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pkgw/pwkit | pwkit/fk10.py | Calculator.set_bfield | def set_bfield(self, B_G):
"""Set the strength of the local magnetic field.
**Call signature**
*B_G*
The magnetic field strength, in Gauss
Returns
*self* for convenience in chaining.
"""
if not (B_G > 0):
raise ValueError('must have B_G >... | python | def set_bfield(self, B_G):
"""Set the strength of the local magnetic field.
**Call signature**
*B_G*
The magnetic field strength, in Gauss
Returns
*self* for convenience in chaining.
"""
if not (B_G > 0):
raise ValueError('must have B_G >... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_bfield_for_s0 | def set_bfield_for_s0(self, s0):
"""Set B to probe a certain harmonic number.
**Call signature**
*s0*
The harmonic number to probe at the lowest frequency
Returns
*self* for convenience in chaining.
This just proceeds from the relation ``nu = s nu_c = s e B... | python | def set_bfield_for_s0(self, s0):
"""Set B to probe a certain harmonic number.
**Call signature**
*s0*
The harmonic number to probe at the lowest frequency
Returns
*self* for convenience in chaining.
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_edist_powerlaw | def set_edist_powerlaw(self, emin_mev, emax_mev, delta, ne_cc):
"""Set the energy distribution function to a power law.
**Call signature**
*emin_mev*
The minimum energy of the distribution, in MeV
*emax_mev*
The maximum energy of the distribution, in MeV
*de... | python | def set_edist_powerlaw(self, emin_mev, emax_mev, delta, ne_cc):
"""Set the energy distribution function to a power law.
**Call signature**
*emin_mev*
The minimum energy of the distribution, in MeV
*emax_mev*
The maximum energy of the distribution, in MeV
*de... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_edist_powerlaw_gamma | def set_edist_powerlaw_gamma(self, gmin, gmax, delta, ne_cc):
"""Set the energy distribution function to a power law in the Lorentz factor
**Call signature**
*gmin*
The minimum Lorentz factor of the distribution
*gmax*
The maximum Lorentz factor of the distribution
... | python | def set_edist_powerlaw_gamma(self, gmin, gmax, delta, ne_cc):
"""Set the energy distribution function to a power law in the Lorentz factor
**Call signature**
*gmin*
The minimum Lorentz factor of the distribution
*gmax*
The maximum Lorentz factor of the distribution
... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_freqs | def set_freqs(self, n, f_lo_ghz, f_hi_ghz):
"""Set the frequency grid on which to perform the calculations.
**Call signature**
*n*
The number of frequency points to sample.
*f_lo_ghz*
The lowest frequency to sample, in GHz.
*f_hi_ghz*
The highest f... | python | def set_freqs(self, n, f_lo_ghz, f_hi_ghz):
"""Set the frequency grid on which to perform the calculations.
**Call signature**
*n*
The number of frequency points to sample.
*f_lo_ghz*
The lowest frequency to sample, in GHz.
*f_hi_ghz*
The highest f... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_obs_angle | def set_obs_angle(self, theta_rad):
"""Set the observer angle relative to the field.
**Call signature**
*theta_rad*
The angle between the ray path and the local magnetic field,
in radians.
Returns
*self* for convenience in chaining.
"""
sel... | python | def set_obs_angle(self, theta_rad):
"""Set the observer angle relative to the field.
**Call signature**
*theta_rad*
The angle between the ray path and the local magnetic field,
in radians.
Returns
*self* for convenience in chaining.
"""
sel... | [
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The angle between the ray path and the local magnetic field,
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_one_freq | def set_one_freq(self, f_ghz):
"""Set the code to calculate results at just one frequency.
**Call signature**
*f_ghz*
The frequency to sample, in GHz.
Returns
*self* for convenience in chaining.
"""
if not (f_ghz >= 0):
raise ValueError(... | python | def set_one_freq(self, f_ghz):
"""Set the code to calculate results at just one frequency.
**Call signature**
*f_ghz*
The frequency to sample, in GHz.
Returns
*self* for convenience in chaining.
"""
if not (f_ghz >= 0):
raise ValueError(... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_padist_gaussian_loss_cone | def set_padist_gaussian_loss_cone(self, boundary_rad, expwidth):
"""Set the pitch-angle distribution to a Gaussian loss cone.
**Call signature**
*boundary_rad*
The angle inside which there are no losses, in radians.
*expwidth*
The characteristic width of the Gaussia... | python | def set_padist_gaussian_loss_cone(self, boundary_rad, expwidth):
"""Set the pitch-angle distribution to a Gaussian loss cone.
**Call signature**
*boundary_rad*
The angle inside which there are no losses, in radians.
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The characteristic width of the Gaussia... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_thermal_background | def set_thermal_background(self, T_K, nth_cc):
"""Set the properties of the background thermal plasma.
**Call signature**
*T_K*
The temperature of the background plasma, in Kelvin.
*nth_cc*
The number density of thermal electrons, in cm^-3.
Returns
... | python | def set_thermal_background(self, T_K, nth_cc):
"""Set the properties of the background thermal plasma.
**Call signature**
*T_K*
The temperature of the background plasma, in Kelvin.
*nth_cc*
The number density of thermal electrons, in cm^-3.
Returns
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pkgw/pwkit | pwkit/fk10.py | Calculator.set_trapezoidal_integration | def set_trapezoidal_integration(self, n):
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**Call signature**
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Returns
*self* for convenience in chaining.
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"""Set the code to use trapezoidal integration.
**Call signature**
*n*
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Returns
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pkgw/pwkit | pwkit/fk10.py | Calculator.find_rt_coefficients | def find_rt_coefficients(self, depth0=None):
"""Figure out emission and absorption coefficients for the current parameters.
**Argument**
*depth0* (default None)
A first guess to use for a good integration depth, in cm. If None,
the most recent value is used.
**Retu... | python | def find_rt_coefficients(self, depth0=None):
"""Figure out emission and absorption coefficients for the current parameters.
**Argument**
*depth0* (default None)
A first guess to use for a good integration depth, in cm. If None,
the most recent value is used.
**Retu... | [
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pkgw/pwkit | pwkit/fk10.py | Calculator.find_rt_coefficients_tot_intens | def find_rt_coefficients_tot_intens(self, depth0=None):
"""Figure out total-intensity emission and absorption coefficients for the
current parameters.
**Argument**
*depth0* (default None)
A first guess to use for a good integration depth, in cm. If None,
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*depth0* (default None)
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pkgw/pwkit | pwkit/io.py | make_path_func | def make_path_func (*baseparts):
"""Return a function that joins paths onto some base directory."""
from os.path import join
base = join (*baseparts)
def path_func (*args):
return join (base, *args)
return path_func | python | def make_path_func (*baseparts):
"""Return a function that joins paths onto some base directory."""
from os.path import join
base = join (*baseparts)
def path_func (*args):
return join (base, *args)
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pkgw/pwkit | pwkit/io.py | djoin | def djoin (*args):
"""'dotless' join, for nicer paths."""
from os.path import join
i = 0
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if i == alen:
return '.'
return join (*args[i:]) | python | def djoin (*args):
"""'dotless' join, for nicer paths."""
from os.path import join
i = 0
alen = len (args)
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pkgw/pwkit | pwkit/io.py | ensure_symlink | def ensure_symlink (src, dst):
"""Ensure the existence of a symbolic link pointing to src named dst. Returns
a boolean indicating whether the symlink already existed.
"""
try:
os.symlink (src, dst)
except OSError as e:
if e.errno == 17: # EEXIST
return True
raise... | python | def ensure_symlink (src, dst):
"""Ensure the existence of a symbolic link pointing to src named dst. Returns
a boolean indicating whether the symlink already existed.
"""
try:
os.symlink (src, dst)
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if e.errno == 17: # EEXIST
return True
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pkgw/pwkit | pwkit/io.py | Path.make_tempfile | def make_tempfile (self, want='handle', resolution='try_unlink', suffix='', **kwargs):
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pkgw/pwkit | pwkit/io.py | Path.try_unlink | def try_unlink (self):
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"""
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pkgw/pwkit | pwkit/io.py | Path.read_pickles | def read_pickles (self):
"""Generate a sequence of objects by opening the path and unpickling items
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"""
try:
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while True:... | python | def read_pickles (self):
"""Generate a sequence of objects by opening the path and unpickling items
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pkgw/pwkit | pwkit/io.py | Path.read_text | def read_text(self, encoding=None, errors=None, newline=None):
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pkgw/pwkit | pwkit/io.py | Path.read_toml | def read_toml(self, encoding=None, errors=None, newline=None, **kwargs):
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"""Read this path as a TOML document.
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pkgw/pwkit | pwkit/io.py | Path.read_yaml | def read_yaml (self, encoding=None, errors=None, newline=None, **kwargs):
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pkgw/pwkit | pwkit/simpleenum.py | enumeration | def enumeration (cls):
"""A very simple decorator for creating enumerations. Unlike Python 3.4
enumerations, this just gives a way to use a class declaration to create
an immutable object containing only the values specified in the class.
If the attribute ``__pickle_compat__`` is set to True in the dec... | python | def enumeration (cls):
"""A very simple decorator for creating enumerations. Unlike Python 3.4
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pkgw/pwkit | pwkit/numutil.py | slice_around_gaps | def slice_around_gaps (values, maxgap):
"""Given an ordered array of values, generate a set of slices that traverse
all of the values. Within each slice, no gap between adjacent values is
larger than `maxgap`. In other words, these slices break the array into
chunks separated by gaps of size larger than... | python | def slice_around_gaps (values, maxgap):
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pkgw/pwkit | pwkit/numutil.py | reduce_data_frame | def reduce_data_frame (df, chunk_slicers,
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minmax_cols=(),
nchunk_colname='nchunk',
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pkgw/pwkit | pwkit/numutil.py | reduce_data_frame_evenly_with_gaps | def reduce_data_frame_evenly_with_gaps (df, valcol, target_len, maxgap, **kwargs):
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pkgw/pwkit | pwkit/numutil.py | usmooth | def usmooth (window, uncerts, *data, **kwargs):
"""Smooth data series according to a window, weighting based on uncertainties.
Arguments:
window
The smoothing window.
uncerts
An array of uncertainties used to weight the smoothing.
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The smoothing window.
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An array of uncertainties used to weight the smoothing.
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pkgw/pwkit | pwkit/numutil.py | weighted_variance | def weighted_variance (x, weights):
"""Return the variance of a weighted sample.
The weighted sample mean is calculated and subtracted off, so the returned
variance is upweighted by ``n / (n - 1)``. If the sample mean is known to
be zero, you should just compute ``np.average (x**2, weights=weights)``.
... | python | def weighted_variance (x, weights):
"""Return the variance of a weighted sample.
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pkgw/pwkit | pwkit/numutil.py | unit_tophat_ee | def unit_tophat_ee (x):
"""Tophat function on the unit interval, left-exclusive and right-exclusive.
Returns 1 if 0 < x < 1, 0 otherwise.
"""
x = np.asarray (x)
x1 = np.atleast_1d (x)
r = ((0 < x1) & (x1 < 1)).astype (x.dtype)
if x.ndim == 0:
return np.asscalar (r)
return r | python | def unit_tophat_ee (x):
"""Tophat function on the unit interval, left-exclusive and right-exclusive.
Returns 1 if 0 < x < 1, 0 otherwise.
"""
x = np.asarray (x)
x1 = np.atleast_1d (x)
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pkgw/pwkit | pwkit/numutil.py | make_tophat_ee | def make_tophat_ee (lower, upper):
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pkgw/pwkit | pwkit/numutil.py | make_tophat_ie | def make_tophat_ie (lower, upper):
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pkgw/pwkit | pwkit/numutil.py | make_tophat_ii | def make_tophat_ii (lower, upper):
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pkgw/pwkit | pwkit/numutil.py | make_step_lcont | def make_step_lcont (transition):
"""Return a ufunc-like step function that is left-continuous. Returns 1 if
x > transition, 0 otherwise.
"""
if not np.isfinite (transition):
raise ValueError ('"transition" argument must be finite number; got %r' % transition)
def step_lcont (x):
x... | python | def make_step_lcont (transition):
"""Return a ufunc-like step function that is left-continuous. Returns 1 if
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pkgw/pwkit | pwkit/numutil.py | make_step_rcont | def make_step_rcont (transition):
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pkgw/pwkit | pwkit/sherpa.py | make_fixed_temp_multi_apec | def make_fixed_temp_multi_apec(kTs, name_template='apec%d', norm=None):
"""Create a model summing multiple APEC components at fixed temperatures.
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An iterable of temperatures for the components, in keV.
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A template to use for the names of each component; it is str... | python | def make_fixed_temp_multi_apec(kTs, name_template='apec%d', norm=None):
"""Create a model summing multiple APEC components at fixed temperatures.
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An iterable of temperatures for the components, in keV.
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pkgw/pwkit | pwkit/sherpa.py | expand_rmf_matrix | def expand_rmf_matrix(rmf):
"""Expand an RMF matrix stored in compressed form.
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An RMF object as might be returned by ``sherpa.astro.ui.get_rmf()``.
Returns:
A non-sparse RMF matrix.
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An RMF object as might be returned by ``sherpa.astro.ui.get_rmf()``.
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pkgw/pwkit | pwkit/sherpa.py | derive_identity_arf | def derive_identity_arf(name, arf):
"""Create an "identity" ARF that has uniform sensitivity.
*name*
The name of the ARF object to be created; passed to Sherpa.
*arf*
An existing ARF object on which to base this one.
Returns:
A new ARF1D object that has a uniform spectral response vec... | python | def derive_identity_arf(name, arf):
"""Create an "identity" ARF that has uniform sensitivity.
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The name of the ARF object to be created; passed to Sherpa.
*arf*
An existing ARF object on which to base this one.
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pkgw/pwkit | pwkit/sherpa.py | get_source_qq_data | def get_source_qq_data(id=None):
"""Get data for a quantile-quantile plot of the source data and model.
*id*
The dataset id for which to get the data; defaults if unspecified.
Returns:
An ndarray of shape ``(3, npts)``. The first slice is the energy axis in
keV; the second is the observed... | python | def get_source_qq_data(id=None):
"""Get data for a quantile-quantile plot of the source data and model.
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The dataset id for which to get the data; defaults if unspecified.
Returns:
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pkgw/pwkit | pwkit/sherpa.py | get_bkg_qq_data | def get_bkg_qq_data(id=None, bkg_id=None):
"""Get data for a quantile-quantile plot of the background data and model.
*id*
The dataset id for which to get the data; defaults if unspecified.
*bkg_id*
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Returns:
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"""Get data for a quantile-quantile plot of the background data and model.
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The dataset id for which to get the data; defaults if unspecified.
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pkgw/pwkit | pwkit/sherpa.py | make_qq_plot | def make_qq_plot(kev, obs, mdl, unit, key_text):
"""Make a quantile-quantile plot comparing events and a model.
*kev*
A 1D, sorted array of event energy bins measured in keV.
*obs*
A 1D array giving the number or rate of events in each bin.
*mdl*
A 1D array giving the modeled number o... | python | def make_qq_plot(kev, obs, mdl, unit, key_text):
"""Make a quantile-quantile plot comparing events and a model.
*kev*
A 1D, sorted array of event energy bins measured in keV.
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pkgw/pwkit | pwkit/sherpa.py | make_multi_qq_plots | def make_multi_qq_plots(arrays, key_text):
"""Make a quantile-quantile plot comparing multiple sets of events and models.
*arrays*
X.
*key_text*
Text describing the quantile-quantile comparison quantity; will be
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Returns:
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"""Make a quantile-quantile plot comparing multiple sets of events and models.
*arrays*
X.
*key_text*
Text describing the quantile-quantile comparison quantity; will be
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pkgw/pwkit | pwkit/sherpa.py | make_spectrum_plot | def make_spectrum_plot(model_plot, data_plot, desc, xmin_clamp=0.01,
min_valid_x=None, max_valid_x=None):
"""Make a plot of a spectral model and data.
*model_plot*
A model plot object returned by Sherpa from a call like `ui.get_model_plot()`
or `ui.get_bkg_model_plot()`.
... | python | def make_spectrum_plot(model_plot, data_plot, desc, xmin_clamp=0.01,
min_valid_x=None, max_valid_x=None):
"""Make a plot of a spectral model and data.
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bibanon/BASC-py4chan | examples/example6-download-thread.py | download_file | def download_file(local_filename, url, clobber=False):
"""Download the given file. Clobber overwrites file if exists."""
dir_name = os.path.dirname(local_filename)
mkdirs(dir_name)
if clobber or not os.path.exists(local_filename):
i = requests.get(url)
# if not exists
if i.stat... | python | def download_file(local_filename, url, clobber=False):
"""Download the given file. Clobber overwrites file if exists."""
dir_name = os.path.dirname(local_filename)
mkdirs(dir_name)
if clobber or not os.path.exists(local_filename):
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bibanon/BASC-py4chan | examples/example6-download-thread.py | download_json | def download_json(local_filename, url, clobber=False):
"""Download the given JSON file, and pretty-print before we output it."""
with open(local_filename, 'w') as json_file:
json_file.write(json.dumps(requests.get(url).json(), sort_keys=True, indent=2, separators=(',', ': '))) | python | def download_json(local_filename, url, clobber=False):
"""Download the given JSON file, and pretty-print before we output it."""
with open(local_filename, 'w') as json_file:
json_file.write(json.dumps(requests.get(url).json(), sort_keys=True, indent=2, separators=(',', ': '))) | [
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pkgw/pwkit | pwkit/data_gui_helpers.py | data_to_argb32 | def data_to_argb32 (data, cmin=None, cmax=None, stretch='linear', cmap='black_to_blue'):
"""Turn arbitrary data values into ARGB32 colors.
There are three steps to this process: clipping the data values to a
maximum and minimum; stretching the spacing between those values; and
converting their amplitud... | python | def data_to_argb32 (data, cmin=None, cmax=None, stretch='linear', cmap='black_to_blue'):
"""Turn arbitrary data values into ARGB32 colors.
There are three steps to this process: clipping the data values to a
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pkgw/pwkit | pwkit/data_gui_helpers.py | data_to_imagesurface | def data_to_imagesurface (data, **kwargs):
"""Turn arbitrary data values into a Cairo ImageSurface.
The method and arguments are the same as data_to_argb32, except that the
data array will be treated as 2D, and higher dimensionalities are not
allowed. The return value is a Cairo ImageSurface object.
... | python | def data_to_imagesurface (data, **kwargs):
"""Turn arbitrary data values into a Cairo ImageSurface.
The method and arguments are the same as data_to_argb32, except that the
data array will be treated as 2D, and higher dimensionalities are not
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ferittuncer/ITU-Turkish-NLP-Pipeline-Caller | pipeline_caller.py | get_token | def get_token(filename=TOKEN_PATH, envvar=TOKEN_ENVVAR):
"""
Returns pipeline_token for API
Tries local file first, then env variable
"""
if os.path.isfile(filename):
with open(filename) as token_file:
token = token_file.readline().strip()
else:
token = os.environ.g... | python | def get_token(filename=TOKEN_PATH, envvar=TOKEN_ENVVAR):
"""
Returns pipeline_token for API
Tries local file first, then env variable
"""
if os.path.isfile(filename):
with open(filename) as token_file:
token = token_file.readline().strip()
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pkgw/pwkit | pwkit/environments/casa/gpdiagnostics.py | GainCal.stats | def stats (self, antnames):
"""XXX may be out of date."""
nbyant = np.zeros (self.nants, dtype=np.int)
sum = np.zeros (self.nants, dtype=np.complex)
sumsq = np.zeros (self.nants)
q = np.abs (self.normvis - 1)
for i in range (self.nsamps):
i1, i2 = self.blidxs... | python | def stats (self, antnames):
"""XXX may be out of date."""
nbyant = np.zeros (self.nants, dtype=np.int)
sum = np.zeros (self.nants, dtype=np.complex)
sumsq = np.zeros (self.nants)
q = np.abs (self.normvis - 1)
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pkgw/pwkit | pwkit/lmmin.py | _qr_factor_packed | def _qr_factor_packed(a, enorm, finfo):
"""Compute the packed pivoting Q-R factorization of a matrix.
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a - An n-by-m matrix, m >= n. This will be *overwritten*
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finfo - A Numpy finfo object.
Returns:
pmut - A... | python | def _qr_factor_packed(a, enorm, finfo):
"""Compute the packed pivoting Q-R factorization of a matrix.
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a - An n-by-m matrix, m >= n. This will be *overwritten*
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pkgw/pwkit | pwkit/lmmin.py | _qr_factor_full | def _qr_factor_full(a, dtype=np.float):
"""Compute the QR factorization of a matrix, with pivoting.
Parameters:
a - An n-by-m arraylike, m >= n.
dtype - (optional) The data type to use for computations.
Default is np.float.
Returns:
q - An m-by-m orthogonal matrix (q q^T = ident)
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"""Compute the QR factorization of a matrix, with pivoting.
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a - An n-by-m arraylike, m >= n.
dtype - (optional) The data type to use for computations.
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pkgw/pwkit | pwkit/lmmin.py | _qrd_solve | def _qrd_solve(r, pmut, ddiag, bqt, sdiag):
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Parameters:
r - **input-output** n-by-n array. The full lower triangle contains
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"""Solve an equation given a QR factored matrix and a diagonal.
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pkgw/pwkit | pwkit/lmmin.py | _qrd_solve_full | def _qrd_solve_full(a, b, ddiag, dtype=np.float):
"""Solve the equation A^T x = B, D x = 0.
Parameters:
a - an n-by-m array, m >= n
b - an m-vector
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Returns:
x - n-vector solving the equation.
s - the n-by-n supplementary matrix s.
p... | python | def _qrd_solve_full(a, b, ddiag, dtype=np.float):
"""Solve the equation A^T x = B, D x = 0.
Parameters:
a - an n-by-m array, m >= n
b - an m-vector
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x - n-vector solving the equation.
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pkgw/pwkit | pwkit/lmmin.py | _calc_covariance | def _calc_covariance(r, pmut, tol=1e-14):
"""Calculate the covariance matrix of the fitted parameters
Parameters:
r - n-by-n matrix, the full upper triangle of R
pmut - n-vector, defines the permutation of R
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tol - scalar, relative column scale for determining rank
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pkgw/pwkit | pwkit/cli/multitool.py | invoke_tool | def invoke_tool (namespace, tool_class=None):
"""Invoke a tool and exit.
`namespace` is a namespace-type dict from which the tool is initialized.
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pkgw/pwkit | pwkit/cli/multitool.py | ArgparsingCommand.get_arg_parser | def get_arg_parser (self, **kwargs):
"""Return an instance of `argparse.ArgumentParser` used to process
this tool's command-line arguments.
"""
import argparse
ap = argparse.ArgumentParser (
prog = kwargs['argv0'],
description = self.summary,
)
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"""Return an instance of `argparse.ArgumentParser` used to process
this tool's command-line arguments.
"""
import argparse
ap = argparse.ArgumentParser (
prog = kwargs['argv0'],
description = self.summary,
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pkgw/pwkit | pwkit/cli/multitool.py | DelegatingCommand.register | def register (self, cmd):
"""Register a new command with the tool. 'cmd' is expected to be an instance
of `Command`, although here only the `cmd.name` attribute is
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"""
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"""Register a new command with the tool. 'cmd' is expected to be an instance
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pkgw/pwkit | pwkit/cli/multitool.py | DelegatingCommand.invoke_command | def invoke_command (self, cmd, args, **kwargs):
"""This function mainly exists to be overridden by subclasses."""
new_kwargs = kwargs.copy ()
new_kwargs['argv0'] = kwargs['argv0'] + ' ' + cmd.name
new_kwargs['parent'] = self
new_kwargs['parent_kwargs'] = kwargs
return cmd... | python | def invoke_command (self, cmd, args, **kwargs):
"""This function mainly exists to be overridden by subclasses."""
new_kwargs = kwargs.copy ()
new_kwargs['argv0'] = kwargs['argv0'] + ' ' + cmd.name
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pkgw/pwkit | pwkit/cli/latexdriver.py | merge_bibtex_collections | def merge_bibtex_collections(citednames, maindict, extradicts, allow_missing=False):
"""There must be a way to be efficient and stream output instead of loading
everything into memory at once, but, meh.
Note that we augment `citednames` with all of the names in `maindict`. The
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"""There must be a way to be efficient and stream output instead of loading
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pkgw/pwkit | pwkit/cli/latexdriver.py | write_bibtex_dict | def write_bibtex_dict(stream, entries):
"""bibtexparser.write converts the entire database to one big string and
writes it out in one go. I'm sure it will always all fit in RAM but some
things just will not stand.
"""
from bibtexparser.bwriter import BibTexWriter
writer = BibTexWriter()
wr... | python | def write_bibtex_dict(stream, entries):
"""bibtexparser.write converts the entire database to one big string and
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things just will not stand.
"""
from bibtexparser.bwriter import BibTexWriter
writer = BibTexWriter()
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pkgw/pwkit | pwkit/cli/latexdriver.py | merge_bibtex_with_aux | def merge_bibtex_with_aux(auxpath, mainpath, extradir, parse=get_bibtex_dict, allow_missing=False):
"""Merge multiple BibTeX files into a single homogeneously-formatted output,
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pkgw/pwkit | pwkit/cli/latexdriver.py | just_smart_bibtools | def just_smart_bibtools(bib_style, aux, bib):
"""Tectonic has taken over most of the features that this tool used to provide,
but here's a hack to keep my smart .bib file generation working.
"""
extradir = Path('.bibtex')
extradir.ensure_dir(parents=True)
bib_export(bib_style, aux, extradir / ... | python | def just_smart_bibtools(bib_style, aux, bib):
"""Tectonic has taken over most of the features that this tool used to provide,
but here's a hack to keep my smart .bib file generation working.
"""
extradir = Path('.bibtex')
extradir.ensure_dir(parents=True)
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pkgw/pwkit | pwkit/environments/casa/closures.py | aap_to_bp | def aap_to_bp (ant1, ant2, pol):
"""Create a basepol from antenna numbers and a CASA polarization code."""
if ant1 < 0:
raise ValueError ('first antenna is below 0: %s' % ant1)
if ant2 < ant1:
raise ValueError ('second antenna is below first: %s' % ant2)
if pol < 1 or pol > 12:
... | python | def aap_to_bp (ant1, ant2, pol):
"""Create a basepol from antenna numbers and a CASA polarization code."""
if ant1 < 0:
raise ValueError ('first antenna is below 0: %s' % ant1)
if ant2 < ant1:
raise ValueError ('second antenna is below first: %s' % ant2)
if pol < 1 or pol > 12:
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pkgw/pwkit | pwkit/environments/casa/closures.py | ClosureCalculator._finish_timeslot | def _finish_timeslot (self):
"""We have loaded in all of the visibilities in one timeslot. We can now
compute the phase closure triples.
XXX: we should only process independent triples. Are we???
"""
for fpol, aps in self.ap_by_fpol.items ():
aps = sorted (aps)
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XXX: we should only process independent triples. Are we???
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pkgw/pwkit | pwkit/environments/casa/closures.py | ClosureCalculator._process_sample | def _process_sample (self, ap1, ap2, ap3, triple, tflags):
"""We have computed one independent phase closure triple in one timeslot.
"""
# Frequency-resolved:
np.divide (triple, np.abs (triple), triple)
phase = np.angle (triple)
self.ap_spec_stats_by_ddid[self.cur_ddid]... | python | def _process_sample (self, ap1, ap2, ap3, triple, tflags):
"""We have computed one independent phase closure triple in one timeslot.
"""
# Frequency-resolved:
np.divide (triple, np.abs (triple), triple)
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pkgw/pwkit | pwkit/phoenix.py | load_spectrum | def load_spectrum(path, smoothing=181, DF=-8.):
"""Load a Phoenix model atmosphere spectrum.
path : string
The file path to load.
smoothing : integer
Smoothing to apply. If None, do not smooth. If an integer, smooth with a
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"""Load a Phoenix model atmosphere spectrum.
path : string
The file path to load.
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Smoothing to apply. If None, do not smooth. If an integer, smooth with a
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pkgw/pwkit | pwkit/ucd_physics.py | lbol_from_spt_dist_mag | def lbol_from_spt_dist_mag (sptnum, dist_pc, jmag, kmag, format='cgs'):
"""Estimate a UCD's bolometric luminosity given some basic parameters.
sptnum: the spectral type as a number; 8 -> M8; 10 -> L0 ; 20 -> T0
Valid values range between 0 and 30, ie M0 to Y0.
dist_pc: distance to the object in parse... | python | def lbol_from_spt_dist_mag (sptnum, dist_pc, jmag, kmag, format='cgs'):
"""Estimate a UCD's bolometric luminosity given some basic parameters.
sptnum: the spectral type as a number; 8 -> M8; 10 -> L0 ; 20 -> T0
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pkgw/pwkit | pwkit/parallel.py | InterruptiblePool.map | def map(self, func, iterable, chunksize=None):
"""Equivalent of `map` built-in, without swallowing KeyboardInterrupt.
func
The function to apply to the items.
iterable
An iterable of items that will have `func` applied to them.
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"""Equivalent of `map` built-in, without swallowing KeyboardInterrupt.
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pkgw/pwkit | pwkit/astutil.py | fmthours | def fmthours (radians, norm='wrap', precision=3, seps='::'):
"""Format an angle as sexagesimal hours in a string.
Arguments are:
radians
The angle, in radians.
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The normalization mode, used for angles outside of the standard range
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The angle, in radians.
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pkgw/pwkit | pwkit/astutil.py | fmtdeglon | def fmtdeglon (radians, norm='wrap', precision=2, seps='::'):
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radians
The angle, in radians.
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The angle, in radians.
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pkgw/pwkit | pwkit/astutil.py | fmtdeglat | def fmtdeglat (radians, norm='raise', precision=2, seps='::'):
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Arguments are:
radians
The angle, in radians.
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The normalization mode, used for angles outside of the standard range
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"""Format a latitudinal angle as sexagesimal degrees in a string.
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radians
The angle, in radians.
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The normalization mode, used for angles outside of the standard range
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pkgw/pwkit | pwkit/astutil.py | fmtradec | def fmtradec (rarad, decrad, precision=2, raseps='::', decseps='::', intersep=' '):
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pkgw/pwkit | pwkit/astutil.py | parsehours | def parsehours (hrstr):
"""Parse a string formatted as sexagesimal hours into an angle.
This function converts a textual representation of an angle, measured in
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pkgw/pwkit | pwkit/astutil.py | parsedeglat | def parsedeglat (latstr):
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pkgw/pwkit | pwkit/astutil.py | sphdist | def sphdist (lat1, lon1, lat2, lon2):
"""Calculate the distance between two locations on a sphere.
lat1
The latitude of the first location.
lon1
The longitude of the first location.
lat2
The latitude of the second location.
lon2
The longitude of the second location.
Ret... | python | def sphdist (lat1, lon1, lat2, lon2):
"""Calculate the distance between two locations on a sphere.
lat1
The latitude of the first location.
lon1
The longitude of the first location.
lat2
The latitude of the second location.
lon2
The longitude of the second location.
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pkgw/pwkit | pwkit/astutil.py | sphbear | def sphbear (lat1, lon1, lat2, lon2, tol=1e-15):
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lon1
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pkgw/pwkit | pwkit/astutil.py | sphofs | def sphofs (lat1, lon1, r, pa, tol=1e-2, rmax=None):
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pkgw/pwkit | pwkit/astutil.py | parang | def parang (hourangle, declination, latitude):
"""Calculate the parallactic angle of a sky position.
This computes the parallactic angle of a sky position expressed in terms
of an hour angle and declination. Arguments:
hourangle
The hour angle of the location on the sky.
declination
Th... | python | def parang (hourangle, declination, latitude):
"""Calculate the parallactic angle of a sky position.
This computes the parallactic angle of a sky position expressed in terms
of an hour angle and declination. Arguments:
hourangle
The hour angle of the location on the sky.
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pkgw/pwkit | pwkit/astutil.py | gaussian_convolve | def gaussian_convolve (maj1, min1, pa1, maj2, min2, pa2):
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Given the shapes of two 2-dimensional Gaussians, this function returns
the shape of their convolution.
Arguments:
maj1
Major axis of input Gaussian 1.
min1
Minor axis of input Gaussia... | python | def gaussian_convolve (maj1, min1, pa1, maj2, min2, pa2):
"""Convolve two Gaussians analytically.
Given the shapes of two 2-dimensional Gaussians, this function returns
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maj1
Major axis of input Gaussian 1.
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pkgw/pwkit | pwkit/astutil.py | gaussian_deconvolve | def gaussian_deconvolve (smaj, smin, spa, bmaj, bmin, bpa):
"""Deconvolve two Gaussians analytically.
Given the shapes of 2-dimensional “source” and “beam” Gaussians, this
returns a deconvolved “result” Gaussian such that the convolution of
“beam” and “result” is “source”.
Arguments:
smaj
... | python | def gaussian_deconvolve (smaj, smin, spa, bmaj, bmin, bpa):
"""Deconvolve two Gaussians analytically.
Given the shapes of 2-dimensional “source” and “beam” Gaussians, this
returns a deconvolved “result” Gaussian such that the convolution of
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smaj
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pkgw/pwkit | pwkit/astutil.py | load_skyfield_data | def load_skyfield_data():
"""Load data files used in Skyfield. This will download files from the
internet if they haven't been downloaded before.
Skyfield downloads files to the current directory by default, which is not
ideal. Here we abuse astropy and use its cache directory to cache the data
fil... | python | def load_skyfield_data():
"""Load data files used in Skyfield. This will download files from the
internet if they haven't been downloaded before.
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pkgw/pwkit | pwkit/astutil.py | get_2mass_epoch | def get_2mass_epoch (tmra, tmdec, debug=False):
"""Given a 2MASS position, look up the epoch when it was observed.
This function uses the CDS Vizier web service to look up information in
the 2MASS point source database. Arguments are:
tmra
The source's J2000 right ascension, in radians.
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"""Given a 2MASS position, look up the epoch when it was observed.
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pkgw/pwkit | pwkit/astutil.py | AstrometryInfo.verify | def verify (self, complain=True):
"""Validate that the attributes are self-consistent.
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ensure that astrometric calculations can legally be performed. If the
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pkgw/pwkit | pwkit/astutil.py | AstrometryInfo.fill_from_simbad | def fill_from_simbad (self, ident, debug=False):
"""Fill in astrometric information using the Simbad web service.
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pkgw/pwkit | pwkit/astutil.py | AstrometryInfo.fill_from_allwise | def fill_from_allwise (self, ident, catalog_ident='II/328/allwise'):
"""Fill in astrometric information from the AllWISE catalog using Astroquery.
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"""Fill in astrometric information from the AllWISE catalog using Astroquery.
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pkgw/pwkit | pwkit/cli/__init__.py | backtrace_on_usr1 | def backtrace_on_usr1 ():
"""Install a signal handler such that this program prints a Python traceback
upon receipt of SIGUSR1. This could be useful for checking that
long-running programs are behaving properly, or for discovering where an
infinite loop is occurring.
Note, however, that the Python ... | python | def backtrace_on_usr1 ():
"""Install a signal handler such that this program prints a Python traceback
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pkgw/pwkit | pwkit/cli/__init__.py | fork_detached_process | def fork_detached_process ():
"""Fork this process, creating a subprocess detached from the current context.
Returns a :class:`pwkit.Holder` instance with information about what
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whoami
A string, either "original" or "forked" depending on which process we are.
pipe
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whoami
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pkgw/pwkit | pwkit/cli/__init__.py | pop_option | def pop_option (ident, argv=None):
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the argument string. Because of the lame behavior, options can't be
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pkgw/pwkit | pwkit/cli/__init__.py | show_usage | def show_usage (docstring, short, stream, exitcode):
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:arg str docstring: the program help text
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pkgw/pwkit | pwkit/cli/__init__.py | wrong_usage | def wrong_usage (docstring, *rest):
"""Print a message indicating invalid command-line arguments and exit with an
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:arg str docstring: the program help text
:arg rest: an optional specific error message
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pkgw/pwkit | pwkit/cli/__init__.py | _InterruptSignalPropagator.excepthook | def excepthook (self, etype, evalue, etb):
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pkgw/pwkit | pwkit/dulk_models.py | calc_nu_b | def calc_nu_b(b):
"""Calculate the cyclotron frequency in Hz given a magnetic field strength in Gauss.
This is in cycles per second not radians per second; i.e. there is a 2π in
the denominator: ν_B = e B / (2π m_e c)
"""
return cgs.e * b / (2 * cgs.pi * cgs.me * cgs.c) | python | def calc_nu_b(b):
"""Calculate the cyclotron frequency in Hz given a magnetic field strength in Gauss.
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pkgw/pwkit | pwkit/dulk_models.py | calc_freefree_snu_ujy | def calc_freefree_snu_ujy(ne, t, width, elongation, dist, ghz):
"""Calculate a flux density from pure free-free emission.
"""
hz = ghz * 1e9
eta = calc_freefree_eta(ne, t, hz)
kappa = calc_freefree_kappa(ne, t, hz)
snu = calc_snu(eta, kappa, width, elongation, dist)
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"""Calculate a flux density from pure free-free emission.
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pkgw/pwkit | pwkit/environments/casa/tasks.py | concat | def concat(invises, outvis, timesort=False):
"""Concatenate visibility measurement sets.
invises (list of str)
Paths to the input measurement sets
outvis (str)
Path to the output measurement set.
timesort (boolean)
If true, sort the output in time after concatenation.
Example::
... | python | def concat(invises, outvis, timesort=False):
"""Concatenate visibility measurement sets.
invises (list of str)
Paths to the input measurement sets
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Path to the output measurement set.
timesort (boolean)
If true, sort the output in time after concatenation.
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Example::
from pwkit.environments.casa import tasks
... | [
"Concatenate",
"visibility",
"measurement",
"sets",
"."
] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L658-L701 | train | 62,393 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | delcal | def delcal(mspath):
"""Delete the ``MODEL_DATA`` and ``CORRECTED_DATA`` columns from a measurement set.
mspath (str)
The path to the MS to modify
Example::
from pwkit.environments.casa import tasks
tasks.delcal('dataset.ms')
"""
wantremove = 'MODEL_DATA CORRECTED_DATA'.split()
... | python | def delcal(mspath):
"""Delete the ``MODEL_DATA`` and ``CORRECTED_DATA`` columns from a measurement set.
mspath (str)
The path to the MS to modify
Example::
from pwkit.environments.casa import tasks
tasks.delcal('dataset.ms')
"""
wantremove = 'MODEL_DATA CORRECTED_DATA'.split()
... | [
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mspath (str)
The path to the MS to modify
Example::
from pwkit.environments.casa import tasks
tasks.delcal('dataset.ms') | [
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] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L732-L758 | train | 62,394 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | delmod_cli | def delmod_cli(argv, alter_logger=True):
"""Command-line access to ``delmod`` functionality.
The ``delmod`` task deletes "on-the-fly" model information from a
Measurement Set. It is so easy to implement that a standalone
function is essentially unnecessary. Just write::
from pwkit.environments.c... | python | def delmod_cli(argv, alter_logger=True):
"""Command-line access to ``delmod`` functionality.
The ``delmod`` task deletes "on-the-fly" model information from a
Measurement Set. It is so easy to implement that a standalone
function is essentially unnecessary. Just write::
from pwkit.environments.c... | [
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"to... | Command-line access to ``delmod`` functionality.
The ``delmod`` task deletes "on-the-fly" model information from a
Measurement Set. It is so easy to implement that a standalone
function is essentially unnecessary. Just write::
from pwkit.environments.casa import util
cb = util.tools.calibrater... | [
"Command",
"-",
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"access",
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"delmod",
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"."
] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L788-L814 | train | 62,395 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | extractbpflags | def extractbpflags(calpath, deststream):
"""Make a flags file out of a bandpass calibration table
calpath (str)
The path to the bandpass calibration table
deststream (stream-like object, e.g. an opened file)
Where to write the flags data
Below is documentation written for the command-line ... | python | def extractbpflags(calpath, deststream):
"""Make a flags file out of a bandpass calibration table
calpath (str)
The path to the bandpass calibration table
deststream (stream-like object, e.g. an opened file)
Where to write the flags data
Below is documentation written for the command-line ... | [
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calpath (str)
The path to the bandpass calibration table
deststream (stream-like object, e.g. an opened file)
Where to write the flags data
Below is documentation written for the command-line interface to this
functionality: | [
"Make",
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] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L976-L1033 | train | 62,396 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | flagmanager_cli | def flagmanager_cli(argv, alter_logger=True):
"""Command-line access to ``flagmanager`` functionality.
The ``flagmanager`` task manages tables of flags associated with
measurement sets. Its features are easy to implement that a standalone
library function is essentially unnecessary. See the source code... | python | def flagmanager_cli(argv, alter_logger=True):
"""Command-line access to ``flagmanager`` functionality.
The ``flagmanager`` task manages tables of flags associated with
measurement sets. Its features are easy to implement that a standalone
library function is essentially unnecessary. See the source code... | [
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The ``flagmanager`` task manages tables of flags associated with
measurement sets. Its features are easy to implement that a standalone
library function is essentially unnecessary. See the source code to this
function for the tool calls that impleme... | [
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"-",
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] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L1192-L1258 | train | 62,397 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | image2fits | def image2fits(mspath, fitspath, velocity=False, optical=False, bitpix=-32,
minpix=0, maxpix=-1, overwrite=False, dropstokes=False, stokeslast=True,
history=True, **kwargs):
"""Convert an image in MS format to FITS format.
mspath (str)
The path to the input MS.
fitspat... | python | def image2fits(mspath, fitspath, velocity=False, optical=False, bitpix=-32,
minpix=0, maxpix=-1, overwrite=False, dropstokes=False, stokeslast=True,
history=True, **kwargs):
"""Convert an image in MS format to FITS format.
mspath (str)
The path to the input MS.
fitspat... | [
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"dropstokes",... | Convert an image in MS format to FITS format.
mspath (str)
The path to the input MS.
fitspath (str)
The path to the output FITS file.
velocity (boolean)
(To be documented.)
optical (boolean)
(To be documented.)
bitpix (integer)
(To be documented.)
minpix (integer)
... | [
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] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L2203-L2240 | train | 62,398 |
pkgw/pwkit | pwkit/environments/casa/tasks.py | importalma | def importalma(asdm, ms):
"""Convert an ALMA low-level ASDM dataset to Measurement Set format.
asdm (str)
The path to the input ASDM dataset.
ms (str)
The path to the output MS dataset.
This implementation automatically infers the value of the "tbuff"
parameter.
Example::
f... | python | def importalma(asdm, ms):
"""Convert an ALMA low-level ASDM dataset to Measurement Set format.
asdm (str)
The path to the input ASDM dataset.
ms (str)
The path to the output MS dataset.
This implementation automatically infers the value of the "tbuff"
parameter.
Example::
f... | [
"def",
"importalma",
"(",
"asdm",
",",
"ms",
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":",
"from",
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"scripting",
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... | Convert an ALMA low-level ASDM dataset to Measurement Set format.
asdm (str)
The path to the input ASDM dataset.
ms (str)
The path to the output MS dataset.
This implementation automatically infers the value of the "tbuff"
parameter.
Example::
from pwkit.environments.casa impor... | [
"Convert",
"an",
"ALMA",
"low",
"-",
"level",
"ASDM",
"dataset",
"to",
"Measurement",
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"format",
"."
] | d40957a1c3d2ea34e7ceac2267ee9635135f2793 | https://github.com/pkgw/pwkit/blob/d40957a1c3d2ea34e7ceac2267ee9635135f2793/pwkit/environments/casa/tasks.py#L2267-L2288 | train | 62,399 |
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