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 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(cspad_cbf_in_memory_phil)
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 __init__(self,
iparams,
write_pickle=True,
write_logs=True,
last_stage='integrate'):
''' Constructor
:param iparams: IOTA params
:param write_pickle: Set to True to write out an integration pickle
'''
self.iparams = iparams
self.write_pickle = write_pickle
self.write_logs = write_logs
self.last_stage = last_stage
self.dlog_bookmark = 0
# Get Processor PHIL and initialize Processor
if self.iparams.cctbx_xfel.target:
with open(self.iparams.cctbx_xfel.target, 'r') as tf:
tphil_string = tf.read()
tparams = phil_scope.fetch(source=parse(tphil_string)).extract()
else:
tparams = phil_scope.extract()
Processor.__init__(self, params=tparams)
# IOTA-specific settings from here
# Turn off all peripheral output
self.params.output.experiments_filename = None
self.params.output.indexed_filename = None
self.params.output.strong_filename = None
self.params.output.refined_experiments_filename = None
self.params.output.integrated_experiments_filename = None
self.params.output.integrated_filename = None
self.params.output.profile_filename = None
# Set customized parameters
beamX = self.iparams.image_import.beam_center.x
beamY = self.iparams.image_import.beam_center.y
if beamX != 0 or beamY != 0:
self.params.geometry.detector.slow_fast_beam_centre = '{} {}'.format(
beamY, beamX)
if self.iparams.image_import.distance != 0:
self.params.geometry.detector.distance = self.iparams.image_import.distance
if self.iparams.image_import.mask is not None:
self.params.spotfinder.lookup.mask = self.iparams.image_import.mask
self.params.integration.lookup.mask = self.iparams.image_import.mask
if self.iparams.cctbx_xfel.target_space_group is not None:
sg = self.iparams.cctbx_xfel.target_space_group
self.params.indexing.known_symmetry.space_group = sg
if self.iparams.cctbx_xfel.target_unit_cell is not None:
uc = self.iparams.cctbx_xfel.target_unit_cell
self.params.indexing.known_symmetry.unit_cell = uc
if not self.params.indexing.stills.method_list:
self.params.indexing.stills.method_list = [
'fft1d', 'real_space_grid_search'
]
if self.iparams.cctbx_xfel.use_fft3d:
self.params.indexing.stills.method_list.insert(2, 'fft3d')
if self.iparams.cctbx_xfel.significance_filter.flag_on:
sigma = self.iparams.cctbx_xfel.significance_filter.sigma
sigma = sigma if sigma else 1
self.params.significance_filter.enable = True
self.params.significance_filter.isigi_cutoff = sigma
# Load reference geometry
self.reference_detector = None
if self.iparams.advanced.reference_geometry:
from dxtbx.model.experiment_list import ExperimentListFactory
try:
ref_experiments = ExperimentListFactory.from_json_file(
str(self.iparams.advanced.reference_geometry),
check_format=False)
except Exception as e:
print('DEBUG: Could not make exp. list because: ', e)
try:
import dxtbx
img = dxtbx.load(
str(self.iparams.advanced.reference_geometry))
except Exception:
print("DEBUG: Couldn't load geometry file {}"
"".format(self.iparams.advanced.reference_geometry))
else:
self.reference_detector = img.get_detector()
else:
assert len(ref_experiments.detectors()) == 1
self.reference_detector = ref_experiments.detectors()[0]
def test_cspad_cbf_in_memory(self):
from os.path import join, exists
import os, dxtbx
from uuid import uuid4
from dials.command_line.stills_process import phil_scope, Processor
from libtbx.phil import parse
from dxtbx.imageset import ImageSet, ImageSetData, MemReader, MemMasker
from dxtbx.datablock import DataBlockFactory
from dxtbx.format.FormatCBFCspad import FormatCBFCspadInMemory
import cPickle as pickle
dirname = 'tmp_%s' % uuid4().hex
os.mkdir(dirname)
os.chdir(dirname)
assert exists(join(self.lcls_path, 'idx-20130301060858801.cbf'))
f = open("process_lcls.phil", 'w')
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
}
""")
f.close()
params = phil_scope.fetch(
parse(file_name="process_lcls.phil")).extract()
params.output.datablock_filename = None
processor = Processor(params)
mem_img = dxtbx.load(join(self.lcls_path, 'idx-20130301060858801.cbf'))
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]), MemMasker([mem_img])))
imgset.set_beam(mem_img.get_beam())
imgset.set_detector(mem_img.get_detector())
datablock = DataBlockFactory.from_imageset(imgset)[0]
processor.process_datablock("20130301060858801",
datablock) # index/integrate the image
result = "idx-20130301060858801_integrated.pickle"
#n_refls = range(140,152) # large ranges to handle platform-specific differences
# 09/20/17 Changes to still indexer: refine candidate basis vectors in target symmetry if supplied
#n_refls = range(128,140) # large ranges to handle platform-specific differences
# 09/27/17 Bugfix for refine_candidates_with_known_symmetry
n_refls = range(
140, 152) # large ranges to handle platform-specific differences
table = pickle.load(open(result, 'rb'))
assert len(table) in n_refls, len(table)
assert 'id' in table
assert (table['id'] == 0).count(False) == 0
print 'OK'
def __init__(self, params, write_pickle=True):
self.phil = params
self.write_pickle = write_pickle
Processor.__init__(self, params=params)
