StripEnergyThresholdFinder for per-strip slow and fast threshold extraction with diagnostics

[JarredMRoberts]

Adds a standalone application, StripEnergyThresholdFinder, for computing per-strip slow and fast energy thresholds. Slow thresholds are determined from ADC spectra using a noise peak and trough method, while fast thresholds are determined from dt0/dt1 timing crossover. The tool reads calibrated HDF5 data via MModuleLoaderMeasurementsHDF, applies strip mapping and energy calibration from a YAML configuration, and produces ROOT diagnostic outputs (energy spectra with thresholds, dt0 vs dt1 per strip, and threshold distributions) along with CSV export files. The implementation is self-contained under apps/ and does not modify existing modules. Tested on COSI datasets with consistent threshold behavior and expected diagnostic results. Target branch is develop/em.

[JarredMRoberts]

I still need to fix all of the code style issues and work on some optimizations to speed the code up a bit.

[fhagemann]

Is this different from #143 or making #143 obsolete?

[fhagemann]

Hi Jarred,
I had an extensive look at this app and finally got this to run.
I replied to all comments in this PR, and opened a separate PR onto your fork/branch, addressing some code changes to

1. get this app running
2. remove the helper classes by replacing them with existing nuclearizer/megalib code

Here is the PR onto your branch with detailed code changes: JarredMRoberts#1

[fhagemann]

Suggested change

	leg->AddEntry(line, "Fast Thresholdeshold", "l");
	leg->AddEntry(line, "Fast Threshold", "l");

[zoglauer]

I second not to have an additional parser linked.
You can use the nuclearizer/megalib XML file format instead; your file then would be:

<strip-threshold-finder>
    <input>
        <data_files>
            <file>/path/to/data/file.hdf5</file>
        </data_files>
        <calibration_file>/path/to/calibration/file.ecal</calibration_file>
        <tac_calibration_file>/path/to/tac/calibration/file.csv</tac_calibration_file>
        <strip_map>/path/to/strip/map/file.map</strip_map>
    </input>

    <analysis>
        <!-- number of skipped strips with minimum statistics -->
        <min_entries>10</min_entries> 
        
        <!-- If a threshold cannot be determined set threshold to default value -->
        <fallback_threshold_keV>20</fallback_threshold_keV> 
        
        <!-- limit for locating the low-energy noise peak -->
        <!-- most noise peaks should be between 100 and 250 -->
        <!-- Worst case the ADC max should be set to ~1000 -->
        <noise_search_max_adc>1800</noise_search_max_adc>
    </analysis>
    
    <output>
        <prefix>output_file_prefix</prefix>
    </output>
</strip-threshold-finder>

[fhagemann]

One more remark: I got this app to run and got reasonable results for the fast and slow thresholds only when using a dataset taken with NN off.
We might want to always filter out NN events, for this app to also run using datasets taken with NN on.