nxtomomill nx-copy

since version xxx nxtomomill contains a function to easily copy an NXtomo from one place to another.

This is helpful mostly for NXtomo generated from bliss and that contains relative links to bliss / lima files. As it will update those.

from the CLI

nxtomomill nx-copy --help
usage: nxtomomill nx-copy [-h] [--entry ENTRIES] [--overwrite] [--debug] [--remove-vds] [nexus_file] [output_file]

copy one or several NXtomo to another location

positional arguments:
  nexus_file            file path to the nexus file containing NXtomo
  output_file           output nexus file

options:
  -h, --help            show this help message and exit
  --entry ENTRIES, --entries ENTRIES
                        NXtomo path(s) to be copied. If none provided then all NXtomo entries will be copied
  --overwrite           Do not ask for user permission to overwrite output files
  --debug               Set logs to debug mode
  --remove-vds          Remove any Virtual dataset to the resulting NXtomo (duplicate detector data - warning: all data will be load in memory before dumping it)

!nxtomomill copy-nx bambou_hercules_0001.nx /other/location/new_nxtomo.nx

from python API

Even if the application is a nxtomomill side the source code is part of nxtomo module.

from nxtomo.application.nxtomo import copy_nxtomo_file as copy_nxtomo

input_file = "/path/to/input/nexus_file.nx"
output_file = "/path/to/output/nexus_file.nx"

copy_nxtomo(
    input_file=input_file,
    output_file=output_file,
    # entries=("entry0000", "entry0001", )  # if we want to copy only a subset of the file
    # overwrite=True,
    # vds_resolution="update", # or "remove". Update will update relative link of the HDF5 Virtual Dataset, remove will replace the HDF5 Virtual Dataset by a default HDF5 dataet
)