def main(xparm_file, spot_file):
import dxtbx
from dxtbx.serialize.xds import to_crystal
models = dxtbx.load(xparm_file)
crystal_model = to_crystal(xparm_file)
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
experiment = Experiment(beam=models.get_beam(),
detector=models.get_detector(),
goniometer=models.get_goniometer(),
scan=models.get_scan(),
crystal=crystal_model)
detector = experiment.detector
beam = experiment.beam
goniometer = experiment.goniometer
scan = experiment.scan
from iotbx.xds import spot_xds
spot_xds_handle = spot_xds.reader()
spot_xds_handle.read_file(spot_file)
from cctbx.array_family import flex
centroids_px = flex.vec3_double(spot_xds_handle.centroid)
miller_indices = flex.miller_index(spot_xds_handle.miller_index)
# only those reflections that were actually indexed
centroids_px = centroids_px.select(miller_indices != (0,0,0))
miller_indices = miller_indices.select(miller_indices != (0,0,0))
ub = crystal_model.get_A()
d_spacings = [1.0 / (ub * mi).length() for mi in miller_indices]
print max(d_spacings)
# Convert Pixel coordinate into mm/rad
x, y, z = centroids_px.parts()
x_mm, y_mm = detector[0].pixel_to_millimeter(flex.vec2_double(x, y)).parts()
z_rad = scan.get_angle_from_array_index(z, deg=False)
centroids_mm = flex.vec3_double(x_mm, y_mm, z_rad)
# then convert detector position to reciprocal space position
# based on code in dials/algorithms/indexing/indexer2.py
s1 = detector[0].get_lab_coord(flex.vec2_double(x_mm, y_mm))
s1 = s1/s1.norms() * (1/beam.get_wavelength())
S = s1 - beam.get_s0()
reciprocal_space_points = S.rotate_around_origin(
goniometer.get_rotation_axis(),
-z_rad)
d_spacings = 1/reciprocal_space_points.norms()
dmax = flex.max(d_spacings)
print dmax
def from_xds(xds_inp, xds_other):
"""Generate an experiment list from XDS files."""
# Get the sequence from the XDS files
sequence = xds.to_imageset(xds_inp, xds_other)
# Get the crystal from the XDS files
crystal = xds.to_crystal(xds_other)
# Create the experiment list
experiments = ExperimentListFactory.from_imageset_and_crystal(sequence, crystal)
# Set the crystal in the experiment list
assert len(experiments) == 1
return experiments
def from_xds(xds_inp, xds_other):
''' Generate an experiment list from XDS files. '''
from dxtbx.serialize import xds
from dxtbx.datablock import DataBlockFactory
# Get the sweep from the XDS files
sweep = xds.to_imageset(xds_inp, xds_other)
# Get the crystal from the XDS files
crystal = xds.to_crystal(xds_other)
# Create the experiment list
experiments = ExperimentListFactory.from_imageset_and_crystal(
sweep, crystal)
# Set the crystal in the experiment list
assert (len(experiments) == 1)
# Return the experiment list
return experiments
def from_xds(xds_inp, xds_other):
''' Generate an experiment list from XDS files. '''
from dxtbx.serialize import xds
from dxtbx.datablock import DataBlockFactory
# Get the sweep from the XDS files
sweep = xds.to_imageset(xds_inp, xds_other)
# Get the crystal from the XDS files
crystal = xds.to_crystal(xds_other)
# Create the experiment list
experiments = ExperimentListFactory.from_imageset_and_crystal(
sweep, crystal)
# Set the crystal in the experiment list
assert(len(experiments) == 1)
# Return the experiment list
return experiments
def _index(self):
"""Actually do the autoindexing using the data prepared by the
previous method."""
self._index_remove_masked_regions()
if self._i_or_ii is None:
self._i_or_ii = self.decide_i_or_ii()
logger.debug("Selecting I or II, chose %s", self._i_or_ii)
idxref = self.Idxref()
for file in ["SPOT.XDS"]:
idxref.set_input_data_file(file, self._indxr_payload[file])
# set the phi start etc correctly
idxref.set_data_range(self._indxr_images[0][0],
self._indxr_images[0][1])
idxref.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
if self._i_or_ii == "i":
blocks = self._index_select_images_i()
for block in blocks[:1]:
starting_frame = block[0]
starting_angle = self.get_scan().get_angle_from_image_index(
starting_frame)
idxref.set_starting_frame(starting_frame)
idxref.set_starting_angle(starting_angle)
idxref.add_spot_range(block[0], block[1])
for block in blocks[1:]:
idxref.add_spot_range(block[0], block[1])
else:
for block in self._indxr_images[:1]:
starting_frame = block[0]
starting_angle = self.get_scan().get_angle_from_image_index(
starting_frame)
idxref.set_starting_frame(starting_frame)
idxref.set_starting_angle(starting_angle)
idxref.add_spot_range(block[0], block[1])
for block in self._indxr_images[1:]:
idxref.add_spot_range(block[0], block[1])
# FIXME need to also be able to pass in the known unit
# cell and lattice if already available e.g. from
# the helper... indirectly
if self._indxr_user_input_lattice:
idxref.set_indexer_user_input_lattice(True)
if self._indxr_input_lattice and self._indxr_input_cell:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
idxref.set_indexer_input_cell(self._indxr_input_cell)
logger.debug("Set lattice: %s", self._indxr_input_lattice)
logger.debug("Set cell: %f %f %f %f %f %f" %
self._indxr_input_cell)
original_cell = self._indxr_input_cell
elif self._indxr_input_lattice:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
original_cell = None
else:
original_cell = None
# FIXED need to set the beam centre here - this needs to come
# from the input .xinfo object or header, and be converted
# to the XDS frame... done.
from dxtbx.serialize.xds import to_xds
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
idxref.set_beam_centre(xds_beam_centre[0], xds_beam_centre[1])
# fixme need to check if the lattice, cell have been set already,
# and if they have, pass these in as input to the indexing job.
done = False
while not done:
try:
done = idxref.run()
# N.B. in here if the IDXREF step was being run in the first
# pass done is FALSE however there should be a refined
# P1 orientation matrix etc. available - so keep it!
except XDSException as e:
# inspect this - if we have complaints about not
# enough reflections indexed, and we have a target
# unit cell, and they are the same, well ignore it
if "solution is inaccurate" in str(e):
logger.debug(
"XDS complains solution inaccurate - ignoring")
done = idxref.continue_from_error()
elif ("insufficient percentage (< 70%)" in str(e)
or "insufficient percentage (< 50%)"
in str(e)) and original_cell:
done = idxref.continue_from_error()
lattice, cell, mosaic = idxref.get_indexing_solution()
# compare solutions
check = PhilIndex.params.xia2.settings.xds_check_cell_deviation
for j in range(3):
# allow two percent variation in unit cell length
if (math.fabs(
(cell[j] - original_cell[j]) / original_cell[j]) >
0.02 and check):
logger.debug("XDS unhappy and solution wrong")
raise e
# and two degree difference in angle
if (math.fabs(cell[j + 3] - original_cell[j + 3]) > 2.0
and check):
logger.debug("XDS unhappy and solution wrong")
raise e
logger.debug("XDS unhappy but solution ok")
elif "insufficient percentage (< 70%)" in str(
e) or "insufficient percentage (< 50%)" in str(e):
logger.debug("XDS unhappy but solution probably ok")
done = idxref.continue_from_error()
else:
raise e
FileHandler.record_log_file(
"%s INDEX" % self.get_indexer_full_name(),
os.path.join(self.get_working_directory(), "IDXREF.LP"),
)
for file in ["SPOT.XDS", "XPARM.XDS"]:
self._indxr_payload[file] = idxref.get_output_data_file(file)
# need to get the indexing solutions out somehow...
self._indxr_other_lattice_cell = idxref.get_indexing_solutions()
(
self._indxr_lattice,
self._indxr_cell,
self._indxr_mosaic,
) = idxref.get_indexing_solution()
xparm_file = os.path.join(self.get_working_directory(), "XPARM.XDS")
models = dxtbx.load(xparm_file)
crystal_model = to_crystal(xparm_file)
# this information gets lost when re-creating the models from the
# XDS results - however is not refined so can simply copy from the
# input - https://github.com/xia2/xia2/issues/372
models.get_detector()[0].set_thickness(
converter.get_detector()[0].get_thickness())
experiment = Experiment(
beam=models.get_beam(),
detector=models.get_detector(),
goniometer=models.get_goniometer(),
scan=models.get_scan(),
crystal=crystal_model,
# imageset=self.get_imageset(),
)
experiment_list = ExperimentList([experiment])
self.set_indexer_experiment_list(experiment_list)
# I will want this later on to check that the lattice was ok
self._idxref_subtree_problem = idxref.get_index_tree_problem()
def _index(self):
'''Actually do the autoindexing using the data prepared by the
previous method.'''
images_str = '%d to %d' % tuple(self._indxr_images[0])
for i in self._indxr_images[1:]:
images_str += ', %d to %d' % tuple(i)
cell_str = None
if self._indxr_input_cell:
cell_str = '%.2f %.2f %.2f %.2f %.2f %.2f' % \
self._indxr_input_cell
# then this is a proper autoindexing run - describe this
# to the journal entry
#if len(self._fp_directory) <= 50:
#dirname = self._fp_directory
#else:
#dirname = '...%s' % self._fp_directory[-46:]
dirname = self.get_directory()
Journal.block(
'autoindexing', self._indxr_sweep_name, 'XDS', {
'images': images_str,
'target cell': cell_str,
'target lattice': self._indxr_input_lattice,
'template': self.get_template(),
'directory': dirname
})
self._index_remove_masked_regions()
if self._i_or_ii is None:
self._i_or_ii = self.decide_i_or_ii()
Debug.write('Selecting I or II, chose %s' % self._i_or_ii)
idxref = self.Idxref()
for file in ['SPOT.XDS']:
idxref.set_input_data_file(file, self._indxr_payload[file])
# set the phi start etc correctly
idxref.set_data_range(self._indxr_images[0][0],
self._indxr_images[0][1])
idxref.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
if self._i_or_ii == 'i':
blocks = self._index_select_images_i()
for block in blocks[:1]:
starting_frame = block[0]
starting_angle = self.get_scan().get_angle_from_image_index(
starting_frame)
idxref.set_starting_frame(starting_frame)
idxref.set_starting_angle(starting_angle)
idxref.add_spot_range(block[0], block[1])
for block in blocks[1:]:
idxref.add_spot_range(block[0], block[1])
else:
for block in self._indxr_images[:1]:
starting_frame = block[0]
starting_angle = self.get_scan().get_angle_from_image_index(
starting_frame)
idxref.set_starting_frame(starting_frame)
idxref.set_starting_angle(starting_angle)
idxref.add_spot_range(block[0], block[1])
for block in self._indxr_images[1:]:
idxref.add_spot_range(block[0], block[1])
# FIXME need to also be able to pass in the known unit
# cell and lattice if already available e.g. from
# the helper... indirectly
if self._indxr_user_input_lattice:
idxref.set_indexer_user_input_lattice(True)
if self._indxr_input_lattice and self._indxr_input_cell:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
idxref.set_indexer_input_cell(self._indxr_input_cell)
Debug.write('Set lattice: %s' % self._indxr_input_lattice)
Debug.write('Set cell: %f %f %f %f %f %f' % \
self._indxr_input_cell)
original_cell = self._indxr_input_cell
elif self._indxr_input_lattice:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
original_cell = None
else:
original_cell = None
# FIXED need to set the beam centre here - this needs to come
# from the input .xinfo object or header, and be converted
# to the XDS frame... done.
#mosflm_beam_centre = self.get_beam_centre()
#xds_beam_centre = beam_centre_mosflm_to_xds(
#mosflm_beam_centre[0], mosflm_beam_centre[1], self.get_header())
from dxtbx.serialize.xds import to_xds
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
idxref.set_beam_centre(xds_beam_centre[0], xds_beam_centre[1])
# fixme need to check if the lattice, cell have been set already,
# and if they have, pass these in as input to the indexing job.
done = False
while not done:
try:
done = idxref.run()
# N.B. in here if the IDXREF step was being run in the first
# pass done is FALSE however there should be a refined
# P1 orientation matrix etc. available - so keep it!
except XDSException as e:
# inspect this - if we have complaints about not
# enough reflections indexed, and we have a target
# unit cell, and they are the same, well ignore it
if 'solution is inaccurate' in str(e):
Debug.write('XDS complains solution inaccurate - ignoring')
done = idxref.continue_from_error()
elif ('insufficient percentage (< 70%)' in str(e) or
'insufficient percentage (< 50%)' in str(e)) and \
original_cell:
done = idxref.continue_from_error()
lattice, cell, mosaic = \
idxref.get_indexing_solution()
# compare solutions
check = PhilIndex.params.xia2.settings.xds_check_cell_deviation
for j in range(3):
# allow two percent variation in unit cell length
if math.fabs((cell[j] - original_cell[j]) / \
original_cell[j]) > 0.02 and check:
Debug.write('XDS unhappy and solution wrong')
raise e
# and two degree difference in angle
if math.fabs(cell[j + 3] - original_cell[j + 3]) \
> 2.0 and check:
Debug.write('XDS unhappy and solution wrong')
raise e
Debug.write('XDS unhappy but solution ok')
elif 'insufficient percentage (< 70%)' in str(e) or \
'insufficient percentage (< 50%)' in str(e):
Debug.write('XDS unhappy but solution probably ok')
done = idxref.continue_from_error()
else:
raise e
FileHandler.record_log_file(
'%s INDEX' % self.get_indexer_full_name(),
os.path.join(self.get_working_directory(), 'IDXREF.LP'))
for file in ['SPOT.XDS', 'XPARM.XDS']:
self._indxr_payload[file] = idxref.get_output_data_file(file)
# need to get the indexing solutions out somehow...
self._indxr_other_lattice_cell = idxref.get_indexing_solutions()
self._indxr_lattice, self._indxr_cell, self._indxr_mosaic = \
idxref.get_indexing_solution()
import dxtbx
from dxtbx.serialize.xds import to_crystal
xparm_file = os.path.join(self.get_working_directory(), 'XPARM.XDS')
models = dxtbx.load(xparm_file)
crystal_model = to_crystal(xparm_file)
from dxtbx.model import Experiment, ExperimentList
experiment = Experiment(
beam=models.get_beam(),
detector=models.get_detector(),
goniometer=models.get_goniometer(),
scan=models.get_scan(),
crystal=crystal_model,
#imageset=self.get_imageset(),
)
experiment_list = ExperimentList([experiment])
self.set_indexer_experiment_list(experiment_list)
# I will want this later on to check that the lattice was ok
self._idxref_subtree_problem = idxref.get_index_tree_problem()
return
def import_xds_as_still(xdsinp, xparm_in):
#from dxtbx.serialize import xds
from dxtbx.datablock import DataBlockFactory
# Get the sweep from the XDS files
#sweep = xds.to_imageset(xds_inp, xds_other)
from iotbx.xds import xds_inp
from dxtbx.imageset import ImageSetFactory
import dxtbx
# Read the input filename
handle = xds_inp.reader()
handle.read_file(xdsinp)
# Get the template
template = handle.name_template_of_data_frames[0]
image_range = handle.data_range
detector_name = handle.detector
#assert image_range[0] == image_range[1]
im_nr = int((image_range[1] - image_range[0] + 1) / 2)
from yamtbx.dataproc.dataset import template_to_filenames
# Create the imageset
#imageset = ImageSetFactory.from_template(template, image_range=image_range, check_format=False)[0]
imageset = ImageSetFactory.make_imageset(
[os.path.realpath(template_to_filenames(template, im_nr, im_nr)[0])])
models = dxtbx.load(xparm_in)
detector = models.get_detector()
if detector_name.strip() in ('PILATUS',
'EIGER') or handle.silicon is not None:
from dxtbx.model import ParallaxCorrectedPxMmStrategy
from cctbx.eltbx import attenuation_coefficient
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))
imageset.set_beam(models.get_beam())
imageset.set_detector(detector)
imageset.set_goniometer(None)
imageset.set_scan(None)
#imageset.set_goniometer(models.get_goniometer())
# take the image range from XDS.INP
#scan = models.get_scan()
#scan.set_image_range(image_range)
#imageset.set_scan(scan)
from dxtbx.serialize import xds
# Get the crystal from the XDS files
crystal = xds.to_crystal(xparm_in)
# Create the experiment list
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
# Set the crystal in the experiment list
assert (len(experiments) == 1)
# Return the experiment list
return experiments
def _index(self):
"""Actually do the autoindexing using the data prepared by the
previous method."""
images_str = "%d to %d" % tuple(self._indxr_images[0])
for i in self._indxr_images[1:]:
images_str += ", %d to %d" % tuple(i)
cell_str = None
if self._indxr_input_cell:
cell_str = "%.2f %.2f %.2f %.2f %.2f %.2f" % self._indxr_input_cell
# then this is a proper autoindexing run - describe this
# to the journal entry
dirname = self.get_directory()
Journal.block(
"autoindexing",
self._indxr_sweep_name,
"XDS",
{
"images": images_str,
"target cell": cell_str,
"target lattice": self._indxr_input_lattice,
"template": self.get_template(),
"directory": dirname,
},
)
idxref = self.Idxref()
self._index_remove_masked_regions()
for file in ["SPOT.XDS"]:
idxref.set_input_data_file(file, self._indxr_payload[file])
# edit SPOT.XDS to remove reflections in untrusted regions of the detector
idxref.set_data_range(self._indxr_images[0][0],
self._indxr_images[0][1])
idxref.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
# set the phi start etc correctly
for block in self._indxr_images[:1]:
starting_frame = block[0]
starting_angle = self.get_scan().get_angle_from_image_index(
starting_frame)
idxref.set_starting_frame(starting_frame)
idxref.set_starting_angle(starting_angle)
idxref.add_spot_range(block[0], block[1])
for block in self._indxr_images[1:]:
idxref.add_spot_range(block[0], block[1])
if self._indxr_user_input_lattice:
idxref.set_indexer_user_input_lattice(True)
if self._indxr_input_lattice and self._indxr_input_cell:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
idxref.set_indexer_input_cell(self._indxr_input_cell)
Debug.write("Set lattice: %s" % self._indxr_input_lattice)
Debug.write("Set cell: %f %f %f %f %f %f" % self._indxr_input_cell)
original_cell = self._indxr_input_cell
elif self._indxr_input_lattice:
idxref.set_indexer_input_lattice(self._indxr_input_lattice)
original_cell = None
else:
original_cell = None
from dxtbx.serialize.xds import to_xds
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
idxref.set_beam_centre(xds_beam_centre[0], xds_beam_centre[1])
# fixme need to check if the lattice, cell have been set already,
# and if they have, pass these in as input to the indexing job.
done = False
while not done:
try:
done = idxref.run()
# N.B. in here if the IDXREF step was being run in the first
# pass done is FALSE however there should be a refined
# P1 orientation matrix etc. available - so keep it!
except XDSException as e:
# inspect this - if we have complaints about not
# enough reflections indexed, and we have a target
# unit cell, and they are the same, well ignore it
if "solution is inaccurate" in str(e):
Debug.write("XDS complains solution inaccurate - ignoring")
done = idxref.continue_from_error()
elif ("insufficient percentage (< 70%)" in str(e)
or "insufficient percentage (< 50%)"
in str(e)) and original_cell:
done = idxref.continue_from_error()
lattice, cell, mosaic = idxref.get_indexing_solution()
# compare solutions FIXME should use xds_cell_deviation
check = PhilIndex.params.xia2.settings.xds_check_cell_deviation
for j in range(3):
# allow two percent variation in unit cell length
if (math.fabs(
(cell[j] - original_cell[j]) / original_cell[j]) >
0.02 and check):
Debug.write("XDS unhappy and solution wrong")
raise e
# and two degree difference in angle
if (math.fabs(cell[j + 3] - original_cell[j + 3]) > 2.0
and check):
Debug.write("XDS unhappy and solution wrong")
raise e
Debug.write("XDS unhappy but solution ok")
elif "insufficient percentage (< 70%)" in str(
e) or "insufficient percentage (< 50%)" in str(e):
Debug.write("XDS unhappy but solution probably ok")
done = idxref.continue_from_error()
else:
raise e
FileHandler.record_log_file(
"%s INDEX" % self.get_indexer_full_name(),
os.path.join(self.get_working_directory(), "IDXREF.LP"),
)
for file in ["SPOT.XDS", "XPARM.XDS"]:
self._indxr_payload[file] = idxref.get_output_data_file(file)
# need to get the indexing solutions out somehow...
self._indxr_other_lattice_cell = idxref.get_indexing_solutions()
self._indxr_lattice, self._indxr_cell, self._indxr_mosaic = (
idxref.get_indexing_solution())
import dxtbx
from dxtbx.serialize.xds import to_crystal
xparm_file = os.path.join(self.get_working_directory(), "XPARM.XDS")
models = dxtbx.load(xparm_file)
crystal_model = to_crystal(xparm_file)
from dxtbx.model import Experiment, ExperimentList
experiment = Experiment(
beam=models.get_beam(),
detector=models.get_detector(),
goniometer=models.get_goniometer(),
scan=models.get_scan(),
crystal=crystal_model,
# imageset=self.get_imageset(),
)
experiment_list = ExperimentList([experiment])
self.set_indexer_experiment_list(experiment_list)
# I will want this later on to check that the lattice was ok
self._idxref_subtree_problem = idxref.get_index_tree_problem()
return