FormatSMVADSCCetaD

newsfragments/770.feature

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+Add ``FormatSMVADSCCetaD`` to allow easier processing of 3DED images from the Ceta-D detector, which have been converted to SMV.

src/dxtbx/format/FormatADSCSMVCetaD.py

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+"""Format class to recognise images from a ThermoFisher Ceta D detector that
+have been converted to an ADSC-like SMV with useful metadata. We
+want to override the beam model to produce an unpolarised beam and to set the
+detector gain to something sensible."""
+
+from __future__ import annotations
+
+import os
+
+from dxtbx.format.FormatSMVADSC import FormatSMVADSC
+from dxtbx.model.beam import Probe
+
+
+# We have to inherit from FormatSMVADSC rather than FormatSMV, so that we can
+# activate this class with an enivronment variable in cases where the
+# BEAMLINE or DETECTOR_SN are not set to anything specific (for example files
+# that lie and set BEAMLINE=ALS831).
+class FormatSMVADSCCetaD(FormatSMVADSC):
+    @staticmethod
+    def understand(image_file):
+        # Allow this class to override FormatSMVADSC with an environment variable
+        if "FORCE_SMV_AS_CETAD" in os.environ:
+            return True
+
+        # Otherwise recognise specific instruments from the header
+        size, header = FormatSMVADSC.get_smv_header(image_file)
+        check = header.get("BEAMLINE", "") + header.get("DETECTOR_SN", "")
+        if "CETAD" in check:
+            return True
+
+        return False
+
+    def _detector(self):
+        distance = float(self._header_dictionary["DISTANCE"])
+        beam_x = float(self._header_dictionary["BEAM_CENTER_X"])
+        beam_y = float(self._header_dictionary["BEAM_CENTER_Y"])
+        pixel_size = float(self._header_dictionary["PIXEL_SIZE"])
+        image_size = (
+            float(self._header_dictionary["SIZE1"]),
+            float(self._header_dictionary["SIZE2"]),
+        )
+        # Ceta has gain of > 26 and saturates at about 8000.0 for binning=1
+        # according to Thermo Fisher
+        binning = {"1x1": 1, "2x2": 2}.get(self._header_dictionary.get("BIN"), 1)
+        gain = float(self._header_dictionary.get("GAIN", 26.0))
+        saturation = 8000 * binning**2
+        trusted_range = (-1000, saturation)
+        pedestal = float(self._header_dictionary.get("IMAGE_PEDESTAL", 0))
+
+        return self._detector_factory.simple(
+            "PAD",
+            distance,
+            (beam_y, beam_x),
+            "+x",
+            "-y",
+            (pixel_size, pixel_size),
+            image_size,
+            trusted_range,
+            [],
+            gain=gain,
+            pedestal=pedestal,
+        )
+
+    def _beam(self):
+        """Return a simple model for an unpolarised beam."""
+
+        wavelength = float(self._header_dictionary["WAVELENGTH"])
+        return self._beam_factory.make_polarized_beam(
+            sample_to_source=(0.0, 0.0, 1.0),
+            wavelength=wavelength,
+            polarization=(0, 1, 0),
+            polarization_fraction=0.5,
+            probe=Probe.electron,
+        )