add : dcm / nii.gz 뷰어 / cvat 컨버터

NII_DCM_Viewer.py

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+"""
+척추 라벨링 데이터 뷰어
+- NII.GZ: 3D 세그멘테이션 마스크
+- PF: MITK PlanarFigure (2D 측정)
+- DCM: DICOM 원본 이미지
+"""
+
+import nibabel as nib
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.widgets import Slider
+from matplotlib.lines import Line2D
+import xml.etree.ElementTree as ET
+from pathlib import Path
+import re
+
+ROOT_PATH = Path(__file__).parent
+BASE_PATH = None
+DCM_FILE = None
+MITK_ORIGIN_Y = 966.81
+SPACING = 0.148
+
+
+def load_nii(filepath):
+    img = nib.load(filepath)
+    return img.get_fdata(), img.header
+
+
+def load_dcm(filepath):
+    import pydicom
+    dcm = pydicom.dcmread(filepath)
+    return dcm.pixel_array
+
+
+def parse_pf(filepath):
+    with open(filepath, 'r', encoding='utf-8') as f:
+        content = f.read()
+    content = re.sub(r'<\?xml[^?]*\?>', '', content)
+    root = ET.fromstring(f'<root>{content}</root>')
+    pf = root.find('PlanarFigure')
+
+    return {
+        'type': pf.get('type'),
+        'vertices': [(float(v.get('x')), float(v.get('y'))) for v in pf.findall('.//Vertex')]
+    }
+
+
+def pf_to_pixel(x, y):
+    """MITK 좌표 -> 픽셀 좌표 변환"""
+    return x / SPACING, (MITK_ORIGIN_Y - y) / SPACING
+
+
+def draw_pf(ax, pf_files, colors):
+    labels = []
+    for i, pf_file in enumerate(pf_files):
+        data = parse_pf(str(pf_file))
+        color = colors[i % len(colors)]
+        transformed = [pf_to_pixel(x, y) for x, y in data['vertices']]
+
+        if 'Line' in data['type']:
+            xs, ys = zip(*transformed)
+            ax.plot(xs, ys, '-o', color=color, linewidth=3, markersize=8)
+        elif 'Circle' in data['type'] and len(transformed) >= 2:
+            center, edge = transformed[0], transformed[1]
+            radius = np.hypot(edge[0]-center[0], edge[1]-center[1])
+            ax.add_patch(plt.Circle(center, radius, fill=False, color=color, linewidth=3))
+            ax.plot(center[0], center[1], 'o', color=color, markersize=8)
+
+        labels.append((color, pf_file.stem))
+    return labels
+
+
+def view_nii_overlay():
+    """모든 NII 마스크를 색상별로 겹쳐서 표시"""
+    nii_files = list(BASE_PATH.glob('*.nii.gz'))
+    first_data, _ = load_nii(str(nii_files[0]))
+    combined = np.zeros(first_data.shape)
+
+    for i, f in enumerate(nii_files, 1):
+        data, _ = load_nii(str(f))
+        combined[data > 0] = i
+
+    fig, ax = plt.subplots(figsize=(10, 10))
+    mid_z = combined.shape[2] // 2
+
+    slider_ax = plt.axes([0.2, 0.02, 0.6, 0.03])
+    slider = Slider(slider_ax, 'Slice', 0, combined.shape[2]-1, valinit=mid_z, valstep=1)
+
+    plt.sca(ax)
+    img_plot = ax.imshow(combined[:, :, mid_z].T, cmap='nipy_spectral', origin='lower')
+    ax.set_title(f'All Vertebrae - Slice {mid_z}')
+    plt.colorbar(img_plot, ax=ax)
+
+    def update(val):
+        idx = int(slider.val)
+        img_plot.set_data(combined[:, :, idx].T)
+        ax.set_title(f'All Vertebrae - Slice {idx}')
+        fig.canvas.draw_idle()
+
+    slider.on_changed(update)
+    plt.show()
+
+
+def view_all_on_dcm():
+    """DCM + NII 마스크 + PF 측정 오버레이"""
+    img = load_dcm(str(DCM_FILE))
+    nii_files = list(BASE_PATH.glob('*.nii.gz'))
+    pf_files = list(BASE_PATH.glob('*.pf'))
+
+    fig, ax = plt.subplots(figsize=(10, 20))
+    ax.imshow(img, cmap='gray', origin='upper')
+
+    # NII 마스크 컨투어
+    cmap = plt.colormaps.get_cmap('tab20').resampled(len(nii_files))
+    nii_labels = []
+    for i, f in enumerate(nii_files):
+        data, _ = load_nii(str(f))
+        proj = np.max(data, axis=2).T  # (W,H,D) -> (H,W)
+        if proj.max() > 0:
+            ax.contour(proj, levels=[0.5], colors=[cmap(i)], linewidths=1.5, alpha=0.8)
+        nii_labels.append((cmap(i), f.stem.split('.')[0]))
+
+    # PF 오버레이
+    pf_labels = draw_pf(ax, pf_files, ['red', 'yellow', 'cyan', 'lime', 'magenta'])
+
+    # 범례
+    legend = [Line2D([0], [0], color=c, label=n) for c, n in nii_labels]
+    legend += [Line2D([0], [0], color=c, marker='o', label=f'[PF] {n}') for c, n in pf_labels]
+    ax.legend(handles=legend, loc='upper left', bbox_to_anchor=(1.02, 1), fontsize=8)
+    ax.set_title('DCM + NII Masks + PF Annotations')
+    plt.tight_layout()
+    plt.show()
+
+
+def select_directory():
+    """디렉토리 선택"""
+    global BASE_PATH, DCM_FILE
+    dirs = sorted([d for d in ROOT_PATH.iterdir() if d.is_dir() and not d.name.startswith('.')])
+
+    if not dirs:
+        print("하위 디렉토리가 없습니다.")
+        return False
+
+    print("\n=== 디렉토리 선택 ===")
+    for i, d in enumerate(dirs, 1):
+        print(f"{i}. {d.name}")
+
+    try:
+        idx = int(input(f"\n선택 (1-{len(dirs)}): ").strip()) - 1
+        if 0 <= idx < len(dirs):
+            BASE_PATH = dirs[idx]
+            dcm_files = list(BASE_PATH.glob('*.dcm'))
+            DCM_FILE = dcm_files[0] if dcm_files else None
+            print(f"선택됨: {BASE_PATH.name}")
+            return True
+    except (ValueError, IndexError):
+        pass
+    print("잘못된 선택")
+    return False
+
+
+if __name__ == '__main__':
+    print("=== 척추 라벨링 뷰어 ===")
+    if not select_directory():
+        exit()
+
+    while True:
+        print(f"\n=== {BASE_PATH.name} ===")
+        print("1. NII 마스크 오버레이 (슬라이더)")
+        print("2. DCM + NII + PF 전체 오버레이")
+        print("q. 종료")
+
+        choice = input("\n선택: ").strip().lower()
+        if choice == 'q':
+            break
+        elif choice == '1':
+            view_nii_overlay()
+        elif choice == '2':
+            if DCM_FILE:
+                view_all_on_dcm()
+            else:
+                print("DCM 파일이 없습니다.")