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Source code for dxtbx.serialize.xds
from __future__ import absolute_import, division, print_function
import warnings
from cctbx import uctbx
from cctbx.eltbx import attenuation_coefficient
from cctbx.sgtbx import space_group, space_group_symbols
from iotbx.xds import xds_inp, xparm
from rstbx.cftbx.coordinate_frame_converter import coordinate_frame_converter
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from scitbx import matrix
import dxtbx
from dxtbx.imageset import ImageSetFactory
from dxtbx.model import Crystal, MosaicCrystalKabsch2010, ParallaxCorrectedPxMmStrategy
from dxtbx.model.detector_helpers_types import detector_helpers_types
[docs]def to_imageset(input_filename, extra_filename=None):
"""Get an image set from the xds input filename plus an extra filename
Params:
input_filename The XDS.INP file
extra_filename A (G)XPARM.XDS, INTGRATE.HKL or XDS_ASCII.HKL file
Returns:
The imageset
"""
# Read the input filename
handle = xds_inp.reader()
handle.read_file(input_filename)
# Get the template
template = handle.name_template_of_data_frames[0].replace("?", "#")
if template.endswith("h5"):
template = template.replace("######", "master")
image_range = handle.data_range
detector_name = handle.detector
if extra_filename is not None:
# we can get all the extra dxtbx models from extra_filename
check_format = False
else:
# we need the image files present to get the dxtbx models
check_format = True
# If an extra filename has been specified, try to load models
if extra_filename:
models = dxtbx.load(extra_filename)
detector = models.get_detector()
if detector_name.strip() in ("PILATUS", "EIGER") or handle.silicon is not None:
if handle.silicon is None:
table = attenuation_coefficient.get_table("Si")
wavelength = models.get_beam().get_wavelength()
mu = table.mu_at_angstrom(wavelength) / 10.0
else:
mu = handle.silicon
t0 = handle.sensor_thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
panel.set_trusted_range(
(handle.minimum_valid_pixel_value, handle.overload)
)
beam = models.get_beam()
detector = models.get_detector()
goniometer = models.get_goniometer()
scan = models.get_scan()
scan.set_image_range(image_range)
else:
beam = None
detector = None
goniometer = None
scan = None
# Create the imageset
imageset = ImageSetFactory.from_template(
template,
image_range=image_range,
check_format=check_format,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
)[0]
# Return the imageset
return imageset
[docs]def to_crystal(filename):
"""Get the crystal model from the xparm file
Params:
filename The xparm/or integrate filename
Return:
The crystal model
"""
# 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")
crystal_space_group = space_group(space_group_symbols(sg).hall())
mosaicity = cfc.get("mosaicity")
# Return the crystal model
if mosaicity is None:
crystal = Crystal(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=crystal_space_group,
)
else:
crystal = MosaicCrystalKabsch2010(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=crystal_space_group,
)
crystal.set_mosaicity(mosaicity)
return crystal
[docs]def xds_detector_name(dxtbx_name):
"""Translate from a xia2 name from the detector library to an XDS detector
name."""
# http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DETECTOR=
if "pilatus" in dxtbx_name:
return "PILATUS"
if "eiger" in dxtbx_name:
return "PILATUS"
if "rayonix" in dxtbx_name:
return "CCDCHESS"
if "adsc" in dxtbx_name:
return "ADSC"
if "holton" in dxtbx_name:
return "ADSC"
if "saturn" in dxtbx_name:
return "SATURN"
if "raxis" in dxtbx_name:
return "RAXIS"
if "mar-345" in dxtbx_name:
return "MAR345"
if "mar" in dxtbx_name:
return "MAR"
if "unknown" in dxtbx_name:
return "ADSC"
raise RuntimeError("detector %s unknown" % dxtbx_name)
[docs]class to_xds(object):
"""A class to export contents of a Sequence as XDS.INP or XPARM.XDS."""
def __init__(self, sequence):
self._sequence = sequence
# detector dimensions in pixels
self.detector_size = [
int(
max(
panel.get_raw_image_offset()[0] + panel.get_image_size()[0]
for panel in self.get_detector()
)
),
int(
max(
panel.get_raw_image_offset()[1] + panel.get_image_size()[1]
for panel in self.get_detector()
)
),
]
self.fast, self.slow = self.detector_size
if len(self.get_detector()) > 1:
fast = self.get_detector()[0].get_parent_fast_axis()
slow = self.get_detector()[0].get_parent_slow_axis()
Rd = align_reference_frame(fast, (1, 0, 0), slow, (0, 1, 0))
origin = Rd * matrix.col(self.get_detector()[0].get_parent_origin())
else:
fast = self.get_detector()[0].get_fast_axis()
slow = self.get_detector()[0].get_slow_axis()
Rd = align_reference_frame(fast, (1, 0, 0), slow, (0, 1, 0))
origin = Rd * matrix.col(self.get_detector()[0].get_origin())
self.detector_x_axis = (Rd * matrix.col(fast)).elems
self.detector_y_axis = (Rd * matrix.col(slow)).elems
F = Rd * matrix.col(fast)
S = Rd * matrix.col(slow)
N = F.cross(S)
self.detector_normal = N.elems
# assume all panels same pixel size
self.pixel_size = self.get_detector()[0].get_pixel_size()
centre = -(origin - origin.dot(N) * N)
x = centre.dot(F)
y = centre.dot(S)
f, s = self.pixel_size
self.detector_distance = origin.dot(N)
# Need to add 0.5 because XDS seems to do centroids in fortran coords
self.detector_origin = (x / f + 0.5, y / f + 0.5)
self.imagecif_to_xds_transformation_matrix = Rd
self.panel_limits = []
self.panel_x_axis = []
self.panel_y_axis = []
self.panel_origin = []
self.panel_distance = []
self.panel_normal = []
for panel_id, panel in enumerate(self.get_detector()):
f = Rd * matrix.col(panel.get_fast_axis())
s = Rd * matrix.col(panel.get_slow_axis())
n = f.cross(s)
xmin, ymin = panel.get_raw_image_offset()
xmax = xmin + panel.get_image_size()[0]
ymax = ymin + panel.get_image_size()[1]
self.panel_limits.append((xmin + 1, xmax, ymin + 1, ymax))
o = Rd * matrix.col(panel.get_origin())
op = o.dot(n) * n
d0 = matrix.col((-x, -y, self.detector_distance))
orgsx = (op - o + d0).dot(f) / self.pixel_size[0] + xmin
orgsy = (op - o + d0).dot(s) / self.pixel_size[1] + ymin
panel_distance = op.dot(n) - d0.dot(n)
# axes in local (i.e. detector) frame
fl = matrix.col(panel.get_local_fast_axis())
sl = matrix.col(panel.get_local_slow_axis())
nl = fl.cross(sl)
self.panel_x_axis.append(fl.elems)
self.panel_y_axis.append(sl.elems)
self.panel_normal.append(nl.elems)
self.panel_origin.append((orgsx, orgsy))
self.panel_distance.append(panel_distance)
# Beam stuff
self.wavelength = self.get_beam().get_wavelength()
self.beam_vector = Rd * matrix.col(
self.get_beam().get_sample_to_source_direction()
)
# just to make sure it is the correct length
self.beam_vector = self.beam_vector.normalize() # / self.wavelength
self.beam_vector = (-self.beam_vector).elems
# Scan and goniometer stuff
self.starting_frame = self.get_scan().get_image_range()[0]
self.starting_angle = self.get_scan().get_oscillation()[0]
self.oscillation_range = self.get_scan().get_oscillation()[1]
self.rotation_axis = (
Rd * matrix.col(self.get_goniometer().get_rotation_axis())
).elems
[docs] def get_template(self):
try:
return self._sequence.get_template()
except AttributeError:
return "FIXME####.h5"
[docs] def XDS_INP(
self,
space_group_number=None,
real_space_a=None,
real_space_b=None,
real_space_c=None,
job_card="XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT",
as_str=None,
):
if as_str:
warnings.warn(
"as_str= parameter is deprecated and will be removed in the future",
DeprecationWarning,
stacklevel=2,
)
result = []
assert [real_space_a, real_space_b, real_space_c].count(None) in (0, 3)
sensor = self.get_detector()[0].get_type()
fast, slow = self.detector_size
f, s = self.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds)
)
trusted = self.get_detector()[0].get_trusted_range()
result.append(
"DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d"
% (detector, trusted[0] + 1, trusted[1])
)
if detector == "PILATUS":
result.append(
"SENSOR_THICKNESS= %.3f" % self.get_detector()[0].get_thickness()
)
if self.get_detector()[0].get_material():
material = self.get_detector()[0].get_material()
table = attenuation_coefficient.get_table(material)
mu = table.mu_at_angstrom(self.wavelength) / 10.0
result.append(
"!SENSOR_MATERIAL / THICKNESS %s %.3f"
% (material, self.get_detector()[0].get_thickness())
)
result.append("!SILICON= %f" % mu)
result.append(
"DIRECTION_OF_DETECTOR_X-AXIS= %.5f %.5f %.5f" % self.detector_x_axis
)
result.append(
"DIRECTION_OF_DETECTOR_Y-AXIS= %.5f %.5f %.5f" % self.detector_y_axis
)
result.append("NX=%d NY=%d QX=%.4f QY=%.4f" % (fast, slow, f, s))
result.append("DETECTOR_DISTANCE= %.6f" % self.detector_distance)
result.append("ORGX= %.2f ORGY= %.2f" % self.detector_origin)
result.append("ROTATION_AXIS= %.5f %.5f %.5f" % self.rotation_axis)
result.append("STARTING_ANGLE= %.3f" % self.starting_angle)
result.append("OSCILLATION_RANGE= %.3f" % self.oscillation_range)
result.append("X-RAY_WAVELENGTH= %.5f" % self.wavelength)
result.append(
"INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f"
% tuple([b / self.wavelength for b in self.beam_vector])
)
# FIXME LATER
if hasattr(self.get_beam(), "get_polarization_fraction"):
result.append(
"FRACTION_OF_POLARIZATION= %.3f"
% self.get_beam().get_polarization_fraction()
)
result.append(
"POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f"
% self.get_beam().get_polarization_normal()
)
template = self.get_template()
if template.endswith("master.h5"):
template = template.replace("master", "??????")
result.append("NAME_TEMPLATE_OF_DATA_FRAMES= %s" % template.replace("#", "?"))
result.append("TRUSTED_REGION= 0.0 1.41")
for panel, (x0, _, y0, _) in zip(self.get_detector(), self.panel_limits):
for f0, s0, f1, s1 in panel.get_mask():
result.append(
"UNTRUSTED_RECTANGLE= %d %d %d %d"
% (f0 + x0 - 1, f1 + x0, s0 + y0 - 1, s1 + y0)
)
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
result.append("DATA_RANGE= %d %d" % start_end)
result.append("JOB=%s" % job_card)
if space_group_number is not None:
result.append("SPACE_GROUP_NUMBER= %i" % space_group_number)
if [real_space_a, real_space_b, real_space_c].count(None) == 0:
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
result.append("UNIT_CELL_A-AXIS= %.6f %.6f %.6f" % unit_cell_a_axis.elems)
result.append("UNIT_CELL_B-AXIS= %.6f %.6f %.6f" % unit_cell_b_axis.elems)
result.append("UNIT_CELL_C-AXIS= %.6f %.6f %.6f" % unit_cell_c_axis.elems)
if len(self.panel_x_axis) > 1:
for panel_id, panel_x_axis in enumerate(self.panel_x_axis):
result.append("")
result.append("!")
result.append("! SEGMENT %d" % (panel_id + 1))
result.append("!")
result.append("SEGMENT= %d %d %d %d" % self.panel_limits[panel_id])
result.append(
"DIRECTION_OF_SEGMENT_X-AXIS= %.5f %.5f %.5f" % panel_x_axis
)
result.append(
"DIRECTION_OF_SEGMENT_Y-AXIS= %.5f %.5f %.5f"
% self.panel_y_axis[panel_id]
)
result.append("SEGMENT_DISTANCE= %.3f" % self.panel_distance[panel_id])
result.append(
"SEGMENT_ORGX= %.2f SEGMENT_ORGY= %.2f"
% self.panel_origin[panel_id]
)
return "\n".join(result)
[docs] def xparm_xds(self, real_space_a, real_space_b, real_space_c, space_group):
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
A_inv = matrix.sqr(
unit_cell_a_axis.elems + unit_cell_b_axis.elems + unit_cell_c_axis.elems
)
metrical_matrix = (A_inv * A_inv.transpose()).as_sym_mat3()
unit_cell = uctbx.unit_cell(metrical_matrix=metrical_matrix)
return xparm.write(
self.starting_frame,
self.starting_angle,
self.oscillation_range,
self.rotation_axis,
self.wavelength,
self.beam_vector,
space_group,
unit_cell.parameters(),
unit_cell_a_axis.elems,
unit_cell_b_axis.elems,
unit_cell_c_axis.elems,
None, # num_segments
self.detector_size,
self.pixel_size,
self.detector_origin,
self.detector_distance,
self.detector_x_axis,
self.detector_y_axis,
self.detector_normal,
segments=None,
orientation=None,
)
