Source code for cyto_dl.image.io.skimage_reader
"""ADAPTED FROM https://github.com/MMV-Lab/mmv_im2im/"""
from typing import Dict, List, Optional, Sequence, Tuple, Union
import numpy as np
from monai.config import PathLike
from monai.data import ImageReader
from monai.data.image_reader import _stack_images
from monai.utils import ensure_tuple, require_pkg
from skimage.io import imread
[docs]@require_pkg(pkg_name="skimage")
class SkimageReader(ImageReader):
def __init__(
self,
channels: Optional[list] = None,
transforms: Optional[list] = None,
):
super().__init__()
self.channels = channels
self.transforms = transforms
[docs] def read(self, data: Union[Sequence[PathLike], PathLike]):
filenames: Sequence[PathLike] = ensure_tuple(data)
img_ = []
for name in filenames:
this_im = imread(f"{name}")
if self.channels:
this_im = this_im[self.channels]
if self.transforms:
for transform in self.transforms:
this_im = transform(this_im)
img_.append(this_im)
return img_ if len(filenames) > 1 else img_[0]
[docs] def get_data(self, img) -> Tuple[np.ndarray, Dict]:
img_array: List[np.ndarray] = []
for img_obj in ensure_tuple(img):
data = img_obj
img_array.append(data)
return _stack_images(img_array, {}), {}