Add disabled channels filter

src/proto_nd_flow/reco/charge/raw_event_generator.py

@@ -401,7 +401,10 @@ def next(self):
         else:
             mc_assn = None
 
-        mask = (block['valid_parity'].astype(bool) & (block['packet_type'] == 0))  # data packets
+        mask_disabled_channels = np.array(
+            [(p[['io_group', 'io_channel', 'chip_id', 'channel_id']]) not in resources['Geometry'].disabled_channels for p in block]
+            , dtype=bool)
+        mask = (block['valid_parity'].astype(bool) & (block['packet_type'] == 0) & mask_disabled_channels)  # data packets
         mask = mask | (block['packet_type'] == 4)  # timestamp packets
         mask = mask | (block['packet_type'] == 7)  # external trigger packets
         mask = mask | (block['packet_type'] == 6)  # sync packets

src/proto_nd_flow/resources/geometry.py

@@ -4,6 +4,7 @@
 import os
 import warnings
 import yaml
+import json
 
 from h5flow.core import H5FlowResource
 from h5flow.core import resources
@@ -89,6 +90,7 @@ class Geometry(H5FlowResource):
     default_det_geometry_file = '-'
     default_crs_geometry_file = ['-']
     default_lrs_geometry_file = '-'
+    default_disabled_channels_file = '-'
     default_beam_direction    = 'z'
     default_drift_direction   = 'x'
     default_crs_geometry_to_module = [0]
@@ -102,6 +104,7 @@ def __init__(self, **params):
         self.charge_only = params.get('charge_only', self.default_charge_only) 
         self.n_io_channels_per_tile = params.get('n_io_channels_per_tile', self.default_n_io_channels_per_tile)
         self.crs_geometry_files = params.get('crs_geometry_files', self.default_crs_geometry_file)
+        self.disabled_channels_file = params.get('disabled_channels_file', self.default_disabled_channels_file)
         self.crs_geometry_to_module = params.get('crs_geometry_to_module', self.default_crs_geometry_to_module)
         self.det_geometry_file = params.get('det_geometry_file', self.default_det_geometry_file)
         self.lrs_geometry_file = params.get('lrs_geometry_file', self.default_lrs_geometry_file)
@@ -111,6 +114,7 @@ def __init__(self, **params):
         self._lar_detector_bounds = None # min and max xyz coordinates for full LAr detector
         self._max_drift_distance = None # max drift distance in each LArTPC (2 TPCs per module)
         self._module_RO_bounds = None # min and max xyz coordinates for each pixel LArTPC module
+        self._disabled_channels = None
 
     def init(self, source_name):
         super(Geometry, self).init(source_name)
@@ -155,6 +159,10 @@ def init(self, source_name):
             write_lut(self.data_manager, self.path, self.pixel_coordinates_2D, 'pixel_coordinates_2D')
             write_lut(self.data_manager, self.path, self.tile_id, 'tile_id')
 
+            self.data_manager.create_dset(self.path+'/disabled_channels', dtype=self.disabled_channels.dtype)
+            disabled_channels_slice = self.data_manager.reserve_data(self.path+'/disabled_channels', len(self.disabled_channels))
+            self.data_manager.write_data(self.path+'/disabled_channels',  disabled_channels_slice, self.disabled_channels)
+
             if not self.charge_only:
                 self.data_manager.set_attrs(self.path, lrs_geometry_file=self.lrs_geometry_file)
                 write_lut(self.data_manager, self.path, self.det_rel_pos, 'det_rel_pos')
@@ -171,6 +179,7 @@ def init(self, source_name):
             self._max_drift_distance = self.data['max_drift_distance']
             self._module_RO_bounds = self.data['module_RO_bounds']
             self._pixel_pitch = self.data['pixel_pitch']
+            self._disabled_channels = self.data_manager.get_dset(self.path+'/disabled_channels')
 
             self._anode_drift_coordinate = read_lut(self.data_manager, self.path, 'anode_drift_coordinate')
             self._drift_dir = read_lut(self.data_manager, self.path, 'drift_dir')
@@ -422,6 +431,9 @@ def _get_module_RO_bounds(self):
 
         self._module_RO_bounds = np.array(self._module_RO_bounds)
 
+    @property
+    def disabled_channels(self):
+        return self._disabled_channels
 
     @staticmethod
     def _rotate_pixel(pixel_pos, tile_orientation):
@@ -850,3 +862,36 @@ def _load_charge_geometry(self):
         #    self._cathode_thickness = abs(anode_to_cathode - self.max_drift_distance) * 2.0
         #else: 
         #    self._cathode_thickness = 0.0
+
+        self._load_disabled_channels()
+
+    def _load_disabled_channels(self):
+
+        # Parses the disabled channels file into a structured array.
+        # The first iteration of the file is a json dictionary where the keys are strings 
+        # '<io_group>-<io_channel>-<chip_id>' and the values are lists of the channel_ids
+
+        disabled_channels_dtype = np.dtype([
+        ('io_group', 'u8'),
+        ('io_channel', 'u8'),
+        ('chip_id', 'u8'),
+        ('channel_id', 'u8')
+        ])
+
+        disabled_channels_list = []
+        if self.disabled_channels_file == '-':
+            self._disabled_channels = np.array([], dtype = disabled_channels_dtype)
+            return
+
+        with open(self.disabled_channels_file, 'r') as f:
+            disabled_channels_json = json.load(f)
+
+        for key in disabled_channels_json:
+
+            io_group, io_channel, chip_id = key.split('-')
+
+            for channel_id in disabled_channels_json[key]:
+
+                disabled_channels_list.append((int(io_group), int(io_channel), int(chip_id), int(channel_id)))
+
+        self._disabled_channels = np.array(disabled_channels_list, dtype = disabled_channels_dtype)

yamls/proto_nd_flow/resources/GeometryMC.yaml

@@ -7,6 +7,7 @@ params:
                        'data/proto_nd_flow/multi_tile_layout-2.5.16_v3.yaml']
   crs_geometry_to_module: [0,0,1,0]
   lrs_geometry_file: 'data/proto_nd_flow/light_module_desc-4.0.0.yaml'
+  disabled_channels_file: 'data/proto_nd_flow/disabled_channels_2x2.json'
   beam_direction: 'z'
   drift_direction: 'x'
   network_agnostic: true

yamls/proto_nd_flow/workflows/charge/charge_event_building_mc.yaml

@@ -9,7 +9,7 @@ flow:
 
 resources:
   - !include yamls/proto_nd_flow/resources/RunDataMC.yaml
-
+  - !include yamls/proto_nd_flow/resources/GeometryMC.yaml
 
 raw_event_generator: # groups time-sorted data packets from larpix datalog files
   !include yamls/proto_nd_flow/reco/charge/RawEventGeneratorMC.yaml