638 lines
23 KiB
Python
638 lines
23 KiB
Python
###
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# Copyright 2008-2011 Diamond Light Source Ltd.
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# This file is part of Diffcalc.
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#
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# Diffcalc is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# Diffcalc is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with Diffcalc. If not, see <http://www.gnu.org/licenses/>.
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###
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from diffcalc.ub.calcstate import decode_ubcalcstate
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from diffcalc.ub.calcstate import UBCalcState
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from diffcalc.ub.crystal import CrystalUnderTest
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from diffcalc.ub.reflections import ReflectionList
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from diffcalc.ub.persistence import UBCalculationJSONPersister, UBCalculationPersister
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from diffcalc.util import DiffcalcException, cross3, dot3, bold
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from math import acos, cos, sin, pi
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from diffcalc.ub.reference import YouReference
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try:
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from numpy import matrix, hstack
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from numpy.linalg import norm
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except ImportError:
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from numjy import matrix, hstack
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from numjy.linalg import norm
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from diffcalc.ub.crystal import CrystalUnderTest
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from diffcalc.ub.reflections import ReflectionList
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from diffcalc.util import DiffcalcException, cross3, dot3
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SMALL = 1e-7
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TODEG = 180 / pi
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WIDTH = 13
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def z(num):
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"""Round to zero if small. This is useful to get rid of erroneous
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minus signs resulting from float representation close to zero.
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"""
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if abs(num) < SMALL:
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num = 0
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return num
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#The UB matrix is used to find or set the orientation of a set of
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#planes described by an hkl vector. The U matrix can be used to find
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#or set the orientation of the crystal lattices' y axis. If there is
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#crystal miscut the crystal lattices y axis is not parallel to the
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#crystals optical surface normal. For surface diffraction experiments,
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#where not only the crystal lattice must be oriented appropriately but
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#so must the crystal's optical surface, two angles tau and sigma are
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#used to describe the difference between the two. Sigma is (minus) the
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#ammount of chi axis rotation and tau (minus) the ammount of phi axis
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#rotation needed to move the surface normal into the direction of the
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class PaperSpecificUbCalcStrategy(object):
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def calculate_q_phi(self, pos):
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"""Calculate hkl in the phi frame in units of 2 * pi / lambda from
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pos object in radians"""
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raise NotImplementedError()
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class UBCalculation:
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"""A UB matrix calculation for an experiment.
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Contains the parameters for the _crystal under test, a list of measured
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reflections and, if its been calculated, a UB matrix to be used by the rest
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of the code.
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"""
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def __init__(self, hardware, diffractometerPluginObject,
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persister, strategy, include_sigtau=True, include_reference=True):
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# The diffractometer geometry is required to map the internal angles
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# into those used by this diffractometer (for display only)
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self._hardware = hardware
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self._geometry = diffractometerPluginObject
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self._persister = persister
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self._strategy = strategy
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self.include_sigtau = include_sigtau
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self.include_reference = include_reference
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self._clear()
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def _get_diffractometer_axes_names(self):
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return self._hardware.get_axes_names()
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def _clear(self, name=None):
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# NOTE the Diffraction calculator is expecting this object to exist in
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# the long run. We can't remove this entire object, and recreate it.
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# It also contains a required link to the angle calculator.
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reflist = ReflectionList(self._geometry, self._get_diffractometer_axes_names())
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reference = YouReference(self._get_UB)
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self._state = UBCalcState(name=name, reflist=reflist, reference=reference)
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self._U = None
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self._UB = None
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self._state.configure_calc_type()
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### State ###
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def start_new(self, name):
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"""start_new(name) --- creates a new blank ub calculation"""
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# Create storage object if name does not exist (TODO)
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if name in self._persister.list():
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print ("No UBCalculation started: There is already a calculation "
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"called: " + name)
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print "Saved calculations: " + repr(self._persister.list())
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return
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self._clear(name)
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self.save()
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def load(self, name):
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state = self._persister.load(name)
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if isinstance(self._persister, UBCalculationJSONPersister):
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self._state = decode_ubcalcstate(state, self._geometry, self._get_diffractometer_axes_names())
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self._state.reference.get_UB = self._get_UB
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elif isinstance(self._persister, UBCalculationPersister):
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self._state = state
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else:
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raise Exception('Unexpected persister type: ' + str(self._persister))
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if self._state.manual_U is not None:
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self.set_U_manually(self._state.manual_U)
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elif self._state.manual_UB is not None:
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self.set_UB_manually(self._state.manual_UB)
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elif self._state.or0 is not None:
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if self._state.or1 is None:
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self.calculate_UB_from_primary_only()
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else:
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self.calculate_UB()
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else:
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pass
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def save(self):
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self.saveas(self._state.name)
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def saveas(self, name):
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self._state.name = name
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self._persister.save(self._state, name)
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def listub(self):
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return self._persister.list()
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def listub_metadata(self):
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return self._persister.list_metadata()
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def remove(self, name):
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self._persister.remove(name)
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if self._state == name:
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self._clear(name)
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def getState(self):
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return self._state.getState()
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def __str__(self):
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if self._state.name is None:
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return "<<< No UB calculation started >>>"
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lines = []
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lines.append(bold("UBCALC"))
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lines.append("")
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lines.append(
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" name:".ljust(WIDTH) + self._state.name.rjust(9))
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if self.include_sigtau:
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lines.append("")
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lines.append(
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" sigma:".ljust(WIDTH) + ("% 9.5f" % self._state.sigma).rjust(9))
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lines.append(
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" tau:".ljust(WIDTH) + ("% 9.5f" % self._state.tau).rjust(9))
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if self.include_reference:
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lines.append("")
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ub_calculated = self._UB is not None
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lines.extend(self._state.reference.repr_lines(ub_calculated, WIDTH))
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lines.append("")
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lines.append(bold("CRYSTAL"))
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lines.append("")
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if self._state.crystal is None:
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lines.append(" <<< none specified >>>")
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else:
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lines.extend(self._state.crystal.str_lines())
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lines.append("")
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lines.append(bold("UB MATRIX"))
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lines.append("")
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if self._UB is None:
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lines.append(" <<< none calculated >>>")
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else:
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lines.extend(self.str_lines_u())
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lines.append("")
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lines.extend(self.str_lines_u_angle_and_axis())
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lines.append("")
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lines.extend(self.str_lines_ub())
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lines.append("")
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lines.append(bold("REFLECTIONS"))
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lines.append("")
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lines.extend(self._state.reflist.str_lines())
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return '\n'.join(lines)
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def str_lines_u(self):
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lines = []
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fmt = "% 9.5f % 9.5f % 9.5f"
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U = self.U
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lines.append(" U matrix:".ljust(WIDTH) +
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fmt % (z(U[0, 0]), z(U[0, 1]), z(U[0, 2])))
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lines.append(' ' * WIDTH + fmt % (z(U[1, 0]), z(U[1, 1]), z(U[1, 2])))
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lines.append(' ' * WIDTH + fmt % (z(U[2, 0]), z(U[2, 1]), z(U[2, 2])))
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return lines
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def str_lines_u_angle_and_axis(self):
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lines = []
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fmt = "% 9.5f % 9.5f % 9.5f"
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y = matrix('0; 0; 1')
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rotation_axis = cross3(y, self.U * y)
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if abs(norm(rotation_axis)) < SMALL:
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lines.append(" U angle:".ljust(WIDTH) + " 0")
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else:
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rotation_axis = rotation_axis * (1 / norm(rotation_axis))
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cos_rotation_angle = dot3(y, self.U * y)
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rotation_angle = acos(cos_rotation_angle)
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lines.append(" angle:".ljust(WIDTH) + "% 9.5f" % (rotation_angle * TODEG))
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lines.append(" axis:".ljust(WIDTH) + fmt % tuple((rotation_axis.T).tolist()[0]))
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return lines
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def str_lines_ub(self):
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lines = []
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fmt = "% 9.5f % 9.5f % 9.5f"
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UB = self.UB
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lines.append(" UB matrix:".ljust(WIDTH) +
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fmt % (z(UB[0, 0]), z(UB[0, 1]), z(UB[0, 2])))
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lines.append(' ' * WIDTH + fmt % (z(UB[1, 0]), z(UB[1, 1]), z(UB[1, 2])))
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lines.append(' ' * WIDTH + fmt % (z(UB[2, 0]), z(UB[2, 1]), z(UB[2, 2])))
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return lines
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@property
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def name(self):
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return self._state.name
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### Lattice ###
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def set_lattice(self, name, *shortform):
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"""
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Converts a list shortform crystal parameter specification to a six-long
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tuple returned as . Returns None if wrong number of input args. See
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set_lattice() for a description of the shortforms supported.
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shortformLattice -- a tuple as follows:
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[a] - assumes cubic
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[a,b]) - assumes tetragonal
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[a,b,c]) - assumes ortho
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[a,b,c,gam]) - assumes mon/hex gam different from 90.
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[a,b,c,alp,bet,gam]) - for arbitrary
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where all measurements in angstroms and angles in degrees
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"""
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self._set_lattice_without_saving(name, *shortform)
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self.save()
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def _set_lattice_without_saving(self, name, *shortform):
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sf = shortform
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if len(sf) == 1:
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fullform = (sf[0], sf[0], sf[0], 90., 90., 90.) # cubic
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elif len(sf) == 2:
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fullform = (sf[0], sf[0], sf[1], 90., 90., 90.) # tetragonal
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elif len(sf) == 3:
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fullform = (sf[0], sf[1], sf[2], 90., 90., 90.) # ortho
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elif len(sf) == 4:
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fullform = (sf[0], sf[1], sf[2], 90., 90., sf[3]) # mon/hex gam
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# not 90
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elif len(sf) == 5:
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raise ValueError("wrong length input to set_lattice")
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elif len(sf) == 6:
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fullform = sf # triclinic/arbitrary
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else:
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raise ValueError("wrong length input to set_lattice")
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self._set_lattice(name, *fullform)
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def _set_lattice(self, name, a, b, c, alpha, beta, gamma):
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"""set lattice parameters in degrees"""
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if self._state.name is None:
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raise DiffcalcException(
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"Cannot set lattice until a UBCalcaluation has been started "
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"with newubcalc")
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self._state.crystal = CrystalUnderTest(name, a, b, c, alpha, beta, gamma)
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# Clear U and UB if these exist
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if self._U is not None: # (UB will also exist)
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print "Warning: the old UB calculation has been cleared."
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print " Use 'calcub' to recalculate with old reflections."
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### Surface normal stuff ###
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def _gettau(self):
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"""
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Returns tau (in degrees): the (minus) ammount of phi axis rotation ,
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that together with some chi axis rotation (minus sigma) brings the
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optical surface normal parallelto the omega axis.
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"""
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return self._state.tau
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def _settau(self, tau):
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self._state.tau = tau
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self.save()
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tau = property(_gettau, _settau)
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def _getsigma(self):
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"""
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Returns sigma (in degrees): the (minus) ammount of phi axis rotation ,
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that together with some phi axis rotation (minus tau) brings the
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optical surface normal parallel to the omega axis.
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"""
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return self._state.sigma
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def _setsigma(self, sigma):
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self.state._sigma = sigma
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self.save()
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sigma = property(_getsigma, _setsigma)
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### Reference vector ###
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def _get_n_phi(self):
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return self._state.reference.n_phi
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n_phi = property(_get_n_phi)
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def set_n_phi_configured(self, n_phi):
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self._state.reference.n_phi_configured = n_phi
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self.save()
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def set_n_hkl_configured(self, n_hkl):
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self._state.reference.n_hkl_configured = n_hkl
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self.save()
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def print_reference(self):
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print '\n'.join(self._state.reference.repr_lines(self.is_ub_calculated()))
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### Reflections ###
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def add_reflection(self, h, k, l, position, energy, tag, time):
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"""add_reflection(h, k, l, position, tag=None) -- adds a reflection
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position is in degrees and in the systems internal representation.
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"""
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if self._state.reflist is None:
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raise DiffcalcException("No UBCalculation loaded")
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self._state.reflist.add_reflection(h, k, l, position, energy, tag, time)
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self.save() # incase autocalculateUbAndReport fails
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# If second reflection has just been added then calculateUB
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if len(self._state.reflist) == 2:
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self._autocalculateUbAndReport()
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self.save()
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def edit_reflection(self, num, h, k, l, position, energy, tag, time):
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"""
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edit_reflection(num, h, k, l, position, tag=None) -- adds a reflection
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position is in degrees and in the systems internal representation.
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"""
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if self._state.reflist is None:
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raise DiffcalcException("No UBCalculation loaded")
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self._state.reflist.edit_reflection(num, h, k, l, position, energy, tag, time)
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# If first or second reflection has been changed and there are at least
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# two reflections then recalculate UB
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if (num == 1 or num == 2) and len(self._state.reflist) >= 2:
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self._autocalculateUbAndReport()
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self.save()
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def get_reflection(self, num):
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"""--> ( [h, k, l], position, energy, tag, time
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num starts at 1, position in degrees"""
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return self._state.reflist.getReflection(num)
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def get_reflection_in_external_angles(self, num):
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"""--> ( [h, k, l], position, energy, tag, time
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num starts at 1, position in degrees"""
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return self._state.reflist.get_reflection_in_external_angles(num)
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def get_number_reflections(self):
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return 0 if self._state.reflist is None else len(self._state.reflist)
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def del_reflection(self, reflectionNumber):
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self._state.reflist.removeReflection(reflectionNumber)
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if ((reflectionNumber == 1 or reflectionNumber == 2) and
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(self._U != None)):
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self._autocalculateUbAndReport()
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self.save()
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def swap_reflections(self, num1, num2):
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self._state.reflist.swap_reflections(num1, num2)
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if ((num1 == 1 or num1 == 2 or num2 == 1 or num2 == 2) and
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(self._U != None)):
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self._autocalculateUbAndReport()
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self.save()
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def _autocalculateUbAndReport(self):
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if len(self._state.reflist) < 2:
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pass
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elif self._state.crystal is None:
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print ("Not calculating UB matrix as no lattice parameters have "
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"been specified.")
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elif not self._state.is_okay_to_autocalculate_ub:
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print ("Not calculating UB matrix as it has been manually set. "
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"Use 'calcub' to explicitly recalculate it.")
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else: # okay to autocalculate
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if self._UB is None:
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print "Calculating UB matrix."
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else:
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print "Recalculating UB matrix."
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self.calculate_UB()
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# @property
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# def reflist(self):
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# return self._state.reflist
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### Calculations ###
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def set_U_manually(self, m):
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"""Manually sets U. matrix must be 3*3 Jama or python matrix.
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Turns off aution UB calcualtion."""
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# Check matrix is a 3*3 Jama matrix
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if m.__class__ != matrix:
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m = matrix(m) # assume its a python matrix
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if m.shape[0] != 3 or m.shape[1] != 3:
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raise ValueError("Expects 3*3 matrix")
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if self._UB is None:
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print "Calculating UB matrix."
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else:
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print "Recalculating UB matrix."
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self._state.configure_calc_type(manual_U=m)
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self._U = m
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if self._state.crystal is None:
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raise DiffcalcException(
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"A crystal must be specified before manually setting U")
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self._UB = self._U * self._state.crystal.B
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print ("NOTE: A new UB matrix will not be automatically calculated "
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"when the orientation reflections are modified.")
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self.save()
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def set_UB_manually(self, m):
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"""Manually sets UB. matrix must be 3*3 Jama or python matrix.
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Turns off aution UB calcualtion."""
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# Check matrix is a 3*3 Jama matrix
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if m.__class__ != matrix:
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m = matrix(m) # assume its a python matrix
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if m.shape[0] != 3 or m.shape[1] != 3:
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raise ValueError("Expects 3*3 matrix")
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self._state.configure_calc_type(manual_UB=m)
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self._UB = m
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self.save()
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@property
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def U(self):
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if self._U is None:
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raise DiffcalcException(
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"No U matrix has been calculated during this ub calculation")
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return self._U
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@property
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def UB(self):
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return self._get_UB()
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def is_ub_calculated(self):
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return self._UB is not None
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def _get_UB(self):
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if not self.is_ub_calculated():
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raise DiffcalcException(
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"No UB matrix has been calculated during this ub calculation")
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else:
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return self._UB
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def calculate_UB(self):
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"""
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Calculate orientation matrix. Uses first two orientation reflections
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as in Busang and Levy, but for the diffractometer in Lohmeier and
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Vlieg.
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"""
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# Major variables:
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# h1, h2: user input reciprical lattice vectors of the two reflections
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# h1c, h2c: user input vectors in cartesian crystal plane
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# pos1, pos2: measured diffractometer positions of the two reflections
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# u1a, u2a: measured reflection vectors in alpha frame
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# u1p, u2p: measured reflection vectors in phi frame
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# Get hkl and angle values for the first two refelctions
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if self._state.reflist is None:
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raise DiffcalcException("Cannot calculate a U matrix until a "
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"UBCalculation has been started with "
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"'newub'")
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try:
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(h1, pos1, _, _, _) = self._state.reflist.getReflection(1)
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(h2, pos2, _, _, _) = self._state.reflist.getReflection(2)
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except IndexError:
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raise DiffcalcException(
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"Two reflections are required to calculate a u matrix")
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h1 = matrix([h1]).T # row->column
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h2 = matrix([h2]).T
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pos1.changeToRadians()
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pos2.changeToRadians()
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# Compute the two reflections' reciprical lattice vectors in the
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# cartesian crystal frame
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B = self._state.crystal.B
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h1c = B * h1
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h2c = B * h2
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u1p = self._strategy.calculate_q_phi(pos1)
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u2p = self._strategy.calculate_q_phi(pos2)
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# Create modified unit vectors t1, t2 and t3 in crystal and phi systems
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t1c = h1c
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t3c = cross3(h1c, h2c)
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t2c = cross3(t3c, t1c)
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t1p = u1p # FIXED from h1c 9July08
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t3p = cross3(u1p, u2p)
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t2p = cross3(t3p, t1p)
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# ...and nornmalise and check that the reflections used are appropriate
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SMALL = 1e-4 # Taken from Vlieg's code
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e = DiffcalcException("Invalid orientation reflection(s)")
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def normalise(m):
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d = norm(m)
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if d < SMALL:
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raise e
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return m / d
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t1c = normalise(t1c)
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t2c = normalise(t2c)
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t3c = normalise(t3c)
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t1p = normalise(t1p)
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t2p = normalise(t2p)
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t3p = normalise(t3p)
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Tc = hstack([t1c, t2c, t3c])
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Tp = hstack([t1p, t2p, t3p])
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self._state.configure_calc_type(or0=1, or1=2)
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self._U = Tp * Tc.I
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self._UB = self._U * B
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self.save()
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def calculate_UB_from_primary_only(self):
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"""
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Calculate orientation matrix with the shortest absolute angle change.
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Uses first orientation reflection
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"""
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# Algorithm from http://www.j3d.org/matrix_faq/matrfaq_latest.html
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# Get hkl and angle values for the first two refelctions
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if self._state.reflist is None:
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raise DiffcalcException(
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"Cannot calculate a u matrix until a UBCalcaluation has been "
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"started with newub")
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try:
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(h, pos, _, _, _) = self._state.reflist.getReflection(1)
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except IndexError:
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raise DiffcalcException(
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"One reflection is required to calculate a u matrix")
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h = matrix([h]).T # row->column
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pos.changeToRadians()
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B = self._state.crystal.B
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h_crystal = B * h
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h_crystal = h_crystal * (1 / norm(h_crystal))
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q_measured_phi = self._strategy.calculate_q_phi(pos)
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q_measured_phi = q_measured_phi * (1 / norm(q_measured_phi))
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rotation_axis = cross3(h_crystal, q_measured_phi)
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rotation_axis = rotation_axis * (1 / norm(rotation_axis))
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cos_rotation_angle = dot3(h_crystal, q_measured_phi)
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rotation_angle = acos(cos_rotation_angle)
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uvw = rotation_axis.T.tolist()[0] # TODO: cleanup
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print "resulting U angle: %.5f deg" % (rotation_angle * TODEG)
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u_repr = (', '.join(['% .5f' % el for el in uvw]))
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print "resulting U axis direction: [%s]" % u_repr
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u, v, w = uvw
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rcos = cos(rotation_angle)
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rsin = sin(rotation_angle)
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m = [[0, 0, 0], [0, 0, 0], [0, 0, 0]] # TODO: tidy
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m[0][0] = rcos + u * u * (1 - rcos)
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m[1][0] = w * rsin + v * u * (1 - rcos)
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m[2][0] = -v * rsin + w * u * (1 - rcos)
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m[0][1] = -w * rsin + u * v * (1 - rcos)
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m[1][1] = rcos + v * v * (1 - rcos)
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m[2][1] = u * rsin + w * v * (1 - rcos)
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m[0][2] = v * rsin + u * w * (1 - rcos)
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m[1][2] = -u * rsin + v * w * (1 - rcos)
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m[2][2] = rcos + w * w * (1 - rcos)
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if self._UB is None:
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print "Calculating UB matrix from the first reflection only."
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else:
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print "Recalculating UB matrix from the first reflection only."
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print ("NOTE: A new UB matrix will not be automatically calculated "
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"when the orientation reflections are modified.")
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self._state.configure_calc_type(or0=1)
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self._U = matrix(m)
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self._UB = self._U * B
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self.save()
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def get_hkl_plane_distance(self, hkl):
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"""Calculates and returns the distance between planes"""
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return self._state.crystal.get_hkl_plane_distance(hkl)
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