"""
Functions to load and reshape examples for extraction development
The basic format for data will be pair data/masks pairs. Data will be
assumed to be a single slide, given that this reduction is expected
to happen beforehand.
The most basic functions were copied from Swain Lab's baby module,
specifically baby/io.py
"""
from importlib_resources import files
import json
import re
from itertools import groupby
from pathlib import Path
from typing import Callable
import numpy as np
from imageio import imread
from extraction.core.functions.distributors import reduce_z
[docs]def load_tiled_image(filename):
tImg = imread(filename)
info = json.loads(tImg.meta.get("Description", "{}"))
tw, th = info.get("tilesize", tImg.shape[0:2])
nt = info.get("ntiles", 1)
nr, nc = info.get("layout", (1, 1))
nc_final_row = np.mod(nt, nc)
img = np.zeros((nt, tw, th), dtype=tImg.dtype)
for i in range(nr):
i_nc = nc_final_row if i + 1 == nr and nc_final_row > 0 else nc
for j in range(i_nc):
ind = i * nc + j
img[ind, :, :] = tImg[i * tw : (i + 1) * tw, j * th : (j + 1) * th]
return img, info
[docs]def load_paired_images(filenames, typeA="Brightfield", typeB="segoutlines"):
re_imlbl = re.compile(r"^(.*)_(" + typeA + r"|" + typeB + r")\.png$")
# For groupby to work, the list needs to be sorted; also has the side
# effect of ensuring filenames is no longer a generator
filenames = sorted(filenames)
matches = [re_imlbl.match(f.name) for f in filenames]
valid = filter(lambda m: m[0], zip(matches, filenames))
grouped = {
k: {m.group(2): f for m, f in v}
for k, v in groupby(valid, key=lambda m: m[0].group(1))
}
valid = [
set(v.keys()).issuperset({typeA, typeB}) for v in grouped.values()
]
if not all(valid):
raise Exception
return {
lbl: {t: load_tiled_image(f) for t, f in g.items()}
for lbl, g in grouped.items()
}
[docs]def load(path=None):
"""
Loads annotated pngs into memory. Only designed for GFP and brightfield.
input
:path: Folder used to look for images
returns
list of dictionaries containing GFP, Brightfield and segoutlines channel
"""
if path is None:
path = (
files("aliby").parent.parent
/ "examples"
/ "extraction"
/ "pairs_data"
)
image_dir = Path(path)
channels = ["Brightfield", "GFP"]
imset = {"segoutlines": {}}
for ch in channels:
imset[ch] = {}
pos = load_paired_images(image_dir.glob("*.png"), typeA=ch)
for key, img in pos.items():
imset[ch][key] = img[ch][0]
imset["segoutlines"][key] = img["segoutlines"][0].astype(bool)
return [{ch: imset[ch][pos] for ch in imset.keys()} for pos in pos.keys()]
[docs]def load_1z(fun: Callable = np.maximum, path: str = None):
"""
---
fun: Function used to reduce the multiple stacks
path: Path to pass to load function
"""
dsets = load(path=path)
dsets_1z = []
for dset in dsets:
tmp = {}
for ch, img in dset.items():
if ch == "segoutlines":
tmp[ch] = img
else:
tmp[ch] = reduce_z(img, fun)
dsets_1z.append(tmp)
return dsets_1z