From 4c26e8852f9dfb1a412f8e883a01196b54b953c0 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Wed, 25 May 2022 19:25:18 +0200
Subject: [PATCH] replace read function
---
src/segment/__main__.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/segment/__main__.py b/src/segment/__main__.py
index e76a9ad..aab8435 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)
--
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