def prepare_dxtbx_models(self, setting_specific_ai, sg, isoform=None):
from dxtbx.model import BeamFactory
beam = BeamFactory.simple(wavelength=self.inputai.wavelength)
from dxtbx.model import DetectorFactory
detector = DetectorFactory.simple(
sensor=DetectorFactory.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 import Crystal
crystal = Crystal(
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,
)
crystal.set_mosaicity(setting_specific_ai.getMosaicity())
if isoform is not None:
newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
crystal.set_B(newB)
from dxtbx.model import Experiment, ExperimentList
experiments = ExperimentList()
experiments.append(
Experiment(beam=beam, detector=detector, crystal=crystal))
print beam
print detector
print crystal
return experiments
def test_crystal_model():
real_space_a = matrix.col((10, 0, 0))
real_space_b = matrix.col((0, 11, 0))
real_space_c = matrix.col((0, 0, 12))
model = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
# This doesn't work as python class uctbx.unit_cell(uctbx_ext.unit_cell)
# so C++ and python classes are different types
# assert isinstance(model.get_unit_cell(), uctbx.unit_cell)
assert model.get_unit_cell().parameters() == (10.0, 11.0, 12.0, 90.0, 90.0,
90.0)
assert approx_equal(model.get_A(),
(1 / 10, 0, 0, 0, 1 / 11, 0, 0, 0, 1 / 12))
assert approx_equal(
matrix.sqr(model.get_A()).inverse(), (10, 0, 0, 0, 11, 0, 0, 0, 12))
assert approx_equal(model.get_B(), model.get_A())
assert approx_equal(model.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert approx_equal(model.get_real_space_vectors(),
(real_space_a, real_space_b, real_space_c))
assert (model.get_crystal_symmetry().unit_cell().parameters() ==
model.get_unit_cell().parameters())
assert model.get_crystal_symmetry().space_group() == model.get_space_group(
)
model2 = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
assert model == model2
model2a = Crystal(model.get_A(), model.get_space_group())
assert model == model2a
model2b = Crystal(
matrix.sqr(model.get_A()).inverse().elems,
model.get_space_group().type().lookup_symbol(),
reciprocal=False,
)
assert model == model2b
# rotate 45 degrees about x-axis
R1 = matrix.sqr((
1,
0,
0,
0,
math.cos(math.pi / 4),
-math.sin(math.pi / 4),
0,
math.sin(math.pi / 4),
math.cos(math.pi / 4),
))
# rotate 30 degrees about y-axis
R2 = matrix.sqr((
math.cos(math.pi / 6),
0,
math.sin(math.pi / 6),
0,
1,
0,
-math.sin(math.pi / 6),
0,
math.cos(math.pi / 6),
))
# rotate 60 degrees about z-axis
R3 = matrix.sqr((
math.cos(math.pi / 3),
-math.sin(math.pi / 3),
0,
math.sin(math.pi / 3),
math.cos(math.pi / 3),
0,
0,
0,
1,
))
R = R1 * R2 * R3
model.set_U(R)
# B is unchanged
assert approx_equal(model.get_B(),
(1 / 10, 0, 0, 0, 1 / 11, 0, 0, 0, 1 / 12))
assert approx_equal(model.get_U(), R)
assert approx_equal(model.get_A(),
matrix.sqr(model.get_U()) * matrix.sqr(model.get_B()))
a_, b_, c_ = model.get_real_space_vectors()
assert approx_equal(a_, R * real_space_a)
assert approx_equal(b_, R * real_space_b)
assert approx_equal(c_, R * real_space_c)
assert (str(model).replace("-0.0000", " 0.0000") == """\
Crystal:
Unit cell: (10.000, 11.000, 12.000, 90.000, 90.000, 90.000)
Space group: P 1
U matrix: {{ 0.4330, -0.7500, 0.5000},
{ 0.7891, 0.0474, -0.6124},
{ 0.4356, 0.6597, 0.6124}}
B matrix: {{ 0.1000, 0.0000, 0.0000},
{ 0.0000, 0.0909, 0.0000},
{ 0.0000, 0.0000, 0.0833}}
A = UB: {{ 0.0433, -0.0682, 0.0417},
{ 0.0789, 0.0043, -0.0510},
{ 0.0436, 0.0600, 0.0510}}
""")
model.set_B((1 / 12, 0, 0, 0, 1 / 12, 0, 0, 0, 1 / 12))
assert approx_equal(model.get_unit_cell().parameters(),
(12, 12, 12, 90, 90, 90))
U = matrix.sqr((0.3455, -0.2589, -0.9020, 0.8914, 0.3909, 0.2293, 0.2933,
-0.8833, 0.3658))
B = matrix.sqr((1 / 13, 0, 0, 0, 1 / 13, 0, 0, 0, 1 / 13))
model.set_A(U * B)
assert approx_equal(model.get_A(), U * B)
assert approx_equal(model.get_U(), U, 1e-4)
assert approx_equal(model.get_B(), B, 1e-5)
model3 = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group=sgtbx.space_group_info("P 222").group(),
)
assert model3.get_space_group().type().hall_symbol() == " P 2 2"
assert model != model3
#
sgi_ref = sgtbx.space_group_info(number=230)
model_ref = Crystal(
real_space_a=(44, 0, 0),
real_space_b=(0, 44, 0),
real_space_c=(0, 0, 44),
space_group=sgi_ref.group(),
)
assert approx_equal(model_ref.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert approx_equal(model_ref.get_B(),
(1 / 44, 0, 0, 0, 1 / 44, 0, 0, 0, 1 / 44))
assert approx_equal(model_ref.get_A(), model_ref.get_B())
assert approx_equal(model_ref.get_unit_cell().parameters(),
(44, 44, 44, 90, 90, 90))
a_ref, b_ref, c_ref = map(matrix.col, model_ref.get_real_space_vectors())
cb_op_to_primitive = sgi_ref.change_of_basis_op_to_primitive_setting()
model_primitive = model_ref.change_basis(cb_op_to_primitive)
cb_op_to_reference = (model_primitive.get_space_group().info().
change_of_basis_op_to_reference_setting())
a_prim, b_prim, c_prim = map(matrix.col,
model_primitive.get_real_space_vectors())
assert (cb_op_to_primitive.as_abc() ==
"-1/2*a+1/2*b+1/2*c,1/2*a-1/2*b+1/2*c,1/2*a+1/2*b-1/2*c")
assert approx_equal(a_prim, -1 / 2 * a_ref + 1 / 2 * b_ref + 1 / 2 * c_ref)
assert approx_equal(b_prim, 1 / 2 * a_ref - 1 / 2 * b_ref + 1 / 2 * c_ref)
assert approx_equal(c_prim, 1 / 2 * a_ref + 1 / 2 * b_ref - 1 / 2 * c_ref)
assert cb_op_to_reference.as_abc() == "b+c,a+c,a+b"
assert approx_equal(a_ref, b_prim + c_prim)
assert approx_equal(b_ref, a_prim + c_prim)
assert approx_equal(c_ref, a_prim + b_prim)
assert approx_equal(
model_primitive.get_U(),
[
-0.5773502691896258,
0.40824829046386285,
0.7071067811865476,
0.5773502691896257,
-0.4082482904638631,
0.7071067811865476,
0.5773502691896257,
0.8164965809277259,
0.0,
],
)
assert approx_equal(
model_primitive.get_B(),
[
0.0262431940540739,
0.0,
0.0,
0.00927837023781507,
0.02783511071344521,
0.0,
0.01607060866333063,
0.01607060866333063,
0.03214121732666125,
],
)
assert approx_equal(
model_primitive.get_A(),
(0, 1 / 44, 1 / 44, 1 / 44, 0, 1 / 44, 1 / 44, 1 / 44, 0),
)
assert approx_equal(
model_primitive.get_unit_cell().parameters(),
[
38.1051177665153,
38.1051177665153,
38.1051177665153,
109.47122063449069,
109.47122063449069,
109.47122063449069,
],
)
assert model_ref != model_primitive
model_ref_recycled = model_primitive.change_basis(cb_op_to_reference)
assert approx_equal(model_ref.get_U(), model_ref_recycled.get_U())
assert approx_equal(model_ref.get_B(), model_ref_recycled.get_B())
assert approx_equal(model_ref.get_A(), model_ref_recycled.get_A())
assert approx_equal(
model_ref.get_unit_cell().parameters(),
model_ref_recycled.get_unit_cell().parameters(),
)
assert model_ref == model_ref_recycled
uc = uctbx.unit_cell(
(58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
sg = sgtbx.space_group_info(symbol="P1").group()
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
cb_op_to_minimum = cs.change_of_basis_op_to_minimum_cell()
# the reciprocal matrix
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
U = random_rotation()
direct_matrix = (U * B).inverse()
model = Crystal(direct_matrix[:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=sg)
assert uc.is_similar_to(model.get_unit_cell())
uc_minimum = uc.change_basis(cb_op_to_minimum)
model_minimum = model.change_basis(cb_op_to_minimum)
assert uc_minimum.is_similar_to(model_minimum.get_unit_cell())
assert model_minimum != model
model_minimum.update(model)
assert model_minimum == model # lgtm
A_static = matrix.sqr(model.get_A())
A_as_scan_points = [A_static]
num_scan_points = 11
for i in range(num_scan_points - 1):
A_as_scan_points.append(
A_as_scan_points[-1] *
matrix.sqr(euler_angles.xyz_matrix(0.1, 0.2, 0.3)))
model.set_A_at_scan_points(A_as_scan_points)
model_minimum = model.change_basis(cb_op_to_minimum)
assert model.num_scan_points == model_minimum.num_scan_points == num_scan_points
M = matrix.sqr(cb_op_to_minimum.c_inv().r().transpose().as_double())
M_inv = M.inverse()
for i in range(num_scan_points):
A_orig = matrix.sqr(model.get_A_at_scan_point(i))
A_min = matrix.sqr(model_minimum.get_A_at_scan_point(i))
assert approx_equal(A_min, A_orig * M_inv)
assert model.get_unit_cell().parameters() == pytest.approx(
(58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
uc = uctbx.unit_cell((10, 11, 12, 91, 92, 93))
model.set_unit_cell(uc)
assert model.get_unit_cell().parameters() == pytest.approx(uc.parameters())
def load(self):
# some parameters
# NOTE: for reference, inside each h5 file there is
# [u'Amatrices', u'Hi', u'bboxes', u'h5_path']
# get the total number of shots using worker 0
if rank == 0:
print("I am root. I am calculating total number of shots")
h5s = [h5py_File(f, "r") for f in self.fnames]
Nshots_per_file = [h["h5_path"].shape[0] for h in h5s]
Nshots_tot = sum(Nshots_per_file)
print("I am root. Total number of shots is %d" % Nshots_tot)
print("I am root. I will divide shots amongst workers.")
shot_tuples = []
for i_f, fname in enumerate(self.fnames):
fidx_shotidx = [(i_f, i_shot)
for i_shot in range(Nshots_per_file[i_f])]
shot_tuples += fidx_shotidx
from numpy import array_split
print("I am root. Number of uniques = %d" % len(set(shot_tuples)))
shots_for_rank = array_split(shot_tuples, size)
# close the open h5s..
for h in h5s:
h.close()
else:
Nshots_tot = None
shots_for_rank = None
h5s = None
#Nshots_tot = comm.bcast( Nshots_tot, root=0)
if has_mpi:
shots_for_rank = comm.bcast(shots_for_rank, root=0)
#h5s = comm.bcast( h5s, root=0) # pull in the open hdf5 files
my_shots = shots_for_rank[rank]
if self.Nload is not None:
my_shots = my_shots[:self.Nload]
# open the unique filenames for this rank
# TODO: check max allowed pointers to open hdf5 file
my_unique_fids = set([fidx for fidx, _ in my_shots])
my_open_files = {
fidx: h5py_File(self.fnames[fidx], "r")
for fidx in my_unique_fids
}
Ntot = 0
self.all_bbox_pixels = []
for img_num, (fname_idx, shot_idx) in enumerate(my_shots):
if img_num == args.Nmax:
#print("Already processed maximum number images!")
continue
h = my_open_files[fname_idx]
# load the dxtbx image data directly:
npz_path = h["h5_path"][shot_idx]
# NOTE take me out!
if args.testmode:
import os
npz_path = os.path.basename(npz_path)
img_handle = numpy_load(npz_path)
img = img_handle["img"]
if len(img.shape) == 2: # if single panel>>
img = np.array([img])
#D = det_from_dict(img_handle["det"][()])
B = beam_from_dict(img_handle["beam"][()])
# get the indexed crystal Amatrix
Amat = h["Amatrices"][shot_idx]
amat_elems = list(sqr(Amat).inverse().elems)
# real space basis vectors:
a_real = amat_elems[:3]
b_real = amat_elems[3:6]
c_real = amat_elems[6:]
# dxtbx indexed crystal model
C = Crystal(a_real, b_real, c_real, "P43212")
# change basis here ? Or maybe just average a/b
a, b, c, _, _, _ = C.get_unit_cell().parameters()
a_init = .5 * (a + b)
c_init = c
# shoe boxes where we expect spots
bbox_dset = h["bboxes"]["shot%d" % shot_idx]
n_bboxes_total = bbox_dset.shape[0]
# is the shoe box within the resolution ring and does it have significant SNR (see filter_bboxes.py)
is_a_keeper = h["bboxes"]["keepers%d" % shot_idx][()]
# tilt plane to the background pixels in the shoe boxes
tilt_abc_dset = h["tilt_abc"]["shot%d" % shot_idx]
try:
panel_ids_dset = h["panel_ids"]["shot%d" % shot_idx]
has_panels = True
except KeyError:
has_panels = False
# apply the filters:
bboxes = [
bbox_dset[i_bb] for i_bb in range(n_bboxes_total)
if is_a_keeper[i_bb]
]
tilt_abc = [
tilt_abc_dset[i_bb] for i_bb in range(n_bboxes_total)
if is_a_keeper[i_bb]
]
if has_panels:
panel_ids = [
panel_ids_dset[i_bb] for i_bb in range(n_bboxes_total)
if is_a_keeper[i_bb]
]
else:
panel_ids = [0] * len(tilt_abc)
# how many pixels do we have
tot_pix = [(j2 - j1) * (i2 - i1) for i1, i2, j1, j2 in bboxes]
Ntot += sum(tot_pix)
# actually load the pixels...
#data_boxes = [ img[j1:j2, i1:i2] for i1,i2,j1,j2 in bboxes]
# Here we will try a per-shot refinement of the unit cell and Umatrix, as well as ncells abc
# and spot scale etc..
# load some ground truth data from the simulation dumps (e.g. spectrum)
h5_fname = h["h5_path"][shot_idx].replace(".npz", "")
# NOTE remove me
if args.testmode:
h5_fname = os.path.basename(h5_fname)
data = h5py_File(h5_fname, "r")
tru = sqr(data["crystalA"][()]).inverse().elems
a_tru = tru[:3]
b_tru = tru[3:6]
c_tru = tru[6:]
C_tru = Crystal(a_tru, b_tru, c_tru, "P43212")
try:
angular_offset_init = compare_with_ground_truth(
a_tru, b_tru, c_tru, [C], symbol="P43212")[0]
except Exception as err:
print(
"Rank %d: Boo cant use the comparison w GT function: %s" %
(rank, err))
fluxes = data["spectrum"][()]
es = data["exposure_s"][()]
fluxes *= es # multiply by the exposure time
spectrum = zip(wavelens, fluxes)
# dont simulate when there are no photons!
spectrum = [(wave, flux) for wave, flux in spectrum
if flux > self.flux_min]
# make a unit cell manager that the refiner will use to track the B-matrix
aa, _, cc, _, _, _ = C_tru.get_unit_cell().parameters()
ucell_man = TetragonalManager(a=a_init, c=c_init)
if args.startwithtruth:
ucell_man = TetragonalManager(a=aa, c=cc)
# create the sim_data instance that the refiner will use to run diffBragg
# create a nanoBragg crystal
nbcryst = nanoBragg_crystal()
nbcryst.dxtbx_crystal = C
if args.startwithtruth:
nbcryst.dxtbx_crystal = C_tru
nbcryst.thick_mm = 0.1
nbcryst.Ncells_abc = 30, 30, 30
nbcryst.miller_array = Fhkl_guess.as_amplitude_array()
nbcryst.n_mos_domains = 1
nbcryst.mos_spread_deg = 0.0
# create a nanoBragg beam
nbbeam = nanoBragg_beam()
nbbeam.size_mm = 0.001
nbbeam.unit_s0 = B.get_unit_s0()
nbbeam.spectrum = spectrum
# sim data instance
SIM = SimData()
SIM.detector = CSPAD
#SIM.detector = D
SIM.crystal = nbcryst
SIM.beam = nbbeam
SIM.panel_id = 0 # default
spot_scale = 12
if args.sad:
spot_scale = 1
SIM.instantiate_diffBragg(default_F=0, oversample=0)
SIM.D.spot_scale = spot_scale
img_in_photons = img / self.gain
print("Rank %d, Starting refinement!" % rank)
try:
RUC = RefineAllMultiPanel(
spot_rois=bboxes,
abc_init=tilt_abc,
img=img_in_photons, # NOTE this is now a multi panel image
SimData_instance=SIM,
plot_images=args.plot,
plot_residuals=args.residual,
ucell_manager=ucell_man)
RUC.panel_ids = panel_ids
RUC.multi_panel = True
RUC.split_evaluation = args.split
RUC.trad_conv = True
RUC.refine_detdist = False
RUC.refine_background_planes = False
RUC.refine_Umatrix = True
RUC.refine_Bmatrix = True
RUC.refine_ncells = True
RUC.use_curvatures = False # args.curvatures
RUC.calc_curvatures = True #args.curvatures
RUC.refine_crystal_scale = True
RUC.refine_gain_fac = False
RUC.plot_stride = args.stride
RUC.poisson_only = False
RUC.trad_conv_eps = 5e-3 # NOTE this is for single panel model
RUC.max_calls = 300
RUC.verbose = False
RUC.use_rot_priors = True
RUC.use_ucell_priors = True
if args.verbose:
if rank == 0: # only show refinement stats for rank 0
RUC.verbose = True
RUC.run()
if RUC.hit_break_to_use_curvatures:
RUC.use_curvatures = True
RUC.run(setup=False)
except AssertionError as err:
print(
"Rank %d, filename %s Hit assertion error during refinement: %s"
% (rank, data.filename, err))
continue
angle, ax = RUC.get_correction_misset(as_axis_angle_deg=True)
if args.startwithtruth:
C = Crystal(a_tru, b_tru, c_tru, "P43212")
C.rotate_around_origin(ax, angle)
C.set_B(RUC.get_refined_Bmatrix())
a_ref, _, c_ref, _, _, _ = C.get_unit_cell().parameters()
# compute missorientation with ground truth model
try:
angular_offset = compare_with_ground_truth(a_tru,
b_tru,
c_tru, [C],
symbol="P43212")[0]
print(
"Rank %d, filename=%s, ang=%f, init_ang=%f, a=%f, init_a=%f, c=%f, init_c=%f"
% (rank, data.filename, angular_offset,
angular_offset_init, a_ref, a_init, c_ref, c_init))
except Exception as err:
print("Rank %d, filename=%s, error %s" %
(rank, data.filename, err))
# free the memory from diffBragg instance
RUC.S.D.free_all()
del img # not sure if needed here..
del img_in_photons
if args.testmode:
exit()
# peak at the memory usage of this rank
mem = getrusage(RUSAGE_SELF).ru_maxrss # peak mem usage in KB
mem = mem / 1e6 # convert to GB
if rank == 0:
print "RANK 0: %.2g total pixels in %d/%d bboxes (file %d / %d); MemUsg=%2.2g GB" \
% (Ntot, len(bboxes), n_bboxes_total, img_num+1, len(my_shots), mem)
# TODO: accumulate all pixels
#self.all_bbox_pixels += data_boxes
for h in my_open_files.values():
h.close()
print("Rank %d; all subimages loaded!" % rank)
