From 4ad0ce5f876fac4c42b43aef7aa23f2c4fdb8ace Mon Sep 17 00:00:00 2001
From: David Waterman <dagewa@users.noreply.github.com>
Date: Wed, 11 Oct 2023 15:20:52 +0100
Subject: [PATCH] Electron probe tweaks (#661)

* Do not overwrite Probe unless requested. Fixes #2515
* Use electron Probe in two ED format classes that were missed before
---
 newsfragments/661.bugfix         | 1 +
 newsfragments/661.feature        | 1 +
 src/dxtbx/format/FormatNXmxED.py | 2 ++
 src/dxtbx/format/FormatSER.py    | 2 ++
 src/dxtbx/model/beam.py          | 3 ++-
 5 files changed, 8 insertions(+), 1 deletion(-)
 create mode 100644 newsfragments/661.bugfix
 create mode 100644 newsfragments/661.feature

diff --git a/newsfragments/661.bugfix b/newsfragments/661.bugfix
new file mode 100644
index 000000000..2cfc35640
--- /dev/null
+++ b/newsfragments/661.bugfix
@@ -0,0 +1 @@
+The beam probe is no longer reset if any geometrical override is provided at import.
diff --git a/newsfragments/661.feature b/newsfragments/661.feature
new file mode 100644
index 000000000..19b0f32b5
--- /dev/null
+++ b/newsfragments/661.feature
@@ -0,0 +1 @@
+Set the beam probe to ``electron`` in both ``FormatNXmxED`` and ``FormatSER``.
diff --git a/src/dxtbx/format/FormatNXmxED.py b/src/dxtbx/format/FormatNXmxED.py
index c02cc63f6..ad70a20c8 100644
--- a/src/dxtbx/format/FormatNXmxED.py
+++ b/src/dxtbx/format/FormatNXmxED.py
@@ -9,6 +9,7 @@
 from dxtbx.format.FormatNXmx import FormatNXmx
 from dxtbx.masking import mask_untrusted_circle, mask_untrusted_polygon
 from dxtbx.model import SimplePxMmStrategy
+from dxtbx.model.beam import Probe
 
 
 class FormatNXmxED(FormatNXmx):
@@ -65,6 +66,7 @@ def _beam(self, index=None):
 
         beam = super()._beam()
         beam.set_polarization_fraction(0.5)
+        beam.set_probe(Probe.electron)
 
         return beam
 
diff --git a/src/dxtbx/format/FormatSER.py b/src/dxtbx/format/FormatSER.py
index d04357f6f..7265323b6 100644
--- a/src/dxtbx/format/FormatSER.py
+++ b/src/dxtbx/format/FormatSER.py
@@ -22,6 +22,7 @@
 from dxtbx import IncorrectFormatError
 from dxtbx.format.Format import Format
 from dxtbx.format.FormatMultiImage import FormatMultiImage
+from dxtbx.model.beam import Probe
 
 
 # The read_emi and _parseEntry_emi functions are taken from openNCEM project
@@ -334,6 +335,7 @@ def cal_wavelength(V0):
             wavelength=wavelength,
             polarization=(0, 1, 0),
             polarization_fraction=0.5,
+            probe=Probe.electron,
         )
 
     def _get_raw_data(self, index):
diff --git a/src/dxtbx/model/beam.py b/src/dxtbx/model/beam.py
index 799d9be32..f16e1fb51 100644
--- a/src/dxtbx/model/beam.py
+++ b/src/dxtbx/model/beam.py
@@ -122,7 +122,8 @@ def from_phil(
             beam.set_flux(params.beam.flux)
         if params.beam.sample_to_source_distance is not None:
             beam.set_sample_to_source_distance(params.beam.sample_to_source_distance)
-        beam.set_probe(Beam.get_probe_from_name(params.beam.probe))
+        if params.beam.probe != "x-ray":
+            beam.set_probe(Beam.get_probe_from_name(params.beam.probe))
 
         return beam