from simtbx.nanoBragg import sim_data from scitbx.matrix import sqr, rec from cctbx import uctbx from dxtbx.model import Crystal ucell = (70, 60, 50, 90.0, 110, 90.0) symbol = "C121" a_real, b_real, c_real = sqr(uctbx.unit_cell(ucell).orthogonalization_matrix()).transpose().as_list_of_lists() C = Crystal(a_real, b_real, c_real, symbol) # random raotation rotation = Rotation.random(num=1, random_state=101)[0] Q = rec(rotation.as_quat(), n=(4, 1)) rot_ang, rot_axis = Q.unit_quaternion_as_axis_and_angle() C.rotate_around_origin(rot_axis, rot_ang) S = sim_data.SimData(use_default_crystal=True) S.crystal.dxtbx_crystal = C spectrum = S.beam.spectrum wave, flux = spectrum[0] Nwave = 5 waves = np.linspace(wave-wave*0.002, wave+wave*0.002, Nwave) fluxes = np.ones(Nwave) * flux / Nwave lambda0_GT = 0 lambda1_GT = 1 S.beam.spectrum = list(zip(waves, fluxes)) S.detector = sim_data.SimData.simple_detector(180, 0.1, (1024, 1024)) S.instantiate_diffBragg(verbose=0, oversample=0, auto_set_spotscale=True)
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)