DaVinci algorithms. (#21)

* Skeleton for FilterInTrees

* Written FilterInTrees lesson

* Addressed Alex's comments

* Fixing build decays too

* First commit of fixing errors

* Make Travis happy

* Make PEP8 happy

* Finalized debug section

01-building-decays.md

@@ -93,7 +93,7 @@ Then, we can build a combiner as
 from Configurables import CombineParticles
 d0 = CombineParticles(
     'Combine_D0',
-    DecayDescriptor='([D0 -> pi- K+]CC)',
+    DecayDescriptor='[D0 -> pi- K+]cc',
     DaughtersCuts=d0_daughters,
     CombinationCut=d0_comb,
     MotherCut=d0_mother

17-switch-mass-hypo.md

@@ -1,6 +1,6 @@
 ---
 layout: page
-title: First steps in LHCb
+title: Seconds steps in LHCb
 subtitle: Replace a mass hypothesis
 minutes: 10
 ---

18-filter-in-trees.md

@@ -0,0 +1,86 @@
+---
+layout: page
+title: Second steps in LHCb
+subtitle: Reuse particles from a decay tree
+minutes: 10
+---
+
+> ## Learning Objectives {.objectives}
+>
+> * Learn how to extract particles from a decay tree
+> * Build a new particle from the extracted particles
+
+Sometimes we want to extract a portion of the decay tree in order to build a different decay.
+To do that, we need to put the particles we're interested in in a new container so they can afterwards be used as inputs to a `CombineParticles` instance (as we saw in [the selection framework lesson](https://lhcb.github.io/second-analysis-steps/01-building-decays.html)).
+To achieve this we can use the `FilterInTrees` algorithm, a simple variation of `FilterDesktop` ([doxygen](https://lhcb-release-area.web.cern.ch/LHCb-release-area/DOC/hlt/latest_doxygen/de/d8e/class_filter_in_trees.html)).
+
+Let's start from the example in [the selection framework lesson](https://lhcb.github.io/second-analysis-steps/01-building-decays.html) and let's check that the $\pi^-$ child of the $D^0$ does not come from a $\rho\to\pi^+\pi^-$.
+To do that, we have to extract the $\pi^-$ from `([D0 -> pi+ K-]CC)` and combine it with all pions in `Phys/StdAllNoPIDsPions/Particles`.
+
+Using `FilterInTrees` is done in the same way we would use `FilterDesktop`:
+
+```python
+from Configurables import FilterInTrees
+from PhysSelPython.Wrappers import Selection, DataOnDemand
+
+decay_tree_location = '/Event/AllStreams/Phys/D2hhCompleteEventPromptDst2D2RSLine/Particles'
+d0_from_dst = FilterInTrees('d0_from_dst_filter', Code="DECTREE('[Charm -> pi+ K-]CC')")
+d0_from_dst_sel = Selection("d0_from_dst_sel",
+                            Algorithm=d0_from_dst,
+                            RequiredSelections=[AutomaticData(Location=decay_tree_location)])
+pions_from_d0 = FilterInTrees('pions_from_d0_filter',Code="('pi+' == ABSID)")
+pions_from_d0_sel = Selection("pions_from_d0_sel",
+                              Algorithm=pions_from_d0,
+                              RequiredSelections=[d0_from_dst_sel])
+```
+
+The output of `pions_from_d0_sel` is a container with all the pions coming from the $D^0$.
+
+> ## Question {.callout}
+> Do you see why we couldn't use something simple like
+> ```python
+pions_from_d0 = FilterInTrees('pions_from_d0_filter', Code="'pi+' == ABSID")
+```
+> ?
+
+Note how we had to do the process in two steps in order to avoid getting the soft pion from the $D^*$.
+Sometimes this makes things quite difficult, but almost all problems can be solved with a smart use of the `DECTREE` container in an intermediate step.
+
+> ## Selecting the soft pion {.challenge}
+> Can you find of a way of selecting the soft pion?
+> Hint: use the `FilterDecays` algorithm, in which you specify a decay descriptor as `Code`, marking the desired particle(s).
+
+The final step is easy, very similar to [building your own decay](https://lhcb.github.io/second-analysis-steps/01-building-decays.html):
+
+```python
+from Configurables import CombineParticles
+from PhysSelPython.Wrappers import Selection, DataOnDemand
+
+Pions = DataOnDemand('Phys/StdAllNoPIDsPions/Particles')
+rho = CombineParticles('rho_particles',
+                       DecayDescriptor=['rho(770)0 -> pi+ pi-'],
+                       CombinationCut="ADAMASS('rho(770)0') < 300*MeV",
+                       MotherCut='(VFASPF(VCHI2/VDOF)< 9)')
+rho_sel = Selection('rho_sel',
+                    Algorithm=rho,
+                    RequiredSelections=[pions_from_d0_sel, Pions])
+```
+
+Unfortunately, the `CombineParticles` example we just wrote is not exactly what we meant, since it will actually build $\rho$ from all pions it gets as input, not using one from our `pions_from_d0` selection and one from `'Phys/StdAllNoPIDsPions/Particles'`.
+How to solve this?
+We have to get creative and use the tools at hand:
+for example, we could use `SubstitutePID` from the previous lesson to change the PID of the pions in the `pions_from_d0` selection to kaon and build `[rho(770)0 -> K+ pi-]CC` and then change again the PID of the kaon to a pion.
+Of course, if we were reconstructing $K^{*}(892)^{0} \to K^{-}\pi^{+}$ with `Phys/StdAllLooseKaons/Particles` instead, for example, we would already have everything we need since the ambiguity wouldn't exist.
+
+> ## An interesting detail {.callout}
+> One can use `FilterInTrees` and `FilterDecays` to select several particles at once and obtain a flattened list.
+> For example, if we had a Stripping line that builds `[B-  -> (^D0 -> ^K- ^pi+) ^pi-]cc` and we wanted to combine the $D^0$ and $\pi^-$ with an external $\pi^0$ to build `[B- -> D0 pi- pi0]cc`, we could do
+> ```python
+flatlist = FilterInTrees ("FlatList", Code="('D0' == ABSID) | ('pi-' == ABSID)")
+from Configurables import CombineParticles
+add_pi0 = CombineParticles("MakeB",
+                           DecayDescriptor = "[B- -> D0 pi- pi0]cc",
+                           ...
+                           Inputs=[flatlist, resolvedPi0])
+```
+> `flatlist` contains both $D^0$ and $\pi^-$, which are then used to build the $B$.

code/06-building-decays/build_decays.py

@@ -25,7 +25,7 @@
 )
 
 d0 = CombineParticles('Combine_D0',
-                      DecayDescriptor='([D0 -> pi- K+]CC)',
+                      DecayDescriptor='[D0 -> pi- K+]cc',
                       DaughtersCuts=d0_daughters,
                       CombinationCut=d0_comb,
                       MotherCut=d0_mother)

code/06-building-decays/davinci.py

@@ -0,0 +1,16 @@
+from Configurables import DaVinci, IoHelper
+
+DaVinci().InputType = 'DST'
+DaVinci().TupleFile = 'DVntuple.root'
+DaVinci().PrintFreq = 1000
+DaVinci().DataType = '2012'
+DaVinci().Simulation = True
+# Only ask for luminosity information when not using simulated data
+DaVinci().Lumi = not DaVinci().Simulation
+DaVinci().EvtMax = 1000
+
+# Use the local input data
+IOHelper().inputFiles([('root://eoslhcb.cern.ch//eos/lhcb/user/a/apearce/'
+                        'Starterkit/Nov2015/'
+                        '00035742_00000001_1.allstreams.dst')],
+                      clear=True)

index.md

@@ -30,9 +30,10 @@ developed][second-ana-repo], or you can [send an email to
 
 1. [Using git to develop LHCb software](02-lb-git.html)
 1. [Building your own decay](01-building-decays.html)
+1. [What to do when something fails](07-fixing-errors.html)
 1. [Run a different stripping line on simulated data](14-rerun-stripping.html)
-1. [Using git to develop LHCb software](02-lb-git.html)
 1. [Replace a mass hypothesis](17-switch-mass-hypo.html)
+1. [Reuse particles from a decay tree](18-filter-in-trees.html)
 1. [HLT intro](18-hlt-intro.html)
 1. [TisTos DIY](18-tistos-diy.html)