Prototype of new alignment configuration

Overview

This MR contains a prototype for configuring alignment jobs using a Moore-like configuration. Its main purpose is documenting the work done during past hackathons and to serve as basis for the next steps. It includes track and vertex selections, adding constraints and defining the elements to be aligned. The fundamental change is making the Alignment project depend on Moore instead of Phys.

Some documentation how to use the new configuration is provided in Alignment/Humboldt/README.md

Next steps and open points are summarised in #17 and #20

Configurations

The configurations added are

Alignment/Humboldt/options/AlignVPHalvesModules.py #example Velo alignment job
Alignment/Humboldt/options/AlignVPHalvesModules_PrKalman.py #example Velo job using PrKalman (see #16)
Alignment/Humboldt/options/AlignFTStationsLayers.py #example SciFi job
Alignment/Humboldt/options/AlignVPHalvesModules_Analyzer.py #run analyser part of example alignment job
Alignment/Humboldt/options/AlignVPHalvesModules_Iterator.py #run iterator part of example alignment job

Helper functions to set up new configuration are in Alignment/Humboldt/python/Humboldt/utils.py.

Central track and particle selections are started to be defined in

Alignment/Humboldt/python/Humboldt/TrackSelections.py
Alignment/Humboldt/python/Humboldt/ParticleSelections.py

New functionality (WIP)

• add AlignIterator taking parts from OnlineAlignment to perform iterator part offline

Tests

• add Alignment/Humboldt/tests/qmtest/humboldt.qms/align-vp-halves-modules.qmt to test new configuration
• add Alignment/Humboldt/tests/qmtest/humboldt.qms/analyzer-vp-halves-modules.qmt to test Analyzer part
• add Alignment/Humboldt/tests/qmtest/humboldt.qms/iterator-vp-halves-modules.qmt to test Iterator part
• add Alignment/Humboldt/tests/qmtest/humboldt.qms/align-vp-halves-modules-splititer.qmt to test gaudisplititer.py (WIP)

Uses Rec!2495 (merged)

Alignment/Humboldt/options/AlignVPHalvesModules_PrKalman.py

+###############################################################################
+# (c) Copyright 2021 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
+
+from Moore import options
+from PyConf.application import configure_input
+from RecoConf.hlt1_tracking import default_ft_decoding_version
+default_ft_decoding_version.global_bind(value=6)
+options.set_input_and_conds_from_testfiledb('upgrade_DC19_01_MinBiasMD')
+#use only a cetain file from testfileDB as some files seem to be corrupt in that sample
+options.input_files = list(
+    set([
+        "root://eoslhcb.cern.ch//eos/lhcb/grid/prod/lhcb/MC/Upgrade/XDIGI/00092857/0000/00092857_00000030_1.xdigi"
+    ]))
+options.evt_max = 10
+# options.use_iosvc = True
+options.event_store = 'EvtStoreSvc'
+options.ntuple_file = "testmonitoring.root"
+options.histo_file = "testmonitoringhist.root"
+
+# set options above this line!
+
+configure_input(options)
+
+# only configure data flow after this line !
+
+from Humboldt.utils import runAlignment
+
+
+# at the moment, define tracks and PVs by hand. Could be changed to centrally defined selection in the future
+def getAlignmentTracksAndPVs():
+    from RecoConf.reconstruction_objects import reconstruction
+    from PyConf.Algorithms import VeloClusterTrackingSIMDFull, PrKalmanFilter
+    # note that the PVs reconstructed by TrackBeamLineVertexFinderSoA do not store the list of associated tracks. Use PatPV3DFuture instead
+    from RecoConf.hlt1_tracking import make_reco_pvs, make_PatPV3DFuture_pvs
+    from RecoConf.hlt2_global_reco import make_fastest_reconstruction
+    from RecoConf.hlt2_global_reco import reconstruction as reconstruction_hook
+    with reconstruction.bind(from_file=False), PrKalmanFilter.bind(
+            FillFitResult=True,
+            ClassicSmoothing=True), reconstruction_hook.bind(
+                make_reconstruction=make_fastest_reconstruction
+            ), make_reco_pvs.bind(
+                make_pvs_from_velo_tracks=make_PatPV3DFuture_pvs
+            ), make_fastest_reconstruction.bind(usePatPVFuture=True):
+        #make tracks and PVs
+        # TODO: in principle the PVs should be an optional input for the alignment
+        reco = reconstruction()
+        hlt2_tracks = reco["Tracks"]
+        best_tracks = hlt2_tracks
+        pvs = reco["PVs"]
+
+        from PyConf.application import default_raw_banks, createODIN
+        odin = createODIN(RawBanks=default_raw_banks(("ODIN"))).ODIN
+        # create input particles, use dummy for now
+        # TODO: in principle these should be composite particles and be an optional input for the alginment
+        from Humboldt.ParticleSelections import DummyParticles
+        particles = DummyParticles()
+
+        #select tracks and PVs
+        from PyConf.Tools import VPTrackSelector
+        from PyConf.Algorithms import TrackListRefiner, VertexListRefiner, TrackSelectionMerger
+        myTrackSelector = VPTrackSelector(
+            TrackTypes=["Long"], MinHits=5, MaxChi2Cut=5)
+        selected_tracks = TrackListRefiner(
+            inputLocation=best_tracks, Selector=myTrackSelector).outputLocation
+
+        myBackwardTrackSelector = VPTrackSelector(
+            TrackTypes=["Velo"],
+            MinHits=5,
+            MaxChi2Cut=5,
+            OnlyBackwardTracks=True)
+        selected_BackwardTracks = TrackListRefiner(
+            inputLocation=best_tracks,
+            Selector=myBackwardTrackSelector).outputLocation
+
+        alignmentTracks = TrackSelectionMerger(
+            InputLocations=[selected_tracks, selected_BackwardTracks
+                            ]).OutputLocation
+
+        selected_pvs = VertexListRefiner(
+            MaxChi2PerDoF=5,
+            MinNumTracks=15,
+            MinNumLongTracks=0,
+            InputLocation=pvs).OutputLocation
+
+        # add track and vertex monitoring
+        from PyConf.Algorithms import TrackMonitor, TrackFitMatchMonitor, TrackVertexMonitor, VPTrackMonitor
+        from RecoConf.mc_checking import vphits_resolution_checker
+        from RecoConf.hlt1_tracking import make_VPClus_hits
+        # TODO: should only use selected PVs
+        myTrackMonitor = TrackMonitor(
+            TracksInContainer=alignmentTracks, PrimaryVertices=pvs)
+        myTrackFitMatchMonitor = TrackFitMatchMonitor(
+            TrackContainer=alignmentTracks)
+        # TODO: check vertices
+        myTrackVertexMonitor = TrackVertexMonitor(
+            TrackContainer=alignmentTracks, PVContainer=pvs)
+        myVPTrackMonitor = VPTrackMonitor(
+            TrackContainer=best_tracks, ClusterContainer=make_VPClus_hits())
+        monitorlist = [
+            myTrackMonitor, myTrackFitMatchMonitor, myTrackVertexMonitor,
+            myVPTrackMonitor,
+            vphits_resolution_checker()
+        ]
+        return alignmentTracks, selected_pvs, particles, odin, monitorlist
+
+
+alignmentTracks, alignmentPVs, particles, odin, monitors = getAlignmentTracksAndPVs(
+)
+
+#define elements and degrees of freedom to be aligned
+from TAlignment.Alignables import Alignables
+elements = Alignables()
+dofs = "TxTyTzRxRyRz"
+dofsmodules = "TxTyTzRxRyRz"
+elements.VPLeft(dofs)
+elements.VPRight(dofs)
+elements.VPModules(dofsmodules)
+
+# add survey constraints
+from Configurables import SurveyConstraints
+from PyConf.Tools import AlignChisqConstraintTool
+surveyconstraints = SurveyConstraints()
+surveyconstraints.VP()
+myAlignChisqConstraintTool = AlignChisqConstraintTool(
+    Constraints=surveyconstraints.Constraints,
+    XmlUncertainties=surveyconstraints.XmlUncertainties,
+    XmlFiles=surveyconstraints.XmlFiles)
+
+# define Lagrange constraints
+constraints = []
+constraints.append("VPHalfAverage : VP/VP(Left|Right) : Tx Ty Tz Rx Ry Rz")
+constraints.append(
+    "VPInternal : VP/VPRight/Module..WithSupport: Tx Ty Tz Rx Ry Rz")
+constraints.append(
+    "VPInternal : VP/VPLeft/Module..WithSupport: Tx Ty Tz Rx Ry Rz")
+
+runAlignment(
+    options,
+    chisqConstraintTool=myAlignChisqConstraintTool,
+    lagrangeConstrains=constraints,
+    alignmentTracks=alignmentTracks,
+    alignmentPVs=alignmentPVs,
+    particles=particles,
+    odin=odin,
+    elementsToAlign=elements,
+    monitorList=monitors)