563 lines
21 KiB
Python
563 lines
21 KiB
Python
import utils.jwtauth
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from flask import request, jsonify, Blueprint
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from models import db, Image, Patient, Office, Case, ImageBbox
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from utils.oss import upload_to_oss, custom_endpoint
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import uuid
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import io
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import os
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import pydicom
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from pydicom.pixel_data_handlers.util import apply_voi_lut
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import nibabel as nib
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import numpy as np
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from PIL import Image as PilImage
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import tempfile
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image_bp = Blueprint('image', __name__)
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def convert_to_png(pixel_array, is_dicom, ds=None):
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"""
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将DICOM或NII文件的像素数组转换为PNG图像字节流。
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如果可用，会为DICOM应用VOI LUT。
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"""
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# 归一化或应用LUT
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if is_dicom and ds and 'VOILUTSequence' in ds:
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# 应用VOI LUT
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arr = apply_voi_lut(pixel_array, ds)
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else:
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# 其他情况进行简单的归一化
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arr = pixel_array.astype(np.float32)
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if np.max(arr) != np.min(arr):
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arr = (arr - np.min(arr)) / (np.max(arr) - np.min(arr)) * 255.0
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else:
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arr = np.zeros_like(arr)
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arr = arr.astype(np.uint8)
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# 转换为灰度PIL图像
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if arr.ndim == 2:
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pil_img = PilImage.fromarray(arr, 'L')
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else: # 对于可能存在的多通道数据，只取第一通道
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pil_img = PilImage.fromarray(arr[:,:,0], 'L')
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# 保存到内存缓冲区
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img_buffer = io.BytesIO()
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pil_img.save(img_buffer, format='PNG')
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img_buffer.seek(0)
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return img_buffer
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@image_bp.route('/api/image/add', methods=['POST'])
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@utils.jwtauth.jwt_required
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def add_image():
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"""
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处理医学影像上传、处理和数据库记录创建。
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"""
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creator_id = request.user_id
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# 1. --- 验证输入 ---
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if 'file' not in request.files:
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return jsonify({'code': 400, 'message': '缺少必要参数: file'}), 400
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name = request.form.get('name')
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img_type = request.form.get('type')
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if not all([name, img_type]):
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return jsonify({'code': 400, 'message': '缺少必要参数: name, type'}), 400
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file = request.files['file']
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if file.filename == '':
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return jsonify({'code': 400, 'message': '未选择文件'}), 400
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patient_id = request.form.get('patient_id') if request.form.get('patient_id') else None
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office_id = request.form.get('office_id') if request.form.get('office_id') else None
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case_id = request.form.get('case_id') if request.form.get('case_id') else None
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note = request.form.get('note')
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# 验证可选的外键是否存在
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if patient_id and not Patient.query.get(patient_id):
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return jsonify({'code': 404, 'message': '病人不存在'}), 404
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if office_id and not Office.query.get(office_id):
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return jsonify({'code': 404, 'message': '科室不存在'}), 404
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if case_id and not Case.query.get(case_id):
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return jsonify({'code': 404, 'message': '病历不存在'}), 404
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# 2. --- 文件分析 ---
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file_bytes = file.read()
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file_size_kb = len(file_bytes) / 1024.0
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file.close()
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file_stream = io.BytesIO(file_bytes)
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ds = None
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nib_img = None
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img_format = 'picture'
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tmp_path = None
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try:
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file_stream.seek(0)
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ds = pydicom.dcmread(file_stream, stop_before_pixels=False)
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img_format = 'dicom'
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except pydicom.errors.InvalidDicomError:
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pass
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if not ds:
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try:
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# 使用临时文件来稳健地处理NII加载
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# 后缀有助于nibabel猜测文件类型
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suffix = os.path.splitext(file.filename)[1] if file.filename and file.filename.endswith(('.nii', '.nii.gz')) else '.tmp'
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with tempfile.NamedTemporaryFile(delete=False, suffix=suffix) as tmp:
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tmp.write(file_bytes)
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tmp_path = tmp.name
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nib_img = nib.load(tmp_path)
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img_format = 'nii'
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except (nib.filebasedimages.ImageFileError, ValueError):
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# 不是一个有效的NII文件。它将被作为 'picture' 处理。
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pass
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# 3. --- 处理并保存 ---
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try:
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# 情况 A: 普通图片
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if img_format == 'picture':
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oss_key = f"hidoc2/images/{uuid.uuid4()}{os.path.splitext(file.filename)[1]}"
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file_stream.seek(0)
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if not upload_to_oss(file_stream, oss_key):
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raise Exception("OSS upload failed")
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new_image = Image(
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name=name, format='picture', type=img_type, dim='2D',
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patient_id=patient_id, creator_id=creator_id,
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office_id=office_id, case_id=case_id, note=note,
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oss_key=oss_key, size=file_size_kb
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)
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db.session.add(new_image)
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db.session.commit()
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return jsonify({'code': 201, 'message': '影像上传成功', 'data': new_image.to_dict()}), 201
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# 情况 B: DICOM 或 NII
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is_dicom = (img_format == 'dicom')
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original_ext = ".dcm" if is_dicom else os.path.splitext(file.filename)[1]
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original_oss_key = f"hidoc2/images/{uuid.uuid4()}{original_ext}"
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file_stream.seek(0)
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if not upload_to_oss(file_stream, original_oss_key):
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raise Exception("Original file OSS upload failed")
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pixel_array = ds.pixel_array if is_dicom else nib_img.get_fdata()
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shape = pixel_array.shape
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is_3d = (hasattr(ds, 'NumberOfFrames') and ds.NumberOfFrames > 1) if is_dicom else (pixel_array.ndim >= 3)
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# B.1 --- 处理3D影像 ---
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if is_3d:
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slice_x, slice_y, slice_z = (shape[2], shape[1], shape[0]) if is_dicom else (shape[0], shape[1], shape[2])
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volume_image = Image(
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name=name, format=img_format, type=img_type, dim='3D',
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patient_id=patient_id, creator_id=creator_id,
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office_id=office_id, case_id=case_id, note=note,
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oss_key=original_oss_key, size=file_size_kb,
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slice_x=slice_x, slice_y=slice_y, slice_z=slice_z
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)
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db.session.add(volume_image)
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db.session.flush()
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parent_id = volume_image.id
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axes = {'x': (slice_x, ' sagittal'), 'y': (slice_y, ' coronal'), 'z': (slice_z, ' axial')}
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for axis_name, (slice_count, axis_label) in axes.items():
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for i in range(slice_count):
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if axis_name == 'z':
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slice_arr = pixel_array[i, :, :] if is_dicom else pixel_array[:, :, i].T
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elif axis_name == 'y':
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slice_arr = pixel_array[:, i, :] if is_dicom else pixel_array[:, i, :].T
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else: # x
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slice_arr = pixel_array[:, :, i] if is_dicom else pixel_array[i, :, :].T
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png_buffer = convert_to_png(slice_arr, is_dicom, ds)
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png_oss_key = f"hidoc2/images/{uuid.uuid4()}.png"
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png_size_kb = len(png_buffer.getvalue()) / 1024.0
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upload_to_oss(png_buffer, png_oss_key)
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slice_img = Image(
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name=f"{name}_{axis_label.strip()}_{i}", format='picture', type=img_type, dim='2D',
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creator_id=creator_id, oss_key=png_oss_key, size=png_size_kb,
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parent_image_id=parent_id, slice_direction=axis_name, slice=i
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)
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db.session.add(slice_img)
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# B.2 --- 处理2D影像 ---
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else:
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slice_y, slice_x = shape[:2]
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main_image = Image(
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name=name, format=img_format, type=img_type, dim='2D',
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patient_id=patient_id, creator_id=creator_id,
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office_id=office_id, case_id=case_id, note=note,
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oss_key=original_oss_key, size=file_size_kb,
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slice_x=slice_x, slice_y=slice_y
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)
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db.session.add(main_image)
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db.session.flush()
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parent_id = main_image.id
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png_buffer = convert_to_png(pixel_array, is_dicom, ds)
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png_oss_key = f"hidoc2/images/{uuid.uuid4()}.png"
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png_size_kb = len(png_buffer.getvalue()) / 1024.0
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upload_to_oss(png_buffer, png_oss_key)
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vis_image = Image(
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name=f"{name}_preview", format='picture', type=img_type, dim='2D',
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creator_id=creator_id, oss_key=png_oss_key, size=png_size_kb,
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parent_image_id=parent_id
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)
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db.session.add(vis_image)
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db.session.commit()
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return jsonify({'code': 201, 'message': '影像处理成功'}), 201
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except Exception as e:
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db.session.rollback()
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import traceback
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traceback.print_exc()
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return jsonify({'code': 500, 'message': f'处理影像时发生内部错误: {str(e)}'}), 500
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finally:
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file_stream.close()
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# 确保在使用完毕后删除临时文件
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if tmp_path and os.path.exists(tmp_path):
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os.remove(tmp_path)
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@image_bp.route('/api/image/<int:image_id>', methods=['GET'])
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@utils.jwtauth.jwt_required
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def get_image_preview(image_id):
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"""
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获取单个影像的预览信息。
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- 对于2D影像，返回源文件URL和单个预览图URL。
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- 对于3D影像，根据direction参数返回对应方向的所有切片URL。
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"""
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image = Image.query.get(image_id)
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if not image:
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return jsonify({'code': 404, 'message': '影像不存在'}), 404
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base_url = custom_endpoint
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response_data = {'image_info': image.to_dict()}
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# --- 3D影像处理 ---
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if image.dim == '3D':
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direction = request.args.get('direction', 'z')
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if direction not in ['x', 'y', 'z']:
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return jsonify({'code': 400, 'message': '无效的direction参数，应为 "x"、"y" 或 "z"'}), 400
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source_url = f"{base_url}/{image.oss_key}"
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slices = Image.query.filter_by(
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parent_image_id=image.id,
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slice_direction=direction
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).order_by(Image.slice.asc()).all()
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slice_previews = [
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{'slice': s.slice, 'url': f"{base_url}/{s.oss_key}", 'id': s.id} for s in slices
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]
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# 查询哪些切片包含标注信息 (Bbox)
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annotated_slices = []
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if slices:
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slice_ids = [s.id for s in slices]
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# 查询所有相关的bbox记录，然后获取有bbox的image_id
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annotated_slice_ids_query = db.session.query(ImageBbox.image_id).filter(
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ImageBbox.image_id.in_(slice_ids)
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).distinct()
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annotated_slice_ids = {row.image_id for row in annotated_slice_ids_query}
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# 过滤出包含标注的切片索引
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annotated_slices = [s.slice for s in slices if s.id in annotated_slice_ids]
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response_data.update({
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'dim': '3D',
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'source_url': source_url,
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'direction': direction,
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'slice_previews': slice_previews,
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'annotated_slices': annotated_slices
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})
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# --- 2D影像处理 ---
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elif image.dim == '2D':
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source_url = f"{base_url}/{image.oss_key}"
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preview_url = source_url # 默认为自身
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# 如果是专业的2D影像格式，则查找其单独生成的预览图
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if image.format in ['dicom', 'nii']:
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preview_image = Image.query.filter_by(parent_image_id=image.id).first()
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if preview_image:
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preview_url = f"{base_url}/{preview_image.oss_key}"
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response_data.update({
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'dim': '2D',
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'source_url': source_url,
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'preview_url': preview_url,
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})
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else:
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return jsonify({'code': 500, 'message': '未知的影像维度'}), 500
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return jsonify({'code': 200, 'message': '获取成功', 'data': response_data})
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@image_bp.route('/api/image/<int:image_id>', methods=['PUT'])
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@utils.jwtauth.jwt_required
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def update_image(image_id):
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"""
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编辑影像备注 (只允许操作主影像)
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"""
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user_id = request.user_id
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data = request.get_json()
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if not data or 'note' not in data:
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return jsonify({'code': 400, 'message': '请求体中缺少必要参数: note'}), 400
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image = Image.query.get(image_id)
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if not image:
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return jsonify({'code': 404, 'message': '影像不存在'}), 404
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# 校验是否为主影像
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if image.parent_image_id is not None:
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return jsonify({'code': 403, 'message': '只允许编辑主影像的备注'}), 403
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# 校验创建者权限
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if image.creator_id != user_id:
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return jsonify({'code': 403, 'message': '您无权编辑此影像'}), 403
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try:
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image.note = data['note']
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db.session.commit()
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return jsonify({'code': 200, 'message': '影像备注更新成功', 'data': image.to_dict()})
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except Exception as e:
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db.session.rollback()
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return jsonify({'code': 500, 'message': f'数据库错误: {str(e)}'}), 500
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@image_bp.route('/api/image/<int:image_id>', methods=['DELETE'])
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@utils.jwtauth.jwt_required
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def delete_image(image_id):
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"""
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删除影像 (只允许操作主影像)
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删除主影像会一并删除其所有子切片和相关标注
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"""
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user_id = request.user_id
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image = Image.query.get(image_id)
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if not image:
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return jsonify({'code': 404, 'message': '影像不存在'}), 404
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# 校验是否为主影像
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if image.parent_image_id is not None:
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return jsonify({'code': 403, 'message': '只允许删除主影像'}), 403
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# 校验创建者权限
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if image.creator_id != user_id:
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return jsonify({'code': 403, 'message': '您无权删除此影像'}), 403
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try:
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# OSS上的文件不会被删除，只删除数据库记录
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db.session.delete(image)
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db.session.commit()
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return jsonify({'code': 200, 'message': '影像删除成功'})
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except Exception as e:
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db.session.rollback()
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return jsonify({'code': 500, 'message': f'数据库错误: {str(e)}'}), 500
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@image_bp.route('/api/image/list', methods=['GET'])
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@utils.jwtauth.jwt_required
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def list_images():
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"""
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获取当前医生创建的所有影像列表 (仅父影像)
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"""
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creator_id = request.user_id
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# 只查询 parent_image_id 为 NULL 的顶层影像
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images = Image.query.filter_by(creator_id=creator_id, parent_image_id=None).order_by(Image.created_at.desc()).all()
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results = []
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base_url = "https://cdn.ember.ac.cn"
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for image in images:
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image_data = image.to_dict()
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source_url = f"{base_url}/{image.oss_key}"
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preview_url = source_url # 默认预览URL为源URL
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# 1. 对于2D picture类型，使用源URL作为预览 (默认行为)
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# 2. 对于2D dicom/nii, 查找其子预览影像
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if image.dim == '2D' and image.format in ['dicom', 'nii']:
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preview_image = Image.query.filter_by(parent_image_id=image.id).first()
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if preview_image:
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preview_url = f"{base_url}/{preview_image.oss_key}"
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# 3. 对于3D dicom/nii, 查找第一个切片作为预览
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elif image.dim == '3D':
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first_slice = Image.query.filter_by(parent_image_id=image.id).order_by(Image.id.asc()).first()
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if first_slice:
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preview_url = f"{base_url}/{first_slice.oss_key}"
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image_data['source_url'] = source_url
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image_data['preview_url'] = preview_url
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results.append(image_data)
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return jsonify({'code': 200, 'message': '查询成功', 'data': results})
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@image_bp.route('/api/image/annotate', methods=['POST'])
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@utils.jwtauth.jwt_required
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def add_annotation():
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"""
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为影像添加标注 (目前仅支持bbox)
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"""
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creator_id = request.user_id
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data = request.get_json()
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if not data:
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return jsonify({'code': 400, 'message': '请求体不能为空'}), 400
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image_id = data.get('image_id')
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anno_type = data.get('anno_type')
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if not all([image_id, anno_type]):
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return jsonify({'code': 400, 'message': '缺少必要参数: image_id, anno_type'}), 400
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image = Image.query.get(image_id)
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if not image:
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return jsonify({'code': 404, 'message': '影像不存在'}), 404
|
||
|
||
# 检查影像是否为可标注的2D图片
|
||
if image.format != 'picture':
|
||
return jsonify({'code': 400, 'message': '标注功能仅支持 picture 格式的影像或切片'}), 400
|
||
|
||
if anno_type == 'bbox':
|
||
required_fields = ['up_left_x', 'up_left_y', 'bottom_right_x', 'bottom_right_y']
|
||
if not all(field in data for field in required_fields):
|
||
return jsonify({'code': 400, 'message': f'缺少bbox必要参数: {required_fields}'}), 400
|
||
|
||
try:
|
||
new_bbox = ImageBbox(
|
||
image_id=image_id,
|
||
creator_id=creator_id,
|
||
up_left_x=int(data['up_left_x']),
|
||
up_left_y=int(data['up_left_y']),
|
||
bottom_right_x=int(data['bottom_right_x']),
|
||
bottom_right_y=int(data['bottom_right_y']),
|
||
note=data.get('note')
|
||
)
|
||
db.session.add(new_bbox)
|
||
db.session.commit()
|
||
return jsonify({'code': 201, 'message': '标注创建成功', 'data': new_bbox.to_dict()}), 201
|
||
except (ValueError, TypeError):
|
||
return jsonify({'code': 400, 'message': '坐标参数必须是有效的整数'}), 400
|
||
except Exception as e:
|
||
db.session.rollback()
|
||
return jsonify({'code': 500, 'message': f'数据库错误: {str(e)}'}), 500
|
||
|
||
elif anno_type == 'mask':
|
||
return jsonify({'code': 501, 'message': 'Mask标注功能暂未实现'}), 501
|
||
else:
|
||
return jsonify({'code': 400, 'message': '无效的anno_type，应为 "bbox" 或 "mask"'}), 400
|
||
|
||
@image_bp.route('/api/image/annotate', methods=['GET'])
|
||
@utils.jwtauth.jwt_required
|
||
def get_annotations():
|
||
"""
|
||
获取影像的标注信息
|
||
"""
|
||
image_id = request.args.get('image_id')
|
||
anno_type = request.args.get('anno_type')
|
||
|
||
if not all([image_id, anno_type]):
|
||
return jsonify({'code': 400, 'message': '缺少必要参数: image_id, anno_type'}), 400
|
||
|
||
if not Image.query.get(image_id):
|
||
return jsonify({'code': 404, 'message': '影像不存在'}), 404
|
||
|
||
if anno_type == 'bbox':
|
||
bboxes = ImageBbox.query.filter_by(image_id=image_id).all()
|
||
data = []
|
||
for bbox in bboxes:
|
||
bbox_data = bbox.to_dict()
|
||
bbox_data['creator_name'] = bbox.creator.name if bbox.creator else '未知'
|
||
data.append(bbox_data)
|
||
return jsonify({'code': 200, 'message': '查询成功', 'data': data})
|
||
|
||
else:
|
||
return jsonify({'code': 400, 'message': '无效的anno_type'}), 400
|
||
|
||
@image_bp.route('/api/image/annotate', methods=['DELETE'])
|
||
@utils.jwtauth.jwt_required
|
||
def delete_annotation():
|
||
"""
|
||
删除指定的标注
|
||
"""
|
||
user_id = request.user_id
|
||
data = request.get_json()
|
||
anno_id = data.get('anno_id')
|
||
anno_type = data.get('anno_type')
|
||
|
||
if not all([anno_id, anno_type]):
|
||
return jsonify({'code': 400, 'message': '请求体中缺少必要参数: anno_id, anno_type'}), 400
|
||
|
||
if anno_type == 'bbox':
|
||
bbox = ImageBbox.query.get(anno_id)
|
||
if not bbox:
|
||
return jsonify({'code': 404, 'message': '标注不存在'}), 404
|
||
|
||
if bbox.creator_id != user_id:
|
||
print(bbox.creator_id, user_id)
|
||
return jsonify({'code': 403, 'message': '您无权删除此标注'}), 403
|
||
|
||
try:
|
||
db.session.delete(bbox)
|
||
db.session.commit()
|
||
return jsonify({'code': 200, 'message': '标注删除成功'})
|
||
except Exception as e:
|
||
db.session.rollback()
|
||
return jsonify({'code': 500, 'message': f'数据库错误: {str(e)}'}), 500
|
||
|
||
else:
|
||
return jsonify({'code': 400, 'message': '无效的anno_type'}), 400
|
||
|
||
@image_bp.route('/api/image/annotate', methods=['PUT'])
|
||
@utils.jwtauth.jwt_required
|
||
def update_annotation():
|
||
"""
|
||
更新指定的标注信息
|
||
"""
|
||
user_id = request.user_id
|
||
data = request.get_json()
|
||
anno_id = data.get('anno_id')
|
||
anno_type = data.get('anno_type')
|
||
|
||
if not all([anno_id, anno_type]):
|
||
return jsonify({'code': 400, 'message': '请求体中缺少必要参数: anno_id, anno_type'}), 400
|
||
|
||
if anno_type == 'bbox':
|
||
bbox = ImageBbox.query.get(anno_id)
|
||
if not bbox:
|
||
return jsonify({'code': 404, 'message': '标注不存在'}), 404
|
||
|
||
if bbox.creator_id != user_id:
|
||
return jsonify({'code': 403, 'message': '您无权编辑此标注'}), 403
|
||
|
||
# 更新字段
|
||
try:
|
||
for key, value in data.items():
|
||
if key in ['up_left_x', 'up_left_y', 'bottom_right_x', 'bottom_right_y']:
|
||
setattr(bbox, key, int(value))
|
||
elif key == 'note':
|
||
setattr(bbox, key, value)
|
||
|
||
db.session.commit()
|
||
return jsonify({'code': 200, 'message': '标注更新成功', 'data': bbox.to_dict()})
|
||
except (ValueError, TypeError):
|
||
return jsonify({'code': 400, 'message': '坐标参数必须是有效的整数'}), 400
|
||
except Exception as e:
|
||
db.session.rollback()
|
||
return jsonify({'code': 500, 'message': f'数据库错误: {str(e)}'}), 500
|
||
|
||
else:
|
||
return jsonify({'code': 400, 'message': '无效的anno_type'}), 400
|
||
|