def __init__(self,
diameter, diameter_variation = None, diameter_spread = None, diameter_variation_n = None,
number = 1., arrival = "synchronised",
position = None, position_variation = None, position_spread = None, position_variation_n = None,
material_type = None, massdensity = None, atomic_composition = None, electron_density = None):
# Initialise base class
AbstractContinuousParticle.__init__(self,
diameter=diameter, diameter_variation=diameter_variation, diameter_spread=diameter_spread, diameter_variation_n=diameter_variation_n,
rotation_values=None, rotation_formalism=None, rotation_mode="extrinsic",
number=number, arrival=arrival,
position=position, position_variation=position_variation, position_spread=position_spread, position_variation_n=position_variation_n,
material_type=material_type, massdensity=massdensity, atomic_composition=atomic_composition, electron_density=electron_density)
def __init__(self,
diameter,
diameter_variation=None,
diameter_spread=None,
diameter_variation_n=None,
flattening=0.75,
flattening_variation=None,
flattening_spread=None,
flattening_variation_n=None,
rotation_values=None,
rotation_formalism=None,
rotation_mode="extrinsic",
number=1.,
arrival="synchronised",
position=None,
position_variation=None,
position_spread=None,
position_variation_n=None,
material_type='water',
massdensity=None,
atomic_composition=None,
electron_density=None):
# Initialise base class
AbstractContinuousParticle.__init__(
self,
diameter=diameter,
diameter_variation=diameter_variation,
diameter_spread=diameter_spread,
diameter_variation_n=diameter_variation_n,
rotation_values=rotation_values,
rotation_formalism=rotation_formalism,
rotation_mode=rotation_mode,
number=number,
arrival=arrival,
position=position,
position_variation=position_variation,
position_spread=position_spread,
position_variation_n=position_variation_n,
material_type=material_type,
massdensity=massdensity,
atomic_composition=atomic_composition,
electron_density=electron_density)
self.flattening_mean = flattening
self.set_flattening_variation(
flattening_variation=flattening_variation,
flattening_spread=flattening_spread,
flattening_variation_n=flattening_variation_n)
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "sphere"
return O
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "sphere"
return O
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "spheroid"
O["flattening"] = self._get_next_flattening()
return O
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "spheroid"
O["flattening"] = self._get_next_flattening()
return O
def __init__(self,
diameter,
diameter_variation = None, diameter_spread = None, diameter_variation_n = None,
flattening = 0.75, flattening_variation = None, flattening_spread = None, flattening_variation_n = None,
rotation_values = None, rotation_formalism = None, rotation_mode = "extrinsic",
number = 1., arrival = "synchronised",
position = None, position_variation = None, position_spread = None, position_variation_n = None,
material_type = 'water', massdensity = None, atomic_composition = None, electron_density = None):
# Initialise base class
AbstractContinuousParticle.__init__(self,
diameter=diameter, diameter_variation=diameter_variation, diameter_spread=diameter_spread, diameter_variation_n=diameter_variation_n,
rotation_values=rotation_values, rotation_formalism=rotation_formalism, rotation_mode=rotation_mode,
number=number, arrival=arrival,
position=position, position_variation=position_variation, position_spread=position_spread, position_variation_n=position_variation_n,
material_type=material_type, massdensity=massdensity, atomic_composition=atomic_composition, electron_density=electron_density)
self.flattening_mean = flattening
self.set_flattening_variation(flattening_variation=flattening_variation, flattening_spread=flattening_spread, flattening_variation_n=flattening_variation_n)
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "map"
O["geometry"] = self.geometry
if self.geometry == "spheroid":
O["flattening"] = self.flattening
return O
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractContinuousParticle.get_next(self)
O["particle_model"] = "map"
O["geometry"] = self.geometry
if self.geometry == "spheroid":
O["flattening"] = self.flattening
return O
def get_conf(sef):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleSphere instance
P1 = condor.ParticleSpheroid(**conf) # P1: new ParticleSphere instance with the same configuration as P0
"""
return AbstractContinuousParticle.get_conf(self)
def get_conf(sef):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleSphere instance
P1 = condor.ParticleSpheroid(**conf) # P1: new ParticleSphere instance with the same configuration as P0
"""
return AbstractContinuousParticle.get_conf(self)
def __init__(self,
diameter,
diameter_variation=None,
diameter_spread=None,
diameter_variation_n=None,
number=1.,
arrival="synchronised",
position=None,
position_variation=None,
position_spread=None,
position_variation_n=None,
material_type=None,
massdensity=None,
atomic_composition=None,
electron_density=None):
# Initialise base class
AbstractContinuousParticle.__init__(
self,
diameter=diameter,
diameter_variation=diameter_variation,
diameter_spread=diameter_spread,
diameter_variation_n=diameter_variation_n,
rotation_values=None,
rotation_formalism=None,
rotation_mode="extrinsic",
number=number,
arrival=arrival,
position=position,
position_variation=position_variation,
position_spread=position_spread,
position_variation_n=position_variation_n,
material_type=material_type,
massdensity=massdensity,
atomic_composition=atomic_composition,
electron_density=electron_density)
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleSpheroid instance
P1 = condor.ParticleSpheroid(**conf) # P1: new ParticleSpheroid instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractContinuousParticle.get_conf(self))
conf["flattening"] = self.flattening_mean
fvar = self._flattening_variation.get_conf()
conf["flattening_variation"] = fvar["mode"]
conf["flattening_spread"] = fvar["spread"]
conf["flattening_variation_n"] = fvar["n"]
return conf
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleSpheroid instance
P1 = condor.ParticleSpheroid(**conf) # P1: new ParticleSpheroid instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractContinuousParticle.get_conf(self))
conf["flattening"] = self.flattening_mean
fvar = self._flattening_variation.get_conf()
conf["flattening_variation"] = fvar["mode"]
conf["flattening_spread"] = fvar["spread"]
conf["flattening_variation_n"] = fvar["n"]
return conf
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleMap instance
P1 = condor.ParticleMap(**conf) # P1: new ParticleMap instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractContinuousParticle.get_conf(self))
conf["geometry"] = self.geometry
if self.geometry == "custom":
m, dx = self.get_original_map()
conf["map3d"] = m
conf["dx"] = dx
if self.geometry == "spheroid":
conf["flattening"] = self.flattening
return conf
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleMap instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleMap instance
P1 = condor.ParticleMap(**conf) # P1: new ParticleMap instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractContinuousParticle.get_conf(self))
conf["geometry"] = self.geometry
if self.geometry == "custom":
m, dx = self.get_original_map()
conf["map3d"] = m
conf["dx"] = dx
if self.geometry == "spheroid":
conf["flattening"] = self.flattening
return conf
def __init__(
self,
geometry,
diameter=None,
diameter_variation=None,
diameter_spread=None,
diameter_variation_n=None,
dx=None,
map3d=None,
map3d_filename=None,
map3d_dataset=None,
emd_id=None,
rotation_values=None,
rotation_formalism=None,
rotation_mode="extrinsic",
flattening=0.75,
number=1.0,
arrival="synchronised",
position=None,
position_variation=None,
position_spread=None,
position_variation_n=None,
material_type=None,
massdensity=None,
atomic_composition=None,
electron_density=None,
):
# Initialise base class
AbstractContinuousParticle.__init__(
self,
diameter=diameter,
diameter_variation=diameter_variation,
diameter_spread=diameter_spread,
diameter_variation_n=diameter_variation_n,
rotation_values=rotation_values,
rotation_formalism=rotation_formalism,
rotation_mode=rotation_mode,
number=number,
arrival=arrival,
position=position,
position_variation=position_variation,
position_spread=position_spread,
position_variation_n=position_variation_n,
material_type=material_type,
massdensity=massdensity,
atomic_composition=atomic_composition,
electron_density=electron_density,
)
# Check for valid geometry
if geometry not in ["icosahedron", "cube", "sphere", "spheroid", "custom"]:
log_and_raise_error(
logger,
"Cannot initialize %s because '%s' is not a valid argument for 'geometry'."
% (kwargs["geometry"], self.__class__.__name__),
)
sys.exit(1)
self.geometry = geometry
# Has effect only for spheroids
self.flattening = flattening
# Init chache
self._cache = {}
self._dx_orig = None
self._map3d_orig = None
if geometry == "custom":
if map3d is not None:
if dx is None:
log_and_raise_error(
logger, "Cannot initialize custom geometry with 'map3d' but without grid spacing 'dx'."
)
sys.exit(1)
else:
log_debug(logger, "Attempting to initialise custom geometry with 'map3d'.")
if map3d_filename is not None or map3d_dataset is not None or emd_id is not None:
log_and_raise_error(
logger, "Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_array(map3d, dx)
elif map3d_filename is not None and map3d_dataset is not None:
if dx is None:
log_and_raise_error(
logger,
"You are trying to initialise the map with an HDF5 file. You also need to provide the grid spacing 'dx'",
)
sys.exit(1)
log_debug(
logger, "Attempting to initialise custom geometry with 'map3d_filename', 'map3d_dataset' and 'dx'."
)
if not map3d_filename.endswith(".h5"):
log_and_raise_error(logger, "Map file is not an HDF5 file!")
sys.exit(1)
if map3d is not None or emd_id is not None:
log_and_raise_error(
logger, "Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_h5file(map3d_filename, map3d_dataset, dx)
elif map3d_filename is not None:
if not map3d_filename.endswith(".map") and not map3d_filename.endswith(".mrc"):
log_and_raise_error(logger, "Map file is not an MRC/MAP file!")
sys.exit(1)
self.set_custom_geometry_by_mrcfile(map3d_filename)
elif emd_id is not None:
log_debug(logger, "Attempting to initialise custom geometry with 'emd_id'.")
if map3d_filename is not None or map3d_dataset is not None or map3d is not None or dx is not None:
log_and_raise_error(
logger, "Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_emd_id(emd_id)
if diameter is None:
self.diameter_mean = self._dx_orig * self._map3d_orig.shape[-1]
def __init__(self,
geometry,
diameter=None,
diameter_variation=None,
diameter_spread=None,
diameter_variation_n=None,
dx=None,
map3d=None,
map3d_filename=None,
map3d_dataset=None,
emd_id=None,
rotation_values=None,
rotation_formalism=None,
rotation_mode="extrinsic",
flattening=0.75,
number=1.,
arrival="synchronised",
position=None,
position_variation=None,
position_spread=None,
position_variation_n=None,
material_type=None,
massdensity=None,
atomic_composition=None,
electron_density=None):
# Initialise base class
AbstractContinuousParticle.__init__(
self,
diameter=diameter,
diameter_variation=diameter_variation,
diameter_spread=diameter_spread,
diameter_variation_n=diameter_variation_n,
rotation_values=rotation_values,
rotation_formalism=rotation_formalism,
rotation_mode=rotation_mode,
number=number,
arrival=arrival,
position=position,
position_variation=position_variation,
position_spread=position_spread,
position_variation_n=position_variation_n,
material_type=material_type,
massdensity=massdensity,
atomic_composition=atomic_composition,
electron_density=electron_density)
# Check for valid geometry
if geometry not in [
"icosahedron", "cube", "sphere", "spheroid", "custom"
]:
log_and_raise_error(
logger,
"Cannot initialize %s because \'%s\' is not a valid argument for \'geometry\'."
% (kwargs["geometry"], self.__class__.__name__))
sys.exit(1)
self.geometry = geometry
# Has effect only for spheroids
self.flattening = flattening
# Init chache
self._cache = {}
self._dx_orig = None
self._map3d_orig = None
if geometry == "custom":
if map3d is not None:
if dx is None:
log_and_raise_error(
logger,
"Cannot initialize custom geometry with \'map3d\' without known grid spacing (\'dx\')."
)
sys.exit(1)
else:
log_debug(
logger,
"Attempting to initialise custom geometry with \'map3d\'."
)
if map3d_filename is not None or map3d_dataset is not None or emd_id is not None:
log_and_raise_error(
logger,
"Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_array(map3d, dx)
elif map3d_filename is not None and map3d_dataset is not None:
if dx is None:
log_and_raise_error(
logger,
"You are trying to initialise the map with an HDF5 file. You also need to provide the grid spacing \'dx\'"
)
sys.exit(1)
log_debug(
logger,
"Attempting to initialise custom geometry with \'map3d_filename\', \'map3d_dataset\' and \'dx\'."
)
if not map3d_filename.endswith(".h5"):
log_and_raise_error(logger,
"Map file is not an HDF5 file!")
sys.exit(1)
if map3d is not None or emd_id is not None:
log_and_raise_error(
logger,
"Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_h5file(map3d_filename,
map3d_dataset, dx)
elif map3d_filename is not None:
if not map3d_filename.endswith(
".map") and not map3d_filename.endswith(".mrc"):
log_and_raise_error(logger,
"Map file is not an MRC/MAP file!")
sys.exit(1)
self.set_custom_geometry_by_mrcfile(map3d_filename)
elif emd_id is not None:
log_debug(
logger,
"Attempting to initialise custom geometry with \'emd_id\'."
)
if map3d_filename is not None or map3d_dataset is not None or map3d is not None or dx is not None:
log_and_raise_error(
logger,
"Cannot initialize custom geometry because of ambiguous keyword arguments."
)
sys.exit(1)
self.set_custom_geometry_by_emd_id(emd_id)
if diameter is None:
self.diameter_mean = self._dx_orig * self._map3d_orig.shape[-1]
