Merge branch 'develop' into feature/aliciavr_XARAPUCA_offline_decoder

Author: bear-is-asleep

sbndcode/CMakeLists.txt

@@ -21,6 +21,7 @@ add_subdirectory(OpT0Finder)
 add_subdirectory(ShowerAna)
 add_subdirectory(Commissioning)
 add_subdirectory(Trigger)
+add_subdirectory(Timing)
 add_subdirectory(PTBAna)
 
 # subdirectory for gallery stuff

sbndcode/Decoders/PMT/CMakeLists.txt

@@ -1,17 +1,20 @@
-art_make(
-	MODULE_LIBRARIES 
+cet_build_plugin( SBNDPMTDecoder art::module
+    SOURCE SBNDPMTDecoder_module.cc	
+    LIBRARIES 
 	sbndaq_artdaq_core::sbndaq-artdaq-core_Overlays_SBND
 	sbnobj::SBND_Timing
-
+    lardata::Utilities
+    canvas::canvas
     lardataobj::RecoBase
-  
+    lardataobj::RawData
+    lardataobj::headers
     art_root_io::TFileService_service
     art_root_io::tfile_support
 	artdaq_core::artdaq-core_Data
-
     ROOT::Core
     ROOT::Tree
-
 )
 
 install_fhicl()
+install_headers()
+install_source()

sbndcode/Decoders/PMT/SBNDPMTDecoder_module.cc

@@ -13,36 +13,46 @@ pmtdecoder:
 
     # configure CAEN inputs 
     caen_fragment_name: [ "CAENV1730", "ContainerCAENV1730" ]
-    ignore_fragid: [8]     # boards to ignore for testing purposes, fragid==8 is the timing board, this is 0-indexed!
+    ignore_fragid: []     # boards to ignore for testing purposes, fragid==8 is the timing board, this is 0-indexed!
     nominal_length: 5000     # expected waveform length
+    raw_ts_correction: 367000 # ns, correction to the rawheader timestamp
 
     # configure SPEC TDC inputs 
     spectdc_product_name: "tdcdecoder" # used if the tdc decoder has been run 
-    spectdc_ftrig_ch: 3 # this should be the channel number of the spec tdc that stores the flash trigger 
-    spectdc_etrig_ch: 4 # this should be the channel number of the spec tdc that stores the event trigger
+    spectdc_ftrig_ch: 3 # channel number of the spec tdc that stores the flash trigger 
+    spectdc_etrig_ch: 4 # channel number of the spec tdc that stores the event trigger
 
-    # configure PTB inputs 
+    # configure PTB inputs; the HLT with the smallest trigger word will be used (within some range to the rawheader timestamp)
     ptb_product_name: "ptbdecoder"
-    ptb_etrig_trigword: 0x0000000000000000
+    ptb_etrig_trigword_min: 1   # minimum trigger word (in decimal) 
+    ptb_etrig_trigword_max: 100000 # maximum trigger word (in decimal)
     ptb_etrig_wordtype: 2
+    ptb_trig_raw_diff_max: 3000000 # the maximum allowed time difference in ns
 
     # configure output options
+    # use time difference between reference + CAEN used to determine rollover and/or weirdness
+    allowed_time_diff: 3000 # us!! not nanoseconds
     # configure the output data product instance names
     pmtInstanceName: "PMTChannels"
     ftrigInstanceName: "FTrigChannels"
+    timingInstanceName: "TimingChannels"
     output_ftrig_wvfm: true # whether or not to output the ftrig as an opdetwaveform (artroot data product)
+    output_timing_wvfm: true # whether or not to output the timing caen wvfms as an opdetwaveform (artroot data product)
+    ignore_timing_ch: [4,5,6,7,8,9,10,11,12,13,14] # only ch0=BES, ch1=RWM, ch2=ETRIG, ch3=MSUM, ch15=FTRIG
 
     # more detailed configurables
     n_maxflashes:    30 # maximum number of flashes anticipated, this is used for memory allocation
-    n_caenboards:    8  # number of caen boards; this is used for memory allocation
+    n_caenboards:    9 # number of caen boards; this is used for memory allocation
+                       # 1-8 = PMT caens, 9th = timing caen 
     threshold_ftrig: 16350 # the threshold for the flash trigger channel
 
     fragid_offset:   40960 # the offset to subtract to get single digit fragids; if use_set_map is true, should set this to 0
     hist_evt:        1  # the # of the event used to generate the histograms, 1st event by default 
 
-    # for when the fragIDs are mapped to the old configuration...
-    set_fragid_map: [3,7,5,9,11,13,15,17,19] # digitizers 0-8 are mapped to these fragids
+    # for when the fragIDs are mapped to the old configuration or you need to hardcode fragids...
+    ## to use this, must set `fragid_offset` to 0!!!
     use_set_map: false
+    set_fragid_map: [3,7,5,9,11,13,15,17,19] # use if `use_set_map` is true: digitizers 0-8 are mapped to these fragids
 
     # ordered in sets of 15 by increasing fragID
     # the PMT_to_Digitizers.txt file in the same directory is the reference for this
@@ -54,7 +64,8 @@ pmtdecoder:
              173,172,227,226,197,196,171,170,225,224,169,168,223,222,167, # digitizer 4
              195,194,221,220,165,164,219,218,193,192,163,162,217,216,166, # digitizer 5
              251,250,305,304,275,274,249,248,303,302,247,246,301,300,245, # digitizer 6
-             273,272,299,298,243,242,297,296,271,270,241,240,295,294,244] # digitizer 7
+             273,272,299,298,243,242,297,296,271,270,241,240,295,294,244, # digitizer 7
+             900,901,902,903,904,905,906,907,908,909,910,911,912,913,914] # digitizer 8 (TIMING CAEN)
 }
 
 END_PROLOG

sbndcode/Decoders/PMT/pmtdecoder.fcl

@@ -24,4 +24,4 @@ physics.reco2: [ pandora, pandoraTrack, pandoraShower, pandoraShowerSBN, pandora
 physics.analyzers.caloskim.G4producer: ""
 physics.analyzers.caloskim.SimChannelproducer: ""
 physics.caloskimana_tpconly: [ caloskim ]
-physics.end_paths: [stream1, caloskimana_tpconly]
+physics.end_paths: [stream1, caloskimana_tpconly]

sbndcode/JobConfigurations/standard/reco/reco2_data.fcl

@@ -0,0 +1,6 @@
+art_dictionary(DICTIONARY_LIBRARIES 
+lardataobj::RawData)
+
+install_headers()
+# install_fhicl()
+# install_source()

sbndcode/Timing/CMakeLists.txt

@@ -0,0 +1,43 @@
+////////////////////////////////////////////////////////////////////////
+//
+// An offline object to associate original CAEN1730 timing information to 
+// the decoded OpDetWaveforms to aid in downstream timing reconstruction
+// author: Lynn Tung
+// with inspiration taken from Tom Junk's offline ptb object
+//
+////////////////////////////////////////////////////////////////////////
+
+#ifndef  sbndtiming_H
+#define  sbndtiming_H
+
+#include <stdint.h>
+#include <vector>
+
+namespace raw {
+    class TimingReferenceInfo {
+      public:
+        TimingReferenceInfo() {}; // constructor
+        TimingReferenceInfo(uint16_t timingType, 
+                        uint16_t timingChannel) :
+        timingType(timingType), timingChannel(timingChannel) {};
+    
+        uint16_t timingType; // e.g. SPECTDC = 0; PTB HLT = 1; CAEN-only = 3
+        uint16_t timingChannel; // e.g. TDC ETRIG = 4; PTB BNB Beam+Light = 2
+    };
+
+  namespace pmt {
+    class BoardTimingInfo {
+      // Associate one of these to every opdetwaveform in the board/digitizer, one per trigger
+      public:
+        BoardTimingInfo() {}; // constructor
+        BoardTimingInfo(uint16_t postPercent, 
+                        std::vector<uint32_t> &triggerTimeTag) :
+        postPercent(postPercent), triggerTimeTag(triggerTimeTag) {};
+
+        uint16_t              postPercent; // # 0-100, represents a percentage
+        std::vector<uint32_t> triggerTimeTag; // ns
+    };
+  }
+}
+
+#endif

sbndcode/Timing/SBNDRawTimingObj.h

@@ -0,0 +1,13 @@
+//File: classes.h
+//Brief: Include directives needed to generate header(s) for the raw::pmt::sbndpmt data product.
+//Author: Lynn Tung
+
+//ART includes
+#include "canvas/Persistency/Common/Wrapper.h"
+#include "canvas/Persistency/Common/Assns.h"
+
+//local includes
+#include "sbndcode/Timing/SBNDRawTimingObj.h"
+
+//larsoft includes
+#include "lardataobj/RawData/OpDetWaveform.h"

sbndcode/Timing/classes.h

@@ -0,0 +1,26 @@
+<!-- 
+  File: classes_def.xml
+  Brief: Data product definitions for pmt timing data products.
+  Author: Lynn Tung
+-->
+
+<lcgdict>
+  <class name="raw::TimingReferenceInfo">
+  </class>
+  <class name="std::vector<raw::TimingReferenceInfo>"/>
+  <class name="art::Wrapper<raw::TimingReferenceInfo>"/>
+  <class name="art::Wrapper<std::vector<raw::TimingReferenceInfo> >"/>
+
+  <class name="raw::pmt::BoardTimingInfo">
+  </class>
+  <class name="std::vector<raw::pmt::BoardTimingInfo>"/>
+  <class name="art::Wrapper<std::vector<raw::pmt::BoardTimingInfo>>"/>
+
+  <class name="std::pair<art::Ptr<raw::pmt::BoardTimingInfo>, art::Ptr<raw::OpDetWaveform>>"/>
+  <class name="std::pair<art::Ptr<raw::OpDetWaveform>, art::Ptr<raw::pmt::BoardTimingInfo>>"/>
+  <class name="art::Assns<raw::pmt::BoardTimingInfo, raw::OpDetWaveform, void>"/>
+  <class name="art::Assns<raw::OpDetWaveform, raw::pmt::BoardTimingInfo, void>"/>
+  <class name="art::Wrapper<art::Assns<raw::pmt::BoardTimingInfo, raw::OpDetWaveform, void>>"/>
+  <class name="art::Wrapper<art::Assns<raw::OpDetWaveform, raw::pmt::BoardTimingInfo, void>>"/>
+
+</lcgdict>

sbndcode/Timing/classes_def.xml

@@ -20,17 +20,21 @@ function(params, anode, field, n, rms_cuts=[])
     // For MicroBooNE, channel groups is a 2D list.  Each element is
     // one group of channels which should be considered together for
     // coherent noise filtering.
-    groups: [std.range(   0 + n * 5638 + g*32,    0 + n * 5638 + (g+1)*32 - 1) for g in std.range(0,149)] +
-            [std.range(4806 + n * 5638 + g*32, 4806 + n * 5638 + (g+1)*32 - 1) for g in std.range(0,25)] ,
+    // 5638 is the number of channels in a single APA, (1984*2 + 1670), including the 6 channel gap.
+    // 4806 is the number of channels for both induction + half of real collection wires + 6 channel gap
+    groups: [std.range(   0 + n * 5638 + g*32,    0 + n * 5638 + (g+1)*32 - 1) for g in std.range(0,150)] +
+            [std.range(4806 + n * 5638 + g*32, 4806 + n * 5638 + (g+1)*32 - 1) for g in std.range(0,26)] ,
 
 
     // Externally determined "bad" channels.
     //
     // Dead channels: 3232:3263 (inclusive) (East V).   4160:4191 (East Y)
+    // Jumpered region: 4800:4805 (inclusive, East Y), 10438:10443 (inclusive, West Y)
+    // No response: 546, 607, 8574
     // Shorted channels:  7169 (West U), 8378 (West V).
     // There are four physically missing wires ( = bad channels) due to combs, in the center of each 1/2 APA.
     // They are 4374 and 5231 (East Y), 10012 and 10869 (West Y).
-    // So in total, there are 76 bad channels.
+    // So in total, there are 88 bad channels.
     // 
     //bad: [],
     bad: [546, 607] + std.range(3232, 3263) + std.range(4160, 4191) + [4374, 4800, 4801, 4802, 4803, 4804, 4805, 5060, 5231, 5636, 5637, 7169, 8378, 8574, 10012, 10869, 10438, 10439, 10440, 10441, 10442, 10443],
@@ -53,15 +57,15 @@ function(params, anode, field, n, rms_cuts=[])
         response_offset: 0.0,  // ticks?
         pad_window_front: 10,  // ticks?
         pad_window_back: 10,  // ticks?
-        decon_limit: 0.02,
+        decon_limit: 0.02, // (SignalProtection, same as upper_decon_limit (default 0.02))
         decon_limit1: 0.09,
-        adc_limit: 15,
+        adc_limit: 10,
         roi_min_max_ratio: 0.8, // default 0.8
         min_rms_cut: 1.0,  // units???
         max_rms_cut: 30.0,  // units???
 
         // parameter used to make "rcrc" spectrum
-        rcrc: 1.1 * wc.millisecond, // 1.1 for collection, 3.3 for induction
+        rcrc: 0.5 * wc.millisecond, // 1.1 for collection, 3.3 for induction
         rc_layers: 1, // default 2
 
         // parameters used to make "config" spectrum