# coding: utf-8
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"""
Application to convert from dx file (HDF5) to NXTomo (HDF5) file
.. code-block:: bash
usage: nxtomomill dxfile2nx [-h] [--input_entry INPUT_ENTRY] [--output_entry OUTPUT_ENTRY] [--file_extension FILE_EXTENSION] [--scan-range SCAN_RANGE] [--pixel-size PIXEL_SIZE] [--fov FIELD_OF_VIEW]
[--distance DISTANCE] [--energy ENERGY] [--overwrite] [--data-copy]
input_file output_file
convert acquisition contained in provided dx file to NXTomo entry
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
--input_entry INPUT_ENTRY
h5py group path to be converted
--output_entry OUTPUT_ENTRY
h5py group path to store the NXTomo
--file_extension FILE_EXTENSION
extension of the output file. Valid values are .h5/.hdf5/.nx
--scan-range SCAN_RANGE
scan range of the projections. Dark and flat will always be considered with rotation angle == scan_range[0]
--pixel-size PIXEL_SIZE
pixel size in meter as (x pixel size, y pixel size)
--fov FIELD_OF_VIEW, --field-of-view FIELD_OF_VIEW
field of view. Can be Full or Half
--distance DISTANCE, --detector-sample-distance DISTANCE
sample to detector distance (in meter)
--energy ENERGY, --incident-beam-energy ENERGY
incident beam energy in keV
--overwrite Do not ask for user permission to overwrite output files
--data-copy Force data duplication of frames. This will permit to have an 'all-embed' file. Otherwise we will have link between the dxfile and the NXTomo.
For a complete tutorial you can have a look at :ref:`dxfile2nxtutorial`
"""
__authors__ = [
"H. Payno",
]
__license__ = "MIT"
__date__ = "18/05/2021"
import argparse
import logging
from pyunitsystem import metricsystem
from nxtomomill import utils
from nxtomomill.converter.dxfile.dxfileconverter import from_dx_to_nx
_logger = logging.getLogger(__name__)
[docs]def convert_2elmts__tuple_to_float(input_str) -> tuple:
if input_str == (None, None):
return input_str
try:
tmp_str = input_str.replace(" ", "")
tmp_str = tmp_str.replace(";", ",")
if tmp_str.startswith("("):
tmp_str = tmp_str[1:]
if tmp_str.startswith(")"):
tmp_str = tmp_str[:-1]
v1, v2 = tmp_str.split(",")
except Exception as e:
raise ValueError(
f"Unable to convert {input_str} to a tuple of two float. Reason is {e}"
)
else:
return float(v1), float(v2)
def _get_pixel_size(input_str) -> tuple:
try:
values = convert_2elmts__tuple_to_float(input_str)
except ValueError:
try:
value = float(input_str)
except Exception:
raise ValueError(
f"Unable to convert {input_str} to pixel size."
f"Should be provided as a tuple (x_pixel_size, y_pixel_size) "
f"or as a single value pixel_size"
)
else:
return value, value
else:
return values
[docs]def main(argv):
""" """
parser = argparse.ArgumentParser(
description="convert acquisition contained in provided dx file to "
"NXTomo entry"
)
parser.add_argument("input_file", help="master file of the " "acquisition")
parser.add_argument("output_file", help="output .nx or .h5 file", default=None)
# usually it looks like the dxfile contains only one acquisition at the
# root level
parser.add_argument(
"--input_entry",
help="h5py group path to be converted",
default="/",
)
parser.add_argument(
"--output_entry",
help="h5py group path to store the NXTomo",
default="entry0000",
)
parser.add_argument(
"--file_extension",
default=".nx",
help="extension of the output file. Valid values are "
"" + "/".join(utils.FileExtension.values()),
)
# as scan range or rotation angle are not stored in dxfile we
# provide the default value which is the "standard" case
parser.add_argument(
"--scan-range",
default="0,180",
help="scan range of the projections. Dark and flat will always be "
"considered with rotation angle == scan_range[0]",
)
# as pixel sizes are not stored in the dxfile and requested for paganin
# we provide some default value
parser.add_argument(
"--pixel-size",
default=(None, None),
help="pixel size in meter as (x pixel size, y pixel size) or as a single value",
)
parser.add_argument(
"--fov",
"--field-of-view",
default=None,
help="field of view. Can be Full or Half",
dest="field_of_view",
)
# as distance is not stored in the dxfile and requested for paganin
# we provide some default value
parser.add_argument(
"--distance",
"--detector-sample-distance",
default=None,
help="sample to detector distance (in meter)",
dest="distance",
)
parser.add_argument(
"--energy",
"--incident-beam-energy",
default=None,
help="incident beam energy in keV",
dest="energy",
)
parser.add_argument(
"--overwrite",
help="Do not ask for user permission to overwrite output files",
action="store_true",
default=False,
)
parser.add_argument(
"--data-copy",
help="Force data duplication of frames. This will permit to have an "
"'all-embed' file. Otherwise we will have link between the dxfile "
"and the NXTomo.",
action="store_true",
dest="duplicate_data",
default=False,
)
options = parser.parse_args(argv[1:])
distance = options.distance
if distance is not None:
distance = float(options.distance)
energy = options.energy
if energy is not None:
energy = float(options.energy) * metricsystem.EnergySI.KILOELECTRONVOLT.value
if options.duplicate_data is False:
_logger.warning(
"Generated file will contain relative links to the "
"(dxfile) source file. You should insure the "
"relative position of the input file and the output "
"stay constant to protect links. (use --copy-data) "
"option to avoid links"
)
from_dx_to_nx(
input_file=options.input_file,
output_file=options.output_file,
file_extension=options.file_extension,
input_entry=options.input_entry,
output_entry=options.output_entry,
scan_range=convert_2elmts__tuple_to_float(options.scan_range),
pixel_size=_get_pixel_size(options.pixel_size),
field_of_view=options.field_of_view,
distance=distance,
overwrite=options.overwrite,
duplicate_data=options.duplicate_data,
energy=energy,
)
