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