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 set_atoms_from_pdb_file(self, pdb_filename):
"""
Specify atomic positions from a PDB file
The PDB file format is described here: `http://www.wwpdb.org/documentation/file-format <http://www.wwpdb.org/documentation/file-format>`
Args:
:pdb_filename (str): Location of the PDB file
"""
import spsim
mol = spsim.get_Molecule_from_pdb(pdb_filename)
self._atomic_numbers, self._atomic_positions = spsim.get_atoms_from_molecule(mol)
spsim.free_mol(mol)
def set_atoms_from_pdb_file(self, pdb_filename):
"""
Specify atomic positions from a PDB file
The PDB file format is described here: `http://www.wwpdb.org/documentation/file-format <http://www.wwpdb.org/documentation/file-format>`
Args:
:pdb_filename (str): Location of the PDB file
"""
import spsim
mol = spsim.get_Molecule_from_pdb(pdb_filename)
self._atomic_numbers, self._atomic_positions = spsim.get_atoms_from_molecule(
mol)
spsim.free_mol(mol)
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 _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