def tst_scan(self):
from dxtbx.serialize import scan
from dxtbx.model import Scan
from scitbx.array_family import flex
s1 = Scan((1, 3), (1.0, 0.2), flex.double([0.1, 0.1, 0.1]), flex.double([0.1, 0.2, 0.3]))
d = scan.to_dict(s1)
s2 = scan.from_dict(d)
assert(d['image_range'] == (1, 3))
assert(d['oscillation'] == (1.0, 0.2))
assert(d['exposure_time'] == [0.1, 0.1, 0.1])
assert(d['epochs'] == [0.1, 0.2, 0.3])
assert(s1 == s2)
# Test with a template and partial dictionary
d2 = { 'exposure_time' : [0.2, 0.2, 0.2] }
s3 = scan.from_dict(d2, d)
assert(s3.get_image_range() == (1, 3))
assert(s3.get_oscillation() == (1.0, 0.2))
assert(list(s3.get_exposure_times()) == [0.2, 0.2, 0.2])
assert(list(s3.get_epochs()) == [0.1, 0.2, 0.3])
assert(s2 != s3)
# Test with a partial epoch
d3 = { 'image_range' : (1, 10), 'epochs' : [0.1, 0.2] }
s4 = scan.from_dict(d3, d)
assert(abs(s4.get_epochs()[2] - 0.3) < 1e-7)
assert(abs(s4.get_epochs()[9] - 1.0) < 1e-7)
print 'OK'
def tst_scan(self):
from dxtbx.serialize import scan
from dxtbx.model import Scan
from scitbx.array_family import flex
s1 = Scan((1, 3), (1.0, 0.2), flex.double([0.1, 0.1, 0.1]),
flex.double([0.1, 0.2, 0.3]))
d = scan.to_dict(s1)
s2 = scan.from_dict(d)
assert (d['image_range'] == (1, 3))
assert (d['oscillation'] == (1.0, 0.2))
assert (d['exposure_time'] == [0.1, 0.1, 0.1])
assert (d['epochs'] == [0.1, 0.2, 0.3])
assert (s1 == s2)
# Test with a template and partial dictionary
d2 = {'exposure_time': [0.2, 0.2, 0.2]}
s3 = scan.from_dict(d2, d)
assert (s3.get_image_range() == (1, 3))
assert (s3.get_oscillation() == (1.0, 0.2))
assert (list(s3.get_exposure_times()) == [0.2, 0.2, 0.2])
assert (list(s3.get_epochs()) == [0.1, 0.2, 0.3])
assert (s2 != s3)
# Test with a partial epoch
d3 = {'image_range': (1, 10), 'epochs': [0.1, 0.2]}
s4 = scan.from_dict(d3, d)
assert (abs(s4.get_epochs()[2] - 0.3) < 1e-7)
assert (abs(s4.get_epochs()[9] - 1.0) < 1e-7)
print 'OK'
def imagesweep_from_dict(d, check_format=True):
'''Construct and image sweep from the dictionary.'''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize import beam, detector, goniometer, scan
from dxtbx.serialize.filename import load_path
# Get the template (required)
template = load_path(str(d['template']))
# If the scan isn't set, find all available files
scan_dict = d.get('scan')
if scan_dict is None:
image_range = None
else:
image_range = scan_dict.get('image_range')
# Construct the sweep
try:
sweep = ImageSetFactory.from_template(
template, image_range, check_format=check_format)[0]
# Get the existing models as dictionaries
beam_dict = beam.to_dict(sweep.get_beam())
gonio_dict = goniometer.to_dict(sweep.get_goniometer())
detector_dict = detector.to_dict(sweep.get_detector())
scan_dict = scan.to_dict(sweep.get_scan())
except Exception:
indices = range(image_range[0], image_range[1] + 1)
sweep = ImageSetFactory.make_sweep(
template, indices, check_format=False)
beam_dict = None
gonio_dict = None
detector_dict = None
scan_dict = None
# Set some external lookups
if 'mask' in d and d['mask'] is not None:
with open(d['mask']) as infile:
sweep.external_lookup.mask.filename = d['mask']
sweep.external_lookup.mask.data = pickle.load(infile)
if 'gain' in d and d['gain'] is not None:
with open(d['gain']) as infile:
sweep.external_lookup.gain.filename = d['gain']
sweep.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in d and d['pedestal'] is not None:
with open(d['pedestal']) as infile:
sweep.external_lookup.pedestal.filename = d['pedestal']
sweep.external_lookup.pedestal.data = pickle.load(infile)
# Set the models with the exisiting models as templates
sweep.set_beam(beam.from_dict(d.get('beam'), beam_dict))
sweep.set_goniometer(goniometer.from_dict(d.get('goniometer'), gonio_dict))
sweep.set_detector(detector.from_dict(d.get('detector'), detector_dict))
sweep.set_scan(scan.from_dict(d.get('scan'), scan_dict))
# Return the sweep
return sweep