FormatSMVCetaD_TUI.py

"""Format class to recognise images from a ThermoFisher Ceta D detector operated
in rolling shutter mode that have been converted to 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


class FormatSMVCetaD_TUI(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)
        if header.get("BEAMLINE") == "CETAD_TUI":
            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,
        )


if __name__ == "__main__":
    import sys

    for arg in sys.argv[1:]:
        print(FormatSMVCetaD_TUI.understand(arg))