from pathlib import Path
import tifffile as tiff
import numpy as np
from minerva.data.readers.base_file_iterator import BaseFileIterator
from minerva.utils.typing import PathLike
from typing import Optional, Union, List
[docs]
class TiffReader(BaseFileIterator):
def __init__(
self,
path: PathLike,
sort_method: Optional[List[str]] = None,
delimiter: Optional[str] = None,
key_index: Union[int, List[int]] = 0,
reverse: bool = False,
):
"""Load image files from a directory.
Parameters
----------
path : Union[Path, str]
The path to the directory containing the image files. Files will be
searched recursively.
sort_method : Optional[List[str]], optional
A list specifying how to sort each part of the filename. Each
element can be either "text" (lexicographical) or "numeric"
(numerically). By default, None, which will use "numeric" if
numeric parts are detected.
delimiter : Optional[str], optional
The delimiter to split filenames into components, by default None.
key_index : Union[int, List[int]], optional
The index (or list of indices) of the part(s) of the filename to
use for sorting. If a list is provided, files will be sorted
based on multiple parts in sequence. Thus, first by the part at
index 0, then by the part at index 1, and so on. By default 0.
reverse : bool, optional
Whether to sort in reverse order, by default False.
Raises
------
NotADirectoryError
If the path is not a directory.
"""
self.root_dir = Path(path)
if not self.root_dir.is_dir():
raise NotADirectoryError(f"{path} is not a directory.")
files = list(self.root_dir.rglob("*.tif*"))
super().__init__(files, sort_method, delimiter, key_index, reverse)
[docs]
def __getitem__(self, index: int) -> np.ndarray:
"""Retrieve the TIFF file at the specified index."""
return tiff.imread(self.files[index].as_posix())
[docs]
def __str__(self) -> str:
return f"TiffReader at '{self.root_dir}' ({len(self.files)} files)"