NXmx: read data_scale_factor (cctbx#756)

New parameter as of nexusformat/definitions#1343. This is not full support of the parameter or of data_offset, but it's one of the use cases needed, namely reading a single gain value

Co-authored-by: Nicholas Devenish <[email protected]>

dependencies.yaml

@@ -74,7 +74,7 @@ run:
   - mrcfile
   - natsort
   - {{ pin_compatible('numpy') }} # [not bootstrap]
-  - nxmx
+  - nxmx >=0.0.4
   - orderedset
   - pint
   - pycbf # [prebuilt_cctbx]

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 | None = None,
 ) -> 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 and 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
+    Includes 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