Fairmat 2024: proposal on atom probe microscopy (APM)

[lukaspie]

Refactored version for NXapm including feedback from the atom probe microscopy/field-ion microscopy community.

This PR depends heavily on others that make changes to existing base classes or introduce base classes that are to be used outside of APM as well. Thus, it will be much smaller once the discussion on these PRs is done and this particular branch here has been rebased:
#1407
#1408
#1410
#1412
#1413
#1414
#1415
#1419
#1420 
#1486

There are however several new base classes that are currently only used within NXapm that are introduced here:

• NXapm_charge_state_analysis
• NXapm_ranging
• NXapm_reconstruction
• NXchemical_composition
• NXcs_filter_boolean_mask
• NXevent_data_apm
• NXinstrument_apm

Aim and design of the appdef is as follows:
NXapm envisaged to be used for documenting measurement and computer simulation of field evaporation experiment.
Instrument part split in two parts:

• ENTRY.measurement.instrument, for all those metadata that do not change when event data are collected
• ENTRY.measurement.events.EVENT_DATA_APM.instrument for all those metadata that do change during events
  This idea allows to not always repeat like with which instrument and hardware components the events were collected

In field evaporation experiment one measures:

• ToF, timing data on at least two delay-line detectors to get ion impact positions
• From this one computes, ions, their chemical and/or nuclides, ultimately resulting in a model of the evaporated specimen the so-called reconstruction. The reconstruction is a point cloud, each point can have an ion label.
• Ion labels are computed based on peak finding and peak identification in calibrated mass-to-charge-state ratio histograms, using methods borrowed from other ToF mass spectrometry and other spectroscopy techniques
• All these processing steps of data are modelled as inheriting from NXprocess

Contrary to the previous version of this proposal:

• We have reduced further the number of new base classes and tried to consolidate them even further.
• We have added references to proprietary concepts of AMETEK/Cameca where known and reliable
• We backup this example with a metastudy where we have collected the majority of datasets that are available online and use NXapm to map the content of these studies into NeXus/HDF5 files via www.github.com/FAIRmat-NFDI/pynxtools-apm

Points of discussion from my side @mkuehbach:

• NXchamber should be replaced by NXcomponent
• NXion should be replaced by NXatom
• NXevent_data_apm could be replaced by NXevent_data but for this last point to happen at least NXevent_data needs to be refactored as currently its scope is limited to neutron science, specifically " NXevent_data is a special group for storing data from neutron
  detectors in event mode."

Note that in FAIRmat we have a comprehensive set of appdefs built around NXapm which we currently do not propose for standardization but it is worthwhile to mention as these explore in many examples the usage of #1421