Support for CAGRA (type 14 GEB format) & (optionally) Grand Raiden at RCNP#110

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csullivan wants to merge 115 commits intopcbend:mainfrom

csullivan:master

Commits on Feb 26, 2016

Adding new TDetector system for parsing
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Commits on Mar 2, 2016

Built out TArgonne(Hit) classes. The raw event
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Commits on Mar 3, 2016

Added ANL kFileType and kDetectorSystem
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(incremental) kFileType::ANL -> kFileType::ANL_RAW
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(incremental) fixed enum miss match in TRawEventSource.
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ANL event building is now fully functional.
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(incremental) Set more members in TArgonneHit.
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Merge branch 'ANL'
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Commits on Mar 4, 2016

(incremental) added clover histograms
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Commits on May 10, 2016

Merge from upstream, updated ANL GEB classes to match new format. Mainly BuildHits is passed the raw_data reference
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Merge branch 'master' of https://github.com/pcbend/GRUTinizer
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Merge branch 'master' of https://github.com/pcbend/GRUTinizer
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Added RCNP Tree source class, needs implementation
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Commits on May 12, 2016

Added templated TTreeSource class for reading preprocessed events from a ROOT TTree
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Made default constructor of TTreeSource private
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Built out TTreeSource. Calling GetEvent effectively calls TTree::GetEntry, creating a NEW event in memory each time.
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Added ability for ROOT file to be a source via TTreeSource. Added functionality to
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Commits on May 19, 2016

Added necessary files for builiding TGrandRaiden data from a root file source.
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Removed trailing whitespace
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Successfully linking against GRAnalyzer data structure RCNPEvent.
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Commits on May 20, 2016

Added TTreeSource<RCNPEvent> which now moves data through and into TGrandRaiden hits where unpacking can be done.
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Commits on May 23, 2016

Added some members to TGrandRaidenHit to test the GR data stream
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Commits on May 24, 2016

Added fake timestamps to GR data to test event correlation. Bug fix in TRawEvent.
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Commits on May 26, 2016

Added histos for all CAGRA boards and channels
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Commits on May 27, 2016

Completely restructured Argonne/CAGRA interface. Instead of
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Updated channel map file to include crystals _and_ segments. The positions now seem to be working.
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Merge pull request #1 from CAGRA-GrandRaiden/RCNPSource
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Added calibrated energy spectra. The calibrations work!
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TCAGRA has been replaced by TCagra due to loss in pinky strength
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Commits on Jun 1, 2016

Bug introduced when refactoring into TANLEvent. Forgot to add check to
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Merging RCNPSource into upstream master. This branch will replace csullivan/master
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Commits on Jun 2, 2016

List of changes:
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Commits on Jun 3, 2016

Commits on Jun 6, 2016

Added source description and status to TTreeSource, data throughput is not a measure of totale filesize in this case,
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Changed initialization of fEvent in TTreeSource
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Now link against new libGRAnalyzer.so for dynamic calling of GR event builder
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Added Grand Raiden analyzer submodule for linking against RCNP routines
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Removed commented lines in makefile
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Added lines to clean rule in makefile
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Updated submodule and granalyzer.cxx example
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Commits on Jun 7, 2016

Added support for RCNPEvent's in ThreadsafeQueue, and also adjusted the granalyzer example
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Added new source for raw RCNP BLD files. GRUTinizer calls GRAnalyzer which prepares RCNPEvents
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Commits on Jun 8, 2016

Now spawn std::async thread which returns a future that can be used to test if the GRAnalyzer is done.
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Added global atomic_int that is set by StoppableThread StopAllClean function, which tells the RCNP
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Added global atomic_int that is set by StoppableThread StopAllClean function, which tells the RCNP
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Added -R option to indicate if the raw RCNP root tree should be saved while analyzing RCNP data.
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Commits on Jun 9, 2016

Added setup script to create the necessary links to the GRAnalyzer git submodule
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Commits on Jun 10, 2016

Changed rcnp gitmodule address
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Commits on Jun 11, 2016

Added line to source thisgrut.sh
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Commits on Jun 12, 2016

Isolated RCNP code a bit so that if you have the correct submodule (GRAnalyzer),
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Removed unnecessary script
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Commits on Jun 14, 2016

Merge remote branch 'origin/RCNPUnified' into RCNPUnified
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Temporarily changing the submodule path for work at RCNP
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Added missing rcnpchannel calibration file to analyzer
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Merge branch 'RCNPUnified' of nsclgw1.nscl.msu.edu:~/ceclub/sullivan/cagragr/GRUTinizer into RCNPUnified
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Commits on Jun 15, 2016

Timestamps bath was absolute, and added <functional> to TCaeser.h
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Commits on Jun 17, 2016

Adding simple program for reading ANL GEB data
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Merge branch 'RCNPUnified' of nsclgw1.nscl.msu.edu:~/ceclub/sullivan/cagragr/GRUTinizer into RCNPUnified
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Changed gitmodules url for submodule to GitHub ssh
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Added functionality for ANL firmware v1.8 (June 2015). July 2015 additions will be necessary.
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Commits on Jun 18, 2016

Major: Added void* fDataPtr to TRawEvent. This allows for TRawEvent to hold user information other than what is in
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Merge branch 'bug_GrandRaiden' into RCNPUnified
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Commits on Jun 19, 2016

Now RCNPEvent is carried through to the rootfile in TGrandRaidenHit.
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Commits on Jun 21, 2016

Improved makefile to check the hist.def file and also added RCNP=1 to makefile. Also added runtime checkt that the hist.def file has not changed from when it was first compiled
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Commits on Jun 24, 2016

Added MPIEventLoop submodule for parallel analysis. Also added fake timestamps back, added histo cut on gr_x.
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Commits on Jun 25, 2016

Fixed error in makefile, and added onlin.bld check to TRawEventSource::EventSource to start RCNP ana in online mode
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Implemented new CFDv18. Untested
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Fixed compile time issues with name mixups between LEDv18 and CFDv18.
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CFDv1.8 seems to be working, but need more rigourous checks, mainly with data
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Updated DigitizerHits histogram. New firmware looks pretty good. Need test with detector and calibration.
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Commits on Jun 26, 2016

Now export the discriminator time to TCagraHit. Need to export previous time too for time difference between events.
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Started to implement pole zero and asymptotic baseline corrections. Needs more work.
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Removed fake timestamp routine as we now have the myriad clock in GR
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Added fast-forward flag and functionality, which will fast-forward to the end of online raw input files.
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Added TGlobRawFile which looks in a directory for new files and attaches to them as they appears.
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Updated GRUTinizer options to utilize TGlobRawFile.
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Commits on Jun 29, 2016

Fully added TGlobRawFile, and removed stalled source functionality as it was preventing the sorting
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Commits on Jun 30, 2016

Many updates:
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Commits on Jul 1, 2016

Commits on Jul 11, 2016

Changed MPIEventLoop submodule remote address to point to CAGRAGR organization
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Added RCNP histos file
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Added Getters for Pre/Post rise sum to TCagraHit, and added new histo loop CAGRA.cxx.
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Commits on Jul 13, 2016

Fixed bug with the saving of TChannel calibration information into the rootfile.
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Error fix in last commit.
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Commits on Jul 15, 2016

Added fix to tcut_tab.py so that Save Cut works when the det_type is not registered. Also added many focal plane corrections.
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Commits on Jul 18, 2016

Commits on Jul 19, 2016

Second pull from upstream merged. 7/19/16
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added logon script and changed rint logon script path in grutrc
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Added delay to StoppableThread::StopAll after shutting down the RCNP thread, to avoid
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Merge branch 'gr_terminate' into merge_upstream
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Removed RCNP online.bld file
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Merge pull request #3 from CAGRA-GrandRaiden/merge_upstream
Chris Sullivan
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Merge branch 'merge_upstream' into style
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Commits on Aug 5, 2016

Updated LaBr hits class in TGrandRaidenHits.
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Merge branch 'labr_hit_update' into merge_upstream
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Merge branch 'master' of https://github.com/pcbend/GRUTinizer into merge_upstream
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Added comment in makefile to indicate how to compile and link against RCNP libGRAnalyzer.so and associated TDetector systems.
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Removed git submodules for merging with upstream.
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Reverted README for merge with upstream.
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Merge pull request #4 from CAGRA-GrandRaiden/merge_upstream
Chris Sullivan
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Commits on Aug 16, 2016

[Pull request #110]
Chris Sullivan
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[Pull request #110]
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[Pull request #110]
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Commits on Aug 22, 2016

[Pull request #110]
Chris Sullivan
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[Pull request #110]
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[Pull request #110]
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Merge from upstream/pcbend to resolve Pull request #110 merge conflict.
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[Pull request #110]
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Commits on Sep 14, 2016

Pole-zero and baseline vectors were missing from TChannel::Copy
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