Add PandoraLArRecoNDBranchFiller

[jback08]

Created the PandoraLArRecoNDBranchFiller class to store the reconstruction information from Pandora's LArRecoND package (used for the DUNE ND). It requires a ROOT file created by the HierarchyAnalysisAlgorithm, which uses Pandora's Hierarchy Tools.

The filled reco branches are rec.nd.lar.pandora.tracks and .rec.nd.lar.pandora.showers. No distinction is made (yet) between tracks and showers, and so the same 3D-cluster Particle Flow Objects (PFOs) are used for both. Here is the list of reco variables used:

1. Start position = cluster vertex point or the first hit position if no vertex is available
2. End position = cluster end position
3. Energy = charge Q
4. Length = primary principal axis length
5. Quality = number of 3D hits.

Any changes needed here can be done mostly in the LArRecoND package, since the CAF just retrieves the output stored by Pandora's hierarchy algorithm.

The MC truth matching uses Pandora's Hierarchy Tools and not TruthMatcher. Pandora requires all MC particles to have a unique ID (even if they originate from different neutrinos), and so the following offsets are applied to the original (ndlar-flow) MC Ids:

1. nuId = orig_nuId + 10^8
2. mcId = orig_mcId + nuIndex * 10^6

where nuIndex = 0 to N-1 for an event with N neutrinos, and the orig_mcId number range restarts from zero for each neutrino. This ensures all IDs are unique, for up to 100 neutrino interactions per event, each containing up to 10^6 hits.

These ID offsets are reversed when the Pandora CAF truth information is filled using the best reco-MC match achieved with Hierarchy Tools, and so the mcId's should then have values consistent with the equivalent input ndlar-flow files. The filled truth information corresponds to:

1. truth.ixn = orig_nuId
2. truth.part = orig_mcId (best match)
3. truth.type = primary, secondary or other
4. truthOverlap = completeness (best match)

H5 input files are first converted to ROOT using h5_to_root_ndlarflow.py before they are used by LArRecoND & Pandora, which in turn creates the hierarchy analysis output file that can be used to make the equivalent CAFs.

For the trigger, the event run numbers are propagated using those originally from the input ndar_flow ROOT files. Also, the start time is currently set using the ts_start variable, but this needs to be updated (in LArRecoND) to use the correct time and units.

Also updated ndcaf_setup.sh and build.sh to use a consistent environment.

[noeroy]

I think that the truth part of it could be an issue, as the truth branches are shared by all reconstructions.

The particles are uniquely identified with two ids, one that identifies the interaction inside a given spill: vertex_id in the flow files, and one that is uniquely identifying for a given interaction which is the Geant4 trajectory id, I believe it is traj_id in the flow files. Those IDs are shared within MLReco and MINERvA so that truth particles are matched to the same id. Would it be possible to have a match between orig_nuId and vertex_id and between orig_mcId and traj_id?

[jback08]

I think this is ready for review now. We have added the unix_ts variable to set the trigger time, and we are using the same MC Id variables as the other reco methods.

[chenel]

Overall looks fine. Just a couple of small grumbles.

[chenel]

A ROOT setup already comes implicitly from the duneanaobj and edepsim requirements (which each depend on ROOT). In the abstract I would prefer to have it explicit, as here, but in practice, if this line conflicts with dependencies inherited from the other products, the resulting environment will have subtle and difficult-to-diagnose inconsistencies. (I've personally wasted hours chasing this sort of thing down in the past.) So unless there's a strong reason to include, I'd like to not add this line.

[jback08]

OK, removed.

[chenel]

any chance we could use unique_ptrs here, instead of manual memory management in 2024? suggestions for the knock-on changes for this suggestion below

[jback08]

Changed to unique pointers.

[chenel]

to use a unique_ptr, this line would look something like

Suggested change

	m_LArRecoNDFile = TFile::Open(pandoraLArRecoNDFilename.c_str(), "read");
	m_LArRecoNDFile.reset(TFile::Open(pandoraLArRecoNDFilename.c_str(), "read"));

[chenel]

similarly, here, you'd have

Suggested change

	m_LArRecoNDTree = dynamic_cast<TTree*>(m_LArRecoNDFile->Get("LArRecoND"));
	m_LArRecoNDTree.reset(dynamic_cast<TTree*>(m_LArRecoNDFile->Get("LArRecoND")));

[chenel]

This might be better as a parameter, rather than hard-coded

[jback08]

Added the LAr density as an optional config parameter with a default value.