def test_imagesetfactory(centroid_files, dials_regression):
from dxtbx.imageset import ImageSetFactory, ImageSweep
filenames = centroid_files
sweep = ImageSetFactory.new(filenames)
assert isinstance(sweep[0], ImageSweep)
template = os.path.join(dials_regression, "centroid_test_data",
"centroid_####.cbf")
image_range = (3, 6)
sweep = ImageSetFactory.from_template(template, image_range)
assert isinstance(sweep[0], ImageSweep)
assert len(sweep[0]) == 4
assert sweep[0].paths()[0].endswith("3.cbf")
assert sweep[0].paths()[-1].endswith("6.cbf")
imageset = ImageSetFactory.make_imageset(filenames)
assert len(imageset) == 9
imageset = ImageSetFactory.make_imageset(filenames, check_format=False)
assert len(imageset) == 9
sweep = ImageSetFactory.make_sweep(template, list(range(1, 9 + 1)))
assert len(sweep) == 9
sweep = ImageSetFactory.make_sweep(template, list(range(3, 6 + 1)))
assert len(sweep) == 4
def test_imagesetfactory(centroid_files, dials_data):
sequence = ImageSetFactory.new(centroid_files)
assert isinstance(sequence[0], ImageSequence)
template = dials_data("centroid_test_data").join(
"centroid_####.cbf").strpath
image_range = (3, 6)
sequence = ImageSetFactory.from_template(template, image_range)
assert isinstance(sequence[0], ImageSequence)
assert len(sequence[0]) == 4
assert sequence[0].paths()[0].endswith("3.cbf")
assert sequence[0].paths()[-1].endswith("6.cbf")
imageset = ImageSetFactory.make_imageset(centroid_files)
assert len(imageset) == 9
imageset = ImageSetFactory.make_imageset(centroid_files,
check_format=False)
assert len(imageset) == 9
sequence = ImageSetFactory.make_sequence(template, list(range(1, 9 + 1)))
assert len(sequence) == 9
sequence = ImageSetFactory.make_sequence(template, list(range(3, 6 + 1)))
assert len(sequence) == 4
def run(self):
from dxtbx.imageset import ImageSetFactory, ImageSweep
from os.path import join
filenames = self.get_file_list()
sweep = ImageSetFactory.new(filenames)
assert(isinstance(sweep[0], ImageSweep) == True)
print 'OK'
template = join(dials_regression, "centroid_test_data", "centroid_####.cbf")
image_range = (3, 6)
sweep = ImageSetFactory.from_template(template, image_range)
assert(isinstance(sweep[0], ImageSweep) == True)
assert len(sweep[0]) == 4
assert sweep[0].paths()[0].endswith("3.cbf")
assert sweep[0].paths()[-1].endswith("6.cbf")
print 'OK'
imageset = ImageSetFactory.make_imageset(filenames)
assert len(imageset) == 9
print 'OK'
imageset = ImageSetFactory.make_imageset(
filenames,
check_format=False)
assert len(imageset) == 9
print 'OK'
sweep = ImageSetFactory.make_sweep(
template,
list(range(1, 9+1)))
assert len(sweep) == 9
print 'OK'
sweep = ImageSetFactory.make_sweep(
template,
list(range(3, 6+1)))
assert len(sweep) == 4
print 'OK'
def _make_stills(self, imageset):
''' Make a still imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
filenames = [load_path(p) for p in imageset['images']]
return ImageSetFactory.make_imageset(
filenames, None, check_format=self._check_format)
def run(self, experiments, reflections):
from dials.util import log
self.logger.log_step_time("INTEGRATE")
logfile = os.path.splitext(
self.logger.rank_log_file_path)[0] + "_integrate.log"
log.config(logfile=logfile)
processor = integrate_only_processor(self.params)
# Re-generate the image sets using their format classes so we can read the raw data
# Integrate the experiments one at a time to not use up memory
all_integrated = flex.reflection_table()
for expt_id, expt in enumerate(experiments):
expt.imageset = ImageSetFactory.make_imageset(
expt.imageset.paths(),
single_file_indices=expt.imageset.indices())
refls = reflections.select(
reflections['exp_id'] == expt.identifier)
idents = refls.experiment_identifiers()
del idents[expt_id]
idents[0] = expt.identifier
refls['id'] = flex.int(len(refls), 0)
integrated = processor.integrate(experiments[expt_id:expt_id + 1],
refls)
idents = integrated.experiment_identifiers()
del idents[0]
idents[expt_id] = expt.identifier
integrated['id'] = flex.int(len(integrated), expt_id)
all_integrated.extend(integrated)
expt.imageset.clear_cache()
return experiments, reflections
def lunus_integrate(self, experiments, is_reference=False):
assert len(experiments) == 1
experiment_params = get_experiment_params(experiments)
p = self.processor
# self.logger.log("LUNUS_INTEGRATE: Passed %s %d" % (experiments[0].imageset.paths()[0],experiments[0].imageset.indices()[0]))
if self.current_path != experiments[0].imageset.paths()[0]:
self.current_imageset = ImageSetFactory.make_imageset(
experiments[0].imageset.paths())
idx = experiments[0].imageset.indices()[0]
experiments[0].imageset = self.current_imageset[idx:idx + 1]
self.logger.log("LUNUS_INTEGRATE: Processing image %s %d" %
(experiments[0].imageset.paths()[0],
experiments[0].imageset.indices()[0]))
data = experiments[0].imageset[0]
if not isinstance(data, tuple):
data = data,
for panel_idx, panel in enumerate(data):
self.processor.set_image(panel_idx, panel)
# self.logger.log("LUNUS_INTEGRATE: file %s panel_idx %d panel[0:10] = %s " % (experiments[0].imageset.paths()[0],panel_idx,str(list(panel[0:10]))))
for pidx in range(len(experiment_params)):
deck_and_extras = self.deck + experiment_params[pidx]
p.LunusSetparamsim(pidx, deck_and_extras)
# self.logger.log("LUNUS: Processing image")
if is_reference:
x = get_experiment_xvectors(experiments)
for pidx in range(len(x)):
p.set_xvectors(pidx, x[pidx])
# We need an amatrix for the next call, to set up the lattice size
if self.params.merging.set_average_unit_cell:
assert 'average_unit_cell' in (self.params.statistics).__dict__
uc = self.params.statistics.__phil_get__('average_unit_cell')
else:
uc = self.params.scaling.unit_cell
assert uc is not None, "Lunus needs a target unit cell"
A_matrix = matrix.sqr(uc.orthogonalization_matrix())
At_flex = A_matrix.transpose().as_flex_double_matrix()
p.set_amatrix(At_flex)
p.LunusProcimlt(0)
else:
crystal = experiments[0].crystal
A_matrix = matrix.sqr(crystal.get_A()).inverse()
At_flex = A_matrix.transpose().as_flex_double_matrix()
p.set_amatrix(At_flex)
p.LunusProcimlt(1)
def _make_stills(self, imageset, format_kwargs=None):
''' Make a still imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
filenames = [load_path(p) for p in imageset['images']]
indices = None
if "single_file_indices" in imageset:
indices = imageset['single_file_indices']
assert len(indices) == len(filenames)
return ImageSetFactory.make_imageset(
filenames, None, check_format=self._check_format,
single_file_indices=indices, format_kwargs=format_kwargs)
def _make_stills(self, imageset, format_kwargs=None):
''' Make a still imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
filenames = [load_path(p) for p in imageset['images']]
indices = None
if "single_file_indices" in imageset:
indices = imageset['single_file_indices']
assert len(indices) == len(filenames)
return ImageSetFactory.make_imageset(
filenames, None, check_format=self._check_format,
single_file_indices=indices, format_kwargs=format_kwargs)
def run(self, experiments, reflections):
self.logger.log_step_time("INTEGRATE")
# Re-generate the image sets using their format classes so we can read the raw data
for expt in experiments:
expt.imageset = ImageSetFactory.make_imageset(
expt.imageset.paths(),
single_file_indices=expt.imageset.indices())
processor = integrate_only_processor(self.params)
reflections = processor.integrate(experiments, reflections)
return experiments, reflections
def run(self, experiments, reflections):
from dials.util import log
self.logger.log_step_time("INTEGRATE")
logfile = os.path.splitext(
self.logger.rank_log_file_path)[0] + "_integrate.log"
log.config(logfile=logfile)
processor = integrate_only_processor(self.params)
# Re-generate the image sets using their format classes so we can read the raw data
# Integrate the experiments one at a time to not use up memory
all_integrated_expts = ExperimentList()
all_integrated_refls = flex.reflection_table()
current_imageset = None
current_imageset_path = None
for expt_id, expt in enumerate(experiments):
assert len(expt.imageset.paths()) == 1 and len(expt.imageset) == 1
self.logger.log("Starting integration experiment %d" % expt_id)
refls = reflections.select(
reflections['exp_id'] == expt.identifier)
if expt.imageset.paths()[0] != current_imageset_path:
current_imageset_path = expt.imageset.paths()[0]
current_imageset = ImageSetFactory.make_imageset(
expt.imageset.paths())
idx = expt.imageset.indices()[0]
expt.imageset = current_imageset[idx:idx + 1]
idents = refls.experiment_identifiers()
del idents[expt_id]
idents[0] = expt.identifier
refls['id'] = flex.int(len(refls), 0)
try:
integrated = processor.integrate(
experiments[expt_id:expt_id + 1], refls)
except RuntimeError:
self.logger.log("Error integrating expt %d" % expt_id)
continue
all_integrated_expts.append(expt)
idents = integrated.experiment_identifiers()
del idents[0]
idents[expt_id] = expt.identifier
integrated['id'] = flex.int(len(integrated),
len(all_integrated_expts) - 1)
all_integrated_refls.extend(integrated)
self.logger.log("Integration done, %d experiments, %d reflections" %
(len(all_integrated_expts), len(all_integrated_refls)))
return all_integrated_expts, all_integrated_refls
def _make_stills(self, imageset, format_kwargs=None):
""" Make a still imageset. """
filenames = [
load_path(p, directory=self._directory) for p in imageset["images"]
]
indices = None
if "single_file_indices" in imageset:
indices = imageset["single_file_indices"]
assert len(indices) == len(filenames)
return ImageSetFactory.make_imageset(
filenames,
None,
check_format=self._check_format,
single_file_indices=indices,
format_kwargs=format_kwargs,
)
def _create_multi_file_imageset(self, format_class, records,
format_kwargs=None):
''' Create a multi file sweep or imageset. '''
from dxtbx.imageset import ImageSetFactory
from os.path import abspath
# Make either an imageset or sweep
if len(records) == 1 and records[0].template is not None:
# Get the image range
image_range = records[0].scan.get_image_range()
image_range = (image_range[0], image_range[1]+1)
# Create the sweep
imageset = ImageSetFactory.make_sweep(
abspath(records[0].template), range(*image_range),
format_class,
records[0].beam, records[0].detector,
records[0].goniometer, records[0].scan,
format_kwargs=format_kwargs)
else:
# Get the filenames
filenames = []
for r in records:
assert(r.template is None)
filenames.append(r.filename)
# make an imageset
imageset = ImageSetFactory.make_imageset(
map(abspath, filenames),
format_class,
format_kwargs=format_kwargs)
for i, r in enumerate(records):
imageset.set_beam(r.beam, i)
imageset.set_detector(r.detector, i)
imageset.set_goniometer(r.goniometer, i)
imageset.set_scan(r.scan, i)
# Return the imageset
return imageset
img = dxtbx.load(imgname)
# detector = img.get_detector()
# beam = img.get_beam()
scan = img.get_scan()
gonio = img.get_goniometer()
print "s0 from ",imgname,": ",beam.get_s0()
print "wavelength from ",imgname,": ",beam.get_wavelength()
crystal = copy.deepcopy(experiments.crystals()[0])
axis = gonio.get_rotation_axis()
start_angle, delta_angle = scan.get_oscillation()
crystal.rotate_around_origin(axis, start_angle + (delta_angle/2), deg=True)
if (output_format == "json"):
exp_list = ExperimentList()
exp_list.append(Experiment(imageset=ImageSetFactory.make_imageset(list([imgname])),
beam=beam,
detector=detector,
goniometer=gonio,
scan=scan,
crystal=crystal))
if (add_background_images==True):
if (len(bkglist) != 1):
bkgname=bkglist[i]
else:
bkgname=bkglist[0]
exp_list[0].imageset.external_lookup.pedestal.filename=os.path.abspath(bkgname)
dump.experiment_list(exp_list,json_dir+"/experiments_for_lunus_{0:05d}.json".format(imnum))
else:
from scitbx import matrix
A_matrix = matrix.sqr(crystal.get_A()).inverse()
def _load_datablocks(self, obj, check_format=True):
''' Create the datablock from a dictionary. '''
from libtbx.containers import OrderedDict
from dxtbx.format.Registry import Registry
from dxtbx.model import Beam, Detector, Scan
from dxtbx.model import Detector
from dxtbx.serialize.filename import load_path
from dxtbx.imageset import ImageSetFactory, ImageGrid
# If we have a list, extract for each dictionary in the list
if isinstance(obj, list):
return [self._load_datablocks(dd, check_format) for dd in obj]
elif not isinstance(obj, dict):
raise RuntimeError('unknown datablock dictionary type')
assert(obj['__id__'] == 'DataBlock')
# Get the list of models
blist = obj.get('beam', [])
dlist = obj.get('detector', [])
glist = obj.get('goniometer', [])
slist = obj.get('scan', [])
def load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
from dxtbx.serialize import goniometer
gonio = goniometer.from_dict(glist[obj['goniometer']])
except Exception:
gonio = None
try:
scan = Scan.from_dict(slist[obj['scan']])
except Exception:
scan = None
return beam, detector, gonio, scan
# Loop through all the imagesets
imagesets = []
for imageset in obj['imageset']:
ident = imageset['__id__']
if "params" in imageset:
format_kwargs = imageset['params']
else:
format_kwargs = {}
if ident == 'ImageSweep':
beam, detector, gonio, scan = load_models(imageset)
if "template" in imageset:
template = load_path(imageset['template'])
i0, i1 = scan.get_image_range()
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format,
format_kwargs=format_kwargs)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
elif "master" in imageset:
template = load_path(imageset['master'])
i0, i1 = scan.get_image_range()
indices = imageset['images']
assert min(indices) == i0-1 and max(indices) == i1-1
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format,
format_kwargs=format_kwargs)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
elif ident == 'ImageSet' or ident == "ImageGrid":
filenames = [image['filename'] for image in imageset['images']]
indices = [image['image'] for image in imageset['images'] if 'image' in image]
assert len(indices) == 0 or len(indices) == len(filenames)
iset = ImageSetFactory.make_imageset(
filenames, None, check_format, indices, format_kwargs=format_kwargs)
if ident == "ImageGrid":
grid_size = imageset['grid_size']
iset = ImageGrid.from_imageset(iset, grid_size)
for i, image in enumerate(imageset['images']):
beam, detector, gonio, scan = load_models(image)
iset.set_beam(beam, i)
iset.set_detector(detector, i)
iset.set_goniometer(gonio, i)
iset.set_scan(scan, i)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
else:
raise RuntimeError('expected ImageSet/ImageSweep, got %s' % ident)
# Return the datablock
return DataBlock(imagesets)
def _load_datablocks(self, obj, check_format=True):
''' Create the datablock from a dictionary. '''
from libtbx.containers import OrderedDict
from dxtbx.format.Registry import Registry
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import HierarchicalDetector
from dxtbx.serialize.filename import load_path
from dxtbx.imageset import ImageSetFactory
import pickle
# If we have a list, extract for each dictionary in the list
if isinstance(obj, list):
return [self._load_datablocks(dd, check_format) for dd in obj]
elif not isinstance(obj, dict):
raise RuntimeError('unknown datablock dictionary type')
assert(obj['__id__'] == 'DataBlock')
# Get the list of models
blist = obj.get('beam', [])
dlist = obj.get('detector', [])
glist = obj.get('goniometer', [])
slist = obj.get('scan', [])
def load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
if 'hierarchy' in dobj:
detector = HierarchicalDetector.from_dict(dobj)
else:
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
gonio = Goniometer.from_dict(glist[obj['goniometer']])
except Exception:
gonio = None
try:
scan = Scan.from_dict(slist[obj['scan']])
except Exception:
scan = None
return beam, detector, gonio, scan
# Loop through all the imagesets
imagesets = []
for imageset in obj['imageset']:
ident = imageset['__id__']
if ident == 'ImageSweep':
beam, detector, gonio, scan = load_models(imageset)
template = load_path(imageset['template'])
i0, i1 = scan.get_image_range()
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
elif ident == 'ImageSet':
filenames = [image['filename'] for image in imageset['images']]
iset = ImageSetFactory.make_imageset(
filenames, None, check_format)
for i, image in enumerate(imageset['images']):
beam, detector, gonio, scan = load_models(image)
iset.set_beam(beam, i)
iset.set_detector(detector, i)
if gonio:
iset.set_goniometer(gonio, i)
if scan:
iset.set_scan(scan, i)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
else:
raise RuntimeError('expected ImageSet/ImageSweep, got %s' % ident)
# Return the datablock
return DataBlock(imagesets)
img = dxtbx.load(imgname)
detector = img.get_detector()
beam = img.get_beam()
scan = img.get_scan()
gonio = img.get_goniometer()
print "s0 from ",imgname,": ",beam.get_s0()
print "wavelength from ",imgname,": ",beam.get_wavelength()
crystal = copy.deepcopy(experiments.crystals()[0])
axis = gonio.get_rotation_axis()
start_angle, delta_angle = scan.get_oscillation()
crystal.rotate_around_origin(axis, start_angle + (delta_angle/2), deg=True)
if (output_format == "json"):
exp_list = ExperimentList()
exp_list.append(Experiment(imageset=ImageSetFactory.make_imageset(list([imgname])),
beam=beam,
detector=detector,
goniometer=gonio,
scan=scan,
crystal=crystal))
if (add_background_images==True):
if (len(bkglist) != 1):
bkgname=bkglist[i]
exp_list[0].imageset.external_lookup.pedestal.filename=os.path.abspath(bkgname)
dump.experiment_list(exp_list,json_dir+"/experiments_for_lunus_{0:05d}.json".format(imnum))
else:
from scitbx import matrix
A_matrix = matrix.sqr(crystal.get_A()).inverse()
At = np.asarray(A_matrix.transpose()).reshape((3,3))
print At
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