diff --git a/src/segment/__main__.py b/src/segment/__main__.py index e76a9ad207dbb27b76251a41ebd8a817094e8c7c..aab8435ef51907de3886a176169b978538db30f9 100644 --- a/src/segment/__main__.py +++ b/src/segment/__main__.py @@ -3,7 +3,7 @@ import os import numpy as np import pandas as pd from segment import seg -from nd2_combine import tools +import nd2 from functools import partial import logging import click @@ -62,7 +62,7 @@ def check_paths(paths:list): def process(path:str='', out_dir_suffix:str='', len_range_px:tuple=(50,500), logger=logging, cpu: int = 1): logger.info(f'Processing {path}') logger.debug(f'len_range_px = {len_range_px}') - reader = tools.read_nd2(path) + reader = nd2.ND2File(path).asarray() dirr = create_results_dir(path, suffix=out_dir_suffix) pfun = partial(seg.crop_and_segment, dirr=dirr, lim_major_axis_length=len_range_px, print_dot=True)