Source code for livecellx.core.io_sc

import tqdm
import numpy as np
from multiprocessing import Pool
from skimage.measure import regionprops, find_contours
from livecellx.livecell_logger import main_info, main_warning
from livecellx.segment.ou_simulator import find_contours_opencv
from livecellx.core.single_cell import SingleCellStatic
from livecellx.core.sc_key_manager import SingleCellMetaKeyManager

# TODO: fix the function below
[docs]def process_scs_from_label_mask(label_mask_dataset, dic_dataset, time, bg_val=0, min_contour_len=10): """process single cells from one label mask. Store labels of single cells in their meta data. Parameters ---------- label_mask_dataset : _type_ _description_ dic_dataset : _type_ _description_ time : _type_ _description_ bg_val : int, optional _description_, by default 0 Returns ------- _type_ _description_ """ label_mask = label_mask_dataset.get_img_by_time(time) labels = set(np.unique(label_mask)) if bg_val in labels: labels.remove(bg_val) contours = [] labels = list(labels) contour_labels = [] for label in labels: bin_mask = (label_mask == label).astype(np.uint8) label_contours = find_contours_opencv(bin_mask) # assert len(label_contours) == 1, "at time {}, label {} has {} contours".format(time, label, len(label_contours)) # contours.append(label_contours[0]) # warn the users filtered_label_contours = [] for contour in label_contours: if len(contour) >= min_contour_len: filtered_label_contours.append(contour) if len(filtered_label_contours) < len(label_contours): main_info( "at time {}, label {} has {} contours found by opencv, {} of them are filtered by contour length threshold: {}".format( time, label, len(label_contours), len(label_contours) - len(filtered_label_contours), min_contour_len, ) ) label_contours = filtered_label_contours if len(label_contours) > 1: main_warning("at time {}, label {} has {} contours".format(time, label, len(label_contours))) main_warning("lengths of each contour: {}".format([len(c) for c in label_contours])) contours.extend(label_contours) contour_labels.extend([label] * len(label_contours)) # contours = find_contours(seg_mask) # skimage: find_contours _scs = [] for i, contour in enumerate(contours): label = int( contour_labels[i] ) # int important here to get rid of numpy.int64 or numpy.int8, etc, to avoid json dump error sc = SingleCellStatic( timeframe=time, img_dataset=dic_dataset, mask_dataset=label_mask_dataset, contour=contour, ) sc.meta[SingleCellMetaKeyManager.MASK_LABEL] = label _scs.append(sc) return _scs
[docs]def process_mask_wrapper(args): return process_scs_from_label_mask(*args)
# TODO: use parallelize function in the future
[docs]def prep_scs_from_mask_dataset(mask_dataset, img_dataset, cores=None): scs = [] inputs = [(mask_dataset, img_dataset, time) for time in mask_dataset.time2url.keys()] pool = Pool(processes=cores) for _scs in tqdm.tqdm(pool.imap_unordered(process_mask_wrapper, inputs), total=len(inputs)): scs.extend(_scs) pool.close() pool.join() return scs