def load(entry, exp_index):
from dxtbx.model.experiment_list import Experiment, ExperimentList
print("Loading NXmx")
# Check file contains the feature
assert "features" in entry
assert 6 in entry["features"][()]
experiment_list = ExperimentList()
# Find all the experiments
entries = find_nx_mx_entries(entry, ".")
if len(entries) > 1:
entries = sorted(entries, key=lambda x: x["dials/index"][()])
assert len(entries) == len(exp_index)
for nxmx, name in zip(entries, exp_index):
assert np.string_(nxmx.name) == name, (nxmx.name, name)
index = []
rotations = []
for name in exp_index:
# Get the entry
nxmx = entry.file[name]
# Get the definition
definition = nxmx["definition"]
assert definition[()] == "NXmx"
assert definition.attrs["version"] == 1
# Get dials specific stuff
nx_dials = get_nx_dials(nxmx, "dials")
# Set index
b = nx_dials["index"].attrs["source"]
d = nx_dials["index"].attrs["detector"]
if "goniometer" in nx_dials["index"].attrs:
g = nx_dials["index"].attrs["goniometer"]
else:
g = None
if "scan" in nx_dials["index"].attrs:
s = nx_dials["index"].attrs["scan"]
else:
s = None
c = nx_dials["index"].attrs["sample"]
index.append((b, d, g, s, c))
# Get the original orientation (dials specific)
transformations = get_nx_transformations(nx_dials, "transformations")
angle = transformations["angle"][()]
assert transformations["angle"].attrs[
"transformation_type"] == "rotation"
axis = transformations["angle"].attrs["vector"]
assert tuple(transformations["angle"].attrs["offset"]) == (0, 0, 0)
assert transformations["angle"].attrs["offset_units"] == "mm"
assert transformations["angle"].attrs["depends_on"] == "."
rotations.append((axis, angle))
# Get the imageset
try:
image_range = nx_dials["template"].attrs["range"]
except Exception:
image_range = None
# Create the experiment
experiment = Experiment()
# Read the models
experiment.beam = load_beam(nxmx)
experiment.detector = load_detector(nxmx)
experiment.goniometer = load_goniometer(nxmx)
experiment.scan = load_scan(nxmx)
experiment.crystal = load_crystal(nxmx)
# Set the image range
if image_range is not None and experiment.scan is not None:
num = image_range[1] - image_range[0] + 1
assert num == len(experiment.scan)
experiment.scan.set_image_range([int(x) for x in image_range])
# Return the experiment list
experiment_list.append(experiment)
# Convert from nexus beam direction
experiment_list = convert_from_nexus_beam_direction(
experiment_list, rotations)
beam = collections.defaultdict(list)
detector = collections.defaultdict(list)
goniometer = collections.defaultdict(list)
scan = collections.defaultdict(list)
crystal = collections.defaultdict(list)
for i, ind in enumerate(index):
beam[ind[0]].append(i)
detector[ind[1]].append(i)
goniometer[ind[2]].append(i)
scan[ind[3]].append(i)
crystal[ind[4]].append(i)
# Set all the shared beams
for value in beam.values():
b1 = experiment_list[value[0]].beam
assert all(experiment_list[v].beam == b1 for v in value[1:])
for v in value[1:]:
experiment_list[v].beam = b1
# Set all the shared detectors
for value in detector.values():
d1 = experiment_list[value[0]].detector
assert all(experiment_list[v].detector == d1 for v in value[1:])
for v in value[1:]:
experiment_list[v].detector = d1
# Set all the shared goniometer
for value in goniometer.values():
g1 = experiment_list[value[0]].goniometer
assert all(experiment_list[v].goniometer == g1 for v in value[1:])
for v in value[1:]:
experiment_list[v].goniometer = g1
# Set all the shared scans
for value in scan.values():
s1 = experiment_list[value[0]].scan
assert all(experiment_list[v].scan == s1 for v in value[1:])
for v in value[1:]:
experiment_list[v].scan = s1
# Set all the shared crystals
for value in crystal.values():
c1 = experiment_list[value[0]].crystal
assert all(experiment_list[v].crystal == c1 for v in value[1:])
for v in value[1:]:
experiment_list[v].crystal = c1
return experiment_list
def split_for_scan_range(self, experiments, reference, scan_range):
''' Update experiments when scan range is set. '''
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
from dials.array_family import flex
# Only do anything is the scan range is set
if scan_range is not None and len(scan_range) > 0:
# Ensure that all experiments have the same imageset and scan
iset = [e.imageset for e in experiments]
scan = [e.scan for e in experiments]
assert (all(x == iset[0] for x in iset))
assert (all(x == scan[0] for x in scan))
# Get the imageset and scan
iset = experiments[0].imageset
scan = experiments[0].scan
# Get the array range
if scan is not None:
frame10, frame11 = scan.get_array_range()
assert (scan.get_num_images() == len(iset))
else:
frame10, frame11 = (0, len(iset))
# Create the new lists
new_experiments = ExperimentList()
new_reference_all = reference.split_by_experiment_id()
new_reference = flex.reflection_table()
for i in range(len(new_reference_all) - len(experiments)):
new_reference_all.append(flex.reflection_table())
assert (len(new_reference_all) == len(experiments))
# Loop through all the scan ranges and create a new experiment list with
# the requested scan ranges.
for frame00, frame01 in scan_range:
assert (frame01 > frame00)
assert (frame00 >= frame10)
assert (frame01 <= frame11)
index0 = frame00 - frame10
index1 = index0 + (frame01 - frame00)
assert (index0 < index1)
assert (index0 >= 0)
assert (index1 <= len(iset))
new_iset = iset[index0:index1]
if scan is None:
new_scan = None
else:
new_scan = scan[index0:index1]
for i, e1 in enumerate(experiments):
e2 = Experiment()
e2.beam = e1.beam
e2.detector = e1.detector
e2.goniometer = e1.goniometer
e2.crystal = e1.crystal
e2.imageset = new_iset
e2.scan = new_scan
new_reference_all[i]['id'] = flex.int(
len(new_reference_all[i]), len(new_experiments))
new_reference.extend(new_reference_all[i])
new_experiments.append(e2)
experiments = new_experiments
reference = new_reference
# Print some information
logger.info(
'Modified experiment list to integrate over requested scan range'
)
for frame00, frame01 in scan_range:
logger.info(' scan_range = %d -> %d' % (frame00, frame01))
logger.info('')
# Return the experiments
return experiments, reference
def split_for_scan_range(self, experiments, reference, scan_range):
""" Update experiments when scan range is set. """
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
# Only do anything is the scan range is set
if scan_range is not None and len(scan_range) > 0:
# Ensure that all experiments have the same imageset and scan
iset = [e.imageset for e in experiments]
scan = [e.scan for e in experiments]
assert all(x == iset[0] for x in iset)
assert all(x == scan[0] for x in scan)
# Get the imageset and scan
iset = experiments[0].imageset
scan = experiments[0].scan
# Get the array range
if scan is not None:
frames_start, frames_end = scan.get_array_range()
assert scan.get_num_images() == len(iset)
else:
frames_start, frames_end = (0, len(iset))
# Create the new lists
new_experiments = ExperimentList()
new_reference_all = reference.split_by_experiment_id()
new_reference = flex.reflection_table()
for i in range(len(new_reference_all) - len(experiments)):
new_reference_all.append(flex.reflection_table())
assert len(new_reference_all) == len(experiments)
# Loop through all the scan ranges and create a new experiment list with
# the requested scan ranges.
for scan_start, scan_end in scan_range:
# Validate the requested scan range
if scan_end == scan_start:
raise Sorry(
"Scan range end must be higher than start; pass {},{} for single image"
.format(scan_start, scan_start + 1))
if scan_end < scan_start:
raise Sorry("Scan range must be in ascending order")
elif scan_start < frames_start or scan_end > frames_end:
raise Sorry(
"Scan range must be within image range {}..{}".format(
frames_start, frames_end))
assert scan_end > scan_start
assert scan_start >= frames_start
assert scan_end <= frames_end
index_start = scan_start - frames_start
index_end = index_start + (scan_end - scan_start)
assert index_start < index_end
assert index_start >= 0
assert index_end <= len(iset)
new_iset = iset[index_start:index_end]
if scan is None:
new_scan = None
else:
new_scan = scan[index_start:index_end]
for i, e1 in enumerate(experiments):
e2 = Experiment()
e2.beam = e1.beam
e2.detector = e1.detector
e2.goniometer = e1.goniometer
e2.crystal = e1.crystal
e2.profile = e1.profile
e2.imageset = new_iset
e2.scan = new_scan
new_reference_all[i]["id"] = flex.int(
len(new_reference_all[i]), len(new_experiments))
new_reference.extend(new_reference_all[i])
new_experiments.append(e2)
experiments = new_experiments
reference = new_reference
# Print some information
logger.info(
"Modified experiment list to integrate over requested scan range"
)
for scan_start, scan_end in scan_range:
logger.info(" scan_range = %d -> %d" % (scan_start, scan_end))
logger.info("")
# Return the experiments
return experiments, reference
def load(entry, exp_index):
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
print "Loading NXmx"
# Check file contains the feature
assert ("features" in entry)
assert (6 in entry['features'].value)
experiment_list = ExperimentList()
# Find all the experiments
entries = find_nx_mx_entries(entry, ".")
if len(entries) > 1:
entries = sorted(entries, key=lambda x: x['dials/index'].value)
assert (len(entries) == len(exp_index))
for nxmx, name in zip(entries, exp_index):
assert (nxmx.name == name)
index = []
rotations = []
for name in exp_index:
# Get the entry
nxmx = entry.file[name]
# Get the definition
definition = nxmx['definition']
assert (definition.value == 'NXmx')
assert (definition.attrs['version'] == 1)
# Get dials specific stuff
nx_dials = get_nx_dials(nxmx, "dials")
# Set index
b = nx_dials['index'].attrs['source']
d = nx_dials['index'].attrs['detector']
if "goniometer" in nx_dials['index'].attrs:
g = nx_dials['index'].attrs['goniometer']
else:
g = None
if "scan" in nx_dials['index'].attrs:
s = nx_dials['index'].attrs['scan']
else:
s = None
c = nx_dials['index'].attrs['sample']
index.append((b, d, g, s, c))
# Get the original orientation (dials specific)
transformations = get_nx_transformations(nx_dials, "transformations")
angle = transformations['angle'].value
assert (transformations['angle'].attrs['transformation_type'] ==
'rotation')
axis = transformations['angle'].attrs['vector']
assert (tuple(transformations['angle'].attrs['offset']) == (0, 0, 0))
assert (transformations['angle'].attrs['offset_units'] == 'mm')
assert (transformations['angle'].attrs['depends_on'] == '.')
rotations.append((axis, angle))
# Get the tmeplate and imageset
try:
template = list(nx_dials['template'])
image_range = None
except Exception:
template = nx_dials['template'].value
if template == "":
template = None
if "range" in nx_dials['template'].attrs:
image_range = nx_dials['template'].attrs['range']
else:
image_range = None
# Create the experiment
experiment = Experiment()
# Read the models
experiment.beam = load_beam(nxmx)
experiment.detector = load_detector(nxmx)
experiment.goniometer = load_goniometer(nxmx)
experiment.scan = load_scan(nxmx)
experiment.crystal = load_crystal(nxmx)
# Set the image range
if image_range is not None and experiment.scan is not None:
num = image_range[1] - image_range[0] + 1
assert (num == len(experiment.scan))
experiment.scan.set_image_range(image_range)
# Return the experiment list
experiment_list.append(experiment)
# Convert from nexus beam direction
experiment_list = convert_from_nexus_beam_direction(
experiment_list, rotations)
from collections import defaultdict
beam = defaultdict(list)
detector = defaultdict(list)
goniometer = defaultdict(list)
scan = defaultdict(list)
crystal = defaultdict(list)
for i, ind in enumerate(index):
beam[ind[0]].append(i)
detector[ind[1]].append(i)
goniometer[ind[2]].append(i)
scan[ind[3]].append(i)
crystal[ind[4]].append(i)
# Set all the shared beams
for key, value in beam.iteritems():
b1 = experiment_list[value[0]].beam
assert (all(experiment_list[v].beam == b1 for v in value[1:]))
for v in value[1:]:
experiment_list[v].beam = b1
# Set all the shared detectors
for key, value in detector.iteritems():
d1 = experiment_list[value[0]].detector
assert (all(experiment_list[v].detector == d1 for v in value[1:]))
for v in value[1:]:
experiment_list[v].detector = d1
# Set all the shared goniometer
for key, value in goniometer.iteritems():
g1 = experiment_list[value[0]].goniometer
assert (all(experiment_list[v].goniometer == g1 for v in value[1:]))
for v in value[1:]:
experiment_list[v].goniometer = g1
# Set all the shared scans
for key, value in scan.iteritems():
s1 = experiment_list[value[0]].scan
assert (all(experiment_list[v].scan == s1 for v in value[1:]))
for v in value[1:]:
experiment_list[v].scan = s1
# Set all the shared crystals
for key, value in crystal.iteritems():
c1 = experiment_list[value[0]].crystal
assert (all(experiment_list[v].crystal == c1 for v in value[1:]))
for v in value[1:]:
experiment_list[v].crystal = c1
return experiment_list
