# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module defines elliptical and elliptical-annulus apertures in both
pixel and sky coordinates.
"""
import math
import astropy.units as u
import numpy as np
from photutils.aperture.attributes import (PixelPositions, PositiveScalar,
PositiveScalarAngle, ScalarAngle,
ScalarAngleOrValue,
SkyCoordPositions)
from photutils.aperture.core import PixelAperture, SkyAperture
from photutils.aperture.mask import ApertureMask
from photutils.geometry import elliptical_overlap_grid
__all__ = ['EllipticalMaskMixin', 'EllipticalAperture', 'EllipticalAnnulus',
'SkyEllipticalAperture', 'SkyEllipticalAnnulus']
[docs]
class EllipticalMaskMixin:
"""
Mixin class to create masks for elliptical and elliptical-annulus
aperture objects.
"""
[docs]
def to_mask(self, method='exact', subpixels=5):
"""
Return a mask for the aperture.
Parameters
----------
method : {'exact', 'center', 'subpixel'}, optional
The method used to determine the overlap of the aperture on
the pixel grid. Not all options are available for all
aperture types. Note that the more precise methods are
generally slower. The following methods are available:
* ``'exact'`` (default):
The the exact fractional overlap of the aperture and
each pixel is calculated. The aperture weights will
contain values between 0 and 1.
* ``'center'``:
A pixel is considered to be entirely in or out of the
aperture depending on whether its center is in or out
of the aperture. The aperture weights will contain
values only of 0 (out) and 1 (in).
* ``'subpixel'``:
A pixel is divided into subpixels (see the
``subpixels`` keyword), each of which are considered
to be entirely in or out of the aperture depending
on whether its center is in or out of the aperture.
If ``subpixels=1``, this method is equivalent to
``'center'``. The aperture weights will contain values
between 0 and 1.
subpixels : int, optional
For the ``'subpixel'`` method, resample pixels by this
factor in each dimension. That is, each pixel is divided
into ``subpixels**2`` subpixels. This keyword is ignored
unless ``method='subpixel'``.
Returns
-------
mask : `~photutils.aperture.ApertureMask` or list of `~photutils.aperture.ApertureMask`
A mask for the aperture. If the aperture is scalar then a
single `~photutils.aperture.ApertureMask` is returned,
otherwise a list of `~photutils.aperture.ApertureMask` is
returned.
"""
use_exact, subpixels = self._translate_mask_mode(method, subpixels)
if hasattr(self, 'a'):
a = self.a
b = self.b
elif hasattr(self, 'a_in'): # annulus
a = self.a_out
b = self.b_out
else:
raise ValueError('Cannot determine the aperture shape.')
masks = []
for bbox, edges in zip(self._bbox, self._centered_edges):
ny, nx = bbox.shape
mask = elliptical_overlap_grid(edges[0], edges[1], edges[2],
edges[3], nx, ny, a, b,
self._theta_radians,
use_exact, subpixels)
# subtract the inner ellipse for an annulus
if hasattr(self, 'a_in'):
mask -= elliptical_overlap_grid(edges[0], edges[1], edges[2],
edges[3], nx, ny, self.a_in,
self.b_in, self._theta_radians,
use_exact, subpixels)
masks.append(ApertureMask(mask, bbox))
if self.isscalar:
return masks[0]
else:
return masks
@staticmethod
def _calc_extents(semimajor_axis, semiminor_axis, theta):
"""
Calculate half of the bounding box extents of an ellipse.
"""
cos_theta = np.cos(theta)
sin_theta = np.sin(theta)
semimajor_x = semimajor_axis * cos_theta
semimajor_y = semimajor_axis * sin_theta
semiminor_x = semiminor_axis * -sin_theta
semiminor_y = semiminor_axis * cos_theta
x_extent = np.sqrt(semimajor_x**2 + semiminor_x**2)
y_extent = np.sqrt(semimajor_y**2 + semiminor_y**2)
return x_extent, y_extent
[docs]
class EllipticalAperture(EllipticalMaskMixin, PixelAperture):
"""
An elliptical aperture defined in pixel coordinates.
The aperture has a single fixed size/shape, but it can have multiple
positions (see the ``positions`` input).
Parameters
----------
positions : array_like
The pixel coordinates of the aperture center(s) in one of the
following formats:
* single ``(x, y)`` pair as a tuple, list, or `~numpy.ndarray`
* tuple, list, or `~numpy.ndarray` of ``(x, y)`` pairs
a : float
The semimajor axis of the ellipse in pixels.
b : float
The semiminor axis of the ellipse in pixels.
theta : float or `~astropy.units.Quantity`, optional
The rotation angle as an angular quantity
(`~astropy.units.Quantity` or `~astropy.coordinates.Angle`) or
value in radians (as a float) from the positive ``x`` axis. The
rotation angle increases counterclockwise.
Raises
------
ValueError : `ValueError`
If either axis (``a`` or ``b``) is negative.
Examples
--------
>>> from astropy.coordinates import Angle
>>> from photutils.aperture import EllipticalAperture
>>> theta = Angle(80, 'deg')
>>> aper = EllipticalAperture([10.0, 20.0], 5.0, 3.0)
>>> aper = EllipticalAperture((10.0, 20.0), 5.0, 3.0, theta=theta)
>>> pos1 = (10.0, 20.0) # (x, y)
>>> pos2 = (30.0, 40.0)
>>> pos3 = (50.0, 60.0)
>>> aper = EllipticalAperture([pos1, pos2, pos3], 5.0, 3.0)
>>> aper = EllipticalAperture((pos1, pos2, pos3), 5.0, 3.0, theta=theta)
"""
_params = ('positions', 'a', 'b', 'theta')
positions = PixelPositions('The center pixel position(s).')
a = PositiveScalar('The semimajor axis in pixels.')
b = PositiveScalar('The semiminor axis in pixels.')
theta = ScalarAngleOrValue('The counterclockwise rotation angle as an '
'angular Quantity or value in radians from '
'the positive x axis.')
def __init__(self, positions, a, b, theta=0.0):
self.positions = positions
self.a = a
self.b = b
self._theta_radians = 0.0 # defined by theta setter
self.theta = theta
@property
def _xy_extents(self):
return self._calc_extents(self.a, self.b, self._theta_radians)
@property
def area(self):
return math.pi * self.a * self.b
def _to_patch(self, origin=(0, 0), **kwargs):
"""
Return a `~matplotlib.patches.patch` for the aperture.
Parameters
----------
origin : array_like, optional
The ``(x, y)`` position of the origin of the displayed
image.
**kwargs : `dict`
Any keyword arguments accepted by
`matplotlib.patches.Patch`.
Returns
-------
patch : `~matplotlib.patches.patch` or list of `~matplotlib.patches.patch`
A patch for the aperture. If the aperture is scalar then a
single `~matplotlib.patches.patch` is returned, otherwise a
list of `~matplotlib.patches.patch` is returned.
"""
import matplotlib.patches as mpatches
xy_positions, patch_kwargs = self._define_patch_params(origin=origin,
**kwargs)
patches = []
theta_deg = self._theta_radians * 180.0 / np.pi
for xy_position in xy_positions:
patches.append(mpatches.Ellipse(xy_position, 2.0 * self.a,
2.0 * self.b, angle=theta_deg,
**patch_kwargs))
if self.isscalar:
return patches[0]
else:
return patches
[docs]
def to_mask(self, method='exact', subpixels=5):
return EllipticalMaskMixin.to_mask(self, method=method,
subpixels=subpixels)
[docs]
def to_sky(self, wcs):
"""
Convert the aperture to a `SkyEllipticalAperture` object defined
in celestial coordinates.
Parameters
----------
wcs : WCS object
A world coordinate system (WCS) transformation that
supports the `astropy shared interface for WCS
<https://docs.astropy.org/en/stable/wcs/wcsapi.html>`_
(e.g., `astropy.wcs.WCS`, `gwcs.wcs.WCS`).
Returns
-------
aperture : `SkyEllipticalAperture` object
A `SkyEllipticalAperture` object.
"""
return SkyEllipticalAperture(**self._to_sky_params(wcs))
[docs]
class EllipticalAnnulus(EllipticalMaskMixin, PixelAperture):
r"""
An elliptical annulus aperture defined in pixel coordinates.
The aperture has a single fixed size/shape, but it can have multiple
positions (see the ``positions`` input).
Parameters
----------
positions : array_like
The pixel coordinates of the aperture center(s) in one of the
following formats:
* single ``(x, y)`` pair as a tuple, list, or `~numpy.ndarray`
* tuple, list, or `~numpy.ndarray` of ``(x, y)`` pairs
a_in : float
The inner semimajor axis of the elliptical annulus in pixels.
a_out : float
The outer semimajor axis of the elliptical annulus in pixels.
b_out : float
The outer semiminor axis of the elliptical annulus in pixels.
b_in : `None` or float, optional
The inner semiminor axis of the elliptical annulus in pixels.
If `None`, then the the inner semiminor axis is calculated as:
.. math:: b_{in} = b_{out}
\left(\frac{a_{in}}{a_{out}}\right)
theta : float or `~astropy.units.Quantity`, optional
The rotation angle as an angular quantity
(`~astropy.units.Quantity` or `~astropy.coordinates.Angle`) or
value in radians (as a float) from the positive ``x`` axis. The
rotation angle increases counterclockwise.
Raises
------
ValueError : `ValueError`
If inner semimajor axis (``a_in``) is greater than outer semimajor
axis (``a_out``).
ValueError : `ValueError`
If either the inner semimajor axis (``a_in``) or the outer semiminor
axis (``b_out``) is negative.
Examples
--------
>>> from astropy.coordinates import Angle
>>> from photutils.aperture import EllipticalAnnulus
>>> theta = Angle(80, 'deg')
>>> aper = EllipticalAnnulus([10.0, 20.0], 3.0, 8.0, 5.0)
>>> aper = EllipticalAnnulus((10.0, 20.0), 3.0, 8.0, 5.0, theta=theta)
>>> pos1 = (10.0, 20.0) # (x, y)
>>> pos2 = (30.0, 40.0)
>>> pos3 = (50.0, 60.0)
>>> aper = EllipticalAnnulus([pos1, pos2, pos3], 3.0, 8.0, 5.0)
>>> aper = EllipticalAnnulus((pos1, pos2, pos3), 3.0, 8.0, 5.0,
... theta=theta)
"""
_params = ('positions', 'a_in', 'a_out', 'b_in', 'b_out', 'theta')
positions = PixelPositions('The center pixel position(s).')
a_in = PositiveScalar('The inner semimajor axis in pixels.')
a_out = PositiveScalar('The outer semimajor axis in pixels.')
b_in = PositiveScalar('The inner semiminor axis in pixels.')
b_out = PositiveScalar('The outer semiminor axis in pixels.')
theta = ScalarAngleOrValue('The counterclockwise rotation angle as an '
'angular Quantity or value in radians from '
'the positive x axis.')
def __init__(self, positions, a_in, a_out, b_out, b_in=None, theta=0.0):
if not a_out > a_in:
raise ValueError('"a_out" must be greater than "a_in".')
self.positions = positions
self.a_in = a_in
self.a_out = a_out
self.b_out = b_out
if b_in is None:
b_in = self.b_out * self.a_in / self.a_out
else:
if not b_out > b_in:
raise ValueError('"b_out" must be greater than "b_in".')
self.b_in = b_in
self._theta_radians = 0.0 # defined by theta setter
self.theta = theta
@property
def _xy_extents(self):
return self._calc_extents(self.a_out, self.b_out, self._theta_radians)
@property
def area(self):
return math.pi * (self.a_out * self.b_out - self.a_in * self.b_in)
def _to_patch(self, origin=(0, 0), **kwargs):
"""
Return a `~matplotlib.patches.patch` for the aperture.
Parameters
----------
origin : array_like, optional
The ``(x, y)`` position of the origin of the displayed
image.
**kwargs : `dict`
Any keyword arguments accepted by
`matplotlib.patches.Patch`.
Returns
-------
patch : `~matplotlib.patches.patch` or list of `~matplotlib.patches.patch`
A patch for the aperture. If the aperture is scalar then a
single `~matplotlib.patches.patch` is returned, otherwise a
list of `~matplotlib.patches.patch` is returned.
"""
import matplotlib.patches as mpatches
xy_positions, patch_kwargs = self._define_patch_params(origin=origin,
**kwargs)
patches = []
theta_deg = self._theta_radians * 180.0 / np.pi
for xy_position in xy_positions:
patch_inner = mpatches.Ellipse(xy_position, 2.0 * self.a_in,
2.0 * self.b_in, angle=theta_deg)
patch_outer = mpatches.Ellipse(xy_position, 2.0 * self.a_out,
2.0 * self.b_out, angle=theta_deg)
path = self._make_annulus_path(patch_inner, patch_outer)
patches.append(mpatches.PathPatch(path, **patch_kwargs))
if self.isscalar:
return patches[0]
else:
return patches
[docs]
def to_mask(self, method='exact', subpixels=5):
return EllipticalMaskMixin.to_mask(self, method=method,
subpixels=subpixels)
[docs]
def to_sky(self, wcs):
"""
Convert the aperture to a `SkyEllipticalAnnulus` object defined
in celestial coordinates.
Parameters
----------
wcs : WCS object
A world coordinate system (WCS) transformation that
supports the `astropy shared interface for WCS
<https://docs.astropy.org/en/stable/wcs/wcsapi.html>`_
(e.g., `astropy.wcs.WCS`, `gwcs.wcs.WCS`).
Returns
-------
aperture : `SkyEllipticalAnnulus` object
A `SkyEllipticalAnnulus` object.
"""
return SkyEllipticalAnnulus(**self._to_sky_params(wcs))
[docs]
class SkyEllipticalAperture(SkyAperture):
"""
An elliptical aperture defined in sky coordinates.
The aperture has a single fixed size/shape, but it can have multiple
positions (see the ``positions`` input).
Parameters
----------
positions : `~astropy.coordinates.SkyCoord`
The celestial coordinates of the aperture center(s). This can be
either scalar coordinates or an array of coordinates.
a : scalar `~astropy.units.Quantity`
The semimajor axis of the ellipse in angular units.
b : scalar `~astropy.units.Quantity`
The semiminor axis of the ellipse in angular units.
theta : scalar `~astropy.units.Quantity`, optional
The position angle (in angular units) of the ellipse semimajor
axis. For a right-handed world coordinate system, the position
angle increases counterclockwise from North (PA=0).
Examples
--------
>>> from astropy.coordinates import SkyCoord
>>> import astropy.units as u
>>> from photutils.aperture import SkyEllipticalAperture
>>> positions = SkyCoord(ra=[10.0, 20.0], dec=[30.0, 40.0], unit='deg')
>>> aper = SkyEllipticalAperture(positions, 1.0*u.arcsec, 0.5*u.arcsec)
"""
_params = ('positions', 'a', 'b', 'theta')
positions = SkyCoordPositions('The center position(s) in sky coordinates.')
a = PositiveScalarAngle('The semimajor axis in angular units.')
b = PositiveScalarAngle('The semiminor axis in angular units.')
theta = ScalarAngle('The position angle in angular units of the ellipse '
'semimajor axis.')
def __init__(self, positions, a, b, theta=0.0 * u.deg):
self.positions = positions
self.a = a
self.b = b
self.theta = theta
[docs]
def to_pixel(self, wcs):
"""
Convert the aperture to an `EllipticalAperture` object defined
in pixel coordinates.
Parameters
----------
wcs : WCS object
A world coordinate system (WCS) transformation that
supports the `astropy shared interface for WCS
<https://docs.astropy.org/en/stable/wcs/wcsapi.html>`_
(e.g., `astropy.wcs.WCS`, `gwcs.wcs.WCS`).
Returns
-------
aperture : `EllipticalAperture` object
An `EllipticalAperture` object.
"""
return EllipticalAperture(**self._to_pixel_params(wcs))
[docs]
class SkyEllipticalAnnulus(SkyAperture):
r"""
An elliptical annulus aperture defined in sky coordinates.
The aperture has a single fixed size/shape, but it can have multiple
positions (see the ``positions`` input).
Parameters
----------
positions : `~astropy.coordinates.SkyCoord`
The celestial coordinates of the aperture center(s). This can be
either scalar coordinates or an array of coordinates.
a_in : scalar `~astropy.units.Quantity`
The inner semimajor axis in angular units.
a_out : scalar `~astropy.units.Quantity`
The outer semimajor axis in angular units.
b_out : scalar `~astropy.units.Quantity`
The outer semiminor axis in angular units.
b_in : `None` or scalar `~astropy.units.Quantity`
The inner semiminor axis in angular units. If `None`, then the
inner semiminor axis is calculated as:
.. math:: b_{in} = b_{out}
\left(\frac{a_{in}}{a_{out}}\right)
theta : scalar `~astropy.units.Quantity`, optional
The position angle (in angular units) of the ellipse semimajor
axis. For a right-handed world coordinate system, the position
angle increases counterclockwise from North (PA=0).
Examples
--------
>>> from astropy.coordinates import SkyCoord
>>> import astropy.units as u
>>> from photutils.aperture import SkyEllipticalAnnulus
>>> positions = SkyCoord(ra=[10.0, 20.0], dec=[30.0, 40.0], unit='deg')
>>> aper = SkyEllipticalAnnulus(positions, 0.5*u.arcsec, 2.0*u.arcsec,
... 1.0*u.arcsec)
"""
_params = ('positions', 'a_in', 'a_out', 'b_in', 'b_out', 'theta')
positions = SkyCoordPositions('The center position(s) in sky coordinates.')
a_in = PositiveScalarAngle('The inner semimajor axis in angular units.')
a_out = PositiveScalarAngle('The outer semimajor axis in angular units.')
b_in = PositiveScalarAngle('The inner semiminor axis in angular units.')
b_out = PositiveScalarAngle('The outer semiminor axis in angular units.')
theta = ScalarAngle('The position angle in angular units of the ellipse '
'semimajor axis.')
def __init__(self, positions, a_in, a_out, b_out, b_in=None,
theta=0.0 * u.deg):
if not a_out > a_in:
raise ValueError('"a_out" must be greater than "a_in".')
self.positions = positions
self.a_in = a_in
self.a_out = a_out
self.b_out = b_out
if b_in is None:
b_in = self.b_out * self.a_in / self.a_out
else:
if not b_out > b_in:
raise ValueError('"b_out" must be greater than "b_in".')
self.b_in = b_in
self.theta = theta
[docs]
def to_pixel(self, wcs):
"""
Convert the aperture to an `EllipticalAnnulus` object defined in
pixel coordinates.
Parameters
----------
wcs : WCS object
A world coordinate system (WCS) transformation that
supports the `astropy shared interface for WCS
<https://docs.astropy.org/en/stable/wcs/wcsapi.html>`_
(e.g., `astropy.wcs.WCS`, `gwcs.wcs.WCS`).
Returns
-------
aperture : `EllipticalAnnulus` object
An `EllipticalAnnulus` object.
"""
return EllipticalAnnulus(**self._to_pixel_params(wcs))