output_format=output_format,
output_vars=output_vars,
output_dir=output_dir,
file_vars=args.file_vars,
fov_count=args.fov_count,
cache_read_order=args.cache_read_order,
channel_slope=args.channel_slope,
channel_intercept=args.channel_intercept,
fov_offset=args.fov_offset,
round_offset=args.round_offset,
channel_offset=args.channel_offset,
aux_file_formats=args.aux_file_formats,
aux_file_vars=aux_file_vars,
aux_names=args.aux_names,
aux_cache_read_order=aux_cache_read_order,
aux_channel_count=args.aux_channel_count,
aux_channel_slope=args.aux_channel_slope,
aux_channel_intercept=args.aux_channel_intercept,
)
if args.codebook_csv:
codebook = parse_codebook(args.codebook_csv)
elif args.codebook_json:
codebook = Codebook.open_json(args.codebook_json)
else:
print("Can't convert notebook, none provided.")
conv_codebook = convert_codebook(codebook, cycles_conv, channels_conv)
codebook.to_json(output_dir + "pround_codebook.json")
conv_codebook.to_json(output_dir + "codebook.json")
p.add_argument("--roi", type=Path)
p.add_argument("--x-size", type=int, nargs="?")
p.add_argument("--y-size", type=int, nargs="?")
p.add_argument("--z-size", type=int, nargs="?")
p.add_argument("--run-ripley", dest="run_ripley", action="store_true")
p.add_argument("--save-pdf", dest="save_pdf", action="store_true")
args = p.parse_args()
print(args)
codebook = False
roi = False
if args.codebook_exp:
codebook = Codebook.open_json(
str(args.codebook_exp) + "/codebook.json")
if (
args.roi
): # NOTE Going to assume 1 FOV for now. Largely used for debugging, not pipeline runs.
exp = starfish.core.experiment.experiment.Experiment.from_json(
str(args.codebook_exp) + "/experiment.json")
img = exp["fov_000"].get_image("primary")
roi = BinaryMaskCollection.from_fiji_roi_set(
path_to_roi_set_zip=args.roi, original_image=img)
elif args.codebook_pkl:
codebook = pickle.load(open(args.codebook_pkl, "rb"))
transcripts = False
if args.transcript_pkl:
transcripts = pickle.load(open(args.transcript_pkl, "rb"))
