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PyAr/fades | fades/envbuilder.py | _FadesEnvBuilder.create_env | def create_env(self, interpreter, is_current, options):
"""Create the virtualenv and return its info."""
if is_current:
# apply pyvenv options
pyvenv_options = options['pyvenv_options']
if "--system-site-packages" in pyvenv_options:
self.system_site_pa... | python | def create_env(self, interpreter, is_current, options):
"""Create the virtualenv and return its info."""
if is_current:
# apply pyvenv options
pyvenv_options = options['pyvenv_options']
if "--system-site-packages" in pyvenv_options:
self.system_site_pa... | [
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PyAr/fades | fades/envbuilder.py | UsageManager.store_usage_stat | def store_usage_stat(self, venv_data, cache):
"""Log an usage record for venv_data."""
with open(self.stat_file_path, 'at') as f:
self._write_venv_usage(f, venv_data) | python | def store_usage_stat(self, venv_data, cache):
"""Log an usage record for venv_data."""
with open(self.stat_file_path, 'at') as f:
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PyAr/fades | fades/envbuilder.py | UsageManager.clean_unused_venvs | def clean_unused_venvs(self, max_days_to_keep):
"""Compact usage stats and remove venvs.
This method loads the complete file usage in memory, for every venv compact all records in
one (the lastest), updates this info for every env deleted and, finally, write the entire
file to disk.
... | python | def clean_unused_venvs(self, max_days_to_keep):
"""Compact usage stats and remove venvs.
This method loads the complete file usage in memory, for every venv compact all records in
one (the lastest), updates this info for every env deleted and, finally, write the entire
file to disk.
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PyAr/fades | fades/helpers.py | logged_exec | def logged_exec(cmd):
"""Execute a command, redirecting the output to the log."""
logger = logging.getLogger('fades.exec')
logger.debug("Executing external command: %r", cmd)
p = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
stdout = []
... | python | def logged_exec(cmd):
"""Execute a command, redirecting the output to the log."""
logger = logging.getLogger('fades.exec')
logger.debug("Executing external command: %r", cmd)
p = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
stdout = []
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PyAr/fades | fades/helpers.py | _get_specific_dir | def _get_specific_dir(dir_type):
"""Get a specific directory, using some XDG base, with sensible default."""
if SNAP_BASEDIR_NAME in os.environ:
logger.debug("Getting base dir information from SNAP_BASEDIR_NAME env var.")
direct = os.path.join(os.environ[SNAP_BASEDIR_NAME], dir_type)
else:
... | python | def _get_specific_dir(dir_type):
"""Get a specific directory, using some XDG base, with sensible default."""
if SNAP_BASEDIR_NAME in os.environ:
logger.debug("Getting base dir information from SNAP_BASEDIR_NAME env var.")
direct = os.path.join(os.environ[SNAP_BASEDIR_NAME], dir_type)
else:
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PyAr/fades | fades/helpers.py | _get_interpreter_info | def _get_interpreter_info(interpreter=None):
"""Return the interpreter's full path using pythonX.Y format."""
if interpreter is None:
# If interpreter is None by default returns the current interpreter data.
major, minor = sys.version_info[:2]
executable = sys.executable
else:
... | python | def _get_interpreter_info(interpreter=None):
"""Return the interpreter's full path using pythonX.Y format."""
if interpreter is None:
# If interpreter is None by default returns the current interpreter data.
major, minor = sys.version_info[:2]
executable = sys.executable
else:
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PyAr/fades | fades/helpers.py | get_interpreter_version | def get_interpreter_version(requested_interpreter):
"""Return a 'sanitized' interpreter and indicates if it is the current one."""
logger.debug('Getting interpreter version for: %s', requested_interpreter)
current_interpreter = _get_interpreter_info()
logger.debug('Current interpreter is %s', current_in... | python | def get_interpreter_version(requested_interpreter):
"""Return a 'sanitized' interpreter and indicates if it is the current one."""
logger.debug('Getting interpreter version for: %s', requested_interpreter)
current_interpreter = _get_interpreter_info()
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PyAr/fades | fades/helpers.py | check_pypi_updates | def check_pypi_updates(dependencies):
"""Return a list of dependencies to upgrade."""
dependencies_up_to_date = []
for dependency in dependencies.get('pypi', []):
# get latest version from PyPI api
try:
latest_version = get_latest_version_number(dependency.project_name)
e... | python | def check_pypi_updates(dependencies):
"""Return a list of dependencies to upgrade."""
dependencies_up_to_date = []
for dependency in dependencies.get('pypi', []):
# get latest version from PyPI api
try:
latest_version = get_latest_version_number(dependency.project_name)
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PyAr/fades | fades/helpers.py | _pypi_head_package | def _pypi_head_package(dependency):
"""Hit pypi with a http HEAD to check if pkg_name exists."""
if dependency.specs:
_, version = dependency.specs[0]
url = BASE_PYPI_URL_WITH_VERSION.format(name=dependency.project_name, version=version)
else:
url = BASE_PYPI_URL.format(name=dependen... | python | def _pypi_head_package(dependency):
"""Hit pypi with a http HEAD to check if pkg_name exists."""
if dependency.specs:
_, version = dependency.specs[0]
url = BASE_PYPI_URL_WITH_VERSION.format(name=dependency.project_name, version=version)
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PyAr/fades | fades/helpers.py | check_pypi_exists | def check_pypi_exists(dependencies):
"""Check if the indicated dependencies actually exists in pypi."""
for dependency in dependencies.get('pypi', []):
logger.debug("Checking if %r exists in PyPI", dependency)
try:
exists = _pypi_head_package(dependency)
except Exception as e... | python | def check_pypi_exists(dependencies):
"""Check if the indicated dependencies actually exists in pypi."""
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PyAr/fades | fades/helpers.py | download_remote_script | def download_remote_script(url):
"""Download the content of a remote script to a local temp file."""
temp_fh = tempfile.NamedTemporaryFile('wt', encoding='utf8', suffix=".py", delete=False)
downloader = _ScriptDownloader(url)
logger.info(
"Downloading remote script from %r using (%r downloader) ... | python | def download_remote_script(url):
"""Download the content of a remote script to a local temp file."""
temp_fh = tempfile.NamedTemporaryFile('wt', encoding='utf8', suffix=".py", delete=False)
downloader = _ScriptDownloader(url)
logger.info(
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PyAr/fades | fades/helpers.py | ExecutionError.dump_to_log | def dump_to_log(self, logger):
"""Send the cmd info and collected stdout to logger."""
logger.error("Execution ended in %s for cmd %s", self._retcode, self._cmd)
for line in self._collected_stdout:
logger.error(STDOUT_LOG_PREFIX + line) | python | def dump_to_log(self, logger):
"""Send the cmd info and collected stdout to logger."""
logger.error("Execution ended in %s for cmd %s", self._retcode, self._cmd)
for line in self._collected_stdout:
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PyAr/fades | fades/helpers.py | _ScriptDownloader._decide | def _decide(self):
"""Find out which method should be applied to download that URL."""
netloc = parse.urlparse(self.url).netloc
name = self.NETLOCS.get(netloc, 'raw')
return name | python | def _decide(self):
"""Find out which method should be applied to download that URL."""
netloc = parse.urlparse(self.url).netloc
name = self.NETLOCS.get(netloc, 'raw')
return name | [
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PyAr/fades | fades/helpers.py | _ScriptDownloader.get | def get(self):
"""Get the script content from the URL using the decided downloader."""
method_name = "_download_" + self.name
method = getattr(self, method_name)
return method() | python | def get(self):
"""Get the script content from the URL using the decided downloader."""
method_name = "_download_" + self.name
method = getattr(self, method_name)
return method() | [
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PyAr/fades | fades/helpers.py | _ScriptDownloader._download_raw | def _download_raw(self, url=None):
"""Download content from URL directly."""
if url is None:
url = self.url
req = request.Request(url, headers=self.HEADERS_PLAIN)
return request.urlopen(req).read().decode("utf8") | python | def _download_raw(self, url=None):
"""Download content from URL directly."""
if url is None:
url = self.url
req = request.Request(url, headers=self.HEADERS_PLAIN)
return request.urlopen(req).read().decode("utf8") | [
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PyAr/fades | fades/helpers.py | _ScriptDownloader._download_linkode | def _download_linkode(self):
"""Download content from Linkode pastebin."""
# build the API url
linkode_id = self.url.split("/")[-1]
if linkode_id.startswith("#"):
linkode_id = linkode_id[1:]
url = "https://linkode.org/api/1/linkodes/" + linkode_id
req = reque... | python | def _download_linkode(self):
"""Download content from Linkode pastebin."""
# build the API url
linkode_id = self.url.split("/")[-1]
if linkode_id.startswith("#"):
linkode_id = linkode_id[1:]
url = "https://linkode.org/api/1/linkodes/" + linkode_id
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PyAr/fades | fades/helpers.py | _ScriptDownloader._download_pastebin | def _download_pastebin(self):
"""Download content from Pastebin itself."""
paste_id = self.url.split("/")[-1]
url = "https://pastebin.com/raw/" + paste_id
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if m is None:
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"""Retrieves package version from the file."""
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install.initialize_options(self)
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install.run(self)
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install.run(self)
# man directory
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PyAr/fades | fades/file_options.py | options_from_file | def options_from_file(args):
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"""
logger.debug("updating options from config files")
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PyAr/fades | fades/cache.py | VEnvsCache._venv_match | def _venv_match(self, installed, requirements):
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if *anything* is not satisified, the venv is no good). Only after
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PyAr/fades | fades/cache.py | VEnvsCache._match_by_uuid | def _match_by_uuid(self, current_venvs, uuid):
"""Select a venv matching exactly by uuid."""
for venv_str in current_venvs:
venv = json.loads(venv_str)
env_path = venv.get('metadata', {}).get('env_path')
_, env_uuid = os.path.split(env_path)
if env_uuid ==... | python | def _match_by_uuid(self, current_venvs, uuid):
"""Select a venv matching exactly by uuid."""
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venv = json.loads(venv_str)
env_path = venv.get('metadata', {}).get('env_path')
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PyAr/fades | fades/cache.py | VEnvsCache._select_better_fit | def _select_better_fit(self, matching_venvs):
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# keep the venvs in a separate array, to pick up the winner, and the (sorted, to compare
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PyAr/fades | fades/cache.py | VEnvsCache._match_by_requirements | def _match_by_requirements(self, current_venvs, requirements, interpreter, options):
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Several venvs can be found in this case, will return the better fit.
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logger.debug("Searching a venv by uuid: %s", uuid)
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PyAr/fades | fades/cache.py | VEnvsCache.get_venv | def get_venv(self, requirements=None, interpreter='', uuid='', options=None):
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PyAr/fades | fades/cache.py | VEnvsCache.store | def store(self, installed_stuff, metadata, interpreter, options):
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PyAr/fades | fades/cache.py | VEnvsCache.remove | def remove(self, env_path):
"""Remove metadata for a given virtualenv from cache."""
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logger.debug("Removing virtualenv from cache: %s" % env_path)
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PyAr/fades | fades/cache.py | VEnvsCache._write_cache | def _write_cache(self, lines, append=False):
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PyAr/fades | fades/pipmanager.py | PipManager.install | def install(self, dependency):
"""Install a new dependency."""
if not self.pip_installed:
logger.info("Need to install a dependency with pip, but no builtin, "
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self._brute_force_install_pip()
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"""Install a new dependency."""
if not self.pip_installed:
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albertyw/csv-ical | csv_ical/convert.py | Convert._generate_configs_from_default | def _generate_configs_from_default(self, overrides=None):
# type: (Dict[str, int]) -> Dict[str, int]
""" Generate configs by inheriting from defaults """
config = DEFAULT_CONFIG.copy()
if not overrides:
overrides = {}
for k, v in overrides.items():
config[... | python | def _generate_configs_from_default(self, overrides=None):
# type: (Dict[str, int]) -> Dict[str, int]
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albertyw/csv-ical | csv_ical/convert.py | Convert.read_ical | def read_ical(self, ical_file_location): # type: (str) -> Calendar
""" Read the ical file """
with open(ical_file_location, 'r') as ical_file:
data = ical_file.read()
self.cal = Calendar.from_ical(data)
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albertyw/csv-ical | csv_ical/convert.py | Convert.make_ical | def make_ical(self, csv_configs=None):
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albertyw/csv-ical | csv_ical/convert.py | Convert.save_ical | def save_ical(self, ical_location): # type: (str) -> None
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planetarypy/planetaryimage | planetaryimage/image.py | PlanetaryImage.open | def open(cls, filename):
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Name of file to read as an image file. This file may be gzip
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planetarypy/planetaryimage | planetaryimage/cubefile.py | CubeFile.apply_numpy_specials | def apply_numpy_specials(self, copy=True):
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planetarypy/planetaryimage | planetaryimage/pds3image.py | Pointer.parse | def parse(cls, value, record_bytes):
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planetarypy/planetaryimage | planetaryimage/pds3image.py | PDS3Image._save | def _save(self, file_to_write, overwrite):
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filename: Set filename for the pds image to be saved.
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planetarypy/planetaryimage | planetaryimage/pds3image.py | PDS3Image._create_label | def _create_label(self, array):
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planetarypy/planetaryimage | planetaryimage/pds3image.py | PDS3Image._update_label | def _update_label(self, label, array):
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It is called by '_create_label' to update label values
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- ^IMAGE, RECORD_BYTES
- STANDARD_DEVIATION
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- MEDIAN, MEAN
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web-push-libs/encrypted-content-encoding | python/http_ece/__init__.py | iv | def iv(base, counter):
"""Generate an initialization vector.
"""
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(mask,) = struct.unpack("!Q", base[4:])
return base[:4] + struct.pack("!Q", counter ^ mask) | python | def iv(base, counter):
"""Generate an initialization vector.
"""
if (counter >> 64) != 0:
raise ECEException(u"Counter too big")
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web-push-libs/encrypted-content-encoding | python/http_ece/__init__.py | encrypt | def encrypt(content, salt=None, key=None,
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rs=4096, version="aes128gcm"):
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:type content: str
:param salt: Encryption salt
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varlink/python | varlink/error.py | VarlinkError.parameters | def parameters(self, namespaced=False):
"""returns the exception varlink error parameters"""
if namespaced:
return json.loads(json.dumps(self.args[0]['parameters']), object_hook=lambda d: SimpleNamespace(**d))
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return self.args[0].get('parameters') | python | def parameters(self, namespaced=False):
"""returns the exception varlink error parameters"""
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varlink/python | varlink/server.py | Service.handle | def handle(self, message, _server=None, _request=None):
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Write any returned bytes to the output stream.
>>> for outgoing_message in service.handle(incoming_message):
>>> connection.write(outgoing_message)
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varlink/python | varlink/server.py | Server.server_close | def server_close(self):
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May be overridden.
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except:
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"""Called to clean-up the server.
May be overridden.
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varlink/python | varlink/client.py | Client.open | def open(self, interface_name, namespaced=False, connection=None):
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varlink/python | varlink/client.py | Client.get_interfaces | def get_interfaces(self, socket_connection=None):
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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):
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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
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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)
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n_datapoints = len(atoms_list)
atoms = atoms_list[0]
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SINGROUP/SOAPLite | soaplite/getBasis.py | getPoly | def getPoly(rCut, nMax):
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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
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SINGROUP/SOAPLite | soaplite/core.py | _format_ase2clusgeo | def _format_ase2clusgeo(obj, all_atomtypes=None):
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obj():
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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
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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
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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):
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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.
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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
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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}}
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----------
**kw
Any keyword arguments ... | [
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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)
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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
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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.
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----------
circulation : array_like (optional)
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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 =... | [
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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)
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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.
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----------
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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... | [
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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
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adrn/gala | gala/coordinates/pm_cov_transform.py | transform_pm_cov | def transform_pm_cov(c, cov, to_frame):
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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.
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The covariance matrix of the proper m... | [
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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
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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
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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... | [
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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`, `... | [
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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.
"""
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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
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"""
Decide how to make the return array. If mmap is False, this returns a
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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):
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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
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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
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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
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----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
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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
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Parameters
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q : array_like, numeric
Position(s) to estimate the circular velocity.
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-------
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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__
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# Delete documentation in this case... | python | def format_doc(*args, **kwargs):
"""
Replaces the docstring of the decorated object and then formats it.
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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
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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.
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const : float
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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
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"""
View inputs as arrays with at least two dimensions.
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arys1, arys2, ... : array_like
One or more array-like sequences. Non-array inputs are converted
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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)
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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`
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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_... | [
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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... | [
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Fit the toy Isochrone potential to the sum of the energy residuals relative
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.. 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
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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... | [
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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 ... | [
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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 ... | [
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Find approximate actions and angles for samples of a phase-space orbit.
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This code is adapted from Jason Sanders'
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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[... | [
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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.
... | [
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A periodic time series.
amplitude_threshold : numeric (optional)
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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.
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Initial conditions.
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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... | [
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coords : `~astropy.coordinates.SkyCoord`
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