"""
Output files parsing for the scanimage dataset
https://docs.scanimage.org/
"""
import re
from pathlib import Path
from typing import Any
import numpy as np
from ScanImageTiffReader import ScanImageTiffReader
from neuralib.util.unstable import unstable
__all__ = ['ScanImageWrapper']
[docs]
@unstable()
class ScanImageWrapper:
META_INFO: dict[str, Any] = {}
[docs]
def __init__(self, sequences: np.ndarray):
self.sequences = sequences
[docs]
@classmethod
def load(cls, file: Path | str) -> 'ScanImageWrapper':
sit = ScanImageTiffReader(file)
cls._parse_meta(sit.metadata())
return ScanImageWrapper(sit.data())
@classmethod
def _parse_meta(cls, meta: str):
"""parse metadata in the tif file"""
pattern = r'(\w+\.\w+)\s*=\s*(.*)'
matches = re.findall(pattern, meta)
for match in matches:
key = match[0]
value = match[1]
if value.isdigit():
value = int(value)
elif value.lower() == 'true':
value = True
elif value.lower() == 'false':
value = False
elif value.startswith("'") and value.endswith("'"):
value = value[1:-1]
elif value.startswith('[') and value.endswith(']'):
value = value[1:-1].split()
if all(item.isdigit() for item in value):
value = [int(item) for item in value]
elif value.startswith('{') and value.endswith('}'):
value = value[1:-1].split()
cls.META_INFO[key] = value