# coding: utf-8
"""
Application to convert a bliss-hdf5 tomography dataset to Nexus - NXtomo (hdf5) format
.. program-output:: nxtomomill h52nx --help
For a complete tutorial you can have a look at: :ref:`Tomoh52nx`
"""
import argparse
import logging
from tqdm import tqdm
from nxtomomill import utils
from nxtomomill.converter import from_h5_to_nx
from nxtomomill.io.config.confighandler import (
SETTABLE_PARAMETERS_UNITS,
TomoHDF5ConfigHandler,
)
logging.basicConfig(level=logging.INFO)
_logger = logging.getLogger(__name__)
def _getPossibleInputParams():
"""
:return: string with param1 (expected unit) ...
"""
res = []
for key, value in SETTABLE_PARAMETERS_UNITS.items():
res.append(f"{key} ({value})")
return ", ".join(res)
def _ask_for_selecting_detector(det_grps: list[str] | tuple[str]) -> str | None:
res = input(
"Several detector found. Only one detector is managed at the "
"time. Please enter the name of the detector you want to use "
f"or 'Cancel' to stop translation ({det_grps})"
)
if res == "Cancel":
return None
elif res in det_grps:
return res
else:
# warning: this is not a debug log !!!
print("detector name not recognized.")
return _ask_for_selecting_detector(det_grps)
[docs]def main(argv):
""" """
parser = argparse.ArgumentParser(
description="convert data acquired as "
"hdf5 from bliss to nexus "
"`NXtomo` classes. For `zseries` it will create one entry per `z`"
)
parser.add_argument(
"input_file", help="master file of the " "acquisition", default=None, nargs="?"
)
parser.add_argument(
"output_file", help="output .nx or .h5 file", default=None, nargs="?"
)
parser.add_argument(
"--file-extension",
"--file_extension",
default=None,
help="extension of the output file. Valid values are "
"" + "/".join([item.value for item in utils.FileExtension]),
)
parser.add_argument(
"--single-file",
help="merge all scan sequence to the same output file. "
"By default create one file per sequence and "
"group all sequence in the output file",
dest="single_file",
action="store_true",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--with-master-file",
help="Creates a master file linking all .nx files",
dest="no_master_file",
action="store_false",
default=None,
)
parser.add_argument(
"--overwrite",
help="Do not ask for user permission to overwrite output files",
action="store_true",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--debug",
help="Set logs to debug mode",
action="store_true",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--entries",
help="Specify (root) entries to be converted. By default it will try "
"to convert all existing entries.",
default=None,
)
parser.add_argument(
"--sub-entries-to-ignore",
"--ignore-sub-entries",
help="Specify (none-root) sub entries to ignore.",
default=None,
)
parser.add_argument(
"--raises-error",
help="Raise errors if some data are not met instead of providing some"
" default values",
action="store_true",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--field-of-view",
help="Force the output to be `Half` or `Full` acquisition. Otherwise "
"parse raw data to find this information.",
default=None,
)
parser.add_argument(
"--no-input",
"--no-input-for-missing-information",
help="The user won't be ask for any inputs",
dest="request_input",
action="store_false",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--data-copy",
"--copy-data",
help="Force data duplication of frames. This will permit to have an "
"'all-embed' file. Otherwise the detector/data dataset will haves "
"links to other files.",
action="store_true",
dest="default_data_copy",
default=None, # default is None and not False for the ConfigHandler so it can knows when set by the user or not
)
parser.add_argument(
"--sample_x_keys",
"--sample-x-keys",
default=None,
help="x translation key in bliss HDF5 file",
)
parser.add_argument(
"--sample_y_keys",
"--sample-y-keys",
default=None,
help="y translation key in bliss HDF5 file",
)
parser.add_argument(
"--translation_z_keys",
"--translation-z-keys",
default=None,
help="z translation key in bliss HDF5 file",
)
parser.add_argument(
"--sample-detector-distance-keys",
"--sample-detector-distance-paths",
"--distance-paths",
default=None,
help="sample detector distance paths",
)
parser.add_argument(
"--valid_camera_names",
"--valid-camera-names",
default=None,
help="Valid NXDetector dataset name to be considered. Otherwise will"
"try to deduce them from NX_class attibute (value should be"
"NXdetector) or from instrument group child structure.",
)
parser.add_argument(
"--rotation_angle_keys",
"--rotation-angle-keys",
"--rot-angle-keys",
"--rot_angle_keys",
default=None,
help="Valid dataset name for rotation angle",
)
parser.add_argument(
"--exposure_time_keys",
"--exposure-time-keys",
"--acq_expo_time_keys",
"--acq-expo-time-keys",
default=None,
help="Valid dataset name for acquisition exposure time",
)
parser.add_argument(
"--sample-x-pixel-size_keys",
"--sample_x_pixel_size_keys",
default=None,
help="X pixel size key to read",
)
parser.add_argument(
"--sample-y-pixel-size_keys",
"--sample_y_pixel_size_keys",
default=None,
help="Y pixel size key to read",
)
# scan titles
parser.add_argument(
"--init_titles",
"--init-titles",
default=None,
help="Titles corresponding to init scans",
)
parser.add_argument(
"--zseries-init-titles",
"--zseries_init_titles",
"--z_series_init_titles",
"--z-series_init_titles",
"--init_zserie_titles",
"--init-zserie-titles",
default=None,
help="Titles corresponding to zserie init scans",
)
parser.add_argument(
"--multitomo-init-titles",
"--multitomo_init_titles",
"--multi-tomo-init-titles",
"--multi_tomo_init_titles",
"--init-multi-tomo-titles",
"--init-pcotomo-titles",
default=None,
help="Titles corresponding to multi-tomo init scans",
)
parser.add_argument(
"--back-and-forth-init-titles",
"--back_and_forth_init_titles",
"--init-back-and-forth-titles",
"--init_back_and_forth_titles",
default=None,
help="Titles corresponding to back-and-forth init scans",
)
parser.add_argument(
"--dark-titles",
"--dark_titles",
default=None,
help="Titles corresponding to dark scans",
)
parser.add_argument(
"--flat-titles",
"--flat_titles",
"--ref_titles",
"--ref-titles",
default=None,
help="Titles corresponding to ref scans",
dest="flat_titles",
)
parser.add_argument(
"--projection_titles",
"--proj_titles",
"--proj-titles",
default=None,
help="Titles corresponding to projection scans",
)
parser.add_argument(
"--alignment-titles",
"--alignment_titles",
"--align_titles",
"--align-titles",
default=None,
help="Titles corresponding to alignment scans",
)
parser.add_argument(
"--set-params",
default=None,
nargs="*",
help="Allow manual definition of some parameters. "
"Valid parameters (and expected input unit) "
f"are: {_getPossibleInputParams()}. Should be added at the end of the command line because "
"will try to cover all text set after this option.",
)
# config file
parser.add_argument(
"--config-file",
"--config",
"--configuration",
"--configuration-file",
default=None,
help="file containing the full configuration to convert from h5 "
"bliss to nexus",
)
options = parser.parse_args(argv[1:])
if options.request_input:
callback_det_sel = _ask_for_selecting_detector
else:
callback_det_sel = None
try:
configuration_handler = TomoHDF5ConfigHandler(options)
except Exception:
_logger.error("Fail to initiate the configuration.", exc_info=True)
return
else:
for title in configuration_handler.configuration.init_titles:
assert title != ""
logging.getLogger("nxtomomill").setLevel(
configuration_handler.configuration.log_level
)
from_h5_to_nx(
configuration=configuration_handler.configuration,
progress=tqdm(desc="h52nx", delay=1, bar_format="{l_bar}{bar}"),
input_callback=None,
detector_sel_callback=callback_det_sel,
)
