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 simulate_xyscan_result(scan_data_file, prefix=None):
"""
scan data is the output of yhe xyscan refinement script
:param scan_data_file: string path
:param prefix: output path prefix where results will be written
:return:
"""
scan_data = np.load(scan_data_file)
idx = int(scan_data['hit_idx'])
if prefix is None:
prefix = "refined_sim%d" % idx
# crystal = scan_data['crystal']
refl = scan_data['refl']
# xR = scan_data['optX']
# yR = scan_data['optY']
optCrystal = scan_data['optCrystal']
fracA = int(scan_data["fracA"])
fracB = int(scan_data["fracB"])
flux = [fracA * 1e14, fracB * 1e14]
energy, fcalc_f = load_fcalc_file(scan_data['fcalc_f'])
P = PatternFactory()
P.adjust_mosaicity(2, 0.05)
sim_A, sim_B = P.make_pattern2(crystal=deepcopy(optCrystal),
flux_per_en=flux,
energies_eV=energy,
fcalcs_at_energies=fcalc_f,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=False,
Op=None) # xR * yR)
if 'optX_fine' in scan_data.keys():
#xR_fine = scan_data['optX_fine']
#yR_fine = scan_data['optY_fine']
optCryst_fine = scan_data["optCrystal_fine"]
sim_A_fine, sim_B_fine = P.make_pattern2(
crystal=deepcopy(optCryst_fine),
flux_per_en=flux,
energies_eV=energy,
fcalcs_at_energies=fcalc_f,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=False,
Op=None) # xR_fine * yR_fine * xR * yR)
fine_scan = True
else:
fine_scan = False
# work this into the data stream, perhaps use experiment lists??
img_file = "/Users/dermen/cxid9114/run62_hits_wtime.h5"
loader = dxtbx.load(img_file)
raw_img = loader.get_raw_data(idx).as_numpy_array()
patts = [sim_A, sim_B, sim_A + sim_B, raw_img]
refls = [refl] * 4
utils.images_and_refls_to_simview(prefix, patts, refls)
if fine_scan:
patts = [sim_A_fine, sim_B_fine, sim_A_fine + sim_B_fine, raw_img]
refls = [refl] * 4
utils.images_and_refls_to_simview(prefix + "_fine", patts, refls)
flux_per_en = [fracA * 1e14, fracB * 1e14]
sim_patt = Patts.make_pattern2(crystal=cryst,
flux_per_en=flux_per_en,
energies_eV=energies,
fcalcs_at_energies=fcalcs_at_en,
mosaic_spread=None,
mosaic_domains=None,
ret_sum=True)
actual_img = loader.get_raw_data(hit_idx).as_numpy_array().astype(
np.float32)
refl = data[hit_idx]['refl']
output_imgs.extend([sim_patt, actual_img])
output_refls.extend([refl, refl])
utils.images_and_refls_to_simview(output_pref, output_imgs, output_refls)
#os.system("dials.image_viewer %s %s" % \
# (output_pref+".h5", output_pref+"_strong.pkl"))
x = col((1., 0., 0.))
y = col((0., 1., 0.))
z = col((0., 0., 1.))
xRot = x.axis_and_angle_as_r3_rotation_matrix
yRot = y.axis_and_angle_as_r3_rotation_matrix
zRot = z.axis_and_angle_as_r3_rotation_matrix
degs = np.linspace(-5., 5., 50) # not sure here..
degs = np.arange(-0.2, 0.2, 0.025) # still not sure about ranges here.
degs = np.arange(-0.4, 0.4, 0.05) # feeling more confident about this range
rotXY_series = [(xRot(i, deg=True), yRot(j, deg=True)) for i in degs
for j in degs]
iset = loader.get_imageset(loader.get_image_file())
dblock = DataBlockFactory.from_imageset(iset[idx:idx + 1])[0]
refl = flex.reflection_table.from_observations(dblock, find_spot_params)
imgs.append(img)
refls.append(refl)
info_fname = image_fname.replace(".h5", ".pkl")
sim_data = utils.open_flex(info_fname)
orient = indexer_two_color(
reflections=count_spots.as_single_shot_reflections(refl,
inplace=False),
imagesets=[iset],
params=indexing_params)
try:
orient.index()
crystals = [o.crystal for o in orient.refined_experiments]
rmsd = orient.best_rmsd
sim_data["sim_indexed_rmsd"] = rmsd
sim_data["sim_indexed_crystals"] = crystals
sim_data["sim_indexed_refls"] = refl
except:
print("FAILED!")
utils.save_flex(sim_data, info_fname + out_tag)
images_and_refls_to_simview(output_pref, imgs, refls)