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def sky_within(self, ra, dec, degin=False):
"""
Test whether a sky position is within this region
Parameters
----------
ra, dec : float
Sky position.
degin : bool
If True the ra/dec is interpreted as degrees, otherwise as radians.
Def... | Test whether a sky position is within this region
Parameters
----------
ra, dec : float
Sky position.
degin : bool
If True the ra/dec is interpreted as degrees, otherwise as radians.
Default = False.
Returns
-------
within : ... | entailment |
def union(self, other, renorm=True):
"""
Add another Region by performing union on their pixlists.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined.
renorm : bool
Perform renormalisation after the operat... | Add another Region by performing union on their pixlists.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined.
renorm : bool
Perform renormalisation after the operation?
Default = True. | entailment |
def without(self, other):
"""
Subtract another Region by performing a difference operation on their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined.
... | Subtract another Region by performing a difference operation on their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined. | entailment |
def intersect(self, other):
"""
Combine with another Region by performing intersection on their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined.
""... | Combine with another Region by performing intersection on their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined. | entailment |
def symmetric_difference(self, other):
"""
Combine with another Region by performing the symmetric difference of their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to ... | Combine with another Region by performing the symmetric difference of their pixlists.
Requires both regions to have the same maxdepth.
Parameters
----------
other : :class:`AegeanTools.regions.Region`
The region to be combined. | entailment |
def write_reg(self, filename):
"""
Write a ds9 region file that represents this region as a set of diamonds.
Parameters
----------
filename : str
File to write
"""
with open(filename, 'w') as out:
for d in range(1, self.maxdepth+1):
... | Write a ds9 region file that represents this region as a set of diamonds.
Parameters
----------
filename : str
File to write | entailment |
def write_fits(self, filename, moctool=''):
"""
Write a fits file representing the MOC of this region.
Parameters
----------
filename : str
File to write
moctool : str
String to be written to fits header with key "MOCTOOL".
Default = ... | Write a fits file representing the MOC of this region.
Parameters
----------
filename : str
File to write
moctool : str
String to be written to fits header with key "MOCTOOL".
Default = '' | entailment |
def _uniq(self):
"""
Create a list of all the pixels that cover this region.
This list contains overlapping pixels of different orders.
Returns
-------
pix : list
A list of HEALPix pixel numbers.
"""
pd = []
for d in range(1, self.maxd... | Create a list of all the pixels that cover this region.
This list contains overlapping pixels of different orders.
Returns
-------
pix : list
A list of HEALPix pixel numbers. | entailment |
def radec2sky(ra, dec):
"""
Convert [ra], [dec] to [(ra[0], dec[0]),....]
and also ra,dec to [(ra,dec)] if ra/dec are not iterable
Parameters
----------
ra, dec : float or iterable
Sky coordinates
Returns
-------
sky : numpy.array
... | Convert [ra], [dec] to [(ra[0], dec[0]),....]
and also ra,dec to [(ra,dec)] if ra/dec are not iterable
Parameters
----------
ra, dec : float or iterable
Sky coordinates
Returns
-------
sky : numpy.array
array of (ra,dec) coordinates. | entailment |
def sky2ang(sky):
"""
Convert ra,dec coordinates to theta,phi coordinates
ra -> phi
dec -> theta
Parameters
----------
sky : numpy.array
Array of (ra,dec) coordinates.
See :func:`AegeanTools.regions.Region.radec2sky`
Returns
... | Convert ra,dec coordinates to theta,phi coordinates
ra -> phi
dec -> theta
Parameters
----------
sky : numpy.array
Array of (ra,dec) coordinates.
See :func:`AegeanTools.regions.Region.radec2sky`
Returns
-------
theta_phi : numpy.a... | entailment |
def sky2vec(cls, sky):
"""
Convert sky positions in to 3d-vectors on the unit sphere.
Parameters
----------
sky : numpy.array
Sky coordinates as an array of (ra,dec)
Returns
-------
vec : numpy.array
Unit vectors as an array of (x... | Convert sky positions in to 3d-vectors on the unit sphere.
Parameters
----------
sky : numpy.array
Sky coordinates as an array of (ra,dec)
Returns
-------
vec : numpy.array
Unit vectors as an array of (x,y,z)
See Also
--------
... | entailment |
def vec2sky(cls, vec, degrees=False):
"""
Convert [x,y,z] vectors into sky coordinates ra,dec
Parameters
----------
vec : numpy.array
Unit vectors as an array of (x,y,z)
degrees
Returns
-------
sky : numpy.array
Sky coord... | Convert [x,y,z] vectors into sky coordinates ra,dec
Parameters
----------
vec : numpy.array
Unit vectors as an array of (x,y,z)
degrees
Returns
-------
sky : numpy.array
Sky coordinates as an array of (ra,dec)
See Also
-... | entailment |
def from_header(cls, header, beam=None, lat=None):
"""
Create a new WCSHelper class from the given header.
Parameters
----------
header : `astropy.fits.HDUHeader` or string
The header to be used to create the WCS helper
beam : :class:`AegeanTools.fits_image.... | Create a new WCSHelper class from the given header.
Parameters
----------
header : `astropy.fits.HDUHeader` or string
The header to be used to create the WCS helper
beam : :class:`AegeanTools.fits_image.Beam` or None
The synthesized beam. If the supplied beam is... | entailment |
def from_file(cls, filename, beam=None):
"""
Create a new WCSHelper class from a given fits file.
Parameters
----------
filename : string
The file to be read
beam : :class:`AegeanTools.fits_image.Beam` or None
The synthesized beam. If the supplie... | Create a new WCSHelper class from a given fits file.
Parameters
----------
filename : string
The file to be read
beam : :class:`AegeanTools.fits_image.Beam` or None
The synthesized beam. If the supplied beam is None then one is constructed form the header.
... | entailment |
def pix2sky(self, pixel):
"""
Convert pixel coordinates into sky coordinates.
Parameters
----------
pixel : (float, float)
The (x,y) pixel coordinates
Returns
-------
sky : (float, float)
The (ra,dec) sky coordinates in degrees
... | Convert pixel coordinates into sky coordinates.
Parameters
----------
pixel : (float, float)
The (x,y) pixel coordinates
Returns
-------
sky : (float, float)
The (ra,dec) sky coordinates in degrees | entailment |
def sky2pix(self, pos):
"""
Convert sky coordinates into pixel coordinates.
Parameters
----------
pos : (float, float)
The (ra, dec) sky coordinates (degrees)
Returns
-------
pixel : (float, float)
The (x,y) pixel coordinates
... | Convert sky coordinates into pixel coordinates.
Parameters
----------
pos : (float, float)
The (ra, dec) sky coordinates (degrees)
Returns
-------
pixel : (float, float)
The (x,y) pixel coordinates | entailment |
def sky2pix_vec(self, pos, r, pa):
"""
Convert a vector from sky to pixel coords.
The vector has a magnitude, angle, and an origin on the sky.
Parameters
----------
pos : (float, float)
The (ra, dec) of the origin of the vector (degrees).
r : float
... | Convert a vector from sky to pixel coords.
The vector has a magnitude, angle, and an origin on the sky.
Parameters
----------
pos : (float, float)
The (ra, dec) of the origin of the vector (degrees).
r : float
The magnitude or length of the vector (degre... | entailment |
def pix2sky_vec(self, pixel, r, theta):
"""
Given and input position and vector in pixel coordinates, calculate
the equivalent position and vector in sky coordinates.
Parameters
----------
pixel : (int,int)
origin of vector in pixel coordinates
r : fl... | Given and input position and vector in pixel coordinates, calculate
the equivalent position and vector in sky coordinates.
Parameters
----------
pixel : (int,int)
origin of vector in pixel coordinates
r : float
magnitude of vector in pixels
theta ... | entailment |
def sky2pix_ellipse(self, pos, a, b, pa):
"""
Convert an ellipse from sky to pixel coordinates.
Parameters
----------
pos : (float, float)
The (ra, dec) of the ellipse center (degrees).
a, b, pa: float
The semi-major axis, semi-minor axis and posi... | Convert an ellipse from sky to pixel coordinates.
Parameters
----------
pos : (float, float)
The (ra, dec) of the ellipse center (degrees).
a, b, pa: float
The semi-major axis, semi-minor axis and position angle of the ellipse (degrees).
Returns
... | entailment |
def pix2sky_ellipse(self, pixel, sx, sy, theta):
"""
Convert an ellipse from pixel to sky coordinates.
Parameters
----------
pixel : (float, float)
The (x, y) coordinates of the center of the ellipse.
sx, sy : float
The major and minor axes (FHWM)... | Convert an ellipse from pixel to sky coordinates.
Parameters
----------
pixel : (float, float)
The (x, y) coordinates of the center of the ellipse.
sx, sy : float
The major and minor axes (FHWM) of the ellipse, in pixels.
theta : float
The rot... | entailment |
def get_pixbeam_pixel(self, x, y):
"""
Determine the beam in pixels at the given location in pixel coordinates.
Parameters
----------
x , y : float
The pixel coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTo... | Determine the beam in pixels at the given location in pixel coordinates.
Parameters
----------
x , y : float
The pixel coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
A beam object, with a/... | entailment |
def get_beam(self, ra, dec):
"""
Determine the beam at the given sky location.
Parameters
----------
ra, dec : float
The sky coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
... | Determine the beam at the given sky location.
Parameters
----------
ra, dec : float
The sky coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
A beam object, with a/b/pa in sky coordinates | entailment |
def get_pixbeam(self, ra, dec):
"""
Determine the beam in pixels at the given location in sky coordinates.
Parameters
----------
ra , dec : float
The sly coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTools.... | Determine the beam in pixels at the given location in sky coordinates.
Parameters
----------
ra , dec : float
The sly coordinates at which the beam is determined.
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
A beam object, with a/b... | entailment |
def get_beamarea_deg2(self, ra, dec):
"""
Calculate the area of the synthesized beam in square degrees.
Parameters
----------
ra, dec : float
The sky coordinates at which the calculation is made.
Returns
-------
area : float
The b... | Calculate the area of the synthesized beam in square degrees.
Parameters
----------
ra, dec : float
The sky coordinates at which the calculation is made.
Returns
-------
area : float
The beam area in square degrees. | entailment |
def get_beamarea_pix(self, ra, dec):
"""
Calculate the beam area in square pixels.
Parameters
----------
ra, dec : float
The sky coordinates at which the calculation is made
dec
Returns
-------
area : float
The beam area i... | Calculate the beam area in square pixels.
Parameters
----------
ra, dec : float
The sky coordinates at which the calculation is made
dec
Returns
-------
area : float
The beam area in square pixels. | entailment |
def sky_sep(self, pix1, pix2):
"""
calculate the GCD sky separation (degrees) between two pixels.
Parameters
----------
pix1, pix2 : (float, float)
The (x,y) pixel coordinates for the two positions.
Returns
-------
dist : float
Th... | calculate the GCD sky separation (degrees) between two pixels.
Parameters
----------
pix1, pix2 : (float, float)
The (x,y) pixel coordinates for the two positions.
Returns
-------
dist : float
The distance between the two points (degrees). | entailment |
def get_psf_sky(self, ra, dec):
"""
Determine the local psf at a given sky location.
The psf is returned in degrees.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
The p... | Determine the local psf at a given sky location.
The psf is returned in degrees.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
The psf semi-major axis, semi-minor axis, and position an... | entailment |
def get_psf_pix(self, ra, dec):
"""
Determine the local psf (a,b,pa) at a given sky location.
The psf is in pixel coordinates.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
... | Determine the local psf (a,b,pa) at a given sky location.
The psf is in pixel coordinates.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
The psf semi-major axis (pixels), semi-minor ax... | entailment |
def get_pixbeam(self, ra, dec):
"""
Get the psf at the location specified in pixel coordinates.
The psf is also in pixel coordinates.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
... | Get the psf at the location specified in pixel coordinates.
The psf is also in pixel coordinates.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
a, b, pa : float
The psf semi-major axis (pixels), semi-mi... | entailment |
def get_beam(self, ra, dec):
"""
Get the psf as a :class:`AegeanTools.fits_image.Beam` object.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
The psf a... | Get the psf as a :class:`AegeanTools.fits_image.Beam` object.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
beam : :class:`AegeanTools.fits_image.Beam`
The psf at the given location. | entailment |
def get_beamarea_pix(self, ra, dec):
"""
Calculate the area of the beam in square pixels.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
area : float
The area of the beam in square pixels.
... | Calculate the area of the beam in square pixels.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
area : float
The area of the beam in square pixels. | entailment |
def get_beamarea_deg2(self, ra, dec):
"""
Calculate the area of the beam in square degrees.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
area : float
The area of the beam in square degrees.
... | Calculate the area of the beam in square degrees.
Parameters
----------
ra, dec : float
The sky position (degrees).
Returns
-------
area : float
The area of the beam in square degrees. | entailment |
def find_start_point(self):
"""
Find the first location in our array that is not empty
"""
for i, row in enumerate(self.data):
for j, _ in enumerate(row):
if self.data[i, j] != 0: # or not np.isfinite(self.data[i,j]):
return i, j | Find the first location in our array that is not empty | entailment |
def step(self, x, y):
"""
Move from the current location to the next
Parameters
----------
x, y : int
The current location
"""
up_left = self.solid(x - 1, y - 1)
up_right = self.solid(x, y - 1)
down_left = self.solid(x - 1, y)
... | Move from the current location to the next
Parameters
----------
x, y : int
The current location | entailment |
def solid(self, x, y):
"""
Determine whether the pixel x,y is nonzero
Parameters
----------
x, y : int
The pixel of interest.
Returns
-------
solid : bool
True if the pixel is not zero.
"""
if not(0 <= x < self.xsi... | Determine whether the pixel x,y is nonzero
Parameters
----------
x, y : int
The pixel of interest.
Returns
-------
solid : bool
True if the pixel is not zero. | entailment |
def walk_perimeter(self, startx, starty):
"""
Starting at a point on the perimeter of a region, 'walk' the perimeter to return
to the starting point. Record the path taken.
Parameters
----------
startx, starty : int
The starting location. Assumed to be on the... | Starting at a point on the perimeter of a region, 'walk' the perimeter to return
to the starting point. Record the path taken.
Parameters
----------
startx, starty : int
The starting location. Assumed to be on the perimeter of a region.
Returns
-------
... | entailment |
def do_march(self):
"""
March about and trace the outline of our object
Returns
-------
perimeter : list
The pixels on the perimeter of the region [[x1, y1], ...]
"""
x, y = self.find_start_point()
perimeter = self.walk_perimeter(x, y)
... | March about and trace the outline of our object
Returns
-------
perimeter : list
The pixels on the perimeter of the region [[x1, y1], ...] | entailment |
def _blank_within(self, perimeter):
"""
Blank all the pixels within the given perimeter.
Parameters
----------
perimeter : list
The perimeter of the region.
"""
# Method:
# scan around the perimeter filling 'up' from each pixel
# stop... | Blank all the pixels within the given perimeter.
Parameters
----------
perimeter : list
The perimeter of the region. | entailment |
def do_march_all(self):
"""
Recursive march in the case that we have a fragmented shape.
Returns
-------
perimeters : [perimeter1, ...]
The perimeters of all the regions in the image.
See Also
--------
:func:`AegeanTools.msq2.MarchingSquares.d... | Recursive march in the case that we have a fragmented shape.
Returns
-------
perimeters : [perimeter1, ...]
The perimeters of all the regions in the image.
See Also
--------
:func:`AegeanTools.msq2.MarchingSquares.do_march` | entailment |
def elliptical_gaussian(x, y, amp, xo, yo, sx, sy, theta):
"""
Generate a model 2d Gaussian with the given parameters.
Evaluate this model at the given locations x,y.
Parameters
----------
x, y : numeric or array-like
locations at which to evaluate the gaussian
amp : float
P... | Generate a model 2d Gaussian with the given parameters.
Evaluate this model at the given locations x,y.
Parameters
----------
x, y : numeric or array-like
locations at which to evaluate the gaussian
amp : float
Peak value.
xo, yo : float
Center of the gaussian.
sx, s... | entailment |
def Cmatrix(x, y, sx, sy, theta):
"""
Construct a correlation matrix corresponding to the data.
The matrix assumes a gaussian correlation function.
Parameters
----------
x, y : array-like
locations at which to evaluate the correlation matirx
sx, sy : float
major/minor axes o... | Construct a correlation matrix corresponding to the data.
The matrix assumes a gaussian correlation function.
Parameters
----------
x, y : array-like
locations at which to evaluate the correlation matirx
sx, sy : float
major/minor axes of the gaussian correlation function (sigmas)
... | entailment |
def Bmatrix(C):
"""
Calculate a matrix which is effectively the square root of the correlation matrix C
Parameters
----------
C : 2d array
A covariance matrix
Returns
-------
B : 2d array
A matrix B such the B.dot(B') = inv(C)
"""
# this version of finding the ... | Calculate a matrix which is effectively the square root of the correlation matrix C
Parameters
----------
C : 2d array
A covariance matrix
Returns
-------
B : 2d array
A matrix B such the B.dot(B') = inv(C) | entailment |
def jacobian(pars, x, y):
"""
Analytical calculation of the Jacobian for an elliptical gaussian
Will work for a model that contains multiple Gaussians, and for which
some components are not being fit (don't vary).
Parameters
----------
pars : lmfit.Model
The model parameters
x, ... | Analytical calculation of the Jacobian for an elliptical gaussian
Will work for a model that contains multiple Gaussians, and for which
some components are not being fit (don't vary).
Parameters
----------
pars : lmfit.Model
The model parameters
x, y : list
Locations at which th... | entailment |
def lmfit_jacobian(pars, x, y, errs=None, B=None, emp=False):
"""
Wrapper around :func:`AegeanTools.fitting.jacobian` and :func:`AegeanTools.fitting.emp_jacobian`
which gives the output in a format that is required for lmfit.
Parameters
----------
pars : lmfit.Model
The model parameters... | Wrapper around :func:`AegeanTools.fitting.jacobian` and :func:`AegeanTools.fitting.emp_jacobian`
which gives the output in a format that is required for lmfit.
Parameters
----------
pars : lmfit.Model
The model parameters
x, y : list
Locations at which the jacobian is being evaluat... | entailment |
def hessian(pars, x, y):
"""
Create a hessian matrix corresponding to the source model 'pars'
Only parameters that vary will contribute to the hessian.
Thus there will be a total of nvar x nvar entries, each of which is a
len(x) x len(y) array.
Parameters
----------
pars : lmfit.Paramet... | Create a hessian matrix corresponding to the source model 'pars'
Only parameters that vary will contribute to the hessian.
Thus there will be a total of nvar x nvar entries, each of which is a
len(x) x len(y) array.
Parameters
----------
pars : lmfit.Parameters
The model
x, y : list... | entailment |
def emp_hessian(pars, x, y):
"""
Calculate the hessian matrix empirically.
Create a hessian matrix corresponding to the source model 'pars'
Only parameters that vary will contribute to the hessian.
Thus there will be a total of nvar x nvar entries, each of which is a
len(x) x len(y) array.
... | Calculate the hessian matrix empirically.
Create a hessian matrix corresponding to the source model 'pars'
Only parameters that vary will contribute to the hessian.
Thus there will be a total of nvar x nvar entries, each of which is a
len(x) x len(y) array.
Parameters
----------
pars : lmfi... | entailment |
def nan_acf(noise):
"""
Calculate the autocorrelation function of the noise
where the noise is a 2d array that may contain nans
Parameters
----------
noise : 2d-array
Noise image.
Returns
-------
acf : 2d-array
The ACF.
"""
corr = np.zeros(noise.shape)
... | Calculate the autocorrelation function of the noise
where the noise is a 2d array that may contain nans
Parameters
----------
noise : 2d-array
Noise image.
Returns
-------
acf : 2d-array
The ACF. | entailment |
def make_ita(noise, acf=None):
"""
Create the matrix ita of the noise where the noise may be a masked array
where ita(x,y) is the correlation between pixel pairs that have the same separation as x and y.
Parameters
----------
noise : 2d-array
The noise image
acf : 2d-array
... | Create the matrix ita of the noise where the noise may be a masked array
where ita(x,y) is the correlation between pixel pairs that have the same separation as x and y.
Parameters
----------
noise : 2d-array
The noise image
acf : 2d-array
The autocorrelation matrix. (None = calcula... | entailment |
def RB_bias(data, pars, ita=None, acf=None):
"""
Calculate the expected bias on each of the parameters in the model pars.
Only parameters that are allowed to vary will have a bias.
Calculation follows the description of Refrieger & Brown 1998 (cite).
Parameters
----------
data : 2d-array
... | Calculate the expected bias on each of the parameters in the model pars.
Only parameters that are allowed to vary will have a bias.
Calculation follows the description of Refrieger & Brown 1998 (cite).
Parameters
----------
data : 2d-array
data that was fit
pars : lmfit.Parameters
... | entailment |
def bias_correct(params, data, acf=None):
"""
Calculate and apply a bias correction to the given fit parameters
Parameters
----------
params : lmfit.Parameters
The model parameters. These will be modified.
data : 2d-array
The data which was used in the fitting
acf : 2d-ar... | Calculate and apply a bias correction to the given fit parameters
Parameters
----------
params : lmfit.Parameters
The model parameters. These will be modified.
data : 2d-array
The data which was used in the fitting
acf : 2d-array
ACF of the data. Default = None.
Retu... | entailment |
def condon_errors(source, theta_n, psf=None):
"""
Calculate the parameter errors for a fitted source
using the description of Condon'97
All parameters are assigned errors, assuming that all params were fit.
If some params were held fixed then these errors are overestimated.
Parameters
-----... | Calculate the parameter errors for a fitted source
using the description of Condon'97
All parameters are assigned errors, assuming that all params were fit.
If some params were held fixed then these errors are overestimated.
Parameters
----------
source : :class:`AegeanTools.models.SimpleSource... | entailment |
def errors(source, model, wcshelper):
"""
Convert pixel based errors into sky coord errors
Parameters
----------
source : :class:`AegeanTools.models.SimpleSource`
The source which was fit.
model : lmfit.Parameters
The model which was fit.
wcshelper : :class:`AegeanTools.wc... | Convert pixel based errors into sky coord errors
Parameters
----------
source : :class:`AegeanTools.models.SimpleSource`
The source which was fit.
model : lmfit.Parameters
The model which was fit.
wcshelper : :class:`AegeanTools.wcs_helpers.WCSHelper`
WCS information.
... | entailment |
def new_errors(source, model, wcshelper): # pragma: no cover
"""
Convert pixel based errors into sky coord errors
Uses covariance matrix for ra/dec errors
and calculus approach to a/b/pa errors
Parameters
----------
source : :class:`AegeanTools.models.SimpleSource`
The source which... | Convert pixel based errors into sky coord errors
Uses covariance matrix for ra/dec errors
and calculus approach to a/b/pa errors
Parameters
----------
source : :class:`AegeanTools.models.SimpleSource`
The source which was fit.
model : lmfit.Parameters
The model which was fit.
... | entailment |
def ntwodgaussian_lmfit(params):
"""
Convert an lmfit.Parameters object into a function which calculates the model.
Parameters
----------
params : lmfit.Parameters
Model parameters, can have multiple components.
Returns
-------
model : func
A function f(x,y) that will ... | Convert an lmfit.Parameters object into a function which calculates the model.
Parameters
----------
params : lmfit.Parameters
Model parameters, can have multiple components.
Returns
-------
model : func
A function f(x,y) that will compute the model. | entailment |
def do_lmfit(data, params, B=None, errs=None, dojac=True):
"""
Fit the model to the data
data may contain 'flagged' or 'masked' data with the value of np.NaN
Parameters
----------
data : 2d-array
Image data
params : lmfit.Parameters
Initial model guess.
B : 2d-array
... | Fit the model to the data
data may contain 'flagged' or 'masked' data with the value of np.NaN
Parameters
----------
data : 2d-array
Image data
params : lmfit.Parameters
Initial model guess.
B : 2d-array
B matrix to be used in residual calculations.
Default = N... | entailment |
def covar_errors(params, data, errs, B, C=None):
"""
Take a set of parameters that were fit with lmfit, and replace the errors
with the 1\sigma errors calculated using the covariance matrix.
Parameters
----------
params : lmfit.Parameters
Model
data : 2d-array
Image data
... | Take a set of parameters that were fit with lmfit, and replace the errors
with the 1\sigma errors calculated using the covariance matrix.
Parameters
----------
params : lmfit.Parameters
Model
data : 2d-array
Image data
errs : 2d-array ?
Image noise.
B : 2d-array
... | entailment |
def barrier(events, sid, kind='neighbour'):
"""
act as a multiprocessing barrier
"""
events[sid].set()
# only wait for the neighbours
if kind=='neighbour':
if sid > 0:
logging.debug("{0} is waiting for {1}".format(sid, sid - 1))
events[sid - 1].wait()
if s... | act as a multiprocessing barrier | entailment |
def sigmaclip(arr, lo, hi, reps=3):
"""
Perform sigma clipping on an array, ignoring non finite values.
During each iteration return an array whose elements c obey:
mean -std*lo < c < mean + std*hi
where mean/std are the mean std of the input array.
Parameters
----------
arr : iterabl... | Perform sigma clipping on an array, ignoring non finite values.
During each iteration return an array whose elements c obey:
mean -std*lo < c < mean + std*hi
where mean/std are the mean std of the input array.
Parameters
----------
arr : iterable
An iterable array of numeric types.
... | entailment |
def _sf2(args):
"""
A shallow wrapper for sigma_filter.
Parameters
----------
args : list
A list of arguments for sigma_filter
Returns
-------
None
"""
# an easier to debug traceback when multiprocessing
# thanks to https://stackoverflow.com/a/16618842/1710603
t... | A shallow wrapper for sigma_filter.
Parameters
----------
args : list
A list of arguments for sigma_filter
Returns
-------
None | entailment |
def sigma_filter(filename, region, step_size, box_size, shape, domask, sid):
"""
Calculate the background and rms for a sub region of an image. The results are
written to shared memory - irms and ibkg.
Parameters
----------
filename : string
Fits file to open
region : list
... | Calculate the background and rms for a sub region of an image. The results are
written to shared memory - irms and ibkg.
Parameters
----------
filename : string
Fits file to open
region : list
Region within the fits file that is to be processed. (row_min, row_max).
step_size :... | entailment |
def filter_mc_sharemem(filename, step_size, box_size, cores, shape, nslice=None, domask=True):
"""
Calculate the background and noise images corresponding to the input file.
The calculation is done via a box-car approach and uses multiple cores and shared memory.
Parameters
----------
filename ... | Calculate the background and noise images corresponding to the input file.
The calculation is done via a box-car approach and uses multiple cores and shared memory.
Parameters
----------
filename : str
Filename to be filtered.
step_size : (int, int)
Step size for the filter.
b... | entailment |
def filter_image(im_name, out_base, step_size=None, box_size=None, twopass=False, cores=None, mask=True, compressed=False, nslice=None):
"""
Create a background and noise image from an input image.
Resulting images are written to `outbase_bkg.fits` and `outbase_rms.fits`
Parameters
----------
i... | Create a background and noise image from an input image.
Resulting images are written to `outbase_bkg.fits` and `outbase_rms.fits`
Parameters
----------
im_name : str or HDUList
Image to filter. Either a string filename or an astropy.io.fits.HDUList.
out_base : str
The output filena... | entailment |
def write_fits(data, header, file_name):
"""
Combine data and a fits header to write a fits file.
Parameters
----------
data : numpy.ndarray
The data to be written.
header : astropy.io.fits.hduheader
The header for the fits file.
file_name : string
The file to writ... | Combine data and a fits header to write a fits file.
Parameters
----------
data : numpy.ndarray
The data to be written.
header : astropy.io.fits.hduheader
The header for the fits file.
file_name : string
The file to write
Returns
-------
None | entailment |
def dec2dec(dec):
"""
Convert sexegessimal RA string into a float in degrees.
Parameters
----------
dec : string
A string separated representing the Dec.
Expected format is `[+- ]hh:mm[:ss.s]`
Colons can be replaced with any whit space character.
Returns
-------
... | Convert sexegessimal RA string into a float in degrees.
Parameters
----------
dec : string
A string separated representing the Dec.
Expected format is `[+- ]hh:mm[:ss.s]`
Colons can be replaced with any whit space character.
Returns
-------
dec : float
The Dec i... | entailment |
def dec2dms(x):
"""
Convert decimal degrees into a sexagessimal string in degrees.
Parameters
----------
x : float
Angle in degrees
Returns
-------
dms : string
String of format [+-]DD:MM:SS.SS
or XX:XX:XX.XX if x is not finite.
"""
if not np.isfinite(x)... | Convert decimal degrees into a sexagessimal string in degrees.
Parameters
----------
x : float
Angle in degrees
Returns
-------
dms : string
String of format [+-]DD:MM:SS.SS
or XX:XX:XX.XX if x is not finite. | entailment |
def dec2hms(x):
"""
Convert decimal degrees into a sexagessimal string in hours.
Parameters
----------
x : float
Angle in degrees
Returns
-------
dms : string
String of format HH:MM:SS.SS
or XX:XX:XX.XX if x is not finite.
"""
if not np.isfinite(x):
... | Convert decimal degrees into a sexagessimal string in hours.
Parameters
----------
x : float
Angle in degrees
Returns
-------
dms : string
String of format HH:MM:SS.SS
or XX:XX:XX.XX if x is not finite. | entailment |
def gcd(ra1, dec1, ra2, dec2):
"""
Calculate the great circle distance between to points using the haversine formula [1]_.
Parameters
----------
ra1, dec1, ra2, dec2 : float
The coordinates of the two points of interest.
Units are in degrees.
Returns
-------
dist : flo... | Calculate the great circle distance between to points using the haversine formula [1]_.
Parameters
----------
ra1, dec1, ra2, dec2 : float
The coordinates of the two points of interest.
Units are in degrees.
Returns
-------
dist : float
The distance between the two poi... | entailment |
def bear(ra1, dec1, ra2, dec2):
"""
Calculate the bearing of point 2 from point 1 along a great circle.
The bearing is East of North and is in [0, 360), whereas position angle is also East of North but (-180,180]
Parameters
----------
ra1, dec1, ra2, dec2 : float
The sky coordinates (de... | Calculate the bearing of point 2 from point 1 along a great circle.
The bearing is East of North and is in [0, 360), whereas position angle is also East of North but (-180,180]
Parameters
----------
ra1, dec1, ra2, dec2 : float
The sky coordinates (degrees) of the two points.
Returns
-... | entailment |
def translate(ra, dec, r, theta):
"""
Translate a given point a distance r in the (initial) direction theta, along a great circle.
Parameters
----------
ra, dec : float
The initial point of interest (degrees).
r, theta : float
The distance and initial direction to translate (d... | Translate a given point a distance r in the (initial) direction theta, along a great circle.
Parameters
----------
ra, dec : float
The initial point of interest (degrees).
r, theta : float
The distance and initial direction to translate (degrees).
Returns
-------
ra, dec ... | entailment |
def dist_rhumb(ra1, dec1, ra2, dec2):
"""
Calculate the Rhumb line distance between two points [1]_.
A Rhumb line between two points is one which follows a constant bearing.
Parameters
----------
ra1, dec1, ra2, dec2 : float
The position of the two points (degrees).
Returns
---... | Calculate the Rhumb line distance between two points [1]_.
A Rhumb line between two points is one which follows a constant bearing.
Parameters
----------
ra1, dec1, ra2, dec2 : float
The position of the two points (degrees).
Returns
-------
dist : float
The distance between... | entailment |
def bear_rhumb(ra1, dec1, ra2, dec2):
"""
Calculate the bearing of point 2 from point 1 along a Rhumb line.
The bearing is East of North and is in [0, 360), whereas position angle is also East of North but (-180,180]
Parameters
----------
ra1, dec1, ra2, dec2 : float
The sky coordinates... | Calculate the bearing of point 2 from point 1 along a Rhumb line.
The bearing is East of North and is in [0, 360), whereas position angle is also East of North but (-180,180]
Parameters
----------
ra1, dec1, ra2, dec2 : float
The sky coordinates (degrees) of the two points.
Returns
---... | entailment |
def translate_rhumb(ra, dec, r, theta):
"""
Translate a given point a distance r in the (initial) direction theta, along a Rhumb line.
Parameters
----------
ra, dec : float
The initial point of interest (degrees).
r, theta : float
The distance and initial direction to translate ... | Translate a given point a distance r in the (initial) direction theta, along a Rhumb line.
Parameters
----------
ra, dec : float
The initial point of interest (degrees).
r, theta : float
The distance and initial direction to translate (degrees).
Returns
-------
ra, dec : fl... | entailment |
def galactic2fk5(l, b):
"""
Convert galactic l/b to fk5 ra/dec
Parameters
----------
l, b : float
Galactic coordinates in radians.
Returns
-------
ra, dec : float
FK5 ecliptic coordinates in radians.
"""
a = SkyCoord(l, b, unit=(u.radian, u.radian), frame='galac... | Convert galactic l/b to fk5 ra/dec
Parameters
----------
l, b : float
Galactic coordinates in radians.
Returns
-------
ra, dec : float
FK5 ecliptic coordinates in radians. | entailment |
def mask_plane(data, wcs, region, negate=False):
"""
Mask a 2d image (data) such that pixels within 'region' are set to nan.
Parameters
----------
data : 2d-array
Image array.
wcs : astropy.wcs.WCS
WCS for the image in question.
region : :class:`AegeanTools.regions.Region`... | Mask a 2d image (data) such that pixels within 'region' are set to nan.
Parameters
----------
data : 2d-array
Image array.
wcs : astropy.wcs.WCS
WCS for the image in question.
region : :class:`AegeanTools.regions.Region`
A region within which the image pixels will be maske... | entailment |
def mask_file(regionfile, infile, outfile, negate=False):
"""
Created a masked version of file, using a region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The image will be masked according to this region.
infile... | Created a masked version of file, using a region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The image will be masked according to this region.
infile : str
Input FITS image.
outfile : str
Output FIT... | entailment |
def mask_table(region, table, negate=False, racol='ra', deccol='dec'):
"""
Apply a given mask (region) to the table, removing all the rows with ra/dec inside the region
If negate=False then remove the rows with ra/dec outside the region.
Parameters
----------
region : :class:`AegeanTools.regio... | Apply a given mask (region) to the table, removing all the rows with ra/dec inside the region
If negate=False then remove the rows with ra/dec outside the region.
Parameters
----------
region : :class:`AegeanTools.regions.Region`
Region to mask.
table : Astropy.table.Table
Table t... | entailment |
def mask_catalog(regionfile, infile, outfile, negate=False, racol='ra', deccol='dec'):
"""
Apply a region file as a mask to a catalog, removing all the rows with ra/dec inside the region
If negate=False then remove the rows with ra/dec outside the region.
Parameters
----------
regionfile : str... | Apply a region file as a mask to a catalog, removing all the rows with ra/dec inside the region
If negate=False then remove the rows with ra/dec outside the region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The catalogue... | entailment |
def mim2reg(mimfile, regfile):
"""
Convert a MIMAS region (.mim) file into a DS9 region (.reg) file.
Parameters
----------
mimfile : str
Input file in MIMAS format.
regfile : str
Output file.
"""
region = Region.load(mimfile)
region.write_reg(regfile)
logging.i... | Convert a MIMAS region (.mim) file into a DS9 region (.reg) file.
Parameters
----------
mimfile : str
Input file in MIMAS format.
regfile : str
Output file. | entailment |
def mim2fits(mimfile, fitsfile):
"""
Convert a MIMAS region (.mim) file into a MOC region (.fits) file.
Parameters
----------
mimfile : str
Input file in MIMAS format.
fitsfile : str
Output file.
"""
region = Region.load(mimfile)
region.write_fits(fitsfile, moctool=... | Convert a MIMAS region (.mim) file into a MOC region (.fits) file.
Parameters
----------
mimfile : str
Input file in MIMAS format.
fitsfile : str
Output file. | entailment |
def box2poly(line):
"""
Convert a string that describes a box in ds9 format, into a polygon that is given by the corners of the box
Parameters
----------
line : str
A string containing a DS9 region command for a box.
Returns
-------
poly : [ra, dec, ...]
The corners of ... | Convert a string that describes a box in ds9 format, into a polygon that is given by the corners of the box
Parameters
----------
line : str
A string containing a DS9 region command for a box.
Returns
-------
poly : [ra, dec, ...]
The corners of the box in clockwise order from ... | entailment |
def circle2circle(line):
"""
Parse a string that describes a circle in ds9 format.
Parameters
----------
line : str
A string containing a DS9 region command for a circle.
Returns
-------
circle : [ra, dec, radius]
The center and radius of the circle.
"""
words =... | Parse a string that describes a circle in ds9 format.
Parameters
----------
line : str
A string containing a DS9 region command for a circle.
Returns
-------
circle : [ra, dec, radius]
The center and radius of the circle. | entailment |
def poly2poly(line):
"""
Parse a string of text containing a DS9 description of a polygon.
This function works but is not very robust due to the constraints of healpy.
Parameters
----------
line : str
A string containing a DS9 region command for a polygon.
Returns
-------
... | Parse a string of text containing a DS9 description of a polygon.
This function works but is not very robust due to the constraints of healpy.
Parameters
----------
line : str
A string containing a DS9 region command for a polygon.
Returns
-------
poly : [ra, dec, ...]
The... | entailment |
def reg2mim(regfile, mimfile, maxdepth):
"""
Parse a DS9 region file and write a MIMAS region (.mim) file.
Parameters
----------
regfile : str
DS9 region (.reg) file.
mimfile : str
MIMAS region (.mim) file.
maxdepth : str
Depth/resolution of the region file.
"... | Parse a DS9 region file and write a MIMAS region (.mim) file.
Parameters
----------
regfile : str
DS9 region (.reg) file.
mimfile : str
MIMAS region (.mim) file.
maxdepth : str
Depth/resolution of the region file. | entailment |
def combine_regions(container):
"""
Return a region that is the combination of those specified in the container.
The container is typically a results instance that comes from argparse.
Order of construction is: add regions, subtract regions, add circles, subtract circles,
add polygons, subtract pol... | Return a region that is the combination of those specified in the container.
The container is typically a results instance that comes from argparse.
Order of construction is: add regions, subtract regions, add circles, subtract circles,
add polygons, subtract polygons.
Parameters
----------
co... | entailment |
def intersect_regions(flist):
"""
Construct a region which is the intersection of all regions described in the given
list of file names.
Parameters
----------
flist : list
A list of region filenames.
Returns
-------
region : :class:`AegeanTools.regions.Region`
The i... | Construct a region which is the intersection of all regions described in the given
list of file names.
Parameters
----------
flist : list
A list of region filenames.
Returns
-------
region : :class:`AegeanTools.regions.Region`
The intersection of all regions, possibly empty... | entailment |
def save_region(region, filename):
"""
Save the given region to a file
Parameters
----------
region : :class:`AegeanTools.regions.Region`
A region.
filename : str
Output file name.
"""
region.save(filename)
logging.info("Wrote {0}".format(filename))
return | Save the given region to a file
Parameters
----------
region : :class:`AegeanTools.regions.Region`
A region.
filename : str
Output file name. | entailment |
def save_as_image(region, filename):
"""
Convert a MIMAS region (.mim) file into a image (eg .png)
Parameters
----------
region : :class:`AegeanTools.regions.Region`
Region of interest.
filename : str
Output filename.
"""
import healpy as hp
pixels = list(region.get... | Convert a MIMAS region (.mim) file into a image (eg .png)
Parameters
----------
region : :class:`AegeanTools.regions.Region`
Region of interest.
filename : str
Output filename. | entailment |
def get_pixinfo(header):
"""
Return some pixel information based on the given hdu header
pixarea - the area of a single pixel in deg2
pixscale - the side lengths of a pixel (assuming they are square)
Parameters
----------
header : HDUHeader or dict
FITS header information
Retur... | Return some pixel information based on the given hdu header
pixarea - the area of a single pixel in deg2
pixscale - the side lengths of a pixel (assuming they are square)
Parameters
----------
header : HDUHeader or dict
FITS header information
Returns
-------
pixarea : float
... | entailment |
def get_beam(header):
"""
Create a :class:`AegeanTools.fits_image.Beam` object from a fits header.
BPA may be missing but will be assumed to be zero.
if BMAJ or BMIN are missing then return None instead of a beam object.
Parameters
----------
header : HDUHeader
The fits header.
... | Create a :class:`AegeanTools.fits_image.Beam` object from a fits header.
BPA may be missing but will be assumed to be zero.
if BMAJ or BMIN are missing then return None instead of a beam object.
Parameters
----------
header : HDUHeader
The fits header.
Returns
-------
beam : ... | entailment |
def fix_aips_header(header):
"""
Search through an image header. If the keywords BMAJ/BMIN/BPA are not set,
but there are AIPS history cards, then we can populate the BMAJ/BMIN/BPA.
Fix the header if possible, otherwise don't. Either way, don't complain.
Parameters
----------
header : HDUH... | Search through an image header. If the keywords BMAJ/BMIN/BPA are not set,
but there are AIPS history cards, then we can populate the BMAJ/BMIN/BPA.
Fix the header if possible, otherwise don't. Either way, don't complain.
Parameters
----------
header : HDUHeader
Fits header which may or ma... | entailment |
def set_pixels(self, pixels):
"""
Set the image data.
Will not work if the new image has a different shape than the current image.
Parameters
----------
pixels : numpy.ndarray
New image data
Returns
-------
None
"""
if... | Set the image data.
Will not work if the new image has a different shape than the current image.
Parameters
----------
pixels : numpy.ndarray
New image data
Returns
-------
None | entailment |
def get_background_rms(self):
"""
Calculate the rms of the image. The rms is calculated from the interqurtile range (IQR), to
reduce bias from source pixels.
Returns
-------
rms : float
The image rms.
Notes
-----
The rms value is cach... | Calculate the rms of the image. The rms is calculated from the interqurtile range (IQR), to
reduce bias from source pixels.
Returns
-------
rms : float
The image rms.
Notes
-----
The rms value is cached after first calculation. | entailment |
def pix2sky(self, pixel):
"""
Get the sky coordinates for a given image pixel.
Parameters
----------
pixel : (float, float)
Image coordinates.
Returns
-------
ra,dec : float
Sky coordinates (degrees)
"""
pixbox = ... | Get the sky coordinates for a given image pixel.
Parameters
----------
pixel : (float, float)
Image coordinates.
Returns
-------
ra,dec : float
Sky coordinates (degrees) | entailment |
def sky2pix(self, skypos):
"""
Get the pixel coordinates for a given sky position (degrees).
Parameters
----------
skypos : (float,float)
ra,dec position in degrees.
Returns
-------
x,y : float
Pixel coordinates.
"""
... | Get the pixel coordinates for a given sky position (degrees).
Parameters
----------
skypos : (float,float)
ra,dec position in degrees.
Returns
-------
x,y : float
Pixel coordinates. | entailment |
def load_sources(filename):
"""
Open a file, read contents, return a list of all the sources in that file.
@param filename:
@return: list of OutputSource objects
"""
catalog = catalogs.table_to_source_list(catalogs.load_table(filename))
logging.info("read {0} sources from {1}".format(len(cat... | Open a file, read contents, return a list of all the sources in that file.
@param filename:
@return: list of OutputSource objects | entailment |
def search_beam(hdulist):
"""
Will search the beam info from the HISTORY
:param hdulist:
:return:
"""
header = hdulist[0].header
history = header['HISTORY']
history_str = str(history)
#AIPS CLEAN BMAJ= 1.2500E-02 BMIN= 1.2500E-02 BPA= 0.00
if 'BMAJ' in history_str:
... | Will search the beam info from the HISTORY
:param hdulist:
:return: | entailment |
def fix_shape(source):
"""
Ensure that a>=b for a given source object.
If a<b then swap a/b and increment pa by 90.
err_a/err_b are also swapped as needed.
Parameters
----------
source : object
any object with a/b/pa/err_a/err_b properties
"""
if source.a < source.b:
... | Ensure that a>=b for a given source object.
If a<b then swap a/b and increment pa by 90.
err_a/err_b are also swapped as needed.
Parameters
----------
source : object
any object with a/b/pa/err_a/err_b properties | entailment |
def theta_limit(theta):
"""
Angle theta is periodic with period pi.
Constrain theta such that -pi/2<theta<=pi/2.
Parameters
----------
theta : float
Input angle.
Returns
-------
theta : float
Rotate angle.
"""
while theta <= -1 * np.pi / 2:
theta += ... | Angle theta is periodic with period pi.
Constrain theta such that -pi/2<theta<=pi/2.
Parameters
----------
theta : float
Input angle.
Returns
-------
theta : float
Rotate angle. | entailment |
def scope2lat(telescope):
"""
Convert a telescope name into a latitude
returns None when the telescope is unknown.
Parameters
----------
telescope : str
Acronym (name) of telescope, eg MWA.
Returns
-------
lat : float
The latitude of the telescope.
Notes
--... | Convert a telescope name into a latitude
returns None when the telescope is unknown.
Parameters
----------
telescope : str
Acronym (name) of telescope, eg MWA.
Returns
-------
lat : float
The latitude of the telescope.
Notes
-----
These values were taken from w... | entailment |
def check_cores(cores):
"""
Determine how many cores we are able to use.
Return 1 if we are not able to make a queue via pprocess.
Parameters
----------
cores : int
The number of cores that are requested.
Returns
-------
cores : int
The number of cores available.
... | Determine how many cores we are able to use.
Return 1 if we are not able to make a queue via pprocess.
Parameters
----------
cores : int
The number of cores that are requested.
Returns
-------
cores : int
The number of cores available. | entailment |
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