def do_work(i, item_list):
processor = Processor(copy.deepcopy(self.params), composite_tag="%04d" % i)
for item in item_list:
tag, filename = item
experiments = do_import(filename)
imagesets = experiments.imagesets()
if len(imagesets) == 0 or len(imagesets[0]) == 0:
logger.info("Zero length imageset in file: %s" % filename)
return
if len(imagesets) > 1:
raise Abort("Found more than one imageset in file: %s" % filename)
if len(imagesets[0]) > 1:
raise Abort(
"Found a multi-image file. Run again with pre_import=True"
)
if self.reference_detector is not None:
imagesets[0].set_detector(
Detector.from_dict(self.reference_detector.to_dict())
)
update_geometry(imagesets[0])
processor.process_experiments(tag, experiments)
processor.finalize()
def test_cspad_cbf_in_memory(dials_regression, run_in_tmpdir):
# Check the data files for this test exist
image_path = os.path.join(
dials_regression,
"image_examples",
"LCLS_cspad_nexus",
"idx-20130301060858801.cbf",
)
assert os.path.isfile(image_path)
with open("process_lcls.phil", "w") as f:
f.write(
"""
dispatch.squash_errors = False
spotfinder {
filter.min_spot_size=2
threshold.dispersion.gain=25
threshold.dispersion.global_threshold=100
}
indexing {
known_symmetry {
space_group = P6122
unit_cell = 92.9 92.9 130.4 90 90 120
}
refinement_protocol.d_min_start=1.7
stills.refine_candidates_with_known_symmetry=True
}
"""
)
params = phil_scope.fetch(parse(file_name="process_lcls.phil")).extract()
params.output.experiments_filename = None
processor = Processor(params)
mem_img = dxtbx.load(image_path)
raw_data = mem_img.get_raw_data() # cache the raw data to prevent swig errors
mem_img = FormatCBFCspadInMemory(mem_img._cbf_handle)
mem_img._raw_data = raw_data
mem_img._cbf_handle = None # drop the file handle to prevent swig errors
imgset = ImageSet(ImageSetData(MemReader([mem_img]), None))
imgset.set_beam(mem_img.get_beam())
imgset.set_detector(mem_img.get_detector())
experiments = ExperimentListFactory.from_imageset_and_crystal(imgset, None)
processor.process_experiments(
"20130301060858801", experiments
) # index/integrate the image
result = "idx-20130301060858801_integrated.refl"
n_refls = list(
range(140, 152)
) # large ranges to handle platform-specific differences
table = flex.reflection_table.from_file(result)
assert len(table) in n_refls, len(table)
assert "id" in table
assert (table["id"] == 0).count(False) == 0
def test_cspad_cbf_in_memory(dials_regression, run_in_tmpdir,
composite_output):
# Check the data files for this test exist
image_path = os.path.join(
dials_regression,
"image_examples",
"LCLS_cspad_nexus",
"idx-20130301060858801.cbf",
)
assert os.path.isfile(image_path)
with open("process_lcls.phil", "w") as f:
f.write(cspad_cbf_in_memory_phil)
params = phil_scope.fetch(parse(file_name="process_lcls.phil")).extract()
params.output.experiments_filename = None
params.output.composite_output = composite_output
if composite_output:
processor = Processor(params, composite_tag="memtest")
else:
processor = Processor(params)
mem_img = dxtbx.load(image_path)
raw_data = mem_img.get_raw_data(
) # cache the raw data to prevent swig errors
mem_img = FormatCBFCspadInMemory(mem_img._cbf_handle)
mem_img._raw_data = raw_data
mem_img._cbf_handle = None # drop the file handle to prevent swig errors
imgset = ImageSet(ImageSetData(MemReader([mem_img]), None))
imgset.set_beam(mem_img.get_beam())
imgset.set_detector(mem_img.get_detector())
experiments = ExperimentListFactory.from_imageset_and_crystal(imgset, None)
processor.process_experiments("20130301060858801",
experiments) # index/integrate the image
if composite_output:
processor.finalize()
result = "idx-memtest_integrated.refl"
else:
result = "idx-20130301060858801_integrated.refl"
n_refls = list(range(
140, 152)) # large ranges to handle platform-specific differences
table = flex.reflection_table.from_file(result)
assert len(table) in n_refls, len(table)
assert "id" in table
assert (table["id"] == 0).count(False) == 0
