Source code for dials.algorithms.spot_prediction.reflection_predictor

import logging

logger = logging.getLogger(__name__)

from libtbx.phil import parse

from dials.util import Sorry

# The phil parameters
phil_scope = parse(
    """

  prediction {

    d_min = None
      .type = float
      .help = "The maximum resolution limit"

    d_max = None
      .type = float
      .help = "The minimum resolution limit"

    margin = 1
      .type = int
      .help = "The margin to use to scan varying prediction"

    force_static = False
      .type = bool
      .help = "For scan-varying prediction force scan-static prediction"

    padding = 1.0
      .type = float(value_min=0)
      .help = "The padding in degrees"
  }
"""
)


class ReflectionPredictor:
    """
    A reflection predictor that takes a number of experiments and does the proper
    prediction for each type of experiment.
    """

    def __init__(
        self, experiment, dmin=None, dmax=None, margin=1, force_static=False, padding=0
    ):
        """
        Initialise a predictor for each experiment.

        :param experiment: The experiment to predict for
        :param dmin: The maximum resolution
        :param dmax: The minimum resolution
        :param margin: The margin of hkl to predict
        :param force_static: force scan varying prediction to be static
        """
        from dxtbx.imageset import ImageSequence

        from dials.algorithms.spot_prediction import (
            ScanStaticReflectionPredictor,
            ScanVaryingReflectionPredictor,
            StillsReflectionPredictor,
        )
        from dials.array_family import flex

        class Predictor:
            def __init__(self, name, func):
                self.name = name
                self.func = func

            def __call__(self):
                result = self.func()
                if dmax is not None:
                    assert dmax > 0
                    result.compute_d_single(experiment)
                    mask = result["d"] > dmax
                    result.del_selected(mask)
                return result

        # Check prediction to maximum resolution is possible
        wl = experiment.beam.get_wavelength()
        if dmin is not None and dmin < 0.5 * wl:
            raise Sorry(
                f"Prediction at d_min of {dmin} is not possible with wavelength {wl}"
            )

        # Select the predictor class
        if isinstance(experiment.imageset, ImageSequence):
            xl_nsp = experiment.crystal.num_scan_points
            bm_nsp = experiment.beam.num_scan_points
            gn_nsp = experiment.goniometer.num_scan_points
            nim = experiment.scan.get_num_images()

            sv_compatible = (xl_nsp == nim + 1) or (bm_nsp == nim + 1)
            if not force_static and sv_compatible:
                predictor = ScanVaryingReflectionPredictor(
                    experiment, dmin=dmin, margin=margin, padding=padding
                )

                if bm_nsp == 0 and gn_nsp == 0:
                    # Only varying crystal
                    A = [
                        experiment.crystal.get_A_at_scan_point(i)
                        for i in range(experiment.crystal.num_scan_points)
                    ]
                    predict = Predictor(
                        "scan varying crystal prediction",
                        lambda: predictor.for_ub(flex.mat3_double(A)),
                    )

                else:
                    # Any allowed model may vary
                    if xl_nsp == nim + 1:
                        A = [
                            experiment.crystal.get_A_at_scan_point(i)
                            for i in range(experiment.crystal.num_scan_points)
                        ]
                    else:
                        A = [experiment.crystal.get_A() for i in range(nim + 1)]
                    if bm_nsp == nim + 1:
                        s0 = [
                            experiment.beam.get_s0_at_scan_point(i)
                            for i in range(experiment.beam.num_scan_points)
                        ]
                    else:
                        s0 = [experiment.beam.get_s0() for i in range(nim + 1)]
                    if gn_nsp == nim + 1:
                        S = [
                            experiment.goniometer.get_setting_rotation_at_scan_point(i)
                            for i in range(experiment.goniometer.num_scan_points)
                        ]
                    else:
                        S = [
                            experiment.goniometer.get_setting_rotation()
                            for i in range(nim + 1)
                        ]
                    predict = Predictor(
                        "scan varying model prediction",
                        lambda: predictor.for_varying_models(
                            flex.mat3_double(A),
                            flex.vec3_double(s0),
                            flex.mat3_double(S),
                        ),
                    )
            else:
                predictor = ScanStaticReflectionPredictor(
                    experiment, dmin=dmin, padding=padding
                )

                # Choose index generation method based on number of images
                # https://github.com/dials/dials/issues/585
                if experiment.scan.get_num_images() > 50:
                    predict_method = predictor.for_ub_old_index_generator
                else:
                    predict_method = predictor.for_ub

                predict = Predictor(
                    "scan static prediction",
                    lambda: predict_method(experiment.crystal.get_A()),
                )
        else:
            predictor = StillsReflectionPredictor(experiment, dmin=dmin)

            predict = Predictor(
                "stills prediction",
                lambda: predictor.for_ub(experiment.crystal.get_A()),
            )

        # Create and add the predictor class
        self._predict = predict

    def __call__(self):
        """
        Predict all the observable reflections.

        :return: A reflection table
        """
        logger.info("Prediction type: %s", self._predict.name)
        table = self._predict()
        logger.info("Predicted %d reflections", len(table))
        return table

    def predictor(self, index):
        """
        Get the predictor for the given experiment index.

        :param index: The experiment index
        :return: The predictor
        """
        return self._predict[index]