/usr/lib/python2.7/dist-packages/photutils/aperture/ellipse.py is in python-photutils 0.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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from __future__ import (absolute_import, division, print_function,
unicode_literals)
import math
import numpy as np
from astropy.coordinates import SkyCoord
from .core import PixelAperture, SkyAperture
from .bounding_box import BoundingBox
from .mask import ApertureMask
from ..geometry import elliptical_overlap_grid
from ..utils.wcs_helpers import assert_angle, assert_angle_or_pixel
__all__ = ['EllipticalMaskMixin', 'EllipticalAperture', 'EllipticalAnnulus',
'SkyEllipticalAperture', 'SkyEllipticalAnnulus']
class EllipticalMaskMixin(object):
"""
Mixin class to create masks for elliptical and elliptical-annulus
aperture objects.
"""
def to_mask(self, method='exact', subpixels=5):
"""
Return a list of `~photutils.ApertureMask` objects, one for each
aperture position.
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 returned mask 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 returned mask 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 returned mask 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.
Returns
-------
mask : list of `~photutils.ApertureMask`
A list of aperture mask objects.
"""
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
b_in = self.a_in * self.b_out / self.a_out
else:
raise ValueError('Cannot determine the aperture shape.')
masks = []
for bbox, edges in zip(self.bounding_boxes, 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,
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,
b_in, self.theta, use_exact,
subpixels)
masks.append(ApertureMask(mask, bbox))
return masks
class EllipticalAperture(EllipticalMaskMixin, PixelAperture):
"""
Elliptical aperture(s), defined in pixel coordinates.
Parameters
----------
positions : array_like or `~astropy.units.Quantity`
Pixel coordinates of the aperture center(s) in one of the
following formats:
* single ``(x, y)`` tuple
* list of ``(x, y)`` tuples
* ``Nx2`` or ``2xN`` `~numpy.ndarray`
* ``Nx2`` or ``2xN`` `~astropy.units.Quantity` in pixel units
Note that a ``2x2`` `~numpy.ndarray` or
`~astropy.units.Quantity` is interpreted as ``Nx2``, i.e. two
rows of (x, y) coordinates.
a : float
The semimajor axis.
b : float
The semiminor axis.
theta : float
The rotation angle in radians of the semimajor axis from the
positive ``x`` axis. The rotation angle increases
counterclockwise.
Raises
------
ValueError : `ValueError`
If either axis (``a`` or ``b``) is negative.
"""
def __init__(self, positions, a, b, theta):
if a < 0 or b < 0:
raise ValueError("'a' and 'b' must be non-negative.")
self.positions = self._sanitize_positions(positions)
self.a = float(a)
self.b = float(b)
self.theta = float(theta)
self._params = ['a', 'b', 'theta']
@property
def bounding_boxes(self):
"""
A list of minimal bounding boxes (`~photutils.BoundingBox`), one
for each position, enclosing the exact elliptical apertures.
"""
cos_theta = np.cos(self.theta)
sin_theta = np.sin(self.theta)
ax = self.a * cos_theta
ay = self.a * sin_theta
bx = self.b * -sin_theta
by = self.b * cos_theta
dx = np.sqrt(ax*ax + bx*bx)
dy = np.sqrt(ay*ay + by*by)
xmin = self.positions[:, 0] - dx
xmax = self.positions[:, 0] + dx
ymin = self.positions[:, 1] - dy
ymax = self.positions[:, 1] + dy
return [BoundingBox._from_float(x0, x1, y0, y1)
for x0, x1, y0, y1 in zip(xmin, xmax, ymin, ymax)]
def area(self):
return math.pi * self.a * self.b
def plot(self, origin=(0, 0), indices=None, ax=None, fill=False,
**kwargs):
import matplotlib.patches as mpatches
plot_positions, ax, kwargs = self._prepare_plot(
origin, indices, ax, fill, **kwargs)
theta_deg = self.theta * 180. / np.pi
for position in plot_positions:
patch = mpatches.Ellipse(position, 2.*self.a, 2.*self.b,
theta_deg, **kwargs)
ax.add_patch(patch)
def to_sky(self, wcs, mode='all'):
"""
Convert the aperture to a `SkyEllipticalAperture` object defined
in celestial coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The world coordinate system (WCS) transformation to use.
mode : {'all', 'wcs'}, optional
Whether to do the transformation including distortions
(``'all'``; default) or only including only the core WCS
transformation (``'wcs'``).
Returns
-------
aperture : `SkyEllipticalAperture` object
A `SkyEllipticalAperture` object.
"""
sky_params = self._to_sky_params(wcs, mode=mode)
return SkyEllipticalAperture(**sky_params)
class EllipticalAnnulus(EllipticalMaskMixin, PixelAperture):
"""
Elliptical annulus aperture(s), defined in pixel coordinates.
Parameters
----------
positions : array_like or `~astropy.units.Quantity`
Pixel coordinates of the aperture center(s) in one of the
following formats:
* single ``(x, y)`` tuple
* list of ``(x, y)`` tuples
* ``Nx2`` or ``2xN`` `~numpy.ndarray`
* ``Nx2`` or ``2xN`` `~astropy.units.Quantity` in pixel units
Note that a ``2x2`` `~numpy.ndarray` or
`~astropy.units.Quantity` is interpreted as ``Nx2``, i.e. two
rows of (x, y) coordinates.
a_in : float
The inner semimajor axis.
a_out : float
The outer semimajor axis.
b_out : float
The outer semiminor axis. The inner semiminor axis is
calculated as:
.. math:: b_{in} = b_{out}
\\left(\\frac{a_{in}}{a_{out}}\\right)
theta : float
The rotation angle in radians of the semimajor axis 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.
"""
def __init__(self, positions, a_in, a_out, b_out, theta):
if not (a_out > a_in):
raise ValueError('"a_out" must be greater than "a_in".')
if a_in < 0 or b_out < 0:
raise ValueError('"a_in" and "b_out" must be non-negative.')
self.positions = self._sanitize_positions(positions)
self.a_in = float(a_in)
self.a_out = float(a_out)
self.b_out = float(b_out)
self.b_in = self.b_out * self.a_in / self.a_out
self.theta = float(theta)
self._params = ['a_in', 'a_out', 'b_out', 'theta']
@property
def bounding_boxes(self):
"""
A list of minimal bounding boxes (`~photutils.BoundingBox`), one
for each position, enclosing the exact elliptical apertures.
"""
cos_theta = np.cos(self.theta)
sin_theta = np.sin(self.theta)
ax = self.a_out * cos_theta
ay = self.a_out * sin_theta
bx = self.b_out * -sin_theta
by = self.b_out * cos_theta
dx = np.sqrt(ax*ax + bx*bx)
dy = np.sqrt(ay*ay + by*by)
xmin = self.positions[:, 0] - dx
xmax = self.positions[:, 0] + dx
ymin = self.positions[:, 1] - dy
ymax = self.positions[:, 1] + dy
return [BoundingBox._from_float(x0, x1, y0, y1)
for x0, x1, y0, y1 in zip(xmin, xmax, ymin, ymax)]
def area(self):
return math.pi * (self.a_out * self.b_out - self.a_in * self.b_in)
def plot(self, origin=(0, 0), indices=None, ax=None, fill=False,
**kwargs):
import matplotlib.patches as mpatches
plot_positions, ax, kwargs = self._prepare_plot(
origin, indices, ax, fill, **kwargs)
theta_deg = self.theta * 180. / np.pi
for position in plot_positions:
patch_inner = mpatches.Ellipse(position, 2.*self.a_in,
2.*self.b_in, theta_deg, **kwargs)
patch_outer = mpatches.Ellipse(position, 2.*self.a_out,
2.*self.b_out, theta_deg, **kwargs)
path = self._make_annulus_path(patch_inner, patch_outer)
patch = mpatches.PathPatch(path, **kwargs)
ax.add_patch(patch)
def to_sky(self, wcs, mode='all'):
"""
Convert the aperture to a `SkyEllipticalAnnulus` object defined
in celestial coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The world coordinate system (WCS) transformation to use.
mode : {'all', 'wcs'}, optional
Whether to do the transformation including distortions
(``'all'``; default) or only including only the core WCS
transformation (``'wcs'``).
Returns
-------
aperture : `SkyEllipticalAnnulus` object
A `SkyEllipticalAnnulus` object.
"""
sky_params = self._to_sky_params(wcs, mode=mode)
return SkyEllipticalAnnulus(**sky_params)
class SkyEllipticalAperture(SkyAperture):
"""
Elliptical aperture(s), defined in sky coordinates.
Parameters
----------
positions : `~astropy.coordinates.SkyCoord`
Celestial coordinates of the aperture center(s). This can be
either scalar coordinates or an array of coordinates.
a : `~astropy.units.Quantity`
The semimajor axis, either in angular or pixel units.
b : `~astropy.units.Quantity`
The semiminor axis, either in angular or pixel units.
theta : `~astropy.units.Quantity`
The position angle (in angular units) of the semimajor axis.
For a right-handed world coordinate system, the position angle
increases counterclockwise from North (PA=0).
"""
def __init__(self, positions, a, b, theta):
if isinstance(positions, SkyCoord):
self.positions = positions
else:
raise TypeError('positions must be a SkyCoord instance')
assert_angle_or_pixel('a', a)
assert_angle_or_pixel('b', b)
assert_angle('theta', theta)
if a.unit.physical_type != b.unit.physical_type:
raise ValueError("a and b should either both be angles "
"or in pixels")
self.a = a
self.b = b
self.theta = theta
self._params = ['a', 'b', 'theta']
def to_pixel(self, wcs, mode='all'):
"""
Convert the aperture to an `EllipticalAperture` object defined
in pixel coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The world coordinate system (WCS) transformation to use.
mode : {'all', 'wcs'}, optional
Whether to do the transformation including distortions
(``'all'``; default) or only including only the core WCS
transformation (``'wcs'``).
Returns
-------
aperture : `EllipticalAperture` object
An `EllipticalAperture` object.
"""
pixel_params = self._to_pixel_params(wcs, mode=mode)
return EllipticalAperture(**pixel_params)
class SkyEllipticalAnnulus(SkyAperture):
"""
Elliptical annulus aperture(s), defined in sky coordinates.
Parameters
----------
positions : `~astropy.coordinates.SkyCoord`
Celestial coordinates of the aperture center(s). This can be
either scalar coordinates or an array of coordinates.
a_in : `~astropy.units.Quantity`
The inner semimajor axis, either in angular or pixel units.
a_out : `~astropy.units.Quantity`
The outer semimajor axis, either in angular or pixel units.
b_out : float
The outer semiminor axis, either in angular or pixel units. The
inner semiminor axis is calculated as:
.. math:: b_{in} = b_{out}
\\left(\\frac{a_{in}}{a_{out}}\\right)
theta : `~astropy.units.Quantity`
The position angle (in angular units) of the semimajor axis.
For a right-handed world coordinate system, the position angle
increases counterclockwise from North (PA=0).
"""
def __init__(self, positions, a_in, a_out, b_out, theta):
if isinstance(positions, SkyCoord):
self.positions = positions
else:
raise TypeError('positions must be a SkyCoord instance')
assert_angle_or_pixel('a_in', a_in)
assert_angle_or_pixel('a_out', a_out)
assert_angle_or_pixel('b_out', b_out)
assert_angle('theta', theta)
if a_in.unit.physical_type != a_out.unit.physical_type:
raise ValueError("a_in and a_out should either both be angles "
"or in pixels")
if a_out.unit.physical_type != b_out.unit.physical_type:
raise ValueError("a_out and b_out should either both be angles "
"or in pixels")
self.a_in = a_in
self.a_out = a_out
self.b_out = b_out
self.theta = theta
self._params = ['a_in', 'a_out', 'b_out', 'theta']
def to_pixel(self, wcs, mode='all'):
"""
Convert the aperture to an `EllipticalAnnulus` object defined in
pixel coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The world coordinate system (WCS) transformation to use.
mode : {'all', 'wcs'}, optional
Whether to do the transformation including distortions
(``'all'``; default) or only including only the core WCS
transformation (``'wcs'``).
Returns
-------
aperture : `EllipticalAnnulus` object
An `EllipticalAnnulus` object.
"""
pixel_params = self._to_pixel_params(wcs, mode=mode)
return EllipticalAnnulus(**pixel_params)
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