def xparm_xds(self,
real_space_a,
real_space_b,
real_space_c,
space_group,
out=None):
from cctbx import uctbx
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)
from iotbx.xds import xparm
writer = xparm.writer(
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,
)
writer.show(out=out)
def xparm_xds(self, real_space_a, real_space_b, real_space_c,
space_group, out=None):
from cctbx import uctbx
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)
from iotbx.xds import xparm
writer = xparm.writer(
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)
writer.show(out=out)
def run(self):
from iotbx.xds import xparm
import os
import libtbx.load_env
from libtbx.test_utils import open_tmp_file
iotbx_dir = libtbx.env.dist_path('iotbx')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 1
handle.read_file(filename)
print('OK')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'NEW_XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 2
handle.read_file(filename)
print('OK')
f = open_tmp_file(suffix='XPARM.XDS', mode='wb')
f.close()
writer = xparm.writer(
handle.starting_frame,
handle.starting_angle,
handle.oscillation_range,
handle.rotation_axis,
handle.wavelength,
handle.beam_vector,
handle.space_group,
handle.unit_cell,
handle.unit_cell_a_axis,
handle.unit_cell_b_axis,
handle.unit_cell_c_axis,
handle.num_segments,
handle.detector_size,
handle.pixel_size,
handle.detector_origin,
handle.detector_distance,
handle.detector_x_axis,
handle.detector_y_axis,
handle.detector_normal,
handle.segments,
handle.orientation)
writer.write_file(f.name)
handle_recycled = xparm.reader()
# make sure we wrote out version 2
assert handle_recycled.find_version(f.name) == 2
handle_recycled.read_file(f.name)
for handle in (handle, handle_recycled):
# Scan and goniometer stuff
assert handle.starting_frame == 1
assert handle.starting_angle == 82.0
assert handle.oscillation_range == 0.1500
assert handle.rotation_axis == (0.999997, -0.001590, -0.001580)
# Beam stuff
assert handle.wavelength == 0.976250
assert handle.beam_vector == (0.001608, 0.004392, 1.024317)
# Detector stuff
assert handle.detector_size == (2463, 2527)
assert handle.pixel_size == (0.172, 0.172)
assert handle.detector_distance == 264.928955
assert handle.detector_origin == (1224.856812, 1187.870972)
assert handle.detector_x_axis == (1.0, 0.0, 0.0)
assert handle.detector_y_axis == (0.0, 1.0, 0.0)
assert handle.detector_normal == (0.0, 0.0, 1.0)
# Crystal stuff
assert handle.space_group == 75
assert handle.unit_cell == (57.7831, 57.7831, 150.0135, 90.000, 90.000, 90.000)
assert handle.unit_cell_a_axis == (-14.918090, -22.358297, 51.151196)
assert handle.unit_cell_b_axis == (-19.858326, 51.608330, 16.766487)
assert handle.unit_cell_c_axis == (-135.447952, -34.400188, -54.539391)
# segment stuff
assert handle_recycled.num_segments == 1
assert handle_recycled.segments == [(1, 1, 2463, 1, 2527)]
assert handle_recycled.orientation == [
(0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0)]
print('OK')
def xparm_xds(self,
real_space_a,
real_space_b,
real_space_c,
space_group,
out=None):
from cctbx import uctbx
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)
from iotbx.xds import xparm
from six.moves import StringIO
b = StringIO()
writer = xparm.writer(
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,
)
writer.show(out=b)
old = b.getvalue()
new = 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,
)
assert old == new
if out:
warnings.warn(
"out= parameter is deprecated. Use return value instead",
DeprecationWarning,
stacklevel=2,
)
print(new, end="", file=out)
return new
def run(self):
from iotbx.xds import xparm
import os
import libtbx.load_env
from libtbx.test_utils import open_tmp_file
iotbx_dir = libtbx.env.dist_path('iotbx')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 1
handle.read_file(filename)
print 'OK'
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'NEW_XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 2
handle.read_file(filename)
print 'OK'
f = open_tmp_file(suffix='XPARM.XDS', mode='wb')
f.close()
writer = xparm.writer(
handle.starting_frame,
handle.starting_angle,
handle.oscillation_range,
handle.rotation_axis,
handle.wavelength,
handle.beam_vector,
handle.space_group,
handle.unit_cell,
handle.unit_cell_a_axis,
handle.unit_cell_b_axis,
handle.unit_cell_c_axis,
handle.num_segments,
handle.detector_size,
handle.pixel_size,
handle.detector_origin,
handle.detector_distance,
handle.detector_x_axis,
handle.detector_y_axis,
handle.detector_normal,
handle.segments,
handle.orientation)
writer.write_file(f.name)
handle_recycled = xparm.reader()
# make sure we wrote out version 2
assert handle_recycled.find_version(f.name) == 2
handle_recycled.read_file(f.name)
for handle in (handle, handle_recycled):
# Scan and goniometer stuff
assert handle.starting_frame == 1
assert handle.starting_angle == 82.0
assert handle.oscillation_range == 0.1500
assert handle.rotation_axis == (0.999997, -0.001590, -0.001580)
# Beam stuff
assert handle.wavelength == 0.976250
assert handle.beam_vector == (0.001608, 0.004392, 1.024317)
# Detector stuff
assert handle.detector_size == (2463, 2527)
assert handle.pixel_size == (0.172, 0.172)
assert handle.detector_distance == 264.928955
assert handle.detector_origin == (1224.856812, 1187.870972)
assert handle.detector_x_axis == (1.0, 0.0, 0.0)
assert handle.detector_y_axis == (0.0, 1.0, 0.0)
assert handle.detector_normal == (0.0, 0.0, 1.0)
# Crystal stuff
assert handle.space_group == 75
assert handle.unit_cell == (57.7831, 57.7831, 150.0135, 90.000, 90.000, 90.000)
assert handle.unit_cell_a_axis == (-14.918090, -22.358297, 51.151196)
assert handle.unit_cell_b_axis == (-19.858326, 51.608330, 16.766487)
assert handle.unit_cell_c_axis == (-135.447952, -34.400188, -54.539391)
# segment stuff
assert handle_recycled.num_segments == 1
assert handle_recycled.segments == [(1, 1, 2463, 1, 2527)]
assert handle_recycled.orientation == [
(0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0)]
print 'OK'
