_linear_path, smd_path, resampled_path, binary_sdf_path,
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binary_erode_path, seg_meta) = res
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for path in [roi_path, binary_path, roi2_path, cortical_path,
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binary_nn_path, binary_linear_path,
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smd_path, resampled_path, binary_sdf_path,
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binary_erode_path]:
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if path is not None:
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flips = standardize_affine(path, seg_dir)
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if flips:
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if std_flips is None:
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std_flips = sorted(flips)
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elif sorted(flips) != std_flips:
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print(f"WARNING: standardize_affine 翻軸不一致 "
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f"({name}): {std_flips} vs {sorted(flips)}")
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# 該 level 的裁切 box（x,y,z 序；imaging/transforms.py 定義）
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boxes = {}
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if seg_meta['has_smd']:
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boxes['smd_resampled'] = seg_meta['bbox2']
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boxes['binary_sdf'] = seg_meta['bbox2']
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boxes['roi'] = seg_meta['bbox2']
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else:
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boxes['roi'] = seg_meta['bbox2']
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if seg_meta['nn_bbox'] is not None:
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boxes['binary_nn'] = seg_meta['nn_bbox']
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if seg_meta['bbox_orig'] is not None:
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boxes['binary'] = seg_meta['bbox_orig']
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boxes['smd'] = margined_box(seg_meta['bbox_orig'],
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image.GetSize(), margin=4)
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level_entries[LABEL_MAP[n]] = {
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'label': int(n),
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'std_flip_axes': list(std_flips) if std_flips is not None else [],
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'boxes': boxes,
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}
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processed.append(n)
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except RuntimeError as e:
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print(f"Label {n} could not be processed, skipping. Error: {e}")
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skipped.append(n)
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# transform.json：每 level 記錄 原始 CT <-> 標準化 grid 的完整座標鏈
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# （box / flip 軸 / ap_flip / 原 CT 幾何），rotated/ 的 R/center/start 由
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# _write_rotated_level 補寫（xfr_preprocess）；供分割後 mask 映回原始座標
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if level_entries:
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try:
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tmeta = build_volume_meta(name, image_path, img_geom(image),
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img_geom(resampled_sitk_img), ap_flip,
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level_entries)
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save_transform(output_dir, tmeta)
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print(f"Transform metadata: {os.path.join(output_dir, 'transform.json')} "
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f"({len(level_entries)} level(s), std_flips={tmeta['levels'][list(level_entries)[0]]['std_flip_axes']})")
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try:
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expected = std_flip_axes_for_direction(image.GetDirection())
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if std_flips is not None and list(std_flips) != expected:
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print(f"WARNING: {name} std_flips {std_flips} != 預期 "
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f"{expected}（依原 CT direction 推斷）")
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elif std_flips is None and expected:
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print(f"WARNING: {name} 預期 std_flips {expected} 但未翻任何軸")
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except ValueError:
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print(f"WARNING: {name} 原 CT direction 非對角 ±1；"
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f"transform.json 的反向映射將無法使用該卷")
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except Exception as e:
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print(f"WARNING: 寫 transform.json 失敗（{name}）：{e}")
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return {
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"processed_labels": processed,
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"missing_labels": skipped
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}
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def process_dataset(image_dir, label_dir, output_dir, labels_to_process=None, max_images=None, post_process=None, max_z_spacing=None, allowed_levels=None, min_levels=None, metadata_cache=None, crop_subdir=False):
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image_files = sorted(glob.glob(os.path.join(image_dir, "*.nii.gz")))
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total_files = len(image_files)
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print(f"Total files: {total_files}")
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PROGRESS_FILE = os.path.join(output_dir, "progress.json")
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progress = load_progress(PROGRESS_FILE)
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all_file_summary = []
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# max_images 統計「實際進入 pipeline 的檔數」：
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# z spacing 超標被跳過的檔不計入配額，繼續掃描後續檔案
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processed_count = 0
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for idx, image_path in enumerate(image_files, 1):
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if max_images is not None and processed_count >= max_images:
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print(f"Reached max_images={max_images}, stopping early.")
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break
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file_name = os.path.basename(image_path)
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name = file_name.replace(".nii.gz", "")
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label_path = os.path.join(label_dir, file_name.replace(".nii.gz", "_seg.nii.gz"))
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file_summary = {
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"file_name": file_name,
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"current_labels": [],
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"missing_labels": []
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}
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if progress.get(name, {}).get("finished", False):
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print(f"[{idx}/{total_files}] Already finished: {file_name}")
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file_summary["current_labels"] = progress[name].get("processed_labels", [])
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file_summary["missing_labels"] = progress[name].get("missing_labels", [])
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processed_count += 1
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all_file_summary.append(file_summary)
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continue
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if not os.path.exists(label_path):
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print(f"[{idx}/{total_files}] Warning: label not found for {file_name}")
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file_summary["note"] = "Label file not found"
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processed_count += 1
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all_file_summary.append(file_summary)
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continue
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try:
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result = process_single_image(image_path, label_path, output_dir_base=output_dir,
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max_z_spacing=max_z_spacing,
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allowed_levels=allowed_levels,
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min_levels=min_levels,
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metadata_cache=metadata_cache,
|
||
crop_subdir=crop_subdir)
|
||
# print(result)
|
||
# exit()
|
||
except Exception as e:
|
||
print(f"[{idx}/{total_files}] Error processing {file_name}: {e}")
|
||
file_summary["note"] = f"Error: {e}"
|
||
processed_count += 1
|
||
all_file_summary.append(file_summary)
|
||
continue
|
||
|
||
if result.get("skipped"):
|
||
# z spacing 超標：不計入 max_images 配額，繼續掃描後續檔案
|
||
print(f"[{idx}/{total_files}] Skipped ({result['skip_reason']}): {file_name}")
|
||
file_summary["note"] = result["skip_reason"]
|
||
all_file_summary.append(file_summary)
|
||
continue
|
||
|
||
processed_count += 1
|
||
file_summary["current_labels"] = result["processed_labels"]
|
||
file_summary["missing_labels"] = result["missing_labels"]
|
||
all_file_summary.append(file_summary)
|
||
|
||
progress[name] = {
|
||
"finished": True,
|
||
"processed_labels": result["processed_labels"],
|
||
"missing_labels": result["missing_labels"]
|
||
}
|
||
save_progress(progress, PROGRESS_FILE)
|
||
|
||
count_msg = f" | processed {processed_count}/{max_images}" if max_images is not None else ""
|
||
print(f"[{idx}/{total_files}] Finished: {file_name} | "
|
||
f"Missing labels: {result['missing_labels'] or 'None'}{count_msg}")
|
||
|
||
if post_process is not None:
|
||
try:
|
||
post_process(os.path.join(output_dir, name), result["processed_labels"])
|
||
except Exception as e:
|
||
print(f"[{idx}/{total_files}] post_process error for {name}: {e}")
|
||
|
||
# --- Summary ---
|
||
summary_path = os.path.join(output_dir, "all_files_label_summary.txt")
|
||
os.makedirs(os.path.dirname(summary_path), exist_ok=True)
|
||
print(f"\nWriting summary to {summary_path}...")
|
||
|
||
with open(summary_path, "w") as f:
|
||
f.write("--- CTSpine1K Dataset Label Summary ---\n")
|
||
f.write(f"Total files processed: {total_files}\n\n")
|
||
|
||
for summary in all_file_summary:
|
||
f.write("================================================\n")
|
||
f.write(f"File: {summary['file_name']}\n")
|
||
|
||
processed_labels_str = ", ".join([str(l) for l in summary['current_labels']])
|
||
f.write(f"Labels processed: {processed_labels_str}\n")
|
||
|
||
if summary['missing_labels']:
|
||
missing_str = ", ".join([f"{l} ({LABEL_MAP.get(l, 'Unknown')})" for l in summary['missing_labels']])
|
||
f.write(f"🚨 Missing Labels: {missing_str}\n")
|
||
else:
|
||
f.write("✅ Missing Labels: None\n")
|
||
|
||
if "note" in summary:
|
||
f.write(f"Note: {summary['note']}\n")
|
||
f.write("================================================\n\n")
|
||
|
||
print("All done! Summary file created.") |