NXmx: read data_scale_factor

newsfragments/756.feature

@@ -0,0 +1 @@
+Add support for reading the detector gain for nexus files

src/dxtbx/format/FormatNXmx.py

@@ -68,10 +68,13 @@ def _start(self):
  nxinstrument = nxentry.instruments[0]
  nxdetector = nxinstrument.detectors[0]
  nxbeam = nxinstrument.beams[0]
+ nxdata = nxmx_obj.entries[0].data[0]
  self._goniometer_model = dxtbx.nexus.get_dxtbx_goniometer(nxsample)
  self._beam_factory = dxtbx.nexus.CachedWavelengthBeamFactory(nxbeam)
  wavelength = self._beam_factory.make_beam(index=0).get_wavelength()
- self._detector_model = dxtbx.nexus.get_dxtbx_detector(nxdetector, wavelength)
+ self._detector_model = dxtbx.nexus.get_dxtbx_detector(
+ nxdetector, wavelength, nxdata
+ )
 
  # if the detector is between the sample and the source, and perpendicular
  # to the beam, then invert the distance vector, as this is probably wrong
@@ -86,7 +89,6 @@ def _start(self):
  if self._scan_model:
  self._num_images = len(self._scan_model)
  else:
- nxdata = nxmx_obj.entries[0].data[0]
  if nxdata.signal:
  data = nxdata[nxdata.signal]
  else:

src/dxtbx/nexus/__init__.py

@@ -245,6 +245,7 @@ def get_dxtbx_scan(
 def get_dxtbx_detector(
  nxdetector: nxmx.NXdetector,
  wavelength: float,
+ nxdata: nxmx.NXdata,
 ) -> dxtbx.model.Detector:
  """Generate a dxtbx detector model from an NXdetector and NXbeam.
 
@@ -461,6 +462,9 @@ def equipment_component_key(dependency):
  p.set_mu(mu)
  p.set_px_mm_strategy(px_mm)
 
+ if nxdata.data_scale_factor and not nxdata.data_scale_factor.shape:
+ p.set_gain(1 / nxdata.data_scale_factor)
+
  return detector
 
 

tests/nexus/test_mpccd_nexus.py

@@ -0,0 +1,24 @@
+from __future__ import annotations
+
+import dxtbx
+
+
+def test_mpccd_nexus_gain(dials_data):
+ """
+ Tests SACLA MPCCD image from CXI.DB 221
+ Includs parameter data_scale_factor, which accounts for a gain of 10
+ """
+
+ try:
+ h5path = (
+ dials_data("image_examples", pathlib=True)
+ / "SACLA-MPCCD-run197287-0-nexus.h5"
+ )
+ except Exception as e:
+ print(type(e), str(e))
+ raise
+ img = dxtbx.load(h5path)
+
+ d = img.get_detector()
+
+ assert d[0].get_gain() == 10