Source code for bioimageloader.collections._bbbc026

from functools import cached_property
from pathlib import Path
from typing import List, Optional

import albumentations
import cv2
import numpy as np
from skimage.util import img_as_float32

from ..base import Dataset
from ..utils import imread_asarray


[docs]class BBBC026(Dataset): """Human Hepatocyte and Murine Fibroblast cells – Co-culture experiment This 384-well plate has images of co-cultured hepatocytes and fibroblasts. Every other well is populated (A01, A03, ..., C01, C03, ...) such that 96 wells comprise the data. Each well has 9 sites and thus 9 images associated, totaling 864 images. For each well there is one field and a single image nuclear image (Hoecsht). Images are in 8-bit PNG format. Parameters ---------- root_dir : str Path to root directory transforms : albumentations.Compose, optional An instance of Compose (albumentations pkg) that defines augmentation in sequence. num_samples : int, optional Useful when ``transforms`` is set. Define the total length of the dataset. If it is set, it overwrites ``__len__``. Notes ----- - Only centers are annotated for 5 imgages (not implemented) References ---------- .. [1] https://bbbc.broadinstitute.org/BBBC026 See Also -------- Dataset : Base class DatasetInterface : Interface """ # Dataset's acronym acronym = 'BBBC026' def __init__( self, root_dir: str, *, transforms: Optional[albumentations.Compose] = None, num_samples: Optional[int] = None, **kwargs ): self._root_dir = root_dir self._transforms = transforms self._num_samples = num_samples
[docs] def get_image(self, p: Path) -> np.ndarray: img = imread_asarray(p) img = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB) return img_as_float32(img)
@cached_property def file_list(self) -> List[Path]: root_dir = self.root_dir parent = 'BBBC026_v1_images' file_list = sorted(root_dir.glob(f'{parent}/*.png')) return file_list