cvds.py

import logging
import click
import converters

logging.basicConfig(format="%(msecs)dms [%(levelname)s]: %(message)s", level=logging.DEBUG)


@click.command()
@click.argument("dataset-dir-or-file-path", type=click.Path(exists=True))
@click.argument("output-dir", type=click.Path(exists=True, dir_okay=True, file_okay=False))
def run(
    dataset_dir_or_file_path: str,
    output_dir: str,
) -> None:
    """Converts CT (or MRI) data into a human readable metadata.txt file and
    chunked, lz4-compressed,  binary chunked volumetric dataSet (CVDS) format.

    CVDS is a simple format that is meant to be consumed directly by Unity with
    very minimal (or none) transformations during runtime.  The format is meant
    to be consumed by Unity's Texture3D.  For instance, if a volume  brick
    (i.e., chunk)  is requested during  rendering,  the chunk is simply
    decompressed and applied directly to the Texture3D.

    Out-of-core conversion is supported  (i.e., dataset is too large to fit  in
    memory all at once). The converter has a minimal memory footprint and keeps
    at most a decoded image raw data (i.e., slice) in memory at once.

    Currently supported CT (or MRI) datasets include:

    IMAGE SEQUENCES (PNG, TIFF):
    a sequence of slice images  ordered  according to their names.  User is
    prompted for crucial and optional volumetric properties such as: width,
    height, color depth, etc.

    DICOM:
    a widely used international standard to transmit, store, retrieve,
    print, process, and display medical imaging information. Everything needed
    to correctly visualize the volumetric data is also provided within the
    same file.

    RAW:
    binary raw format. Users are prompted for crucial volumetric properties
    such as: width, height, color depth, etc.
    """
    uvds_converter = converters.Converter.factory(dataset_dir_or_file_path)
    uvds_converter.import_dataset(dataset_dir_or_file_path)
    uvds_converter.write_metadata(output_dir)
    uvds_converter.write_binary_chunks(output_dir)
    logging.info("done")


if __name__ == "__main__":
    run()