{Axes.ROUND.value: 1, Axes.CH.value: 3, Features.CODE_VALUE: 1},
{Axes.ROUND.value: 2, Axes.CH.value: 1, Features.CODE_VALUE: 1},
{Axes.ROUND.value: 3, Axes.CH.value: 2, Features.CODE_VALUE: 1}
],
Features.TARGET: "ACTB_human"
},
{
Features.CODEWORD: [
{Axes.ROUND.value: 0, Axes.CH.value: 3, Features.CODE_VALUE: 1},
{Axes.ROUND.value: 1, Axes.CH.value: 1, Features.CODE_VALUE: 1},
{Axes.ROUND.value: 2, Axes.CH.value: 1, Features.CODE_VALUE: 1},
{Axes.ROUND.value: 3, Axes.CH.value: 2, Features.CODE_VALUE: 1}
],
Features.TARGET: "ACTB_mouse"
},
]
codebook = Codebook.from_code_array(codebook_array)
codebook_json_filename = "codebook.json"
codebook.to_json(os.path.join(output_dir, codebook_json_filename))
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("input_dir", type=FsExistsType())
parser.add_argument("output_dir", type=FsExistsType())
parser.add_argument("--d", help="Download data", type=bool)
args = parser.parse_args()
format_data(args.input_dir, args.output_dir, args.d)
}
write_experiment_json(output_dir,
num_fovs,
tile_format=ImageFormat.TIFF,
primary_image_dimensions=primary_image_dimensions,
aux_name_to_dimensions=aux_name_to_dimensions,
primary_tile_fetcher=MERFISHTileFetcher(
input_dir, is_dapi=False),
aux_tile_fetcher={
'nuclei':
MERFISHTileFetcher(input_dir, is_dapi=True),
},
postprocess_func=add_scale_factors,
default_shape=SHAPE)
if __name__ == "__main__":
s3_bucket = "s3://czi.starfish.data.public/browse/raw/20180820/merfish_u2os/"
input_help_msg = "Path to raw data. Raw data can be downloaded from: {}".format(
s3_bucket)
output_help_msg = "Path to output experment.json and all formatted images it references"
parser = argparse.ArgumentParser()
parser.add_argument("input_dir", type=FsExistsType(), help=input_help_msg)
parser.add_argument("output_dir",
type=FsExistsType(),
help=output_help_msg)
args = parser.parse_args()
format_data(args.input_dir, args.output_dir)
