sensospot_parser/sensospot_data/__init__.py

""" Sensospot Data Parser

Parsing the numerical output from Sensovations Sensospot image analysis.
"""

__version__ = "0.4.0"

VERSION_TABLE_NAME = f"v{__version__}".replace(".", "_")


from pathlib import Path

import click

from .parser import (  # noqa: F401
    CACHE_FILE_NAME,
    parse_file,
    parse_folder,
    process_folder,
    parse_multiple_files,
)
from .parameters import ExposureInfo  # noqa: F401
from .normalisation import split_channels, normalize_channel  # noqa: F401


@click.command()
@click.argument(
    "source",
    type=click.Path(
        exists=True,
        file_okay=False,
        dir_okay=True,
        readable=True,
        writable=True,
    ),
)
@click.option(
    "-o",
    "--outfile",
    default="raw_data.h5",
    help="Output file path, relative to source dir",
)
def run(source, outfile):
    source_path = Path(source)
    # read the raw data of a folder
    raw_data = parse_folder(source_path)
    hdf5_path = source_path / outfile
    raw_data.to_hdf(hdf5_path, key="raw_data", format="table")