From 1646a43fbf243a477a72b8c8a80848a12ded6f34 Mon Sep 17 00:00:00 2001
From: davidmcdonagh <davidnmcdonagh@gmail.com>
Date: Mon, 4 Mar 2024 13:25:00 +0000
Subject: [PATCH] Added filter to TOFSpotFinder._post_process to filter
 reflections outside of the time of flight range.

---
 newsfragments/XXX.misc                      |  1 +
 src/dials/algorithms/centroid/__init__.py   |  2 +-
 src/dials/algorithms/spot_finding/finder.py | 14 ++++++++++++++
 3 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 newsfragments/XXX.misc

diff --git a/newsfragments/XXX.misc b/newsfragments/XXX.misc
new file mode 100644
index 0000000000..e2a302055d
--- /dev/null
+++ b/newsfragments/XXX.misc
@@ -0,0 +1 @@
+Add filter in `TOFSpotFinder._post_process` to remove any reflections outside of the time of flight range
diff --git a/src/dials/algorithms/centroid/__init__.py b/src/dials/algorithms/centroid/__init__.py
index d650f9232b..f78ce90bab 100644
--- a/src/dials/algorithms/centroid/__init__.py
+++ b/src/dials/algorithms/centroid/__init__.py
@@ -79,7 +79,7 @@ def tof_centroid_px_to_mm_panel(panel, scan, position, variance, sd_error):
 
     pixel_size = panel.get_pixel_size()
     tof = scan.get_property("time_of_flight")  # (usec)
-    frames = [i + 1 for i in range(len(tof))]
+    frames = list(range(len(tof)))
     frame_to_tof = frame_to_tof_interpolator(frames, tof)
 
     if isinstance(position, tuple):
diff --git a/src/dials/algorithms/spot_finding/finder.py b/src/dials/algorithms/spot_finding/finder.py
index 1db461537a..93ead73dd2 100644
--- a/src/dials/algorithms/spot_finding/finder.py
+++ b/src/dials/algorithms/spot_finding/finder.py
@@ -930,6 +930,20 @@ def _post_process(self, reflections):
 
         reflections = self._correct_centroid_tof(reflections)
 
+        # Filter any reflections outside of the tof range
+        for i, expt in enumerate(self.experiments):
+            _, _, frame = reflections["xyzobs.px.value"].parts()
+            tof_frame_range = (0, len(expt.scan.get_property("time_of_flight")) - 1)
+            if "imageset_id" in reflections:
+                sel_expt = reflections["imageset_id"] == i
+            else:
+                sel_expt = reflections["id"] == i
+
+            sel = sel_expt & (
+                (frame > tof_frame_range[1]) | (frame < tof_frame_range[0])
+            )
+            reflections = reflections.select(~sel)
+
         n_rows = reflections.nrows()
         panel_numbers = flex.size_t(reflections["panel"])
         reflections["L1"] = flex.double(n_rows)