You've already forked DataMate
37 lines
1.2 KiB
Python
37 lines
1.2 KiB
Python
# -- encoding: utf-8 --
|
|
|
|
"""
|
|
Description: 医疗图片解析载入
|
|
Create: 2025/02/08 11:00
|
|
"""
|
|
|
|
import time
|
|
from typing import Dict, Any
|
|
|
|
from loguru import logger
|
|
|
|
from datamate.core.base_op import Mapper
|
|
|
|
|
|
class SlideFormatter(Mapper):
|
|
|
|
def __init__(self, *args, **kwargs):
|
|
super(SlideFormatter, self).__init__(*args, **kwargs)
|
|
|
|
def execute(self, sample: Dict[str, Any]) -> Dict[str, Any]:
|
|
'''
|
|
Read medical image and corresponding mask file, each as Image type in COntent value. Return Content.
|
|
'''
|
|
start = time.time()
|
|
file_type = sample[self.filetype_key]
|
|
types_openslide = ['svs', 'tif', 'dcm', 'vms', 'vmu',
|
|
'ndpi', 'scn', 'mrxs', 'tiff', 'svslide',
|
|
'bif', 'czi', 'sdpc']
|
|
if file_type not in types_openslide:
|
|
raise TypeError(f"Format not supported: {file_type}. Supported formats are: {', '.join(types_openslide)}.")
|
|
|
|
file_name = sample[self.filename_key]
|
|
logger.info(f"fileName: {file_name}, method: SlideFormatter costs {(time.time() - start):6f} s")
|
|
# Not really loading the slide, instead, use path as lazy loading.
|
|
return sample
|