Add sub-reader for PHI Versaprobe data

lukaspie commented 5 months ago

Phi Parser:

Parser for PHI Versaprobe .spe (regular spectra) and .pro (sputter depth profiling)
New config file to account for these data sets
Correct parsing of binary encoded data
Mapping of optional instrument devices (sputter source, neutral ion gun, C60 gun, defect positioner) to the config file

Other changes:

The main reader supports energy reading as well as more options for writing raw detector data (i.e., write scan data if there is no data for the individual channels

Error fixes:

Links that are broken (see #2) are temporarily removed from config files until that bug is fixed.
The mapping of keys and the renaming of ENTRY[entry] to the actual entries (e.g. `ENTRY[MeasurementGroup_Survey]) has been streamlined and harmonized across all subreaders

Still missing:

[ ] Example data for this reader (pending approval by data provider)
[ ] Test data for this reader (pending approval by data provider)

This PR depends on FAIRmat-NFDI/pynxtools#220 and should be merged afterwards/together. EDIT: FAIRmat-NFDI/pynxtools#220 merged into pynxools-xps@main.

Resolves FAIRmat-NFDI/pynxtools-xps#1.

github-actions[bot] commented 4 months ago

Pull Request Test Coverage Report for Build 8465335526

Details

704 of 731 (96.31%) changed or added relevant lines in 11 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+10.0%) to 58.792%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pynxtools_xps/sle/sle_specs.py	0	1	0.0%
pynxtools_xps/txt/txt_vamas_export.py	0	1	0.0%
pynxtools_xps/txt/txt_scienta.py	0	2	0.0%
pynxtools_xps/vms/vamas.py	3	13	23.08%
pynxtools_xps/phi/spe_pro_phi.py	328	341	96.19%
<!--	Total:	704	731	96.31%	-->

Totals
Change from base Build 8427529939:	10.0%
Covered Lines:	1956
Relevant Lines:	3327

💛 - Coveralls

lukaspie commented 3 months ago

An additional consideration we already discussed in discord is adding an additional axis for the depth profile so you can view it in one NXdata. Depending on the effort this can either be handled here or in a separate PR.

I realized that this is a bit of an involved effort because the XPS reader so far only works for one-dimensional datasets with an energy axis. In principle, I think I should redesign it such that not every scan gets an axis in NXdata, but rather the scan numbers, measurement cycle numbers, sputter cycle numbers, are axes to one NXdata. However, this requires quite a bit of effort to disentangle in the main reader, so I suggest that I will do it in a separate PR.

Thus, I would just simply wait for the approval that the example/test data can be included here and then it would merge this PR.

domna commented 3 months ago

Thus, I would just simply wait for the approval that the example/test data can be included here and then it would merge this PR.

Sounds reasonable. I'll approve this already. Feel free to add the test data and merge when ready

FAIRmat-NFDI / pynxtools-xps