Merge branch 'develop' into feature/aliciavr_XARAPUCA_offline_decoder-to-production

Author: bear-is-asleep

sbndcode/Calibration/DQM/FilterChoppy_module.cc

@@ -105,8 +105,13 @@ namespace filt{
     // exit if the data isn't present
     if (!timestamp_handle.isValid()) {
       std::cerr << "Error: missing timestamps with producer (" << "daq" << ")" << std::endl;
-      return false;
+      return true; // don't want to filter out events missing TPC data (e.g. CRT-only runs)
     }
+    if (timestamp_handle->size() == 0) {
+      std::cerr << "Error: missing timestamps with producer (" << "daq" << ")" << std::endl;
+      return true; // don't want to filter out events missing TPC data (e.g. CRT-only runs)
+    }
+    
     art::fill_ptr_vector(raw_timestamps_handle, timestamp_handle);
 
     // collect TS

sbndcode/Decoders/XARAPUCA/SBNDXARAPUCADecoder_module.cc

@@ -1,4 +1,5 @@
 #include "xarapucadecoder.fcl"
+#include "spectdc_decoder_sbnd.fcl"
 
 process_name: XARAPUCADecoder
 
@@ -21,6 +22,7 @@ outputs: {
 physics: {
 
     producers: {
+        tdcdecoder: @local::spec_tdc_decoder_sbnd
         xarapucadecoder: @local::xarapucadecoder    
     }
 
@@ -29,7 +31,7 @@ physics: {
     analyzers:{}
 
 
-    reco: [xarapucadecoder]
+    reco: [tdcdecoder, xarapucadecoder]
 
 
     # Defines the output stream, there could be more than one if using filters.

sbndcode/Decoders/XARAPUCA/run_xarapucadecoder.fcl

@@ -14,15 +14,22 @@ xarapucadecoder:
     fragment_id_offset: 41216                                   # Offset to be applied to the fragment IDs (0xA100).
     board_id_list: [7, 13, 16, 19]                              # Slots where the boards are installed.
     # - Timing configuration.
+    timing_priority: 0                                          # 0 SPEC-TDC ETT, 1 CAEN-only.
     ns_per_sample: 16                                           # Nanoseconds per sample.
+    # - SPEC-TDC access configuration
+    spectdc_product_name:  "tdcdecoder"                         # Name for getting SPEC-TDC Decoder products.
+    spectdc_ftrig_ch: 3                                         # Channel assigned to flash triggers.
+    spectdc_etrig_ch: 4                                         # Channel assigned to event triggers.
 
     # OUTPUT configuration:
     # - Output data product instance name.
-    product_instance_name: "XARAPUCAChannels"                   # Name for the instance product created.
-    store_debug_waveforms: 0                                   # Number of waveforms to store (0: none, -1: all, n: first n waveforms).
+    waveforms_instance_name: "XARAPUCAChannels"                 # Name for the instance product containing the raw decoded waveforms.
+    timing_instance_name: ""                                    # Name for the instance product containing the timing reference information.
+    store_debug_waveforms: 0                                    # Number of waveforms to store (0: none, -1: all, n: first n waveforms).
     # - Debug options.
     debug_all: false                                            # (De)activates all debug options.
-    debug_handle: false                                         # (De)activates art::Handle data printing.
+    debug_tdc_handle: false                                     # (De)activates SPEC-TDC art::Handle information printing.
+    debug_fragments_handle: false                               # (De)activates V1740B CAEN fragments art::Handle information printing.
     debug_timing: false                                         # (De)activates timing data printing. 
     debug_buffer: false                                         # (De)activates buffer status printing.
     debug_waveforms: false                                      # (De)activates waveforms decoding printing.

sbndcode/Decoders/XARAPUCA/xarapucadecoder.fcl

@@ -32,7 +32,7 @@ sbnd_data_badchannels_west_plane0_shorted: [ 7169 ]
 sbnd_data_badchannels_west_plane1_shorted: [ 8378 ]
 
 #No response from channels
-sbnd_data_badchannels_no_response: [ 546, 607, 8574 ]
+sbnd_data_badchannels_no_response: [ 546, 607, 2781, 7167, 8574, 8395, 11147 ]
 
 #noisy channels
 sbnd_data_badchannels_noisy: [ 5060, 5636, 5637 ]

sbndcode/Utilities/badchannels_sbnd.fcl

@@ -20,24 +20,32 @@ 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.
-    // 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)] ,
+    // 5638 is the number of channels in a single APA, (1984*2 + 1670), 
+    // including the 6 channel gap.
+    // The induction planes have to types of ch grouping (due to FEMB), 
+    // one where the grouping is 32 channels wide and one where it is 128 channels wide.
+    // The collection planes are grouped by 64. 
 
+    groups: [std.range(   0 + n * 5638 + g*32 ,    0 + n * 5638 + (g+1)*32  - 1) for g in std.range(0,26)] + # first section of u 
+            [std.range( 832 + n * 5638 + g*128,  832 + n * 5638 + (g+1)*128 - 1) for g in std.range(0,9)] +  # second section of u
+            [std.range(1984 + n * 5638 + g*128, 1984 + n * 5638 + (g+1)*128 - 1) for g in std.range(0,9)] +  # first section of v
+            [std.range(3136 + n * 5638 + g*32 , 3136 + n * 5638 + (g+1)*32  - 1) for g in std.range(0,26)] + # second section of v 
+            [std.range(3974 + n * 5638 + g*64 , 3974 + n * 5638 + (g+1)*64  - 1) for g in std.range(0,13)] + # first half of w
+            [std.range(4806 + n * 5638 + g*64 , 4806 + n * 5638 + (g+1)*64  - 1) for g in std.range(0,13)] , # second half of w
 
     // 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).
+    // Unresponsive channels: 546, 607, 2781, 7167, 8574, 8395, 11147
     // 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 88 bad channels.
+    // So in total, there are 76 bad channels + 12 from jumpered region + 4 missing 
     // 
     //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],
+    bad: [546, 607, 2781] + std.range(3232, 3263) + std.range(4160, 4191) + [4374, 4800, 4801, 4802, 4803, 4804, 4805, 5060, 5231, 5636, 5637, 7167, 7169, 8378, 8395, 8574, 10012, 10869, 10438, 10439, 10440, 10441, 10442, 10443, 11147],
 
     // Overide defaults for specific channels.  If an info is
     // mentioned for a particular channel in multiple objects in this

sbndcode/WireCell/cfg/pgrapher/experiment/sbnd/chndb-base.jsonnet

@@ -20,22 +20,32 @@ 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.
+    // The induction planes have to types of ch grouping (due to FEMB), 
+    // one where the grouping is 32 channels wide and one where it is 128 channels wide.
+    // The collection planes are grouped by 64. 
 
+    groups: [std.range(   0 + n * 5638 + g*32 ,    0 + n * 5638 + (g+1)*32  - 1) for g in std.range(0,26)] + # first section of u 
+            [std.range( 832 + n * 5638 + g*128,  832 + n * 5638 + (g+1)*128 - 1) for g in std.range(0,9)] +  # second section of u
+            [std.range(1984 + n * 5638 + g*128, 1984 + n * 5638 + (g+1)*128 - 1) for g in std.range(0,9)] +  # first section of v
+            [std.range(3136 + n * 5638 + g*32 , 3136 + n * 5638 + (g+1)*32  - 1) for g in std.range(0,26)] + # second section of v 
+            [std.range(3974 + n * 5638 + g*64 , 3974 + n * 5638 + (g+1)*64  - 1) for g in std.range(0,13)] + # first half of w
+            [std.range(4806 + n * 5638 + g*64 , 4806 + n * 5638 + (g+1)*64  - 1) for g in std.range(0,13)] , # second half of w
 
     // 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).
+    // Unresponsive channels: 546, 607, 2781, 7167, 8574, 8395, 11147
     // 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 88 bad channels.
+    // So in total, there are 76 bad channels + 12 from jumpered region + 4 missing 
     // 
     //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],
+    bad: [546, 607, 2781] + std.range(3232, 3263) + std.range(4160, 4191) + [4374, 4800, 4801, 4802, 4803, 4804, 4805, 5060, 5231, 5636, 5637, 7167, 7169, 8378, 8395, 8574, 10012, 10869, 10438, 10439, 10440, 10441, 10442, 10443, 11147],
 
     // Overide defaults for specific channels.  If an info is
     // mentioned for a particular channel in multiple objects in this

sbndcode/WireCell/cfg/pgrapher/experiment/sbnd/chndb-perfect.jsonnet

@@ -61,7 +61,7 @@ function(params, anode, chndbobj, n, name='', dft=default_dft)
           wc.tn(single),
         ],
         grouped_filters: [
-          // wc.tn(grouped),
+          wc.tn(grouped),
         ],
         channel_status_filters: [
         ],

sbndcode/WireCell/cfg/pgrapher/experiment/sbnd/nf.jsonnet

@@ -123,7 +123,7 @@ base {
         // The "absolute" time (ie, relative to trigger time?) that the lower edge
         // of final readout tick #0 should correspond to.  This is a
         // "fixed" notion.
-        local tick0_time = -200*wc.us,
+        local tick0_time = -205*wc.us, // updated in January 2025, front porch in data = 410 ticks
 
         // Open the ductor's gate a bit early.
         local response_time_offset = $.det.response_plane / $.lar.drift_speed,

sbndcode/WireCell/cfg/pgrapher/experiment/sbnd/params.jsonnet

@@ -75,7 +75,7 @@ local wf(name, data={}) = {
 [
   lf('ROI_tight_lf', { tau: 0.0185 * wc.megahertz }),  // 0.02 
   lf('ROI_tighter_lf', { tau: 0.145 * wc.megahertz }),  // 0.1 
-  lf('ROI_loose_lf', { tau: 0.00175 * wc.megahertz }),  // 0.0025 
+  lf('ROI_loose_lf', { tau: 0.006 * wc.megahertz }),  // updated from 0.00175 for data teardrop removal
 
   hf('Gaus_tight'),
   hf('Gaus_wide', { sigma: 0.10 * wc.megahertz }),