def tst_goniometer(self):
from dxtbx.serialize import goniometer
from dxtbx.model import Goniometer
g1 = Goniometer((1, 0, 0), (1, 0, 0, 0, 1, 0, 0, 0, 1))
d = goniometer.to_dict(g1)
g2 = goniometer.from_dict(d)
assert(d['rotation_axis'] == (1, 0, 0))
assert(d['fixed_rotation'] == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert(g1 == g2)
# Test with a template and partial dictionary
d2 = { 'rotation_axis' : (0, 1, 0) }
g3 = goniometer.from_dict(d2, d)
assert(g3.get_rotation_axis() == (0, 1, 0))
assert(g3.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert(g2 != g3)
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
def tst_goniometer(self):
from dxtbx.serialize import goniometer
from dxtbx.model import Goniometer
g1 = Goniometer((1, 0, 0), (1, 0, 0, 0, 1, 0, 0, 0, 1))
d = goniometer.to_dict(g1)
g2 = goniometer.from_dict(d)
assert (d['rotation_axis'] == (1, 0, 0))
assert (d['fixed_rotation'] == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert (g1 == g2)
# Test with a template and partial dictionary
d2 = {'rotation_axis': (0, 1, 0)}
g3 = goniometer.from_dict(d2, d)
assert (g3.get_rotation_axis() == (0, 1, 0))
assert (g3.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert (g2 != g3)
print 'OK'
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
def _goniometer_from_dict(obj): ''' Get the goniometer from a dictionary. ''' from dxtbx.serialize import goniometer return goniometer.from_dict(obj)
