Copying a NXtomo

With Recent Software Versions

Usually, the NXtomo contains relative links, so you cannot simply copy and paste it.

Starting from Nxtomomill 1.0, you can access the nxtomomill nx-copy function. You can also use the nxtomo Python API of the NXtomo object. The copy_nxtomo_file function is used as follows:

from nxtomo.application.nxtomo import copy_nxtomo_file
copy_nxtomo_file(
    input_file="/path/to/my_nx.nx",
    output_file="/new/path/new_nx.nx",
    entries=None,  # or a tuple of existing NXtomo entries
)

With Older Software Versions

The simplest way to copy such a file is to use the nxtomomill.nexus module. You can load it with the default parameters (detector_data_as=”as_data_url”) and save it to a new location.

from nxtomo.application.nxtomo import NXtomo
from tomwer.core.scan.nxtomoscan import NXtomoScan

if in_data is not None:
    scan = in_data
    nx_tomo = NXtomo().load(scan.master_file, scan.entry)  # load data
    new_location = "/my/path/to/nexus.nx"
    new_entry = scan.entry  # or any data path in the HDF5 file you like
    nx_tomo.save(new_location, new_entry)
    print(f"Created new NXtomo to {new_entry}@{new_location}")
    # provide the new scan in output if some processing must be done on this new NXtomo
    out_data = NXtomoScan(scan=new_location, entry=new_entry)

Warning

Be careful! The saved file will still contain relative links to the original data. You can avoid this by setting the load function option detector_data_as to as_numpy_array. However, this will load all the data into memory.

Warning

Only the frames are shared; other datasets (rotation angle, energy, etc.) will be decoupled. So if you edit one dataset in the NXtomo, it won’t affect the other one.