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"""
Application to convert a bliss-hdf5 tomography dataset to Nexus - NXtomo (hdf5) format
.. code-block:: console
usage: nxtomomill h52nx [-h] [--file-extension FILE_EXTENSION] [--single-file] [--overwrite] [--debug] [--entries ENTRIES] [--ignore-sub-entries IGNORE_SUB_ENTRIES] [--raises-error]
[--field-of-view FIELD_OF_VIEW] [--no-input] [--data-copy] [--x_trans_keys X_TRANS_KEYS] [--y_trans_keys Y_TRANS_KEYS] [--z_trans_keys Z_TRANS_KEYS]
[--sample-detector-distance-paths SAMPLE_DETECTOR_DISTANCE_PATHS] [--valid_camera_names VALID_CAMERA_NAMES] [--rot_angle_keys ROT_ANGLE_KEYS] [--acq_expo_time_keys ACQ_EXPO_TIME_KEYS]
[--x_pixel_size_key X_PIXEL_SIZE_KEY] [--y_pixel_size_key Y_PIXEL_SIZE_KEY] [--init_titles INIT_TITLES] [--init_zserie_titles INIT_ZSERIE_TITLES] [--dark_titles DARK_TITLES]
[--ref_titles REF_TITLES] [--proj_titles PROJ_TITLES] [--align_titles ALIGN_TITLES] [--set-params [SET_PARAMS [SET_PARAMS ...]]] [--format FORMAT] [--config CONFIG]
[input_file] [output_file]
convert data acquired as hdf5 from bliss to nexus `NXtomo` classes. For `zseries` it will create one entry per `z`
positional arguments:
input_file master file of the acquisition
output_file output .nx or .h5 file
optional arguments:
-h, --help show this help message and exit
--file-extension FILE_EXTENSION, --file_extension FILE_EXTENSION
extension of the output file. Valid values are .h5/.hdf5/.nx
--single-file merge all scan sequence to the same output file. By default create one file per sequence and group all sequence in the output file
--overwrite Do not ask for user permission to overwrite output files
--debug Set logs to debug mode
--entries ENTRIES Specify (root) entries to be converted. By default it will try to convert all existing entries.
--ignore-sub-entries IGNORE_SUB_ENTRIES
Specify (none-root) sub entries to ignore.
--raises-error Raise errors if some data are not met instead of providing some default values
--field-of-view FIELD_OF_VIEW
Force the output to be `Half` or `Full` acquisition. Otherwise parse raw data to find this information.
--no-input, --no-input-for-missing-information
The user won't be ask for any inputs
--data-copy, --copy-data
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.
--x_trans_keys X_TRANS_KEYS, --x-trans-keys X_TRANS_KEYS
x translation key in bliss HDF5 file
--y_trans_keys Y_TRANS_KEYS, --y-trans-keys Y_TRANS_KEYS
y translation key in bliss HDF5 file
--z_trans_keys Z_TRANS_KEYS, --z-trans-keys Z_TRANS_KEYS
z translation key in bliss HDF5 file
--sample-detector-distance-paths SAMPLE_DETECTOR_DISTANCE_PATHS, --distance SAMPLE_DETECTOR_DISTANCE_PATHS
sample detector distance
--valid_camera_names VALID_CAMERA_NAMES, --valid-camera-names VALID_CAMERA_NAMES
Valid NXDetector dataset name to be considered. Otherwise willtry to deduce them from NX_class attibute (value should beNXdetector) or from instrument group child structure.
--rot_angle_keys ROT_ANGLE_KEYS, --rot-angle-keys ROT_ANGLE_KEYS
Valid dataset name for rotation angle
--acq_expo_time_keys ACQ_EXPO_TIME_KEYS, --acq-expo-time-keys ACQ_EXPO_TIME_KEYS
Valid dataset name for acquisition exposure time
--x_pixel_size_key X_PIXEL_SIZE_KEY, --x-pixel-size-key X_PIXEL_SIZE_KEY
X pixel size key to read
--y_pixel_size_key Y_PIXEL_SIZE_KEY, --y-pixel-size-key Y_PIXEL_SIZE_KEY
Y pixel size key to read
--init_titles INIT_TITLES, --init-titles INIT_TITLES
Titles corresponding to init scans
--init_zserie_titles INIT_ZSERIE_TITLES, --init-zserie-titles INIT_ZSERIE_TITLES
Titles corresponding to zserie init scans
--dark_titles DARK_TITLES, --dark-titles DARK_TITLES
Titles corresponding to dark scans
--flat_titles --flat-titles --ref_titles REF_TITLES, --ref-titles FLAT_TITLES
Titles corresponding to ref scans
--proj_titles PROJ_TITLES, --proj-titles PROJ_TITLES
Titles corresponding to projection scans
--align_titles ALIGN_TITLES, --align-titles ALIGN_TITLES
Titles corresponding to alignment scans
--set-params [SET_PARAMS [SET_PARAMS ...]]
Allow manual definition of some parameters. Valid parameters (and expected input unit) are: energy (kev), x_pixel_size (m), y_pixel_size (m). Should be added at the end of the command
line because will try to cover all text set after this option.
--format FORMAT Input format. Standard by default. Should be 'xrd-ct' otherwise
--config CONFIG, --config-file CONFIG, --configuration CONFIG, --configuration-file CONFIG
file containing the full configuration to convert from h5 bliss to nexus
For a complete tutorial you can have a look at: :ref:`Tomoh52nx`
"""
__authors__ = ["C. Nemoz", "H. Payno", "A.Sole"]
__license__ = "MIT"
__date__ = "16/01/2020"
import argparse
import logging
from collections.abc import Iterable
from nxtomomill import utils
from nxtomomill.converter import from_h5_to_nx
from nxtomomill.io.config.confighandler import (
SETTABLE_PARAMETERS_UNITS,
TomoHDF5ConfigHandler,
)
from nxtomomill.utils import Format, Progress
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: Iterable):
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(utils.FileExtension.values()),
)
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(
"--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(
"--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="duplicate_data",
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(
"--x_trans_keys",
"--x-trans-keys",
default=None,
help="x translation key in bliss HDF5 file",
)
parser.add_argument(
"--y_trans_keys",
"--y-trans-keys",
default=None,
help="y translation key in bliss HDF5 file",
)
parser.add_argument(
"--z_trans_keys",
"--z-trans-keys",
default=None,
help="z translation key in bliss HDF5 file",
)
parser.add_argument(
"--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(
"--rot_angle_keys",
"--rot-angle-keys",
default=None,
help="Valid dataset name for rotation angle",
)
parser.add_argument(
"--acq_expo_time_keys",
"--acq-expo-time-keys",
default=None,
help="Valid dataset name for acquisition exposure time",
)
parser.add_argument(
"--x_pixel_size_key",
"--x-pixel-size-key",
default=None,
help="X pixel size key to read",
)
parser.add_argument(
"--y_pixel_size_key",
"--y-pixel-size-key",
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(
"--init_zserie_titles",
"--init-zserie-titles",
default=None,
help="Titles corresponding to zserie init scans",
)
parser.add_argument(
"--init_pcotomo_titles",
"--init-pcotomo-titles",
default=None,
help="Titles corresponding to pcotomo 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(
"--proj_titles",
"--proj-titles",
default=None,
help="Titles corresponding to projection scans",
)
parser.add_argument(
"--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.",
)
parser.add_argument(
"--format",
default=None,
help="Input format. Standard by default. Should be 'xrd-ct' otherwise",
)
# config file
parser.add_argument(
"--config",
"--config-file",
"--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, raise_error=True)
except Exception as e:
_logger.error(e)
return
else:
if options.format is not None:
try:
configuration_handler.configuration.format = Format.from_value(
options.format
)
except ValueError:
raise RuntimeError(f"Invalid format provided: {options.format}")
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=Progress(""),
input_callback=None,
detector_sel_callback=callback_det_sel,
)
