[REMI] Add and enhance plots, more documentation, clean-up and some deprecation

Description

A collection of minor changes by themselves, aggregated to an MR for simplicty. I tried to be diligent about each commit though and will describe them individually:

• 1994e74d Requested by operators to quickly visualize how the detector is wired (i.e. digitizer channel to detector signal) and discriminated (discrimination settings are set by digitizer channel but conceptualized by detector signal). [1]

• 42371701 Ongoing effort to remove EXtra-remi and proper use of notebook parameters, here code to open DataCollection, calculate time calibration and hide some already deprecated keys in the user YAML file.

• 59cc7816 A more detailed version of the pulse height distribution already added in !822 (merged) to visualize it as a function of TOF. This can help to understand a different detector response for different particles (e.g. a highly charged and/or fast ion typically causes larger analog signals, also visible in example) [2]

• 88ea35b8 More captions and explanatory text all over the place on how to read figures or what's going on.

• d9738483 This figure was too large to fit on a single report page and always clipped. Bonus code styling fix.

• ce238900 Also part of clean-up, these parameters are kind of useless. Why would we have a configuration to break the format? I've seen them in proposal config though, so preserve them for compatibility.

• 47de13a2 Adding figures in between makes a mess of numbers, so use descriptive labels instead.

How Has This Been Tested?

This should work out of the box:

run = 290  # Run ID.
in_folder = '/gpfs/exfel/exp/SQS/202102/p002676/raw'
out_folder = '<someplace>'
calib_config_path = '/gpfs/exfel/exp/SQS/202102/p002676/usr/remi_proc_config.yaml'

Alternatively for report creation:

xfel-calibrate remi correct --in-folder /gpfs/exfel/exp/SQS/202102/p002676/raw --run 290 --out-folder <someplace> --calib-config-path /gpfs/exfel/exp/SQS/202102/p002676/usr/remi_proc_config.yaml

Relevant Documents

[1]

[2]

Types of changes

• New feature (non-breaking change which adds functionality)
• Docs (changes to the documentation)
• Style (formatting changes only, no code changes)
• Refactor (refactoring code with no functionality changes)
• Chore (non-code changes, e.g. comments, readme, grammar, etc...)

Checklist:

Reviewers

@ahmedk @kluyvert