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.
47 lines
1.3 KiB
Python
47 lines
1.3 KiB
Python
import os
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import numpy as np
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import nibabel as nib
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def standardize_affine(file_path, output_dir):
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"""翻轉 affine 對角為負的軸（資料 flip + 平移修正）後重寫同目錄同名檔。
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回傳：實際翻轉的軸 index list（未翻為 []）。呼叫端（transform 記錄）
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需要這份 ground truth：反 index 鏈路用「N-1-i」鏡射補回翻軸。"""
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img = nib.load(file_path)
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data = img.get_fdata()
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affine = img.affine.copy()
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# 初始化翻轉軸
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flip_axes = []
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# 檢查 X 軸方向
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if affine[0, 0] < 0:
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flip_axes.append(0)
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affine[0, 0] *= -1
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affine[0, 3] *= -1 # 修正平移部分
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# 檢查 Y 軸方向
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if affine[1, 1] < 0:
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flip_axes.append(1)
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affine[1, 1] *= -1
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affine[1, 3] *= -1 # 修正平移部分
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# 檢查 Z 軸方向
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if affine[2, 2] < 0:
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flip_axes.append(2)
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affine[2, 2] *= -1
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affine[2, 3] *= -1 # 修正平移部分
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# 翻轉數據（如果需要）
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if flip_axes:
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data = np.flip(data, axis=tuple(flip_axes))
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# 保存修正後的影像
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standardized_img = nib.Nifti1Image(data, affine)
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output_path = os.path.join(output_dir, os.path.basename(file_path))
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os.makedirs(os.path.dirname(output_path), exist_ok=True)
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nib.save(standardized_img, output_path)
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return flip_axes
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