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"""
Application to convert a tomo dataset written in edf into and hdf5/nexus file.
.. code-block:: bash
usage: nxtomomill edf2nx [-h] [--dataset-basename DATASET_BASENAME] [--info-file INFO_FILE] [--config CONFIG] [scan_path] [output_file]
convert data acquired as edf to hdf5 - nexus compliant file format.
positional arguments:
scan_path folder containing the edf files
output_file foutput .h5 file
optional arguments:
-h, --help show this help message and exit
--dataset-basename DATASET_BASENAME, --file-prefix DATASET_BASENAME
file prefix to be used to deduce projections
--info-file INFO_FILE
.info file containing acquisition information (ScanRange, Energy, TOMO_N...)
--config CONFIG, --configuration-file CONFIG, --configuration CONFIG
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
For a complete tutorial you can have a look at :ref:`edf2nxtutorial`
"""
__authors__ = ["C. Nemoz", "H. Payno", "A.Sole"]
__license__ = "MIT"
__date__ = "16/01/2020"
import argparse
import logging
from nxtomomill import converter
from nxtomomill.io.utils import convert_str_to_tuple
from nxtomomill.io.config.edfconfig import TomoEDFConfig
from nxtomomill.utils import Progress
logging.basicConfig(level=logging.INFO)
[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",
)
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
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=Progress(""),
)
