replace read function

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)