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allows --all channels to work in CLI #949

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Merged
carsen-stringer merged 1 commit into from
Sep 7, 2024
Merged

allows --all channels to work in CLI #949

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12 changes: 11 additions & 1 deletion cellpose/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,16 +155,26 @@ def main():
builtin_size = False
if args.all_channels:
channels = None
img = io.imread(image_names[0])
if img.ndim == 3:
nchan = min(img.shape)
elif img.ndim == 2:
nchan = 1
channels = None
else:
nchan = 2

pretrained_model = None if model_type is not None else pretrained_model
if restore_type is None:
model = models.CellposeModel(gpu=gpu, device=device,
pretrained_model=pretrained_model,
model_type=model_type,
nchan=nchan,
backbone=backbone)
else:
model = denoise.CellposeDenoiseModel(
gpu=gpu, device=device, pretrained_model=pretrained_model,
model_type=model_type, restore_type=restore_type,
model_type=model_type, restore_type=restore_type, nchan=nchan,
chan2_restore=args.chan2_restore)

# handle diameters
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