Refactor image conversion functions for improved clarity and error ha…

[mrariden]

better tests for transforms to catch things we missed previously.

3d image reading fixes and explicit guessing about what the order is in the gui. API is more robust.

[mrariden]

full test passing on ubuntu

[mrariden]

gui appears to be working too

Guessing will fail for some images:

cellpose/cellpose/io.py

Lines 236 to 266 in 9cb3c29

	def imread_3D(img_file):
	"""
	Read in a 3D image file and convert it to have a channel axis last. Attempts to do this for multi-channel and grayscale images.
	Args:
	img_file (str): The path to the image file.
	Returns:
	img_out (numpy.ndarray): The image data as a NumPy array.
	"""
	img = imread(img_file)
	dimension_lengths = list(img.shape)
	# guess at channel axis:
	channel_axis = np.argmin(img.shape)
	del dimension_lengths[channel_axis]
	# guess at z axis:
	z_axis = np.argmin(dimension_lengths)
	# grayscale images:
	if img.ndim == 3:
	channel_axis = None
	try:
	return transforms.convert_image(img, channel_axis=channel_axis, z_axis=z_axis, do_3D=True)
	except Exception as e:
	io_logger.critical("ERROR: could not read file, %s" % e)
	io_logger.critical("ERROR: Guessed z_axis: %s, channel_axis: %s" % (z_axis, channel_axis))
	return None