Source code for dxtbx.model.goniometer

import math

import pycbf

import libtbx.phil
from scitbx.array_family import flex

from dxtbx_model_ext import Goniometer, KappaGoniometer, MultiAxisGoniometer

__all__ = [
    "Goniometer",
    "GoniometerFactory",
    "KappaGoniometer",
    "MultiAxisGoniometer",
    "goniometer_phil_scope",
]

goniometer_phil_scope = libtbx.phil.parse(
    """
  goniometer
    .expert_level = 1
    .short_caption = "Goniometer overrides"
  {

    axis = None
      .type = floats(size=3)
      .help = "Override the axis for a single axis goniometer. Equivalent to"
              "providing a single 3D vector to 'axes'."
      .short_caption="Goniometer axis"

    axes = None
      .type = floats
      .help = "Override the goniometer axes. Axes must be provided in the"
              "order crystal-to-goniometer, i.e. for a Kappa goniometer"
              "phi,kappa,omega"
      .short_caption="Goniometer axes"

    angles = None
      .type = floats
      .help = "Override the goniometer angles. Axes must be provided in the"
              "order crystal-to-goniometer, i.e. for a Kappa goniometer"
              "phi,kappa,omega"
      .short_caption = "Goniometer angles"

    names = None
      .type = str
      .help = "The multi axis goniometer axis names"
      .short_caption = "The axis names"

    scan_axis = None
      .type = int
      .help = "The scan axis"
      .short_caption = "The scan axis"

    fixed_rotation = None
      .type = floats(size=9)
      .help = "Override the fixed rotation matrix"
      .short_caption = "Fixed rotation matrix"

    setting_rotation = None
      .type = floats(size=9)
      .help = "Override the setting rotation matrix"
      .short_caption = "Setting rotation matrix"

    invert_rotation_axis = False
      .type = bool
      .help = "Invert the rotation axis"
      .short_caption = "Invert rotation axis"

  }
"""
)


[docs]class GoniometerFactory: """A factory class for goniometer objects, which will encapsulate some standard goniometer designs to make it a little easier to get started with all of this - for cases when we are not using a CBF. When we have a CBF just use that factory method and everything will be peachy."""
[docs] @staticmethod def single_axis_goniometer_from_phil(params, reference=None): """ Generate or overwrite a single axis goniometer """ # Check the axis parameter and copy from axes if required if params.goniometer.axis is None: params.goniometer.axis = params.goniometer.axes if params.goniometer.axis is not None and len(params.goniometer.axis) != 3: raise RuntimeError("Single axis goniometer requires 3 axis values") # Check the angles parameter if params.goniometer.angles is not None: raise RuntimeError("Single axis goniometer requires angles == None") # Check the names parameter if params.goniometer.names is not None: raise RuntimeError("Single axis goniometer requires names == None") # Init the gonionmeter if reference is None: goniometer = Goniometer() else: goniometer = reference # Set the parameters if params.goniometer.axis is not None: goniometer.set_rotation_axis_datum(params.goniometer.axis) if params.goniometer.fixed_rotation is not None: goniometer.set_fixed_rotation(params.goniometer.fixed_rotation) if params.goniometer.setting_rotation is not None: goniometer.set_setting_rotation(params.goniometer.setting_rotation) if params.goniometer.invert_rotation_axis is True: rotation_axis = goniometer.get_rotation_axis_datum() goniometer.set_rotation_axis_datum([-x for x in rotation_axis]) return goniometer
[docs] @staticmethod def multi_axis_goniometer_from_phil(params, reference=None): # Check the axes parameter if params.goniometer.axes is not None: if len(params.goniometer.axes) % 3: raise RuntimeError( "Number of values for axes parameter must be multiple of 3." ) # Check the fixed rotation if params.goniometer.fixed_rotation is not None: raise RuntimeError("Multi-axis goniometer requires fixed_rotation == None") # Check the setting rotation if params.goniometer.setting_rotation is not None: raise RuntimeError( "Multi-axis goniometer requires setting_rotation == None" ) # Check the input if reference is None: if params.goniometer.axes is None: raise RuntimeError("No axes set") # Create the axes axes = flex.vec3_double( params.goniometer.axes[i * 3 : (i * 3) + 3] for i in range(len(params.goniometer.axes) // 3) ) # Invert the rotation axis if params.goniometer.invert_rotation_axis is True: axes = flex.vec3_double([[-x for x in v] for v in axes]) # Create the angles if params.goniometer.angles is not None: angles = params.goniometer.angles if len(angles) != len(axes): raise RuntimeError("Number of angles must match axes") else: angles = flex.double([0] * len(axes)) # Create the names if params.goniometer.names is not None: names = params.goniometer.names if len(names) != len(axes): raise RuntimeError("Number of names must match axes") else: names = flex.std_string([""] * len(axes)) # Create the scan axis if params.goniometer.scan_axis is not None: scan_axis = params.goniometer.scan_axis else: scan_axis = 0 # Create the model goniometer = MultiAxisGoniometer(axes, angles, names, scan_axis) else: goniometer = reference # Set the axes if params.goniometer.axes is not None: axes = flex.vec3_double( params.goniometer.axes[i * 3 : (i * 3) + 3] for i in range(len(params.goniometer.axes) // 3) ) if len(goniometer.get_axes()) != len(axes): raise RuntimeError( "Number of axes must match the current goniometer (%s)" % len(goniometer.get_axes()) ) goniometer.set_axes(axes) # Invert rotation axis if params.goniometer.invert_rotation_axis is True: axes = flex.vec3_double( [[-x for x in v] for v in goniometer.get_axes()] ) goniometer.set_axes(axes) # Set the angles if params.goniometer.angles is not None: if len(goniometer.get_angles()) != len(params.goniometer.angles): raise RuntimeError( "Number of angles must match the current goniometer (%s)" % len(goniometer.get_angles()) ) goniometer.set_angles(params.goniometer.angles) # Set the namess if params.goniometer.names is not None: if len(goniometer.get_names()) != len(params.goniometer.names): raise RuntimeError( "Number of names must match the current goniometer (%s)" % len(goniometer.get_names()) ) goniometer.set_names(params.goniometer.names) # Set the scan axis if params.goniometer.scan_axis is not None: raise RuntimeError("Can not override scan axis") return goniometer
[docs] @staticmethod def from_phil(params, reference=None): """ Convert the phil parameters into a goniometer model """ if params.goniometer.axis and params.goniometer.axes: raise ValueError("Only one of axis or axes should be set") if reference is not None: if isinstance(reference, MultiAxisGoniometer): goniometer = GoniometerFactory.multi_axis_goniometer_from_phil( params, reference ) else: goniometer = GoniometerFactory.single_axis_goniometer_from_phil( params, reference ) else: if params.goniometer.axes and len(params.goniometer.axes) > 3: goniometer = GoniometerFactory.multi_axis_goniometer_from_phil(params) elif params.goniometer.axis or params.goniometer.axes: goniometer = GoniometerFactory.single_axis_goniometer_from_phil(params) else: return None return goniometer
[docs] @staticmethod def from_dict(d, t=None): """Convert the dictionary to a goniometer model Params: d The dictionary of parameters t The template dictionary to use Returns: The goniometer model """ if d is None and t is None: return None joint = t.copy() if t else {} joint.update(d) # Create the model from the joint dictionary if {"axes", "angles", "scan_axis"}.issubset(joint): return MultiAxisGoniometer.from_dict(joint) return Goniometer.from_dict(joint)
[docs] @staticmethod def make_goniometer(rotation_axis, fixed_rotation): return Goniometer( tuple(map(float, rotation_axis)), tuple(map(float, fixed_rotation)) )
[docs] @staticmethod def make_kappa_goniometer(alpha, omega, kappa, phi, direction, scan_axis): omega_axis = (1, 0, 0) phi_axis = (1, 0, 0) c = math.cos(alpha * math.pi / 180) s = math.sin(alpha * math.pi / 180) if direction == "+y": kappa_axis = (c, s, 0.0) elif direction == "+z": kappa_axis = (c, 0.0, s) elif direction == "-y": kappa_axis = (c, -s, 0.0) elif direction == "-z": kappa_axis = (c, 0.0, -s) else: raise RuntimeError("Invalid direction") if scan_axis == "phi": scan_axis = 0 else: scan_axis = 2 axes = flex.vec3_double((phi_axis, kappa_axis, omega_axis)) angles = flex.double((phi, kappa, omega)) names = flex.std_string(("PHI", "KAPPA", "OMEGA")) return GoniometerFactory.make_multi_axis_goniometer( axes, angles, names, scan_axis )
[docs] @staticmethod def make_multi_axis_goniometer(axes, angles, names, scan_axis): return MultiAxisGoniometer(axes, angles, names, scan_axis)
[docs] @staticmethod def single_axis(): """Construct a single axis goniometer which is canonical in the CBF reference frame.""" axis = (1, 0, 0) fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1) return GoniometerFactory.make_goniometer(axis, fixed)
[docs] @staticmethod def single_axis_reverse(): """Construct a single axis goniometer which is canonical in the CBF reference frame, but reversed in rotation.""" axis = (-1, 0, 0) fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1) return GoniometerFactory.make_goniometer(axis, fixed)
[docs] @staticmethod def known_axis(axis): """Return an goniometer instance for a known rotation axis, assuming that nothing is known about the fixed element of the rotation axis.""" assert len(axis) == 3 fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1) return Goniometer(axis, fixed)
[docs] @staticmethod def kappa(alpha, omega, kappa, phi, direction, scan_axis): """Return a kappa goniometer where omega is the primary axis (i,e. aligned with X in the CBF coordinate frame) and has the kappa arm with angle alpha attached to it, aligned with -z, +y, +z or -y at omega = 0, that being the direction, which in turn has phi fixed to it which should initially be coincident with omega. We also need to know which axis is being used for the scan i.e. phi or omega. All angles should be given in degrees. This will work by first constructing the rotation axes and then composing them to the scan axis and fixed component of the rotation.""" return GoniometerFactory.make_kappa_goniometer( alpha, omega, kappa, phi, direction, scan_axis )
[docs] @staticmethod def multi_axis(axes, angles, names, scan_axis): """ """ return GoniometerFactory.make_multi_axis_goniometer( axes, angles, names, scan_axis )
[docs] @staticmethod def imgCIF(cif_file): """Initialize a goniometer model from an imgCIF file.""" # FIXME in here work out how to get the proper setting matrix if != 1 cbf_handle = pycbf.cbf_handle_struct() cbf_handle.read_file(cif_file.encode(), pycbf.MSG_DIGEST) return GoniometerFactory.imgCIF_H(cbf_handle)
[docs] @staticmethod def imgCIF_H(cbf_handle): """Initialize a goniometer model from an imgCIF file handle, where it is assumed that the file has already been read.""" # find the goniometer axes and dependencies axis_names = flex.std_string() depends_on = flex.std_string() axes = flex.vec3_double() angles = flex.double() scan_axis = None cbf_handle.find_category(b"axis") for i in range(cbf_handle.count_rows()): cbf_handle.find_column(b"equipment") if cbf_handle.get_value() == b"goniometer": cbf_handle.find_column(b"id") axis_names.append(cbf_handle.get_value()) axis = [] for i in range(3): cbf_handle.find_column(b"vector[%i]" % (i + 1)) axis.append(float(cbf_handle.get_value())) axes.append(axis) cbf_handle.find_column(b"depends_on") depends_on.append(cbf_handle.get_value()) cbf_handle.next_row() # find the starting angles of each goniometer axis and figure out which one # is the scan axis (i.e. non-zero angle_increment) cbf_handle.find_category(b"diffrn_scan_axis") for i in range(cbf_handle.count_rows()): cbf_handle.find_column(b"axis_id") axis_name = cbf_handle.get_value() if axis_name.decode() not in axis_names: cbf_handle.next_row() continue cbf_handle.find_column(b"angle_start") axis_angle = float(cbf_handle.get_value()) cbf_handle.find_column(b"angle_increment") increment = float(cbf_handle.get_value()) angles.append(axis_angle) if abs(increment) > 0: assert ( scan_axis is None ), "More than one scan axis is defined: not currently supported" scan_axis = flex.first_index(axis_names, axis_name) cbf_handle.next_row() assert axes.size() == angles.size() if scan_axis is None: # probably a still shot -> scan axis arbitrary as no scan scan_axis = 0 # figure out the order of the axes from the depends_on values order = flex.size_t() for i in range(axes.size()): if depends_on[i] == ".": o = 0 else: o = flex.first_index(axis_names, depends_on[i]) + 1 assert o not in order order.append(o) # multi-axis gonio requires axes in order as viewed from crystal to gonio base # i.e. the reverse of the order we have from cbf header order = order.reversed() axes = axes.select(order) angles = angles.select(order) axis_names = axis_names.select(order) scan_axis = axes.size() - scan_axis - 1 # construct a multi-axis goniometer gonio = GoniometerFactory.multi_axis(axes, angles, axis_names, scan_axis) return gonio