Add the preliminary ALERT timeline to the main branch

[Sangbaek]

This PR consists of three major commits and two minor fixes for the ALERT timeline.
These are all prelim in sense that it only produces the ATOF TDC peak location/ sigma/ integral (normalized to the trigger.)
It is timeliy to include in the main branch to get the feedbacks from the ALERT experts.

1. Add the prelim ALERT monitoring

• Add the ALERT.java to save the histograms in out_ALERT_runnum.hipo
• Edit the run_histograms.java to include the ALERT histograms in the task list

2. Add the prelim ALERT timeline scripts

• Add the alert_atof_tdc.groovy to produce the timeline of peak location/ sigma/ normalized integral .
• Edit the run_analysis.java to include the ALERT timeline in the task list

3. Include the ALERT in the detector timeline list

• Edit the run-detectors-timelines.sh to include the alert in the task list.

4. Clarify the meaning of the timeline variable

• Clarify the meaning of normalized integral by changing it from integral_per_trigger to integral_normalized_to_trigger

5. Save the timeline hipo file for each sector/layer

• Initialize the timeline per each sector/layer.

[c-dilks]

Looks good to me, thanks!

I do have a review comment however: this PR nearly doubles the number of timelines; do you really need so many, or can you combine them?

    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector0_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector0_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector0_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector0_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector10_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector10_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector10_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector10_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector11_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector11_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector11_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector11_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector12_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector12_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector12_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector12_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector13_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector13_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector13_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector13_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector14_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector14_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector14_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector14_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector1_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector1_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector1_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector1_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector2_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector2_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector2_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector2_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector3_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector3_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector3_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector3_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector4_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector4_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector4_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector4_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector5_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector5_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector5_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector5_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector6_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector6_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector6_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector6_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector7_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector7_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector7_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector7_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector8_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector8_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector8_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector8_layer3.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector9_layer0.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector9_layer1.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector9_layer2.hipo
    │   │   ├── alert_atof_tdc_integral_normalized_to_trigger_sector9_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector0_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector0_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector0_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector0_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector10_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector10_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector10_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector10_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector11_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector11_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector11_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector11_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector12_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector12_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector12_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector12_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector13_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector13_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector13_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector13_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector14_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector14_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector14_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector14_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector1_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector1_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector1_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector1_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector2_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector2_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector2_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector2_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector3_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector3_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector3_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector3_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector4_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector4_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector4_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector4_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector5_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector5_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector5_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector5_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector6_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector6_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector6_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector6_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector7_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector7_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector7_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector7_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector8_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector8_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector8_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector8_layer3.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector9_layer0.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector9_layer1.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector9_layer2.hipo
    │   │   ├── alert_atof_tdc_peak_location_sector9_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector0_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector0_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector0_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector0_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector10_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector10_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector10_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector10_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector11_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector11_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector11_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector11_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector12_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector12_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector12_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector12_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector13_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector13_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector13_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector13_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector14_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector14_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector14_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector14_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector1_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector1_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector1_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector1_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector2_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector2_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector2_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector2_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector3_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector3_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector3_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector3_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector4_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector4_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector4_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector4_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector5_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector5_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector5_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector5_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector6_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector6_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector6_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector6_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector7_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector7_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector7_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector7_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector8_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector8_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector8_layer2.hipo
    │   │   ├── alert_atof_tdc_sigma_sector8_layer3.hipo
    │   │   ├── alert_atof_tdc_sigma_sector9_layer0.hipo
    │   │   ├── alert_atof_tdc_sigma_sector9_layer1.hipo
    │   │   ├── alert_atof_tdc_sigma_sector9_layer2.hipo
    │   │   └── alert_atof_tdc_sigma_sector9_layer3.hipo

[Sangbaek]

Thank you, Chris.

Yes, I anticipate that the scroll in the clas12mon's alert web page will be super busy.
But each sector/layer comes with 12 combinations of components and orders ( 10 for wedges and 2 for bar), so I don't know if we want to sacrifice the readability in lieu of the number of hipos.
I'll have to ask Whit about optimizing the visualization, and I think this PR will catalyze the discussion, by helping Noemie to produce the timeline.

I think you might want include the options to suppress the ALERT for other run groups except for RG-L. when you publish the new module with this update.

I haven't heard from Raphael about the AHDC input yet, and I didn't include anything for the AHDC.
They might need similar plots with AHDC::adc, so I expect I'm going to submit a follow-up PR shortly.

[Sangbaek]

Related issue: #305

[c-dilks]

Sounds good, thanks!

It looks like the default behavior when ALERT data are not available is to fill ALERT timelines with flat zero, which is the current convention for other detectors, so that's not a problem for other run groups. Eventually we can add the ability to just not publish irrelevant timelines (you're welcome to send a PR on that if you can think of a general way to do it!)