repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
varlink/python | varlink/server.py | Server.server_bind | def server_bind(self):
"""Called by constructor to bind the socket.
May be overridden.
"""
if self.allow_reuse_address:
self.socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
self.socket.setblocking(True)
if not self.listen_fd:
self.s... | python | def server_bind(self):
"""Called by constructor to bind the socket.
May be overridden.
"""
if self.allow_reuse_address:
self.socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
self.socket.setblocking(True)
if not self.listen_fd:
self.s... | Called by constructor to bind the socket.
May be overridden. | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/server.py#L443-L463 |
varlink/python | varlink/server.py | Server.server_close | def server_close(self):
"""Called to clean-up the server.
May be overridden.
"""
if self.remove_file:
try:
os.remove(self.remove_file)
except:
pass
self.socket.close() | python | def server_close(self):
"""Called to clean-up the server.
May be overridden.
"""
if self.remove_file:
try:
os.remove(self.remove_file)
except:
pass
self.socket.close() | Called to clean-up the server.
May be overridden. | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/server.py#L473-L484 |
varlink/python | varlink/server.py | Server.shutdown_request | def shutdown_request(self, request):
"""Called to shutdown and close an individual request."""
try:
# explicitly shutdown. socket.close() merely releases
# the socket and waits for GC to perform the actual close.
request.shutdown(socket.SHUT_RDWR)
except:
... | python | def shutdown_request(self, request):
"""Called to shutdown and close an individual request."""
try:
# explicitly shutdown. socket.close() merely releases
# the socket and waits for GC to perform the actual close.
request.shutdown(socket.SHUT_RDWR)
except:
... | Called to shutdown and close an individual request. | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/server.py#L502-L511 |
varlink/python | varlink/client.py | Client.open | def open(self, interface_name, namespaced=False, connection=None):
"""Open a new connection and get a client interface handle with the varlink methods installed.
:param interface_name: an interface name, which the service this client object is
connected to, provides.
... | python | def open(self, interface_name, namespaced=False, connection=None):
"""Open a new connection and get a client interface handle with the varlink methods installed.
:param interface_name: an interface name, which the service this client object is
connected to, provides.
... | Open a new connection and get a client interface handle with the varlink methods installed.
:param interface_name: an interface name, which the service this client object is
connected to, provides.
:param namespaced: If arguments and return values are instances of SimpleN... | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/client.py#L585-L606 |
varlink/python | varlink/client.py | Client.get_interfaces | def get_interfaces(self, socket_connection=None):
"""Returns the a list of Interface objects the service implements."""
if not socket_connection:
socket_connection = self.open_connection()
close_socket = True
else:
close_socket = False
# noinspection ... | python | def get_interfaces(self, socket_connection=None):
"""Returns the a list of Interface objects the service implements."""
if not socket_connection:
socket_connection = self.open_connection()
close_socket = True
else:
close_socket = False
# noinspection ... | Returns the a list of Interface objects the service implements. | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/client.py#L615-L630 |
varlink/python | varlink/client.py | Client.add_interface | def add_interface(self, interface):
"""Manually add or overwrite an interface definition from an Interface object.
:param interface: an Interface() object
"""
if not isinstance(interface, Interface):
raise TypeError
self._interfaces[interface.name] = interface | python | def add_interface(self, interface):
"""Manually add or overwrite an interface definition from an Interface object.
:param interface: an Interface() object
"""
if not isinstance(interface, Interface):
raise TypeError
self._interfaces[interface.name] = interface | Manually add or overwrite an interface definition from an Interface object.
:param interface: an Interface() object | https://github.com/varlink/python/blob/b021a29dd9def06b03416d20e8b37be39c3edd33/varlink/client.py#L650-L659 |
SINGROUP/SOAPLite | utilities/rematch_example.py | rematch_entry | def rematch_entry(envkernel, gamma = 0.1, threshold = 1e-6):
"""
Compute the global similarity between two structures A and B.
It uses the Sinkhorn algorithm as reported in:
Phys. Chem. Chem. Phys., 2016, 18, p. 13768
Args:
envkernel: NxM matrix of structure A with
N and structu... | python | def rematch_entry(envkernel, gamma = 0.1, threshold = 1e-6):
"""
Compute the global similarity between two structures A and B.
It uses the Sinkhorn algorithm as reported in:
Phys. Chem. Chem. Phys., 2016, 18, p. 13768
Args:
envkernel: NxM matrix of structure A with
N and structu... | Compute the global similarity between two structures A and B.
It uses the Sinkhorn algorithm as reported in:
Phys. Chem. Chem. Phys., 2016, 18, p. 13768
Args:
envkernel: NxM matrix of structure A with
N and structure B with M atoms
gamma: parameter to control between best match ... | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/utilities/rematch_example.py#L15-L59 |
SINGROUP/SOAPLite | utilities/batchSoapPy.py | create | def create(atoms_list,N, L, cutoff = 0, all_atomtypes=[]):
"""Takes a trajectory xyz file and writes soap features
"""
myAlphas, myBetas = genBasis.getBasisFunc(cutoff, N)
# get information about feature length
n_datapoints = len(atoms_list)
atoms = atoms_list[0]
x = get_lastatom_soap(atoms,... | python | def create(atoms_list,N, L, cutoff = 0, all_atomtypes=[]):
"""Takes a trajectory xyz file and writes soap features
"""
myAlphas, myBetas = genBasis.getBasisFunc(cutoff, N)
# get information about feature length
n_datapoints = len(atoms_list)
atoms = atoms_list[0]
x = get_lastatom_soap(atoms,... | Takes a trajectory xyz file and writes soap features | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/utilities/batchSoapPy.py#L21-L44 |
SINGROUP/SOAPLite | soaplite/getBasis.py | getPoly | def getPoly(rCut, nMax):
"""Used to calculate discrete vectors for the polynomial basis functions.
Args:
rCut(float): Radial cutoff
nMax(int): Number of polynomial radial functions
"""
rCutVeryHard = rCut+5.0
rx = 0.5*rCutVeryHard*(x + 1)
basisFunctions = []
for i in range(... | python | def getPoly(rCut, nMax):
"""Used to calculate discrete vectors for the polynomial basis functions.
Args:
rCut(float): Radial cutoff
nMax(int): Number of polynomial radial functions
"""
rCutVeryHard = rCut+5.0
rx = 0.5*rCutVeryHard*(x + 1)
basisFunctions = []
for i in range(... | Used to calculate discrete vectors for the polynomial basis functions.
Args:
rCut(float): Radial cutoff
nMax(int): Number of polynomial radial functions | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/getBasis.py#L303-L342 |
SINGROUP/SOAPLite | soaplite/core.py | _format_ase2clusgeo | def _format_ase2clusgeo(obj, all_atomtypes=None):
""" Takes an ase Atoms object and returns numpy arrays and integers
which are read by the internal clusgeo. Apos is currently a flattened
out numpy array
Args:
obj():
all_atomtypes():
sort():
"""
#atoms metadata
total... | python | def _format_ase2clusgeo(obj, all_atomtypes=None):
""" Takes an ase Atoms object and returns numpy arrays and integers
which are read by the internal clusgeo. Apos is currently a flattened
out numpy array
Args:
obj():
all_atomtypes():
sort():
"""
#atoms metadata
total... | Takes an ase Atoms object and returns numpy arrays and integers
which are read by the internal clusgeo. Apos is currently a flattened
out numpy array
Args:
obj():
all_atomtypes():
sort(): | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/core.py#L11-L44 |
SINGROUP/SOAPLite | soaplite/core.py | _get_supercell | def _get_supercell(obj, rCut=5.0):
rCutHard = rCut + 5 # Giving extra space for hard cutOff
""" Takes atoms object (with a defined cell) and a radial cutoff.
Returns a supercell centered around the original cell
generously extended to contain all spheres with the given radial
cutoff centered around... | python | def _get_supercell(obj, rCut=5.0):
rCutHard = rCut + 5 # Giving extra space for hard cutOff
""" Takes atoms object (with a defined cell) and a radial cutoff.
Returns a supercell centered around the original cell
generously extended to contain all spheres with the given radial
cutoff centered around... | Takes atoms object (with a defined cell) and a radial cutoff.
Returns a supercell centered around the original cell
generously extended to contain all spheres with the given radial
cutoff centered around the original atoms. | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/core.py#L47-L77 |
SINGROUP/SOAPLite | soaplite/core.py | get_soap_locals | def get_soap_locals(obj, Hpos, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for the given positions in a finite system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
Hpos: Positio... | python | def get_soap_locals(obj, Hpos, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for the given positions in a finite system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
Hpos: Positio... | Get the RBF basis SOAP output for the given positions in a finite system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
Hpos: Positions at which to calculate SOAP
alp: Alphas
bet: Betas
rCut: Radial cutoff.
nMax: Maximum ... | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/core.py#L80-L169 |
SINGROUP/SOAPLite | soaplite/core.py | get_soap_structure | def get_soap_structure(obj, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for atoms in a finite structure.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp: Alphas
bet: Be... | python | def get_soap_structure(obj, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for atoms in a finite structure.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp: Alphas
bet: Be... | Get the RBF basis SOAP output for atoms in a finite structure.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp: Alphas
bet: Betas
rCut: Radial cutoff.
nMax: Maximum nmber of radial basis functions
Lmax: Maximum spherica... | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/core.py#L172-L195 |
SINGROUP/SOAPLite | soaplite/core.py | get_periodic_soap_locals | def get_periodic_soap_locals(obj, Hpos, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for the given position in a periodic system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp... | python | def get_periodic_soap_locals(obj, Hpos, alp, bet, rCut=5.0, nMax=5, Lmax=5, crossOver=True, all_atomtypes=None, eta=1.0):
"""Get the RBF basis SOAP output for the given position in a periodic system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp... | Get the RBF basis SOAP output for the given position in a periodic system.
Args:
obj(ase.Atoms): Atomic structure for which the SOAP output is
calculated.
alp: Alphas
bet: Betas
rCut: Radial cutoff.
nMax: Maximum nmber of radial basis functions
Lmax: Maxi... | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/soaplite/core.py#L198-L221 |
SINGROUP/SOAPLite | utilities/get_sitecenteredsoap_from_structures.py | get_nnsoap | def get_nnsoap(obj, first_shell, alphas, betas, rcut=6, nmax=10, lmax=9, all_atomtypes=[]):
"""Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector from left... | python | def get_nnsoap(obj, first_shell, alphas, betas, rcut=6, nmax=10, lmax=9, all_atomtypes=[]):
"""Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector from left... | Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector from left to right. | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/utilities/get_sitecenteredsoap_from_structures.py#L57-L82 |
SINGROUP/SOAPLite | utilities/get_sitecenteredsoap_from_structures.py | get_sitecenteredsoap | def get_sitecenteredsoap(obj, first_shell, alphas, betas, rcut=6, nmax=10, lmax=9, all_atomtypes=[]):
"""Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector... | python | def get_sitecenteredsoap(obj, first_shell, alphas, betas, rcut=6, nmax=10, lmax=9, all_atomtypes=[]):
"""Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector... | Takes cluster structure and nearest neighbour information of a datapoint,
Returns concatenated soap vectors for each nearest
neighbour (up to 3). Top, bridge, hollow fill the initial
zero soap vector from left to right. | https://github.com/SINGROUP/SOAPLite/blob/80e27cc8d5b4c887011542c5a799583bfc6ff643/utilities/get_sitecenteredsoap_from_structures.py#L84-L99 |
adrn/gala | gala/dynamics/orbit.py | Orbit.w | def w(self, units=None):
"""
This returns a single array containing the phase-space positions.
Parameters
----------
units : `~gala.units.UnitSystem` (optional)
The unit system to represent the position and velocity in
before combining into the full array... | python | def w(self, units=None):
"""
This returns a single array containing the phase-space positions.
Parameters
----------
units : `~gala.units.UnitSystem` (optional)
The unit system to represent the position and velocity in
before combining into the full array... | This returns a single array containing the phase-space positions.
Parameters
----------
units : `~gala.units.UnitSystem` (optional)
The unit system to represent the position and velocity in
before combining into the full array.
Returns
-------
w ... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L142-L166 |
adrn/gala | gala/dynamics/orbit.py | Orbit.represent_as | def represent_as(self, new_pos, new_vel=None):
"""
Represent the position and velocity of the orbit in an alternate
coordinate system. Supports any of the Astropy coordinates
representation classes.
Parameters
----------
new_pos : :class:`~astropy.coordinates.Bas... | python | def represent_as(self, new_pos, new_vel=None):
"""
Represent the position and velocity of the orbit in an alternate
coordinate system. Supports any of the Astropy coordinates
representation classes.
Parameters
----------
new_pos : :class:`~astropy.coordinates.Bas... | Represent the position and velocity of the orbit in an alternate
coordinate system. Supports any of the Astropy coordinates
representation classes.
Parameters
----------
new_pos : :class:`~astropy.coordinates.BaseRepresentation`
The type of representation to generate... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L171-L195 |
adrn/gala | gala/dynamics/orbit.py | Orbit.to_hdf5 | def to_hdf5(self, f):
"""
Serialize this object to an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file.
"""
f = super(Orbit, self).to_hdf5(f)
if self.potential ... | python | def to_hdf5(self, f):
"""
Serialize this object to an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file.
"""
f = super(Orbit, self).to_hdf5(f)
if self.potential ... | Serialize this object to an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L214-L236 |
adrn/gala | gala/dynamics/orbit.py | Orbit.from_hdf5 | def from_hdf5(cls, f):
"""
Load an object from an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file.
"""
# TODO: this is duplicated code from PhaseSpacePosition
if... | python | def from_hdf5(cls, f):
"""
Load an object from an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file.
"""
# TODO: this is duplicated code from PhaseSpacePosition
if... | Load an object from an HDF5 file.
Requires ``h5py``.
Parameters
----------
f : str, :class:`h5py.File`
Either the filename or an open HDF5 file. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L239-L292 |
adrn/gala | gala/dynamics/orbit.py | Orbit.orbit_gen | def orbit_gen(self):
"""
Generator for iterating over each orbit.
"""
if self.norbits == 1:
yield self
else:
for i in range(self.norbits):
yield self[:, i] | python | def orbit_gen(self):
"""
Generator for iterating over each orbit.
"""
if self.norbits == 1:
yield self
else:
for i in range(self.norbits):
yield self[:, i] | Generator for iterating over each orbit. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L294-L303 |
adrn/gala | gala/dynamics/orbit.py | Orbit.potential_energy | def potential_energy(self, potential=None):
r"""
The potential energy *per unit mass*:
.. math::
E_\Phi = \Phi(\boldsymbol{q})
Returns
-------
E : :class:`~astropy.units.Quantity`
The potential energy.
"""
if self.hamiltonian is ... | python | def potential_energy(self, potential=None):
r"""
The potential energy *per unit mass*:
.. math::
E_\Phi = \Phi(\boldsymbol{q})
Returns
-------
E : :class:`~astropy.units.Quantity`
The potential energy.
"""
if self.hamiltonian is ... | r"""
The potential energy *per unit mass*:
.. math::
E_\Phi = \Phi(\boldsymbol{q})
Returns
-------
E : :class:`~astropy.units.Quantity`
The potential energy. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L309-L328 |
adrn/gala | gala/dynamics/orbit.py | Orbit.energy | def energy(self, hamiltonian=None):
r"""
The total energy *per unit mass*:
Returns
-------
E : :class:`~astropy.units.Quantity`
The total energy.
"""
if self.hamiltonian is None and hamiltonian is None:
raise ValueError("To compute the to... | python | def energy(self, hamiltonian=None):
r"""
The total energy *per unit mass*:
Returns
-------
E : :class:`~astropy.units.Quantity`
The total energy.
"""
if self.hamiltonian is None and hamiltonian is None:
raise ValueError("To compute the to... | r"""
The total energy *per unit mass*:
Returns
-------
E : :class:`~astropy.units.Quantity`
The total energy. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L330-L360 |
adrn/gala | gala/dynamics/orbit.py | Orbit._max_helper | def _max_helper(self, arr, approximate=False,
interp_kwargs=None, minimize_kwargs=None):
"""
Helper function for computing extrema (apocenter, pericenter, z_height)
and times of extrema.
Parameters
----------
arr : `numpy.ndarray`
"""
... | python | def _max_helper(self, arr, approximate=False,
interp_kwargs=None, minimize_kwargs=None):
"""
Helper function for computing extrema (apocenter, pericenter, z_height)
and times of extrema.
Parameters
----------
arr : `numpy.ndarray`
"""
... | Helper function for computing extrema (apocenter, pericenter, z_height)
and times of extrema.
Parameters
----------
arr : `numpy.ndarray` | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L362-L407 |
adrn/gala | gala/dynamics/orbit.py | Orbit.pericenter | def pericenter(self, return_times=False, func=np.mean,
interp_kwargs=None, minimize_kwargs=None,
approximate=False):
"""
Estimate the pericenter(s) of the orbit by identifying local minima in
the spherical radius and interpolating between timesteps near the
... | python | def pericenter(self, return_times=False, func=np.mean,
interp_kwargs=None, minimize_kwargs=None,
approximate=False):
"""
Estimate the pericenter(s) of the orbit by identifying local minima in
the spherical radius and interpolating between timesteps near the
... | Estimate the pericenter(s) of the orbit by identifying local minima in
the spherical radius and interpolating between timesteps near the
minima.
By default, this returns the mean of all local minima (pericenters). To
get, e.g., the minimum pericenter, pass in ``func=np.min``. To get
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L422-L484 |
adrn/gala | gala/dynamics/orbit.py | Orbit.zmax | def zmax(self, return_times=False, func=np.mean,
interp_kwargs=None, minimize_kwargs=None,
approximate=False):
"""
Estimate the maximum ``z`` height of the orbit by identifying local
maxima in the absolute value of the ``z`` position and interpolating
between ti... | python | def zmax(self, return_times=False, func=np.mean,
interp_kwargs=None, minimize_kwargs=None,
approximate=False):
"""
Estimate the maximum ``z`` height of the orbit by identifying local
maxima in the absolute value of the ``z`` position and interpolating
between ti... | Estimate the maximum ``z`` height of the orbit by identifying local
maxima in the absolute value of the ``z`` position and interpolating
between timesteps near the maxima.
By default, this returns the mean of all local maxima. To get, e.g., the
largest ``z`` excursion, pass in ``func=np... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L550-L612 |
adrn/gala | gala/dynamics/orbit.py | Orbit.eccentricity | def eccentricity(self, **kw):
r"""
Returns the eccentricity computed from the mean apocenter and
mean pericenter.
.. math::
e = \frac{r_{\rm apo} - r_{\rm per}}{r_{\rm apo} + r_{\rm per}}
Parameters
----------
**kw
Any keyword arguments ... | python | def eccentricity(self, **kw):
r"""
Returns the eccentricity computed from the mean apocenter and
mean pericenter.
.. math::
e = \frac{r_{\rm apo} - r_{\rm per}}{r_{\rm apo} + r_{\rm per}}
Parameters
----------
**kw
Any keyword arguments ... | r"""
Returns the eccentricity computed from the mean apocenter and
mean pericenter.
.. math::
e = \frac{r_{\rm apo} - r_{\rm per}}{r_{\rm apo} + r_{\rm per}}
Parameters
----------
**kw
Any keyword arguments passed to ``apocenter()`` and
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L614-L637 |
adrn/gala | gala/dynamics/orbit.py | Orbit.estimate_period | def estimate_period(self, radial=True):
"""
Estimate the period of the orbit. By default, computes the radial
period. If ``radial==False``, this returns period estimates for
each dimension of the orbit.
Parameters
----------
radial : bool (optional)
W... | python | def estimate_period(self, radial=True):
"""
Estimate the period of the orbit. By default, computes the radial
period. If ``radial==False``, this returns period estimates for
each dimension of the orbit.
Parameters
----------
radial : bool (optional)
W... | Estimate the period of the orbit. By default, computes the radial
period. If ``radial==False``, this returns period estimates for
each dimension of the orbit.
Parameters
----------
radial : bool (optional)
What period to estimate. If ``True``, estimates the radial
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L639-L675 |
adrn/gala | gala/dynamics/orbit.py | Orbit.circulation | def circulation(self):
"""
Determine which axes the Orbit circulates around by checking
whether there is a change of sign of the angular momentum
about an axis. Returns a 2D array with ``ndim`` integers per orbit
point. If a box orbit, all integers will be 0. A 1 indicates
... | python | def circulation(self):
"""
Determine which axes the Orbit circulates around by checking
whether there is a change of sign of the angular momentum
about an axis. Returns a 2D array with ``ndim`` integers per orbit
point. If a box orbit, all integers will be 0. A 1 indicates
... | Determine which axes the Orbit circulates around by checking
whether there is a change of sign of the angular momentum
about an axis. Returns a 2D array with ``ndim`` integers per orbit
point. If a box orbit, all integers will be 0. A 1 indicates
circulation about the corresponding axis.... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L680-L731 |
adrn/gala | gala/dynamics/orbit.py | Orbit.align_circulation_with_z | def align_circulation_with_z(self, circulation=None):
"""
If the input orbit is a tube orbit, this function aligns the circulation
axis with the z axis and returns a copy.
Parameters
----------
circulation : array_like (optional)
Array of bits that specify th... | python | def align_circulation_with_z(self, circulation=None):
"""
If the input orbit is a tube orbit, this function aligns the circulation
axis with the z axis and returns a copy.
Parameters
----------
circulation : array_like (optional)
Array of bits that specify th... | If the input orbit is a tube orbit, this function aligns the circulation
axis with the z axis and returns a copy.
Parameters
----------
circulation : array_like (optional)
Array of bits that specify the axis about which the orbit
circulates. If not provided, will... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L733-L800 |
adrn/gala | gala/dynamics/orbit.py | Orbit.to_frame | def to_frame(self, frame, current_frame=None, **kwargs):
"""
TODO:
Parameters
----------
frame : `gala.potential.CFrameBase`
The frame to transform to.
current_frame : `gala.potential.CFrameBase` (optional)
If the Orbit has no associated Hamiltoni... | python | def to_frame(self, frame, current_frame=None, **kwargs):
"""
TODO:
Parameters
----------
frame : `gala.potential.CFrameBase`
The frame to transform to.
current_frame : `gala.potential.CFrameBase` (optional)
If the Orbit has no associated Hamiltoni... | TODO:
Parameters
----------
frame : `gala.potential.CFrameBase`
The frame to transform to.
current_frame : `gala.potential.CFrameBase` (optional)
If the Orbit has no associated Hamiltonian, this specifies the
current frame of the orbit.
Retur... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/orbit.py#L885-L916 |
adrn/gala | gala/coordinates/greatcircle.py | greatcircle_to_greatcircle | def greatcircle_to_greatcircle(from_greatcircle_coord,
to_greatcircle_frame):
"""Transform between two greatcircle frames."""
# This transform goes through the parent frames on each side.
# from_frame -> from_frame.origin -> to_frame.origin -> to_frame
intermediate_from =... | python | def greatcircle_to_greatcircle(from_greatcircle_coord,
to_greatcircle_frame):
"""Transform between two greatcircle frames."""
# This transform goes through the parent frames on each side.
# from_frame -> from_frame.origin -> to_frame.origin -> to_frame
intermediate_from =... | Transform between two greatcircle frames. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/greatcircle.py#L21-L31 |
adrn/gala | gala/coordinates/greatcircle.py | reference_to_greatcircle | def reference_to_greatcircle(reference_frame, greatcircle_frame):
"""Convert a reference coordinate to a great circle frame."""
# Define rotation matrices along the position angle vector, and
# relative to the origin.
pole = greatcircle_frame.pole.transform_to(coord.ICRS)
ra0 = greatcircle_frame.ra... | python | def reference_to_greatcircle(reference_frame, greatcircle_frame):
"""Convert a reference coordinate to a great circle frame."""
# Define rotation matrices along the position angle vector, and
# relative to the origin.
pole = greatcircle_frame.pole.transform_to(coord.ICRS)
ra0 = greatcircle_frame.ra... | Convert a reference coordinate to a great circle frame. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/greatcircle.py#L34-L70 |
adrn/gala | gala/coordinates/greatcircle.py | pole_from_endpoints | def pole_from_endpoints(coord1, coord2):
"""Compute the pole from a great circle that connects the two specified
coordinates.
This assumes a right-handed rule from coord1 to coord2: the pole is the
north pole under that assumption.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCo... | python | def pole_from_endpoints(coord1, coord2):
"""Compute the pole from a great circle that connects the two specified
coordinates.
This assumes a right-handed rule from coord1 to coord2: the pole is the
north pole under that assumption.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCo... | Compute the pole from a great circle that connects the two specified
coordinates.
This assumes a right-handed rule from coord1 to coord2: the pole is the
north pole under that assumption.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCoord`
Coordinate of one point on a great ... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/greatcircle.py#L270-L296 |
adrn/gala | gala/coordinates/greatcircle.py | sph_midpoint | def sph_midpoint(coord1, coord2):
"""Compute the midpoint between two points on the sphere.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCoord`
Coordinate of one point on a great circle.
coord2 : `~astropy.coordinates.SkyCoord`
Coordinate of the other point on a great cir... | python | def sph_midpoint(coord1, coord2):
"""Compute the midpoint between two points on the sphere.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCoord`
Coordinate of one point on a great circle.
coord2 : `~astropy.coordinates.SkyCoord`
Coordinate of the other point on a great cir... | Compute the midpoint between two points on the sphere.
Parameters
----------
coord1 : `~astropy.coordinates.SkyCoord`
Coordinate of one point on a great circle.
coord2 : `~astropy.coordinates.SkyCoord`
Coordinate of the other point on a great circle.
Returns
-------
midpt :... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/greatcircle.py#L299-L322 |
adrn/gala | gala/coordinates/pm_cov_transform.py | get_uv_tan | def get_uv_tan(c):
"""Get tangent plane basis vectors on the unit sphere at the given
spherical coordinates.
"""
l = c.spherical.lon
b = c.spherical.lat
p = np.array([-np.sin(l), np.cos(l), np.zeros_like(l.value)]).T
q = np.array([-np.cos(l)*np.sin(b), -np.sin(l)*np.sin(b), np.cos(b)]).T
... | python | def get_uv_tan(c):
"""Get tangent plane basis vectors on the unit sphere at the given
spherical coordinates.
"""
l = c.spherical.lon
b = c.spherical.lat
p = np.array([-np.sin(l), np.cos(l), np.zeros_like(l.value)]).T
q = np.array([-np.cos(l)*np.sin(b), -np.sin(l)*np.sin(b), np.cos(b)]).T
... | Get tangent plane basis vectors on the unit sphere at the given
spherical coordinates. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/pm_cov_transform.py#L8-L18 |
adrn/gala | gala/coordinates/pm_cov_transform.py | get_transform_matrix | def get_transform_matrix(from_frame, to_frame):
"""Compose sequential matrix transformations (static or dynamic) to get a
single transformation matrix from a given path through the Astropy
transformation machinery.
Parameters
----------
from_frame : `~astropy.coordinates.BaseCoordinateFrame` su... | python | def get_transform_matrix(from_frame, to_frame):
"""Compose sequential matrix transformations (static or dynamic) to get a
single transformation matrix from a given path through the Astropy
transformation machinery.
Parameters
----------
from_frame : `~astropy.coordinates.BaseCoordinateFrame` su... | Compose sequential matrix transformations (static or dynamic) to get a
single transformation matrix from a given path through the Astropy
transformation machinery.
Parameters
----------
from_frame : `~astropy.coordinates.BaseCoordinateFrame` subclass
The *class* of the frame you're transfor... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/pm_cov_transform.py#L21-L59 |
adrn/gala | gala/coordinates/pm_cov_transform.py | transform_pm_cov | def transform_pm_cov(c, cov, to_frame):
"""Transform a proper motion covariance matrix to a new frame.
Parameters
----------
c : `~astropy.coordinates.SkyCoord`
The sky coordinates of the sources in the initial coordinate frame.
cov : array_like
The covariance matrix of the proper m... | python | def transform_pm_cov(c, cov, to_frame):
"""Transform a proper motion covariance matrix to a new frame.
Parameters
----------
c : `~astropy.coordinates.SkyCoord`
The sky coordinates of the sources in the initial coordinate frame.
cov : array_like
The covariance matrix of the proper m... | Transform a proper motion covariance matrix to a new frame.
Parameters
----------
c : `~astropy.coordinates.SkyCoord`
The sky coordinates of the sources in the initial coordinate frame.
cov : array_like
The covariance matrix of the proper motions. Must have same length as
the in... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/pm_cov_transform.py#L62-L121 |
adrn/gala | gala/potential/frame/builtin/transformations.py | rodrigues_axis_angle_rotate | def rodrigues_axis_angle_rotate(x, vec, theta):
"""
Rotated the input vector or set of vectors `x` around the axis
`vec` by the angle `theta`.
Parameters
----------
x : array_like
The vector or array of vectors to transform. Must have shape
"""
x = np.array(x).T
vec = np.a... | python | def rodrigues_axis_angle_rotate(x, vec, theta):
"""
Rotated the input vector or set of vectors `x` around the axis
`vec` by the angle `theta`.
Parameters
----------
x : array_like
The vector or array of vectors to transform. Must have shape
"""
x = np.array(x).T
vec = np.a... | Rotated the input vector or set of vectors `x` around the axis
`vec` by the angle `theta`.
Parameters
----------
x : array_like
The vector or array of vectors to transform. Must have shape | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/frame/builtin/transformations.py#L10-L29 |
adrn/gala | gala/potential/frame/builtin/transformations.py | z_angle_rotate | def z_angle_rotate(xy, theta):
"""
Rotated the input vector or set of vectors `xy` by the angle `theta`.
Parameters
----------
xy : array_like
The vector or array of vectors to transform. Must have shape
"""
xy = np.array(xy).T
theta = np.array(theta).T
out = np.zeros_lik... | python | def z_angle_rotate(xy, theta):
"""
Rotated the input vector or set of vectors `xy` by the angle `theta`.
Parameters
----------
xy : array_like
The vector or array of vectors to transform. Must have shape
"""
xy = np.array(xy).T
theta = np.array(theta).T
out = np.zeros_lik... | Rotated the input vector or set of vectors `xy` by the angle `theta`.
Parameters
----------
xy : array_like
The vector or array of vectors to transform. Must have shape | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/frame/builtin/transformations.py#L31-L49 |
adrn/gala | gala/potential/frame/builtin/transformations.py | static_to_constantrotating | def static_to_constantrotating(frame_i, frame_r, w, t=None):
"""
Transform from an inertial static frame to a rotating frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `~gala.dynam... | python | def static_to_constantrotating(frame_i, frame_r, w, t=None):
"""
Transform from an inertial static frame to a rotating frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `~gala.dynam... | Transform from an inertial static frame to a rotating frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `~gala.dynamics.Orbit`
t : quantity_like (optional)
Required if input coo... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/frame/builtin/transformations.py#L100-L120 |
adrn/gala | gala/potential/frame/builtin/transformations.py | constantrotating_to_static | def constantrotating_to_static(frame_r, frame_i, w, t=None):
"""
Transform from a constantly rotating frame to a static, inertial frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `... | python | def constantrotating_to_static(frame_r, frame_i, w, t=None):
"""
Transform from a constantly rotating frame to a static, inertial frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `... | Transform from a constantly rotating frame to a static, inertial frame.
Parameters
----------
frame_i : `~gala.potential.StaticFrame`
frame_r : `~gala.potential.ConstantRotatingFrame`
w : `~gala.dynamics.PhaseSpacePosition`, `~gala.dynamics.Orbit`
t : quantity_like (optional)
Required i... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/frame/builtin/transformations.py#L122-L142 |
adrn/gala | gala/potential/potential/io.py | from_dict | def from_dict(d, module=None):
"""
Convert a dictionary potential specification into a
:class:`~gala.potential.PotentialBase` subclass object.
Parameters
----------
d : dict
Dictionary specification of a potential.
module : namespace (optional)
"""
# need this here for circ... | python | def from_dict(d, module=None):
"""
Convert a dictionary potential specification into a
:class:`~gala.potential.PotentialBase` subclass object.
Parameters
----------
d : dict
Dictionary specification of a potential.
module : namespace (optional)
"""
# need this here for circ... | Convert a dictionary potential specification into a
:class:`~gala.potential.PotentialBase` subclass object.
Parameters
----------
d : dict
Dictionary specification of a potential.
module : namespace (optional) | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/io.py#L70-L117 |
adrn/gala | gala/potential/potential/io.py | to_dict | def to_dict(potential):
"""
Turn a potential object into a dictionary that fully specifies the
state of the object.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object.
"""
from .. import potent... | python | def to_dict(potential):
"""
Turn a potential object into a dictionary that fully specifies the
state of the object.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object.
"""
from .. import potent... | Turn a potential object into a dictionary that fully specifies the
state of the object.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/io.py#L148-L179 |
adrn/gala | gala/potential/potential/io.py | load | def load(f, module=None):
"""
Read a potential specification file and return a
:class:`~gala.potential.PotentialBase` object instantiated with parameters
specified in the spec file.
Parameters
----------
f : str, file_like
A block of text, filename, or file-like object to parse and ... | python | def load(f, module=None):
"""
Read a potential specification file and return a
:class:`~gala.potential.PotentialBase` object instantiated with parameters
specified in the spec file.
Parameters
----------
f : str, file_like
A block of text, filename, or file-like object to parse and ... | Read a potential specification file and return a
:class:`~gala.potential.PotentialBase` object instantiated with parameters
specified in the spec file.
Parameters
----------
f : str, file_like
A block of text, filename, or file-like object to parse and read
a potential from.
mod... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/io.py#L183-L203 |
adrn/gala | gala/potential/potential/io.py | save | def save(potential, f):
"""
Write a :class:`~gala.potential.PotentialBase` object out to a text (YAML)
file.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object.
f : str, file_like
A filename... | python | def save(potential, f):
"""
Write a :class:`~gala.potential.PotentialBase` object out to a text (YAML)
file.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object.
f : str, file_like
A filename... | Write a :class:`~gala.potential.PotentialBase` object out to a text (YAML)
file.
Parameters
----------
potential : :class:`~gala.potential.PotentialBase`
The instantiated :class:`~gala.potential.PotentialBase` object.
f : str, file_like
A filename or file-like object to write the in... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/io.py#L205-L224 |
adrn/gala | gala/integrate/core.py | Integrator._prepare_ws | def _prepare_ws(self, w0, mmap, n_steps):
"""
Decide how to make the return array. If mmap is False, this returns a
full array of zeros, but with the correct shape as the output. If mmap
is True, return a pointer to a memory-mapped array. The latter is
particularly useful for int... | python | def _prepare_ws(self, w0, mmap, n_steps):
"""
Decide how to make the return array. If mmap is False, this returns a
full array of zeros, but with the correct shape as the output. If mmap
is True, return a pointer to a memory-mapped array. The latter is
particularly useful for int... | Decide how to make the return array. If mmap is False, this returns a
full array of zeros, but with the correct shape as the output. If mmap
is True, return a pointer to a memory-mapped array. The latter is
particularly useful for integrating a large number of orbits or
integrating a lar... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/integrate/core.py#L44-L78 |
adrn/gala | gala/dynamics/nonlinear.py | fast_lyapunov_max | def fast_lyapunov_max(w0, hamiltonian, dt, n_steps, d0=1e-5,
n_steps_per_pullback=10, noffset_orbits=2, t1=0.,
atol=1E-10, rtol=1E-10, nmax=0, return_orbit=True):
"""
Compute the maximum Lyapunov exponent using a C-implemented estimator
that uses the DOPRI853 inte... | python | def fast_lyapunov_max(w0, hamiltonian, dt, n_steps, d0=1e-5,
n_steps_per_pullback=10, noffset_orbits=2, t1=0.,
atol=1E-10, rtol=1E-10, nmax=0, return_orbit=True):
"""
Compute the maximum Lyapunov exponent using a C-implemented estimator
that uses the DOPRI853 inte... | Compute the maximum Lyapunov exponent using a C-implemented estimator
that uses the DOPRI853 integrator.
Parameters
----------
w0 : `~gala.dynamics.PhaseSpacePosition`, array_like
Initial conditions.
hamiltonian : `~gala.potential.Hamiltonian`
dt : numeric
Timestep.
n_steps ... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/nonlinear.py#L12-L95 |
adrn/gala | gala/dynamics/nonlinear.py | surface_of_section | def surface_of_section(orbit, plane_ix, interpolate=False):
"""
Generate and return a surface of section from the given orbit.
.. warning::
This is an experimental function and the API may change.
Parameters
----------
orbit : `~gala.dynamics.Orbit`
plane_ix : int
Integer ... | python | def surface_of_section(orbit, plane_ix, interpolate=False):
"""
Generate and return a surface of section from the given orbit.
.. warning::
This is an experimental function and the API may change.
Parameters
----------
orbit : `~gala.dynamics.Orbit`
plane_ix : int
Integer ... | Generate and return a surface of section from the given orbit.
.. warning::
This is an experimental function and the API may change.
Parameters
----------
orbit : `~gala.dynamics.Orbit`
plane_ix : int
Integer that represents the coordinate to record crossings in. For
examp... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/nonlinear.py#L207-L263 |
adrn/gala | gala/potential/potential/core.py | PotentialBase._remove_units | def _remove_units(self, x):
"""
Always returns an array. If a Quantity is passed in, it converts to the
units associated with this object and returns the value.
"""
if hasattr(x, 'unit'):
x = x.decompose(self.units).value
else:
x = np.array(x)
... | python | def _remove_units(self, x):
"""
Always returns an array. If a Quantity is passed in, it converts to the
units associated with this object and returns the value.
"""
if hasattr(x, 'unit'):
x = x.decompose(self.units).value
else:
x = np.array(x)
... | Always returns an array. If a Quantity is passed in, it converts to the
units associated with this object and returns the value. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L96-L107 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.energy | def energy(self, q, t=0.):
"""
Compute the potential energy at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input pos... | python | def energy(self, q, t=0.):
"""
Compute the potential energy at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input pos... | Compute the potential energy at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input position object has no units (i.e. is an `~numpy.n... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L126-L147 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.gradient | def gradient(self, q, t=0.):
"""
Compute the gradient of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
... | python | def gradient(self, q, t=0.):
"""
Compute the gradient of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
... | Compute the gradient of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input position object has no units (i.e. is an ... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L149-L170 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.density | def density(self, q, t=0.):
"""
Compute the density value at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input posit... | python | def density(self, q, t=0.):
"""
Compute the density value at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input posit... | Compute the density value at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input position object has no units (i.e. is an `~numpy.ndar... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L172-L194 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.hessian | def hessian(self, q, t=0.):
"""
Compute the Hessian of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
... | python | def hessian(self, q, t=0.):
"""
Compute the Hessian of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
... | Compute the Hessian of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input position object has no units (i.e. is an `... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L196-L224 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.mass_enclosed | def mass_enclosed(self, q, t=0.):
"""
Estimate the mass enclosed within the given position by assuming the potential
is spherical.
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
Position(s) to estimate the... | python | def mass_enclosed(self, q, t=0.):
"""
Estimate the mass enclosed within the given position by assuming the potential
is spherical.
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
Position(s) to estimate the... | Estimate the mass enclosed within the given position by assuming the potential
is spherical.
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
Position(s) to estimate the enclossed mass.
Returns
-------
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L246-L291 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.circular_velocity | def circular_velocity(self, q, t=0.):
"""
Estimate the circular velocity at the given position assuming the
potential is spherical.
Parameters
----------
q : array_like, numeric
Position(s) to estimate the circular velocity.
Returns
-------
... | python | def circular_velocity(self, q, t=0.):
"""
Estimate the circular velocity at the given position assuming the
potential is spherical.
Parameters
----------
q : array_like, numeric
Position(s) to estimate the circular velocity.
Returns
-------
... | Estimate the circular velocity at the given position assuming the
potential is spherical.
Parameters
----------
q : array_like, numeric
Position(s) to estimate the circular velocity.
Returns
-------
vcirc : `~astropy.units.Quantity`
Circu... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L293-L318 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.plot_contours | def plot_contours(self, grid, filled=True, ax=None, labels=None,
subplots_kw=dict(), **kwargs):
"""
Plot equipotentials contours. Computes the potential energy on a grid
(specified by the array `grid`).
.. warning:: Right now the grid input must be arrays and must ... | python | def plot_contours(self, grid, filled=True, ax=None, labels=None,
subplots_kw=dict(), **kwargs):
"""
Plot equipotentials contours. Computes the potential energy on a grid
(specified by the array `grid`).
.. warning:: Right now the grid input must be arrays and must ... | Plot equipotentials contours. Computes the potential energy on a grid
(specified by the array `grid`).
.. warning:: Right now the grid input must be arrays and must already
be in the unit system of the potential. Quantity support is coming...
Parameters
----------
g... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L396-L497 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.total_energy | def total_energy(self, x, v):
"""
Compute the total energy (per unit mass) of a point in phase-space
in this potential. Assumes the last axis of the input position /
velocity is the dimension axis, e.g., for 100 points in 3-space,
the arrays should have shape (100,3).
Pa... | python | def total_energy(self, x, v):
"""
Compute the total energy (per unit mass) of a point in phase-space
in this potential. Assumes the last axis of the input position /
velocity is the dimension axis, e.g., for 100 points in 3-space,
the arrays should have shape (100,3).
Pa... | Compute the total energy (per unit mass) of a point in phase-space
in this potential. Assumes the last axis of the input position /
velocity is the dimension axis, e.g., for 100 points in 3-space,
the arrays should have shape (100,3).
Parameters
----------
x : array_like... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L649-L667 |
adrn/gala | gala/potential/potential/core.py | PotentialBase.replace_units | def replace_units(self, units, copy=True):
"""Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optio... | python | def replace_units(self, units, copy=True):
"""Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optio... | Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optional)
If True, returns a copy, if False, ch... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L691-L714 |
adrn/gala | gala/potential/potential/core.py | CompositePotential.replace_units | def replace_units(self, units, copy=True):
"""Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optio... | python | def replace_units(self, units, copy=True):
"""Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optio... | Change the unit system of this potential.
Parameters
----------
units : `~gala.units.UnitSystem`
Set of non-reducable units that specify (at minimum) the
length, mass, time, and angle units.
copy : bool (optional)
If True, returns a copy, if False, ch... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/core.py#L810-L834 |
adrn/gala | gala/potential/potential/util.py | from_equation | def from_equation(expr, vars, pars, name=None, hessian=False):
r"""
Create a potential class from an expression for the potential.
.. note::
This utility requires having `Sympy <http://www.sympy.org/>`_ installed.
.. warning::
These potentials are *not* pickle-able and cannot be writ... | python | def from_equation(expr, vars, pars, name=None, hessian=False):
r"""
Create a potential class from an expression for the potential.
.. note::
This utility requires having `Sympy <http://www.sympy.org/>`_ installed.
.. warning::
These potentials are *not* pickle-able and cannot be writ... | r"""
Create a potential class from an expression for the potential.
.. note::
This utility requires having `Sympy <http://www.sympy.org/>`_ installed.
.. warning::
These potentials are *not* pickle-able and cannot be written
out to YAML files (using `~gala.potential.PotentialBase... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/util.py#L18-L162 |
adrn/gala | gala/potential/potential/util.py | format_doc | def format_doc(*args, **kwargs):
"""
Replaces the docstring of the decorated object and then formats it.
Modeled after astropy.utils.decorators.format_doc
"""
def set_docstring(obj):
# None means: use the objects __doc__
doc = obj.__doc__
# Delete documentation in this case... | python | def format_doc(*args, **kwargs):
"""
Replaces the docstring of the decorated object and then formats it.
Modeled after astropy.utils.decorators.format_doc
"""
def set_docstring(obj):
# None means: use the objects __doc__
doc = obj.__doc__
# Delete documentation in this case... | Replaces the docstring of the decorated object and then formats it.
Modeled after astropy.utils.decorators.format_doc | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/potential/potential/util.py#L165-L184 |
adrn/gala | gala/io.py | quantity_from_hdf5 | def quantity_from_hdf5(dset):
"""
Return an Astropy Quantity object from a key in an HDF5 file,
group, or dataset. This checks to see if the input file/group/dataset
contains a ``'unit'`` attribute (e.g., in `f.attrs`).
Parameters
----------
dset : :class:`h5py.DataSet`
Returns
---... | python | def quantity_from_hdf5(dset):
"""
Return an Astropy Quantity object from a key in an HDF5 file,
group, or dataset. This checks to see if the input file/group/dataset
contains a ``'unit'`` attribute (e.g., in `f.attrs`).
Parameters
----------
dset : :class:`h5py.DataSet`
Returns
---... | Return an Astropy Quantity object from a key in an HDF5 file,
group, or dataset. This checks to see if the input file/group/dataset
contains a ``'unit'`` attribute (e.g., in `f.attrs`).
Parameters
----------
dset : :class:`h5py.DataSet`
Returns
-------
q : `astropy.units.Quantity`, `nu... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/io.py#L4-L25 |
adrn/gala | gala/io.py | quantity_to_hdf5 | def quantity_to_hdf5(f, key, q):
"""
Turn an Astropy Quantity object into something we can write out to
an HDF5 file.
Parameters
----------
f : :class:`h5py.File`, :class:`h5py.Group`, :class:`h5py.DataSet`
key : str
The name.
q : float, `astropy.units.Quantity`
The quan... | python | def quantity_to_hdf5(f, key, q):
"""
Turn an Astropy Quantity object into something we can write out to
an HDF5 file.
Parameters
----------
f : :class:`h5py.File`, :class:`h5py.Group`, :class:`h5py.DataSet`
key : str
The name.
q : float, `astropy.units.Quantity`
The quan... | Turn an Astropy Quantity object into something we can write out to
an HDF5 file.
Parameters
----------
f : :class:`h5py.File`, :class:`h5py.Group`, :class:`h5py.DataSet`
key : str
The name.
q : float, `astropy.units.Quantity`
The quantity. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/io.py#L27-L48 |
adrn/gala | gala/units.py | UnitSystem.decompose | def decompose(self, q):
"""
A thin wrapper around :meth:`astropy.units.Quantity.decompose` that
knows how to handle Quantities with physical types with non-default
representations.
Parameters
----------
q : :class:`~astropy.units.Quantity`
An instance... | python | def decompose(self, q):
"""
A thin wrapper around :meth:`astropy.units.Quantity.decompose` that
knows how to handle Quantities with physical types with non-default
representations.
Parameters
----------
q : :class:`~astropy.units.Quantity`
An instance... | A thin wrapper around :meth:`astropy.units.Quantity.decompose` that
knows how to handle Quantities with physical types with non-default
representations.
Parameters
----------
q : :class:`~astropy.units.Quantity`
An instance of an astropy Quantity object.
Ret... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/units.py#L133-L158 |
adrn/gala | gala/units.py | UnitSystem.get_constant | def get_constant(self, name):
"""
Retrieve a constant with specified name in this unit system.
Parameters
----------
name : str
The name of the constant, e.g., G.
Returns
-------
const : float
The value of the constant represented... | python | def get_constant(self, name):
"""
Retrieve a constant with specified name in this unit system.
Parameters
----------
name : str
The name of the constant, e.g., G.
Returns
-------
const : float
The value of the constant represented... | Retrieve a constant with specified name in this unit system.
Parameters
----------
name : str
The name of the constant, e.g., G.
Returns
-------
const : float
The value of the constant represented in this unit system.
Examples
--... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/units.py#L160-L187 |
adrn/gala | gala/util.py | rolling_window | def rolling_window(arr, window_size, stride=1, return_idx=False):
"""
There is an example of an iterator for pure-Python objects in:
http://stackoverflow.com/questions/6822725/rolling-or-sliding-window-iterator-in-python
This is a rolling-window iterator Numpy arrays, with window size and
stride con... | python | def rolling_window(arr, window_size, stride=1, return_idx=False):
"""
There is an example of an iterator for pure-Python objects in:
http://stackoverflow.com/questions/6822725/rolling-or-sliding-window-iterator-in-python
This is a rolling-window iterator Numpy arrays, with window size and
stride con... | There is an example of an iterator for pure-Python objects in:
http://stackoverflow.com/questions/6822725/rolling-or-sliding-window-iterator-in-python
This is a rolling-window iterator Numpy arrays, with window size and
stride control. See examples below for demos.
Parameters
----------
arr : a... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/util.py#L48-L111 |
adrn/gala | gala/util.py | atleast_2d | def atleast_2d(*arys, **kwargs):
"""
View inputs as arrays with at least two dimensions.
Parameters
----------
arys1, arys2, ... : array_like
One or more array-like sequences. Non-array inputs are converted
to arrays. Arrays that already have two or more dimensions are
pre... | python | def atleast_2d(*arys, **kwargs):
"""
View inputs as arrays with at least two dimensions.
Parameters
----------
arys1, arys2, ... : array_like
One or more array-like sequences. Non-array inputs are converted
to arrays. Arrays that already have two or more dimensions are
pre... | View inputs as arrays with at least two dimensions.
Parameters
----------
arys1, arys2, ... : array_like
One or more array-like sequences. Non-array inputs are converted
to arrays. Arrays that already have two or more dimensions are
preserved.
insert_axis : int (optional)
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/util.py#L113-L170 |
adrn/gala | gala/util.py | assert_angles_allclose | def assert_angles_allclose(x, y, **kwargs):
"""
Like numpy's assert_allclose, but for angles (in radians).
"""
c2 = (np.sin(x)-np.sin(y))**2 + (np.cos(x)-np.cos(y))**2
diff = np.arccos((2.0 - c2)/2.0) # a = b = 1
assert np.allclose(diff, 0.0, **kwargs) | python | def assert_angles_allclose(x, y, **kwargs):
"""
Like numpy's assert_allclose, but for angles (in radians).
"""
c2 = (np.sin(x)-np.sin(y))**2 + (np.cos(x)-np.cos(y))**2
diff = np.arccos((2.0 - c2)/2.0) # a = b = 1
assert np.allclose(diff, 0.0, **kwargs) | Like numpy's assert_allclose, but for angles (in radians). | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/util.py#L176-L182 |
adrn/gala | gala/coordinates/quaternion.py | Quaternion.from_v_theta | def from_v_theta(cls, v, theta):
"""
Create a quaternion from unit vector v and rotation angle theta.
Returns
-------
q : :class:`gala.coordinates.Quaternion`
A ``Quaternion`` instance.
"""
theta = np.asarray(theta)
v = np.asarray(v)
... | python | def from_v_theta(cls, v, theta):
"""
Create a quaternion from unit vector v and rotation angle theta.
Returns
-------
q : :class:`gala.coordinates.Quaternion`
A ``Quaternion`` instance.
"""
theta = np.asarray(theta)
v = np.asarray(v)
... | Create a quaternion from unit vector v and rotation angle theta.
Returns
-------
q : :class:`gala.coordinates.Quaternion`
A ``Quaternion`` instance. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/quaternion.py#L27-L45 |
adrn/gala | gala/coordinates/quaternion.py | Quaternion.v_theta | def v_theta(self):
"""
Return the ``(v, theta)`` equivalent of the (normalized) quaternion.
Returns
-------
v : float
theta : float
"""
# compute theta
norm = np.sqrt(np.sum(self.wxyz**2))
theta = 2 * np.arccos(self.wxyz[0] / norm)
... | python | def v_theta(self):
"""
Return the ``(v, theta)`` equivalent of the (normalized) quaternion.
Returns
-------
v : float
theta : float
"""
# compute theta
norm = np.sqrt(np.sum(self.wxyz**2))
theta = 2 * np.arccos(self.wxyz[0] / norm)
... | Return the ``(v, theta)`` equivalent of the (normalized) quaternion.
Returns
-------
v : float
theta : float | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/quaternion.py#L66-L84 |
adrn/gala | gala/coordinates/quaternion.py | Quaternion.rotation_matrix | def rotation_matrix(self):
"""
Compute the rotation matrix of the (normalized) quaternion.
Returns
-------
R : :class:`~numpy.ndarray`
A 3 by 3 rotation matrix (has shape ``(3,3)``).
"""
v, theta = self.v_theta
c = np.cos(theta)
s = n... | python | def rotation_matrix(self):
"""
Compute the rotation matrix of the (normalized) quaternion.
Returns
-------
R : :class:`~numpy.ndarray`
A 3 by 3 rotation matrix (has shape ``(3,3)``).
"""
v, theta = self.v_theta
c = np.cos(theta)
s = n... | Compute the rotation matrix of the (normalized) quaternion.
Returns
-------
R : :class:`~numpy.ndarray`
A 3 by 3 rotation matrix (has shape ``(3,3)``). | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/quaternion.py#L87-L109 |
adrn/gala | gala/coordinates/quaternion.py | Quaternion.random | def random(cls):
"""
Randomly sample a Quaternion from a distribution uniform in
3D rotation angles.
https://www-preview.ri.cmu.edu/pub_files/pub4/kuffner_james_2004_1/kuffner_james_2004_1.pdf
Returns
-------
q : :class:`gala.coordinates.Quaternion`
... | python | def random(cls):
"""
Randomly sample a Quaternion from a distribution uniform in
3D rotation angles.
https://www-preview.ri.cmu.edu/pub_files/pub4/kuffner_james_2004_1/kuffner_james_2004_1.pdf
Returns
-------
q : :class:`gala.coordinates.Quaternion`
... | Randomly sample a Quaternion from a distribution uniform in
3D rotation angles.
https://www-preview.ri.cmu.edu/pub_files/pub4/kuffner_james_2004_1/kuffner_james_2004_1.pdf
Returns
-------
q : :class:`gala.coordinates.Quaternion`
A randomly sampled ``Quaternion`` ins... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/quaternion.py#L112-L137 |
adrn/gala | gala/integrate/pyintegrators/leapfrog.py | LeapfrogIntegrator.step | def step(self, t, x_im1, v_im1_2, dt):
"""
Step forward the positions and velocities by the given timestep.
Parameters
----------
dt : numeric
The timestep to move forward.
"""
x_i = x_im1 + v_im1_2 * dt
F_i = self.F(t, np.vstack((x_i, v_im1_... | python | def step(self, t, x_im1, v_im1_2, dt):
"""
Step forward the positions and velocities by the given timestep.
Parameters
----------
dt : numeric
The timestep to move forward.
"""
x_i = x_im1 + v_im1_2 * dt
F_i = self.F(t, np.vstack((x_i, v_im1_... | Step forward the positions and velocities by the given timestep.
Parameters
----------
dt : numeric
The timestep to move forward. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/integrate/pyintegrators/leapfrog.py#L93-L110 |
adrn/gala | gala/integrate/pyintegrators/leapfrog.py | LeapfrogIntegrator._init_v | def _init_v(self, t, w0, dt):
"""
Leapfrog updates the velocities offset a half-step from the
position updates. If we're given initial conditions aligned in
time, e.g. the positions and velocities at the same 0th step,
then we have to initially scoot the velocities forward by a h... | python | def _init_v(self, t, w0, dt):
"""
Leapfrog updates the velocities offset a half-step from the
position updates. If we're given initial conditions aligned in
time, e.g. the positions and velocities at the same 0th step,
then we have to initially scoot the velocities forward by a h... | Leapfrog updates the velocities offset a half-step from the
position updates. If we're given initial conditions aligned in
time, e.g. the positions and velocities at the same 0th step,
then we have to initially scoot the velocities forward by a half
step to prime the integrator.
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/integrate/pyintegrators/leapfrog.py#L112-L131 |
adrn/gala | gala/dynamics/actionangle.py | generate_n_vectors | def generate_n_vectors(N_max, dx=1, dy=1, dz=1, half_lattice=True):
r"""
Generate integer vectors, :math:`\boldsymbol{n}`, with
:math:`|\boldsymbol{n}| < N_{\rm max}`.
If ``half_lattice=True``, only return half of the three-dimensional
lattice. If the set N = {(i,j,k)} defines the lattice, we restr... | python | def generate_n_vectors(N_max, dx=1, dy=1, dz=1, half_lattice=True):
r"""
Generate integer vectors, :math:`\boldsymbol{n}`, with
:math:`|\boldsymbol{n}| < N_{\rm max}`.
If ``half_lattice=True``, only return half of the three-dimensional
lattice. If the set N = {(i,j,k)} defines the lattice, we restr... | r"""
Generate integer vectors, :math:`\boldsymbol{n}`, with
:math:`|\boldsymbol{n}| < N_{\rm max}`.
If ``half_lattice=True``, only return half of the three-dimensional
lattice. If the set N = {(i,j,k)} defines the lattice, we restrict to
the cases such that ``(k > 0)``, ``(k = 0, j > 0)``, and
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L23-L76 |
adrn/gala | gala/dynamics/actionangle.py | fit_isochrone | def fit_isochrone(orbit, m0=2E11, b0=1., minimize_kwargs=None):
r"""
Fit the toy Isochrone potential to the sum of the energy residuals relative
to the mean energy by minimizing the function
.. math::
f(m,b) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm iso}(x_i\,|\,m,b) - <E>)^2
TODO: This shou... | python | def fit_isochrone(orbit, m0=2E11, b0=1., minimize_kwargs=None):
r"""
Fit the toy Isochrone potential to the sum of the energy residuals relative
to the mean energy by minimizing the function
.. math::
f(m,b) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm iso}(x_i\,|\,m,b) - <E>)^2
TODO: This shou... | r"""
Fit the toy Isochrone potential to the sum of the energy residuals relative
to the mean energy by minimizing the function
.. math::
f(m,b) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm iso}(x_i\,|\,m,b) - <E>)^2
TODO: This should fail if the Hamiltonian associated with the orbit has
a... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L78-L140 |
adrn/gala | gala/dynamics/actionangle.py | fit_harmonic_oscillator | def fit_harmonic_oscillator(orbit, omega0=[1., 1, 1], minimize_kwargs=None):
r"""
Fit the toy harmonic oscillator potential to the sum of the energy
residuals relative to the mean energy by minimizing the function
.. math::
f(\boldsymbol{\omega}) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm sho}(x_i... | python | def fit_harmonic_oscillator(orbit, omega0=[1., 1, 1], minimize_kwargs=None):
r"""
Fit the toy harmonic oscillator potential to the sum of the energy
residuals relative to the mean energy by minimizing the function
.. math::
f(\boldsymbol{\omega}) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm sho}(x_i... | r"""
Fit the toy harmonic oscillator potential to the sum of the energy
residuals relative to the mean energy by minimizing the function
.. math::
f(\boldsymbol{\omega}) = \sum_i (\frac{1}{2}v_i^2 + \Phi_{\rm sho}(x_i\,|\,\boldsymbol{\omega}) - <E>)^2
TODO: This should fail if the Hamiltonian... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L142-L194 |
adrn/gala | gala/dynamics/actionangle.py | fit_toy_potential | def fit_toy_potential(orbit, force_harmonic_oscillator=False):
"""
Fit a best fitting toy potential to the orbit provided. If the orbit is a
tube (loop) orbit, use the Isochrone potential. If the orbit is a box
potential, use the harmonic oscillator potential. An option is available to
force using t... | python | def fit_toy_potential(orbit, force_harmonic_oscillator=False):
"""
Fit a best fitting toy potential to the orbit provided. If the orbit is a
tube (loop) orbit, use the Isochrone potential. If the orbit is a box
potential, use the harmonic oscillator potential. An option is available to
force using t... | Fit a best fitting toy potential to the orbit provided. If the orbit is a
tube (loop) orbit, use the Isochrone potential. If the orbit is a box
potential, use the harmonic oscillator potential. An option is available to
force using the harmonic oscillator (`force_harmonic_oscillator`).
See the docstrin... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L196-L235 |
adrn/gala | gala/dynamics/actionangle.py | check_angle_sampling | def check_angle_sampling(nvecs, angles):
"""
Returns a list of the index of elements of n which do not have adequate
toy angle coverage. The criterion is that we must have at least one sample
in each Nyquist box when we project the toy angles along the vector n.
Parameters
----------
nvecs ... | python | def check_angle_sampling(nvecs, angles):
"""
Returns a list of the index of elements of n which do not have adequate
toy angle coverage. The criterion is that we must have at least one sample
in each Nyquist box when we project the toy angles along the vector n.
Parameters
----------
nvecs ... | Returns a list of the index of elements of n which do not have adequate
toy angle coverage. The criterion is that we must have at least one sample
in each Nyquist box when we project the toy angles along the vector n.
Parameters
----------
nvecs : array_like
Array of integer vectors.
an... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L237-L283 |
adrn/gala | gala/dynamics/actionangle.py | _action_prepare | def _action_prepare(aa, N_max, dx, dy, dz, sign=1., throw_out_modes=False):
"""
Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" actions and generating
function values, `x` (see Equations 12-14 in Sanders & Binney (2014)).
.. todo::
... | python | def _action_prepare(aa, N_max, dx, dy, dz, sign=1., throw_out_modes=False):
"""
Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" actions and generating
function values, `x` (see Equations 12-14 in Sanders & Binney (2014)).
.. todo::
... | Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" actions and generating
function values, `x` (see Equations 12-14 in Sanders & Binney (2014)).
.. todo::
Wrong shape for aa -- should be (6,n) as usual...
Parameters
----------
a... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L285-L353 |
adrn/gala | gala/dynamics/actionangle.py | _angle_prepare | def _angle_prepare(aa, t, N_max, dx, dy, dz, sign=1.):
"""
Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" angles, frequencies, and
generating function derivatives, `x` (see Appendix of
Sanders & Binney (2014)).
.. todo::
Wron... | python | def _angle_prepare(aa, t, N_max, dx, dy, dz, sign=1.):
"""
Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" angles, frequencies, and
generating function derivatives, `x` (see Appendix of
Sanders & Binney (2014)).
.. todo::
Wron... | Given toy actions and angles, `aa`, compute the matrix `A` and
vector `b` to solve for the vector of "true" angles, frequencies, and
generating function derivatives, `x` (see Appendix of
Sanders & Binney (2014)).
.. todo::
Wrong shape for aa -- should be (6,n) as usual...
Parameters
-... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L355-L441 |
adrn/gala | gala/dynamics/actionangle.py | _single_orbit_find_actions | def _single_orbit_find_actions(orbit, N_max, toy_potential=None,
force_harmonic_oscillator=False):
"""
Find approximate actions and angles for samples of a phase-space orbit,
`w`, at times `t`. Uses toy potentials with known, analytic action-angle
transformations to approx... | python | def _single_orbit_find_actions(orbit, N_max, toy_potential=None,
force_harmonic_oscillator=False):
"""
Find approximate actions and angles for samples of a phase-space orbit,
`w`, at times `t`. Uses toy potentials with known, analytic action-angle
transformations to approx... | Find approximate actions and angles for samples of a phase-space orbit,
`w`, at times `t`. Uses toy potentials with known, analytic action-angle
transformations to approximate the true coordinates as a Fourier sum.
This code is adapted from Jason Sanders'
`genfunc <https://github.com/jlsanders/genfunc>... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L443-L537 |
adrn/gala | gala/dynamics/actionangle.py | find_actions | def find_actions(orbit, N_max, force_harmonic_oscillator=False, toy_potential=None):
r"""
Find approximate actions and angles for samples of a phase-space orbit.
Uses toy potentials with known, analytic action-angle transformations to
approximate the true coordinates as a Fourier sum.
This code is ... | python | def find_actions(orbit, N_max, force_harmonic_oscillator=False, toy_potential=None):
r"""
Find approximate actions and angles for samples of a phase-space orbit.
Uses toy potentials with known, analytic action-angle transformations to
approximate the true coordinates as a Fourier sum.
This code is ... | r"""
Find approximate actions and angles for samples of a phase-space orbit.
Uses toy potentials with known, analytic action-angle transformations to
approximate the true coordinates as a Fourier sum.
This code is adapted from Jason Sanders'
`genfunc <https://github.com/jlsanders/genfunc>`_
Pa... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/actionangle.py#L539-L591 |
adrn/gala | gala/integrate/timespec.py | parse_time_specification | def parse_time_specification(units, dt=None, n_steps=None, nsteps=None, t1=None, t2=None, t=None):
"""
Return an array of times given a few combinations of kwargs that are
accepted -- see below.
Parameters
----------
dt, n_steps[, t1] : (numeric, int[, numeric])
A fixed timestep dt and ... | python | def parse_time_specification(units, dt=None, n_steps=None, nsteps=None, t1=None, t2=None, t=None):
"""
Return an array of times given a few combinations of kwargs that are
accepted -- see below.
Parameters
----------
dt, n_steps[, t1] : (numeric, int[, numeric])
A fixed timestep dt and ... | Return an array of times given a few combinations of kwargs that are
accepted -- see below.
Parameters
----------
dt, n_steps[, t1] : (numeric, int[, numeric])
A fixed timestep dt and a number of steps to run for.
dt, t1, t2 : (numeric, numeric, numeric)
A fixed timestep dt, an init... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/integrate/timespec.py#L13-L110 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | angact_ho | def angact_ho(x,omega):
""" Calculate angle and action variable in sho potential with
parameter omega """
action = (x[3:]**2+(omega*x[:3])**2)/(2.*omega)
angle = np.array([np.arctan(-x[3+i]/omega[i]/x[i]) if x[i]!=0. else -np.sign(x[3+i])*np.pi/2. for i in range(3)])
for i in range(3):
if(x[... | python | def angact_ho(x,omega):
""" Calculate angle and action variable in sho potential with
parameter omega """
action = (x[3:]**2+(omega*x[:3])**2)/(2.*omega)
angle = np.array([np.arctan(-x[3+i]/omega[i]/x[i]) if x[i]!=0. else -np.sign(x[3+i])*np.pi/2. for i in range(3)])
for i in range(3):
if(x[... | Calculate angle and action variable in sho potential with
parameter omega | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L18-L26 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | findbestparams_ho | def findbestparams_ho(xsamples):
""" Minimize sum of square differences of H_sho-<H_sho> for timesamples """
return np.abs(leastsq(deltaH_ho,np.array([10.,10.,10.]), Dfun = Jac_deltaH_ho, args=(xsamples,))[0])[:3] | python | def findbestparams_ho(xsamples):
""" Minimize sum of square differences of H_sho-<H_sho> for timesamples """
return np.abs(leastsq(deltaH_ho,np.array([10.,10.,10.]), Dfun = Jac_deltaH_ho, args=(xsamples,))[0])[:3] | Minimize sum of square differences of H_sho-<H_sho> for timesamples | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L39-L41 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | cart2spol | def cart2spol(X):
""" Performs coordinate transformation from cartesian
to spherical polar coordinates with (r,phi,theta) having
usual meanings. """
x,y,z,vx,vy,vz=X
r=np.sqrt(x*x+y*y+z*z)
p=np.arctan2(y,x)
t=np.arccos(z/r)
vr=(vx*np.cos(p)+vy*np.sin(p))*np.sin(t)+np.cos(t)*vz
vp=-vx... | python | def cart2spol(X):
""" Performs coordinate transformation from cartesian
to spherical polar coordinates with (r,phi,theta) having
usual meanings. """
x,y,z,vx,vy,vz=X
r=np.sqrt(x*x+y*y+z*z)
p=np.arctan2(y,x)
t=np.arccos(z/r)
vr=(vx*np.cos(p)+vy*np.sin(p))*np.sin(t)+np.cos(t)*vz
vp=-vx... | Performs coordinate transformation from cartesian
to spherical polar coordinates with (r,phi,theta) having
usual meanings. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L46-L57 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | H_iso | def H_iso(x,params):
""" Isochrone Hamiltonian = -GM/(b+sqrt(b**2+(r-r0)**2))"""
#r = (np.sqrt(np.sum(x[:3]**2))-params[2])**2
r = np.sum(x[:3]**2)
return 0.5*np.sum(x[3:]**2)-Grav*params[0]/(params[1]+np.sqrt(params[1]**2+r)) | python | def H_iso(x,params):
""" Isochrone Hamiltonian = -GM/(b+sqrt(b**2+(r-r0)**2))"""
#r = (np.sqrt(np.sum(x[:3]**2))-params[2])**2
r = np.sum(x[:3]**2)
return 0.5*np.sum(x[3:]**2)-Grav*params[0]/(params[1]+np.sqrt(params[1]**2+r)) | Isochrone Hamiltonian = -GM/(b+sqrt(b**2+(r-r0)**2)) | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L60-L64 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | angact_iso | def angact_iso(x,params):
""" Calculate angle and action variable in isochrone potential with
parameters params = (M,b) """
GM = Grav*params[0]
E = H_iso(x,params)
r,p,t,vr,vphi,vt=cart2spol(x)
st=np.sin(t)
Lz=r*vphi*st
L=np.sqrt(r*r*vt*vt+Lz*Lz/st/st)
if(E>0.): # Unbound
re... | python | def angact_iso(x,params):
""" Calculate angle and action variable in isochrone potential with
parameters params = (M,b) """
GM = Grav*params[0]
E = H_iso(x,params)
r,p,t,vr,vphi,vt=cart2spol(x)
st=np.sin(t)
Lz=r*vphi*st
L=np.sqrt(r*r*vt*vt+Lz*Lz/st/st)
if(E>0.): # Unbound
re... | Calculate angle and action variable in isochrone potential with
parameters params = (M,b) | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L67-L113 |
adrn/gala | gala/dynamics/_genfunc/toy_potentials.py | findbestparams_iso | def findbestparams_iso(xsamples):
""" Minimize sum of square differences of H_iso-<H_iso> for timesamples"""
p = 0.5*np.sum(xsamples.T[3:]**2,axis=0)
r = np.sum(xsamples.T[:3]**2,axis=0)
return np.abs(leastsq(deltaH_iso,np.array([10.,10.]), Dfun = None , col_deriv=1,args=(p,r,))[0]) | python | def findbestparams_iso(xsamples):
""" Minimize sum of square differences of H_iso-<H_iso> for timesamples"""
p = 0.5*np.sum(xsamples.T[3:]**2,axis=0)
r = np.sum(xsamples.T[:3]**2,axis=0)
return np.abs(leastsq(deltaH_iso,np.array([10.,10.]), Dfun = None , col_deriv=1,args=(p,r,))[0]) | Minimize sum of square differences of H_iso-<H_iso> for timesamples | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/toy_potentials.py#L130-L134 |
adrn/gala | gala/dynamics/util.py | peak_to_peak_period | def peak_to_peak_period(t, f, amplitude_threshold=1E-2):
"""
Estimate the period of the input time series by measuring the average
peak-to-peak time.
Parameters
----------
t : array_like
Time grid aligned with the input time series.
f : array_like
A periodic time series.
... | python | def peak_to_peak_period(t, f, amplitude_threshold=1E-2):
"""
Estimate the period of the input time series by measuring the average
peak-to-peak time.
Parameters
----------
t : array_like
Time grid aligned with the input time series.
f : array_like
A periodic time series.
... | Estimate the period of the input time series by measuring the average
peak-to-peak time.
Parameters
----------
t : array_like
Time grid aligned with the input time series.
f : array_like
A periodic time series.
amplitude_threshold : numeric (optional)
A tolerance paramet... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/util.py#L17-L68 |
adrn/gala | gala/dynamics/util.py | estimate_dt_n_steps | def estimate_dt_n_steps(w0, hamiltonian, n_periods, n_steps_per_period,
dE_threshold=1E-9, func=np.nanmax,
**integrate_kwargs):
"""
Estimate the timestep and number of steps to integrate an orbit for
given its initial conditions and a potential object.
Pa... | python | def estimate_dt_n_steps(w0, hamiltonian, n_periods, n_steps_per_period,
dE_threshold=1E-9, func=np.nanmax,
**integrate_kwargs):
"""
Estimate the timestep and number of steps to integrate an orbit for
given its initial conditions and a potential object.
Pa... | Estimate the timestep and number of steps to integrate an orbit for
given its initial conditions and a potential object.
Parameters
----------
w0 : `~gala.dynamics.PhaseSpacePosition`, array_like
Initial conditions.
potential : :class:`~gala.potential.PotentialBase`
The potential to... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/util.py#L94-L169 |
adrn/gala | gala/dynamics/util.py | combine | def combine(objs):
"""Combine the specified `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects.
Parameters
----------
objs : iterable
An iterable of either `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects.
"""
from .orbit import Orbit
... | python | def combine(objs):
"""Combine the specified `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects.
Parameters
----------
objs : iterable
An iterable of either `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects.
"""
from .orbit import Orbit
... | Combine the specified `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects.
Parameters
----------
objs : iterable
An iterable of either `~gala.dynamics.PhaseSpacePosition` or
`~gala.dynamics.Orbit` objects. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/util.py#L171-L277 |
adrn/gala | gala/coordinates/reflex.py | reflex_correct | def reflex_correct(coords, galactocentric_frame=None):
"""Correct the input Astropy coordinate object for solar reflex motion.
The input coordinate instance must have distance and radial velocity information. If the radial velocity is not known, fill the
Parameters
----------
coords : `~astropy.co... | python | def reflex_correct(coords, galactocentric_frame=None):
"""Correct the input Astropy coordinate object for solar reflex motion.
The input coordinate instance must have distance and radial velocity information. If the radial velocity is not known, fill the
Parameters
----------
coords : `~astropy.co... | Correct the input Astropy coordinate object for solar reflex motion.
The input coordinate instance must have distance and radial velocity information. If the radial velocity is not known, fill the
Parameters
----------
coords : `~astropy.coordinates.SkyCoord`
The Astropy coordinate object with... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/coordinates/reflex.py#L5-L40 |
adrn/gala | gala/dynamics/plot.py | _get_axes | def _get_axes(dim, subplots_kwargs=dict()):
"""
Parameters
----------
dim : int
Dimensionality of the orbit.
subplots_kwargs : dict (optional)
Dictionary of kwargs passed to :func:`~matplotlib.pyplot.subplots`.
"""
import matplotlib.pyplot as plt
if dim > 1:
n_p... | python | def _get_axes(dim, subplots_kwargs=dict()):
"""
Parameters
----------
dim : int
Dimensionality of the orbit.
subplots_kwargs : dict (optional)
Dictionary of kwargs passed to :func:`~matplotlib.pyplot.subplots`.
"""
import matplotlib.pyplot as plt
if dim > 1:
n_p... | Parameters
----------
dim : int
Dimensionality of the orbit.
subplots_kwargs : dict (optional)
Dictionary of kwargs passed to :func:`~matplotlib.pyplot.subplots`. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/plot.py#L6-L32 |
adrn/gala | gala/dynamics/plot.py | plot_projections | def plot_projections(x, relative_to=None, autolim=True, axes=None,
subplots_kwargs=dict(), labels=None, plot_function=None,
**kwargs):
"""
Given N-dimensional quantity, ``x``, make a figure containing 2D projections
of all combinations of the axes.
Parameters
... | python | def plot_projections(x, relative_to=None, autolim=True, axes=None,
subplots_kwargs=dict(), labels=None, plot_function=None,
**kwargs):
"""
Given N-dimensional quantity, ``x``, make a figure containing 2D projections
of all combinations of the axes.
Parameters
... | Given N-dimensional quantity, ``x``, make a figure containing 2D projections
of all combinations of the axes.
Parameters
----------
x : array_like
Array of values. ``axis=0`` is assumed to be the dimensionality,
``axis=1`` is the time axis. See :ref:`shape-conventions` for more
... | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/plot.py#L34-L120 |
adrn/gala | gala/dynamics/_genfunc/genfunc_3d.py | check_angle_solution | def check_angle_solution(ang,n_vec,toy_aa,timeseries):
""" Plots the toy angle solution against the toy angles ---
Takes true angles and frequencies ang,
the Fourier vectors n_vec,
the toy action-angles toy_aa
and the timeseries """
f,a=plt.subplots(3,1)
for i in range(3):
... | python | def check_angle_solution(ang,n_vec,toy_aa,timeseries):
""" Plots the toy angle solution against the toy angles ---
Takes true angles and frequencies ang,
the Fourier vectors n_vec,
the toy action-angles toy_aa
and the timeseries """
f,a=plt.subplots(3,1)
for i in range(3):
... | Plots the toy angle solution against the toy angles ---
Takes true angles and frequencies ang,
the Fourier vectors n_vec,
the toy action-angles toy_aa
and the timeseries | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/genfunc_3d.py#L30-L44 |
adrn/gala | gala/dynamics/_genfunc/genfunc_3d.py | eval_mean_error_functions | def eval_mean_error_functions(act,ang,n_vec,toy_aa,timeseries,withplot=False):
""" Calculates sqrt(mean(E)) and sqrt(mean(F)) """
Err = np.zeros(6)
NT = len(timeseries)
size = len(ang[6:])/3
UA = ua(toy_aa.T[3:].T,np.ones(3))
fig,axis=None,None
if(withplot):
fig,axis=plt.subplots(3,... | python | def eval_mean_error_functions(act,ang,n_vec,toy_aa,timeseries,withplot=False):
""" Calculates sqrt(mean(E)) and sqrt(mean(F)) """
Err = np.zeros(6)
NT = len(timeseries)
size = len(ang[6:])/3
UA = ua(toy_aa.T[3:].T,np.ones(3))
fig,axis=None,None
if(withplot):
fig,axis=plt.subplots(3,... | Calculates sqrt(mean(E)) and sqrt(mean(F)) | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/genfunc_3d.py#L63-L94 |
adrn/gala | gala/dynamics/_genfunc/genfunc_3d.py | box_actions | def box_actions(results, times, N_matrix, ifprint):
"""
Finds actions, angles and frequencies for box orbit.
Takes a series of phase-space points from an orbit integration at times t and returns
L = (act,ang,n_vec,toy_aa, pars) -- explained in find_actions() below.
"""
if(ifprint):
... | python | def box_actions(results, times, N_matrix, ifprint):
"""
Finds actions, angles and frequencies for box orbit.
Takes a series of phase-space points from an orbit integration at times t and returns
L = (act,ang,n_vec,toy_aa, pars) -- explained in find_actions() below.
"""
if(ifprint):
... | Finds actions, angles and frequencies for box orbit.
Takes a series of phase-space points from an orbit integration at times t and returns
L = (act,ang,n_vec,toy_aa, pars) -- explained in find_actions() below. | https://github.com/adrn/gala/blob/ea95575a0df1581bb4b0986aebd6eea8438ab7eb/gala/dynamics/_genfunc/genfunc_3d.py#L96-L135 |
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