def exercise_similarity():

  model_1 = crystal_model(real_space_a=(10,0,0),
                          real_space_b=(0,11,0),
                          real_space_c=(0,0,12),
                          space_group_symbol="P 1",
                          mosaicity=0.5)
  model_2 = crystal_model(real_space_a=(10,0,0),
                          real_space_b=(0,11,0),
                          real_space_c=(0,0,12),
                          space_group_symbol="P 1",
                          mosaicity=0.5)
  assert model_1.is_similar_to(model_2)

  # mosaicity tests
  model_1.set_mosaicity(-1)
  model_2.set_mosaicity(-0.5)
  assert model_1.is_similar_to(model_2) # test ignores negative mosaicity
  model_1.set_mosaicity(0.5)
  model_2.set_mosaicity(0.63) # outside tolerance
  assert not model_1.is_similar_to(model_2)
  model_2.set_mosaicity(0.625) #just inside tolerance
  assert model_1.is_similar_to(model_2)

  # orientation tests
  R = model_2.get_U()
  dr1 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0101, deg=True)
  dr2 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0099, deg=True)
  model_2.set_U(dr1 * R)
  assert not model_1.is_similar_to(model_2) # outside tolerance
  model_2.set_U(dr2 * R)
  assert model_1.is_similar_to(model_2) # inside tolerance

  # unit_cell.is_similar_to is tested elsewhere
  return
def exercise():
  from dials.algorithms.indexing import compare_orientation_matrices
  from dxtbx.model.crystal import crystal_model
  from cctbx import sgtbx
  from scitbx import matrix
  from scitbx.math import euler_angles as euler

  # try and see if we can get back the original rotation matrix and euler angles
  real_space_a = matrix.col((10,0,0))
  real_space_b = matrix.col((0,10,10))
  real_space_c = matrix.col((0,0,10))
  euler_angles = (1.3, 5.6, 7.8)
  R = matrix.sqr(
    euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
  crystal_a = crystal_model(real_space_a,
                            real_space_b,
                            real_space_c,
                            space_group=sgtbx.space_group('P 1'))
  crystal_b = crystal_model(R * real_space_a,
                            R * real_space_b,
                            R * real_space_c,
                            space_group=sgtbx.space_group('P 1'))
  assert approx_equal(crystal_b.get_U() * crystal_a.get_U().transpose(), R)
  best_R_ab, best_axis, best_angle, best_cb_op = \
    compare_orientation_matrices.difference_rotation_matrix_axis_angle(
      crystal_a,
      crystal_b)
  best_euler_angles = euler.xyz_angles(best_R_ab)
  assert approx_equal(best_euler_angles, euler_angles)
  assert best_cb_op.is_identity_op()
  assert approx_equal(best_R_ab, R)

  # now see if we can deconvolute the original euler angles after applying
  # a change of basis to one of the crystals
  crystal_a = crystal_model(real_space_a,
                            real_space_b,
                            real_space_c,
                            space_group=sgtbx.space_group('I 2 3'))
  crystal_b = crystal_model(R * real_space_a,
                            R * real_space_b,
                            R * real_space_c,
                            space_group=sgtbx.space_group('I 2 3'))
  cb_op = sgtbx.change_of_basis_op('z,x,y')
  crystal_b = crystal_b.change_basis(cb_op)
  best_R_ab, best_axis, best_angle, best_cb_op = \
    compare_orientation_matrices.difference_rotation_matrix_axis_angle(
      crystal_a,
      crystal_b)
  best_euler_angles = euler.xyz_angles(best_R_ab)
  assert approx_equal(best_euler_angles, euler_angles)
  assert best_cb_op.c() == cb_op.inverse().c()
  assert approx_equal(best_R_ab, R)
Esempio n. 3
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  def tst_dump_empty_sweep(self):
    from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model
    from uuid import uuid4

    imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
    imageset.set_beam(Beam((1, 0, 0)))
    imageset.set_detector(Detector())
    imageset.set_goniometer(Goniometer())
    imageset.set_scan(Scan((1, 3), (0.0, 1.0)))

    crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)

    experiments = ExperimentListFactory.from_imageset_and_crystal(
      imageset, crystal)

    dump = ExperimentListDumper(experiments)
    filename = 'temp%s.json' % uuid4().hex
    dump.as_json(filename)
    experiments2 = ExperimentListFactory.from_json_file(filename,
                                                        check_format=False)
    self.check(experiments, experiments2)

    print 'OK'
  def tst_dump_empty_sweep(self):
    from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model
    from uuid import uuid4

    imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
    imageset.set_beam(Beam((1, 0, 0)))
    imageset.set_detector(Detector())
    imageset.set_goniometer(Goniometer())
    imageset.set_scan(Scan((1, 3), (0.0, 1.0)))

    crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)

    experiments = ExperimentListFactory.from_imageset_and_crystal(
      imageset, crystal)

    dump = ExperimentListDumper(experiments)
    filename = 'temp%s.json' % uuid4().hex
    dump.as_json(filename)
    experiments2 = ExperimentListFactory.from_json_file(filename,
                                                        check_format=False)
    self.check(experiments, experiments2)

    print 'OK'
Esempio n. 5
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def to_crystal(filename):
  ''' Get the crystal model from the xparm file

  Params:
      filename The xparm/or integrate filename

  Return:
      The crystal model

  '''
  from rstbx.cftbx.coordinate_frame_converter import \
      coordinate_frame_converter
  from dxtbx.model.crystal import crystal_model
  from cctbx.sgtbx import space_group, space_group_symbols

  # Get the real space coordinate frame
  cfc = coordinate_frame_converter(filename)
  real_space_a = cfc.get('real_space_a')
  real_space_b = cfc.get('real_space_b')
  real_space_c = cfc.get('real_space_c')
  sg = cfc.get('space_group_number')
  space_group = space_group(space_group_symbols(sg).hall())
  mosaicity = cfc.get('mosaicity')

  # Return the crystal model
  return crystal_model(
      real_space_a=real_space_a,
      real_space_b=real_space_b,
      real_space_c=real_space_c,
      space_group=space_group,
      mosaicity=mosaicity)
  def tst_from_datablock(self):
    from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.datablock import DataBlockFactory
    from dxtbx.model.crystal import crystal_model

    imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
    imageset.set_beam(Beam())
    imageset.set_detector(Detector())
    imageset.set_goniometer(Goniometer())
    imageset.set_scan(Scan((1, 2), (0, 1)))

    crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)

    datablock = DataBlockFactory.from_imageset(imageset)

    experiments = ExperimentListFactory.from_datablock_and_crystal(
      datablock, crystal)

    assert(len(experiments) == 1)
    assert(experiments[0].imageset is not None)
    assert(experiments[0].beam is not None)
    assert(experiments[0].detector is not None)
    assert(experiments[0].goniometer is not None)
    assert(experiments[0].scan is not None)
    assert(experiments[0].crystal is not None)

    print 'OK'
    pass
Esempio n. 7
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  def __init__(self, obj):
    from dxtbx.model.crystal import crystal_model
    import cctbx.uctbx
    from scitbx import matrix

    # Get the crystal parameters
    unit_cell_parameters = list(obj.handle['unit_cell'][0])
    unit_cell = cctbx.uctbx.unit_cell(unit_cell_parameters)
    U = list(obj.handle['orientation_matrix'][0].flatten())
    U = matrix.sqr(U)
    B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
    A = U * B
    Ai = A.inverse()
    real_space_a = Ai[0:3]
    real_space_b = Ai[3:6]
    real_space_c = Ai[6:9]

    # Get the space group symbol
    space_group_symbol = obj.handle['unit_cell_group'][()]

    # Create the model
    self.model = crystal_model(
      real_space_a,
      real_space_b,
      real_space_c,
      space_group_symbol)
Esempio n. 8
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def to_crystal(filename):
    ''' Get the crystal model from the xparm file

  Params:
      filename The xparm/or integrate filename

  Return:
      The crystal model

  '''
    from rstbx.cftbx.coordinate_frame_converter import \
        coordinate_frame_converter
    from dxtbx.model.crystal import crystal_model
    from cctbx.sgtbx import space_group, space_group_symbols

    # Get the real space coordinate frame
    cfc = coordinate_frame_converter(filename)
    real_space_a = cfc.get('real_space_a')
    real_space_b = cfc.get('real_space_b')
    real_space_c = cfc.get('real_space_c')
    sg = cfc.get('space_group_number')
    space_group = space_group(space_group_symbols(sg).hall())
    mosaicity = cfc.get('mosaicity')

    # Return the crystal model
    return crystal_model(real_space_a=real_space_a,
                         real_space_b=real_space_b,
                         real_space_c=real_space_c,
                         space_group=space_group,
                         mosaicity=mosaicity)
Esempio n. 9
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  def tst_crystal(self):
    from dxtbx.serialize.crystal import to_dict, from_dict
    from dxtbx.model.crystal import crystal_model
    from scitbx import matrix

    real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
    real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
    real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))

    c1 = crystal_model(
        real_space_a=real_space_a,
        real_space_b=real_space_b,
        real_space_c=real_space_c,
        space_group_symbol="P 1 2/m 1",
        mosaicity=0.1)

    d = to_dict(c1)
    c2 = from_dict(d)
    eps = 1e-7
    assert(abs(matrix.col(d['real_space_a']) - real_space_a) <= eps)
    assert(abs(matrix.col(d['real_space_b']) - real_space_b) <= eps)
    assert(abs(matrix.col(d['real_space_c']) - real_space_c) <= eps)
    assert(d['space_group_hall_symbol'] == "-P 2y")
    assert(d['mosaicity'] == 0.1)
    assert(c1 == c2)
    print 'OK'
    def predict_once(args):
        from dxtbx.model.experiment.experiment_list import Experiment

        U = args[0]
        A = U * B
        direct_matrix = A.inverse()
        cryst_model = crystal_model(
            direct_matrix[0:3],
            direct_matrix[3:6],
            direct_matrix[6:9],
            space_group=space_group,
        )
        experiment = Experiment(
            imageset=sweep,
            beam=sweep.get_beam(),
            detector=sweep.get_detector(),
            goniometer=sweep.get_goniometer(),
            scan=sweep.get_scan(),
            crystal=cryst_model,
        )
        predicted_reflections = flex.reflection_table.from_predictions(experiment)
        miller_indices = predicted_reflections["miller_index"]
        miller_set = miller.set(crystal_symmetry, miller_indices, anomalous_flag=True)
        if params.d_min is not None:
            resolution_sel = miller_set.d_spacings().data() > params.d_min
            predicted_reflections = predicted_reflections.select(resolution_sel)
        return len(predicted_reflections)
Esempio n. 11
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  def tst_crystal_with_scan_points(self):
    from dxtbx.serialize.crystal import to_dict, from_dict
    from dxtbx.model.crystal import crystal_model
    from scitbx import matrix

    real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
    real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
    real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))

    c1 = crystal_model(
        real_space_a=real_space_a,
        real_space_b=real_space_b,
        real_space_c=real_space_c,
        space_group_symbol="P 1 2/m 1",
        mosaicity=0.1)

    A = c1.get_A()
    c1.set_A_at_scan_points([A for i in range(5)])

    d = to_dict(c1)
    c2 = from_dict(d)
    eps = 1e-9
    for Acomp in (d['A_at_scan_points']):
      for e1, e2 in zip(A, Acomp):
        assert(abs(e1 - e2) <= eps)
    assert(c1 == c2)
    print 'OK'
Esempio n. 12
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  def tst_from_datablock(self):
    from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.datablock import DataBlockFactory
    from dxtbx.model.crystal import crystal_model

    imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
    imageset.set_beam(Beam())
    imageset.set_detector(Detector())
    imageset.set_goniometer(Goniometer())
    imageset.set_scan(Scan((1, 2), (0, 1)))

    crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)

    datablock = DataBlockFactory.from_imageset(imageset)

    experiments = ExperimentListFactory.from_datablock_and_crystal(
      datablock, crystal)

    assert(len(experiments) == 1)
    assert(experiments[0].imageset is not None)
    assert(experiments[0].beam is not None)
    assert(experiments[0].detector is not None)
    assert(experiments[0].goniometer is not None)
    assert(experiments[0].scan is not None)
    assert(experiments[0].crystal is not None)

    print 'OK'
  def test_random(self):
    """Test random initial orientations, random parameter shifts and random
    times"""

    attempts = 100
    failures = 0
    null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))

    for i in range(attempts):

      # make a new P1 random crystal and parameterise it
      a = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((1, 0, 0)))
      b = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((0, 1, 0)))
      c = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((0, 0, 1)))
      xl = crystal_model(a, b, c, space_group_symbol="P 1")

      xl_op = TestOrientationModel(50, xl, self.image_range, 5)

      # How many parameters?
      num_param = xl_op.num_free()

      # apply random parameter shifts to the orientation (2.0 mrad each
      # checkpoint)
      p_vals = xl_op.get_param_vals()
      sigmas = [2.0] * len(p_vals)
      new_vals = random_param_shift(p_vals, sigmas)
      xl_op.set_param_vals(new_vals)

      # select random time point at which to make comparisons
      t = random.uniform(*self.image_range)
      xl_op.set_time_point(t)

      # compare analytical and finite difference derivatives
      xl_op_an_ds_dp = xl_op.get_ds_dp()
      xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
                                        num_param)

      for j in range(num_param):
        try:
          assert(approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
                              null_mat, eps = 1.e-6))
        except Exception:
          failures += 1
          print "for try", i
          print "failure for parameter number", j
          print "of the orientation parameterisation"
          print "with fd_ds_dp = "
          print xl_op_fd_ds_dp[j]
          print "and an_ds_dp = "
          print xl_op_an_ds_dp[j]
          print "so that difference fd_ds_dp - an_ds_dp ="
          print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]

    if failures == 0: print "OK"
def create_Bmat():
    """Create a random crystal model, in P1 for maximum generality. Return the
  B matrix of this crystal"""

    from dxtbx.model.crystal import crystal_model

    vecs = map(random_vector_close_to, [(20, 0, 0), (0, 20, 0), (0, 0, 20)])

    return crystal_model(*vecs, space_group_symbol="P 1").get_B()
  def test_random(self):
    """Test random initial orientations, random parameter shifts and random
    times"""

    attempts = 100
    failures = 0
    null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))

    for i in range(attempts):

      # make a new P1 random crystal and parameterise it
      a = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((1, 0, 0)))
      b = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((0, 1, 0)))
      c = random.uniform(10,50) * \
              self.random_direction_close_to(matrix.col((0, 0, 1)))
      xl = crystal_model(a, b, c, space_group_symbol="P 1")

      xl_op = TestOrientationModel(50, xl, self.image_range, 5)

      # How many parameters?
      num_param = xl_op.num_free()

      # apply random parameter shifts to the orientation (2.0 mrad each
      # checkpoint)
      p_vals = xl_op.get_param_vals()
      sigmas = [2.0] * len(p_vals)
      new_vals = random_param_shift(p_vals, sigmas)
      xl_op.set_param_vals(new_vals)

      # select random time point at which to make comparisons
      t = random.uniform(*self.image_range)
      xl_op.set_time_point(t)

      # compare analytical and finite difference derivatives
      xl_op_an_ds_dp = xl_op.get_ds_dp()
      xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
                                        num_param)

      for j in range(num_param):
        try:
          assert(approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
                              null_mat, eps = 1.e-6))
        except Exception:
          failures += 1
          print "for try", i
          print "failure for parameter number", j
          print "of the orientation parameterisation"
          print "with fd_ds_dp = "
          print xl_op_fd_ds_dp[j]
          print "and an_ds_dp = "
          print xl_op_an_ds_dp[j]
          print "so that difference fd_ds_dp - an_ds_dp ="
          print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]

    if failures == 0: print "OK"
Esempio n. 16
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  def build_crystal(self):

    vecs = map(self._build_cell_vec,
               [self._params.crystal.a,
                self._params.crystal.b,
                self._params.crystal.c])

    sg = self._params.crystal.space_group_symbol

    self.crystal = crystal_model(*vecs, space_group_symbol = sg)
Esempio n. 17
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def generate_crystal(unit_cell, space_group):
  from dxtbx.model.crystal import crystal_model

  B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
  U = random_rotation()
  A = U * B
  direct_matrix = A.inverse()
  return crystal_model(direct_matrix[0:3],
                       direct_matrix[3:6],
                       direct_matrix[6:9],
                       space_group=space_group)
Esempio n. 18
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def dials_crystal_from_orientation(crystal_orientation,space_group):
  dm = crystal_orientation.direct_matrix()
  AA = col((dm[0],dm[1],dm[2]))
  BB = col((dm[3],dm[4],dm[5]))
  CC = col((dm[6],dm[7],dm[8]))

  from dxtbx.model.crystal import crystal_model

  cryst = crystal_model(real_space_a=AA, real_space_b=BB, real_space_c=CC,
                        space_group=space_group)
  return cryst
Esempio n. 19
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def generate_crystal(unit_cell, space_group):
    from dxtbx.model.crystal import crystal_model

    B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
    U = random_rotation()
    A = U * B
    direct_matrix = A.inverse()
    return crystal_model(direct_matrix[0:3],
                         direct_matrix[3:6],
                         direct_matrix[6:9],
                         space_group=space_group)
  def tst_equality(self):

    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    # Create a load of models
    b1 = Beam()
    d1 = Detector()
    g1 = Goniometer()
    s1 = Scan()
    c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create a load of models that look the same but aren't
    b2 = Beam()
    d2 = Detector()
    g2 = Goniometer()
    s2 = Scan()
    c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create an experiment
    e1 = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Create an experiment
    e2 = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Create an experiment
    e3 = Experiment(
      beam=b2, detector=d2, goniometer=g2,
      scan=s2, crystal=c2, imageset=None)

    # Check e1 equals e2 but not e3
    assert(e1 == e2)
    assert(e1 != e3)
    assert(e2 != e3)

    # Test passed
    print 'OK'
Esempio n. 21
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  def tst_equality(self):

    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    # Create a load of models
    b1 = Beam()
    d1 = Detector()
    g1 = Goniometer()
    s1 = Scan()
    c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create a load of models that look the same but aren't
    b2 = Beam()
    d2 = Detector()
    g2 = Goniometer()
    s2 = Scan()
    c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create an experiment
    e1 = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Create an experiment
    e2 = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Create an experiment
    e3 = Experiment(
      beam=b2, detector=d2, goniometer=g2,
      scan=s2, crystal=c2, imageset=None)

    # Check e1 equals e2 but not e3
    assert(e1 == e2)
    assert(e1 != e3)
    assert(e2 != e3)

    # Test passed
    print 'OK'
  def __init__(self,params):
    import cPickle as pickle
    from dxtbx.model.beam import beam_factory
    from dxtbx.model.detector import detector_factory
    from dxtbx.model.crystal import crystal_model
    from cctbx.crystal_orientation import crystal_orientation,basis_type
    from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
    from scitbx import matrix
    self.experiments = ExperimentList()
    self.unique_file_names = []

    self.params = params
    data = pickle.load(open(self.params.output.prefix+"_frame.pickle","rb"))
    frames_text = data.split("\n")

    for item in frames_text:
      tokens = item.split(' ')
      wavelength = float(tokens[order_dict["wavelength"]])

      beam = beam_factory.simple(wavelength = wavelength)

      detector = detector_factory.simple(
        sensor = detector_factory.sensor("PAD"), # XXX shouldn't hard code for XFEL
        distance = float(tokens[order_dict["distance"]]),
        beam_centre = [float(tokens[order_dict["beam_x"]]), float(tokens[order_dict["beam_y"]])],
        fast_direction = "+x",
        slow_direction = "+y",
        pixel_size = [self.params.pixel_size,self.params.pixel_size],
        image_size = [1795,1795],  # XXX obviously need to figure this out
        )

      reciprocal_matrix = matrix.sqr([float(tokens[order_dict[k]]) for k in [
'res_ori_1','res_ori_2','res_ori_3','res_ori_4','res_ori_5','res_ori_6','res_ori_7','res_ori_8','res_ori_9']])
      ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
      direct = matrix.sqr(ORI.direct_matrix())
      crystal = crystal_model(
        real_space_a = matrix.row(direct[0:3]),
        real_space_b = matrix.row(direct[3:6]),
        real_space_c = matrix.row(direct[6:9]),
        space_group_symbol = "P63",  # XXX obviously another gap in the database paradigm
        mosaicity = float(tokens[order_dict["half_mosaicity_deg"]]),
      )
      crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
      #if isoform is not None:
      #  newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
      #  crystal.set_B(newB)

      self.experiments.append(Experiment(beam=beam,
                                  detector=None, #dummy for now
                                  crystal=crystal))
      self.unique_file_names.append(tokens[order_dict["unique_file_name"]])

    self.show_summary()
Esempio n. 23
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  def tst_contains(self):
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    # Create a load of models
    b1 = Beam()
    d1 = Detector()
    g1 = Goniometer()
    s1 = Scan()
    c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create an experiment
    e = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Check experiment contains model
    assert(b1 in e)
    assert(d1 in e)
    assert(g1 in e)
    assert(s1 in e)
    assert(c1 in e)

    # Create a load of models that look the same but aren't
    b2 = Beam()
    d2 = Detector()
    g2 = Goniometer()
    s2 = Scan()
    c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Check experiment doesn't contain model
    assert(b2 not in e)
    assert(d2 not in e)
    assert(g2 not in e)
    assert(s2 not in e)
    assert(c2 not in e)

    # Test passed
    print 'OK'
  def tst_contains(self):
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    # Create a load of models
    b1 = Beam()
    d1 = Detector()
    g1 = Goniometer()
    s1 = Scan()
    c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Create an experiment
    e = Experiment(
      beam=b1, detector=d1, goniometer=g1,
      scan=s1, crystal=c1, imageset=None)

    # Check experiment contains model
    assert(b1 in e)
    assert(d1 in e)
    assert(g1 in e)
    assert(s1 in e)
    assert(c1 in e)

    # Create a load of models that look the same but aren't
    b2 = Beam()
    d2 = Detector()
    g2 = Goniometer()
    s2 = Scan()
    c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)

    # Check experiment doesn't contain model
    assert(b2 not in e)
    assert(d2 not in e)
    assert(g2 not in e)
    assert(s2 not in e)
    assert(c2 not in e)

    # Test passed
    print 'OK'
Esempio n. 25
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  def __init__(self, test_nave_model = False):

    # Set up experimental models with regular geometry
    from dxtbx.model.experiment import beam_factory
    from dxtbx.model.experiment import goniometer_factory
    from dxtbx.model.experiment import detector_factory

    from dxtbx.model.crystal import crystal_model

    # Beam along the Z axis
    self.beam = beam_factory.make_beam(unit_s0 = matrix.col((0, 0, 1)),
                                       wavelength = 1.0)

    # Goniometer (used only for index generation) along X axis
    self.goniometer = goniometer_factory.known_axis(matrix.col((1, 0, 0)))

    # Detector fast, slow along X, -Y; beam in the centre, 200 mm distance
    dir1 = matrix.col((1, 0, 0))
    dir2 = matrix.col((0, -1, 0))
    n = matrix.col((0, 0, 1))
    centre = matrix.col((0, 0, 200))
    npx_fast = npx_slow = 1000
    pix_size = 0.2
    origin = centre - (0.5 * npx_fast * pix_size * dir1 +
                       0.5 * npx_slow * pix_size * dir2)
    self.detector = detector_factory.make_detector("PAD",
                        dir1, dir2, origin,
                        (pix_size, pix_size),
                        (npx_fast, npx_slow),
                        (0, 1.e6))

    # Cubic 100 A^3 crystal
    a = matrix.col((100, 0, 0))
    b = matrix.col((0, 100, 0))
    c = matrix.col((0, 0, 100))
    self.crystal = crystal_model(a, b, c, space_group_symbol = "P 1")

    if test_nave_model:
      self.crystal._ML_half_mosaicity_deg = 500
      self.crystal._ML_domain_size_ang = 0.2

    # Collect these models in an Experiment (ignoring the goniometer)
    from dxtbx.model.experiment.experiment_list import Experiment
    self.experiment = Experiment(beam=self.beam, detector=self.detector,
      goniometer=None, scan=None, crystal=self.crystal, imageset=None)

    # Generate some reflections
    self.reflections = self.generate_reflections()

    return
Esempio n. 26
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 def expt_crystal_maker(self):
   """Construct the crystal object for the experiments file."""
   a, b, c = self.ucell.parameters()[0:3]
   direct_matrix = self.ori.direct_matrix()
   real_a = direct_matrix[0:3]
   real_b = direct_matrix[3:6]
   real_c = direct_matrix[6:9]
   lattice = self.ucell.lattice_symmetry_group()
   self.crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=lattice)
   self.crystal.set_mosaicity(self.data['mosaicity'])
   self.crystal._ML_half_mosaicity_deg = self.data['ML_half_mosaicity_deg'][0]
   self.crystal._ML_domain_size_ang = self.data['ML_domain_size_ang'][0]
   if self.data['identified_isoform'] is not None:
     self.crystal.identified_isoform = self.data['identified_isoform']
Esempio n. 27
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def exercise_similarity():

    model_1 = crystal_model(real_space_a=(10, 0, 0),
                            real_space_b=(0, 11, 0),
                            real_space_c=(0, 0, 12),
                            space_group_symbol="P 1",
                            mosaicity=0.5)
    model_2 = crystal_model(real_space_a=(10, 0, 0),
                            real_space_b=(0, 11, 0),
                            real_space_c=(0, 0, 12),
                            space_group_symbol="P 1",
                            mosaicity=0.5)
    assert model_1.is_similar_to(model_2)

    # mosaicity tests
    model_1.set_mosaicity(-1)
    model_2.set_mosaicity(-0.5)
    assert model_1.is_similar_to(model_2)  # test ignores negative mosaicity
    model_1.set_mosaicity(0.5)
    model_2.set_mosaicity(0.63)  # outside tolerance
    assert not model_1.is_similar_to(model_2)
    model_2.set_mosaicity(0.625)  #just inside tolerance
    assert model_1.is_similar_to(model_2)

    # orientation tests
    R = model_2.get_U()
    dr1 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0101,
                                                                     deg=True)
    dr2 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0099,
                                                                     deg=True)
    model_2.set_U(dr1 * R)
    assert not model_1.is_similar_to(model_2)  # outside tolerance
    model_2.set_U(dr2 * R)
    assert model_1.is_similar_to(model_2)  # inside tolerance

    # unit_cell.is_similar_to is tested elsewhere
    return
Esempio n. 28
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def from_dict(d):
  ''' Convert the dictionary to a crystal model

  Params:
      d The dictionary of parameters

  Returns:
      The crystal model

  '''
  from dxtbx.model.crystal import crystal_model

  # If None, return None
  if d is None:
    return None

  # Check the version and id
  if str(d['__id__']) != "crystal":
    raise ValueError("\"__id__\" does not equal \"crystal\"")

  # Extract from the dictionary
  real_space_a = d['real_space_a']
  real_space_b = d['real_space_b']
  real_space_c = d['real_space_c']
  # str required to force unicode to ascii conversion
  space_group  = str("Hall:" + d['space_group_hall_symbol'])
  mosaicity    = d['mosaicity']
  xl = crystal_model(real_space_a, real_space_b, real_space_c,
                     space_group_symbol=space_group,
                     mosaicity=mosaicity)
  # New parameters for maximum likelihood values
  try:
    xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
  except KeyError:
    pass
  try:
    xl._ML_domain_size_ang = d['ML_domain_size_ang']
  except KeyError:
    pass

  # Extract scan point setting matrices, if present
  try:
    A_at_scan_points = d['A_at_scan_points']
    xl.set_A_at_scan_points(A_at_scan_points)
  except KeyError:
    pass

  return xl
Esempio n. 29
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def trumpet_wrapper(result, postx, file_name, params, out):
    from scitbx import matrix
    from dxtbx.model.beam import beam_factory
    beam = beam_factory.make_beam(s0=(0, 0, -1. / result["wavelength"]))
    from dxtbx.model.experiment import experiment_list
    from dxtbx.model import crystal

    obs_to_plot = postx.observations_original_index_pair1_selected  # XXX uses a private interface

    HKL = obs_to_plot.indices()
    i_sigi = obs_to_plot.data() / obs_to_plot.sigmas()
    direct_matrix = result["current_orientation"][0].direct_matrix()
    real_a = direct_matrix[0:3]
    real_b = direct_matrix[3:6]
    real_c = direct_matrix[6:9]
    SG = obs_to_plot.space_group()
    crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=SG)
    q = experiment_list.Experiment(beam=beam, crystal=crystal)

    TPL = trumpet_plot()
    from xfel.cxi.data_utils import reduction
    RED = reduction(filename=file_name,
                    experiment=q,
                    HKL=HKL,
                    i_sigi=i_sigi,
                    measurements=obs_to_plot,
                    params=params)
    TPL.set_reduction(RED)

    # first plot: before postrefinement
    TPL.reduction.experiment.crystal.set_A(
        matrix.sqr(result["current_orientation"][0].reciprocal_matrix()))
    TPL.set_refined(
        dict(half_mosaic_rotation_deg=result["ML_half_mosaicity_deg"][0],
             mosaic_domain_size_ang=result["ML_domain_size_ang"][0]))
    TPL.plot_one_model(nrow=0, out=out)

    # second plot after postrefinement
    values = postx.get_parameter_values()
    TPL.reduction.experiment.crystal.set_A(
        postx.refined_mini.refinery.get_eff_Astar(values))
    TPL.refined["red_curve_domain_size_ang"] = 1 / values.RS
    TPL.refined[
        "partiality_array"] = postx.refined_mini.refinery.get_partiality_array(
            values)
    TPL.plot_one_model(nrow=1, out=out)

    TPL.show()
  def __init__(self, plots = False):

    # Do we make scatterplots?
    self.do_plots = plots

    # Let's say we have a scan of 100 images
    self.image_range = (1, 100)

    # Make a random P1 crystal
    a = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((1, 0, 0)))
    b = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 1, 0)))
    c = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 0, 1)))
    self.xl = crystal_model(a, b, c, space_group_symbol = "P 1")
Esempio n. 31
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def get_random_predictions():
    """ Return a DIALS reflection table representing predictions using the given models.
  Assumes a Ewald proximity model for mosaicity """
    # The U matrix to calculate A*
    rot = flex.random_double_r3_rotation_matrix()
    A = sqr(rot) * sqr(uc.reciprocal().orthogonalization_matrix())
    A_inv = A.inverse()

    # Use the matrix to create a crystal model
    a = col(A_inv[:3])
    b = col(A_inv[3:6])
    c = col(A_inv[6:])
    cm = crystal_model(a, b, c, space_group=spgrp)

    # This DIALS object has no gonio or scan which will identify it as a still
    expt = Experiment(beam=beam, detector=detector, goniometer=None, scan=None, crystal=cm)

    # Predict the reflections
    return flex.reflection_table.from_predictions(expt)
  def prepare_dxtbx_models(self,setting_specific_ai,sg,isoform=None):

    from dxtbx.model.beam import beam_factory
    beam = beam_factory.simple(wavelength = self.inputai.wavelength)

    from dxtbx.model.detector import detector_factory
    detector = detector_factory.simple(
      sensor = detector_factory.sensor("PAD"),
      distance = setting_specific_ai.distance(),
      beam_centre = [setting_specific_ai.xbeam(), setting_specific_ai.ybeam()],
      fast_direction = "+x",
      slow_direction = "+y",
      pixel_size = [self.pixel_size,self.pixel_size],
      image_size = [self.inputpd['size1'],self.inputpd['size1']],
      )

    direct = matrix.sqr(setting_specific_ai.getOrientation().direct_matrix())
    from dxtbx.model.crystal import crystal_model
    crystal = crystal_model(
      real_space_a = matrix.row(direct[0:3]),
      real_space_b = matrix.row(direct[3:6]),
      real_space_c = matrix.row(direct[6:9]),
      space_group_symbol = sg,
      mosaicity = setting_specific_ai.getMosaicity()
    )
    if isoform is not None:
      newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
      crystal.set_B(newB)

    from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
    experiments = ExperimentList()
    experiments.append(Experiment(beam=beam,
                                  detector=detector,
                                  crystal=crystal))

    print beam
    print detector
    print crystal
    return experiments
Esempio n. 33
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def trumpet_wrapper(result, postx, file_name, params, out):
      from scitbx import matrix
      from dxtbx.model.beam import beam_factory
      beam = beam_factory.make_beam(s0=(0,0,-1./result["wavelength"]))
      from dxtbx.model.experiment import experiment_list
      from dxtbx.model import crystal

      obs_to_plot = postx.observations_original_index_pair1_selected # XXX uses a private interface

      HKL=obs_to_plot.indices()
      i_sigi=obs_to_plot.data()/obs_to_plot.sigmas()
      direct_matrix = result["current_orientation"][0].direct_matrix()
      real_a = direct_matrix[0:3]
      real_b = direct_matrix[3:6]
      real_c = direct_matrix[6:9]
      SG = obs_to_plot.space_group()
      crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=SG)
      q = experiment_list.Experiment(beam=beam, crystal=crystal)

      TPL = trumpet_plot()
      from xfel.cxi.data_utils import reduction
      RED = reduction(filename = file_name, experiment = q, HKL = HKL, i_sigi = i_sigi,
                    measurements = obs_to_plot, params = params)
      TPL.set_reduction(RED)

      # first plot: before postrefinement
      TPL.reduction.experiment.crystal.set_A(matrix.sqr(result["current_orientation"][0].reciprocal_matrix()))
      TPL.set_refined(dict(half_mosaic_rotation_deg=result["ML_half_mosaicity_deg"][0],
                             mosaic_domain_size_ang=result["ML_domain_size_ang"][0]))
      TPL.plot_one_model(nrow=0,out=out)

      # second plot after postrefinement
      values = postx.get_parameter_values()
      TPL.reduction.experiment.crystal.set_A(postx.refined_mini.refinery.get_eff_Astar(values))
      TPL.refined["red_curve_domain_size_ang"]=1/values.RS
      TPL.refined["partiality_array"]=postx.refined_mini.refinery.get_partiality_array(values)
      TPL.plot_one_model(nrow=1,out=out)

      TPL.show()
Esempio n. 34
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  def tst_from_imageset(self):
    from dxtbx.imageset import ImageSet, NullReader
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    imageset = ImageSet(NullReader(["filename.cbf"]))
    imageset.set_beam(Beam(), 0)
    imageset.set_detector(Detector(), 0)

    crystal = crystal_model(
      (1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)

    experiments = ExperimentListFactory.from_imageset_and_crystal(
      imageset, crystal)


    assert(len(experiments) == 1)
    assert(experiments[0].imageset is not None)
    assert(experiments[0].beam is not None)
    assert(experiments[0].detector is not None)
    assert(experiments[0].crystal is not None)

    print 'OK'
Esempio n. 35
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def get_random_predictions():
    """Return a DIALS reflection table representing predictions using the given models.
    Assumes a Ewald proximity model for mosaicity"""
    # The U matrix to calculate A*
    rot = flex.random_double_r3_rotation_matrix()
    A = sqr(rot) * sqr(uc.reciprocal().orthogonalization_matrix())
    A_inv = A.inverse()

    # Use the matrix to create a crystal model
    a = col(A_inv[:3])
    b = col(A_inv[3:6])
    c = col(A_inv[6:])
    cm = crystal_model(a, b, c, space_group=spgrp)

    # This DIALS object has no gonio or scan which will identify it as a still
    expt = Experiment(beam=beam,
                      detector=detector,
                      goniometer=None,
                      scan=None,
                      crystal=cm)

    # Predict the reflections
    return flex.reflection_table.from_predictions(expt)
  def tst_from_imageset(self):
    from dxtbx.imageset import ImageSet, NullReader
    from dxtbx.model import Beam, Detector, Goniometer, Scan
    from dxtbx.model.crystal import crystal_model

    imageset = ImageSet(NullReader(["filename.cbf"]))
    imageset.set_beam(Beam(), 0)
    imageset.set_detector(Detector(), 0)

    crystal = crystal_model(
      (1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)

    experiments = ExperimentListFactory.from_imageset_and_crystal(
      imageset, crystal)


    assert(len(experiments) == 1)
    assert(experiments[0].imageset is not None)
    assert(experiments[0].beam is not None)
    assert(experiments[0].detector is not None)
    assert(experiments[0].crystal is not None)

    print 'OK'
Esempio n. 37
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    def __init__(self, obj):
        from dxtbx.model.crystal import crystal_model
        import cctbx.uctbx
        from scitbx import matrix

        # Get the crystal parameters
        unit_cell_parameters = list(obj.handle['unit_cell'][0])
        unit_cell = cctbx.uctbx.unit_cell(unit_cell_parameters)
        U = list(obj.handle['orientation_matrix'][0].flatten())
        U = matrix.sqr(U)
        B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
        A = U * B
        Ai = A.inverse()
        real_space_a = Ai[0:3]
        real_space_b = Ai[3:6]
        real_space_c = Ai[6:9]

        # Get the space group symbol
        space_group_symbol = obj.handle['unit_cell_group'][()]

        # Create the model
        self.model = crystal_model(real_space_a, real_space_b, real_space_c,
                                   space_group_symbol)
 def predict_once(args):
   from dxtbx.model.experiment.experiment_list import Experiment
   U = args[0]
   A = U * B
   direct_matrix = A.inverse()
   cryst_model = crystal_model(direct_matrix[0:3],
                               direct_matrix[3:6],
                               direct_matrix[6:9],
                               space_group=space_group)
   experiment = Experiment(imageset=sweep,
                           beam=sweep.get_beam(),
                           detector=sweep.get_detector(),
                           goniometer=sweep.get_goniometer(),
                           scan=sweep.get_scan(),
                           crystal=cryst_model)
   predicted_reflections = flex.reflection_table.from_predictions(
     experiment)
   miller_indices = predicted_reflections['miller_index']
   miller_set = miller.set(
     crystal_symmetry, miller_indices, anomalous_flag=True)
   if params.d_min is not None:
     resolution_sel = miller_set.d_spacings().data() > params.d_min
     predicted_reflections = predicted_reflections.select(resolution_sel)
   return len(predicted_reflections)
  def __init__(self, plots = False):

    # Do we make scatterplots?
    self.do_plots = plots

    # Let's say we have a scan of 100 images
    self.image_range = (1, 100)

    # Make a random P1 crystal
    a = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((1, 0, 0)))
    b = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 1, 0)))
    c = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 0, 1)))
    self.xl = crystal_model(a, b, c, space_group_symbol = "P 1")

    # Make a beam with wavelength in the range 0.8--1.2 and s0 direction close
    # to 0,0,1
    s0 = random.uniform(0.8, 1.2) * \
        self.random_direction_close_to(matrix.col((0, 0, 1)))
    self.beam = Beam(s0)

    # Make a standard goniometer model along X
    self.goniometer = Goniometer((1,0,0))

    # Make a simple single panel detector
    d1 = matrix.col((1, 0, 0))
    d2 = matrix.col((0, -1, 0))
    npx_fast = 1475
    npx_slow = 1679
    pix_size_f = pix_size_s = 0.172
    from dxtbx.model.experiment import detector_factory
    self.detector = detector_factory.make_detector("PAD", d1, d2,
      matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
      (npx_fast, npx_slow), (0, 2e20))
  def __init__(self, plots = False):

    # Do we make scatterplots?
    self.do_plots = plots

    # Let's say we have a scan of 100 images
    self.image_range = (1, 100)

    # Make a random P1 crystal
    a = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((1, 0, 0)))
    b = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 1, 0)))
    c = random.uniform(10,50) * \
        self.random_direction_close_to(matrix.col((0, 0, 1)))
    self.xl = crystal_model(a, b, c, space_group_symbol = "P 1")

    # Make a beam with wavelength in the range 0.8--1.2 and s0 direction close
    # to 0,0,1
    s0 = random.uniform(0.8, 1.2) * \
        self.random_direction_close_to(matrix.col((0, 0, 1)))
    self.beam = Beam(s0)

    # Make a standard goniometer model along X
    self.goniometer = Goniometer((1,0,0))

    # Make a simple single panel detector
    d1 = matrix.col((1, 0, 0))
    d2 = matrix.col((0, -1, 0))
    npx_fast = 1475
    npx_slow = 1679
    pix_size_f = pix_size_s = 0.172
    from dxtbx.model.experiment import detector_factory
    self.detector = detector_factory.make_detector("PAD", d1, d2,
      matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
      (npx_fast, npx_slow), (0, 2e20))
def test1():

    dials_regression = libtbx.env.find_in_repositories(
        relative_path="dials_regression", test=os.path.isdir)

    # use a datablock that contains a CS-PAD detector description
    data_dir = os.path.join(dials_regression, "refinement_test_data",
                            "hierarchy_test")
    datablock_path = os.path.join(data_dir, "datablock.json")
    assert os.path.exists(datablock_path)

    # load models
    from dxtbx.datablock import DataBlockFactory
    datablock = DataBlockFactory.from_serialized_format(datablock_path,
                                                        check_format=False)
    im_set = datablock[0].extract_imagesets()[0]
    from copy import deepcopy
    detector = deepcopy(im_set.get_detector())
    beam = im_set.get_beam()

    # we'll invent a crystal, goniometer and scan for this test
    from dxtbx.model.crystal import crystal_model
    crystal = crystal_model((40., 0., 0.), (0., 40., 0.), (0., 0., 40.),
                            space_group_symbol="P1")

    from dxtbx.model.experiment import goniometer_factory
    goniometer = goniometer_factory.known_axis((1., 0., 0.))

    # Build a mock scan for a 180 degree sweep
    from dxtbx.model.scan import scan_factory
    sf = scan_factory()
    scan = sf.make_scan(image_range=(1, 1800),
                        exposure_times=0.1,
                        oscillation=(0, 0.1),
                        epochs=range(1800),
                        deg=True)
    sweep_range = scan.get_oscillation_range(deg=False)
    im_width = scan.get_oscillation(deg=False)[1]
    assert sweep_range == (0., pi)
    assert approx_equal(im_width, 0.1 * pi / 180.)

    from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment

    # Build an experiment list
    experiments = ExperimentList()
    experiments.append(
        Experiment(beam=beam,
                   detector=detector,
                   goniometer=goniometer,
                   scan=scan,
                   crystal=crystal,
                   imageset=None))

    # simulate some reflections
    refs, ref_predictor = generate_reflections(experiments)

    # move the detector quadrants apart by 2mm both horizontally and vertically
    from dials.algorithms.refinement.parameterisation \
      import DetectorParameterisationHierarchical
    det_param = DetectorParameterisationHierarchical(detector, level=1)
    det_p_vals = det_param.get_param_vals()
    p_vals = list(det_p_vals)
    p_vals[1] += 2
    p_vals[2] -= 2
    p_vals[7] += 2
    p_vals[8] += 2
    p_vals[13] -= 2
    p_vals[14] += 2
    p_vals[19] -= 2
    p_vals[20] -= 2
    det_param.set_param_vals(p_vals)

    # reparameterise the detector at the new perturbed geometry
    det_param = DetectorParameterisationHierarchical(detector, level=1)

    # parameterise other models
    from dials.algorithms.refinement.parameterisation.beam_parameters import \
        BeamParameterisation
    from dials.algorithms.refinement.parameterisation.crystal_parameters import \
        CrystalOrientationParameterisation, CrystalUnitCellParameterisation
    beam_param = BeamParameterisation(beam, goniometer)
    xlo_param = CrystalOrientationParameterisation(crystal)
    xluc_param = CrystalUnitCellParameterisation(crystal)

    # fix beam
    beam_param.set_fixed([True] * 3)

    # fix crystal
    xluc_param.set_fixed([True] * 6)
    xlo_param.set_fixed([True] * 3)

    # parameterisation of the prediction equation
    from dials.algorithms.refinement.parameterisation.prediction_parameters import \
        XYPhiPredictionParameterisation
    from dials.algorithms.refinement.parameterisation.parameter_report import \
        ParameterReporter
    pred_param = XYPhiPredictionParameterisation(experiments, [det_param],
                                                 [beam_param], [xlo_param],
                                                 [xluc_param])
    param_reporter = ParameterReporter([det_param], [beam_param], [xlo_param],
                                       [xluc_param])

    # reflection manager and target function
    from dials.algorithms.refinement.target import \
      LeastSquaresPositionalResidualWithRmsdCutoff
    from dials.algorithms.refinement.reflection_manager import ReflectionManager
    refman = ReflectionManager(refs, experiments, nref_per_degree=20)

    # set a very tight rmsd target of 1/10000 of a pixel
    target = LeastSquaresPositionalResidualWithRmsdCutoff(
        experiments,
        ref_predictor,
        refman,
        pred_param,
        restraints_parameterisation=None,
        frac_binsize_cutoff=0.0001)

    # minimisation engine
    from dials.algorithms.refinement.engine \
      import LevenbergMarquardtIterations as Refinery
    refinery = Refinery(target=target,
                        prediction_parameterisation=pred_param,
                        log=None,
                        verbosity=0,
                        track_step=False,
                        track_gradient=False,
                        track_parameter_correlation=False,
                        max_iterations=20)

    # Refiner
    from dials.algorithms.refinement.refiner import Refiner
    refiner = Refiner(reflections=refs,
                      experiments=experiments,
                      pred_param=pred_param,
                      param_reporter=param_reporter,
                      refman=refman,
                      target=target,
                      refinery=refinery,
                      verbosity=0)

    history = refiner.run()
    assert history.reason_for_termination == "RMSD target achieved"

    #compare detector with original detector
    orig_det = im_set.get_detector()
    refined_det = refiner.get_experiments()[0].detector

    from scitbx import matrix
    import math
    for op, rp in zip(orig_det, refined_det):
        # compare the origin vectors by...
        o1 = matrix.col(op.get_origin())
        o2 = matrix.col(rp.get_origin())
        # ...their relative lengths
        assert approx_equal(math.fabs(o1.length() - o2.length()) / o1.length(),
                            0,
                            eps=1e-5)
        # ...the angle between them
        assert approx_equal(o1.accute_angle(o2), 0, eps=1e-5)

    print "OK"
    return
Esempio n. 42
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def from_dict(d):
    ''' Convert the dictionary to a crystal model

  Params:
      d The dictionary of parameters

  Returns:
      The crystal model

  '''
    from dxtbx.model.crystal import crystal_model

    # If None, return None
    if d is None:
        return None

    # Check the version and id
    if str(d['__id__']) != "crystal":
        raise ValueError("\"__id__\" does not equal \"crystal\"")

    # Extract from the dictionary
    real_space_a = d['real_space_a']
    real_space_b = d['real_space_b']
    real_space_c = d['real_space_c']
    # str required to force unicode to ascii conversion
    space_group = str("Hall:" + d['space_group_hall_symbol'])
    mosaicity = d['mosaicity']
    xl = crystal_model(real_space_a,
                       real_space_b,
                       real_space_c,
                       space_group_symbol=space_group,
                       mosaicity=mosaicity)
    # New parameters for maximum likelihood values
    try:
        xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
    except KeyError:
        pass
    try:
        xl._ML_domain_size_ang = d['ML_domain_size_ang']
    except KeyError:
        pass

    # Isoforms used for stills
    try:
        xl.identified_isoform = d['identified_isoform']
    except KeyError:
        pass

    # Extract scan point setting matrices, if present
    try:
        A_at_scan_points = d['A_at_scan_points']
        xl.set_A_at_scan_points(A_at_scan_points)
    except KeyError:
        pass

    # Extract covariance of B, if present
    try:
        cov_B = d['B_covariance']
        xl.set_B_covariance(cov_B)
    except KeyError:
        pass

    return xl
Esempio n. 43
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    def __init__(self, params):
        import cPickle as pickle
        from dxtbx.model import BeamFactory
        from dxtbx.model import DetectorFactory
        from dxtbx.model.crystal import crystal_model
        from cctbx.crystal_orientation import crystal_orientation, basis_type
        from dxtbx.model import Experiment, ExperimentList
        from scitbx import matrix
        self.experiments = ExperimentList()
        self.unique_file_names = []

        self.params = params
        data = pickle.load(
            open(self.params.output.prefix + "_frame.pickle", "rb"))
        frames_text = data.split("\n")

        for item in frames_text:
            tokens = item.split(' ')
            wavelength = float(tokens[order_dict["wavelength"]])

            beam = BeamFactory.simple(wavelength=wavelength)

            detector = DetectorFactory.simple(
                sensor=DetectorFactory.sensor(
                    "PAD"),  # XXX shouldn't hard code for XFEL
                distance=float(tokens[order_dict["distance"]]),
                beam_centre=[
                    float(tokens[order_dict["beam_x"]]),
                    float(tokens[order_dict["beam_y"]])
                ],
                fast_direction="+x",
                slow_direction="+y",
                pixel_size=[self.params.pixel_size, self.params.pixel_size],
                image_size=[1795,
                            1795],  # XXX obviously need to figure this out
            )

            reciprocal_matrix = matrix.sqr([
                float(tokens[order_dict[k]]) for k in [
                    'res_ori_1', 'res_ori_2', 'res_ori_3', 'res_ori_4',
                    'res_ori_5', 'res_ori_6', 'res_ori_7', 'res_ori_8',
                    'res_ori_9'
                ]
            ])
            ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
            direct = matrix.sqr(ORI.direct_matrix())
            crystal = crystal_model(
                real_space_a=matrix.row(direct[0:3]),
                real_space_b=matrix.row(direct[3:6]),
                real_space_c=matrix.row(direct[6:9]),
                space_group_symbol=self.params.target_space_group.type().
                lookup_symbol(),
                mosaicity=float(tokens[order_dict["half_mosaicity_deg"]]),
            )
            crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
            #if isoform is not None:
            #  newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
            #  crystal.set_B(newB)

            self.experiments.append(
                Experiment(
                    beam=beam,
                    detector=None,  #dummy for now
                    crystal=crystal))
            self.unique_file_names.append(
                tokens[order_dict["unique_file_name"]])

        self.show_summary()
Esempio n. 44
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    from cctbx.uctbx import unit_cell

    def random_direction_close_to(vector):
        return vector.rotate_around_origin(matrix.col(
            (random.random(), random.random(), random.random())).normalize(),
                                           random.gauss(0, 1.0),
                                           deg=True)

    # make a random P1 crystal and parameterise it
    a = random.uniform(10, 50) * random_direction_close_to(
        matrix.col((1, 0, 0)))
    b = random.uniform(10, 50) * random_direction_close_to(
        matrix.col((0, 1, 0)))
    c = random.uniform(10, 50) * random_direction_close_to(
        matrix.col((0, 0, 1)))
    xl = crystal_model(a, b, c, space_group_symbol="P 1")

    xl_op = CrystalOrientationParameterisation(xl)
    xl_ucp = CrystalUnitCellParameterisation(xl)

    null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))

    # compare analytical and finite difference derivatives
    an_ds_dp = xl_op.get_ds_dp()
    fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi / 180] * 3)
    for e, f in zip(an_ds_dp, fd_ds_dp):
        assert (approx_equal((e - f), null_mat, eps=1.e-6))

    an_ds_dp = xl_ucp.get_ds_dp()
    fd_ds_dp = get_fd_gradients(xl_ucp, [1.e-7] * xl_ucp.num_free())
    for e, f in zip(an_ds_dp, fd_ds_dp):
Esempio n. 45
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def run(args):
    import libtbx.load_env
    from libtbx.utils import Sorry

    usage = "%s [options] experiments.json indexed.pickle" % libtbx.env.dispatcher_name

    parser = OptionParser(
        usage=usage,
        phil=phil_scope,
        read_reflections=True,
        read_experiments=True,
        check_format=False,
        epilog=help_message,
    )

    params, options = parser.parse_args(show_diff_phil=True)

    reflections = flatten_reflections(params.input.reflections)
    experiments = flatten_experiments(params.input.experiments)
    if len(experiments) == 0 and len(reflections) == 0:
        parser.print_help()
        return
    elif len(experiments.crystals()) > 1:
        raise Sorry("Only one crystal can be processed at a time")
    if params.change_of_basis_op is None:
        raise Sorry("Please provide a change_of_basis_op.")

    reference_crystal = None
    if params.reference is not None:
        from dxtbx.serialize import load

        reference_experiments = load.experiment_list(params.reference, check_format=False)
        assert len(reference_experiments.crystals()) == 1
        reference_crystal = reference_experiments.crystals()[0]

    if len(experiments) and params.change_of_basis_op is libtbx.Auto:
        if reference_crystal is not None:
            from dials.algorithms.indexing.compare_orientation_matrices import (
                difference_rotation_matrix_and_euler_angles,
            )

            cryst = experiments.crystals()[0]
            R, euler_angles, change_of_basis_op = difference_rotation_matrix_and_euler_angles(cryst, reference_crystal)
            print "Change of basis op: %s" % change_of_basis_op
            print "Rotation matrix to transform input crystal to reference::"
            print R.mathematica_form(format="%.3f", one_row_per_line=True)
            print "Euler angles (xyz): %.2f, %.2f, %.2f" % euler_angles

        elif len(reflections):
            assert len(reflections) == 1

            # always re-map reflections to reciprocal space
            from dials.algorithms.indexing import indexer

            refl_copy = flex.reflection_table()
            for i, imageset in enumerate(experiments.imagesets()):
                if "imageset_id" in reflections[0]:
                    sel = reflections[0]["imageset_id"] == i
                else:
                    sel = reflections[0]["id"] == i
                refl = indexer.indexer_base.map_spots_pixel_to_mm_rad(
                    reflections[0].select(sel), imageset.get_detector(), imageset.get_scan()
                )

                indexer.indexer_base.map_centroids_to_reciprocal_space(
                    refl, imageset.get_detector(), imageset.get_beam(), imageset.get_goniometer()
                )
                refl_copy.extend(refl)

            # index the reflection list using the input experiments list
            refl_copy["id"] = flex.int(len(refl_copy), -1)
            from dials.algorithms.indexing import index_reflections

            index_reflections(refl_copy, experiments, tolerance=0.2)
            hkl_expt = refl_copy["miller_index"]
            hkl_input = reflections[0]["miller_index"]

            change_of_basis_op = derive_change_of_basis_op(hkl_input, hkl_expt)

            # reset experiments list since we don't want to reindex this
            experiments = []

    else:
        change_of_basis_op = sgtbx.change_of_basis_op(params.change_of_basis_op)

    if len(experiments):
        experiment = experiments[0]
        cryst_orig = copy.deepcopy(experiment.crystal)
        cryst_reindexed = cryst_orig.change_basis(change_of_basis_op)
        if params.space_group is not None:
            a, b, c = cryst_reindexed.get_real_space_vectors()
            cryst_reindexed = crystal_model(a, b, c, space_group=params.space_group.group())
        experiment.crystal.update(cryst_reindexed)

        print "Old crystal:"
        print cryst_orig
        print
        print "New crystal:"
        print cryst_reindexed
        print

        print "Saving reindexed experimental models to %s" % params.output.experiments
        dump.experiment_list(experiments, params.output.experiments)

    if len(reflections):
        assert len(reflections) == 1
        reflections = reflections[0]

        miller_indices = reflections["miller_index"]

        if params.hkl_offset is not None:
            h, k, l = miller_indices.as_vec3_double().parts()
            h += params.hkl_offset[0]
            k += params.hkl_offset[1]
            l += params.hkl_offset[2]
            miller_indices = flex.miller_index(h.iround(), k.iround(), l.iround())
        non_integral_indices = change_of_basis_op.apply_results_in_non_integral_indices(miller_indices)
        if non_integral_indices.size() > 0:
            print "Removing %i/%i reflections (change of basis results in non-integral indices)" % (
                non_integral_indices.size(),
                miller_indices.size(),
            )
        sel = flex.bool(miller_indices.size(), True)
        sel.set_selected(non_integral_indices, False)
        miller_indices_reindexed = change_of_basis_op.apply(miller_indices.select(sel))
        reflections["miller_index"].set_selected(sel, miller_indices_reindexed)
        reflections["miller_index"].set_selected(~sel, (0, 0, 0))

        print "Saving reindexed reflections to %s" % params.output.reflections
        easy_pickle.dump(params.output.reflections, reflections)
def test1():

  dials_regression = libtbx.env.find_in_repositories(
    relative_path="dials_regression",
    test=os.path.isdir)

  # use a datablock that contains a CS-PAD detector description
  data_dir = os.path.join(dials_regression, "refinement_test_data",
                          "hierarchy_test")
  datablock_path = os.path.join(data_dir, "datablock.json")
  assert os.path.exists(datablock_path)

  # load models
  from dxtbx.datablock import DataBlockFactory
  datablock = DataBlockFactory.from_serialized_format(datablock_path, check_format=False)
  im_set = datablock[0].extract_imagesets()[0]
  from copy import deepcopy
  detector = deepcopy(im_set.get_detector())
  beam = im_set.get_beam()

  # we'll invent a crystal, goniometer and scan for this test
  from dxtbx.model.crystal import crystal_model
  crystal = crystal_model((40.,0.,0.) ,(0.,40.,0.), (0.,0.,40.),
                          space_group_symbol = "P1")

  from dxtbx.model.experiment import goniometer_factory
  goniometer = goniometer_factory.known_axis((1., 0., 0.))

  # Build a mock scan for a 180 degree sweep
  from dxtbx.model.scan import scan_factory
  sf = scan_factory()
  scan = sf.make_scan(image_range = (1,1800),
                      exposure_times = 0.1,
                      oscillation = (0, 0.1),
                      epochs = range(1800),
                      deg = True)
  sweep_range = scan.get_oscillation_range(deg=False)
  im_width = scan.get_oscillation(deg=False)[1]
  assert sweep_range == (0., pi)
  assert approx_equal(im_width, 0.1 * pi / 180.)

  from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment

  # Build an experiment list
  experiments = ExperimentList()
  experiments.append(Experiment(
        beam=beam, detector=detector, goniometer=goniometer,
        scan=scan, crystal=crystal, imageset=None))

  # simulate some reflections
  refs, ref_predictor = generate_reflections(experiments)

  # move the detector quadrants apart by 2mm both horizontally and vertically
  from dials.algorithms.refinement.parameterisation \
    import DetectorParameterisationHierarchical
  det_param = DetectorParameterisationHierarchical(detector, level=1)
  det_p_vals = det_param.get_param_vals()
  p_vals = list(det_p_vals)
  p_vals[1] += 2
  p_vals[2] -= 2
  p_vals[7] += 2
  p_vals[8] += 2
  p_vals[13] -= 2
  p_vals[14] += 2
  p_vals[19] -= 2
  p_vals[20] -= 2
  det_param.set_param_vals(p_vals)

  # reparameterise the detector at the new perturbed geometry
  det_param = DetectorParameterisationHierarchical(detector, level=1)

  # parameterise other models
  from dials.algorithms.refinement.parameterisation.beam_parameters import \
      BeamParameterisation
  from dials.algorithms.refinement.parameterisation.crystal_parameters import \
      CrystalOrientationParameterisation, CrystalUnitCellParameterisation
  beam_param = BeamParameterisation(beam, goniometer)
  xlo_param = CrystalOrientationParameterisation(crystal)
  xluc_param = CrystalUnitCellParameterisation(crystal)

  # fix beam
  beam_param.set_fixed([True]*3)

  # fix crystal
  xluc_param.set_fixed([True]*6)
  xlo_param.set_fixed([True]*3)

  # parameterisation of the prediction equation
  from dials.algorithms.refinement.parameterisation.prediction_parameters import \
      XYPhiPredictionParameterisation
  from dials.algorithms.refinement.parameterisation.parameter_report import \
      ParameterReporter
  pred_param = XYPhiPredictionParameterisation(experiments,
    [det_param], [beam_param], [xlo_param], [xluc_param])
  param_reporter = ParameterReporter([det_param], [beam_param],
                                     [xlo_param], [xluc_param])

  # reflection manager and target function
  from dials.algorithms.refinement.target import \
    LeastSquaresPositionalResidualWithRmsdCutoff
  from dials.algorithms.refinement.reflection_manager import ReflectionManager
  refman = ReflectionManager(refs, experiments, nref_per_degree=20)

  # set a very tight rmsd target of 1/10000 of a pixel
  target = LeastSquaresPositionalResidualWithRmsdCutoff(experiments,
      ref_predictor, refman, pred_param, restraints_parameterisation=None,
      frac_binsize_cutoff=0.0001)

  # minimisation engine
  from dials.algorithms.refinement.engine \
    import LevenbergMarquardtIterations as Refinery
  refinery = Refinery(target = target,
                      prediction_parameterisation = pred_param,
                      log = None,
                      verbosity = 0,
                      track_step = False,
                      track_gradient = False,
                      track_parameter_correlation = False,
                      max_iterations = 20)

  # Refiner
  from dials.algorithms.refinement.refiner import Refiner
  refiner = Refiner(reflections=refs,
                    experiments=experiments,
                    pred_param=pred_param,
                    param_reporter=param_reporter,
                    refman=refman,
                    target=target,
                    refinery=refinery,
                    verbosity=0)

  history = refiner.run()
  assert history.reason_for_termination == "RMSD target achieved"

  #compare detector with original detector
  orig_det = im_set.get_detector()
  refined_det = refiner.get_experiments()[0].detector

  from scitbx import matrix
  import math
  for op, rp in zip(orig_det, refined_det):
    # compare the origin vectors by...
    o1 = matrix.col(op.get_origin())
    o2 = matrix.col(rp.get_origin())
    # ...their relative lengths
    assert approx_equal(
      math.fabs(o1.length() - o2.length()) / o1.length(), 0, eps=1e-5)
    # ...the angle between them
    assert approx_equal(o1.accute_angle(o2), 0, eps=1e-5)

  print "OK"
  return
Esempio n. 47
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def run(space_group_info):
    datablock_json = os.path.join(dials_regression, "indexing_test_data",
                                  "i04_weak_data", "datablock_orig.json")

    datablock = load.datablock(datablock_json, check_format=False)[0]
    sweep = datablock.extract_imagesets()[0]

    sweep._indices = sweep._indices[:20]
    sweep.set_scan(sweep.get_scan()[:20])

    import random
    space_group = space_group_info.group()
    unit_cell = space_group_info.any_compatible_unit_cell(
        volume=random.uniform(1e4, 1e6))

    crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
                                        space_group=space_group)
    crystal_symmetry.show_summary()

    # the reciprocal matrix
    B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
    U = random_rotation()
    A = U * B

    direct_matrix = A.inverse()
    cryst_model = crystal_model(direct_matrix[0:3],
                                direct_matrix[3:6],
                                direct_matrix[6:9],
                                space_group=space_group)
    experiment = Experiment(imageset=sweep,
                            beam=sweep.get_beam(),
                            detector=sweep.get_detector(),
                            goniometer=sweep.get_goniometer(),
                            scan=sweep.get_scan(),
                            crystal=cryst_model)
    predicted_reflections = flex.reflection_table.from_predictions(experiment)
    use_fraction = 0.3
    use_sel = flex.random_selection(
        len(predicted_reflections),
        int(use_fraction * len(predicted_reflections)))
    predicted_reflections = predicted_reflections.select(use_sel)
    miller_indices = predicted_reflections['miller_index']
    miller_set = miller.set(crystal_symmetry,
                            miller_indices,
                            anomalous_flag=True)
    predicted_reflections['xyzobs.mm.value'] = predicted_reflections[
        'xyzcal.mm']
    predicted_reflections['id'] = flex.int(len(predicted_reflections), 0)
    from dials.algorithms.indexing.indexer import indexer_base
    indexer_base.map_centroids_to_reciprocal_space(predicted_reflections,
                                                   sweep.get_detector(),
                                                   sweep.get_beam(),
                                                   sweep.get_goniometer())

    # check that local and global indexing worked equally well in absence of errors
    result = compare_global_local(experiment, predicted_reflections,
                                  miller_indices)
    assert result.misindexed_local == 0
    assert result.misindexed_global == 0

    a, b, c = cryst_model.get_real_space_vectors()
    relative_error = 0.02
    a *= (1 + relative_error)
    b *= (1 + relative_error)
    c *= (1 + relative_error)

    cryst_model2 = crystal_model(a, b, c, space_group=space_group)
    experiment.crystal = cryst_model2

    result = compare_global_local(experiment, predicted_reflections,
                                  miller_indices)

    # check that the local indexing did a better job given the errors in the basis vectors
    #assert result.misindexed_local < result.misindexed_global
    assert result.misindexed_local == 0
    assert result.correct_local > result.correct_global
    # usually the number misindexed is much smaller than this
    assert result.misindexed_local < (0.001 * len(result.reflections_local))

    # the reciprocal matrix
    A = cryst_model.get_A()
    A = random_rotation(angle_max=0.03) * A

    direct_matrix = A.inverse()
    cryst_model2 = crystal_model(direct_matrix[0:3],
                                 direct_matrix[3:6],
                                 direct_matrix[6:9],
                                 space_group=space_group)
    experiment.crystal = cryst_model2

    result = compare_global_local(experiment, predicted_reflections,
                                  miller_indices)

    # check that the local indexing did a better job given the errors in the basis vectors
    assert result.misindexed_local <= result.misindexed_global, (
        result.misindexed_local, result.misindexed_global)
    assert result.misindexed_local < 0.01 * result.correct_local
    assert result.correct_local > result.correct_global
    # usually the number misindexed is much smaller than this
    assert result.misindexed_local < (0.001 * len(result.reflections_local))
Esempio n. 48
0
def exercise_crystal_model():

  real_space_a = matrix.col((10,0,0))
  real_space_b = matrix.col((0,11,0))
  real_space_c = matrix.col((0,0,12))
  model = crystal_model(real_space_a=(10,0,0),
                        real_space_b=(0,11,0),
                        real_space_c=(0,0,12),
                        space_group_symbol="P 1")
  assert isinstance(model.get_unit_cell(), uctbx.unit_cell)
  assert model.get_unit_cell().parameters() == (
    10.0, 11.0, 12.0, 90.0, 90.0, 90.0)
  assert approx_equal(model.get_A(), (1/10, 0, 0, 0, 1/11, 0, 0, 0, 1/12))
  assert approx_equal(model.get_A().inverse(), (10, 0, 0, 0, 11, 0, 0, 0, 12))
  assert approx_equal(model.get_B(), model.get_A())
  assert approx_equal(model.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
  assert approx_equal(model.get_real_space_vectors(),
                      (real_space_a, real_space_b, real_space_c))
  assert approx_equal(model.get_mosaicity(), 0)

  model2 = crystal_model(real_space_a=(10,0,0),
                         real_space_b=(0,11,0),
                         real_space_c=(0,0,12),
                         space_group_symbol="P 1")
  assert model == model2
  model2.set_mosaicity(0.01)
  assert model != model2
  # rotate 45 degrees about x-axis
  R1 = matrix.sqr((1, 0, 0,
                   0, math.cos(math.pi/4), -math.sin(math.pi/4),
                   0, math.sin(math.pi/4), math.cos(math.pi/4)))
  # rotate 30 degrees about y-axis
  R2 = matrix.sqr((math.cos(math.pi/6), 0, math.sin(math.pi/6),
                   0, 1, 0,
                   -math.sin(math.pi/6), 0, math.cos(math.pi/6)))
  # rotate 60 degrees about z-axis
  R3 = matrix.sqr((math.cos(math.pi/3), -math.sin(math.pi/3), 0,
                   math.sin(math.pi/3), math.cos(math.pi/3), 0,
                   0, 0, 1))
  R = R1 * R2 * R3
  model.set_U(R)
  # B is unchanged
  assert approx_equal(model.get_B(), (1/10, 0, 0, 0, 1/11, 0, 0, 0, 1/12))
  assert approx_equal(model.get_U(), R)
  assert approx_equal(model.get_A(), model.get_U() * model.get_B())
  a_, b_, c_ = model.get_real_space_vectors()
  assert approx_equal(a_, R * real_space_a)
  assert approx_equal(b_, R * real_space_b)
  assert approx_equal(c_, R * real_space_c)
  s = StringIO()
  print >> s, model
  assert not show_diff(s.getvalue().replace("-0.0000", " 0.0000"), """\
Crystal:
    Unit cell: (10.000, 11.000, 12.000, 90.000, 90.000, 90.000)
    Space group: P 1
    U matrix:  {{ 0.4330, -0.7500,  0.5000},
                { 0.7891,  0.0474, -0.6124},
                { 0.4356,  0.6597,  0.6124}}
    B matrix:  {{ 0.1000,  0.0000,  0.0000},
                { 0.0000,  0.0909,  0.0000},
                { 0.0000,  0.0000,  0.0833}}
    A = UB:    {{ 0.0433, -0.0682,  0.0417},
                { 0.0789,  0.0043, -0.0510},
                { 0.0436,  0.0600,  0.0510}}

""")
  model.set_B((1/12, 0, 0, 0, 1/12, 0, 0, 0, 1/12))
  assert approx_equal(model.get_unit_cell().parameters(),
                      (12, 12, 12, 90, 90, 90))

  U = matrix.sqr((
    0.3455, -0.2589, -0.9020, 0.8914, 0.3909, 0.2293, 0.2933, -0.8833, 0.3658))
  B = matrix.sqr((1/13, 0, 0, 0, 1/13, 0, 0, 0, 1/13))
  model.set_A(U * B)
  assert approx_equal(model.get_A(), U * B)
  assert approx_equal(model.get_U(), U, 1e-4)
  assert approx_equal(model.get_B(), B, 1e-5)

  model3 = crystal_model(
    real_space_a=(10,0,0),
    real_space_b=(0,11,0),
    real_space_c=(0,0,12),
    space_group=sgtbx.space_group_info("P 222").group(),
    mosaicity=0.01)
  assert model3.get_space_group().type().hall_symbol() == " P 2 2"
  assert model != model3
  #
  sgi_ref = sgtbx.space_group_info(number=230)
  model_ref = crystal_model(
    real_space_a=(44,0,0),
    real_space_b=(0,44,0),
    real_space_c=(0,0,44),
    space_group=sgi_ref.group())
  assert approx_equal(model_ref.get_U(), (1,0,0,0,1,0,0,0,1))
  assert approx_equal(model_ref.get_B(), (1/44,0,0,0,1/44,0,0,0,1/44))
  assert approx_equal(model_ref.get_A(), model_ref.get_B())
  assert approx_equal(model_ref.get_unit_cell().parameters(),
                      (44,44,44,90,90,90))
  a_ref, b_ref, c_ref = model_ref.get_real_space_vectors()
  cb_op_to_primitive = sgi_ref.change_of_basis_op_to_primitive_setting()
  model_primitive = model_ref.change_basis(cb_op_to_primitive)
  cb_op_to_reference = model_primitive.get_space_group().info()\
    .change_of_basis_op_to_reference_setting()
  a_prim, b_prim, c_prim = model_primitive.get_real_space_vectors()
  #print cb_op_to_primitive.as_abc()
  ##'-1/2*a+1/2*b+1/2*c,1/2*a-1/2*b+1/2*c,1/2*a+1/2*b-1/2*c'
  assert approx_equal(a_prim, -1/2 * a_ref + 1/2 * b_ref + 1/2 * c_ref)
  assert approx_equal(b_prim, 1/2 * a_ref - 1/2 * b_ref + 1/2 * c_ref)
  assert approx_equal(c_prim, 1/2 * a_ref + 1/2 * b_ref - 1/2 * c_ref)
  #print cb_op_to_reference.as_abc()
  ##b+c,a+c,a+b
  assert approx_equal(a_ref, b_prim + c_prim)
  assert approx_equal(b_ref, a_prim + c_prim)
  assert approx_equal(c_ref, a_prim + b_prim)
  assert approx_equal(
    model_primitive.get_U(),
  [-0.5773502691896258, 0.40824829046386285, 0.7071067811865476,
   0.5773502691896257, -0.4082482904638631, 0.7071067811865476,
   0.5773502691896257, 0.8164965809277259, 0.0])
  assert approx_equal(
    model_primitive.get_B(),
    [0.0262431940540739, 0.0, 0.0, 0.00927837023781507, 0.02783511071344521,
     0.0, 0.01607060866333063, 0.01607060866333063, 0.03214121732666125])
  assert approx_equal(
    model_primitive.get_A(), (0, 1/44, 1/44, 1/44, 0, 1/44, 1/44, 1/44, 0))
  assert approx_equal(
    model_primitive.get_unit_cell().parameters(),
    [38.1051177665153, 38.1051177665153, 38.1051177665153,
     109.47122063449069, 109.47122063449069, 109.47122063449069])
  assert model_ref != model_primitive
  model_ref_recycled = model_primitive.change_basis(cb_op_to_reference)
  assert approx_equal(model_ref.get_U(), model_ref_recycled.get_U())
  assert approx_equal(model_ref.get_B(), model_ref_recycled.get_B())
  assert approx_equal(model_ref.get_A(), model_ref_recycled.get_A())
  assert approx_equal(model_ref.get_unit_cell().parameters(),
                      model_ref_recycled.get_unit_cell().parameters())
  assert model_ref == model_ref_recycled
  #
  uc = uctbx.unit_cell((58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
  sg = sgtbx.space_group_info(symbol="P1").group()
  cs = crystal.symmetry(unit_cell=uc, space_group=sg)
  cb_op_to_minimum = cs.change_of_basis_op_to_minimum_cell()
  # the reciprocal matrix
  B = matrix.sqr(uc.fractionalization_matrix()).transpose()
  U = random_rotation()
  direct_matrix = (U * B).inverse()
  model = crystal_model(direct_matrix[:3],
                        direct_matrix[3:6],
                        direct_matrix[6:9],
                        space_group=sg)
  assert uc.is_similar_to(model.get_unit_cell())
  uc_minimum = uc.change_basis(cb_op_to_minimum)
  model_minimum = model.change_basis(cb_op_to_minimum)
  assert uc_minimum.is_similar_to(model_minimum.get_unit_cell())
  assert model_minimum != model
  model_minimum.update(model)
  assert model_minimum == model
  #
  from scitbx.math import euler_angles
  A_static = model.get_A()
  A_as_scan_points = [A_static]
  num_scan_points = 11
  for i in range(num_scan_points-1):
    A_as_scan_points.append(
      A_as_scan_points[-1] * matrix.sqr(euler_angles.xyz_matrix(0.1,0.2,0.3)))
  model.set_A_at_scan_points(A_as_scan_points)
  model_minimum = model.change_basis(cb_op_to_minimum)
  assert model.num_scan_points == model_minimum.num_scan_points == num_scan_points
  M = matrix.sqr(cb_op_to_minimum.c_inv().r().transpose().as_double())
  M_inv = M.inverse()
  for i in range(num_scan_points):
    A_orig = model.get_A_at_scan_point(i)
    A_min = model_minimum.get_A_at_scan_point(i)
    assert A_min == A_orig * M_inv
Esempio n. 49
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def write_par_file(file_name, experiment):
    from scitbx import matrix
    from dxtbx.model.crystal import crystal_model
    from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
    from dials.command_line.refine_bravais_settings import short_space_group_name

    imageset = experiment.imageset
    detector = imageset.get_detector()
    goniometer = imageset.get_goniometer()
    beam = imageset.get_beam()
    scan = imageset.get_scan()

    R_to_mosflm = align_reference_frame(beam.get_s0(), (1.0, 0.0, 0.0),
                                        goniometer.get_rotation_axis(),
                                        (0.0, 0.0, 1.0))

    cryst = experiment.crystal
    cryst = cryst.change_basis(
      cryst.get_space_group().info()\
        .change_of_basis_op_to_reference_setting())
    A = cryst.get_A()
    A_inv = A.inverse()

    real_space_a = R_to_mosflm * A_inv.elems[:3]
    real_space_b = R_to_mosflm * A_inv.elems[3:6]
    real_space_c = R_to_mosflm * A_inv.elems[6:9]

    cryst_mosflm = crystal_model(real_space_a,
                                 real_space_b,
                                 real_space_c,
                                 space_group=cryst.get_space_group(),
                                 mosaicity=cryst.get_mosaicity())
    A_mosflm = cryst_mosflm.get_A()
    U_mosflm = cryst_mosflm.get_U()
    B_mosflm = cryst_mosflm.get_B()
    UB_mosflm = U_mosflm * B_mosflm
    uc_params = cryst_mosflm.get_unit_cell().parameters()
    assert U_mosflm.is_r3_rotation_matrix(), U_mosflm

    symmetry = cryst_mosflm.get_space_group().type().number()
    beam_centre = tuple(reversed(detector[0].get_beam_centre(beam.get_s0())))
    distance = detector[0].get_directed_distance()
    polarization = R_to_mosflm * matrix.col(beam.get_polarization_normal())
    rotation = matrix.col(goniometer.get_rotation_axis())
    if (rotation.angle(matrix.col(detector[0].get_fast_axis())) <
            rotation.angle(matrix.col(detector[0].get_slow_axis()))):
        direction = 'FAST'
    else:
        direction = 'SLOW'
    rotation = R_to_mosflm * rotation

    with open(file_name, 'wb') as f:  #
        print >> f, '# parameter file for BEST'
        print >> f, 'TITLE          From DIALS'
        print >> f, 'DETECTOR       PILA'
        print >> f, 'SITE           Not set'
        print >> f, 'DIAMETER       %6.2f' % (max(
            detector[0].get_image_size()) * detector[0].get_pixel_size()[0])
        print >> f, 'PIXEL          %s' % detector[0].get_pixel_size()[0]
        print >> f, 'ROTAXIS        %4.2f %4.2f %4.2f' % rotation.elems, direction
        print >> f, 'POLAXIS        %4.2f %4.2f %4.2f' % polarization.elems
        print >> f, 'GAIN               1.00'  # correct for Pilatus images
        print >> f, 'CMOSAIC            %.2f' % experiment.profile.sigma_m()
        print >> f, 'PHISTART           %.2f' % scan.get_oscillation_range()[0]
        print >> f, 'PHIWIDTH           %.2f' % scan.get_oscillation()[1]
        print >> f, 'DISTANCE        %7.2f' % distance
        print >> f, 'WAVELENGTH      %.5f' % beam.get_wavelength()
        print >> f, 'POLARISATION    %7.5f' % beam.get_polarization_fraction()
        print >> f, 'SYMMETRY       %s' % short_space_group_name(
            cryst.get_space_group())
        print >> f, 'UB             %9.2f %9.2f %9.2f' % UB_mosflm[:3]
        print >> f, '               %9.2f %9.2f %9.2f' % UB_mosflm[3:6]
        print >> f, '               %9.2f %9.2f %9.2f' % UB_mosflm[6:]
        print >> f, 'CELL           %8.2f %8.2f %8.2f %6.2f %6.2f %6.2f' % uc_params
        print >> f, 'RASTER           13  13   7   3   4'
        print >> f, 'SEPARATION      2.960  2.960'
        print >> f, 'BEAM           %8.3f %8.3f' % beam_centre
        print >> f, '# end of parameter file for BEST'
Esempio n. 50
0
  def extract_varying_crystal(integrate_lp, experiments):
    '''Extract a varying crystal model from an INTEGRATE.LP file (static
    in blocks with step changes) and write it to the provided
    experiments
    '''

    if len(experiments) > 1:
      print "Can only read a varying crystal model for a single " +\
            "experiment. Skipping."
      return
    experiment = experiments[0]

    # read required records from the file. Relies on them being in the
    # right order as we read through once
    xds_axis = None
    xds_beam = None
    blocks, a_axis, b_axis, c_axis = [], [], [], []
    with open(integrate_lp) as f:
      for record in f:
        if record.lstrip().startswith("ROTATION_AXIS="):
          xds_axis = record.split("ROTATION_AXIS=")[1].split()
          break
      for record in f:
        if record.lstrip().startswith("INCIDENT_BEAM_DIRECTION="):
          xds_beam = record.split("INCIDENT_BEAM_DIRECTION=")[1].split()
          break
      for record in f:
        if record.lstrip().startswith("PROCESSING OF IMAGES"):
          blocks.append(record.split("PROCESSING OF IMAGES")[1])
          continue
        if record.lstrip().startswith("COORDINATES OF UNIT CELL A-AXIS"):
          a_axis.append(record.split("COORDINATES OF UNIT CELL A-AXIS")[1])
          continue
        if record.lstrip().startswith("COORDINATES OF UNIT CELL B-AXIS"):
          b_axis.append(record.split("COORDINATES OF UNIT CELL B-AXIS")[1])
          continue
        if record.lstrip().startswith("COORDINATES OF UNIT CELL C-AXIS"):
          c_axis.append(record.split("COORDINATES OF UNIT CELL C-AXIS")[1])
          continue

    # sanity checks
    msg = "INTEGRATE.LP is not in the expected format"
    nblocks = len(blocks)
    try:
      assert len(a_axis) == len(b_axis) == len(c_axis) == nblocks
      assert (xds_axis, xds_beam).count(None) == 0
    except AssertionError:
      print msg
      return

    # conversions to numeric
    try:
      blocks = [map(int, block.split("...")) for block in blocks]
      a_axis = [map(float, axis.split()) for axis in a_axis]
      b_axis = [map(float, axis.split()) for axis in b_axis]
      c_axis = [map(float, axis.split()) for axis in c_axis]
      xds_beam = [float(e) for e in xds_beam]
      xds_axis = [float(e) for e in xds_axis]
    except ValueError:
      print msg
      return

    # coordinate frame conversions
    from scitbx import matrix
    dbeam = matrix.col(experiment.beam.get_direction())
    daxis = matrix.col(experiment.goniometer.get_rotation_axis())
    xbeam = matrix.col(xds_beam).normalize()
    xaxis = matrix.col(xds_axis).normalize()

    # want to align XDS -s0 vector...
    from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
    R = align_reference_frame(- xbeam, dbeam, xaxis, daxis)

    # Make a static crystal for each block
    from dxtbx.model.crystal import crystal_model
    crystals = []
    sg = experiment.crystal.get_space_group()
    for a, b, c in zip(a_axis, b_axis, c_axis):
      a = R * matrix.col(a)
      b = R * matrix.col(b)
      c = R * matrix.col(c)
      crystals.append(crystal_model(a, b, c, space_group=sg))

    # construct a list of scan points
    A_list = []
    for block, crystal in zip(blocks, crystals):
      A = crystal.get_A()
      for im in range(block[0], block[1] + 1):
        A_list.append(A)
    # Need a final scan point at the end of the final image
    A_list.append(A)

    # set the scan-varying crystal
    experiment.crystal.set_A_at_scan_points(A_list)

    return
Esempio n. 51
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def test_refinement():
  '''Test a refinement run'''

  dials_regression = libtbx.env.find_in_repositories(
    relative_path="dials_regression",
    test=os.path.isdir)

  # Get a beam and detector from a datablock. This one has a CS-PAD, but that
  # is irrelevant
  data_dir = os.path.join(dials_regression, "refinement_test_data",
                          "hierarchy_test")
  datablock_path = os.path.join(data_dir, "datablock.json")
  assert os.path.exists(datablock_path)

  # load models
  from dxtbx.datablock import DataBlockFactory
  datablock = DataBlockFactory.from_serialized_format(datablock_path, check_format=False)
  im_set = datablock[0].extract_imagesets()[0]
  from copy import deepcopy
  detector = deepcopy(im_set.get_detector())
  beam = im_set.get_beam()

  # Invent a crystal, goniometer and scan for this test
  from dxtbx.model.crystal import crystal_model
  crystal = crystal_model((40.,0.,0.) ,(0.,40.,0.), (0.,0.,40.),
                          space_group_symbol = "P1")
  orig_xl = deepcopy(crystal)

  from dxtbx.model.experiment import goniometer_factory
  goniometer = goniometer_factory.known_axis((1., 0., 0.))

  # Build a mock scan for a 180 degree sweep
  from dxtbx.model.scan import scan_factory
  sf = scan_factory()
  scan = sf.make_scan(image_range = (1,1800),
                      exposure_times = 0.1,
                      oscillation = (0, 0.1),
                      epochs = range(1800),
                      deg = True)
  sweep_range = scan.get_oscillation_range(deg=False)
  im_width = scan.get_oscillation(deg=False)[1]
  assert sweep_range == (0., pi)
  assert approx_equal(im_width, 0.1 * pi / 180.)

  from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment

  # Build an experiment list
  experiments = ExperimentList()
  experiments.append(Experiment(
        beam=beam, detector=detector, goniometer=goniometer,
        scan=scan, crystal=crystal, imageset=None))

  # simulate some reflections
  refs, _ = generate_reflections(experiments)

  # change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
  # alpha and beta angles)
  from dials.algorithms.refinement.parameterisation.crystal_parameters import \
    CrystalUnitCellParameterisation
  xluc_param = CrystalUnitCellParameterisation(crystal)
  xluc_p_vals = xluc_param.get_param_vals()
  cell_params = crystal.get_unit_cell().parameters()
  cell_params = [a + b for a, b in zip(cell_params, [0.1, -0.1, 0.1, 0.1,
                                                     -0.1, 0.0])]
  from cctbx.uctbx import unit_cell
  from rstbx.symmetry.constraints.parameter_reduction import \
      symmetrize_reduce_enlarge
  from scitbx import matrix
  new_uc = unit_cell(cell_params)
  newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
  S = symmetrize_reduce_enlarge(crystal.get_space_group())
  S.set_orientation(orientation=newB)
  X = tuple([e * 1.e5 for e in S.forward_independent_parameters()])
  xluc_param.set_param_vals(X)

  # reparameterise the crystal at the perturbed geometry
  xluc_param = CrystalUnitCellParameterisation(crystal)

  # Dummy parameterisations for other models
  beam_param = None
  xlo_param = None
  det_param = None

  # parameterisation of the prediction equation
  from dials.algorithms.refinement.parameterisation.parameter_report import \
      ParameterReporter
  pred_param = TwoThetaPredictionParameterisation(experiments,
    det_param, beam_param, xlo_param, [xluc_param])
  param_reporter = ParameterReporter(det_param, beam_param,
                                     xlo_param, [xluc_param])

  # reflection manager
  refman = TwoThetaReflectionManager(refs, experiments, nref_per_degree=20,
    verbosity=2)

  # reflection predictor
  ref_predictor = TwoThetaExperimentsPredictor(experiments)

  # target function
  target = TwoThetaTarget(experiments, ref_predictor, refman, pred_param)

  # minimisation engine
  from dials.algorithms.refinement.engine \
    import LevenbergMarquardtIterations as Refinery
  refinery = Refinery(target = target,
                      prediction_parameterisation = pred_param,
                      log = None,
                      verbosity = 0,
                      track_step = False,
                      track_gradient = False,
                      track_parameter_correlation = False,
                      max_iterations = 20)

  # Refiner
  from dials.algorithms.refinement.refiner import Refiner
  refiner = Refiner(reflections=refs,
                    experiments=experiments,
                    pred_param=pred_param,
                    param_reporter=param_reporter,
                    refman=refman,
                    target=target,
                    refinery=refinery,
                    verbosity=1)

  history = refiner.run()

  # compare crystal with original crystal
  refined_xl = refiner.get_experiments()[0].crystal

  #print refined_xl
  assert refined_xl.is_similar_to(orig_xl, uc_rel_length_tolerance=0.001,
    uc_abs_angle_tolerance=0.01)

  #print "Unit cell esds:"
  #print refined_xl.get_cell_parameter_sd()

  return
Esempio n. 52
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def dump(experiments, directory):
    '''
  Dump the experiments in mosflm format

  :param experiments: The experiments to dump
  :param directory: The directory to write to

  '''
    for i, experiment in enumerate(experiments):
        suffix = ""
        if len(experiments) > 1:
            suffix = "_%i" % (i + 1)

        sub_dir = "%s%s" % (directory, suffix)
        if not os.path.isdir(sub_dir):
            os.makedirs(sub_dir)
        detector = experiment.detector
        beam = experiment.beam
        scan = experiment.scan
        goniometer = experiment.goniometer

        # XXX imageset is getting the experimental geometry from the image files
        # rather than the input experiments.json file
        imageset = experiment.imageset

        from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
        R_to_mosflm = align_reference_frame(beam.get_s0(), (1.0, 0.0, 0.0),
                                            goniometer.get_rotation_axis(),
                                            (0.0, 0.0, 1.0))
        #print R_to_mosflm

        cryst = experiment.crystal
        cryst = cryst.change_basis(
          cryst.get_space_group().info()\
            .change_of_basis_op_to_reference_setting())
        A = cryst.get_A()
        A_inv = A.inverse()

        real_space_a = R_to_mosflm * A_inv.elems[:3]
        real_space_b = R_to_mosflm * A_inv.elems[3:6]
        real_space_c = R_to_mosflm * A_inv.elems[6:9]

        cryst_mosflm = crystal_model(real_space_a,
                                     real_space_b,
                                     real_space_c,
                                     space_group=cryst.get_space_group(),
                                     mosaicity=cryst.get_mosaicity())
        A_mosflm = cryst_mosflm.get_A()
        U_mosflm = cryst_mosflm.get_U()
        assert U_mosflm.is_r3_rotation_matrix(), U_mosflm
        w = beam.get_wavelength()

        index_mat = os.path.join(sub_dir, "index.mat")
        mosflm_in = os.path.join(sub_dir, "mosflm.in")
        print "Exporting experiment to %s and %s" % (index_mat, mosflm_in)

        with open(index_mat, "wb") as f:
            print >> f, format_mosflm_mat(w * A_mosflm, U_mosflm,
                                          cryst.get_unit_cell())

        directory, template = os.path.split(imageset.get_template())
        symmetry = cryst_mosflm.get_space_group().type().number()
        beam_centre = tuple(
            reversed(detector[0].get_beam_centre(beam.get_s0())))
        distance = detector[0].get_directed_distance()

        with open(mosflm_in, "wb") as f:
            print >> f, write_mosflm_input(directory=directory,
                                           template=template,
                                           symmetry=symmetry,
                                           beam_centre=beam_centre,
                                           distance=distance,
                                           mat_file="index.mat")

    return
Esempio n. 53
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def run(space_group_info):
  datablock_json = os.path.join(
    dials_regression, "indexing_test_data",
    "i04_weak_data", "datablock_orig.json")

  datablock = load.datablock(datablock_json, check_format=False)[0]
  sweep = datablock.extract_imagesets()[0]

  sweep._indices = sweep._indices[:20]
  sweep.set_scan(sweep.get_scan()[:20])

  import random
  space_group = space_group_info.group()
  unit_cell = space_group_info.any_compatible_unit_cell(volume=random.uniform(1e4,1e6))

  crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
                                      space_group=space_group)
  crystal_symmetry.show_summary()

  # the reciprocal matrix
  B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
  U = random_rotation()
  A = U * B

  direct_matrix = A.inverse()
  cryst_model = crystal_model(direct_matrix[0:3],
                              direct_matrix[3:6],
                              direct_matrix[6:9],
                              space_group=space_group)
  experiment = Experiment(imageset=sweep,
                          beam=sweep.get_beam(),
                          detector=sweep.get_detector(),
                          goniometer=sweep.get_goniometer(),
                          scan=sweep.get_scan(),
                          crystal=cryst_model)
  predicted_reflections = flex.reflection_table.from_predictions(
    experiment)
  use_fraction = 0.3
  use_sel = flex.random_selection(
    len(predicted_reflections), int(use_fraction*len(predicted_reflections)))
  predicted_reflections = predicted_reflections.select(use_sel)
  miller_indices = predicted_reflections['miller_index']
  miller_set = miller.set(
    crystal_symmetry, miller_indices, anomalous_flag=True)
  predicted_reflections['xyzobs.mm.value'] = predicted_reflections['xyzcal.mm']
  predicted_reflections['id'] = flex.int(len(predicted_reflections), 0)
  from dials.algorithms.indexing.indexer import indexer_base
  indexer_base.map_centroids_to_reciprocal_space(
    predicted_reflections, sweep.get_detector(), sweep.get_beam(),
    sweep.get_goniometer())


  # check that local and global indexing worked equally well in absence of errors
  result = compare_global_local(experiment, predicted_reflections,
                                miller_indices)
  assert result.misindexed_local == 0
  assert result.misindexed_global == 0

  a, b, c = cryst_model.get_real_space_vectors()
  relative_error = 0.02
  a *= (1+relative_error)
  b *= (1+relative_error)
  c *= (1+relative_error)

  cryst_model2 = crystal_model(a, b, c, space_group=space_group)
  experiment.crystal = cryst_model2

  result = compare_global_local(experiment, predicted_reflections,
                                miller_indices)

  # check that the local indexing did a better job given the errors in the basis vectors
  #assert result.misindexed_local < result.misindexed_global
  assert result.misindexed_local == 0
  assert result.correct_local > result.correct_global
  # usually the number misindexed is much smaller than this
  assert result.misindexed_local < (0.001 * len(result.reflections_local))

  # the reciprocal matrix
  A = cryst_model.get_A()
  A = random_rotation(angle_max=0.03) * A

  direct_matrix = A.inverse()
  cryst_model2 = crystal_model(direct_matrix[0:3],
                               direct_matrix[3:6],
                               direct_matrix[6:9],
                               space_group=space_group)
  experiment.crystal = cryst_model2

  result = compare_global_local(experiment, predicted_reflections,
                                miller_indices)

  # check that the local indexing did a better job given the errors in the basis vectors
  assert result.misindexed_local <= result.misindexed_global, (
    result.misindexed_local, result.misindexed_global)
  assert result.misindexed_local < 0.01 * result.correct_local
  assert result.correct_local > result.correct_global
  # usually the number misindexed is much smaller than this
  assert result.misindexed_local < (0.001 * len(result.reflections_local))