Source code for photutils.aperture.ellipse

# 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 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, strict=True): 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] 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): """ The exact geometric area of the aperture shape. """ 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, optional 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) theta_deg = self._theta_radians * 180.0 / np.pi patches = [mpatches.Ellipse(xy_position, 2.0 * self.a, 2.0 * self.b, angle=theta_deg, **patch_kwargs) for xy_position in xy_positions] if self.isscalar: return patches[0] 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 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 elif 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): """ The exact geometric area of the aperture shape. """ 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, optional 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] 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 elif 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))