else:
P.init.Nabc = SIM.crystal.Ncells_abc
if "detz_shift" in args.perturb:
P.init.detz_shift = 1
else:
P.init.detz_shift = 0
if "eta" in args.perturb:
P.init.eta_abc = [0.12, 0.13, 0.14]
P.simulator.crystal.num_mosaicity_samples = 250 # in practive, the number of mosaic domains we model should be smaller than whats in the crystal .. .
P.simulator.crystal.has_isotropic_mosaicity = False
P.fix.eta_abc = False
E.detector = SIM.detector
E.beam = SIM.D.beam
E.imageset = make_imageset([img], E.beam, E.detector)
#refls = utils.refls_from_sims([img], E.detector, E.beam, thresh=18)
refls = utils.refls_from_sims([spots], E.detector, E.beam, thresh=18)
print("%d REFLS" % len(refls))
utils.refls_to_q(refls, E.detector, E.beam, update_table=True)
utils.refls_to_hkl(refls, E.detector, E.beam, E.crystal, update_table=True)
P.roi.shoebox_size = 20
P.relative_tilt = False
P.roi.fit_tilt = False
P.roi.pad_shoebox_for_background_estimation = 10
P.roi.reject_edge_reflections = False
P.refiner.sigma_r = SIM.D.readout_noise_adu
P.refiner.adu_per_photon = SIM.D.quantum_gain
P.simulator.init_scale = 1 #SIM.D.spot_scale
from __future__ import division
from simtbx.diffBragg import utils
from simtbx.nanoBragg.tst_nanoBragg_basic import pdb_lines
from simtbx.diffBragg.phil import hopper_phil, philz
from libtbx.phil import parse
from simtbx.nanoBragg import tst_nanoBragg_multipanel
from dxtbx.model import Experiment
import numpy as np
# make a dummie experiment
expt = Experiment()
expt.detector = tst_nanoBragg_multipanel.whole_det
expt.beam = tst_nanoBragg_multipanel.beam
expt.crystal = tst_nanoBragg_multipanel.cryst
# write a dummie PDB file
PDB = "1234.pdb"
o = open(PDB, "w")
o.write(pdb_lines)
o.close()
# Create a miller array from on-disk PDB file
F = utils.get_complex_fcalc_from_pdb(PDB,
wavelength=expt.beam.get_wavelength(),
dmin=2, dmax=20, k_sol=0.2, b_sol=20)
F = F.as_amplitude_array()
Fmap = {h: amp for h,amp in zip(F.indices(), F.data())}
# Create a sim_data class instance as would be done for hopper_utils.refine for example
phil_scope = parse(hopper_phil+philz)
iset = isets[i]
path = iset.get_path(0)
d = df2_filt0.query("imgpaths=='%s'" % path)
if has_master:
master_index = iset.indices()[0]
d = d.query("master_indices==%d" % master_index)
if len(d) != 1:
continue
A = d.Amats.values[0]
#break
C = deepcopy(crystals[i])
#C.set_A(A)
Ex = Experiment()
Ex.crystal = C
Ex.imageset = iset
Ex.beam = beams[i]
Ex.detector = D
El2.append(Ex)
Rsel = R.select(R['id']==i)
nref = len(Rsel)
Rsel['id'] = flex.int(nref, new_id)
R2.extend(Rsel)
new_id += 1
print (new_id)
el_file = "%s.expt" % args.tag
R_file = "%s.refl" % args.tag
El2.as_file(el_file)
print("Saved experiment %s" % el_file )
R2.as_file(R_file)