The LeftRight method determines the sign of the wire
distance for each hit in the spacepoint by looping
through all combinations of wire signs and fitting each
combination with a line  and selecting
the combination with the lowest chi-squared.
The fit to the line is known as the "stub" which
is an array of the x,dx/dz, y and dy/dz of the fit
and is associated each spacepoint. The stubs are
used later in LinkStubs method
to match spacepoints between two chambers to give a
possible tracks.

Previously the LeftRight method would only fit a
stub for a spacepoint with 4 hits in the chamber if the
parameter flag  HMSStyleChamber was true.
HMSStyleChamber refers to the 6 GeV HMS chambers
and we do not have them anymore.
But not fitting the spacepoint, the stub
was filled with zeros for x,dx/dz,y and dy/dz
and these spacepoints would never be matched with
other spacepoints to form a possible track.

This includes a particularly nasty leak in the shower code that caused
several hundred bytes to be lost _per event_.

instead of using GetParent() every hit to get DC version.

  Add doxygen groups "Apparatuses" and "Decoders"
  Make sure every class is in a group
  Make sure most classes have a \brief description
  Improve comments for some classes including THcHallCSpectrometer
     and hodoscope classes
  Change some Doxyfile defaults.  Include sources files.

THcSpacePoint
  1) added fSetStubFlag which is intialized
     to kFALSE in constructor and set to kTRUE
     when SetStub is called.
   2) added method GetSetStubFlag which
      returns fSetStubFlag.

THcDriftchamber
   1) In ProcessHits increased fHits reserve to 40
   2) In FindSpacePoints use fSpacePoints->Delete();
   3) In LeftRight ,only SetStub if the Stub is fit.

THcDC
   1) In LinkStubs
      a) only link stubs if number of total spacepoints <10
      b) only link stubs if both spacepoints have SetStubFlag true

THcDCHit.h
   1) In constructor initalize fLR to 0

THcDCTrack.cxx
   1) AddSpacePoint check if fnSP < 10

In LeftRight method when using SmallAngle Approximation and
 additional condition that the wires in adjacent plane have to
 be within 0.51cm.

1) Add to tree variable arrays stub_x,stub_xp,stub_y and stub_yp
    and ncombos. These are arrays of the number of spacepoints in
    the chamber.

2) In ReadDatabase
   a) new variable  fRatio_xpfp_to_xfp which is set differently
       for HMS and SHMS. Used in method LeftRight
   b) Set default value of optional parameter fStubMaxXPDiff = 999.

3)  Modified method LeftRight
   a) Previously only for the old fHMSStyleChambers would
      the code only select LR combinations where
      the difference between stub_xp to space_point_X*ratio is
        with in the fStubMaxXPDiff .
      The ratio came from the HMS optics.
   b) Changed LeftRight so that if fStubMaxXPDiff < 100
         then the code will only select LR combinations where
      the difference between stub_xp to space_point_X*ratio is
        with in the fStubMaxXPDiff . The ratio is
      set in ReadDataBase according to the spectrometer.


5) In FindSpacePoints add some comments.

1) Add X,Y offsets parameter for each plane, instead of X,Y offset per chamber
2) ModifyTHcDriftChamber::CorrectHitTimes to work with SHMS chambers
3) Add GetReadoutSide method to THcDCHit class.

Fixed minor bug
   FindStub was using the uncorrected drift distance
   from the hit object that was not corrected in
   CorrectHitTimes method. Need to use the corrected
   drift distance that with the spacepoint Hit structure

  Modify THcFormula and THcParmList to match changes to THaFormula
     (needed for reports)
  Small changes in THcInterface and detector classes for compatibility
     with new OO decoder and podd 1.6

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

This reverts commit e9ce1040.

Conflicts:
	src/THcHallCSpectrometer.cxx

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

First, in h_pattern_recognition.f we have:

https://github.com/zahmed9/engine/blob/mkj/HTRACKING/h_pattern_recognition.f#L139
(hdc_wire_center(yy)-hdc_wire_center(yyprime))**2 .lt. (hspace_point_criterion(ich))

So I changed
https://github.com/zahmed9/hcana/blob/develop/src/THcDriftChamber.cxx#L292
TMath::Abs(fHits[plane_hitind]->GetPos() - fHits[planep_hitind]->GetPos()) < fSpacePointCriterion

to

pow((fHits[plane_hitind]->GetPos() - fHits[planep_hitind]->GetPos()),2) < fSpacePointCriterion

Second, the value of MAX_SPACE_POINTS in ENGINE is 100 so in hcana I changed it from 50 to 100.

Found when doing valgrind --tool=memcheck --track-origins=yes --leak-check=full hcana
Return errors like below
==14467== Invalid write of size 1
==14467==    at 0x4A0794F: __GI_strcpy (mc_replace_strmem.c:313)
==14467==    by 0x57137A3: THcHodoscope::Setup(char const*, char const*) (THcHodoscope.cxx:112)
==14467==    by 0x5713A7E: THcHodoscope::Init(TDatime const&) (THcHodoscope.cxx:142)
==14467==    by 0x4D38C29: THaApparatus::Init(TDatime const&) (THaApparatus.C:193)
==14467==    by 0x4D67E57: THaAnalyzer::InitModules(TList const*, TDatime&, int, char const*) (THaAnalyzer.C:433)
==14467==    by 0x4D68B1F: THaAnalyzer::DoInit(THaRunBase*) (THaAnalyzer.C:667)
==14467==    by 0x4D68126: THaAnalyzer::Init(THaRunBase*) (THaAnalyzer.C:467)
==14467==    by 0x4D6B31A: THaAnalyzer::Process(THaRunBase*) (THaAnalyzer.C:1289)
==14467==    by 0x4E21E97: G__haDict_704_0_6(G__value*, char const*, G__param*, int) (haDict.C:23491)
==14467==    by 0x6DB6148: Cint::G__ExceptionWrapper(int (*)(G__value*, char const*, G__param*, int), G__value*, char*, G__param*, int) (in /u/apps/root/5.34.13/root/lib/libCint.so.5.34)
==14467==    by 0x6E5A3A0: G__execute_call (in /u/apps/root/5.34.13/root/lib/libCint.so.5.34)
==14467==    by 0x6E5B201: G__call_cppfunc (in /u/apps/root/5.34.13/root/lib/libCint.so.5.34)
==14467==  Address 0xd7636a2 is 0 bytes after a block of size 2 alloc'd
==14467==    at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==14467==    by 0x5713757: THcHodoscope::Setup(char const*, char const*) (THcHodoscope.cxx:111)
==14467==    by 0x5713A7E: THcHodoscope::Init(TDatime const&) (THcHodoscope.cxx:142)
==14467==    by 0x4D38C29: THaApparatus::Init(TDatime const&) (THaApparatus.C:193)
==14467==    by 0x4D67E57: THaAnalyzer::InitModules(TList const*, TDatime&, int, char const*) (THaAnalyzer.C:433)
==14467==    by 0x4D68B1F: THaAnalyzer::DoInit(THaRunBase*) (THaAnalyzer.C:667)
==14467==    by 0x4D68126: THaAnalyzer::Init(THaRunBase*) (THaAnalyzer.C:467)
==14467==    by 0x4D6B31A: THaAnalyzer::Process(THaRunBase*) (THaAnalyzer.C:1289)
==14467==    by 0x4E21E97: G__haDict_704_0_6(G__value*, char const*, G__param*, int) (haDict.C:23491)
==14467==    by 0x6DB6148: Cint::G__ExceptionWrapper(int (*)(G__value*, char const*, G__param*, int), G__value*, char*, G__param*, int) (in /u/apps/root/5

In tree they are called tnhit and trawhit.
Created two new variables for THcDriftChamber, fNthits and fN_True_RawHits.
In tree they are called tnhit and trawhit.
THcDC defined subdetector THcDriftChamber to have name Ch1 and Ch2 to do used in the tree.
THcDriftChamberPlane defined new method GetNRawhits to return fNRawhits for each plane.
Added member fNRawhits to THcDriftChamberPlane

  Fix from Mark Jones with additional cleanup for
  saw's misunderstanding of space point criterion

  Compare wire coordinate, not wire number

  THcDriftChamber::AddPlane didn't know if style was HMS, because
  style was only determined in Init.  Now fHMSStyleFlag is set in
  only one place.  Right now determined from spectrometer name, but
  could be a parameter in the future.

Modified ReadDatabase : Added fdebugstubchisq and Corrected fhdebugflagpr to be Int
Added PrintDecode( void ) to print the drift chamber info in fHits
Modified FindSpacePoints to use the proper PlaneInd and PlanePInd
    for HMS and SOS style chambers
Changed THcDriftChamber::FindEasySpacePoint(Int_t yplane_hitind,Int_t yplanep_hitind) to
THcDriftChamber::FindEasySpacePoint_HMS(Int_t yplane_hitind,Int_t yplanep_hitind)
Added  THcDriftChamber::FindEasySpacePoint_SOS(Int_t xplane_hitind,Int_t xplanep_hitind)
commented out many fhdebugflagpr  output statements

Should compare (pindex1%2), not pindex1, to determine evenness.

  THcDriftChamber
    New flag fHMSStyleChambers to determine if HMS or SOS style
    tracking should be done.  Flag is set on if the spectrometer
    name begins with 'h'.
    THcDriftChamber::LeftRight fSmallAngleApprox must be set and
    fHMSStyleChambers must be off to do SOS style.
    If not HMS style, ignore all the Yplane optimizations
  THcDC
    SOS code does "project to chamber" in link stubs.  Need to evaluate
    if this is necessary, or if HMS style should also do it.