def from_parameters(reflections,
experiments,
known_crystal_models=None,
params=None):
if known_crystal_models is not None:
from dials.algorithms.indexing.known_orientation import (
IndexerKnownOrientation, )
if params.indexing.known_symmetry.space_group is None:
params.indexing.known_symmetry.space_group = (
known_crystal_models[0].get_space_group().info())
idxr = IndexerKnownOrientation(reflections, experiments, params,
known_crystal_models)
else:
has_stills = False
has_sequences = False
for expt in experiments:
if isinstance(expt.imageset, ImageSequence):
has_sequences = True
else:
has_stills = True
if has_stills and has_sequences:
raise ValueError(
"Please provide only stills or only sequences, not both")
use_stills_indexer = has_stills
if not (params.indexing.stills.indexer is libtbx.Auto
or params.indexing.stills.indexer.lower() == "auto"):
if params.indexing.stills.indexer == "stills":
use_stills_indexer = True
elif params.indexing.stills.indexer == "sequences":
use_stills_indexer = False
else:
assert False
if params.indexing.basis_vector_combinations.max_refine is libtbx.Auto:
if use_stills_indexer:
params.indexing.basis_vector_combinations.max_refine = 5
else:
params.indexing.basis_vector_combinations.max_refine = 50
if use_stills_indexer:
# Ensure the indexer and downstream applications treat this as set of stills
from dxtbx.imageset import ImageSet # , MemImageSet
for experiment in experiments:
experiment.imageset = ImageSet(
experiment.imageset.data(),
experiment.imageset.indices())
# if isinstance(imageset, MemImageSet):
# imageset = MemImageSet(imagesequence._images, imagesequence.indices())
# else:
# imageset = ImageSet(imagesequence.reader(), imagesequence.indices())
# imageset._models = imagesequence._models
experiment.imageset.set_scan(None)
experiment.imageset.set_goniometer(None)
experiment.scan = None
experiment.goniometer = None
IndexerType = None
for entry_point in pkg_resources.iter_entry_points(
"dials.index.basis_vector_search"):
if params.indexing.method == entry_point.name:
if use_stills_indexer:
# do something
from dials.algorithms.indexing.stills_indexer import (
StillsIndexerBasisVectorSearch as IndexerType, )
else:
from dials.algorithms.indexing.lattice_search import (
BasisVectorSearch as IndexerType, )
if IndexerType is None:
for entry_point in pkg_resources.iter_entry_points(
"dials.index.lattice_search"):
if params.indexing.method == entry_point.name:
if use_stills_indexer:
from dials.algorithms.indexing.stills_indexer import (
StillsIndexerLatticeSearch as IndexerType, )
else:
from dials.algorithms.indexing.lattice_search import (
LatticeSearch as IndexerType, )
assert IndexerType is not None
idxr = IndexerType(reflections, experiments, params=params)
return idxr
def from_parameters(reflections,
experiments,
known_crystal_models=None,
params=None):
if known_crystal_models is not None:
from dials.algorithms.indexing.known_orientation import (
IndexerKnownOrientation, )
if params.indexing.known_symmetry.space_group is None:
params.indexing.known_symmetry.space_group = (
known_crystal_models[0].get_space_group().info())
idxr = IndexerKnownOrientation(reflections, experiments, params,
known_crystal_models)
else:
has_stills = False
has_sweeps = False
for expt in experiments:
if (expt.goniometer is None or expt.scan is None
or expt.scan.get_oscillation()[1] == 0):
if has_sweeps:
raise Sorry(
"Please provide only stills or only sweeps, not both"
)
has_stills = True
else:
if has_stills:
raise Sorry(
"Please provide only stills or only sweeps, not both"
)
has_sweeps = True
assert not (has_stills and has_sweeps)
use_stills_indexer = has_stills
if not (params.indexing.stills.indexer is libtbx.Auto
or params.indexing.stills.indexer.lower() == "auto"):
if params.indexing.stills.indexer == "stills":
use_stills_indexer = True
elif params.indexing.stills.indexer == "sweeps":
use_stills_indexer = False
else:
assert False
if params.indexing.basis_vector_combinations.max_refine is libtbx.Auto:
if use_stills_indexer:
params.indexing.basis_vector_combinations.max_refine = 5
else:
params.indexing.basis_vector_combinations.max_refine = 50
if use_stills_indexer:
# Ensure the indexer and downstream applications treat this as set of stills
from dxtbx.imageset import ImageSet # , MemImageSet
for experiment in experiments:
experiment.imageset = ImageSet(
experiment.imageset.data(),
experiment.imageset.indices())
# if isinstance(imageset, MemImageSet):
# imageset = MemImageSet(imagesweep._images, imagesweep.indices())
# else:
# imageset = ImageSet(imagesweep.reader(), imagesweep.indices())
# imageset._models = imagesweep._models
experiment.imageset.set_scan(None)
experiment.imageset.set_goniometer(None)
experiment.scan = None
experiment.goniometer = None
if params.indexing.method in ("fft1d", "fft3d",
"real_space_grid_search"):
if use_stills_indexer:
# do something
from dials.algorithms.indexing.stills_indexer import (
StillsIndexerBasisVectorSearch as BasisVectorSearch, )
else:
from dials.algorithms.indexing.lattice_search import (
BasisVectorSearch, )
idxr = BasisVectorSearch(reflections,
experiments,
params=params)
return idxr