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"))