def test_experimentlist_factory_from_args(dials_regression):
pytest.importorskip("dials")
os.environ["DIALS_REGRESSION"] = dials_regression
# Get all the filenames
filenames = [
os.path.join(dials_regression, "experiment_test_data",
"experiment_1.json"),
# os.path.join(dials_regression, 'experiment_test_data', 'experiment_2.json'),
os.path.join(dials_regression, "experiment_test_data",
"experiment_3.json"),
os.path.join(dials_regression, "experiment_test_data",
"experiment_4.json"),
]
# Get the experiments from a list of filenames
experiments = ExperimentListFactory.from_args(filenames, verbose=True)
assert len(experiments) == 3
for experiment in experiments:
assert experiment.imageset
assert experiment.beam
assert experiment.detector
assert experiment.goniometer
assert experiment.scan
def test_experimentlist_factory_from_args(monkeypatch, dials_regression):
pytest.importorskip("dials")
# Get all the filenames
filenames = [
os.path.join(dials_regression, "experiment_test_data",
"experiment_1.json"),
# os.path.join(dials_regression, 'experiment_test_data', 'experiment_2.json'),
os.path.join(dials_regression, "experiment_test_data",
"experiment_3.json"),
os.path.join(dials_regression, "experiment_test_data",
"experiment_4.json"),
]
# Get the experiments from a list of filenames
with monkeypatch.context() as m:
m.setenv("DIALS_REGRESSION", dials_regression)
experiments = ExperimentListFactory.from_args(filenames)
assert len(experiments) == 3
for experiment in experiments:
assert experiment.imageset
assert experiment.beam
assert experiment.detector
assert experiment.goniometer
assert experiment.scan
def test_experimentlist_factory_from_args(dials_regression):
pytest.importorskip('dials')
os.environ['DIALS_REGRESSION'] = dials_regression
# Get all the filenames
filenames = [
os.path.join(dials_regression, 'experiment_test_data',
'experiment_1.json'),
#os.path.join(dials_regression, 'experiment_test_data', 'experiment_2.json'),
os.path.join(dials_regression, 'experiment_test_data',
'experiment_3.json'),
os.path.join(dials_regression, 'experiment_test_data',
'experiment_4.json')
]
# Get the experiments from a list of filenames
experiments = ExperimentListFactory.from_args(filenames, verbose=True)
# Have 4 experiment
assert len(experiments) == 3
for i in range(3):
assert experiments[i].imageset is not None
assert experiments[i].beam is not None
assert experiments[i].detector is not None
assert experiments[i].goniometer is not None
assert experiments[i].scan is not None
def tst_from_args(self):
from os.path import join
from glob import glob
# Get all the filenames
filenames = [
join(self.path, 'experiment_test_data', 'experiment_1.json'),
#join(self.path, 'experiment_test_data', 'experiment_2.json'),
join(self.path, 'experiment_test_data', 'experiment_3.json'),
join(self.path, 'experiment_test_data', 'experiment_4.json')
]
# Get the experiments from a list of filenames
experiments = ExperimentListFactory.from_args(filenames)
# Have 4 experiment
assert (len(experiments) == 3)
for i in range(3):
assert (experiments[i].imageset is not None)
assert (experiments[i].beam is not None)
assert (experiments[i].detector is not None)
assert (experiments[i].goniometer is not None)
assert (experiments[i].scan is not None)
# Test passed
print 'OK'
def build_hist(nproc=1):
# FIXME use proper optionparser here. This works for now
if len(sys.argv) >= 2 and sys.argv[1].startswith("nproc="):
nproc = int(sys.argv[1][6:])
sys.argv = sys.argv[1:]
experiments = ExperimentListFactory.from_args(sys.argv[1:])
if len(experiments) == 0:
experiments = ExperimentListFactory.from_filenames(sys.argv[1:])
for experiment in experiments:
imageset = experiment.imageset
limit = experiment.detector[0].get_trusted_range()[1]
n0, n1 = experiment.scan.get_image_range()
image_count = n1 - n0 + 1
binfactor = 5 # register up to 500% counts
histmax = (limit * binfactor) + 0.0
histbins = int(limit * binfactor) + 1
use_python_counter = histbins > 90000000 # empirically determined
print("Processing %d images in %d processes using %s\n" % (
image_count,
nproc,
"python Counter" if use_python_counter else "flex arrays",
))
def process_image(process):
last_update = start = timeit.default_timer()
i = process
if use_python_counter:
local_hist = Counter()
else:
local_hist = flex.histogram(flex.double(),
data_min=0.0,
data_max=histmax,
n_slots=histbins)
max_images = image_count // nproc
if process >= image_count % nproc:
max_images += 1
while i < image_count:
data = imageset.get_raw_data(i)[0]
if not use_python_counter:
data = flex.histogram(
data.as_double().as_1d(),
data_min=0.0,
data_max=histmax,
n_slots=histbins,
)
local_hist.update(data)
i = i + nproc
if process == 0:
if timeit.default_timer() > (last_update + 3):
last_update = timeit.default_timer()
if sys.stdout.isatty():
sys.stdout.write("\033[A")
print("Processed %d%% (%d seconds remain) " % (
100 * i // image_count,
round((image_count - i) * (last_update - start) /
(i + 1)),
))
return local_hist
results = easy_mp.parallel_map(
func=process_image,
iterable=range(nproc),
processes=nproc,
preserve_exception_message=True,
)
print("Merging results")
result_hist = None
for hist in results:
if result_hist is None:
result_hist = hist
else:
result_hist.update(hist)
if not use_python_counter:
# reformat histogram into dictionary
result = list(result_hist.slots())
result_hist = {
b: count
for b, count in enumerate(result) if count > 0
}
results = {
"scale_factor": 1 / limit,
"overload_limit": limit,
"counts": result_hist,
}
print("Writing results to overload.json")
with open("overload.json", "w") as fh:
json.dump(results, fh, indent=1, sort_keys=True)
