def __init__(self,
pickle_path,
sweep_path,
extra_args,
expected_unit_cell,
expected_rmsds,
expected_hall_symbol,
n_expected_lattices=1,
relative_length_tolerance=0.005,
absolute_angle_tolerance=0.5):
args = ["dials.index", pickle_path, sweep_path] + extra_args
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory(suffix="test_dials_index")
os.chdir(tmp_dir)
command = " ".join(args)
print command
result = easy_run.fully_buffered(command=command).raise_if_errors()
os.chdir(cwd)
assert os.path.exists(os.path.join(tmp_dir, "experiments.json"))
experiments_list = dxtbx_load.experiment_list(
os.path.join(tmp_dir, "experiments.json"), check_format=False)
assert len(experiments_list.crystals()) == n_expected_lattices, (
len(experiments_list.crystals()), n_expected_lattices)
assert os.path.exists(os.path.join(tmp_dir, "indexed.pickle"))
from libtbx.utils import time_log
unpickling_timer = time_log("unpickling")
self.calc_rmsds_timer = time_log("calc_rmsds")
unpickling_timer.start()
self.indexed_reflections = load.reflections(os.path.join(tmp_dir, "indexed.pickle"))
unpickling_timer.stop()
for i in range(len(experiments_list)):
experiment = experiments_list[i]
self.crystal_model = experiment.crystal
#assert self.crystal_model.get_unit_cell().is_similar_to(
#expected_unit_cell,
#relative_length_tolerance=relative_length_tolerance,
#absolute_angle_tolerance=absolute_angle_tolerance), (
#self.crystal_model.get_unit_cell().parameters(),
#expected_unit_cell.parameters())
assert unit_cells_are_similar(
self.crystal_model.get_unit_cell(),expected_unit_cell,
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance), (
self.crystal_model.get_unit_cell().parameters(),
expected_unit_cell.parameters())
sg = self.crystal_model.get_space_group()
assert sg.type().hall_symbol() == expected_hall_symbol, (
sg.type().hall_symbol(), expected_hall_symbol)
reflections = self.indexed_reflections.select(
self.indexed_reflections['id'] == i)
mi = reflections['miller_index']
assert (mi != (0,0,0)).count(False) == 0
reflections = reflections.select(mi != (0,0,0))
self.rmsds = self.get_rmsds_obs_pred(reflections, experiment)
for actual, expected in zip(self.rmsds, expected_rmsds):
assert actual <= expected, "%s %s" %(self.rmsds, expected_rmsds)
if 0:
print self.calc_rmsds_timer.legend
print unpickling_timer.report()
print self.calc_rmsds_timer.report()
def load_input(exp_path, ref_path): refs = load_dials.reflections(ref_path) exp = load_dxtbx.experiment_list(exp_path , check_format=False)[0] return refs, exp
def load_input(exp_path, ref_path):
refs = load_dials.reflections(ref_path)
exp = load_dxtbx.experiment_list(exp_path, check_format=False)[0]
return refs, exp
from __future__ import division
if __name__ == '__main__':
import sys
from dials.model.serialize import load
from matplotlib import pylab
from scitbx.array_family import flex
rlist = load.reflections(sys.argv[1])
I = [r.intensity for r in rlist]
for r in rlist:
print "Background: %f, Intensity: %f" % (
flex.mean(r.shoebox_background), r.intensity)
pylab.plot(I)
pylab.show()
from dials.model.serialize import load
spots2 = load.reflections('strong2.pickle')
print spots2[52776]
#for i, s in enumerate(spots2):
# x, y, z = s.centroid_position
# if z >= 357 and z < 372:
# if x >= 1240 and x < 1250:
# print i, x, y, z
# if i == 49807:
# print s
spots = load.reflections('strong.pickle')
#dx, dy, dz = [], [], []
#for s1, s2 in zip(spots, spots2):
# dx.append(s1.centroid_variance[0] - s2.centroid_variance[0])
# dx.append(s1.centroid_variance[1] - s2.centroid_variance[1])
# dx.append(s1.centroid_variance[2] - s2.centroid_variance[2])
#from matplotlib import pylab
#pylab.plot(dx)
#pylab.show()
#for s1, s2 in zip(spots, spots2):
# print s1.centroid_variance, s2.centroid_variance
#from dials.algorithms.centroid import ComputeCentroid
try:
assert(abs(a - b) < eps)
except Exception, e:
print a, b
raise e
import sys
from dials.model.data import ReflectionList
filename1 = sys.argv[1]
filename2 = sys.argv[2]
from dials.model.serialize import load
from cctbx.array_family import flex
refl1 = load.reflections(filename1)
refl2 = load.reflections(filename2)
print "Length: ", len(refl1), len(refl2)
#assert(len(refl1) == len(refl2))
refl1 = ReflectionList([r for r in refl1 if r.is_valid()])
refl2 = ReflectionList([r for r in refl2 if r.is_valid()])
num_valid1 = len([r for r in refl1 if r.is_valid()])
num_valid2 = len([r for r in refl2 if r.is_valid()])
print "Valid: ", num_valid1, num_valid2
assert(num_valid1 == num_valid2)
from scitbx import matrix
print "Checking"
for r1, r2 in zip(refl1, refl2):
from __future__ import division
from __future__ import print_function
if __name__ == "__main__":
import sys
from dials.model.serialize import load
from matplotlib import pylab
from scitbx.array_family import flex
rlist = load.reflections(sys.argv[1])
I = [r.intensity for r in rlist]
for r in rlist:
print("Background: %f, Intensity: %f" %
(flex.mean(r.shoebox_background), r.intensity))
pylab.plot(I)
pylab.show()
def __init__(self,
pickle_path,
sweep_path,
extra_args,
expected_unit_cell,
expected_rmsds,
expected_hall_symbol,
n_expected_lattices=1,
relative_length_tolerance=0.005,
absolute_angle_tolerance=0.5):
args = ["dials.index", pickle_path, sweep_path] + extra_args
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory(suffix="test_dials_index")
os.chdir(tmp_dir)
command = " ".join(args)
print command
result = easy_run.fully_buffered(command=command).raise_if_errors()
os.chdir(cwd)
assert os.path.exists(os.path.join(tmp_dir, "experiments.json"))
experiments_list = dxtbx_load.experiment_list(os.path.join(
tmp_dir, "experiments.json"),
check_format=False)
assert len(experiments_list.crystals()) == n_expected_lattices, (len(
experiments_list.crystals()), n_expected_lattices)
assert os.path.exists(os.path.join(tmp_dir, "indexed.pickle"))
from libtbx.utils import time_log
unpickling_timer = time_log("unpickling")
self.calc_rmsds_timer = time_log("calc_rmsds")
unpickling_timer.start()
self.indexed_reflections = load.reflections(
os.path.join(tmp_dir, "indexed.pickle"))
unpickling_timer.stop()
for i in range(len(experiments_list)):
experiment = experiments_list[i]
self.crystal_model = experiment.crystal
#assert self.crystal_model.get_unit_cell().is_similar_to(
#expected_unit_cell,
#relative_length_tolerance=relative_length_tolerance,
#absolute_angle_tolerance=absolute_angle_tolerance), (
#self.crystal_model.get_unit_cell().parameters(),
#expected_unit_cell.parameters())
assert unit_cells_are_similar(
self.crystal_model.get_unit_cell(),
expected_unit_cell,
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance), (
self.crystal_model.get_unit_cell().parameters(),
expected_unit_cell.parameters())
sg = self.crystal_model.get_space_group()
assert sg.type().hall_symbol() == expected_hall_symbol, (
sg.type().hall_symbol(), expected_hall_symbol)
reflections = self.indexed_reflections.select(
self.indexed_reflections['id'] == i)
mi = reflections['miller_index']
assert (mi != (0, 0, 0)).count(False) == 0
reflections = reflections.select(mi != (0, 0, 0))
self.rmsds = self.get_rmsds_obs_pred(reflections, experiment)
for actual, expected in zip(self.rmsds, expected_rmsds):
assert actual <= expected, "%s %s" % (self.rmsds,
expected_rmsds)
if 0:
print self.calc_rmsds_timer.legend
print unpickling_timer.report()
print self.calc_rmsds_timer.report()
assert abs(a - b) < eps
except Exception as e:
print(a, b)
raise e
import sys
from dials.model.data import ReflectionList
filename1 = sys.argv[1]
filename2 = sys.argv[2]
from dials.model.serialize import load
from cctbx.array_family import flex
refl1 = load.reflections(filename1)
refl2 = load.reflections(filename2)
print("Length: ", len(refl1), len(refl2))
# assert(len(refl1) == len(refl2))
refl1 = ReflectionList([r for r in refl1 if r.is_valid()])
refl2 = ReflectionList([r for r in refl2 if r.is_valid()])
num_valid1 = len([r for r in refl1 if r.is_valid()])
num_valid2 = len([r for r in refl2 if r.is_valid()])
print("Valid: ", num_valid1, num_valid2)
assert num_valid1 == num_valid2
from scitbx import matrix
print("Checking")
from __future__ import print_function
from dials.model.serialize import load
spots2 = load.reflections("strong2.pickle")
print(spots2[52776])
# for i, s in enumerate(spots2):
# x, y, z = s.centroid_position
# if z >= 357 and z < 372:
# if x >= 1240 and x < 1250:
# print i, x, y, z
# if i == 49807:
# print s
spots = load.reflections("strong.pickle")
# dx, dy, dz = [], [], []
# for s1, s2 in zip(spots, spots2):
# dx.append(s1.centroid_variance[0] - s2.centroid_variance[0])
# dx.append(s1.centroid_variance[1] - s2.centroid_variance[1])
# dx.append(s1.centroid_variance[2] - s2.centroid_variance[2])
# from matplotlib import pylab
# pylab.plot(dx)
# pylab.show()
# for s1, s2 in zip(spots, spots2):
# print s1.centroid_variance, s2.centroid_variance
# from dials.algorithms.centroid import ComputeCentroid