Tool to produce a time calibration HDF5 file

[Bultako]

This PR is the continuation of #533 developed in a forked repo and now with the code placed in a branch of lstchain repo.

It adds a new Tool lstchain_create_time_calibration_file

Generate a HDF5 file with time calibration coefficients

Options
=======
The options below are convenience aliases to configurable class-options,
as listed in the "Equivalent to" description-line of the aliases.
To see all configurable class-options for some <cmd>, use:
    <cmd> --help-all

--debug
    Set log-level to debug, for the most verbose logging.
    Equivalent to: [--Application.log_level=10]
--show-config
    Show the application's configuration (human-readable format)
    Equivalent to: [--Application.show_config=True]
--show-config-json
    Show the application's configuration (json format)
    Equivalent to: [--Application.show_config_json=True]
-q, --quiet
    Disable console logging.
    Equivalent to: [--Tool.quiet=True]
-i, --input=<Path>
    Path to the fits.fz events file or directory to glob
    Default: None
    Equivalent to: [--TimeCalibrationHDF5Writer.input]
-o, --output=<Unicode>
    Path to the time calibration file
    Default: ''
    Equivalent to: [--TimeCorrectionCalculate.calib_file_path]
--glob=<Unicode>
    Filename pattern to glob files in the directory
    Default: '*.fits.fz'
    Equivalent to: [--TimeCalibrationHDF5Writer.glob]
--max-events=<Int>
    Maximum number of events that will be read from the file
    Default: None
    Equivalent to: [--LSTEventSource.max_events]
--pedestal=<telescopeparameter-item-1>...
    Path to the LST pedestal file
    Default: [('type', '*', None)]
    Equivalent to: [--LSTR0Corrections.drs4_pedestal_path]
--run-summary-path=<telescopeparameter-item-1>...
    Path to the run summary for the correct night. If given, dragon reference
    counters are read from this file. Explicitly given values override values
    read from the file.
    Default: [('type', '*', None)]
    Equivalent to: [--EventTimeCalculator.run_summary_path]
--config=<Path>
    name of a configuration file with parameters to load in addition to command-
    line parameters
    Default: None
    Equivalent to: [--Tool.config_file]
--log-level=<Enum>
    Set the log level by value or name.
    Choices: any of [0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL']
    Default: 30
    Equivalent to: [--Tool.log_level]
-l, --log-file=<Path>
    Filename for the log
    Default: None
    Equivalent to: [--Tool.log_file]
--log-file-level=<Enum>
    Logging Level for File Logging
    Choices: any of [0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL']
    Default: 'INFO'
    Equivalent to: [--Tool.log_file_level]

To see all available configurables, use `--help-all`.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.91%. Comparing base (96ae165) to head (777cea2).
Report is 1980 commits behind head on main.

Additional details and impacted files

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[Bultako]

I guess that for testing this PR we need bigger raw files than those already present in test_data. I have the exception below when testing with LST-1.1.Run02008.0000_first50.fits.fz

Caught unexpected exception: Not enough events to coverage all capacitor. 
Please use more events to time calibration file.

[maxnoe]

@Bultako is that an option? Could you run the test with less required events?

And maybe fix the language of the error?

[rlopezcoto]

@Bultako is that an option? Could you run the test with less required events?

And maybe fix the language of the error?

For the time calibration it is complicated because you need to cover all capacitors to be able to calculate the time correction for all of them. In principle the exception is right and you should not be able to produce a time calibration file without covering all capacitors.
I cannot think on any way of performing tests without that, but maybe @FrancaCassol or @pawel21 have some idea.

[maxnoe]

We can also try to look for the smallest possible file.

Unfortunately that will be around 1000 events or so I think.

[rlopezcoto]

this one was reviewed and approved, could you re-approve @maxnoe so we can also include it in the next release?

[maxnoe]

I think we need to adapt the onsite scripts so that actually the new tool is called, right?

[rlopezcoto]

I would get this tool in the release before, and then lstosa can be later updated to use it

[maxnoe]

I am not talking about osa, I am talking about the onsite scripts in this repo.

[FrancaCassol]

I think we should concentrate towards what is blocking release 0.8.0
This tool should replace the script, so I think it should be merged when the lstchain script is removed and the onsite script is adapted. But I will personally not approve any further change in the calibration scripts before 0.8.0

[rlopezcoto]

ok, let's leave this for lstchain > v0.8

[vuillaut]

Should be closed?

[maxnoe]

Yes, all the calibration related tools have been moved to the new lstcam-calib project, we shouldn't update the ones here