Hit indices

src/dxtbx/format/FormatXTC.py

@@ -3,6 +3,7 @@
 import functools
 import sys
 import time
+from itertools import groupby
 
 import numpy as np
 import serialtbx.detector.xtc
@@ -32,11 +33,15 @@
     psana = None
 
 locator_str = """
+  hits_file = None
+    .type = str
+    .help = path to a file where each line is 2 numbers separated by a space, a run index, and an event index in the XTC stream
   experiment = None
     .type = str
     .help = Experiment identifier, e.g. mfxo1916
   run = None
-    .type = ints
+    .type = int
+    .multiple = True
     .help = Run number or a list of runs to process
   mode = idx
     .type = str
@@ -147,6 +152,7 @@
 
         self._ds = FormatXTC._get_datasource(image_file, self.params)
         self._evr = None
+        self._load_hit_indices()
         self.populate_events()
 
         self._cached_psana_detectors = {}
@@ -162,6 +168,17 @@
         else:
             self._spectrum_pedestal = None
 
+    def _load_hit_indices(self):
+        self._hit_inds = None
+        if self.params.hits_file is not None:
+            assert self.params.mode == "idx"
+            hits = np.loadtxt(self.params.hits_file, int)
+            hits = list(map(tuple, hits))
+            key = lambda x: x[0]
+            gb = groupby(sorted(hits, key=key), key=key)
+            # dictionary where key is run number, and vals are indices of hits
+            self._hit_inds = {r:[ind for _,ind in group] for r,group in gb}
+
     @staticmethod
     def understand(image_file):
         """Extracts the datasource and detector_address from the image_file and then feeds it to PSANA
@@ -229,18 +246,27 @@
         self.run_mapping = {}
 
         if self.params.mode == "idx":
-            for run in self._psana_runs.values():
+            for run_num, run in self._psana_runs.items():
                 times = run.times()
+                if self._hit_inds is not None and run_num not in self._hit_inds:
+                    continue
+                if self._hit_inds is not None and run_num in self._hit_inds:
+                    temp = []
+                    for i_hit in self._hit_inds[run_num]:
+                        temp.append( times[i_hit] )
+                    times = tuple(temp)
                 if (
                     self.params.filter.required_present_codes
                     or self.params.filter.required_absent_codes
                 ) and self.params.filter.pre_filter:
                     times = [t for t in times if self.filter_event(run.event(t))]
-                self.run_mapping[run.run()] = (
+
+                self.run_mapping[run_num] = (
                     len(self.times),
                     len(self.times) + len(times),
                     run,
                 )
+
                 self.times.extend(times)
             self.n_images = len(self.times)