!-----------------------------------------------------------------------------
! Package     : Tb/TbAlgorithms
! Responsible :
! Purpose     : Algorithms for Timepix3 testbeam analysis
!-----------------------------------------------------------------------------

! 2016-02-23 - Heinrich Schindler
 - TbClustering: apply eta corrections if available.
 - TbSimpleTracking: add option to remove outliers from a candidate track.

! 2016-02-04 - Heinrich Schindler
 - TbClustering: assign different cluster errors depending on the 
   number of rows/columns covered by the cluster.
 - TbSimpleTracking: add cut on max. cluster width,
   deactivate monitoring by default.

! 2016-01-31 - Heinrich Schindler
 - TbClustering: move timing histograms to TbClusterPlots. 
 - TbClusterAssociator: add track chi2 cut.

! 2016-01-28 - Heinrich Schindler
 - TbHitMonitor: add profile histograms of ToT/charge as function of column.
 - TbClusterPlots: add ToT histograms.

! 2016-01-26 - Heinrich Schindler
 - TbSimpleTracking: apply charge and cluster size cuts also at seeding stage.

! 2015-12-14 - Heinrich Schindler
 - Add options to TbClusterAssociator to use hit or cluster coordinates and
   to skip used clusters.
 
! 2015-12-02 - Tim Evans
 - Add new synchronisation method to TbCalibration.

! 2015-11-12 - Dan Saunders
 - Update default settings for clustering and tracking. 
 - Add new cuts and function to recover missed hits to TbSimpleTracking.

! 2015-10-29 - Heinrich Schindler
 - Speed up TbClustering.

! 2015-10-23 - Heinrich Schindler
 - Fix compiler warnings uncovered by clang (signed vs unsigned int).

!========================= TbAlgorithms v2r2 2015-05-19 =======================

! 2015-05-19 - Heinrich Schindler
 - Undo latest changes to TbAlignment. To be put back after the release.

! 2015-05-18 - Tim Evans
 - Added new features to the alignment, can run multiple alignment 
   algorithms from the same job
 - Added DeviceSurvey alignment algorithm, that uses time alignment 
   to survey align a single device (i.e. the DuT)
 - Options to only use a single trigger channel in the trigger 
   associator

! 2015-03-24 - Heinrich Schindler
 - Add property TrackFitTool to TbTrackPlots, TbAlignment, TbTracking, 
   TbSimpleTracking, TbVertexTracking.
 - Small speed ups in TbTrackVolume and TbTracking.

! 2015-03-09 - Heinrich Schindler
 - Add TbDUTMonitor.
 - TbTracking: avoid new/delete of TbTrackVolume for each seed cluster.

! 2015-03-05 - Heinrich Schindler
 - TbClusterPlots: bugfix in cluster width plot.
 - TbTrackPlots: fix tracking efficiency plot titles.

! 2015-03-03 - Heinrich Schindler
 - Fix typo in previous commit.
 - Allow tracking algorithms to pick up existing track containers 
   (in case of multiple pattern recognition instances).

! 2015-03-02 - Heinrich Schindler
 - Tidy up TbAlignment (bug fix in technique 3, specify device to align and 
   reference plane by plane index instead of device ID).

! 2015-01-26 - Heinrich Schindler
 - TbAlignment: remove unused class members.
 - TbClustering: use scol instead of col in hitTouchesCluster. 

! 2015-01-24 - Heinrich Schindler
 - TbAlignment: pick up clusters in TbTrack::associatedClusters for technique 3.
 - TbHitMonitor: plot scol instead of col in hit map.

! 2015-01-21 - Heinrich Schindler
 - TbClustering: use pixelToPosition function of TbGeometrySvc to 
   compute the local cluster position.
 - Fix bug in TbClusterPlots pointed out by Panos.
 - Use TbHit::charge instead of ToT to compute the cluster charge.

! 2015-01-20 - Heinrich Schindler
 - Add algorithm TbClusterAssociator.

! 2014-12-30 - Heinrich Schindler
 - TbTrackVolume: remove unused functions and variables, 
   separate public and private members, tag associated clusters in TbTracking.

! 2014-12-28 - Heinrich Schindler
 - Follow removal of TbCluster::endCluster, vertexed, volumed.

! 2014-12-13 - Heinrich Schindler
 - TbAlignment: add alignment technique 3 (similar to technique 2 but without 
   requiring the device to align to be in the tracking. 

! 2014-12-13 - Heinrich Schindler
 - TbMillepede: use values instead of pointers for class members, 
   remove unused variables.

! 2014-12-12 - Heinrich Schindler
 - Follow renaming of TbHit::plane to TbHit::device.

! 2014-12-07 - Heinrich Schindler
 - TbClustering: add member m_used to keep track of which hits are clustered.

!========================= TbAlgorithms v2r1 2014-11-30 =======================

! 2014-11-30 - Heinrich Schindler
 - Convert TbMillepede to a Gaudi tool.

! 2014-11-20 - Heinrich Schindler
 - Convert TbClusterFinder to a Gaudi tool and move it to TbKernel.

! 2014-11-11 - Dan Saunders
 - Add TbVertexTracking.

! 2014-10-26 - Dan Saunders
 - Add efficiency calculation algorithm.

! 2014-10-08 - Tim Evans
 - Added simple algorithm TbCalibration which takes histograms from the 
   tracking and the hitmonitor and produces pixel masks and per plane
   time calibration constants

! 2014-09-26 - Dan Saunders
 - Added simple estimates of cluster position errors, and incorporated into 
   TbTrackFit.
 - Added optional new pattern recognition shape "sqDiabolo" (not yet default). 

! 2014-09-19 - Heinrich Schindler
 - Fix in TbAlignment technique 2 (use only clusters on device to align for
   chi2 calculation).

! 2014-08-26 - Christoph Hombach
 - Improvements to MILLEPEDE

!========================= TbAlgorithms v2r0 2014-08-18 =======================

! 2014-08-15 - Heinrich Schindler
 - Move spatial efficiency calculation in TbClusterPlots to external script. 
 - Remove unused class TbAlignmentPlots.
 - Fix compiler warning in TbAlignment (replace array by vector).

! 2014-08-04 - Heinrich Schindler
 - Sort clusters on track by z-position.

! 2014-08-03 - Angelo Di Canto
 - Minor update to TbAlignment (more configurable properties)

! 2014-08-02 - Dan Saunders
 - Fixed TbClustering inefficiency (now as good as previous slower version).

! 2014-08-02 - Heinrich Schindler
 - More residual plots for Paula.

! 2014-08-01 - Dan Saunders  
  - Updated TbClustering for speed/
  - Extra plots (pull distributions) to TbTrackPlots.

! 2014-08-01 - Christoph Hombach        
  - Added alignment monitoring plots to TbTrackPlots
  
! 2014-07-30 - Christoph Hombach
  - Update Millepede
  
! 2014-07-31 - Dan Saunders
  - Changed default ordering of cluster hits to increasing in TOA.
  - Added a few extra plots to TbTrackPlots.
  - Updated example.py to use run1024 (assuming eos is mounted). 

! 2014-07-29 - Heinrich Schindler
 - Add TbTriggerAssociator.

! 2014-07-21 - Christop Hombach
 - Added residual plots, which can be called after alignment procedure in TbAlignment

! 2014-07-21 - Tim Evans
 - Added trigger data packets

! 2014-07-21 - Angelo Di Canto
 - Added checks for masked planes in TbAlignment
 - Millepede renamed into TbMillepede
 
! 2014-07-19 - Heinrich Schindler
 - Add TbHeaderDecoder tool which reads and optionally dumps the Spidr header.
 - TbEventBuilder: retrieve device ID from header and check if it matches 
   with the alignment file.  
 - Move TbAlgorithm to TbKernel.
 - Millepede: clang-format and other cosmetic changes.

! 2014-07-18 Christoph Hombach
 - Removed DUT from Millepede fit -> Next step DUT separate 
 - Added shell script to run alignment loop

! 2014-07-18 - Heinrich Schindler
 - Use htime instead of global time for time windows.

! 2014-07-17 - Christoph Hombach
 - Working implementation of Millepede
 - Need to clean up code....

! 2014-07-17 - Tim Evans
 - Added extended timestamp functionality
 - Added option to manually set the header size

! 2014-07-14 - Dan Saunders
 - Added hit maps to TbTrackPlots. 
 - Few temporary additions to TbEventBuilder (all commented out), present for
   DQM testing.
 
! 2014-07-14 - Heinrich Schindler
 - Add new class TbAlgorithm (base class for other testbeam algorithms).
 
 ! 2014-07-14 - Dan Saunders
 - New plots to TbTrackPlots, and separated filling into separate functions
   for different categories of plot.
 - New option in TbTracking to ignore listed planes during tracking.

! 2014-07-09 - Heinrich Schindler
 - Speed improvements in TbClusterFinder.
 - TbClusterPlots: add configurable histogram parameters, 
   histogram labels.
 - TbTrackPlots: configurable histograms, add local residual plots. 

! 2014-07-08 - Hella Snoek
 - Added option to search for hits further away in TbClustering.
 - Added some printout statements to info printing the configurables.

! 2014-07-08 - Dan Saunders
 - Added safety checks for using TbClusterFinder with empty planes.

! 2014-07-08 - Heinrich Schindler
 - Adapt TbTupleWriter to new TES locations.
 - TbTracking: use Gaudi counter for nbr. of tracks; inline geomSvc; 
   initialize planeSearchOrder directly.
 - Follow renaming from "chip" to "plane" in TbHit and TbCluster.
 - Run clang-format.
 - Member functions to start consistently with lower case letter.
 - Separate hit monitor histograms for each plane.
 - Add one/two/three/four-pixel cluster ToT distributions to TbClusterPlots.

! 2014-07-07 - Tim Evans
 - Updated TbEventBuilder to use different TES locations for the different 
   chips.

! 2014-07-07 - Heinrich Schindler
 - Fix compiler warnings in TbAlignmentPlots and TbAlignment.
 - Update TbAlignment survey method to work with separate TES cluster locations.
 
! 2014-07-07 - Dan Saunders
 - Updated tracking and clustering to use different TES locations for hits and
   clusters on different chips. 

! 2014-07-04 - Dan Saunders
 - Tidied up TbTrackPlots and TbClusterPlots
 - Allowed for varying track sizes - minimum number of clusters set by 
   TbTracking().MinNClusters = 5. Priority is given to more complete tracks.

! 2014-07-03 - Angelo Di Canto 
 - Speed improvements in TbAlignment
 - Fixed bug in definition of alignment constants in TbAlignment

! 2014-07-01 - Angelo Di Canto 
 - Fixed few typos/bugs in TbAlignment

! 2014-07-01 - Dan Saunders
 - Tidied up TbTracking.

! 2014-07-01 - Heinrich Schindler
 - Add samples plot to TbClusterPlots.

! 2014-06-30 - Heinrich Schindler
 - TbClustering: remove monitoring plots (to be added to TbClusterPlots);
   merge some short functions; use STL sort.

! 2014-06-27 - Tim Evans
 - Added reading of the header classes to TbEventBuilder
 - Added TbRawFile class as a wrapper for input files to cleanup eventbuilder
 - Moved raw bank decoding into event definitions
 - Fixed read order dependence

! 2014-06-25 - Heinrich Schindler
 - Reduce finalise output of TbTupleWriter.
 - Delete alignment tracks in destructor of TbAlignment.
 - TbClustering: consistent definition of local and global coordinates.
 - Fix compiler warnings.

! 2014-06-19 - Heinrich Schindler
 - Add TbTupleWriter.

! 2014-06-16 - Dan Saunders
 - Speed improvements in TbTracking.

! 2014-06-06 - Heinrich Schindler
 - TbHitMonitor: fix binning in 2D hitmap.

!========================= TbAlgorithms v1r0 2014-05-30 =======================

! 2014-05-29 - Heinrich Schindler
 - Initialise geometry service pointers to NULL in constructor.
 - TbEventBuilder::finalize: empty cache, close files.
 - TbTracking: Get the number of planes from the geometry service.
 - TbAlignment: change return value of techniqueX from StatusCode to bool.
 - Follow renaming of chip_num to chip in TbCluster.
 - Mask (for now) unused variable warnings in TbTrackVolume.
 - Move TbTestMC and TbTrackFitter to Tb/TbSimulation.
 
! 2014-05-28 - Heinrich Schindler
 - TbTestMC: use Gaudi random number generators instead of TRandom3.
 - Call finalize functions of actual base classes.
 - Trivial formatting changes.

! 2014-05-26 - Heinrich Schindler
 - TbClustering: add new clusters directly to TbClusters container.
 - TbTracking: idem; also use on-demand booking of histograms.

! 2014-05-24 - Heinrich Schindler
 - Follow changes in event classes; cosmetic modifications.
 - Fix compiler warning in TbTrackFitter.
 - TbEventBuilder: allow processing of all files in a given directory.

! 2014-05-23 - Panagiotis Tsopelas
 - In TbAlignment.cpp, TbTrackFitter, TbTrackPlots : 
   Renamed "chi2" -> "chi2PerNdof" after change in TbTrack
   Changed  every call to a first state parameter (x0, y0, tx, ty)
   to a call through the "firstState" 

! 2014-05-21 - Heinrich Schindler
 - Fix signed/unsigned comparison compiler warnings.
 - Transfer ownership to TES ("put") directly after newing.
 - Remove unnecessary include statements.
 - Remove setters/getters from algorithms (use declareProperty instead). 
 - TbEventBuilder: change return type of retrieve function to bool 
   and make it private.
 - Run clang-format.
 - TbEventBuilder, TbHitMonitor: add header guards
 - Remove do-nothing finalize methods.

! 2014-05-15 - Dan Saunders
 - Added MC genorator and first version of tracking. This including a plot object
   and prototype track object (TbTrackVolume) used during the track finding.
   
 - Clustering also updated to consider hits separated diagonally.

! 2014-05-15 - Marco Clemencic
 - Fixed CMake configuration.

! 2014-05-06 - Panagiotis Tsopelas

 - Added TbTrackFitter. In this class random cluster positions are assigned to the planes
   and pseudoTbTracks are formed. Then the TbTrackFit::fit() method is called to fit the 
   TbTracks. Residuals are also calculated.

! 2014-04-29 - Dan Saunders
 - Updated TbClustering
 - Added a TbClusterPlots object - note: need to change local positions to global

! 2014-04-11 - Heinrich Schindler
 - TbEventBuilder: call stopRun after reaching end of file
 - Run clang-format to get consistent formatting
 - Change get to getIfExists
 - Remove do-nothing finalize method

! 2014-04-02 - Tim Evans
 - Added TbEventBuilder and TbHitMonitor classes

! 2014-03-31 - Heinrich Schindler
 - Initial import