From 0c96a6548734a93920b5f0cee4dfd3786ebf214c Mon Sep 17 00:00:00 2001 From: Giovanni Cardone Date: Fri, 7 May 2021 17:01:40 +0200 Subject: [PATCH] Fix issue #257 when model is cyto2 and diameter is zero --- cellpose/__main__.py | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/cellpose/__main__.py b/cellpose/__main__.py index c54df6c0..c19b4548 100644 --- a/cellpose/__main__.py +++ b/cellpose/__main__.py @@ -138,16 +138,6 @@ def main(): imf=imf, look_one_level_down=args.look_one_level_down) nimg = len(image_names) - if args.diameter==0: - if args.pretrained_model=='cyto' or args.pretrained_model=='nuclei': - diameter = None - logger.info('>>>> estimating diameter for each image') - else: - logger.info('>>>> using user-specified model, no auto-diameter estimation available') - diameter = model.diam_mean - else: - diameter = args.diameter - logger.info('>>>> using diameter %0.2f for all images'%diameter) cstr0 = ['GRAY', 'RED', 'GREEN', 'BLUE'] cstr1 = ['NONE', 'RED', 'GREEN', 'BLUE'] @@ -167,6 +157,17 @@ def main(): pretrained_model=cpmodel_path, torch=(not args.mxnet)) + if args.diameter==0: + if args.pretrained_model=='cyto' or args.pretrained_model=='nuclei' or args.pretrained_model=='cyto2': + diameter = None + logger.info('>>>> estimating diameter for each image') + else: + logger.info('>>>> using user-specified model, no auto-diameter estimation available') + diameter = model.diam_mean + else: + diameter = args.diameter + logger.info('>>>> using diameter %0.2f for all images'%diameter) + tqdm_out = utils.TqdmToLogger(logger,level=logging.INFO) for image_name in tqdm(image_names, file=tqdm_out): image = io.imread(image_name)