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
beam = BeamFactory.simple(params.wavelength).get_s0()
beam_center = (0,0)
data = numpy.zeros((11840,194))
if annulus:
inner = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.annulus_inner)))
outer = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.annulus_outer)))
print "Inner (mm):", inner
print "Outer (mm):", outer
if params.resolution is not None:
radius = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.resolution)))
print "Radius (mm):", radius
print "Panel:",; sys.stdout.flush()
for p_id, panel in enumerate(img.get_detector()):
print p_id,; sys.stdout.flush()
for y in range(185):
for x in range(194):
lx, ly, lz = panel.get_pixel_lab_coord((x,y))
if annulus:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],outer) or point_inside_circle(lx,ly,beam_center[0],beam_center[1],inner):
data[(p_id*185)+y,x] = 1
if params.resolution is not None:
if annulus:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],radius):
data[(p_id*185)+y,x] = 0
else:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],radius):
data[(p_id*185)+y,x] = 1
print
beam = beam_factory.simple(params.wavelength).get_s0()
beam_center = (0,0)
data = numpy.zeros((11840,194))
if annulus:
inner = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.annulus_inner)))
outer = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.annulus_outer)))
print "Inner (mm):", inner
print "Outer (mm):", outer
if params.resolution is not None:
radius = params.distance * math.tan(2*math.sinh(params.wavelength/(2*params.resolution)))
print "Radius (mm):", radius
print "Panel:",; sys.stdout.flush()
for p_id, panel in enumerate(img.get_detector()):
print p_id,; sys.stdout.flush()
for y in xrange(185):
for x in xrange(194):
lx, ly, lz = panel.get_pixel_lab_coord((x,y))
if annulus:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],outer) or point_inside_circle(lx,ly,beam_center[0],beam_center[1],inner):
data[(p_id*185)+y,x] = 1
if params.resolution is not None:
if annulus:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],radius):
data[(p_id*185)+y,x] = 0
else:
if not point_inside_circle(lx,ly,beam_center[0],beam_center[1],radius):
data[(p_id*185)+y,x] = 1
print
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'
