# coding: utf-8
"""
Application to convert a fluo-tomo dataset, after PyMCA (https://www.silx.org/doc/PyMca/dev/index.html) fit, into an hdf5/nexus file.
.. code-block:: bash
usage: nxtomomill fluo2nx [-h] [--info-file INFO_FILE] [--config CONFIG] [scan_path] [output_file]
convert fluo-tomo data (after PyMCA fit) to hdf5 - nexus compliant file format.
positional arguments:
scan_path folder containing the tiff files
output_file foutput .h5 file
dataset_basename File prefix to be used to deduce projection file names.
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 fluo files to nexus. Default configuration file can be created from `nxtomomill fluo-config` command
"""
import argparse
import logging
import os
from nxtomomill import utils
from nxtomomill import converter
from nxtomomill.io.config.fluoconfig import TomoFluoConfig
from tqdm import tqdm
logging.basicConfig(level=logging.INFO)
[docs]def main(argv):
""" """
parser = argparse.ArgumentParser(
description="Converts fluo-tomo data (after PyMca fit) "
"to hdf5 - nexus compliant file format."
)
parser.add_argument(
"scan_path", help="folder containing the projection tiff files", nargs=1
)
parser.add_argument(
"output_file",
help="File produced by the converter. '.nx' extension recommended.",
nargs=1,
)
parser.add_argument(
"dataset_basename",
help="file prefix to be used to deduce projections. ",
nargs=1,
)
parser.add_argument(
"--detectors",
nargs="*",
default=list(),
help="Define a list of detector names used for the exp (coma separated values). E.g. 'falcon, xmap'.",
)
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 (PyMCA-computed) fluo projections to nexus. "
"Default configuration file can be created from `nxtomomill fluo-config` command",
)
parser.add_argument(
"--mode",
default="newfile",
help="What to do if file exists:"
"- 'newfile': program will fail if file already exists."
"- 'overwrite': program will overwrite existing file or existing entries in file.",
)
options = parser.parse_args(argv[1:])
config = TomoFluoConfig()
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[0]
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[0]
if options.output_file is not None:
config.output_file = options.output_file[0]
if options.detectors is not None:
config.detectors = options.detectors
fileout_h5 = utils.get_file_name(
file_name=config.output_file,
extension=config.file_extension,
check=True,
)
if os.path.exists(fileout_h5):
if options.mode == "newfile":
raise FileExistsError(
f"The file {fileout_h5} already exists. Please remove it before running the program."
)
elif options.mode == "overwrite":
config.overwrite = True
else:
raise RuntimeError(
f"The value entered for --mode is not valid. Should be either 'newfile' or 'overwrite'. {options.mode} was given."
)
converter.from_fluo_to_nx(
configuration=config,
progress=tqdm("fluo2nx"),
)
