def tst_crystal(self):
from dxtbx.serialize.crystal import to_dict, from_dict
from dxtbx.model.crystal import crystal_model
from scitbx import matrix
real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))
c1 = crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group_symbol="P 1 2/m 1",
mosaicity=0.1)
d = to_dict(c1)
c2 = from_dict(d)
eps = 1e-7
assert(abs(matrix.col(d['real_space_a']) - real_space_a) <= eps)
assert(abs(matrix.col(d['real_space_b']) - real_space_b) <= eps)
assert(abs(matrix.col(d['real_space_c']) - real_space_c) <= eps)
assert(d['space_group_hall_symbol'] == "-P 2y")
assert(d['mosaicity'] == 0.1)
assert(c1 == c2)
print 'OK'
def tst_crystal_with_scan_points(self):
from dxtbx.serialize.crystal import to_dict, from_dict
from dxtbx.model.crystal import crystal_model
from scitbx import matrix
real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))
c1 = crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group_symbol="P 1 2/m 1",
mosaicity=0.1)
A = c1.get_A()
c1.set_A_at_scan_points([A for i in range(5)])
d = to_dict(c1)
c2 = from_dict(d)
eps = 1e-9
for Acomp in (d['A_at_scan_points']):
for e1, e2 in zip(A, Acomp):
assert(abs(e1 - e2) <= eps)
assert(c1 == c2)
print 'OK'
def work(filename, cl=None):
if cl is None:
cl = []
import libtbx.phil
phil_scope = libtbx.phil.parse('''\
index = False
.type = bool
integrate = False
.type = bool
indexing_min_spots = 10
.type = int(value_min=1)
''')
if not os.access(filename, os.R_OK):
raise RuntimeError("Server does not have read access to file %s" %filename)
interp = phil_scope.command_line_argument_interpreter()
params, unhandled = interp.process_and_fetch(
cl, custom_processor='collect_remaining')
index = params.extract().index
integrate = params.extract().integrate
indexing_min_spots = params.extract().indexing_min_spots
from dials.command_line.find_spots import phil_scope as find_spots_phil_scope
from dxtbx.datablock import DataBlockFactory
from dials.array_family import flex
interp = find_spots_phil_scope.command_line_argument_interpreter()
phil_scope, unhandled = interp.process_and_fetch(
unhandled, custom_processor='collect_remaining')
logger.info('The following spotfinding parameters have been modified:')
logger.info(find_spots_phil_scope.fetch_diff(source=phil_scope).as_str())
params = phil_scope.extract()
# no need to write the hot mask in the server/client
params.spotfinder.write_hot_mask = False
datablock = DataBlockFactory.from_filenames([filename])[0]
t0 = time.time()
reflections = flex.reflection_table.from_observations(datablock, params)
t1 = time.time()
logger.info('Spotfinding took %.2f seconds' %(t1-t0))
from dials.algorithms.spot_finding import per_image_analysis
imageset = datablock.extract_imagesets()[0]
scan = imageset.get_scan()
if scan is not None:
i = scan.get_array_range()[0]
else:
i = 0
stats = per_image_analysis.stats_single_image(
imageset, reflections, i=i, plot=False)
stats = stats.__dict__
t2 = time.time()
logger.info('Resolution analysis took %.2f seconds' %(t2-t1))
if index and stats['n_spots_no_ice'] > indexing_min_spots:
import logging
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
from dials.algorithms.indexing import indexer
from dxtbx.serialize.crystal import to_dict
interp = indexer.master_phil_scope.command_line_argument_interpreter()
phil_scope, unhandled = interp.process_and_fetch(
unhandled, custom_processor='collect_remaining')
imagesets = [imageset]
logger.info('The following indexing parameters have been modified:')
indexer.master_phil_scope.fetch_diff(source=phil_scope).show()
params = phil_scope.extract()
params.indexing.scan_range=[]
if (imageset.get_goniometer() is not None and
imageset.get_scan() is not None and
imageset.get_scan().get_oscillation()[1] == 0):
imageset.set_goniometer(None)
imageset.set_scan(None)
try:
idxr = indexer.indexer_base.from_parameters(
reflections, imagesets, params=params)
indexing_results = []
indexed_sel = idxr.refined_reflections.get_flags(
idxr.refined_reflections.flags.indexed)
indexed_sel &= ~(idxr.refined_reflections.get_flags(
idxr.refined_reflections.flags.centroid_outlier))
for i_expt, expt in enumerate(idxr.refined_experiments):
sel = idxr.refined_reflections['id'] == i_expt
sel &= indexed_sel
indexing_results.append({
'crystal': to_dict(expt.crystal),
'n_indexed': sel.count(True),
'fraction_indexed': sel.count(True)/sel.size()})
stats['lattices'] = indexing_results
stats['n_indexed'] = indexed_sel.count(True)
stats['fraction_indexed'] = indexed_sel.count(True)/len(reflections)
except Exception, e:
logger.error(e)
stats['error'] = str(e)
#stats.crystal = None
#stats.n_indexed = None
#stats.fraction_indexed = None
finally:
