def get_values(invert_y):
from dxtbx.model.beam import beam_factory
beam = beam_factory.simple(wavelength=1)
if invert_y:
y_direction = "-y"
else:
y_direction = "+y"
from dxtbx.model.detector import detector_factory
detector = detector_factory.simple(
sensor=detector_factory.sensor("PAD"),
distance=100,
beam_centre=[50, 50],
fast_direction="+x",
slow_direction=y_direction,
pixel_size=[0.1, 0.1],
image_size=[1000, 1000])
from dxtbx.model import ParallaxCorrectedPxMmStrategy
from cctbx.eltbx import attenuation_coefficient
wavelength = beam.get_wavelength()
thickness = 0.5
table = attenuation_coefficient.get_table("Si")
mu = table.mu_at_angstrom(wavelength) / 10.0
t0 = thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
v1 = detector[0].pixel_to_millimeter((0, 0))
v2 = detector[0].pixel_to_millimeter((1000, 1000))
return v1, v2
def _beam(self):
'''
Create the beam model
'''
from dxtbx.model.beam import beam_factory
configuration = self.header['configuration']
return beam_factory.simple(configuration['wavelength'])
def _beam(self):
'''
Create the beam model
'''
from dxtbx.model.beam import beam_factory
configuration = self.header['configuration']
return beam_factory.simple(configuration['wavelength'])
def __init__(self,params):
import cPickle as pickle
from dxtbx.model.beam import beam_factory
from dxtbx.model.detector import detector_factory
from dxtbx.model.crystal import crystal_model
from cctbx.crystal_orientation import crystal_orientation,basis_type
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
from scitbx import matrix
self.experiments = ExperimentList()
self.unique_file_names = []
self.params = params
data = pickle.load(open(self.params.output.prefix+"_frame.pickle","rb"))
frames_text = data.split("\n")
for item in frames_text:
tokens = item.split(' ')
wavelength = float(tokens[order_dict["wavelength"]])
beam = beam_factory.simple(wavelength = wavelength)
detector = detector_factory.simple(
sensor = detector_factory.sensor("PAD"), # XXX shouldn't hard code for XFEL
distance = float(tokens[order_dict["distance"]]),
beam_centre = [float(tokens[order_dict["beam_x"]]), float(tokens[order_dict["beam_y"]])],
fast_direction = "+x",
slow_direction = "+y",
pixel_size = [self.params.pixel_size,self.params.pixel_size],
image_size = [1795,1795], # XXX obviously need to figure this out
)
reciprocal_matrix = matrix.sqr([float(tokens[order_dict[k]]) for k in [
'res_ori_1','res_ori_2','res_ori_3','res_ori_4','res_ori_5','res_ori_6','res_ori_7','res_ori_8','res_ori_9']])
ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
direct = matrix.sqr(ORI.direct_matrix())
crystal = crystal_model(
real_space_a = matrix.row(direct[0:3]),
real_space_b = matrix.row(direct[3:6]),
real_space_c = matrix.row(direct[6:9]),
space_group_symbol = "P63", # XXX obviously another gap in the database paradigm
mosaicity = float(tokens[order_dict["half_mosaicity_deg"]]),
)
crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
#if isoform is not None:
# newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
# crystal.set_B(newB)
self.experiments.append(Experiment(beam=beam,
detector=None, #dummy for now
crystal=crystal))
self.unique_file_names.append(tokens[order_dict["unique_file_name"]])
self.show_summary()
def prepare_dxtbx_models(self,setting_specific_ai,sg,isoform=None):
from dxtbx.model.beam import beam_factory
beam = beam_factory.simple(wavelength = self.inputai.wavelength)
from dxtbx.model.detector import detector_factory
detector = detector_factory.simple(
sensor = detector_factory.sensor("PAD"),
distance = setting_specific_ai.distance(),
beam_centre = [setting_specific_ai.xbeam(), setting_specific_ai.ybeam()],
fast_direction = "+x",
slow_direction = "+y",
pixel_size = [self.pixel_size,self.pixel_size],
image_size = [self.inputpd['size1'],self.inputpd['size1']],
)
direct = matrix.sqr(setting_specific_ai.getOrientation().direct_matrix())
from dxtbx.model.crystal import crystal_model
crystal = crystal_model(
real_space_a = matrix.row(direct[0:3]),
real_space_b = matrix.row(direct[3:6]),
real_space_c = matrix.row(direct[6:9]),
space_group_symbol = sg,
mosaicity = setting_specific_ai.getMosaicity()
)
if isoform is not None:
newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
crystal.set_B(newB)
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
experiments = ExperimentList()
experiments.append(Experiment(beam=beam,
detector=detector,
crystal=crystal))
print beam
print detector
print crystal
return experiments
def __init__(self, params):
import cPickle as pickle
from dxtbx.model.beam import beam_factory
from dxtbx.model.detector import detector_factory
from dxtbx.model.crystal import crystal_model
from cctbx.crystal_orientation import crystal_orientation, basis_type
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
from scitbx import matrix
self.experiments = ExperimentList()
self.unique_file_names = []
self.params = params
data = pickle.load(
open(self.params.output.prefix + "_frame.pickle", "rb"))
frames_text = data.split("\n")
for item in frames_text:
tokens = item.split(' ')
wavelength = float(tokens[order_dict["wavelength"]])
beam = beam_factory.simple(wavelength=wavelength)
detector = detector_factory.simple(
sensor=detector_factory.sensor(
"PAD"), # XXX shouldn't hard code for XFEL
distance=float(tokens[order_dict["distance"]]),
beam_centre=[
float(tokens[order_dict["beam_x"]]),
float(tokens[order_dict["beam_y"]])
],
fast_direction="+x",
slow_direction="+y",
pixel_size=[self.params.pixel_size, self.params.pixel_size],
image_size=[1795,
1795], # XXX obviously need to figure this out
)
reciprocal_matrix = matrix.sqr([
float(tokens[order_dict[k]]) for k in [
'res_ori_1', 'res_ori_2', 'res_ori_3', 'res_ori_4',
'res_ori_5', 'res_ori_6', 'res_ori_7', 'res_ori_8',
'res_ori_9'
]
])
ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
direct = matrix.sqr(ORI.direct_matrix())
crystal = crystal_model(
real_space_a=matrix.row(direct[0:3]),
real_space_b=matrix.row(direct[3:6]),
real_space_c=matrix.row(direct[6:9]),
space_group_symbol=self.params.target_space_group.type().
lookup_symbol(),
mosaicity=float(tokens[order_dict["half_mosaicity_deg"]]),
)
crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
#if isoform is not None:
# newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
# crystal.set_B(newB)
self.experiments.append(
Experiment(
beam=beam,
detector=None, #dummy for now
crystal=crystal))
self.unique_file_names.append(
tokens[order_dict["unique_file_name"]])
self.show_summary()
(-float(fs_x.rstrip('x')), float(fs_y.rstrip('y')), 0.0))
slow = matrix.col(
(-float(ss_x.rstrip('x')), float(ss_y.rstrip('y')), 0.0))
origin = matrix.col(
(-float(geom[key]['corner_x']) * params.pixel_size,
float(geom[key]['corner_y']) * params.pixel_size, 0.0))
# OBS! you need to set the panel to a root before set local frame...
p = root.add_panel()
p.set_name('panel-%s' % key)
p.set_image_size((512, 1024))
p.set_trusted_range((-1, 1000000))
p.set_pixel_size((params.pixel_size, params.pixel_size))
p.set_local_frame(fast.elems, slow.elems, origin.elems)
from dxtbx.model.beam import beam_factory
wavelength = params.wavelength
beam = beam_factory.simple(wavelength)
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList, ExperimentListDumper
experiments = ExperimentList()
experiment = Experiment(detector=detector, beam=beam)
experiments.append(experiment)
dump = ExperimentListDumper(experiments)
dump.as_json("geometry.json")
if __name__ == "__main__":
run(sys.argv[1:])
from xfel.cftbx.detector.cspad_cbf_tbx import read_slac_metrology, get_cspad_cbf_handle
from dxtbx.format.FormatCBFCspad import FormatCBFCspadInMemory
from dxtbx.model.beam import beam_factory
metro = read_slac_metrology(path=params.optical_metrology_path)
cbf = get_cspad_cbf_handle(None,
metro,
'cbf',
None,
"test",
None,
params.distance,
verbose=True,
header_only=True)
img = FormatCBFCspadInMemory(cbf)
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 "Generating annular gain mask between %f and %f angstroms, assuming a distance %s mm and wavelength %s angstroms" % \
(params.annulus_inner, params.annulus_outer, params.distance, params.wavelength)
else:
print "Generating annular gain mask between %f and %f angstroms, assuming a distance %s mm and wavelength %s angstroms. Also, pixels higher than %f angstroms will be set to low gain." % \
(params.annulus_inner, params.annulus_outer, params.distance, params.wavelength, params.resolution)
elif params.resolution is not None:
print "Generating circular gain mask %s angstroms, assuming a distance %s mm and wavelength %s angstroms" % \
(params.resolution, params.distance, params.wavelength)
from xfel.cftbx.detector.cspad_cbf_tbx import read_slac_metrology, get_cspad_cbf_handle
from dxtbx.format.FormatCBFCspad import FormatCBFCspadInMemory
from dxtbx.model.beam import beam_factory
metro = read_slac_metrology(path = params.optical_metrology_path)
cbf = get_cspad_cbf_handle(None, metro, 'cbf', None, "test", None, params.distance, verbose = True, header_only = True)
img = FormatCBFCspadInMemory(cbf)
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()):
slow = matrix.col((-float(ss_x.rstrip('x')),float(ss_y.rstrip('y')), 0.0))
origin = matrix.col((-float(geom[key]['corner_x']) * params.pixel_size,
float(geom[key]['corner_y']) * params.pixel_size,
0.0))
# OBS! you need to set the panel to a root before set local frame...
p = root.add_panel()
p.set_name('panel-%s' % key)
p.set_image_size((512, 1024))
p.set_trusted_range((-1, 1000000))
p.set_pixel_size((params.pixel_size, params.pixel_size))
p.set_local_frame(
fast.elems,
slow.elems,
origin.elems)
from dxtbx.model.beam import beam_factory
wavelength = params.wavelength
beam = beam_factory.simple(wavelength)
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList, ExperimentListDumper
experiments = ExperimentList()
experiment = Experiment(detector = detector, beam = beam)
experiments.append(experiment)
dump = ExperimentListDumper(experiments)
dump.as_json("geometry.json")
if __name__ == "__main__":
run(sys.argv[1:])
