def save_results(data_img, crystal, refl, fcalc_file, Xang, Yang, filename):
x = col((1, 0, 0))
y = col((0, 1, 0))
rX = x.axis_and_angle_as_r3_rotation_matrix(Xang, deg=True)
rY = y.axis_and_angle_as_r3_rotation_matrix(Yang, deg=True)
energies, fcalc_at_en = sim_utils.load_fcalc_file(fcalc_file)
Patts = PatternFactory()
Patts.adjust_mosaicity(2, 0.05)
#flux_per_en = [fracA*Patts.SIM2.flux, fracB*Patts.SIM2.flux]
flux_per_en = [fracA * 1e14, fracB * 1e14]
sim_patt = Patts.make_pattern2(crystal=deepcopy(crystal),
flux_per_en=flux_per_en,
energies_eV=energies,
fcalcs_at_energies=fcalcs_at_en,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=True,
Op=None)
sim_patt_R = Patts.make_pattern2(crystal=deepcopy(crystal),
flux_per_en=flux_per_en,
energies_eV=energies,
fcalcs_at_energies=fcalcs_at_en,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=True,
Op=rX * rY)
refls = [refl] * 3
imgs = [sim_patt, data_img, sim_patt_R]
utils.images_and_refls_to_simview(filename, imgs, refls)
def refine_cell(data):
spot_mask = spot_utils.strong_spot_mask(data['refl'], (1800, 1800))
Patts = sim_utils.PatternFactory()
Patts.adjust_mosaicity(2, 0.5)
energy, fcalc = sim_utils.load_fcalc_file(data['fcalc_f'])
crystal = data['crystal']
a, b, c, _, _, _ = crystal.get_unit_cell().parameters()
optX, optY = data['optX'], data['optY']
optX_fine, optY_fine = data['optX_fine'], data['optY_fine']
Op = optX_fine * optY_fine * optX * optY
crystal.set_U(Op)
overlaps = []
imgs_all = []
percs = np.arange(-0.005, 0.006, 0.001)
crystals = []
for i in percs:
for j in percs:
crystal2 = deepcopy(crystal)
a2 = a + a * i
c2 = c + c * j
B2 = sqr((a2, 0, 0, 0, a2, 0, 0, 0, c2)).inverse()
crystal2.set_B(B2)
sim_patt = Patts.make_pattern2(
crystal=crystal2,
flux_per_en=[data['fracA'] * 1e14, data['fracB'] * 1e14],
energies_eV=energy,
fcalcs_at_energies=fcalc,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=True,
Op=None)
sim_sig_mask = sim_patt > 0
overlaps.append(np.sum(sim_sig_mask * spot_mask))
crystals.append(deepcopy(crystal2))
imgs_all.append(sim_patt)
refls_all = [data["refl"]] * len(imgs_all)
utils.images_and_refls_to_simview("cell_refine", imgs_all, refls_all)
return overlaps, crystals
def xyscan_multi(crystal,
fcalcs_file,
fracA,
fracB,
strong,
rot_series,
n_jobs,
scan_func=xyscan,
use_weights=False,
raw_image=None):
"""
:param crystal_file:
:param energies:
:param fcalcs_file:
:param fracA:
:param fracB:
:param strong_file:
:param rotxy_series:
:param n_jobs:
:return:
"""
from joblib import Parallel, delayed
nscans = len(rot_series)
scan_idx = np.array_split(range(nscans), n_jobs)
scan_split = []
for idx in scan_idx:
scan_split.append([rot_series[i] for i in idx])
energy, fcalcs = sim_utils.load_fcalc_file(fcalcs_file)
results = Parallel(n_jobs=n_jobs)(delayed(scan_func)\
(crystal=crystal,
fcalcs_energies=energy,
fcalcs = fcalcs,
fracA=fracA, fracB=fracB,
strong=strong,jid=jid,
use_weights=use_weights, raw_image=raw_image,
rotxy_series=scan_split[jid]) \
for jid in range(n_jobs))
results = np.concatenate(results)
return results
idx = hit_idx[0]
iset = loader.get_imageset(img_f)[idx:idx + 1]
dblock = DataBlockFactory.from_imageset(iset)[0]
refls = info_f[idx]['refl']
fracA = info_f[idx]['fracA']
fracB = info_f[idx]['fracB']
cryst_orig = info_f[idx]['crystals'][0]
# load a test crystal
#crystal = utils.open_flex( sim_utils.cryst_f )
# fraction of two color energy
# simulate the pattern
#Patts = sim_utils.PatternFactory()
en, fcalc = sim_utils.load_fcalc_file("../sim/fcalc_slim.pkl")
flux = [fracA * 1e14, fracB * 1e14]
#imgA, imgB = Patts.make_pattern2(crystal, flux, en, fcalc, 20, 0.1, False)
# here we can index each 1 color pattern as well as the two color pattern
# for fun
# ==================================
# 2 color indexer of 2 color pattern
# ==================================
sad_index_params.indexing.multiple_lattice_search.max_lattices = 1
sad_index_params.indexing.stills.refine_all_candidates = True #False
sad_index_params.indexing.stills.refine_candidates_with_known_symmetry = True #False
sad_index_params.indexing.stills.candidate_outlier_rejection = True # False
sad_index_params.indexing.stills.rmsd_min_px = 10
#sad_index_params.indexing.refinement_protocol.mode = "ignore"