Save dark and flat fields in nexus file produced with NEXUSDataWriter

[lauramurgatroyd]

The NXTomo format has the flat and dark fields included in the data, with a key to specify the indices where they are located.

We would like to read in an NXTomo file and write out a nexus file with the NEXUSDataWriter, without losing the information about the dark and flat fields.

The NEXUSDataWriter currently writes the dataset to:

CIL/Wrappers/Python/cil/io/NEXUSDataWriter.py

Line 80 in 39b6f7a

ds_data = f.create_dataset('entry1/tomo_entry/data/data',

We could either:

• Write the dark and flat fields there along with the data, and also save the key. Other nexus files previously written out with the NEXUSDataWriter won't have a key, but in the NEXUSDataReader we could assume no dark and flat fields are present in the data in the case that a key doesn't exist.

or

• Save the dark and flat fields as separate entries in the nexus file, along with a list of angles where they were taken.

[lauramurgatroyd]

Closing this, because instead of writing dark and flat fields to the CIL Nexus file, we are going to keep the data as NXTomo format until we get to a processing step (e.g. Centre of Rotation Correction) where we need to specifically write out CIL info (such as the geometry). The other steps just modify the data which will be saved in an NXTomo anyway.
Therefore we will just need the NXTomo reader and writers (see #939 and #949)