def _conf_to_spsim_opts(D_source,D_particle,D_detector):
import spsim
# Create temporary file for pdb file
tmpf_pdb = tempfile.NamedTemporaryFile(mode='w+b', bufsize=-1, suffix='.conf', prefix='tmp_spsim', dir=None, delete=False)
tmpf_pdb_name = tmpf_pdb.name
tmpf_pdb.close()
# Write pdb file
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"], D_particle["atomic_positions"])
spsim.write_pdb_from_mol(tmpf_pdb_name, mol)
spsim.free_mol(mol)
# Start with default spsim configuration
opts = spsim.set_defaults()
# Create temporary file for spsim configuration
tmpf_conf = tempfile.NamedTemporaryFile(mode='w+b', bufsize=-1, suffix='.conf', prefix='tmp_spsim', dir=None, delete=False)
# Write string sequence from configuration dicts
s = []
s += "# THIS FILE WAS CREATED AUTOMATICALLY BY CONDOR\n"
s += "# Temporary configuration file for spsim\n"
s += "verbosity_level = 0;\n"
s += "number_of_dimensions = 2;\n"
s += "number_of_patterns = 1;\n"
s += "origin_to_com = 1;\n"
s += "input_type = \"pdb\";\n"
#s += "pdb_filename = \"%s\";\n" % D_particle["pdb_filename"]
s += "pdb_filename = \"%s\";\n" % tmpf_pdb_name
s += "detector_distance = %.6e;\n" % D_detector["distance"]
s += "detector_width = %.6e;\n" % (D_detector["pixel_size"] * D_detector["nx"])
s += "detector_height = %.6e;\n" % (D_detector["pixel_size"] * D_detector["ny"])
s += "detector_pixel_width = %.6e;\n" % D_detector["pixel_size"]
s += "detector_pixel_height = %.6e;\n" % D_detector["pixel_size"]
s += "detector_center_x = %.6e;\n" % (D_detector["pixel_size"] * (D_detector["cx"] - (D_detector["nx"]-1)/2.))
s += "detector_center_y = %.6e;\n" % (D_detector["pixel_size"] * (D_detector["cy"] - (D_detector["ny"]-1)/2.))
s += "detector_binning = 1;\n"
s += "experiment_wavelength = %.6e;\n" % D_source["wavelength"]
s += "experiment_beam_intensity = %.6e;\n" % D_particle["intensity"]
#s += "use_cuda = 0;\n"
intrinsic_rotation = condor.utils.rotation.Rotation(values=D_particle["extrinsic_quaternion"],formalism="quaternion")
intrinsic_rotation.invert()
e0, e1, e2 = intrinsic_rotation.get_as_euler_angles("zxz")
s += "phi = %.6e;\n" % e0
s += "theta = %.6e;\n" % e1
s += "psi = %.6e;\n" % e2
s += "random_orientation = 0;\n"
# Write string sequence to file
tmpf_conf.writelines(s)
# Close temporary file
tmpf_conf_name = tmpf_conf.name
tmpf_conf.close()
# Read configuration into options struct
spsim.read_options_file(tmpf_conf_name, opts)
# This deletes the temporary files
os.unlink(tmpf_pdb_name)
os.unlink(tmpf_conf_name)
return opts
def _conf_to_spsim_opts(D_source,
D_particle,
D_detector,
ndim=2,
qn=None,
qmax=None):
if ndim == 2:
if qn is not None or qmax is not None:
log_warning(
logger,
"As ndim=2 the passed values for qn and qmax take no effect.")
if ndim == 3:
if qn is None and qmax is None:
log_and_raise_error(
logger, "As ndim=3 both qn and qmax must be not None.")
return
import spsim
# Create temporary file for pdb file
tmpf_pdb = tempfile.NamedTemporaryFile(mode='w+b',
bufsize=-1,
suffix='.conf',
prefix='tmp_spsim',
dir=None,
delete=False)
tmpf_pdb_name = tmpf_pdb.name
tmpf_pdb.close()
# Write pdb file
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"],
D_particle["atomic_positions"])
spsim.write_pdb_from_mol(tmpf_pdb_name, mol)
spsim.free_mol(mol)
# Start with default spsim configuration
opts = spsim.set_defaults()
# Create temporary file for spsim configuration
tmpf_conf = tempfile.NamedTemporaryFile(mode='w+b',
bufsize=-1,
suffix='.conf',
prefix='tmp_spsim',
dir=None,
delete=False)
# Write string sequence from configuration dicts
s = []
s += "# THIS FILE WAS CREATED AUTOMATICALLY BY CONDOR\n"
s += "# Temporary configuration file for spsim\n"
s += "verbosity_level = 0;\n"
s += "number_of_dimensions = %i;\n" % ndim
s += "number_of_patterns = 1;\n"
s += "origin_to_com = 1;\n"
s += "input_type = \"pdb\";\n"
#s += "pdb_filename = \"%s\";\n" % D_particle["pdb_filename"]
s += "pdb_filename = \"%s\";\n" % tmpf_pdb_name
if ndim == 2:
D = D_detector["distance"]
Lx = D_detector["pixel_size"] * D_detector["nx"]
Ly = D_detector["pixel_size"] * D_detector["ny"]
else:
k0 = 2. * numpy.pi / D_source["wavelength"]
D = qn / 2. * D_detector["pixel_size"] * k0 / qmax
Lx = Ly = Lz = D_detector["pixel_size"] * qn
s += "detector_distance = %.12e;\n" % D
s += "detector_width = %.12e;\n" % Lx
s += "detector_height = %.12e;\n" % Ly
if ndim == 3:
s += "detector_depth = %.12e;\n" % Lz
s += "detector_pixel_width = %.12e;\n" % D_detector["pixel_size"]
s += "detector_pixel_height = %.12e;\n" % D_detector["pixel_size"]
if ndim == 3:
s += "detector_pixel_depth = %.12e;\n" % D_detector["pixel_size"]
if ndim == 2:
s += "detector_center_x = %.12e;\n" % (D_detector["pixel_size"] *
(D_detector["cx"] -
(D_detector["nx"] - 1) / 2.))
s += "detector_center_y = %.12e;\n" % (D_detector["pixel_size"] *
(D_detector["cy"] -
(D_detector["ny"] - 1) / 2.))
else:
s += "detector_center_x = 0;\n"
s += "detector_center_y = 0;\n"
s += "detector_center_z = 0;\n"
s += "detector_binning = 1;\n"
s += "experiment_wavelength = %.12e;\n" % D_source["wavelength"]
s += "experiment_beam_intensity = %.12e;\n" % D_particle["intensity"]
s += "experiment_polarization = \"ignore\";\n" # polarization correction will be done in Condor if needed (see experiment.py)
#s += "use_cuda = 0;\n"
intrinsic_rotation = condor.utils.rotation.Rotation(
values=D_particle["extrinsic_quaternion"], formalism="quaternion")
intrinsic_rotation.invert()
e0, e1, e2 = intrinsic_rotation.get_as_euler_angles("zxz")
if not numpy.isfinite(e0):
print "ERROR: phi is not finite"
if not numpy.isfinite(e1):
print "ERROR: theta is not finite"
if not numpy.isfinite(e2):
print "ERROR: psi is not finite"
s += "phi = %.12e;\n" % e0
s += "theta = %.12e;\n" % e1
s += "psi = %.12e;\n" % e2
s += "random_orientation = 0;\n"
# Write string sequence to file
tmpf_conf.writelines(s)
# Close temporary file
tmpf_conf_name = tmpf_conf.name
tmpf_conf.close()
# Read configuration into options struct
spsim.read_options_file(tmpf_conf_name, opts)
# This deletes the temporary files
os.unlink(tmpf_pdb_name)
os.unlink(tmpf_conf_name)
return opts
def propagate(self, save_map3d = False, save_qmap = False):
log_debug(logger, "Start propagation")
# Iterate objects
D_source = self.source.get_next()
D_particles = self._get_next_particles()
D_detector = self.detector.get_next()
# Pull out variables
nx = D_detector["nx"]
ny = D_detector["ny"]
cx = D_detector["cx"]
cy = D_detector["cy"]
pixel_size = D_detector["pixel_size"]
detector_distance = D_detector["distance"]
wavelength = D_source["wavelength"]
# Qmap without rotation
Y,X = numpy.meshgrid(numpy.float64(numpy.arange(ny))-cy,
numpy.float64(numpy.arange(nx))-cx,
indexing="ij")
qmap0 = condor.utils.scattering_vector.generate_qmap(X, Y, pixel_size, detector_distance, wavelength, extrinsic_rotation=None)
qmap_singles = {}
F_tot = None
# Calculate patterns of all single particles individually
for particle_key, D_particle in D_particles.items():
p = D_particle["_class_instance"]
# Intensity at interaction point
pos = D_particle["position"]
D_particle["intensity"] = self.source.get_intensity(pos, "ph/m2", pulse_energy=D_source["pulse_energy"])
I_0 = D_particle["intensity"]
# Calculate primary wave amplitude
# F0 = sqrt(I_0) 2pi/wavelength^2
F0 = numpy.sqrt(I_0)*2*numpy.pi/wavelength**2
D_particle["F0"] = F0
# 3D Orientation
extrinsic_rotation = Rotation(values=D_particle["extrinsic_quaternion"], formalism="quaternion")
# Resolution
dx_required = self.detector.get_resolution_element_r(wavelength, cx=cx, cy=cy, center_variation=False)
dx_suggested = self.detector.get_resolution_element_r(wavelength, center_variation=True)
# UNIFORM SPHERE
if isinstance(p, condor.particle.ParticleSphere):
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None)
q = numpy.sqrt(qmap[:,:,0]**2+qmap[:,:,1]**2)
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*dn)**2
# Geometrical factor
Omega_p = self.detector.get_all_pixel_solid_angles(cx, cy)
# Pattern
F = condor.utils.sphere_diffraction.F_sphere_diffraction(K, q, R) * numpy.sqrt(Omega_p)
# UNIFORM SPHEROID
elif isinstance(p, condor.particle.ParticleSpheroid):
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None, order="xyz")
qx = qmap[:,:,0]
qy = qmap[:,:,1]
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*abs(dn))**2
# Geometrical factors
a = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_a(D_particle["diameter"], D_particle["flattening"])
c = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_c(D_particle["diameter"], D_particle["flattening"])
Omega_p = self.detector.get_all_pixel_solid_angles(cx, cy)
# Pattern
# Spheroid axis before rotation
v0 = numpy.array([0.,1.,0.])
v1 = extrinsic_rotation.rotate_vector(v0)
theta = numpy.arcsin(v1[2])
phi = numpy.arctan2(-v1[0],v1[1])
F = condor.utils.spheroid_diffraction.F_spheroid_diffraction(K, qx, qy, a, c, theta, phi) * numpy.sqrt(Omega_p)
# MAP
elif isinstance(p, condor.particle.ParticleMap):
# Scattering vectors (the nfft requires order z,y,x)
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=extrinsic_rotation, order="zyx")
# Geometrical factor
Omega_p = self.detector.get_all_pixel_solid_angles(cx, cy)
# Generate map
map3d_dn, dx = p.get_new_dn_map(D_particle, dx_required, dx_suggested, wavelength)
log_debug(logger, "Sampling of map: dx_required = %e m, dx_suggested = %e m, dx = %e m" % (dx_required, dx_suggested, dx))
if save_map3d:
D_particle["map3d_dn"] = map3d_dn
D_particle["dx"] = dx
# Rescale and shape qmap for nfft
qmap_scaled = dx * qmap / (2. * numpy.pi)
qmap_shaped = qmap_scaled.reshape(qmap_scaled.shape[0]*qmap_scaled.shape[1], 3)
# For Jing:
#D_particle["qmap3d"] = detector.generate_qmap_ori(nfft_scaled=True)
# Check inputs
invalid_mask = ((qmap_shaped>=-0.5) * (qmap_shaped<0.5)) == False
if (invalid_mask).sum() > 0:
qmap_shaped[invalid_mask] = 0.
log_warning(logger, "%i invalid pixel positions." % invalid_mask.sum())
log_debug(logger, "Map3d input shape: (%i,%i,%i), number of dimensions: %i, sum %f" % (map3d_dn.shape[0], map3d_dn.shape[1], map3d_dn.shape[2], len(list(map3d_dn.shape)), abs(map3d_dn).sum()))
if (numpy.isfinite(abs(map3d_dn))==False).sum() > 0:
log_warning(logger, "There are infinite values in the dn map of the object.")
log_debug(logger, "Scattering vectors shape: (%i,%i); Number of dimensions: %i" % (qmap_shaped.shape[0], qmap_shaped.shape[1], len(list(qmap_shaped.shape))))
if (numpy.isfinite(qmap_shaped)==False).sum() > 0:
log_warning(logger, "There are infinite values in the scattering vectors.")
# NFFT
fourier_pattern = log_execution_time(logger)(condor.utils.nfft.nfft)(map3d_dn, qmap_shaped)
# Check output - masking in case of invalid values
if (invalid_mask).sum() > 0:
fourier_pattern[numpy.any(invalid_mask)] = numpy.nan
# reshaping
fourier_pattern = numpy.reshape(fourier_pattern, (qmap_scaled.shape[0], qmap_scaled.shape[1]))
log_debug(logger, "Got pattern of %i x %i pixels." % (fourier_pattern.shape[1], fourier_pattern.shape[0]))
#F = F0 * fourier_pattern * dx_required**3 * numpy.sqrt(Omega_p)
F = F0 * fourier_pattern * dx**3 * numpy.sqrt(Omega_p)
# ATOMS
elif isinstance(p, condor.particle.ParticleAtoms):
# Import only here (otherwise errors if spsim library not installed)
import spsim
# Create options struct
opts = condor.utils.config._conf_to_spsim_opts(D_source, D_particle, D_detector)
spsim.write_options_file("./spsim.confout",opts)
# Create molecule struct
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"], D_particle["atomic_positions"])
# Always recenter molecule
spsim.origin_to_center_of_mass(mol)
spsim.write_pdb_from_mol("./mol.pdbout", mol)
# Calculate diffraction pattern
pat = spsim.simulate_shot(mol, opts)
# Extract complex Fourier values from spsim output
F_img = spsim.make_cimage(pat.F, pat.rot, opts)
phot_img = spsim.make_image(opts.detector.photons_per_pixel, pat.rot, opts)
F = numpy.sqrt(abs(phot_img.image[:])) * numpy.exp(1.j * numpy.angle(F_img.image[:]))
spsim.sp_image_free(F_img)
spsim.sp_image_free(phot_img)
# Extract qmap from spsim output
qmap_img = spsim.sp_image_alloc(3,D_detector["nx"], D_detector["ny"])
spsim.array_to_image(pat.HKL_list, qmap_img)
qmap = numpy.zeros(shape=(D_detector["ny"], D_detector["nx"], 3))
qmap[:,:,0] = 2*numpy.pi*qmap_img.image.real[:,:,0]
qmap[:,:,1] = 2*numpy.pi*qmap_img.image.real[:,:,1]
qmap[:,:,2] = 2*numpy.pi*qmap_img.image.real[:,:,2]
spsim.sp_image_free(qmap_img)
spsim.free_diffraction_pattern(pat)
spsim.free_output_in_options(opts)
else:
log_and_raise_error(logger, "No valid particles initialized.")
sys.exit(0)
if save_qmap:
qmap_singles[particle_key] = qmap
# Superimpose patterns
if F_tot is None:
F_tot = numpy.zeros_like(F)
v = D_particle["position"]
F_tot = F_tot + F * numpy.exp(-1.j*(v[0]*qmap0[:,:,0]+v[1]*qmap0[:,:,1]+v[2]*qmap0[:,:,2]))
I_tot, M_tot = self.detector.detect_photons(abs(F_tot)**2)
IXxX_tot, MXxX_tot = self.detector.bin_photons(I_tot, M_tot)
if self.detector.binning is not None:
FXxX_tot, MXxX_tot = condor.utils.resample.downsample(F_tot, self.detector.binning, mode="integrate",
mask2d0=M_tot, bad_bits=PixelMask.PIXEL_IS_IN_MASK, min_N_pixels=1)
M_tot_binary = M_tot == 0
MXxX_tot_binary = None if MXxX_tot is None else (MXxX_tot == 0)
O = {}
O["source"] = D_source
O["particles"] = D_particles
O["detector"] = D_detector
O["entry_1"] = {}
data_1 = {}
data_1["data_fourier"] = F_tot
data_1["data"] = I_tot
data_1["mask"] = M_tot
data_1["full_period_resolution"] = 2 * self.detector.get_max_resolution(wavelength)
O["entry_1"]["data_1"] = data_1
if self.detector.binning is not None:
data_2 = {}
data_2["data_fourier"] = FXxX_tot
data_2["data"] = IXxX_tot
data_2["mask"] = MXxX_tot
O["entry_1"]["data_2"] = data_2
O = remove_from_dict(O, "_")
return O
def _propagate(self, save_map3d=False, save_qmap=False, ndim=2, qn=None, qmax=None):
if ndim not in [2,3]:
log_and_raise_error(logger, "ndim = %i is an invalid input. Has to be either 2 or 3." % ndim)
log_debug(logger, "Start propagation")
# Iterate objects
D_source = self.source.get_next()
D_particles = self._get_next_particles()
D_detector = self.detector.get_next()
# Pull out variables
nx = D_detector["nx"]
ny = D_detector["ny"]
cx = D_detector["cx"]
cy = D_detector["cy"]
pixel_size = D_detector["pixel_size"]
detector_distance = D_detector["distance"]
wavelength = D_source["wavelength"]
# Qmap without rotation
if ndim == 2:
qmap0 = self.detector.generate_qmap(wavelength, cx=cx, cy=cy, extrinsic_rotation=None)
else:
qmax = numpy.sqrt((self.detector.get_q_max(wavelength, pos="edge")**2).sum())
qn = max([nx, ny])
qmap0 = self.detector.generate_qmap_3d(wavelength, qn=qn, qmax=qmax, extrinsic_rotation=None, order='xyz')
if self.detector.solid_angle_correction:
log_and_raise_error(logger, "Carrying out solid angle correction for a simulation of a 3D Fourier volume does not make sense. Please set solid_angle_correction=False for your Detector and try again.")
return
qmap_singles = {}
F_tot = 0.
# Calculate patterns of all single particles individually
for particle_key, D_particle in D_particles.items():
p = D_particle["_class_instance"]
# Intensity at interaction point
pos = D_particle["position"]
D_particle["intensity"] = self.source.get_intensity(pos, "ph/m2", pulse_energy=D_source["pulse_energy"])
I_0 = D_particle["intensity"]
# Calculate primary wave amplitude
# F0 = sqrt(I_0) 2pi/wavelength^2
F0 = numpy.sqrt(I_0)*2*numpy.pi/wavelength**2
D_particle["F0"] = F0
# 3D Orientation
extrinsic_rotation = Rotation(values=D_particle["extrinsic_quaternion"], formalism="quaternion")
if isinstance(p, condor.particle.ParticleSphere) or isinstance(p, condor.particle.ParticleSpheroid) or isinstance(p, condor.particle.ParticleMap):
# Solid angles
if self.detector.solid_angle_correction:
Omega_p = self.detector.get_all_pixel_solid_angles(cx, cy)
else:
Omega_p = pixel_size**2 / detector_distance**2
# UNIFORM SPHERE
if isinstance(p, condor.particle.ParticleSphere):
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
if ndim == 2:
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None)
else:
qmap = qmap0
q = numpy.sqrt((qmap**2).sum(axis=ndim))
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*dn)**2
# Pattern
F = condor.utils.sphere_diffraction.F_sphere_diffraction(K, q, R) * numpy.sqrt(Omega_p)
# UNIFORM SPHEROID
elif isinstance(p, condor.particle.ParticleSpheroid):
if ndim == 3:
log_and_raise_error(logger, "Spheroid simulation with ndim = 3 is not supported.")
return
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None, order="xyz")
qx = qmap[:,:,0]
qy = qmap[:,:,1]
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*abs(dn))**2
# Geometrical factors
a = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_a(D_particle["diameter"], D_particle["flattening"])
c = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_c(D_particle["diameter"], D_particle["flattening"])
# Pattern
# Spheroid axis before rotation
v0 = numpy.array([0.,1.,0.])
v1 = extrinsic_rotation.rotate_vector(v0)
theta = numpy.arcsin(v1[2])
phi = numpy.arctan2(-v1[0],v1[1])
F = condor.utils.spheroid_diffraction.F_spheroid_diffraction(K, qx, qy, a, c, theta, phi) * numpy.sqrt(Omega_p)
# MAP
elif isinstance(p, condor.particle.ParticleMap):
# Resolution
dx_required = self.detector.get_resolution_element_r(wavelength, cx=cx, cy=cy, center_variation=False)
dx_suggested = self.detector.get_resolution_element_r(wavelength, center_variation=True)
# Scattering vectors (the nfft requires order z,y,x)
if ndim == 2:
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=extrinsic_rotation, order="zyx")
else:
qmap = self.detector.generate_qmap_3d(wavelength=wavelength, qn=qn, qmax=qmax, extrinsic_rotation=extrinsic_rotation, order="zyx")
# Generate map
map3d_dn, dx = p.get_new_dn_map(D_particle, dx_required, dx_suggested, wavelength)
log_debug(logger, "Sampling of map: dx_required = %e m, dx_suggested = %e m, dx = %e m" % (dx_required, dx_suggested, dx))
if save_map3d:
D_particle["map3d_dn"] = map3d_dn
D_particle["dx"] = dx
# Rescale and shape qmap for nfft
qmap_scaled = dx * qmap / (2. * numpy.pi)
qmap_shaped = qmap_scaled.reshape(qmap_scaled.size/3, 3)
# Check inputs
invalid_mask = ~((qmap_shaped>=-0.5) * (qmap_shaped<0.5))
if numpy.any(invalid_mask):
qmap_shaped[invalid_mask] = 0.
log_warning(logger, "%i invalid pixel positions." % invalid_mask.sum())
log_debug(logger, "Map3d input shape: (%i,%i,%i), number of dimensions: %i, sum %f" % (map3d_dn.shape[0], map3d_dn.shape[1], map3d_dn.shape[2], len(list(map3d_dn.shape)), abs(map3d_dn).sum()))
if (numpy.isfinite(abs(map3d_dn))==False).sum() > 0:
log_warning(logger, "There are infinite values in the dn map of the object.")
log_debug(logger, "Scattering vectors shape: (%i,%i); Number of dimensions: %i" % (qmap_shaped.shape[0], qmap_shaped.shape[1], len(list(qmap_shaped.shape))))
if (numpy.isfinite(qmap_shaped)==False).sum() > 0:
log_warning(logger, "There are infinite values in the scattering vectors.")
# NFFT
fourier_pattern = log_execution_time(logger)(condor.utils.nfft.nfft)(map3d_dn, qmap_shaped)
# Check output - masking in case of invalid values
if numpy.any(invalid_mask):
fourier_pattern[invalid_mask.any(axis=1)] = numpy.nan
# reshaping
fourier_pattern = numpy.reshape(fourier_pattern, tuple(list(qmap_scaled.shape)[:-1]))
log_debug(logger, "Generated pattern of shape %s." % str(fourier_pattern.shape))
F = F0 * fourier_pattern * dx**3 * numpy.sqrt(Omega_p)
# ATOMS
elif isinstance(p, condor.particle.ParticleAtoms):
# Import here to make other functionalities of Condor independent of spsim
import spsim
# Check version
from distutils.version import StrictVersion
spsim_version_min = "0.1.0"
if not hasattr(spsim, "__version__") or StrictVersion(spsim.__version__) < StrictVersion(spsim_version_min):
log_and_raise_error(logger, "Your spsim version is too old. Please install the newest spsim version and try again.")
sys.exit(0)
# Create options struct
opts = condor.utils.config._conf_to_spsim_opts(D_source, D_particle, D_detector, ndim=ndim, qn=qn, qmax=qmax)
spsim.write_options_file("./spsim.confout",opts)
# Create molecule struct
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"], D_particle["atomic_positions"])
# Always recenter molecule
spsim.origin_to_center_of_mass(mol)
spsim.write_pdb_from_mol("./mol.pdbout", mol)
# Calculate diffraction pattern
pat = spsim.simulate_shot(mol, opts)
# Extract complex Fourier values from spsim output
F_img = spsim.make_cimage(pat.F, pat.rot, opts)
phot_img = spsim.make_image(opts.detector.photons_per_pixel, pat.rot, opts)
F = numpy.sqrt(abs(phot_img.image[:])) * numpy.exp(1.j * numpy.angle(F_img.image[:]))
spsim.sp_image_free(F_img)
spsim.sp_image_free(phot_img)
# Extract qmap from spsim output
if ndim == 2:
qmap_img = spsim.sp_image_alloc(3, nx, ny)
else:
qmap_img = spsim.sp_image_alloc(3*qn, qn, qn)
spsim.array_to_image(pat.HKL_list, qmap_img)
if ndim == 2:
qmap = 2*numpy.pi * qmap_img.image.real
else:
qmap = 2*numpy.pi * numpy.reshape(qmap_img.image.real, (qn, qn, qn, 3))
spsim.sp_image_free(qmap_img)
spsim.free_diffraction_pattern(pat)
spsim.free_output_in_options(opts)
else:
log_and_raise_error(logger, "No valid particles initialized.")
sys.exit(0)
if save_qmap:
qmap_singles[particle_key] = qmap
v = D_particle["position"]
# Calculate phase factors if needed
if not numpy.allclose(v, numpy.zeros_like(v), atol=1E-12):
if ndim == 2:
F = F * numpy.exp(-1.j*(v[0]*qmap0[:,:,0]+v[1]*qmap0[:,:,1]+v[2]*qmap0[:,:,2]))
else:
F = F * numpy.exp(-1.j*(v[0]*qmap0[:,:,:,0]+v[1]*qmap0[:,:,:,1]+v[2]*qmap0[:,:,:,2]))
# Superimpose patterns
F_tot = F_tot + F
# Polarization correction
if ndim == 2:
P = self.detector.calculate_polarization_factors(cx=cx, cy=cy, polarization=self.source.polarization)
else:
if self.source.polarization != "ignore":
log_and_raise_error(logger, "polarization=\"%s\" for a 3D propagation does not make sense. Set polarization=\"ignore\" in your Source configuration and try again." % self.source.polarization)
return
P = 1.
F_tot = numpy.sqrt(P) * F_tot
# Photon detection
I_tot, M_tot = self.detector.detect_photons(abs(F_tot)**2)
if ndim == 2:
M_tot_binary = M_tot == 0
if self.detector.binning is not None:
IXxX_tot, MXxX_tot = self.detector.bin_photons(I_tot, M_tot)
FXxX_tot, MXxX_tot = condor.utils.resample.downsample(F_tot, self.detector.binning, mode="integrate",
mask2d0=M_tot, bad_bits=PixelMask.PIXEL_IS_IN_MASK, min_N_pixels=1)
MXxX_tot_binary = None if MXxX_tot is None else (MXxX_tot == 0)
else:
M_tot_binary = None
O = {}
O["source"] = D_source
O["particles"] = D_particles
O["detector"] = D_detector
O["entry_1"] = {}
data_1 = {}
data_1["data_fourier"] = F_tot
data_1["data"] = I_tot
data_1["mask"] = M_tot
data_1["full_period_resolution"] = 2 * self.detector.get_max_resolution(wavelength)
O["entry_1"]["data_1"] = data_1
if self.detector.binning is not None:
data_2 = {}
data_2["data_fourier"] = FXxX_tot
data_2["data"] = IXxX_tot
data_2["mask"] = MXxX_tot
O["entry_1"]["data_2"] = data_2
O = remove_from_dict(O, "_")
return O
def _propagate(self, save_map3d=False, save_qmap=False, ndim=2, qn=None, qmax=None):
if ndim not in [2,3]:
log_and_raise_error(logger, "ndim = %i is an invalid input. Has to be either 2 or 3." % ndim)
log_debug(logger, "Start propagation")
# Iterate objects
D_source = self.source.get_next()
D_particles = self._get_next_particles()
D_detector = self.detector.get_next()
# Pull out variables
nx = D_detector["nx"]
ny = D_detector["ny"]
cx = D_detector["cx"]
cy = D_detector["cy"]
pixel_size = D_detector["pixel_size"]
detector_distance = D_detector["distance"]
wavelength = D_source["wavelength"]
# Qmap without rotation
if ndim == 2:
qmap0 = self.detector.generate_qmap(wavelength, cx=cx, cy=cy, extrinsic_rotation=None)
else:
qmax = numpy.sqrt((self.detector.get_q_max(wavelength, pos="edge")**2).sum())
qn = max([nx, ny])
qmap0 = self.detector.generate_qmap_3d(wavelength, qn=qn, qmax=qmax, extrinsic_rotation=None, order='xyz')
if self.detector.solid_angle_correction:
log_and_raise_error(logger, "Carrying out solid angle correction for a simulation of a 3D Fourier volume does not make sense. Please set solid_angle_correction=False for your Detector and try again.")
return
qmap_singles = {}
F_tot = 0.
# Calculate patterns of all single particles individually
for particle_key, D_particle in D_particles.items():
p = D_particle["_class_instance"]
# Intensity at interaction point
pos = D_particle["position"]
D_particle["intensity"] = self.source.get_intensity(pos, "ph/m2", pulse_energy=D_source["pulse_energy"])
I_0 = D_particle["intensity"]
# Calculate primary wave amplitude
# F0 = sqrt(I_0) 2pi/wavelength^2
F0 = numpy.sqrt(I_0)*2*numpy.pi/wavelength**2
D_particle["F0"] = F0
# 3D Orientation
extrinsic_rotation = Rotation(values=D_particle["extrinsic_quaternion"], formalism="quaternion")
if isinstance(p, condor.particle.ParticleSphere) or isinstance(p, condor.particle.ParticleSpheroid) or isinstance(p, condor.particle.ParticleMap):
# Solid angles
if self.detector.solid_angle_correction:
Omega_p = self.detector.get_all_pixel_solid_angles(cx, cy)
else:
Omega_p = pixel_size**2 / detector_distance**2
# UNIFORM SPHERE
if isinstance(p, condor.particle.ParticleSphere):
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
if ndim == 2:
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None)
else:
qmap = qmap0
q = numpy.sqrt((qmap**2).sum(axis=ndim))
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*dn)**2
# Pattern
F = condor.utils.sphere_diffraction.F_sphere_diffraction(K, q, R) * numpy.sqrt(Omega_p)
# UNIFORM SPHEROID
elif isinstance(p, condor.particle.ParticleSpheroid):
if ndim == 3:
log_and_raise_error(logger, "Spheroid simulation with ndim = 3 is not supported.")
return
# Refractive index
dn = p.get_dn(wavelength)
# Scattering vectors
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=None, order="xyz")
qx = qmap[:,:,0]
qy = qmap[:,:,1]
# Intensity scaling factor
R = D_particle["diameter"]/2.
V = 4/3.*numpy.pi*R**3
K = (F0*V*abs(dn))**2
# Geometrical factors
a = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_a(D_particle["diameter"], D_particle["flattening"])
c = condor.utils.spheroid_diffraction.to_spheroid_semi_diameter_c(D_particle["diameter"], D_particle["flattening"])
# Pattern
# Spheroid axis before rotation
v0 = numpy.array([0.,1.,0.])
v1 = extrinsic_rotation.rotate_vector(v0)
theta = numpy.arcsin(v1[2])
phi = numpy.arctan2(-v1[0],v1[1])
F = condor.utils.spheroid_diffraction.F_spheroid_diffraction(K, qx, qy, a, c, theta, phi) * numpy.sqrt(Omega_p)
# MAP
elif isinstance(p, condor.particle.ParticleMap):
# Resolution
dx_required = self.detector.get_resolution_element_r(wavelength, cx=cx, cy=cy, center_variation=False)
dx_suggested = self.detector.get_resolution_element_r(wavelength, center_variation=True)
# Scattering vectors (the nfft requires order z,y,x)
if ndim == 2:
qmap = self.get_qmap(nx=nx, ny=ny, cx=cx, cy=cy, pixel_size=pixel_size, detector_distance=detector_distance, wavelength=wavelength, extrinsic_rotation=extrinsic_rotation, order="zyx")
else:
qmap = self.detector.generate_qmap_3d(wavelength=wavelength, qn=qn, qmax=qmax, extrinsic_rotation=extrinsic_rotation, order="zyx")
# Generate map
map3d_dn, dx = p.get_new_dn_map(D_particle, dx_required, dx_suggested, wavelength)
log_debug(logger, "Sampling of map: dx_required = %e m, dx_suggested = %e m, dx = %e m" % (dx_required, dx_suggested, dx))
if save_map3d:
D_particle["map3d_dn"] = map3d_dn
D_particle["dx"] = dx
# Rescale and shape qmap for nfft
qmap_scaled = dx * qmap / (2. * numpy.pi)
qmap_shaped = qmap_scaled.reshape(int(qmap_scaled.size/3), 3)
# Check inputs
invalid_mask = ~((qmap_shaped>=-0.5) * (qmap_shaped<0.5))
if numpy.any(invalid_mask):
qmap_shaped[invalid_mask] = 0.
log_warning(logger, "%i invalid pixel positions." % invalid_mask.sum())
log_debug(logger, "Map3d input shape: (%i,%i,%i), number of dimensions: %i, sum %f" % (map3d_dn.shape[0], map3d_dn.shape[1], map3d_dn.shape[2], len(list(map3d_dn.shape)), abs(map3d_dn).sum()))
if (numpy.isfinite(abs(map3d_dn))==False).sum() > 0:
log_warning(logger, "There are infinite values in the dn map of the object.")
log_debug(logger, "Scattering vectors shape: (%i,%i); Number of dimensions: %i" % (qmap_shaped.shape[0], qmap_shaped.shape[1], len(list(qmap_shaped.shape))))
if (numpy.isfinite(qmap_shaped)==False).sum() > 0:
log_warning(logger, "There are infinite values in the scattering vectors.")
# NFFT
fourier_pattern = log_execution_time(logger)(condor.utils.nfft.nfft)(map3d_dn, qmap_shaped)
# Check output - masking in case of invalid values
if numpy.any(invalid_mask):
fourier_pattern[invalid_mask.any(axis=1)] = numpy.nan
# reshaping
fourier_pattern = numpy.reshape(fourier_pattern, tuple(list(qmap_scaled.shape)[:-1]))
log_debug(logger, "Generated pattern of shape %s." % str(fourier_pattern.shape))
F = F0 * fourier_pattern * dx**3 * numpy.sqrt(Omega_p)
# ATOMS
elif isinstance(p, condor.particle.ParticleAtoms):
# Import here to make other functionalities of Condor independent of spsim
import spsim
# Check version
from distutils.version import StrictVersion
spsim_version_min = "0.1.0"
if not hasattr(spsim, "__version__") or StrictVersion(spsim.__version__) < StrictVersion(spsim_version_min):
log_and_raise_error(logger, "Your spsim version is too old. Please install the newest spsim version and try again.")
sys.exit(0)
# Create options struct
opts = condor.utils.config._conf_to_spsim_opts(D_source, D_particle, D_detector, ndim=ndim, qn=qn, qmax=qmax)
spsim.write_options_file("./spsim.confout",opts)
# Create molecule struct
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"], D_particle["atomic_positions"])
# Always recenter molecule
spsim.origin_to_center_of_mass(mol)
spsim.write_pdb_from_mol("./mol.pdbout", mol)
# Calculate diffraction pattern
pat = spsim.simulate_shot(mol, opts)
# Extract complex Fourier values from spsim output
F_img = spsim.make_cimage(pat.F, pat.rot, opts)
phot_img = spsim.make_image(opts.detector.photons_per_pixel, pat.rot, opts)
F = numpy.sqrt(abs(phot_img.image[:])) * numpy.exp(1.j * numpy.angle(F_img.image[:]))
spsim.sp_image_free(F_img)
spsim.sp_image_free(phot_img)
# Extract qmap from spsim output
if ndim == 2:
qmap_img = spsim.sp_image_alloc(3, nx, ny)
else:
qmap_img = spsim.sp_image_alloc(3*qn, qn, qn)
spsim.array_to_image(pat.HKL_list, qmap_img)
if ndim == 2:
qmap = 2*numpy.pi * qmap_img.image.real
else:
qmap = 2*numpy.pi * numpy.reshape(qmap_img.image.real, (qn, qn, qn, 3))
self._qmap_cache = {
"qmap" : qmap,
"nx" : nx,
"ny" : ny,
"cx" : cx,
"cy" : cy,
"pixel_size" : pixel_size,
"detector_distance" : detector_distance,
"wavelength" : wavelength,
"extrinsic_rotation": copy.deepcopy(extrinsic_rotation),
"order" : 'zyx',
}
spsim.sp_image_free(qmap_img)
spsim.free_diffraction_pattern(pat)
spsim.free_output_in_options(opts)
else:
log_and_raise_error(logger, "No valid particles initialized.")
sys.exit(0)
if save_qmap:
qmap_singles[particle_key] = qmap
v = D_particle["position"]
# Calculate phase factors if needed
if not numpy.allclose(v, numpy.zeros_like(v), atol=1E-12):
if ndim == 2:
F = F * numpy.exp(-1.j*(v[0]*qmap0[:,:,0]+v[1]*qmap0[:,:,1]+v[2]*qmap0[:,:,2]))
else:
F = F * numpy.exp(-1.j*(v[0]*qmap0[:,:,:,0]+v[1]*qmap0[:,:,:,1]+v[2]*qmap0[:,:,:,2]))
# Superimpose patterns
F_tot = F_tot + F
# Polarization correction
if ndim == 2:
P = self.detector.calculate_polarization_factors(cx=cx, cy=cy, polarization=self.source.polarization)
else:
if self.source.polarization != "ignore":
log_and_raise_error(logger, "polarization=\"%s\" for a 3D propagation does not make sense. Set polarization=\"ignore\" in your Source configuration and try again." % self.source.polarization)
return
P = 1.
F_tot = numpy.sqrt(P) * F_tot
# Photon detection
I_tot, M_tot = self.detector.detect_photons(abs(F_tot)**2)
if ndim == 2:
M_tot_binary = M_tot == 0
if self.detector.binning is not None:
IXxX_tot, MXxX_tot = self.detector.bin_photons(I_tot, M_tot)
FXxX_tot, MXxX_tot = condor.utils.resample.downsample(F_tot, self.detector.binning, mode="integrate",
mask2d0=M_tot, bad_bits=PixelMask.PIXEL_IS_IN_MASK, min_N_pixels=1)
MXxX_tot_binary = None if MXxX_tot is None else (MXxX_tot == 0)
else:
M_tot_binary = None
O = {}
O["source"] = D_source
O["particles"] = D_particles
O["detector"] = D_detector
O["entry_1"] = {}
data_1 = {}
data_1["data_fourier"] = F_tot
data_1["data"] = I_tot
data_1["mask"] = M_tot
data_1["full_period_resolution"] = 2 * self.detector.get_max_resolution(wavelength)
O["entry_1"]["data_1"] = data_1
if self.detector.binning is not None:
data_2 = {}
data_2["data_fourier"] = FXxX_tot
data_2["data"] = IXxX_tot
data_2["mask"] = MXxX_tot
O["entry_1"]["data_2"] = data_2
O = remove_from_dict(O, "_")
return O
def _conf_to_spsim_opts(D_source,D_particle,D_detector,ndim=2,qn=None,qmax=None):
if ndim == 2:
if qn is not None or qmax is not None:
log_warning(logger, "As ndim=2 the passed values for qn and qmax take no effect.")
if ndim == 3:
if qn is None and qmax is None:
log_and_raise_error(logger, "As ndim=3 both qn and qmax must be not None.")
return
import spsim
# Create temporary file for pdb file
tmpf_pdb = tempfile.NamedTemporaryFile(mode='w+', suffix='.conf', prefix='tmp_spsim', dir=None, delete=False)
tmpf_pdb_name = tmpf_pdb.name
tmpf_pdb.close()
# Write pdb file
mol = spsim.get_molecule_from_atoms(D_particle["atomic_numbers"], D_particle["atomic_positions"])
spsim.write_pdb_from_mol(tmpf_pdb_name, mol)
spsim.free_mol(mol)
# Start with default spsim configuration
opts = spsim.set_defaults()
# Create temporary file for spsim configuration
tmpf_conf = tempfile.NamedTemporaryFile(mode='w+', suffix='.conf', prefix='tmp_spsim', dir=None, delete=False)
# Write string sequence from configuration dicts
s = []
s += "# THIS FILE WAS CREATED AUTOMATICALLY BY CONDOR\n"
s += "# Temporary configuration file for spsim\n"
s += "verbosity_level = 0;\n"
s += "number_of_dimensions = %i;\n" % ndim
s += "number_of_patterns = 1;\n"
s += "origin_to_com = 1;\n"
s += "input_type = \"pdb\";\n"
#s += "pdb_filename = \"%s\";\n" % D_particle["pdb_filename"]
s += "pdb_filename = \"%s\";\n" % tmpf_pdb_name
if ndim == 2:
D = D_detector["distance"]
Lx = D_detector["pixel_size"] * D_detector["nx"]
Ly = D_detector["pixel_size"] * D_detector["ny"]
else:
k0 = 2. * numpy.pi / D_source["wavelength"]
D = qn / 2. * D_detector["pixel_size"] * k0 / qmax
Lx = Ly = Lz = D_detector["pixel_size"] * qn
s += "detector_distance = %.12e;\n" % D
s += "detector_width = %.12e;\n" % Lx
s += "detector_height = %.12e;\n" % Ly
if ndim == 3:
s += "detector_depth = %.12e;\n" % Lz
s += "detector_pixel_width = %.12e;\n" % D_detector["pixel_size"]
s += "detector_pixel_height = %.12e;\n" % D_detector["pixel_size"]
if ndim == 3:
s += "detector_pixel_depth = %.12e;\n" % D_detector["pixel_size"]
if ndim == 2:
s += "detector_center_x = %.12e;\n" % (D_detector["pixel_size"] * (D_detector["cx"] - (D_detector["nx"]-1)/2.))
s += "detector_center_y = %.12e;\n" % (D_detector["pixel_size"] * (D_detector["cy"] - (D_detector["ny"]-1)/2.))
else:
s += "detector_center_x = 0;\n"
s += "detector_center_y = 0;\n"
s += "detector_center_z = 0;\n"
s += "detector_binning = 1;\n"
s += "experiment_wavelength = %.12e;\n" % D_source["wavelength"]
s += "experiment_beam_intensity = %.12e;\n" % D_particle["intensity"]
s += "experiment_polarization = \"ignore\";\n" # polarization correction will be done in Condor if needed (see experiment.py)
#s += "use_cuda = 0;\n"
intrinsic_rotation = condor.utils.rotation.Rotation(values=D_particle["extrinsic_quaternion"],formalism="quaternion")
intrinsic_rotation.invert()
e0, e1, e2 = intrinsic_rotation.get_as_euler_angles("zxz")
if not numpy.isfinite(e0):
print("ERROR: phi is not finite")
if not numpy.isfinite(e1):
print("ERROR: theta is not finite")
if not numpy.isfinite(e2):
print("ERROR: psi is not finite")
s += "phi = %.12e;\n" % e0
s += "theta = %.12e;\n" % e1
s += "psi = %.12e;\n" % e2
s += "random_orientation = 0;\n"
# Write string sequence to file
tmpf_conf.writelines(s)
# Close temporary file
tmpf_conf_name = tmpf_conf.name
tmpf_conf.close()
# Read configuration into options struct
spsim.read_options_file(tmpf_conf_name, opts)
# This deletes the temporary files
os.unlink(tmpf_pdb_name)
os.unlink(tmpf_conf_name)
return opts