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11,044 | burnman.classes.polytope | set_return_type |
Sets the return_type for the polytope object. Also deletes the cached
endmember_occupancies property.
:param return_fractions: Choose whether the generated polytope object
should return fractions or floats.
:type return_fractions: bool
| def set_return_type(self, return_fractions=False):
"""
Sets the return_type for the polytope object. Also deletes the cached
endmember_occupancies property.
:param return_fractions: Choose whether the generated polytope object
should return fractions or floats.
:type return_fractions: bool
"""
try:
del self.__dict__["endmember_occupancies"]
except KeyError:
pass
self.return_fractions = return_fractions
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11,045 | burnman.classes.polytope | subpolytope_from_independent_endmember_limits |
Returns a smaller polytope by applying additional limits to the amounts
of the independent endmembers.
| def subpolytope_from_independent_endmember_limits(self, limits):
"""
Returns a smaller polytope by applying additional limits to the amounts
of the independent endmembers.
"""
modified_limits = self.independent_endmember_polytope.get_inequalities().copy()
modified_limits.extend(limits, linear=False)
return cdd.Polyhedron(modified_limits)
| (self, limits) | [
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11,046 | burnman.classes.polytope | subpolytope_from_site_occupancy_limits |
Returns a smaller polytope by applying additional limits to the
individual site occupancies.
| def subpolytope_from_site_occupancy_limits(self, limits):
"""
Returns a smaller polytope by applying additional limits to the
individual site occupancies.
"""
modified_limits = self.polytope_matrix.copy()
modified_limits.extend(limits, linear=False)
return cdd.Polyhedron(modified_limits)
| (self, limits) | [
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11,047 | burnman.classes.mineral | Mineral |
This is the base class for all minerals. States of the mineral
can only be queried after setting the pressure and temperature
using set_state(). The method for computing properties of
the material is set using set_method(). This is done during
initialisation if the param 'equation_of_state' has been defined.
The method can be overridden later by the user.
This class is available as ``burnman.Mineral``.
If deriving from this class, set the properties in self.params
to the desired values. For more complicated materials you
can overwrite set_state(), change the params and then call
set_state() from this class.
All the material parameters are expected to be in plain SI units. This
means that the elastic moduli should be in Pascals and NOT Gigapascals,
and the Debye temperature should be in K not C. Additionally, the
reference volume should be in m^3/(mol molecule) and not in unit cell
volume and 'n' should be the number of atoms per molecule. Frequently in
the literature the reference volume is given in Angstrom^3 per unit cell.
To convert this to m^3/(mol of molecule) you should multiply by 10^(-30) *
N_a / Z, where N_a is Avogadro's number and Z is the number of formula units per
unit cell. You can look up Z in many places, including www.mindat.org
| class Mineral(Material):
"""
This is the base class for all minerals. States of the mineral
can only be queried after setting the pressure and temperature
using set_state(). The method for computing properties of
the material is set using set_method(). This is done during
initialisation if the param 'equation_of_state' has been defined.
The method can be overridden later by the user.
This class is available as ``burnman.Mineral``.
If deriving from this class, set the properties in self.params
to the desired values. For more complicated materials you
can overwrite set_state(), change the params and then call
set_state() from this class.
All the material parameters are expected to be in plain SI units. This
means that the elastic moduli should be in Pascals and NOT Gigapascals,
and the Debye temperature should be in K not C. Additionally, the
reference volume should be in m^3/(mol molecule) and not in unit cell
volume and 'n' should be the number of atoms per molecule. Frequently in
the literature the reference volume is given in Angstrom^3 per unit cell.
To convert this to m^3/(mol of molecule) you should multiply by 10^(-30) *
N_a / Z, where N_a is Avogadro's number and Z is the number of formula units per
unit cell. You can look up Z in many places, including www.mindat.org
"""
def __init__(self, params=None, property_modifiers=None):
Material.__init__(self)
if params is not None:
self.params = params
elif "params" not in self.__dict__:
self.params = {}
if property_modifiers is not None:
self.property_modifiers = property_modifiers
elif "property_modifiers" not in self.__dict__:
self.property_modifiers = []
self.method = None
if "equation_of_state" in self.params:
self.set_method(self.params["equation_of_state"])
if "name" in self.params:
self.name = self.params["name"]
def set_method(self, equation_of_state):
"""
Set the equation of state to be used for this mineral.
Takes a string corresponding to any of the predefined
equations of state: 'bm2', 'bm3', 'mgd2', 'mgd3', 'slb2', 'slb3',
'mt', 'hp_tmt', or 'cork'. Alternatively, you can pass a user defined
class which derives from the equation_of_state base class.
After calling set_method(), any existing derived properties
(e.g., elastic parameters or thermodynamic potentials) will be out
of date, so set_state() will need to be called again.
"""
if equation_of_state is None:
self.method = None
return
new_method = eos.create(equation_of_state)
if self.method is not None and "equation_of_state" in self.params:
self.method = eos.create(self.params["equation_of_state"])
if type(new_method).__name__ == "instance":
raise Exception(
"Please derive your method from object (see python old style classes)"
)
if (
self.method is not None
and isinstance(new_method, type(self.method)) is False
):
# Warn user that they are changing the EoS
warnings.warn(
"Warning, you are changing the method to "
f"{new_method.__class__.__name__} even though the "
"material is designed to be used with the method "
f"{self.method.__class__.__name__}. "
"This does not overwrite any mineral attributes",
stacklevel=2,
)
self.reset()
self.method = new_method
# Validate the params object on the requested EOS.
try:
self.method.validate_parameters(self.params)
except Exception as e:
print(
f"Mineral {self.to_string()} failed to validate parameters "
f'with message: "{e.message}"'
)
raise
# Invalidate the cache upon resetting the method
self.reset()
def to_string(self):
"""
Returns the name of the mineral class
"""
return (
"'"
+ self.__class__.__module__.replace(".minlib_", ".")
+ "."
+ self.__class__.__name__
+ "'"
)
def debug_print(self, indent=""):
print("%s%s" % (indent, self.to_string()))
def unroll(self):
return ([self], [1.0])
@copy_documentation(Material.set_state)
def set_state(self, pressure, temperature):
Material.set_state(self, pressure, temperature)
self._property_modifiers = (
eos.property_modifiers.calculate_property_modifications(self)
)
if self.method is None:
raise AttributeError(
"no method set for mineral, or equation_of_state given in mineral.params"
)
"""
Properties from equations of state
We choose the P, T properties (e.g. Gibbs(P, T) rather than Helmholtz(V, T)),
as it allows us to more easily apply corrections to the free energy
"""
@material_property
@copy_documentation(Material.molar_gibbs)
def molar_gibbs(self):
return (
self.method.gibbs_free_energy(
self.pressure,
self.temperature,
self._molar_volume_unmodified,
self.params,
)
+ self._property_modifiers["G"]
)
@material_property
def _molar_volume_unmodified(self):
return self.method.volume(self.pressure, self.temperature, self.params)
@material_property
@copy_documentation(Material.molar_volume)
def molar_volume(self):
return self._molar_volume_unmodified + self._property_modifiers["dGdP"]
@material_property
@copy_documentation(Material.molar_entropy)
def molar_entropy(self):
return (
self.method.entropy(
self.pressure,
self.temperature,
self._molar_volume_unmodified,
self.params,
)
- self._property_modifiers["dGdT"]
)
@material_property
@copy_documentation(Material.isothermal_bulk_modulus)
def isothermal_bulk_modulus(self):
K_T_orig = self.method.isothermal_bulk_modulus(
self.pressure, self.temperature, self._molar_volume_unmodified, self.params
)
return self.molar_volume / (
(self._molar_volume_unmodified / K_T_orig)
- self._property_modifiers["d2GdP2"]
)
@material_property
@copy_documentation(Material.molar_heat_capacity_p)
def molar_heat_capacity_p(self):
return (
self.method.molar_heat_capacity_p(
self.pressure,
self.temperature,
self._molar_volume_unmodified,
self.params,
)
- self.temperature * self._property_modifiers["d2GdT2"]
)
@material_property
@copy_documentation(Material.thermal_expansivity)
def thermal_expansivity(self):
return (
(
self.method.thermal_expansivity(
self.pressure,
self.temperature,
self._molar_volume_unmodified,
self.params,
)
* self._molar_volume_unmodified
)
+ self._property_modifiers["d2GdPdT"]
) / self.molar_volume
@material_property
@copy_documentation(Material.shear_modulus)
def shear_modulus(self):
G = self.method.shear_modulus(
self.pressure, self.temperature, self._molar_volume_unmodified, self.params
)
if G < np.finfo("float").eps:
warnings.formatwarning = (
lambda msg, *a: "Warning from file '{0}', line {1}:\n{2}\n\n".format(
a[1], a[2], msg
)
)
warnings.warn(
"You are trying to calculate sh | (params=None, property_modifiers=None) | [
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11,048 | burnman.classes.mineral | __init__ | null | def __init__(self, params=None, property_modifiers=None):
Material.__init__(self)
if params is not None:
self.params = params
elif "params" not in self.__dict__:
self.params = {}
if property_modifiers is not None:
self.property_modifiers = property_modifiers
elif "property_modifiers" not in self.__dict__:
self.property_modifiers = []
self.method = None
if "equation_of_state" in self.params:
self.set_method(self.params["equation_of_state"])
if "name" in self.params:
self.name = self.params["name"]
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11,059 | burnman.classes.perplex | PerplexMaterial |
This is the base class for a PerpleX material. States of the material
can only be queried after setting the pressure and temperature
using set_state().
Instances of this class are initialised with
a 2D PerpleX tab file. This file should be in the standard format
(as output by werami), and should have columns with the following names:
'rho,kg/m3', 'alpha,1/K', 'beta,1/bar', 'Ks,bar', 'Gs,bar', 'v0,km/s',
'vp,km/s', 'vs,km/s', 's,J/K/kg', 'h,J/kg', 'cp,J/K/kg', 'V,J/bar/mol'.
The order of these names is not important.
Properties of the material are determined by linear interpolation from
the PerpleX grid. They are all returned in SI units on a molar basis,
even though the PerpleX tab file is not in these units.
This class is available as ``burnman.PerplexMaterial``.
| class PerplexMaterial(Material):
"""
This is the base class for a PerpleX material. States of the material
can only be queried after setting the pressure and temperature
using set_state().
Instances of this class are initialised with
a 2D PerpleX tab file. This file should be in the standard format
(as output by werami), and should have columns with the following names:
'rho,kg/m3', 'alpha,1/K', 'beta,1/bar', 'Ks,bar', 'Gs,bar', 'v0,km/s',
'vp,km/s', 'vs,km/s', 's,J/K/kg', 'h,J/kg', 'cp,J/K/kg', 'V,J/bar/mol'.
The order of these names is not important.
Properties of the material are determined by linear interpolation from
the PerpleX grid. They are all returned in SI units on a molar basis,
even though the PerpleX tab file is not in these units.
This class is available as ``burnman.PerplexMaterial``.
"""
def __init__(self, tab_file, name="Perple_X material"):
self.name = name
self.params = {"name": name}
(
self._property_interpolators,
self.params["molar_mass"],
self.bounds,
) = self._read_2D_perplex_file(tab_file)
Material.__init__(self)
def _read_2D_perplex_file(self, filename):
with open(filename, "r") as f:
datastream = f.read()
lines = [
line.strip().split() for line in datastream.split("\n") if line.strip()
]
if lines[2][0] != "2":
raise Exception("This is not a 2D PerpleX table")
bounds = [
(float(lines[4][0]), float(lines[5][0]), int(lines[6][0])),
(float(lines[8][0]), float(lines[9][0]), int(lines[10][0])),
]
if lines[3][0] == "P(bar)" and lines[7][0] == "T(K)":
Pmin, Pint, nP = bounds[0]
Tmin, Tint, nT = bounds[1]
elif lines[3][0] == "T(K)" and lines[7][0] == "P(bar)":
Pmin, Pint, nP = bounds[1]
Tmin, Tint, nT = bounds[0]
else:
raise Exception(
"This file does not have a recognised PerpleX structure.\n"
"Are the independent variables P(bar) and T(K)?"
)
Pmin = Pmin * 1.0e5 # bar to Pa
Pint = Pint * 1.0e5 # bar to Pa
Pmax = Pmin + Pint * (nP - 1.0)
Tmax = Tmin + Tint * (nT - 1.0)
pressures = np.linspace(Pmin, Pmax, nP)
temperatures = np.linspace(Tmin, Tmax, nT)
n_properties = int(lines[11][0])
property_list = lines[12]
# property_table[i][j][k] returns the kth property at the ith pressure and jth temperature
table = np.array(
[[float(string) for string in line] for line in lines[13 : 13 + nP * nT]]
)
if lines[3][0] == "P(bar)":
property_table = np.swapaxes(table.reshape(nT, nP, n_properties), 0, 1)
else:
property_table = table.reshape(nP, nT, n_properties)
ordered_property_list = [
"rho,kg/m3",
"alpha,1/K",
"beta,1/bar",
"Ks,bar",
"Gs,bar",
"v0,km/s",
"vp,km/s",
"vs,km/s",
"s,J/K/kg",
"h,J/kg",
"cp,J/K/kg",
"V,J/bar/mol",
]
p_indices = [
i
for i, p in enumerate(property_list)
for ordered_p in ordered_property_list
if p == ordered_p
]
properties = {}
for i, p_idx in enumerate(p_indices):
# Fill in NaNs as long as they aren't in the corners of the P-T grid
a = np.array(property_table[:, :, [p_idx]][:, :, 0])
x, y = np.indices(a.shape)
a[np.isnan(a)] = griddata(
(x[~np.isnan(a)], y[~np.isnan(a)]), # points we know
a[~np.isnan(a)], # values we know
(x[np.isnan(a)], y[np.isnan(a)]),
)
# Fill any remaining NaNs with zeros
properties[ordered_property_list[i]] = np.nan_to_num(a, 0.0)
densities = properties["rho,kg/m3"]
volumes = 1.0e-5 * properties["V,J/bar/mol"]
molar_masses = densities * volumes
molar_mass = np.mean(molar_masses)
property_interpolators = {
"rho": RegularGridInterpolator(
(pressures, temperatures), densities, bounds_error=True
),
"alpha": RegularGridInterpolator(
(pressures, temperatures), properties["alpha,1/K"], bounds_error=True
),
"K_T": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 / properties["beta,1/bar"],
bounds_error=True,
),
"K_S": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 * properties["Ks,bar"],
bounds_error=True,
),
"G_S": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 * properties["Gs,bar"],
bounds_error=True,
),
"bulk_sound_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["v0,km/s"],
bounds_error=True,
),
"p_wave_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["vp,km/s"],
bounds_error=True,
),
"s_wave_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["vs,km/s"],
bounds_error=True,
),
"S": RegularGridInterpolator(
(pressures, temperatures),
properties["s,J/K/kg"] * molar_masses,
bounds_error=True,
),
"H": RegularGridInterpolator(
(pressures, temperatures),
properties["h,J/kg"] * molar_masses,
bounds_error=True,
),
"C_p": RegularGridInterpolator(
(pressures, temperatures),
properties["cp,J/K/kg"] * molar_masses,
bounds_error=True,
),
"V": RegularGridInterpolator(
(pressures, temperatures), volumes, bounds_error=True
),
}
bounds = [[Pmin, Pmax], [Tmin, Tmax]]
return property_interpolators, molar_mass, bounds
@copy_documentation(Material.set_state)
def set_state(self, pressure, temperature):
if not np.logical_and(
np.all(self.bounds[0][0] <= pressure), np.all(pressure <= self.bounds[0][1])
):
raise ValueError(
"The set_state pressure ({0:.4f}) is outside the bounds of this rock ({1:.4f}-{2:.4f} GPa)".format(
pressure, self.bounds[0][0] / 1.0e9, self.bounds[0][1] / 1.0e9
)
)
if not np.logical_and(
np.all(self.bounds[1][0] <= temperature),
np.all(temperature <= self.bounds[1][1]),
):
raise ValueError(
"The set_state temperature ({0:.1f}) is outside the bounds of this rock ({1:.1f}-{2:.1f} K)".format(
temperature, self.bounds[1][0], self.bounds[1][1]
)
)
Material.set_state(self, pressure, temperature)
"""
Properties by linear interpolation of Perple_X output
"""
@material_property
@copy_documentation(Material.molar_volume)
def molar_volume(self):
return self._property_interpolators["V"]([self.pressure, self.temperature])[0]
@material_property
@copy_documentation(Material.molar_enthalpy)
def molar_enthalpy(self):
return self._property_interpolators["H"]([self.pressure, self.temperature])[0]
@material_property
@copy_documentation(Material.molar_entropy)
def molar_entropy(self):
return self._property_interpolators["S"]([self.pressure, self.temperature])[0]
@material_property
@copy_documentation(Material.isothermal_bulk_modulus)
def isothermal_bul | (tab_file, name='Perple_X material') | [
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] |
11,060 | burnman.classes.perplex | __init__ | null | def __init__(self, tab_file, name="Perple_X material"):
self.name = name
self.params = {"name": name}
(
self._property_interpolators,
self.params["molar_mass"],
self.bounds,
) = self._read_2D_perplex_file(tab_file)
Material.__init__(self)
| (self, tab_file, name='Perple_X material') | [
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11,061 | burnman.classes.perplex | _read_2D_perplex_file | null | def _read_2D_perplex_file(self, filename):
with open(filename, "r") as f:
datastream = f.read()
lines = [
line.strip().split() for line in datastream.split("\n") if line.strip()
]
if lines[2][0] != "2":
raise Exception("This is not a 2D PerpleX table")
bounds = [
(float(lines[4][0]), float(lines[5][0]), int(lines[6][0])),
(float(lines[8][0]), float(lines[9][0]), int(lines[10][0])),
]
if lines[3][0] == "P(bar)" and lines[7][0] == "T(K)":
Pmin, Pint, nP = bounds[0]
Tmin, Tint, nT = bounds[1]
elif lines[3][0] == "T(K)" and lines[7][0] == "P(bar)":
Pmin, Pint, nP = bounds[1]
Tmin, Tint, nT = bounds[0]
else:
raise Exception(
"This file does not have a recognised PerpleX structure.\n"
"Are the independent variables P(bar) and T(K)?"
)
Pmin = Pmin * 1.0e5 # bar to Pa
Pint = Pint * 1.0e5 # bar to Pa
Pmax = Pmin + Pint * (nP - 1.0)
Tmax = Tmin + Tint * (nT - 1.0)
pressures = np.linspace(Pmin, Pmax, nP)
temperatures = np.linspace(Tmin, Tmax, nT)
n_properties = int(lines[11][0])
property_list = lines[12]
# property_table[i][j][k] returns the kth property at the ith pressure and jth temperature
table = np.array(
[[float(string) for string in line] for line in lines[13 : 13 + nP * nT]]
)
if lines[3][0] == "P(bar)":
property_table = np.swapaxes(table.reshape(nT, nP, n_properties), 0, 1)
else:
property_table = table.reshape(nP, nT, n_properties)
ordered_property_list = [
"rho,kg/m3",
"alpha,1/K",
"beta,1/bar",
"Ks,bar",
"Gs,bar",
"v0,km/s",
"vp,km/s",
"vs,km/s",
"s,J/K/kg",
"h,J/kg",
"cp,J/K/kg",
"V,J/bar/mol",
]
p_indices = [
i
for i, p in enumerate(property_list)
for ordered_p in ordered_property_list
if p == ordered_p
]
properties = {}
for i, p_idx in enumerate(p_indices):
# Fill in NaNs as long as they aren't in the corners of the P-T grid
a = np.array(property_table[:, :, [p_idx]][:, :, 0])
x, y = np.indices(a.shape)
a[np.isnan(a)] = griddata(
(x[~np.isnan(a)], y[~np.isnan(a)]), # points we know
a[~np.isnan(a)], # values we know
(x[np.isnan(a)], y[np.isnan(a)]),
)
# Fill any remaining NaNs with zeros
properties[ordered_property_list[i]] = np.nan_to_num(a, 0.0)
densities = properties["rho,kg/m3"]
volumes = 1.0e-5 * properties["V,J/bar/mol"]
molar_masses = densities * volumes
molar_mass = np.mean(molar_masses)
property_interpolators = {
"rho": RegularGridInterpolator(
(pressures, temperatures), densities, bounds_error=True
),
"alpha": RegularGridInterpolator(
(pressures, temperatures), properties["alpha,1/K"], bounds_error=True
),
"K_T": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 / properties["beta,1/bar"],
bounds_error=True,
),
"K_S": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 * properties["Ks,bar"],
bounds_error=True,
),
"G_S": RegularGridInterpolator(
(pressures, temperatures),
1.0e5 * properties["Gs,bar"],
bounds_error=True,
),
"bulk_sound_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["v0,km/s"],
bounds_error=True,
),
"p_wave_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["vp,km/s"],
bounds_error=True,
),
"s_wave_velocity": RegularGridInterpolator(
(pressures, temperatures),
1.0e3 * properties["vs,km/s"],
bounds_error=True,
),
"S": RegularGridInterpolator(
(pressures, temperatures),
properties["s,J/K/kg"] * molar_masses,
bounds_error=True,
),
"H": RegularGridInterpolator(
(pressures, temperatures),
properties["h,J/kg"] * molar_masses,
bounds_error=True,
),
"C_p": RegularGridInterpolator(
(pressures, temperatures),
properties["cp,J/K/kg"] * molar_masses,
bounds_error=True,
),
"V": RegularGridInterpolator(
(pressures, temperatures), volumes, bounds_error=True
),
}
bounds = [[Pmin, Pmax], [Tmin, Tmax]]
return property_interpolators, molar_mass, bounds
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11,072 | burnman.classes.planet | Planet |
A class to build (self-consistent) Planets made out of Layers
(:class:`burnman.Layer`). By default the planet is set to be self-consistent
(with zero pressure at the surface and zero gravity at the center),
but this can be overwritte using the set_pressure_mode().
Pressure_modes defined in the individual layers will be ignored.
If temperature modes are already set for each of the layers, when the
planet is initialized, the planet will be built immediately.
| class Planet(object):
"""
A class to build (self-consistent) Planets made out of Layers
(:class:`burnman.Layer`). By default the planet is set to be self-consistent
(with zero pressure at the surface and zero gravity at the center),
but this can be overwritte using the set_pressure_mode().
Pressure_modes defined in the individual layers will be ignored.
If temperature modes are already set for each of the layers, when the
planet is initialized, the planet will be built immediately.
"""
def __init__(
self, name, layers, n_max_iterations=50, max_delta=1.0e-5, verbose=False
):
"""
:param name: Name of planet.
:type name: str
:param layers: Layers to build the planet out of
(layers are sorted within the planet).
:type layers: list of :class:`burnman.Layer`
:param n_max_iterations: Maximum number of iterations to reach
self-consistent planet.
:type n_max_iterations: int
:param max_delta: Relative update to the center pressure of the planet between
iterations to stop iterations.
:type max_delta: float
"""
# sort layers
self.layers = sorted(layers, key=lambda x: x.inner_radius)
# assert layers attach to one another
if len(self.layers) > 1:
for i in range(1, len(self.layers)):
assert self.layers[i].inner_radius == self.layers[i - 1].outer_radius
self.name = name
self.radii = self.evaluate(["radii"])
self.n_slices = len(self.radii)
self.radius_planet = max(self.radii)
self.volume = 4.0 / 3.0 * np.pi * np.power(self.radius_planet, 3.0)
for layer in self.layers:
layer.n_start = np.where(self.radii == layer.inner_radius)[0][-1]
layer.n_end = np.where(self.radii == layer.outer_radius)[0][0] + 1
self._cached = {}
self.verbose = verbose
self.set_pressure_mode(n_max_iterations=n_max_iterations, max_delta=max_delta)
def __iter__(self):
"""
Planet object will iterate over Layers.
"""
return list(self.layers).__iter__()
def __str__(self):
"""
Prints details of the planet
"""
writing = "{0} consists of {1} layers:\n".format(self.name, len(self.layers))
for layer in self:
writing = writing + layer.__str__()
return writing
def reset(self):
"""
Resets all cached material properties.
It is typically not required for the user to call this function.
"""
self._cached = {}
def get_layer(self, name):
"""
Returns a layer with a given name
:param name: Given name of a layer
:type name: str
:returns: Layer with the given name.
:rtype: :class:`burnman.Layer`
"""
for layer in self.layers:
if layer.name == name:
return layer
raise LookupError()
def get_layer_by_radius(self, radius):
"""
Returns a layer in which this radius lies
:param radius: Radius at which to evaluate the layer.
:type radius: float
:returns: Layer in which the radius lies.
:rtype: :class:`burnman.Layer`
"""
for layer in self.layers:
if layer.outer_radius >= radius:
return layer
raise LookupError()
def evaluate(self, properties, radlist=None):
"""
Function that is generally used to evaluate properties
of the different layers and stitch them together.
If asking for different radii than the internal radlist,
pressure and temperature values are interpolated and the
layer material evaluated at those pressures and
temperatures.
:param properties: List of properties to evaluate
:type properties: list of strings
:param radlist: Radii to evaluate properties at. If left empty,
internal radius lists are used.
:type radlist: array of floats
:returns: 1D or 2D array of requested properties
(1D if only one property was requested)
:rtype: numpy.array
"""
if radlist is None:
values = np.empty(
[len(properties), np.sum([len(layer.radii) for layer in self.layers])]
)
for i, prop in enumerate(properties):
if prop == "depth":
values[i] = np.array(
[
self.radius_planet - r
for layer in self.layers
for r in layer.radii
]
)
else:
j = 0
for layer in self.layers:
vals = getattr(layer, prop)
values[i, j : j + len(vals)] = vals
j += len(vals)
else:
values = np.empty([len(properties), len(radlist)])
l_idx = [
i
for i, layer in enumerate(self.layers)
for r in radlist
if r >= layer.inner_radius and r <= layer.outer_radius
]
for j, r in enumerate(radlist):
values[:, j] = (
self.layers[l_idx[j]]
.evaluate(properties, [r], self.radius_planet)
.T[0]
)
if values.shape[0] == 1:
values = values[0]
return values
def set_pressure_mode(
self,
pressure_mode="self-consistent",
pressures=None,
pressure_top=0.0,
gravity_bottom=0.0,
n_max_iterations=50,
max_delta=1.0e-5,
):
"""
Sets the pressure mode of the planet by user-defined values are in a
self-consistent fashion.
pressure_mode is 'user-defined' or 'self-consistent'.
The default for the planet is self-consistent, with zero pressure at
the surface and zero pressure at the center.
:param pressure_mode: This can be set to 'user-defined' or 'self-consistent'.
:type pressure_mode: str
:param pressures: Pressures (Pa) to set layer to ('user-defined').
This should be the same length as defined radius array for the layer.
:type pressures: array of floats
:param pressure_top: Pressure (Pa) at the top of the layer.
:type pressure_top: float
:param gravity_bottom: Gravity (m/s^2) at the bottom the layer
:type gravity_bottom: float
:param n_max_iterations: Maximum number of iterations to reach
self-consistent pressures.
:type n_max_iterations: int
"""
self.reset()
assert pressure_mode == "user-defined" or pressure_mode == "self-consistent"
self.pressure_mode = pressure_mode
self.gravity_bottom = gravity_bottom
if pressure_mode == "user-defined":
assert len(pressures) == len(self.radii)
self._pressures = pressures
warnings.warn(
"User-defined pressures mean that the planet is "
"unlikely to be self-consistent"
)
if pressure_mode == "self-consistent":
self.pressure_top = pressure_top
self.n_max_iterations = n_max_iterations
self.max_delta = max_delta
def make(self):
"""
This routine needs to be called before evaluating any properties.
If pressures and temperatures are self-consistent, they
are computed across the planet here. Also initializes an array of materials
in each Layer to compute properties from.
"""
self.reset()
for layer in self.layers:
assert layer.temperature_mode is not None
if self.pressure_mode == "user-defined":
self._temperatures = self._evaluate_temperature(self._pressures)
if self.pressure_mode == "self-consistent":
new_press = (
self.press | (name, layers, n_max_iterations=50, max_delta=1e-05, verbose=False) | [
0.0847201868891716,
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0.0021796890068799257,
-0.013425433076918125,
-0.07779494673013687,
-0.03311261162161827,
-0.03674110770225525,
0.03431519865989685,
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0.024901846423745155,
0.003338215872645378,
0.06444208323955536,
-0.03468841686844826,
0.00662977946922183,
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0.05332851782441139,
0.033879779279232025,
0.01726127229630947,
0.019842686131596565,
0.029027964919805527,
0.018380921334028244,
-0.02172950468957424,
-0.004844041541218758,
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11,073 | burnman.classes.planet | __init__ |
:param name: Name of planet.
:type name: str
:param layers: Layers to build the planet out of
(layers are sorted within the planet).
:type layers: list of :class:`burnman.Layer`
:param n_max_iterations: Maximum number of iterations to reach
self-consistent planet.
:type n_max_iterations: int
:param max_delta: Relative update to the center pressure of the planet between
iterations to stop iterations.
:type max_delta: float
| def __init__(
self, name, layers, n_max_iterations=50, max_delta=1.0e-5, verbose=False
):
"""
:param name: Name of planet.
:type name: str
:param layers: Layers to build the planet out of
(layers are sorted within the planet).
:type layers: list of :class:`burnman.Layer`
:param n_max_iterations: Maximum number of iterations to reach
self-consistent planet.
:type n_max_iterations: int
:param max_delta: Relative update to the center pressure of the planet between
iterations to stop iterations.
:type max_delta: float
"""
# sort layers
self.layers = sorted(layers, key=lambda x: x.inner_radius)
# assert layers attach to one another
if len(self.layers) > 1:
for i in range(1, len(self.layers)):
assert self.layers[i].inner_radius == self.layers[i - 1].outer_radius
self.name = name
self.radii = self.evaluate(["radii"])
self.n_slices = len(self.radii)
self.radius_planet = max(self.radii)
self.volume = 4.0 / 3.0 * np.pi * np.power(self.radius_planet, 3.0)
for layer in self.layers:
layer.n_start = np.where(self.radii == layer.inner_radius)[0][-1]
layer.n_end = np.where(self.radii == layer.outer_radius)[0][0] + 1
self._cached = {}
self.verbose = verbose
self.set_pressure_mode(n_max_iterations=n_max_iterations, max_delta=max_delta)
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11,074 | burnman.classes.planet | __iter__ |
Planet object will iterate over Layers.
| def __iter__(self):
"""
Planet object will iterate over Layers.
"""
return list(self.layers).__iter__()
| (self) | [
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] |
11,075 | burnman.classes.planet | __str__ |
Prints details of the planet
| def __str__(self):
"""
Prints details of the planet
"""
writing = "{0} consists of {1} layers:\n".format(self.name, len(self.layers))
for layer in self:
writing = writing + layer.__str__()
return writing
| (self) | [
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] |
11,076 | burnman.classes.planet | _compute_gravity |
Calculate the gravity of the planet, based on a density profile.
This integrates Poisson's equation in radius, under the assumption
that the planet is laterally homogeneous.
Used to update the gravity profile in _evaluate_eos()
| def _compute_gravity(self, density, gravity_bottom):
"""
Calculate the gravity of the planet, based on a density profile.
This integrates Poisson's equation in radius, under the assumption
that the planet is laterally homogeneous.
Used to update the gravity profile in _evaluate_eos()
"""
start_gravity = gravity_bottom
grav = []
for layer in self.layers:
grav.extend(
layer._compute_gravity(
density[layer.n_start : layer.n_end], start_gravity
)
)
start_gravity = grav[-1]
return np.array(grav)
| (self, density, gravity_bottom) | [
0.06810642033815384,
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0.0002899034006986767,
0.014599427580833435,
0.0023862700909376144,
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11,077 | burnman.classes.planet | _compute_pressure |
Calculate the pressure profile based on density and gravity.
This integrates the equation for hydrostatic equilibrium P = rho g z.
Used to update the pressure profile in _evaluate_eos()
| def _compute_pressure(self, density, gravity, pressure_top):
"""
Calculate the pressure profile based on density and gravity.
This integrates the equation for hydrostatic equilibrium P = rho g z.
Used to update the pressure profile in _evaluate_eos()
"""
start_pressure = pressure_top
press = []
for layer in self.layers[::-1]:
press.extend(
layer._compute_pressure(
density[layer.n_start : layer.n_end],
gravity[layer.n_start : layer.n_end],
start_pressure,
)[::-1]
)
start_pressure = press[-1]
return np.array(press)[::-1]
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] |
11,078 | burnman.classes.planet | _evaluate_density |
Used to update the density profile in _evaluate_eos()
| def _evaluate_density(self, pressures, temperatures):
"""
Used to update the density profile in _evaluate_eos()
"""
density = []
for layer in self.layers:
density.append(
layer.material.evaluate(
["density"],
pressures[layer.n_start : layer.n_end],
temperatures[layer.n_start : layer.n_end],
)
)
return np.squeeze(np.hstack(density))
| (self, pressures, temperatures) | [
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11,079 | burnman.classes.planet | _evaluate_eos |
Used to update the pressure profile in set_state()
| def _evaluate_eos(self, pressures, temperatures, gravity_bottom, pressure_top):
"""
Used to update the pressure profile in set_state()
"""
density = self._evaluate_density(pressures, temperatures)
grav = self._compute_gravity(density, gravity_bottom)
press = self._compute_pressure(density, grav, pressure_top)
return grav, press
| (self, pressures, temperatures, gravity_bottom, pressure_top) | [
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] |
11,080 | burnman.classes.planet | _evaluate_temperature |
Returns the temperatures of different layers for given pressures.
Used by set_state()
| def _evaluate_temperature(self, pressures):
"""
Returns the temperatures of different layers for given pressures.
Used by set_state()
"""
temps = []
temperature_top = None
for layer in self.layers[::-1]:
if temperature_top is None or layer.temperature_top is not None:
temperature_top = layer.temperature_top
temps.extend(
layer._evaluate_temperature(
(pressures[layer.n_start : layer.n_end]), temperature_top
)[::-1]
)
temperature_top = temps[-1]
return np.hstack(np.squeeze(temps))[::-1]
| (self, pressures) | [
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-0.07698752731084824,
0.022717341780662537,
0.03164137899875641,
0.002605057554319501,
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] |
11,081 | burnman.classes.planet | evaluate |
Function that is generally used to evaluate properties
of the different layers and stitch them together.
If asking for different radii than the internal radlist,
pressure and temperature values are interpolated and the
layer material evaluated at those pressures and
temperatures.
:param properties: List of properties to evaluate
:type properties: list of strings
:param radlist: Radii to evaluate properties at. If left empty,
internal radius lists are used.
:type radlist: array of floats
:returns: 1D or 2D array of requested properties
(1D if only one property was requested)
:rtype: numpy.array
| def evaluate(self, properties, radlist=None):
"""
Function that is generally used to evaluate properties
of the different layers and stitch them together.
If asking for different radii than the internal radlist,
pressure and temperature values are interpolated and the
layer material evaluated at those pressures and
temperatures.
:param properties: List of properties to evaluate
:type properties: list of strings
:param radlist: Radii to evaluate properties at. If left empty,
internal radius lists are used.
:type radlist: array of floats
:returns: 1D or 2D array of requested properties
(1D if only one property was requested)
:rtype: numpy.array
"""
if radlist is None:
values = np.empty(
[len(properties), np.sum([len(layer.radii) for layer in self.layers])]
)
for i, prop in enumerate(properties):
if prop == "depth":
values[i] = np.array(
[
self.radius_planet - r
for layer in self.layers
for r in layer.radii
]
)
else:
j = 0
for layer in self.layers:
vals = getattr(layer, prop)
values[i, j : j + len(vals)] = vals
j += len(vals)
else:
values = np.empty([len(properties), len(radlist)])
l_idx = [
i
for i, layer in enumerate(self.layers)
for r in radlist
if r >= layer.inner_radius and r <= layer.outer_radius
]
for j, r in enumerate(radlist):
values[:, j] = (
self.layers[l_idx[j]]
.evaluate(properties, [r], self.radius_planet)
.T[0]
)
if values.shape[0] == 1:
values = values[0]
return values
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11,082 | burnman.classes.planet | get_layer |
Returns a layer with a given name
:param name: Given name of a layer
:type name: str
:returns: Layer with the given name.
:rtype: :class:`burnman.Layer`
| def get_layer(self, name):
"""
Returns a layer with a given name
:param name: Given name of a layer
:type name: str
:returns: Layer with the given name.
:rtype: :class:`burnman.Layer`
"""
for layer in self.layers:
if layer.name == name:
return layer
raise LookupError()
| (self, name) | [
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11,083 | burnman.classes.planet | get_layer_by_radius |
Returns a layer in which this radius lies
:param radius: Radius at which to evaluate the layer.
:type radius: float
:returns: Layer in which the radius lies.
:rtype: :class:`burnman.Layer`
| def get_layer_by_radius(self, radius):
"""
Returns a layer in which this radius lies
:param radius: Radius at which to evaluate the layer.
:type radius: float
:returns: Layer in which the radius lies.
:rtype: :class:`burnman.Layer`
"""
for layer in self.layers:
if layer.outer_radius >= radius:
return layer
raise LookupError()
| (self, radius) | [
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] |
11,084 | burnman.classes.planet | make |
This routine needs to be called before evaluating any properties.
If pressures and temperatures are self-consistent, they
are computed across the planet here. Also initializes an array of materials
in each Layer to compute properties from.
| def make(self):
"""
This routine needs to be called before evaluating any properties.
If pressures and temperatures are self-consistent, they
are computed across the planet here. Also initializes an array of materials
in each Layer to compute properties from.
"""
self.reset()
for layer in self.layers:
assert layer.temperature_mode is not None
if self.pressure_mode == "user-defined":
self._temperatures = self._evaluate_temperature(self._pressures)
if self.pressure_mode == "self-consistent":
new_press = (
self.pressure_top + (-self.radii + max(self.radii)) * 1.0e3
) # initial pressure curve guess
temperatures = self._evaluate_temperature(new_press)
# Make it self-consistent!!!
i = 0
while i < self.n_max_iterations:
i += 1
ref_press = new_press
new_grav, new_press = self._evaluate_eos(
new_press, temperatures, self.gravity_bottom, self.pressure_top
)
temperatures = self._evaluate_temperature(new_press)
rel_err = abs((max(ref_press) - max(new_press)) / max(new_press))
if self.verbose:
print(
f"Iteration {i:0d} maximum relative pressure error: "
f"{rel_err:.1e}"
)
if rel_err < self.max_delta:
break
self.pressures = new_press
self.temperatures = temperatures
self._gravity = new_grav
for layer in self.layers:
layer.sublayers = []
layer.pressures = self.pressures[layer.n_start : layer.n_end]
layer.temperatures = self.temperatures[layer.n_start : layer.n_end]
layer.gravity_bottom = self._gravity[layer.n_start - 1]
layer.pressure_mode = "set-in-planet"
for i in range(len(layer.radii)):
layer.sublayers.append(layer.material.copy())
layer.sublayers[i].set_state(layer.pressures[i], layer.temperatures[i])
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11,085 | burnman.classes.planet | reset |
Resets all cached material properties.
It is typically not required for the user to call this function.
| def reset(self):
"""
Resets all cached material properties.
It is typically not required for the user to call this function.
"""
self._cached = {}
| (self) | [
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11,086 | burnman.classes.planet | set_pressure_mode |
Sets the pressure mode of the planet by user-defined values are in a
self-consistent fashion.
pressure_mode is 'user-defined' or 'self-consistent'.
The default for the planet is self-consistent, with zero pressure at
the surface and zero pressure at the center.
:param pressure_mode: This can be set to 'user-defined' or 'self-consistent'.
:type pressure_mode: str
:param pressures: Pressures (Pa) to set layer to ('user-defined').
This should be the same length as defined radius array for the layer.
:type pressures: array of floats
:param pressure_top: Pressure (Pa) at the top of the layer.
:type pressure_top: float
:param gravity_bottom: Gravity (m/s^2) at the bottom the layer
:type gravity_bottom: float
:param n_max_iterations: Maximum number of iterations to reach
self-consistent pressures.
:type n_max_iterations: int
| def set_pressure_mode(
self,
pressure_mode="self-consistent",
pressures=None,
pressure_top=0.0,
gravity_bottom=0.0,
n_max_iterations=50,
max_delta=1.0e-5,
):
"""
Sets the pressure mode of the planet by user-defined values are in a
self-consistent fashion.
pressure_mode is 'user-defined' or 'self-consistent'.
The default for the planet is self-consistent, with zero pressure at
the surface and zero pressure at the center.
:param pressure_mode: This can be set to 'user-defined' or 'self-consistent'.
:type pressure_mode: str
:param pressures: Pressures (Pa) to set layer to ('user-defined').
This should be the same length as defined radius array for the layer.
:type pressures: array of floats
:param pressure_top: Pressure (Pa) at the top of the layer.
:type pressure_top: float
:param gravity_bottom: Gravity (m/s^2) at the bottom the layer
:type gravity_bottom: float
:param n_max_iterations: Maximum number of iterations to reach
self-consistent pressures.
:type n_max_iterations: int
"""
self.reset()
assert pressure_mode == "user-defined" or pressure_mode == "self-consistent"
self.pressure_mode = pressure_mode
self.gravity_bottom = gravity_bottom
if pressure_mode == "user-defined":
assert len(pressures) == len(self.radii)
self._pressures = pressures
warnings.warn(
"User-defined pressures mean that the planet is "
"unlikely to be self-consistent"
)
if pressure_mode == "self-consistent":
self.pressure_top = pressure_top
self.n_max_iterations = n_max_iterations
self.max_delta = max_delta
| (self, pressure_mode='self-consistent', pressures=None, pressure_top=0.0, gravity_bottom=0.0, n_max_iterations=50, max_delta=1e-05) | [
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11,087 | burnman.classes.solution | Solution |
This is the base class for all solutions.
Site occupancies, endmember activities and the constant
and pressure and temperature dependencies of the excess
properties can be queried after using set_composition().
States of the solution can only be queried after setting
the pressure, temperature and composition using set_state().
This class is available as :class:`burnman.Solution`.
It uses an instance of :class:`burnman.SolutionModel` to
calculate interaction terms between endmembers.
All the solution parameters are expected to be in SI units. This
means that the interaction parameters should be in J/mol, with the T
and P derivatives in J/K/mol and m^3/mol.
The parameters are relevant to all solution models. Please
see the documentation for individual models for details about
other parameters.
:param name: Name of the solution.
:type name: string
:param solution_model: The SolutionModel object defining the properties
of the solution.
:type solution_model: :class:`burnman.SolutionModel`
:param molar_fractions: The molar fractions of each endmember in the solution.
Can be reset using the set_composition() method.
:type molar_fractions: numpy.array
| class Solution(Mineral):
"""
This is the base class for all solutions.
Site occupancies, endmember activities and the constant
and pressure and temperature dependencies of the excess
properties can be queried after using set_composition().
States of the solution can only be queried after setting
the pressure, temperature and composition using set_state().
This class is available as :class:`burnman.Solution`.
It uses an instance of :class:`burnman.SolutionModel` to
calculate interaction terms between endmembers.
All the solution parameters are expected to be in SI units. This
means that the interaction parameters should be in J/mol, with the T
and P derivatives in J/K/mol and m^3/mol.
The parameters are relevant to all solution models. Please
see the documentation for individual models for details about
other parameters.
:param name: Name of the solution.
:type name: string
:param solution_model: The SolutionModel object defining the properties
of the solution.
:type solution_model: :class:`burnman.SolutionModel`
:param molar_fractions: The molar fractions of each endmember in the solution.
Can be reset using the set_composition() method.
:type molar_fractions: numpy.array
"""
def __init__(self, name=None, solution_model=None, molar_fractions=None):
"""
Set up matrices to speed up calculations for when P, T, X is defined.
"""
Mineral.__init__(self)
# Solution needs a method attribute to call Mineral.set_state().
# Note that set_method() below will not change self.method
self.method = "SolutionMethod"
if name is not None:
self.name = name
if solution_model is not None:
self.solution_model = solution_model
# Equation of state
for i in range(self.n_endmembers):
self.solution_model.endmembers[i][0].set_method(
self.solution_model.endmembers[i][0].params["equation_of_state"]
)
# Molar fractions
if molar_fractions is not None:
self.set_composition(molar_fractions)
@cached_property
def endmembers(self):
return self.solution_model.endmembers
def set_composition(self, molar_fractions):
"""
Set the composition for this solution.
Resets cached properties.
:param molar_fractions: Molar abundance for each endmember, needs to sum to one.
:type molar_fractions: list of float
"""
assert len(self.solution_model.endmembers) == len(molar_fractions)
if type(self.solution_model) != MechanicalSolution:
assert sum(molar_fractions) > 0.9999
assert sum(molar_fractions) < 1.0001
if type(self.solution_model) == PolynomialSolution:
self.solution_model.set_composition(molar_fractions)
self.reset()
self.molar_fractions = np.array(molar_fractions)
def set_method(self, method):
for i in range(self.n_endmembers):
self.solution_model.endmembers[i][0].set_method(method)
# note: do not set self.method here!
self.reset()
def set_state(self, pressure, temperature):
if type(self.solution_model) == PolynomialSolution:
self.solution_model.set_state(pressure, temperature)
Mineral.set_state(self, pressure, temperature)
for i in range(self.n_endmembers):
self.solution_model.endmembers[i][0].set_state(pressure, temperature)
@material_property
def formula(self):
"""
Returns molar chemical formula of the solution.
:rtype: Counter
"""
return sum_formulae(self.endmember_formulae, self.molar_fractions)
@material_property
def site_occupancies(self):
"""
:returns: The fractional occupancies of species on each site.
:rtype: list of OrderedDicts
"""
occs = np.einsum(
"ij, i", self.solution_model.endmember_occupancies, self.molar_fractions
)
site_occs = []
k = 0
for i in range(self.solution_model.n_sites):
site_occs.append(OrderedDict())
for j in range(len(self.solution_model.sites[i])):
site_occs[-1][self.solution_model.sites[i][j]] = occs[k]
k += 1
return site_occs
def site_formula(self, precision=2):
"""
Returns the molar chemical formula of the solution with site occupancies.
For example, [Mg0.4Fe0.6]2SiO4.
:param precision: Precision with which to print the site occupancies
:type precision: int
:returns: Molar chemical formula of the solution with site occupancies
:rtype: str
"""
split_empty = self.solution_model.empty_formula.split("[")
formula = split_empty[0]
for i, site_occs in enumerate(self.site_occupancies):
formula += "["
for species, occ in site_occs.items():
formula += f"{species}{occ:0.{precision}f}"
formula += split_empty[i + 1]
return formula
@material_property
def activities(self):
"""
Returns a list of endmember activities [unitless].
"""
return self.solution_model.activities(
self.pressure, self.temperature, self.molar_fractions
)
@material_property
def activity_coefficients(self):
"""
Returns a list of endmember activity coefficients
(gamma = activity / ideal activity) [unitless].
"""
return self.solution_model.activity_coefficients(
self.pressure, self.temperature, self.molar_fractions
)
@material_property
def molar_internal_energy(self):
"""
Returns molar internal energy of the mineral [J/mol].
Aliased with self.energy
"""
return self.molar_helmholtz + self.temperature * self.molar_entropy
@material_property
def excess_partial_gibbs(self):
"""
Returns excess partial molar gibbs free energy [J/mol].
Property specific to solutions.
"""
return self.solution_model.excess_partial_gibbs_free_energies(
self.pressure, self.temperature, self.molar_fractions
)
@material_property
def excess_partial_volumes(self):
"""
Returns excess partial volumes [m^3].
Property specific to solutions.
"""
return self.solution_model.excess_partial_volumes(
self.pressure, self.temperature, self.molar_fractions
)
@material_property
def excess_partial_entropies(self):
"""
Returns excess partial entropies [J/K].
Property specific to solutions.
"""
return self.solution_model.excess_partial_entropies(
self.pressure, self.temperature, self.molar_fractions
)
@material_property
def partial_gibbs(self):
"""
Returns endmember partial molar gibbs free energy [J/mol].
Property specific to solutions.
"""
return (
np.array(
[
self.solution_model.endmembers[i][0].gibbs
for i in range(self.n_endmembers)
]
)
+ self.excess_partial_gibbs
)
@material_property
def partial_volumes(self):
"""
Returns endmember partial volumes [m^3].
Property specific to solutions.
"""
return (
np.array(
[
self.solution_model.endmembers[i][0].molar_volume
for i in range(self.n_endmembers)
]
)
+ self.excess_partial_volumes
)
@material_property
def partial_entropies(self):
"""
Returns endmember partial entropies [J/K].
Property specific to solutions.
"""
return (
np.array(
[
self.solution_model.endmembers[i][0].molar_entropy
f | (name=None, solution_model=None, molar_fractions=None) | [
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11,088 | burnman.classes.solution | __init__ |
Set up matrices to speed up calculations for when P, T, X is defined.
| def __init__(self, name=None, solution_model=None, molar_fractions=None):
"""
Set up matrices to speed up calculations for when P, T, X is defined.
"""
Mineral.__init__(self)
# Solution needs a method attribute to call Mineral.set_state().
# Note that set_method() below will not change self.method
self.method = "SolutionMethod"
if name is not None:
self.name = name
if solution_model is not None:
self.solution_model = solution_model
# Equation of state
for i in range(self.n_endmembers):
self.solution_model.endmembers[i][0].set_method(
self.solution_model.endmembers[i][0].params["equation_of_state"]
)
# Molar fractions
if molar_fractions is not None:
self.set_composition(molar_fractions)
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] |
11,094 | burnman.classes.solution | set_composition |
Set the composition for this solution.
Resets cached properties.
:param molar_fractions: Molar abundance for each endmember, needs to sum to one.
:type molar_fractions: list of float
| def set_composition(self, molar_fractions):
"""
Set the composition for this solution.
Resets cached properties.
:param molar_fractions: Molar abundance for each endmember, needs to sum to one.
:type molar_fractions: list of float
"""
assert len(self.solution_model.endmembers) == len(molar_fractions)
if type(self.solution_model) != MechanicalSolution:
assert sum(molar_fractions) > 0.9999
assert sum(molar_fractions) < 1.0001
if type(self.solution_model) == PolynomialSolution:
self.solution_model.set_composition(molar_fractions)
self.reset()
self.molar_fractions = np.array(molar_fractions)
| (self, molar_fractions) | [
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11,096 | burnman.classes.solution | set_state | null | def set_state(self, pressure, temperature):
if type(self.solution_model) == PolynomialSolution:
self.solution_model.set_state(pressure, temperature)
Mineral.set_state(self, pressure, temperature)
for i in range(self.n_endmembers):
self.solution_model.endmembers[i][0].set_state(pressure, temperature)
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] |
11,098 | burnman.classes.solution | site_formula |
Returns the molar chemical formula of the solution with site occupancies.
For example, [Mg0.4Fe0.6]2SiO4.
:param precision: Precision with which to print the site occupancies
:type precision: int
:returns: Molar chemical formula of the solution with site occupancies
:rtype: str
| def site_formula(self, precision=2):
"""
Returns the molar chemical formula of the solution with site occupancies.
For example, [Mg0.4Fe0.6]2SiO4.
:param precision: Precision with which to print the site occupancies
:type precision: int
:returns: Molar chemical formula of the solution with site occupancies
:rtype: str
"""
split_empty = self.solution_model.empty_formula.split("[")
formula = split_empty[0]
for i, site_occs in enumerate(self.site_occupancies):
formula += "["
for species, occ in site_occs.items():
formula += f"{species}{occ:0.{precision}f}"
formula += split_empty[i + 1]
return formula
| (self, precision=2) | [
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11,116 | burnman.tools.partitioning | calculate_nakajima_fp_pv_partition_coefficient |
Calculate the partitioning of iron between periclase and bridgmanite as given
by Nakajima et al., 2012.
:param pressure: Equilibrium pressure [Pa]
:type pressure: float
:param temperature: Equilibrium temperature [K]
:type temperature: float
:param bulk_composition_mol: Bulk composition [mol].
Only Mg, Fe, and Si are assumed to explicitly affect the partitioning
with Al playing an implicit role.
:type bulk_composition_mol: dict
:param initial_distribution_coefficient: The distribution coefficient (Kd_0)
at 25 GPa and 0 K.
:type initial_distribution_coefficient: float
:returns: The proportion of Fe in ferropericlase and perovskite, respectively
:rtype: tuple
| def calculate_nakajima_fp_pv_partition_coefficient(
pressure, temperature, bulk_composition_mol, initial_distribution_coefficient
):
"""
Calculate the partitioning of iron between periclase and bridgmanite as given
by Nakajima et al., 2012.
:param pressure: Equilibrium pressure [Pa]
:type pressure: float
:param temperature: Equilibrium temperature [K]
:type temperature: float
:param bulk_composition_mol: Bulk composition [mol].
Only Mg, Fe, and Si are assumed to explicitly affect the partitioning
with Al playing an implicit role.
:type bulk_composition_mol: dict
:param initial_distribution_coefficient: The distribution coefficient (Kd_0)
at 25 GPa and 0 K.
:type initial_distribution_coefficient: float
:returns: The proportion of Fe in ferropericlase and perovskite, respectively
:rtype: tuple
"""
norm = bulk_composition_mol["Mg"] + bulk_composition_mol["Fe"]
f_FeO = bulk_composition_mol["Fe"] / norm
f_SiO2 = bulk_composition_mol["Si"] / norm
Kd_0 = initial_distribution_coefficient
delV = 2.0e-7 # in m^3/mol, average taken from Nakajima et al 2012, JGR
# eq 5 Nakajima et al 2012, JGR. Solved for ln(K(P,T,X))
rs = ((25.0e9 - pressure) * delV / (constants.gas_constant * temperature)) + np.log(
Kd_0
)
# The exchange coefficent at P and T. K(P,T,X) in eq 5 Nakajima et al 2012
K = np.exp(rs)
# Solving equation 6 in Nakajima et al., 2012 for X_Fe_fp and X_Fe_pv
# Solved using the definition of the distribution coefficient
# to define X_Fe_fp as a function of X_Fe_pv
num_to_sqrt = (-4.0 * f_FeO * (K - 1.0) * K * f_SiO2) + (
pow(1.0 + (f_FeO * (K - 1)) + ((K - 1.0) * f_SiO2), 2.0)
)
X_Fe_pv = (
-1.0 + f_FeO - (f_FeO * K) + f_SiO2 - (f_SiO2 * K) + np.sqrt(num_to_sqrt)
) / (2.0 * f_SiO2 * (1.0 - K))
X_Fe_fp = X_Fe_pv / (((1.0 - X_Fe_pv) * K) + X_Fe_pv)
return (X_Fe_fp, X_Fe_pv)
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11,118 | burnman.utils.unitcell | cell_parameters_to_vectors |
Converts cell parameters to unit cell vectors.
:param cell_parameters: An array containing the three lengths of the
unit cell vectors [m], and the three angles [degrees].
The first angle (:math:`\alpha`) corresponds to the angle between the
second and the third cell vectors, the second (:math:`\beta`) to the
angle between the first and third cell vectors, and the third
(:math:`\gamma`) to the angle between the first and second vectors.
:type cell_parameters: numpy.array (1D)
:returns: The three vectors defining the parallelopiped cell [m].
This function assumes that the first cell vector is colinear with the
x-axis, and the second is perpendicular to the z-axis, and the third is
defined in a right-handed sense.
:rtype: numpy.array (2D)
| def cell_parameters_to_vectors(cell_parameters):
"""
Converts cell parameters to unit cell vectors.
:param cell_parameters: An array containing the three lengths of the
unit cell vectors [m], and the three angles [degrees].
The first angle (:math:`\\alpha`) corresponds to the angle between the
second and the third cell vectors, the second (:math:`\\beta`) to the
angle between the first and third cell vectors, and the third
(:math:`\\gamma`) to the angle between the first and second vectors.
:type cell_parameters: numpy.array (1D)
:returns: The three vectors defining the parallelopiped cell [m].
This function assumes that the first cell vector is colinear with the
x-axis, and the second is perpendicular to the z-axis, and the third is
defined in a right-handed sense.
:rtype: numpy.array (2D)
"""
a, b, c, alpha_deg, beta_deg, gamma_deg = cell_parameters
alpha = np.radians(alpha_deg)
beta = np.radians(beta_deg)
gamma = np.radians(gamma_deg)
n2 = (np.cos(alpha) - np.cos(gamma) * np.cos(beta)) / np.sin(gamma)
M = np.array(
[
[a, 0, 0],
[b * np.cos(gamma), b * np.sin(gamma), 0],
[c * np.cos(beta), c * n2, c * np.sqrt(np.sin(beta) ** 2 - n2**2)],
]
)
return M
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] |
11,119 | burnman.utils.unitcell | cell_vectors_to_parameters |
Converts unit cell vectors to cell parameters.
:param M: The three vectors defining the parallelopiped cell [m].
This function assumes that the first cell vector is colinear with the
x-axis, the second is perpendicular to the z-axis, and the third is
defined in a right-handed sense.
:type M: numpy.array (2D)
:returns: An array containing the three lengths of the unit cell vectors [m],
and the three angles [degrees].
The first angle (:math:`\alpha`) corresponds to the angle between the
second and the third cell vectors, the second (:math:`\beta`) to the
angle between the first and third cell vectors, and the third
(:math:`\gamma`) to the angle between the first and second vectors.
:rtype: numpy.array (1D)
| def cell_vectors_to_parameters(M):
"""
Converts unit cell vectors to cell parameters.
:param M: The three vectors defining the parallelopiped cell [m].
This function assumes that the first cell vector is colinear with the
x-axis, the second is perpendicular to the z-axis, and the third is
defined in a right-handed sense.
:type M: numpy.array (2D)
:returns: An array containing the three lengths of the unit cell vectors [m],
and the three angles [degrees].
The first angle (:math:`\\alpha`) corresponds to the angle between the
second and the third cell vectors, the second (:math:`\\beta`) to the
angle between the first and third cell vectors, and the third
(:math:`\\gamma`) to the angle between the first and second vectors.
:rtype: numpy.array (1D)
"""
assert M[0, 1] == 0
assert M[0, 2] == 0
assert M[1, 2] == 0
a = M[0, 0]
b = np.sqrt(np.power(M[1, 0], 2.0) + np.power(M[1, 1], 2.0))
c = np.sqrt(
np.power(M[2, 0], 2.0) + np.power(M[2, 1], 2.0) + np.power(M[2, 2], 2.0)
)
gamma = np.arccos(M[1, 0] / b)
beta = np.arccos(M[2, 0] / c)
alpha = np.arccos(M[2, 1] / c * np.sin(gamma) + np.cos(gamma) * np.cos(beta))
gamma_deg = np.degrees(gamma)
beta_deg = np.degrees(beta)
alpha_deg = np.degrees(alpha)
return np.array([a, b, c, alpha_deg, beta_deg, gamma_deg])
| (M) | [
0.037104636430740356,
0.057343531399965286,
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0.016587737947702408,
0.003996347542852163,
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11,125 | burnman.tools.equilibration | equilibrate |
A function that finds the thermodynamic equilibrium state of an
assemblage subject to given equality constraints by solving a set of
nonlinear equations related to the chemical potentials and
other state variables of the system.
The user chooses an assemblage (e.g. olivine, garnet and orthopyroxene)
and :math:`2+n_c` equality constraints, where :math:`n_c` is the number of
bulk compositional degrees of freedom. The equilibrate function attempts to
find the remaining unknowns that satisfy those constraints.
There are a number of equality constraints implemented in burnman. These are
given as a list of lists. Each constraint should have the form:
[<constraint type>, <constraint>], where
<constraint type> is one of 'P', 'T', 'S', 'V', 'X', 'PT_ellipse',
'phase_fraction', or 'phase_composition'. The format of the
<constraint> object depends on the constraint type:
- P: float or numpy.array of
pressures [Pa]
- T: float or numpy.array of
temperatures [K]
- S: float or numpy.array of
entropies [J/K]
- V: float or numpy.array of
volumes [m:math:`^3`]
- PT_ellipse: list of two floats or numpy.arrays, where the equality
satifies the equation norm(([P, T] - arr[0])/arr[1]) = 1
- phase_fraction: tuple with the form (<phase> <fraction(s)>),
where <phase> is one of the phase objects in the assemblage
and <fraction(s)> is a float or numpy.array corresponding
to the desired phase fractions.
- phase_composition: tuple with the form (<phase> <constraint>),
where <phase> is one of the phase objects in the assemblage
and <constraint> has the form (site_names, n, d, v),
where :math:`(nx)/(dx) = v`, n and d are constant vectors of
site coefficients, and v is a float or numpy.array. For example,
a constraint of the form ([Mg_A, Fe_A], [1., 0.], [1., 1.], [0.5])
would correspond to equal amounts Mg and Fe on the A site
(Mg_A / (Mg_A + Fe_A) = 0.5).
- X: list of a numpy.array and a float or numpy.array,
where the equality satisfies the linear equation arr[0] x = arr[1].
The first numpy.array is fixed, and the second is to be looped over
by the equilibrate function.
This is a generic compositional equality constraint.
:param composition: The bulk composition that the assemblage must satisfy.
:type composition: dict
:param assemblage: The assemblage to be equilibrated.
:type assemblage: :class:`burnman.Composite`
:param equality_constraints: The list of equality constraints. See above
for valid formats.
:type equality_constraints: list of list
:param free_compositional_vectors: A list of dictionaries containing
the compositional freedom of the solution. For example, if the list
contains the vector {'Mg': 1., 'Fe': -1}, that implies that the bulk
composition is equal to composition + :math:`a` (n_Mg - n_Fe),
where the value of :math:`a` is to be determined by the solve.
Vector given in atomic (molar) units of elements.
:type free_compositional_vectors: list of dict
:param tol: The tolerance for the nonlinear solver.
:type tol: float
:param store_iterates: Whether to store the parameter values for
each iteration in each solution object.
:type store_iterates: bool
:param store_assemblage: Whether to store a copy of the assemblage
object in each solution object.
:type store_assemblage: bool
:param max_iterations: The maximum number of iterations for the
nonlinear solver.
:type max_iterations: int
:param verbose: Whether to print output updating the user on the status of
equilibration.
:type verbose: bool
:returns: Solver solution object (or a list, or a 2D list of solution objects)
created by :func:`burnman.optimize.nonlinear_solvers.damped_newton_solve`,
and a namedtuple object created by
:func:`burnman.tools.equilibration.get_equilibration_parameters`. See
documentation of these functions for the return types. If store_assemblage
is True, each solution object also has an attribute called `assemblage`,
which contains a copy of the input assemblage with the equilibrated
properties. So, for a 2D grid of solution objects, one could call either
sols[0][1].x[0] or sols[0][1].assemblage.pressure to get the pressure.
:rtype: tuple
| def equilibrate(
composition,
assemblage,
equality_constraints,
free_compositional_vectors=[],
tol=1.0e-3,
store_iterates=False,
store_assemblage=True,
max_iterations=100.0,
verbose=False,
):
"""
A function that finds the thermodynamic equilibrium state of an
assemblage subject to given equality constraints by solving a set of
nonlinear equations related to the chemical potentials and
other state variables of the system.
The user chooses an assemblage (e.g. olivine, garnet and orthopyroxene)
and :math:`2+n_c` equality constraints, where :math:`n_c` is the number of
bulk compositional degrees of freedom. The equilibrate function attempts to
find the remaining unknowns that satisfy those constraints.
There are a number of equality constraints implemented in burnman. These are
given as a list of lists. Each constraint should have the form:
[<constraint type>, <constraint>], where
<constraint type> is one of 'P', 'T', 'S', 'V', 'X', 'PT_ellipse',
'phase_fraction', or 'phase_composition'. The format of the
<constraint> object depends on the constraint type:
- P: float or numpy.array of
pressures [Pa]
- T: float or numpy.array of
temperatures [K]
- S: float or numpy.array of
entropies [J/K]
- V: float or numpy.array of
volumes [m:math:`^3`]
- PT_ellipse: list of two floats or numpy.arrays, where the equality
satifies the equation norm(([P, T] - arr[0])/arr[1]) = 1
- phase_fraction: tuple with the form (<phase> <fraction(s)>),
where <phase> is one of the phase objects in the assemblage
and <fraction(s)> is a float or numpy.array corresponding
to the desired phase fractions.
- phase_composition: tuple with the form (<phase> <constraint>),
where <phase> is one of the phase objects in the assemblage
and <constraint> has the form (site_names, n, d, v),
where :math:`(nx)/(dx) = v`, n and d are constant vectors of
site coefficients, and v is a float or numpy.array. For example,
a constraint of the form ([Mg_A, Fe_A], [1., 0.], [1., 1.], [0.5])
would correspond to equal amounts Mg and Fe on the A site
(Mg_A / (Mg_A + Fe_A) = 0.5).
- X: list of a numpy.array and a float or numpy.array,
where the equality satisfies the linear equation arr[0] x = arr[1].
The first numpy.array is fixed, and the second is to be looped over
by the equilibrate function.
This is a generic compositional equality constraint.
:param composition: The bulk composition that the assemblage must satisfy.
:type composition: dict
:param assemblage: The assemblage to be equilibrated.
:type assemblage: :class:`burnman.Composite`
:param equality_constraints: The list of equality constraints. See above
for valid formats.
:type equality_constraints: list of list
:param free_compositional_vectors: A list of dictionaries containing
the compositional freedom of the solution. For example, if the list
contains the vector {'Mg': 1., 'Fe': -1}, that implies that the bulk
composition is equal to composition + :math:`a` (n_Mg - n_Fe),
where the value of :math:`a` is to be determined by the solve.
Vector given in atomic (molar) units of elements.
:type free_compositional_vectors: list of dict
:param tol: The tolerance for the nonlinear solver.
:type tol: float
:param store_iterates: Whether to store the parameter values for
each iteration in each solution object.
:type store_iterates: bool
:param store_assemblage: Whether to store a copy of the assemblage
object in each solution object.
:type store_assemblage: bool
:param max_iterations: The maximum number of iterations for the
nonlinear solver.
:type max_iterations: int
:param verbose: Whether to print output updating the user on the status of
equilibration.
:type verbose: bool
:returns: Solver solution object (or a list, or a 2D list of solution objects)
created by :func:`burnman.optimize.nonlinear_solvers.damped_newton_solve`,
and a namedtuple object created by
:func:`burnman.tools.equilibration.get_equilibration_parameters`. See
documentation of these functions for the return types. If store_assemblage
is True, each solution object also has an attribute called `assemblage`,
which contains a copy of the input assemblage with the equilibrated
properties. So, for a 2D grid of solution objects, one could call either
sols[0][1].x[0] or sols[0][1].assemblage.pressure to get the pressure.
:rtype: tuple
"""
for ph in assemblage.phases:
if isinstance(ph, Solution) and not hasattr(ph, "molar_fractions"):
raise Exception(
f"set_composition for solution {ph} before running equilibrate."
)
if assemblage.molar_fractions is None:
n_phases = len(assemblage.phases)
f = 1.0 / float(n_phases)
assemblage.set_fractions([f for i in range(n_phases)])
assemblage.n_moles = sum(composition.values()) / sum(assemblage.formula.values())
n_equality_constraints = len(equality_constraints)
n_free_compositional_vectors = len(free_compositional_vectors)
if n_equality_constraints != n_free_compositional_vectors + 2:
raise Exception(
"The number of equality constraints "
f"(currently {n_equality_constraints}) "
"must be two more than the number of "
"free_compositional vectors "
f"(currently {n_free_compositional_vectors})."
)
for v in free_compositional_vectors:
if np.abs(sum(v.values())) > 1.0e-12:
raise Exception(
"The amounts of each free_compositional_vector" "must sum to zero"
)
# Make parameter tuple
prm = get_equilibration_parameters(
assemblage, composition, free_compositional_vectors
)
# Check equality constraints have the correct structure
# Convert into the format readable by the function and jacobian functions
eq_constraint_lists = process_eq_constraints(equality_constraints, assemblage, prm)
# Set up solves
nc = [len(eq_constraint_list) for eq_constraint_list in eq_constraint_lists]
# Find the initial state (could be none here)
initial_state = [assemblage.pressure, assemblage.temperature]
# Reset initial state if equality constraints
# are related to pressure or temperature
for i in range(n_equality_constraints):
if eq_constraint_lists[i][0][0] == "P":
initial_state[0] = eq_constraint_lists[i][0][1]
elif eq_constraint_lists[i][0][0] == "T":
initial_state[1] = eq_constraint_lists[i][0][1]
elif eq_constraint_lists[i][0][0] == "PT_ellipse":
initial_state = eq_constraint_lists[i][0][1][1]
if initial_state[0] is None:
initial_state[0] = 5.0e9
if initial_state[1] is None:
initial_state[1] = 1200.0
assemblage.set_state(*initial_state)
parameters = get_parameters(assemblage, n_free_compositional_vectors)
# Solve the system of equations, loop over input parameters
sol_array = np.empty(shape=tuple(nc), dtype="object")
# Loop over problems
problems = list(product(*[list(range(nc[i])) for i in range(len(nc))]))
n_problems = len(problems)
for i_problem, i_c in enumerate(problems):
if verbose:
string = "Processing solution"
for i in range(len(i_c)):
string += " {0}/{1}".format(i_c[i] + 1, nc[i])
print(string + ":")
equality_constraints = [eq_constraint_lists[i][i_c[i]] for i in range(len(nc))]
# Set the initial fractions and compositions
# of the phases in the assemblage:
sol = damped_newton_solve(
F=lambda x: F(
x,
assemb | (composition, assemblage, equality_constraints, free_compositional_vectors=[], tol=0.001, store_iterates=False, store_assemblage=True, max_iterations=100.0, verbose=False) | [
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] |
11,129 | burnman.classes.material | material_property |
Decorator @material_property to be used for cached properties of materials.
To be used on function in Material or derived classes that should be exposed
as read-only properties that are cached. The function Material.reset() will
reset the cached values.
Internally, the values are stored in a dictionary member called _cached, which
is emptied by .reset().
| def material_property(func):
"""
Decorator @material_property to be used for cached properties of materials.
To be used on function in Material or derived classes that should be exposed
as read-only properties that are cached. The function Material.reset() will
reset the cached values.
Internally, the values are stored in a dictionary member called _cached, which
is emptied by .reset().
"""
class mat_obj:
def __init__(self, func):
self.func = func
self.varname = self.func.__name__
def get(self, obj):
if not hasattr(obj, "_cached"):
raise Exception(
"The material_property decorator could not find "
"class member _cached. "
"Did you forget to call Material.__init__(self) in __init___?"
)
cache_array = getattr(obj, "_cached")
if self.varname not in cache_array:
cache_array[self.varname] = self.func(obj)
return cache_array[self.varname]
return property(mat_obj(func).get, doc=func.__doc__)
| (func) | [
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0.031918130815029144,
-0.006999513134360313,
0.01235259510576725
] |
11,137 | smtpapi | SMTPAPIHeader | null | class SMTPAPIHeader(object):
def __init__(self):
self.data = {}
def add_to(self, to):
if 'to' not in self.data:
self.data['to'] = []
if type(to) is list:
self.data['to'] += to
else:
self.data['to'].append(to)
def set_tos(self, tos):
self.data['to'] = tos
def add_substitution(self, key, value):
if 'sub' not in self.data:
self.data['sub'] = {}
if key not in self.data['sub']:
self.data['sub'][key] = []
self.data['sub'][key].append(value)
def set_substitutions(self, subs):
self.data['sub'] = subs
def _add_key_value(self, index, key, value):
if index not in self.data:
self.data[index] = {}
self.data[index][key] = value
def _add_key(self, index, key):
if index not in self.data:
self.data[index] = []
self.data[index].append(key)
def add_unique_arg(self, key, value):
self._add_key_value('unique_args', key, value)
def set_unique_args(self, value):
self.data['unique_args'] = value
def add_category(self, category):
self._add_key('category', category)
def set_categories(self, category):
self.data['category'] = category
def add_section(self, key, section):
self._add_key_value('section', key, section)
def set_sections(self, value):
self.data['section'] = value
def add_send_each_at(self, time):
self._add_key('send_each_at', time)
def set_send_each_at(self, time):
self.data['send_each_at'] = time
def set_send_at(self, time):
self.data['send_at'] = time
def add_filter(self, app, setting, val):
if 'filters' not in self.data:
self.data['filters'] = {}
if app not in self.data['filters']:
self.data['filters'][app] = {}
if 'settings' not in self.data['filters'][app]:
self.data['filters'][app]['settings'] = {}
self.data['filters'][app]['settings'][setting] = val
def set_asm_group_id(self, value):
if not bool(value):
self.data['asm_group_id'] = {}
else:
self.data['asm_group_id'] = value
def set_ip_pool(self, value):
if bool(value):
self.data['ip_pool'] = value
else:
self.data['ip_pool'] = {}
def json_string(self):
result = {}
for key in self.data.keys():
if self.data[key] != [] and self.data[key] != {}:
result[key] = self.data[key]
return json.dumps(result, cls=_CustomJSONEncoder)
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11,138 | smtpapi | __init__ | null | def __init__(self):
self.data = {}
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11,139 | smtpapi | _add_key | null | def _add_key(self, index, key):
if index not in self.data:
self.data[index] = []
self.data[index].append(key)
| (self, index, key) | [
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11,140 | smtpapi | _add_key_value | null | def _add_key_value(self, index, key, value):
if index not in self.data:
self.data[index] = {}
self.data[index][key] = value
| (self, index, key, value) | [
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] |
11,141 | smtpapi | add_category | null | def add_category(self, category):
self._add_key('category', category)
| (self, category) | [
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11,142 | smtpapi | add_filter | null | def add_filter(self, app, setting, val):
if 'filters' not in self.data:
self.data['filters'] = {}
if app not in self.data['filters']:
self.data['filters'][app] = {}
if 'settings' not in self.data['filters'][app]:
self.data['filters'][app]['settings'] = {}
self.data['filters'][app]['settings'][setting] = val
| (self, app, setting, val) | [
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11,143 | smtpapi | add_section | null | def add_section(self, key, section):
self._add_key_value('section', key, section)
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11,144 | smtpapi | add_send_each_at | null | def add_send_each_at(self, time):
self._add_key('send_each_at', time)
| (self, time) | [
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11,145 | smtpapi | add_substitution | null | def add_substitution(self, key, value):
if 'sub' not in self.data:
self.data['sub'] = {}
if key not in self.data['sub']:
self.data['sub'][key] = []
self.data['sub'][key].append(value)
| (self, key, value) | [
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11,146 | smtpapi | add_to | null | def add_to(self, to):
if 'to' not in self.data:
self.data['to'] = []
if type(to) is list:
self.data['to'] += to
else:
self.data['to'].append(to)
| (self, to) | [
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11,147 | smtpapi | add_unique_arg | null | def add_unique_arg(self, key, value):
self._add_key_value('unique_args', key, value)
| (self, key, value) | [
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11,148 | smtpapi | json_string | null | def json_string(self):
result = {}
for key in self.data.keys():
if self.data[key] != [] and self.data[key] != {}:
result[key] = self.data[key]
return json.dumps(result, cls=_CustomJSONEncoder)
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] |
11,149 | smtpapi | set_asm_group_id | null | def set_asm_group_id(self, value):
if not bool(value):
self.data['asm_group_id'] = {}
else:
self.data['asm_group_id'] = value
| (self, value) | [
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11,150 | smtpapi | set_categories | null | def set_categories(self, category):
self.data['category'] = category
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11,151 | smtpapi | set_ip_pool | null | def set_ip_pool(self, value):
if bool(value):
self.data['ip_pool'] = value
else:
self.data['ip_pool'] = {}
| (self, value) | [
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11,152 | smtpapi | set_sections | null | def set_sections(self, value):
self.data['section'] = value
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11,153 | smtpapi | set_send_at | null | def set_send_at(self, time):
self.data['send_at'] = time
| (self, time) | [
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] |
11,154 | smtpapi | set_send_each_at | null | def set_send_each_at(self, time):
self.data['send_each_at'] = time
| (self, time) | [
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11,155 | smtpapi | set_substitutions | null | def set_substitutions(self, subs):
self.data['sub'] = subs
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11,156 | smtpapi | set_tos | null | def set_tos(self, tos):
self.data['to'] = tos
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] |
11,157 | smtpapi | set_unique_args | null | def set_unique_args(self, value):
self.data['unique_args'] = value
| (self, value) | [
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11,158 | smtpapi | _CustomJSONEncoder | null | class _CustomJSONEncoder(json.JSONEncoder):
def default(self, o):
if isinstance(o, decimal.Decimal):
return float(o)
# Provide a fallback to the default encoder if we haven't implemented
# special support for the object's class
return super(_CustomJSONEncoder, self).default(o)
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] |
11,159 | json.encoder | __init__ | Constructor for JSONEncoder, with sensible defaults.
If skipkeys is false, then it is a TypeError to attempt
encoding of keys that are not str, int, float or None. If
skipkeys is True, such items are simply skipped.
If ensure_ascii is true, the output is guaranteed to be str
objects with all incoming non-ASCII characters escaped. If
ensure_ascii is false, the output can contain non-ASCII characters.
If check_circular is true, then lists, dicts, and custom encoded
objects will be checked for circular references during encoding to
prevent an infinite recursion (which would cause an RecursionError).
Otherwise, no such check takes place.
If allow_nan is true, then NaN, Infinity, and -Infinity will be
encoded as such. This behavior is not JSON specification compliant,
but is consistent with most JavaScript based encoders and decoders.
Otherwise, it will be a ValueError to encode such floats.
If sort_keys is true, then the output of dictionaries will be
sorted by key; this is useful for regression tests to ensure
that JSON serializations can be compared on a day-to-day basis.
If indent is a non-negative integer, then JSON array
elements and object members will be pretty-printed with that
indent level. An indent level of 0 will only insert newlines.
None is the most compact representation.
If specified, separators should be an (item_separator, key_separator)
tuple. The default is (', ', ': ') if *indent* is ``None`` and
(',', ': ') otherwise. To get the most compact JSON representation,
you should specify (',', ':') to eliminate whitespace.
If specified, default is a function that gets called for objects
that can't otherwise be serialized. It should return a JSON encodable
version of the object or raise a ``TypeError``.
| def __init__(self, *, skipkeys=False, ensure_ascii=True,
check_circular=True, allow_nan=True, sort_keys=False,
indent=None, separators=None, default=None):
"""Constructor for JSONEncoder, with sensible defaults.
If skipkeys is false, then it is a TypeError to attempt
encoding of keys that are not str, int, float or None. If
skipkeys is True, such items are simply skipped.
If ensure_ascii is true, the output is guaranteed to be str
objects with all incoming non-ASCII characters escaped. If
ensure_ascii is false, the output can contain non-ASCII characters.
If check_circular is true, then lists, dicts, and custom encoded
objects will be checked for circular references during encoding to
prevent an infinite recursion (which would cause an RecursionError).
Otherwise, no such check takes place.
If allow_nan is true, then NaN, Infinity, and -Infinity will be
encoded as such. This behavior is not JSON specification compliant,
but is consistent with most JavaScript based encoders and decoders.
Otherwise, it will be a ValueError to encode such floats.
If sort_keys is true, then the output of dictionaries will be
sorted by key; this is useful for regression tests to ensure
that JSON serializations can be compared on a day-to-day basis.
If indent is a non-negative integer, then JSON array
elements and object members will be pretty-printed with that
indent level. An indent level of 0 will only insert newlines.
None is the most compact representation.
If specified, separators should be an (item_separator, key_separator)
tuple. The default is (', ', ': ') if *indent* is ``None`` and
(',', ': ') otherwise. To get the most compact JSON representation,
you should specify (',', ':') to eliminate whitespace.
If specified, default is a function that gets called for objects
that can't otherwise be serialized. It should return a JSON encodable
version of the object or raise a ``TypeError``.
"""
self.skipkeys = skipkeys
self.ensure_ascii = ensure_ascii
self.check_circular = check_circular
self.allow_nan = allow_nan
self.sort_keys = sort_keys
self.indent = indent
if separators is not None:
self.item_separator, self.key_separator = separators
elif indent is not None:
self.item_separator = ','
if default is not None:
self.default = default
| (self, *, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None) | [
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11,160 | smtpapi | default | null | def default(self, o):
if isinstance(o, decimal.Decimal):
return float(o)
# Provide a fallback to the default encoder if we haven't implemented
# special support for the object's class
return super(_CustomJSONEncoder, self).default(o)
| (self, o) | [
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] |
11,161 | json.encoder | encode | Return a JSON string representation of a Python data structure.
>>> from json.encoder import JSONEncoder
>>> JSONEncoder().encode({"foo": ["bar", "baz"]})
'{"foo": ["bar", "baz"]}'
| def encode(self, o):
"""Return a JSON string representation of a Python data structure.
>>> from json.encoder import JSONEncoder
>>> JSONEncoder().encode({"foo": ["bar", "baz"]})
'{"foo": ["bar", "baz"]}'
"""
# This is for extremely simple cases and benchmarks.
if isinstance(o, str):
if self.ensure_ascii:
return encode_basestring_ascii(o)
else:
return encode_basestring(o)
# This doesn't pass the iterator directly to ''.join() because the
# exceptions aren't as detailed. The list call should be roughly
# equivalent to the PySequence_Fast that ''.join() would do.
chunks = self.iterencode(o, _one_shot=True)
if not isinstance(chunks, (list, tuple)):
chunks = list(chunks)
return ''.join(chunks)
| (self, o) | [
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] |
11,162 | json.encoder | iterencode | Encode the given object and yield each string
representation as available.
For example::
for chunk in JSONEncoder().iterencode(bigobject):
mysocket.write(chunk)
| def iterencode(self, o, _one_shot=False):
"""Encode the given object and yield each string
representation as available.
For example::
for chunk in JSONEncoder().iterencode(bigobject):
mysocket.write(chunk)
"""
if self.check_circular:
markers = {}
else:
markers = None
if self.ensure_ascii:
_encoder = encode_basestring_ascii
else:
_encoder = encode_basestring
def floatstr(o, allow_nan=self.allow_nan,
_repr=float.__repr__, _inf=INFINITY, _neginf=-INFINITY):
# Check for specials. Note that this type of test is processor
# and/or platform-specific, so do tests which don't depend on the
# internals.
if o != o:
text = 'NaN'
elif o == _inf:
text = 'Infinity'
elif o == _neginf:
text = '-Infinity'
else:
return _repr(o)
if not allow_nan:
raise ValueError(
"Out of range float values are not JSON compliant: " +
repr(o))
return text
if (_one_shot and c_make_encoder is not None
and self.indent is None):
_iterencode = c_make_encoder(
markers, self.default, _encoder, self.indent,
self.key_separator, self.item_separator, self.sort_keys,
self.skipkeys, self.allow_nan)
else:
_iterencode = _make_iterencode(
markers, self.default, _encoder, self.indent, floatstr,
self.key_separator, self.item_separator, self.sort_keys,
self.skipkeys, _one_shot)
return _iterencode(o, 0)
| (self, o, _one_shot=False) | [
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11,233 | ffmpeg_editlist | atomic_write | Atomically write into the given fname.
Returns a NamedTemporaryFile that will be moved (atomically,
os.replace). Use [returnvalue].name to access the file's name.
| def main(argv=sys.argv[1:]):
parser = argparse.ArgumentParser()
parser.add_argument('editlist')
parser.add_argument('input', type=Path,
help="Input file or directory of files.")
parser.add_argument('--output', '-o', default='.', type=Path,
help='Output directory')
parser.add_argument('--srt', action='store_true',
help='Also convert subtitles')
parser.add_argument('--limit', '-l', action='append',
help='Limit to only outputs matching this pattern. There is no wildcarding. This option can be given multiple times.')
parser.add_argument('--check', '-c', action='store_true',
help="Don't encode or generate output files, just check consistency of the YAML file. This *will* override the .info.txt output file.")
parser.add_argument('--force', '-f', action='store_true',
help='Overwrite existing output files without prompting')
parser.add_argument('--verbose', '-v', action='store_true',
help='Verbose (put ffmpeg in normal mode, otherwise ffmpeg is quiet.)')
parser.add_argument('--reencode', action='store_true',
help='Re-encode all segments of the video. See --preset and --crf to adjust parameters.'
'This is needed when you start a snipet in the middle of a video, since the video decoding '
'can only begin at a key frame. '
'Default false.')
parser.add_argument('--crf', default=20, type=int,
help='x264 crf (preceived quality) to use for re-encoding, lower is higher quality. '
'Reasonable options are 20 (extremely good) to 30 (lower quality) (the absolute range 1 - 51); '
'higher numbers take less time to encode.'
'Default is 20, which should be good enough for any purpose.')
parser.add_argument('--preset', default='veryslow',
help='x264 preset to use for re-encoding, basically the encoding speed. '
'Changing this affects how much time it will take to compress to get the --crf quality target '
'you request; slower=better compression by using more expensive codec features. '
'Example options you might use include veryslow, slow, medium, fast, and ultrafast. '
'Default is veryslow, use ultrafast for fast testing.')
parser.add_argument('--threads', type=int,
help='Number of encoding threads. Default: unset, autodetect')
parser.add_argument('--wait', action='store_true',
help='Wait after each encoding (don\'t clean up the temporary directory right away')
parser.add_argument('--list', action='store_true',
help="Don't do anything, just list all outputs that would be processed (and nothing else)")
args = parser.parse_args(argv)
if args.threads:
FFMPEG_VIDEO_ENCODE.extend(['-threads', str(args.threads)])
FFMPEG_VIDEO_ENCODE.extend(['-preset', args.preset])
FFMPEG_VIDEO_ENCODE.extend(['-crf', str(args.crf)])
if args.srt:
import srt
all_inputs = set()
# Open the input file. Parse out of markdown if it is markdown:
data = open(args.editlist).read()
if '```' in data:
matches = re.findall(r'`{3,}[^\n]*\n(.*?)\n`{3,}', data, re.MULTILINE|re.DOTALL)
#print(matches)
data = '\n'.join([m for m in matches])
#print(data)
data = yaml.safe_load(data)
PWD = Path(os.getcwd())
LOGLEVEL = 31
if args.verbose:
LOGLEVEL = 40
workshop_title = None
workshop_description = None
options_ffmpeg_global = [ ]
#
# For each output file
#
input0 = args.input
for segment in data:
#print(segment)
tmp_outputs = [ ]
TOC = [ ]
segment_list = [ ]
cumulative_time = 0
filters = [ ]
covers = [ ]
options_ffmpeg_output = [ ]
subtitles = [ ]
with tempfile.TemporaryDirectory() as tmpdir:
# Find input
if 'input' in segment:
input0 = segment['input']
if 'workshop_description' in segment:
workshop_description = segment['workshop_description'].strip()
if 'workshop_title' in segment:
workshop_title = segment['workshop_title']
if 'crop' in segment:
# -filter:v "crop=w:h:x:y" - x:y is top-left corner
options_ffmpeg_output.extend(generate_crop(**segment['crop']))
if 'output' not in segment:
continue
allow_reencode = segment.get('reencode', True)
# Exclude non-matching files if '--limit' specified.
if args.limit and not any(limit_match in segment['output'] for limit_match in args.limit):
continue
if args.list:
print(segment['output'])
continue
input1 = input0
editlist = segment.get('editlist', segment.get('time'))
if editlist is None:
continue
#
# For each segment in the output
#
options_ffmpeg_segment = [ ]
segment_type = 'video'
segment_number = 0
for i, command in enumerate(editlist):
# Is this a command to cover a part of the video?
if isinstance(command, dict) and 'cover' in command:
cover = command['cover']
covers.append((segment_number, seconds(cover['begin'])))
filters.append(generate_cover(**cover))
continue
# Input command: change input files
elif isinstance(command, dict) and 'input' in command:
input1 = command['input']
# Handle png images
if 'duration' in command:
start = 0
stop = seconds(command['duration'])
segment_type = 'image'
segment_number += 1
else:
continue
# Start command: start a segment
elif isinstance(command, dict) and 'start' in command:
segment_number += 1
start = command['start']
continue
elif isinstance(command, dict) and 'begin' in command:
segment_number += 1
start = command['begin']
continue
# End command: process this segment and all queued commands
elif isinstance(command, dict) and 'stop' in command:
stop = command['stop']
# Continue below to process this segment
elif isinstance(command, dict) and 'end' in command:
stop = command['end']
# Continue below to process this segment
# Is this a TOC entry?
# If it's a dict, it is a table of contents entry that will be
# mapped to the correct time in the procesed video.
# This is a TOC entry
elif isinstance(command, dict):
( (time, title), ) = list(command.items())
if time == '-':
time = start
if title in {'stop', 'start', 'begin', 'end', 'cover', 'input'}:
LOG.error("ERROR: Suspicious TOC entry name, aborting encoding: %s", title)
sys.exit(1)
#print(start, title)
#print('TOC', start, title, segment)
TOC.append((segment_number, seconds(time), title))
continue
# The end of our time segment (from 'start' to 'stop'). | (fname, mode='w+b') | [
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11,237 | ffmpeg_editlist | ensure_filedir_exists | Ensure a a directory exists, that can hold the file given as argument | def ensure_filedir_exists(filename):
"""Ensure a a directory exists, that can hold the file given as argument"""
dirname = os.path.dirname(filename)
if dirname == '':
return
if not os.path.isdir(dirname):
os.makedirs(dirname)
| (filename) | [
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11,238 | ffmpeg_editlist | generate_cover | null | def generate_cover(begin, end, w=10000, h=10000, x=0, y=0):
begin = seconds(begin)
end = seconds(end)
return FFMPEG_COVER.format(**locals())
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] |
11,239 | ffmpeg_editlist | generate_crop | null | def generate_crop(w, h, x, y):
return ['-filter:v', f"crop={w}:{h}:{x}:{y}"]
| (w, h, x, y) | [
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11,240 | ffmpeg_editlist | humantime | null | def humantime(x):
hou = x // 3600
min = (x % 3600) // 60
sec = x % 60
if hou:
return "%d:%02d:%02d"%(hou, min, floor(sec))
return "%02d:%02d"%(min, floor(sec))
| (x) | [
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11,241 | ffmpeg_editlist | is_time | null | def is_time(x):
m = re.match(r'((\d{1,2}:)?\d{1,2}:)?\d{1,2}(\.\d*)?$', x)
return bool(m)
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11,244 | ffmpeg_editlist | main | null | def main(argv=sys.argv[1:]):
parser = argparse.ArgumentParser()
parser.add_argument('editlist')
parser.add_argument('input', type=Path,
help="Input file or directory of files.")
parser.add_argument('--output', '-o', default='.', type=Path,
help='Output directory')
parser.add_argument('--srt', action='store_true',
help='Also convert subtitles')
parser.add_argument('--limit', '-l', action='append',
help='Limit to only outputs matching this pattern. There is no wildcarding. This option can be given multiple times.')
parser.add_argument('--check', '-c', action='store_true',
help="Don't encode or generate output files, just check consistency of the YAML file. This *will* override the .info.txt output file.")
parser.add_argument('--force', '-f', action='store_true',
help='Overwrite existing output files without prompting')
parser.add_argument('--verbose', '-v', action='store_true',
help='Verbose (put ffmpeg in normal mode, otherwise ffmpeg is quiet.)')
parser.add_argument('--reencode', action='store_true',
help='Re-encode all segments of the video. See --preset and --crf to adjust parameters.'
'This is needed when you start a snipet in the middle of a video, since the video decoding '
'can only begin at a key frame. '
'Default false.')
parser.add_argument('--crf', default=20, type=int,
help='x264 crf (preceived quality) to use for re-encoding, lower is higher quality. '
'Reasonable options are 20 (extremely good) to 30 (lower quality) (the absolute range 1 - 51); '
'higher numbers take less time to encode.'
'Default is 20, which should be good enough for any purpose.')
parser.add_argument('--preset', default='veryslow',
help='x264 preset to use for re-encoding, basically the encoding speed. '
'Changing this affects how much time it will take to compress to get the --crf quality target '
'you request; slower=better compression by using more expensive codec features. '
'Example options you might use include veryslow, slow, medium, fast, and ultrafast. '
'Default is veryslow, use ultrafast for fast testing.')
parser.add_argument('--threads', type=int,
help='Number of encoding threads. Default: unset, autodetect')
parser.add_argument('--wait', action='store_true',
help='Wait after each encoding (don\'t clean up the temporary directory right away')
parser.add_argument('--list', action='store_true',
help="Don't do anything, just list all outputs that would be processed (and nothing else)")
args = parser.parse_args(argv)
if args.threads:
FFMPEG_VIDEO_ENCODE.extend(['-threads', str(args.threads)])
FFMPEG_VIDEO_ENCODE.extend(['-preset', args.preset])
FFMPEG_VIDEO_ENCODE.extend(['-crf', str(args.crf)])
if args.srt:
import srt
all_inputs = set()
# Open the input file. Parse out of markdown if it is markdown:
data = open(args.editlist).read()
if '```' in data:
matches = re.findall(r'`{3,}[^\n]*\n(.*?)\n`{3,}', data, re.MULTILINE|re.DOTALL)
#print(matches)
data = '\n'.join([m for m in matches])
#print(data)
data = yaml.safe_load(data)
PWD = Path(os.getcwd())
LOGLEVEL = 31
if args.verbose:
LOGLEVEL = 40
workshop_title = None
workshop_description = None
options_ffmpeg_global = [ ]
#
# For each output file
#
input0 = args.input
for segment in data:
#print(segment)
tmp_outputs = [ ]
TOC = [ ]
segment_list = [ ]
cumulative_time = 0
filters = [ ]
covers = [ ]
options_ffmpeg_output = [ ]
subtitles = [ ]
with tempfile.TemporaryDirectory() as tmpdir:
# Find input
if 'input' in segment:
input0 = segment['input']
if 'workshop_description' in segment:
workshop_description = segment['workshop_description'].strip()
if 'workshop_title' in segment:
workshop_title = segment['workshop_title']
if 'crop' in segment:
# -filter:v "crop=w:h:x:y" - x:y is top-left corner
options_ffmpeg_output.extend(generate_crop(**segment['crop']))
if 'output' not in segment:
continue
allow_reencode = segment.get('reencode', True)
# Exclude non-matching files if '--limit' specified.
if args.limit and not any(limit_match in segment['output'] for limit_match in args.limit):
continue
if args.list:
print(segment['output'])
continue
input1 = input0
editlist = segment.get('editlist', segment.get('time'))
if editlist is None:
continue
#
# For each segment in the output
#
options_ffmpeg_segment = [ ]
segment_type = 'video'
segment_number = 0
for i, command in enumerate(editlist):
# Is this a command to cover a part of the video?
if isinstance(command, dict) and 'cover' in command:
cover = command['cover']
covers.append((segment_number, seconds(cover['begin'])))
filters.append(generate_cover(**cover))
continue
# Input command: change input files
elif isinstance(command, dict) and 'input' in command:
input1 = command['input']
# Handle png images
if 'duration' in command:
start = 0
stop = seconds(command['duration'])
segment_type = 'image'
segment_number += 1
else:
continue
# Start command: start a segment
elif isinstance(command, dict) and 'start' in command:
segment_number += 1
start = command['start']
continue
elif isinstance(command, dict) and 'begin' in command:
segment_number += 1
start = command['begin']
continue
# End command: process this segment and all queued commands
elif isinstance(command, dict) and 'stop' in command:
stop = command['stop']
# Continue below to process this segment
elif isinstance(command, dict) and 'end' in command:
stop = command['end']
# Continue below to process this segment
# Is this a TOC entry?
# If it's a dict, it is a table of contents entry that will be
# mapped to the correct time in the procesed video.
# This is a TOC entry
elif isinstance(command, dict):
( (time, title), ) = list(command.items())
if time == '-':
time = start
if title in {'stop', 'start', 'begin', 'end', 'cover', 'input'}:
LOG.error("ERROR: Suspicious TOC entry name, aborting encoding: %s", title)
sys.exit(1)
#print(start, title)
#print('TOC', start, title, segment)
TOC.append((segment_number, seconds(time), title))
continue
# The end of our time segment (from 'start' to 'stop'). | (argv=['--package', 'ffmpeg-editlist', '--s3_bucket', '/data']) | [
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] |
11,245 | ffmpeg_editlist | map_time | Map a time from source time to output time
| def map_time(seg_n, lookup_table, time):
"""Map a time from source time to output time
"""
time_lookup_vals = [(x[0], x[1]) for x in lookup_table]
i = bisect.bisect_right(time_lookup_vals, (seg_n, time))
#print(f"lookup of {seg_n},{time} found at i={i}")
if lookup_table[i-1][1] is None:
#LOG.error("%s", lookup_table)
#LOG.error("%s", time)
LOG.error("Bad time lookup (type 1) for %s(=%ss)", humantime(time), time)
sys.exit(1)
if lookup_table[i-1][2] is None:
#LOG.error("%s", lookup_table)
#LOG.error("%s", time)
LOG.error("Bad time lookup (type 2) for %s(=%ss)", humantime(time), time)
sys.exit(1)
return time - lookup_table[i-1][1] + lookup_table[i-1][2]
| (seg_n, lookup_table, time) | [
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11,248 | ffmpeg_editlist | seconds | Convert HH:MM:SS.SS or S to seconds | def seconds(x):
"""Convert HH:MM:SS.SS or S to seconds"""
if isinstance(x, (int, float)):
return x
x = x.split(':')
sec = float(x[-1])
if len(x) >= 2:
sec += float(x[-2]) * 60
if len(x) >= 3:
sec += float(x[-3]) * 3600
return sec
| (x) | [
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11,249 | ffmpeg_editlist | shell_join | null | def shell_join(x):
return ' '.join(shlex.quote(str(_)) for _ in x)
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11,255 | ffmpeg_editlist | test_humantime | null | def test_humantime():
assert humantime(30) == "00:30"
assert humantime(90) == "01:30"
assert humantime(150) == "02:30"
assert humantime(3690) == "1:01:30"
assert humantime(3690.5) == "1:01:30"
assert humantime(7350) == "2:02:30"
assert humantime(43950) == "12:12:30"
| () | [
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] |
11,256 | ffmpeg_editlist | test_is_time | null | def test_is_time():
assert is_time('10')
assert is_time('10.')
assert is_time('10:10.5')
assert is_time('10:10:10.5')
assert not is_time('1e5')
assert not is_time('string')
assert not is_time('.5')
assert not is_time('Exercise: aoeu')
| () | [
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11,257 | ffmpeg_editlist | test_seconds | null | def test_seconds():
assert seconds(30) == 30
assert seconds(30.5) == 30.5
assert seconds('30') == 30
assert seconds('1:30') == 90
assert seconds('1:1:30') == 3690
assert seconds('1:1:30.5') == 3690.5
| () | [
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11,260 | rarfile | AES_CBC_Decrypt | Decrypt API | class AES_CBC_Decrypt:
"""Decrypt API"""
def __init__(self, key, iv):
if _have_crypto == 2:
self.decrypt = AES.new(key, AES.MODE_CBC, iv).decrypt
else:
ciph = Cipher(algorithms.AES(key), modes.CBC(iv), default_backend())
self.decrypt = ciph.decryptor().update
| (key, iv) | [
0.06094679608941078,
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0.014770828187465668,
0.0460754856467247,
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11,261 | rarfile | __init__ | null | def __init__(self, key, iv):
if _have_crypto == 2:
self.decrypt = AES.new(key, AES.MODE_CBC, iv).decrypt
else:
ciph = Cipher(algorithms.AES(key), modes.CBC(iv), default_backend())
self.decrypt = ciph.decryptor().update
| (self, key, iv) | [
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0.052870191633701324,
0.04405249282717705
] |
11,262 | rarfile | BadRarFile | Incorrect data in archive. | class BadRarFile(Error):
"""Incorrect data in archive."""
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11,263 | rarfile | BadRarName | Cannot guess multipart name components. | class BadRarName(Error):
"""Cannot guess multipart name components."""
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] |
11,264 | rarfile | Blake2SP | Blake2sp hash context.
| class Blake2SP:
"""Blake2sp hash context.
"""
__slots__ = ["_thread", "_buf", "_cur", "_digest"]
digest_size = 32
block_size = 64
parallelism = 8
def __init__(self, data=None):
self._buf = b""
self._cur = 0
self._digest = None
self._thread = []
for i in range(self.parallelism):
ctx = self._blake2s(i, 0, i == (self.parallelism - 1))
self._thread.append(ctx)
if data:
self.update(data)
def _blake2s(self, ofs, depth, is_last):
return blake2s(node_offset=ofs, node_depth=depth, last_node=is_last,
depth=2, inner_size=32, fanout=self.parallelism)
def _add_block(self, blk):
self._thread[self._cur].update(blk)
self._cur = (self._cur + 1) % self.parallelism
def update(self, data):
"""Hash data.
"""
view = memoryview(data)
bs = self.block_size
if self._buf:
need = bs - len(self._buf)
if len(view) < need:
self._buf += view.tobytes()
return
self._add_block(self._buf + view[:need].tobytes())
view = view[need:]
while len(view) >= bs:
self._add_block(view[:bs])
view = view[bs:]
self._buf = view.tobytes()
def digest(self):
"""Return final digest value.
"""
if self._digest is None:
if self._buf:
self._add_block(self._buf)
self._buf = b""
ctx = self._blake2s(0, 1, True)
for t in self._thread:
ctx.update(t.digest())
self._digest = ctx.digest()
return self._digest
def hexdigest(self):
"""Hexadecimal digest."""
return hexlify(self.digest()).decode("ascii")
| (data=None) | [
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11,265 | rarfile | __init__ | null | def __init__(self, data=None):
self._buf = b""
self._cur = 0
self._digest = None
self._thread = []
for i in range(self.parallelism):
ctx = self._blake2s(i, 0, i == (self.parallelism - 1))
self._thread.append(ctx)
if data:
self.update(data)
| (self, data=None) | [
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11,266 | rarfile | _add_block | null | def _add_block(self, blk):
self._thread[self._cur].update(blk)
self._cur = (self._cur + 1) % self.parallelism
| (self, blk) | [
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11,267 | rarfile | _blake2s | null | def _blake2s(self, ofs, depth, is_last):
return blake2s(node_offset=ofs, node_depth=depth, last_node=is_last,
depth=2, inner_size=32, fanout=self.parallelism)
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] |
11,268 | rarfile | digest | Return final digest value.
| def digest(self):
"""Return final digest value.
"""
if self._digest is None:
if self._buf:
self._add_block(self._buf)
self._buf = b""
ctx = self._blake2s(0, 1, True)
for t in self._thread:
ctx.update(t.digest())
self._digest = ctx.digest()
return self._digest
| (self) | [
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11,269 | rarfile | hexdigest | Hexadecimal digest. | def hexdigest(self):
"""Hexadecimal digest."""
return hexlify(self.digest()).decode("ascii")
| (self) | [
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11,270 | rarfile | update | Hash data.
| def update(self, data):
"""Hash data.
"""
view = memoryview(data)
bs = self.block_size
if self._buf:
need = bs - len(self._buf)
if len(view) < need:
self._buf += view.tobytes()
return
self._add_block(self._buf + view[:need].tobytes())
view = view[need:]
while len(view) >= bs:
self._add_block(view[:bs])
view = view[bs:]
self._buf = view.tobytes()
| (self, data) | [
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] |
11,271 | rarfile | CRC32Context | Hash context that uses CRC32. | class CRC32Context:
"""Hash context that uses CRC32."""
__slots__ = ["_crc"]
def __init__(self, data=None):
self._crc = 0
if data:
self.update(data)
def update(self, data):
"""Process data."""
self._crc = crc32(data, self._crc)
def digest(self):
"""Final hash."""
return self._crc
def hexdigest(self):
"""Hexadecimal digest."""
return "%08x" % self.digest()
| (data=None) | [
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11,272 | rarfile | __init__ | null | def __init__(self, data=None):
self._crc = 0
if data:
self.update(data)
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11,273 | rarfile | digest | Final hash. | def digest(self):
"""Final hash."""
return self._crc
| (self) | [
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11,274 | rarfile | hexdigest | Hexadecimal digest. | def hexdigest(self):
"""Hexadecimal digest."""
return "%08x" % self.digest()
| (self) | [
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] |
11,275 | rarfile | update | Process data. | def update(self, data):
"""Process data."""
self._crc = crc32(data, self._crc)
| (self, data) | [
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11,276 | rarfile | CommonParser | Shared parser parts. | class CommonParser:
"""Shared parser parts."""
_main = None
_hdrenc_main = None
_needs_password = False
_fd = None
_expect_sig = None
_parse_error = None
_password = None
comment = None
def __init__(self, rarfile, password, crc_check, charset, strict,
info_cb, sfx_offset, part_only):
self._rarfile = rarfile
self._password = password
self._crc_check = crc_check
self._charset = charset
self._strict = strict
self._info_callback = info_cb
self._info_list = []
self._info_map = {}
self._vol_list = []
self._sfx_offset = sfx_offset
self._part_only = part_only
def is_solid(self):
"""Returns True if archive uses solid compression.
"""
if self._main:
if self._main.flags & RAR_MAIN_SOLID:
return True
return False
def has_header_encryption(self):
"""Returns True if headers are encrypted
"""
if self._hdrenc_main:
return True
if self._main:
if self._main.flags & RAR_MAIN_PASSWORD:
return True
return False
def setpassword(self, pwd):
"""Set cached password."""
self._password = pwd
def volumelist(self):
"""Volume files"""
return self._vol_list
def needs_password(self):
"""Is password required"""
return self._needs_password
def strerror(self):
"""Last error"""
return self._parse_error
def infolist(self):
"""List of RarInfo records.
"""
return self._info_list
def getinfo(self, member):
"""Return RarInfo for filename
"""
if isinstance(member, RarInfo):
fname = member.filename
elif isinstance(member, Path):
fname = str(member)
else:
fname = member
if fname.endswith("/"):
fname = fname.rstrip("/")
try:
return self._info_map[fname]
except KeyError:
raise NoRarEntry("No such file: %s" % fname) from None
def getinfo_orig(self, member):
inf = self.getinfo(member)
if inf.file_redir:
redir_type, redir_flags, redir_name = inf.file_redir
# cannot leave to unrar as it expects copied file to exist
if redir_type in (RAR5_XREDIR_FILE_COPY, RAR5_XREDIR_HARD_LINK):
inf = self.getinfo(redir_name)
return inf
def parse(self):
"""Process file."""
self._fd = None
try:
self._parse_real()
finally:
if self._fd:
self._fd.close()
self._fd = None
def _parse_real(self):
"""Actually read file.
"""
fd = XFile(self._rarfile)
self._fd = fd
fd.seek(self._sfx_offset, 0)
sig = fd.read(len(self._expect_sig))
if sig != self._expect_sig:
raise NotRarFile("Not a Rar archive")
volume = 0 # first vol (.rar) is 0
more_vols = False
endarc = False
volfile = self._rarfile
self._vol_list = [self._rarfile]
raise_need_first_vol = False
while True:
if endarc:
h = None # don"t read past ENDARC
else:
h = self._parse_header(fd)
if not h:
if raise_need_first_vol:
# did not find ENDARC with VOLNR
raise NeedFirstVolume("Need to start from first volume", None)
if more_vols and not self._part_only:
volume += 1
fd.close()
try:
volfile = self._next_volname(volfile)
fd = XFile(volfile)
except IOError:
self._set_error("Cannot open next volume: %s", volfile)
break
self._fd = fd
sig = fd.read(len(self._expect_sig))
if sig != self._expect_sig:
self._set_error("Invalid volume sig: %s", volfile)
break
more_vols = False
endarc = False
self._vol_list.append(volfile)
self._main = None
self._hdrenc_main = None
continue
break
h.volume = volume
h.volume_file = volfile
if h.type == RAR_BLOCK_MAIN and not self._main:
self._main = h
if volume == 0 and (h.flags & RAR_MAIN_NEWNUMBERING) and not self._part_only:
# RAR 2.x does not set FIRSTVOLUME,
# so check it only if NEWNUMBERING is used
if (h.flags & RAR_MAIN_FIRSTVOLUME) == 0:
if getattr(h, "main_volume_number", None) is not None:
# rar5 may have more info
raise NeedFirstVolume(
"Need to start from first volume (current: %r)"
% (h.main_volume_number,),
h.main_volume_number
)
# delay raise until we have volnr from ENDARC
raise_need_first_vol = True
if h.flags & RAR_MAIN_PASSWORD:
self._needs_password = True
if not self._password:
break
elif h.type == RAR_BLOCK_ENDARC:
# use flag, but also allow RAR 2.x logic below to trigger
if h.flags & RAR_ENDARC_NEXT_VOLUME:
more_vols = True
endarc = True
if raise_need_first_vol and (h.flags & RAR_ENDARC_VOLNR) > 0:
raise NeedFirstVolume(
"Need to start from first volume (current: %r)"
% (h.endarc_volnr,),
h.endarc_volnr
)
elif h.type == RAR_BLOCK_FILE:
# RAR 2.x does not write RAR_BLOCK_ENDARC
if h.flags & RAR_FILE_SPLIT_AFTER:
more_vols = True
# RAR 2.x does not set RAR_MAIN_FIRSTVOLUME
if volume == 0 and h.flags & RAR_FILE_SPLIT_BEFORE:
if not self._part_only:
raise_need_first_vol = True
if h.needs_password():
self._needs_password = True
# store it
self.process_entry(fd, h)
if self._info_callback:
self._info_callback(h)
# go to next header
if h.add_size > 0:
fd.seek(h.data_offset + h.add_size, 0)
def process_entry(self, fd, item):
"""Examine item, add into lookup cache."""
raise NotImplementedError()
def _decrypt_header(self, fd):
raise NotImplementedError("_decrypt_header")
def _parse_block_header(self, fd):
raise NotImplementedError("_parse_block_header")
def _open_hack(self, inf, pwd):
raise NotImplementedError("_open_hack")
def _parse_header(self, fd):
"""Read single header
"""
try:
# handle encrypted headers
if (self._main and self._main.flags & RAR_MAIN_PASSWORD) or self._hdrenc_main:
if not self._password:
return None
fd = self._decrypt_header(fd)
# now read actual header
return self._parse_block_header(fd)
except struct.error:
self._set_error("Broken header in RAR file")
return None
def _next_volname(self, volfile):
"""Given current vol name, construct next one
"""
if is_filelike(volfile):
raise IOError("Working on single FD")
if self._main.flags & RAR_MAIN_NEWNUMBERING:
return _next_newvol(volfile)
return _next_oldvol(volfile)
def _se | (rarfile, password, crc_check, charset, strict, info_cb, sfx_offset, part_only) | [
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] |
11,277 | rarfile | __init__ | null | def __init__(self, rarfile, password, crc_check, charset, strict,
info_cb, sfx_offset, part_only):
self._rarfile = rarfile
self._password = password
self._crc_check = crc_check
self._charset = charset
self._strict = strict
self._info_callback = info_cb
self._info_list = []
self._info_map = {}
self._vol_list = []
self._sfx_offset = sfx_offset
self._part_only = part_only
| (self, rarfile, password, crc_check, charset, strict, info_cb, sfx_offset, part_only) | [
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11,278 | rarfile | _decrypt_header | null | def _decrypt_header(self, fd):
raise NotImplementedError("_decrypt_header")
| (self, fd) | [
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] |
11,279 | rarfile | _next_volname | Given current vol name, construct next one
| def _next_volname(self, volfile):
"""Given current vol name, construct next one
"""
if is_filelike(volfile):
raise IOError("Working on single FD")
if self._main.flags & RAR_MAIN_NEWNUMBERING:
return _next_newvol(volfile)
return _next_oldvol(volfile)
| (self, volfile) | [
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11,280 | rarfile | _open_clear | null | def _open_clear(self, inf):
if FORCE_TOOL:
return self._open_unrar(self._rarfile, inf)
return DirectReader(self, inf)
| (self, inf) | [
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11,281 | rarfile | _open_hack | null | def _open_hack(self, inf, pwd):
raise NotImplementedError("_open_hack")
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11,282 | rarfile | _open_hack_core | null | def _open_hack_core(self, inf, pwd, prefix, suffix):
size = inf.compress_size + inf.header_size
rf = XFile(inf.volume_file, 0)
rf.seek(inf.header_offset)
tmpfd, tmpname = mkstemp(suffix=".rar", dir=HACK_TMP_DIR)
tmpf = os.fdopen(tmpfd, "wb")
try:
tmpf.write(prefix)
while size > 0:
if size > BSIZE:
buf = rf.read(BSIZE)
else:
buf = rf.read(size)
if not buf:
raise BadRarFile("read failed: " + inf.filename)
tmpf.write(buf)
size -= len(buf)
tmpf.write(suffix)
tmpf.close()
rf.close()
except BaseException:
rf.close()
tmpf.close()
os.unlink(tmpname)
raise
return self._open_unrar(tmpname, inf, pwd, tmpname)
| (self, inf, pwd, prefix, suffix) | [
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] |
11,283 | rarfile | _open_unrar | Extract using unrar
| def _open_unrar(self, rarfile, inf, pwd=None, tmpfile=None, force_file=False):
"""Extract using unrar
"""
setup = tool_setup()
# not giving filename avoids encoding related problems
fn = None
if not tmpfile or force_file:
fn = inf.filename.replace("/", os.path.sep)
# read from unrar pipe
cmd = setup.open_cmdline(pwd, rarfile, fn)
return PipeReader(self, inf, cmd, tmpfile)
| (self, rarfile, inf, pwd=None, tmpfile=None, force_file=False) | [
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11,284 | rarfile | _open_unrar_membuf | Write in-memory archive to temp file, needed for solid archives.
| def _open_unrar_membuf(self, memfile, inf, pwd):
"""Write in-memory archive to temp file, needed for solid archives.
"""
tmpname = membuf_tempfile(memfile)
return self._open_unrar(tmpname, inf, pwd, tmpname, force_file=True)
| (self, memfile, inf, pwd) | [
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11,285 | rarfile | _parse_block_header | null | def _parse_block_header(self, fd):
raise NotImplementedError("_parse_block_header")
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] |
11,286 | rarfile | _parse_header | Read single header
| def _parse_header(self, fd):
"""Read single header
"""
try:
# handle encrypted headers
if (self._main and self._main.flags & RAR_MAIN_PASSWORD) or self._hdrenc_main:
if not self._password:
return None
fd = self._decrypt_header(fd)
# now read actual header
return self._parse_block_header(fd)
except struct.error:
self._set_error("Broken header in RAR file")
return None
| (self, fd) | [
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] |
11,287 | rarfile | _parse_real | Actually read file.
| def _parse_real(self):
"""Actually read file.
"""
fd = XFile(self._rarfile)
self._fd = fd
fd.seek(self._sfx_offset, 0)
sig = fd.read(len(self._expect_sig))
if sig != self._expect_sig:
raise NotRarFile("Not a Rar archive")
volume = 0 # first vol (.rar) is 0
more_vols = False
endarc = False
volfile = self._rarfile
self._vol_list = [self._rarfile]
raise_need_first_vol = False
while True:
if endarc:
h = None # don"t read past ENDARC
else:
h = self._parse_header(fd)
if not h:
if raise_need_first_vol:
# did not find ENDARC with VOLNR
raise NeedFirstVolume("Need to start from first volume", None)
if more_vols and not self._part_only:
volume += 1
fd.close()
try:
volfile = self._next_volname(volfile)
fd = XFile(volfile)
except IOError:
self._set_error("Cannot open next volume: %s", volfile)
break
self._fd = fd
sig = fd.read(len(self._expect_sig))
if sig != self._expect_sig:
self._set_error("Invalid volume sig: %s", volfile)
break
more_vols = False
endarc = False
self._vol_list.append(volfile)
self._main = None
self._hdrenc_main = None
continue
break
h.volume = volume
h.volume_file = volfile
if h.type == RAR_BLOCK_MAIN and not self._main:
self._main = h
if volume == 0 and (h.flags & RAR_MAIN_NEWNUMBERING) and not self._part_only:
# RAR 2.x does not set FIRSTVOLUME,
# so check it only if NEWNUMBERING is used
if (h.flags & RAR_MAIN_FIRSTVOLUME) == 0:
if getattr(h, "main_volume_number", None) is not None:
# rar5 may have more info
raise NeedFirstVolume(
"Need to start from first volume (current: %r)"
% (h.main_volume_number,),
h.main_volume_number
)
# delay raise until we have volnr from ENDARC
raise_need_first_vol = True
if h.flags & RAR_MAIN_PASSWORD:
self._needs_password = True
if not self._password:
break
elif h.type == RAR_BLOCK_ENDARC:
# use flag, but also allow RAR 2.x logic below to trigger
if h.flags & RAR_ENDARC_NEXT_VOLUME:
more_vols = True
endarc = True
if raise_need_first_vol and (h.flags & RAR_ENDARC_VOLNR) > 0:
raise NeedFirstVolume(
"Need to start from first volume (current: %r)"
% (h.endarc_volnr,),
h.endarc_volnr
)
elif h.type == RAR_BLOCK_FILE:
# RAR 2.x does not write RAR_BLOCK_ENDARC
if h.flags & RAR_FILE_SPLIT_AFTER:
more_vols = True
# RAR 2.x does not set RAR_MAIN_FIRSTVOLUME
if volume == 0 and h.flags & RAR_FILE_SPLIT_BEFORE:
if not self._part_only:
raise_need_first_vol = True
if h.needs_password():
self._needs_password = True
# store it
self.process_entry(fd, h)
if self._info_callback:
self._info_callback(h)
# go to next header
if h.add_size > 0:
fd.seek(h.data_offset + h.add_size, 0)
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