Merge pull request #158 from DUNE/feature_nd_config

update the ndlar yaml configuration

yamls/ndlar_flow/reco/charge/CalibHitBuilderMC.yaml

@@ -0,0 +1,34 @@
+classname: CalibHitBuilder # reco/charge/calib_hit_builder.py
+path: proto_nd_flow.reco.charge.calib_prompt_hits
+requires:
+  - 'charge/events'
+  - 'charge/raw_hits'
+  - 'charge/packets'
+  - 'combined/t0'
+  - name: 'charge/packets_index'
+    path: ['charge/packets']
+    index_only: True
+  - name: 'packet_frac_backtrack'
+    path: ['charge/packets','mc_truth/packet_fraction']
+  - name: 'packet_seg_backtrack'
+    path: ['charge/packets','mc_truth/segments']
+
+params:
+  # inputs
+  events_dset_name: 'charge/events'
+  packets_dset_name: 'charge/packets'
+  packets_index_name: 'charge/packets_index'
+  raw_hits_dset_name: 'charge/raw_hits'
+  t0_dset_name: 'combined/t0'
+  max_contrib_segments: 10
+
+  # output
+  calib_hits_dset_name: 'charge/calib_prompt_hits'
+  mc_hit_frac_dset_name: 'mc_truth/calib_prompt_hit_backtrack'
+
+  # configuration parameters
+  pedestal_mv: 580.0
+  vref_mv: 1568.0 #M0-like: 1300 #2x2: 1568.0
+  vcm_mv: 478.1 #M0-like:288 #478.0 #2x2: 478.1
+  adc_counts: 256
+  gain: 4.522 #datasheet: 4 #measurement(?): 4.522

yamls/ndlar_flow/reco/charge/CalibNoiseFilter.yaml

@@ -0,0 +1,40 @@
+# This class implements several filters to remove irregularities in data from LArPix bugs or configuration issues.
+# References on these issues can be found here:
+# - https://docs.dunescience.org/cgi-bin/private/RetrieveFile?docid=32080&filename=2x2_Charge_Readout_Features_July2024_Data.pdf&version=1
+#
+# Further information on the implementation of the filters can be found here:
+# - https://indico.fnal.gov/event/65995/contributions/298818/attachments/181069/248231/Aug%2027%2C%202024_%20sim_calib%20update%20on%20post-hit%20filtering.pdf
+# - https://indico.fnal.gov/event/66399/contributions/300891/attachments/182225/250160/adc%20droop%20and%20data%20features%20-%20sim_calib%2010_01_2024.pdf
+#
+
+
+classname: CalibNoiseFilter # reco/charge/calib_noise_filter
+path: proto_nd_flow.reco.charge.calib_noise_filter
+requires:
+  - 'charge/events'
+  - 'charge/calib_prompt_hits'
+  - name: 'hits_frac_backtrack'
+    path: ['charge/calib_prompt_hits','mc_truth/calib_prompt_hit_backtrack']
+
+params:
+  # inputs
+  events_dset_name: 'charge/events'
+  hits_name: 'charge/calib_prompt_hits'
+  filter_function_names: ['hot_pixel_filter','correlated_post_trigger_filter', 'low_current_filter'] #which filter functions to apply (this is an ordered list, but all filters will be "OR'd")
+
+  #params specific to each cut
+  low_current_filter__threshold: 6.0 #
+  hot_pixel_filter__max_n_hits: 35 
+    #hot_pixel_filter__max_n_hits: 
+    # - maximum number of hits on a channel in single event before filtering all hits from channel
+    # - 35 chosen by hand scanning events. in a 200us event, 35 hits corresponds to ~50% of the maximum data rate from a LArPix channel
+    #
+    # low_current_filter__threshold:
+    # - minimum Q for filter
+    # - 6 chosen from hand scanning, and to be ~1ke- above the mean 2x2 thresholds. This is currently crude, and this should be implemented in the future as a per-channel threshold.
+
+
+  # outputs
+  calib_hits_dset_name: 'charge/calib_final_hits'
+  mc_hit_frac_dset_name: 'mc_truth/calib_final_hit_backtrack'
+

yamls/ndlar_flow/reco/charge/EventBuilder.yaml

@@ -0,0 +1,12 @@
+classname: EventBuilder
+path: proto_nd_flow.reco.charge.event_builder
+requires:
+  - 'charge/raw_hits'
+  - 'charge/ext_trigs'
+params:
+  # inputs
+  hits_dset_name: 'charge/raw_hits'
+  ext_trigs_dset_name: 'charge/ext_trigs'
+
+  # output
+  events_dset_name: 'charge/events'

yamls/ndlar_flow/reco/charge/ExternalTriggerFinder.yaml

@@ -0,0 +1,17 @@
+classname: ExternalTriggerFinder
+path: proto_nd_flow.reco.charge.external_trigger_finder
+requires:
+  - 'charge/packets'
+  - name: 'charge/packets_corr_ts'
+    path: ['charge/packets', 'charge/packets_corr_ts']
+params:
+  # inputs
+  packets_dset_name: 'charge/packets'
+  ts_dset_name: 'charge/packets_corr_ts'
+
+  # output
+  ext_trigs_dset_name: 'charge/ext_trigs'
+
+  # configuration parameters
+  pacman_trigger_enabled: True
+  pacman_trigger_word_filter: 2

yamls/ndlar_flow/reco/charge/RawHitBuilder.yaml

@@ -0,0 +1,13 @@
+classname: RawHitBuilder # reco/charge/raw_hit_builder.py
+path: proto_nd_flow.reco.charge.raw_hit_builder
+requires:
+  - 'charge/packets'
+  - name: 'charge/packets_corr_ts'
+    path: ['charge/packets', 'charge/packets_corr_ts']
+params:
+  # inputs
+  packets_dset_name: 'charge/packets'
+  ts_dset_name: 'charge/packets_corr_ts'
+
+  # output
+  hits_dset_name: 'charge/raw_hits'

yamls/ndlar_flow/reco/charge/TimestampCorrectorMC.yaml

@@ -0,0 +1,86 @@
+classname: TimestampCorrector
+path: proto_nd_flow.reco.charge.timestamp_corrector
+requires:
+  - 'charge/packets'
+  - name: 'charge/packets_index'
+    path: 'charge/packets'
+    index_only: True
+params:
+  # input
+  packets_dset_name: 'charge/packets'
+
+  # output
+  ts_dset_name: 'charge/packets_corr_ts' # new dataset
+
+  # configuration parameters
+  correction:
+    1: [0., 0.]
+    2: [0., 0.]
+    3: [0., 0.]
+    4: [0., 0.]
+    5: [0., 0.]
+    6: [0., 0.]
+    7: [0., 0.]
+    8: [0., 0.]
+    9: [0., 0.]
+    10: [0., 0.]
+    11: [0., 0.]
+    12: [0., 0.]
+    13: [0., 0.]
+    14: [0., 0.]
+    15: [0., 0.]
+    16: [0., 0.]
+    17: [0., 0.]
+    18: [0., 0.]
+    19: [0., 0.]
+    20: [0., 0.]
+    21: [0., 0.]
+    22: [0., 0.]
+    23: [0., 0.]
+    24: [0., 0.]
+    25: [0., 0.]
+    26: [0., 0.]
+    27: [0., 0.]
+    28: [0., 0.]
+    29: [0., 0.]
+    30: [0., 0.]
+    31: [0., 0.]
+    32: [0., 0.]
+    33: [0., 0.]
+    34: [0., 0.]
+    35: [0., 0.]
+    36: [0., 0.]
+    37: [0., 0.]
+    38: [0., 0.]
+    39: [0., 0.]
+    40: [0., 0.]
+    41: [0., 0.]
+    42: [0., 0.]
+    43: [0., 0.]
+    44: [0., 0.]
+    45: [0., 0.]
+    46: [0., 0.]
+    47: [0., 0.]
+    48: [0., 0.]
+    49: [0., 0.]
+    50: [0., 0.]
+    51: [0., 0.]
+    52: [0., 0.]
+    53: [0., 0.]
+    54: [0., 0.]
+    55: [0., 0.]
+    56: [0., 0.]
+    57: [0., 0.]
+    58: [0., 0.]
+    59: [0., 0.]
+    60: [0., 0.]
+    61: [0., 0.]
+    62: [0., 0.]
+    63: [0., 0.]
+    64: [0., 0.]
+    65: [0., 0.]
+    66: [0., 0.]
+    67: [0., 0.]
+    68: [0., 0.]
+    69: [0., 0.]
+    70: [0., 0.]

yamls/ndlar_flow/resources/LArData.yaml

@@ -0,0 +1,17 @@
+classname: LArData
+path: proto_nd_flow.resources.lar_data
+params:
+  path: 'lar_info'
+  # electron_lifetime_file: 'data/module0_flow/ElecLifetimeFit_Module0.npz'
+  # download link: https://portal.nersc.gov/project/dune/data/Module0/electronLifetime/ElecLifetimeFit_Module0.root
+  electron_lifetime: 2200 # us
+  #: Recombination :math:`\alpha` constant for the Box model
+  box_alpha: 0.93
+  #: Recombination :math:`\beta` value for the Box model in :math:`(kV/cm)(g/cm^2)/MeV`
+  box_beta: 0.207 #0.3 (MeV/cm)^-1 * 1.383 (g/cm^3)* 0.5 (kV/cm), R. Acciarri et al JINST 8 (2013) P08005
+  #: Recombination :math:`A_b` value for the Birks Model
+  birks_Ab: 0.800
+  #: Recombination :math:`k_b` value for the Birks Model in :math:`(kV/cm)(g/cm^2)/MeV`
+  birks_kb: 0.0486 # g/cm2/MeV Amoruso, et al NIM A 523 (2004) 275
+  #: Average energy expended per ion pair in LAr in :math:`eV` from Phys. Rev. A 10, 1452
+  W_ion: 23.6

yamls/ndlar_flow/workflows/charge/charge_event_building.yaml → yamls/ndlar_flow/workflows/charge/charge_event_building_mc.yaml

@@ -8,9 +8,9 @@ flow:
 
 
 resources:
-  - !include yamls/ndlar_flow/resources/RunData.yaml
+  - !include yamls/ndlar_flow/resources/RunDataMC.yaml
 
 
 raw_event_generator: # groups time-sorted data packets from larpix datalog files
-  !include yamls/ndlar_flow/reco/charge/RawEventGenerator.yaml
+  !include yamls/ndlar_flow/reco/charge/RawEventGeneratorMC.yaml
 

yamls/ndlar_flow/workflows/charge/charge_event_reconstruction.yaml → yamls/ndlar_flow/workflows/charge/charge_event_reconstruction_mc.yaml

@@ -8,8 +8,8 @@ flow:
 
 
 resources:
-  - !include yamls/ndlar_flow/resources/RunData.yaml
-  - !include yamls/ndlar_flow/resources/Geometry.yaml
+  - !include yamls/ndlar_flow/resources/RunDataMC.yaml
+  - !include yamls/ndlar_flow/resources/GeometryMC.yaml
 
 
 raw_events:
@@ -21,17 +21,17 @@ raw_events:
 
 
 timestamp_corrector:
-  !include yamls/proto_nd_flow/reco/charge/TimestampCorrector.yaml
+  !include yamls/ndlar_flow/reco/charge/TimestampCorrectorMC.yaml
 
 
 ext_trig_finder:
-  !include yamls/proto_nd_flow/reco/charge/ExternalTriggerFinder.yaml
+  !include yamls/ndlar_flow/reco/charge/ExternalTriggerFinder.yaml
 
 
 raw_hit_builder:
-  !include yamls/proto_nd_flow/reco/charge/RawHitBuilder.yaml
+  !include yamls/ndlar_flow/reco/charge/RawHitBuilder.yaml
 
 
 event_builder:
-  !include yamls/proto_nd_flow/reco/charge/EventBuilder.yaml
+  !include yamls/ndlar_flow/reco/charge/EventBuilder.yaml
 

yamls/ndlar_flow/workflows/charge/final_calibration_mc.yaml

@@ -0,0 +1,24 @@
+# Generates the mid-level event built data for charge data (i.e. hits and
+# external triggers)
+
+flow:
+  source: raw_events
+  stages: [calib_noise_filter]
+  drop: []
+
+
+resources:
+  - !include yamls/ndlar_flow/resources/RunDataMC.yaml
+  - !include yamls/ndlar_flow/resources/LArData.yaml
+  - !include yamls/ndlar_flow/resources/GeometryMC.yaml
+
+raw_events:
+  classname: H5FlowDatasetLoopGenerator
+  path: h5flow.modules
+  dset_name: 'charge/raw_events'
+  params:
+    chunk_size: 32
+
+calib_noise_filter:
+  !include yamls/ndlar_flow/reco/charge/CalibNoiseFilter.yaml
+

yamls/ndlar_flow/workflows/charge/prompt_calibration.yaml → yamls/ndlar_flow/workflows/charge/prompt_calibration_mc.yaml

@@ -8,9 +8,9 @@ flow:
 
 
 resources:
-  - !include yamls/ndlar_flow/resources/RunData.yaml
-  - !include yamls/proto_nd_flow/resources/LArData.yaml
-  - !include yamls/ndlar_flow/resources/Geometry.yaml
+  - !include yamls/ndlar_flow/resources/RunDataMC.yaml
+  - !include yamls/ndlar_flow/resources/LArData.yaml
+  - !include yamls/ndlar_flow/resources/GeometryMC.yaml
 
 
 raw_events:
@@ -21,5 +21,5 @@ raw_events:
     chunk_size: 128
 
 calib_hit_builder:
-  !include yamls/proto_nd_flow/reco/charge/CalibHitBuilder.yaml
+  !include yamls/ndlar_flow/reco/charge/CalibHitBuilderMC.yaml
 

yamls/ndlar_flow/workflows/combined/combined_reconstruction.yaml → yamls/ndlar_flow/workflows/combined/combined_reconstruction_mc.yaml

@@ -14,8 +14,8 @@ events:
     chunk_size: 32
 
 resources:
-  - !include yamls/ndlar_flow/resources/RunData.yaml
-  - !include yamls/ndlar_flow/resources/Geometry.yaml
+  - !include yamls/ndlar_flow/resources/RunDataMC.yaml
+  - !include yamls/ndlar_flow/resources/GeometryMC.yaml
   - !include yamls/proto_nd_flow/resources/LArData.yaml
 #  - !include yamls/proto_nd_flow/resources/DisabledChannels.yaml