added option --no_norm in CLI (MouseLand#466)

cellpose/__main__.py

@@ -59,6 +59,7 @@ def main():
  algorithm_args.add_argument('--no_resample', action='store_true', help="disable dynamics on full image (makes algorithm faster for images with large diameters)")
  algorithm_args.add_argument('--net_avg', action='store_true', help='run 4 networks instead of 1 and average results')
  algorithm_args.add_argument('--no_interp', action='store_true', help='do not interpolate when running dynamics (was default)')
+ algorithm_args.add_argument('--no_norm', action='store_true', help='do not normalize images (normalize=False)')
  algorithm_args.add_argument('--do_3D', action='store_true', help='process images as 3D stacks of images (nplanes x nchan x Ly x Lx')
  algorithm_args.add_argument('--diameter', required=False, default=30., type=float, 
  help='cell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image')
@@ -237,6 +238,7 @@ def main():
  invert=args.invert,
  batch_size=args.batch_size,
  interp=(not args.no_interp),
+ normalize=(not args.no_norm),
  channel_axis=args.channel_axis,
  z_axis=args.z_axis,
  anisotropy=args.anisotropy,

docs/command.rst

@@ -139,6 +139,7 @@ You can run the help string and see all the options:
  for images with large diameters)
  --net_avg run 4 networks instead of 1 and average results
  --no_interp do not interpolate when running dynamics (was default)
+ --no_norm do not normalize images (normalize=False)
  --do_3D process images as 3D stacks of images (nplanes x nchan
  x Ly x Lx
  --diameter DIAMETER cell diameter, if 0 will use the diameter of the