# coding: utf-8
"""
Application to convert a tomo dataset written in edf into and hdf5/nexus file.
.. program-output:: nxtomomill edf2nx --help
For a complete tutorial you can have a look at :ref:`edf2nxtutorial`
"""
import argparse
import logging
from nxtomomill import converter
from nxtomomill.models.utils import convert_str_to_tuple
from nxtomomill.io.config.edfconfig import TomoEDFConfig
from nxtomomill.settings import Tomo
from tqdm import tqdm
logging.basicConfig(level=logging.INFO)
fabio_logger = logging.getLogger("fabio.edfimage")
fabio_logger.setLevel(logging.ERROR)
[docs]def main(argv):
""" """
parser = argparse.ArgumentParser(
description="convert data acquired as "
"edf to hdf5 - nexus "
"compliant file format."
)
parser.add_argument("scan_path", help="folder containing the edf files", nargs="?")
parser.add_argument("output_file", help="foutput .h5 file", nargs="?")
parser.add_argument(
"--dataset-basename",
"--file-prefix",
default=None,
help="file prefix to be used to deduce projections",
)
parser.add_argument(
"--info-file",
default=None,
help=".info file containing acquisition information (ScanRange, Energy, TOMO_N...)",
)
parser.add_argument(
"--config",
"--configuration-file",
"--configuration",
default=None,
help="file containing the full configuration to convert from SPEC-EDF to bliss to nexus. "
"Default configuration file can be created from `nxtomomill edf-config` command",
)
parser.add_argument(
"--delete-edf",
"--delete-edf-source",
"--delete-edf-source-files",
default=False,
action="store_true",
help="if you are duplicating data (default behavior) you can ask to delete used edf files to free space",
)
parser.add_argument(
"--output-checks",
default=tuple(),
help="Define list of check to be run once the conversion is finished (raise an error if check fails). This is done before removing edf if asked. So if check fails source edf files won't be removed",
)
parser.add_argument(
"--use-existing-angles",
"--no-angle-recalculcation",
default=None,
action="store_true",
help=f"By default the angle will be recomputed to have equally spaced angles from the min and the max angles. If this option is set then angles defined in edf headers ({','.join(Tomo.EDF.ROT_ANGLE)}) will be used.",
)
options = parser.parse_args(argv[1:])
config = TomoEDFConfig()
if options.config is not None:
config = config.from_cfg_file(options.config)
check_input = {
"dataset basename": (options.dataset_basename, config.dataset_basename),
"scan path": (options.scan_path, config.input_folder),
"output file": (options.output_file, config.output_file),
"info file": (options.info_file, config.dataset_info_file),
}
for input_name, (opt_value, config_value) in check_input.items():
if (
opt_value is not None
and config_value is not None
and opt_value != config_value
):
raise ValueError(
f"two values for {input_name} are provided from arguments and configuration file ({opt_value, config_value})"
)
if options.dataset_basename is not None:
config.dataset_basename = options.dataset_basename
if options.info_file is not None:
config.dataset_info_file = options.info_file
if options.scan_path is not None:
config.input_folder = options.scan_path
if options.output_file is not None:
config.output_file = options.output_file
config.delete_edf_source_files = options.delete_edf
if options.use_existing_angles is not None:
config.force_angle_calculation = not options.use_existing_angles
config.output_checks = convert_str_to_tuple(options.output_checks)
assert isinstance(
config.output_checks, tuple
), f"config.output_checks is expected to be a tuple. Gets {type(config.output_checks)}"
converter.from_edf_to_nx(
configuration=config,
progress=tqdm(desc="edf2nx", bar_format="{l_bar}{bar}{postfix}"),
)
