/usr/lib/python3/dist-packages/photutils/aperture/ellipse.py is in python3-photutils 0.3-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 | # Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import math
import numpy as np
from astropy.coordinates import SkyCoord
import astropy.units as u
from astropy.wcs.utils import skycoord_to_pixel
from .core import (PixelAperture, SkyAperture, ApertureMask,
_sanitize_pixel_positions, _translate_mask_method,
_make_annulus_path)
from ..geometry import elliptical_overlap_grid
from ..utils.wcs_helpers import (skycoord_to_pixel_scale_angle, 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 `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.
"""
if method not in ('center', 'subpixel', 'exact'):
raise ValueError('"{0}" method is not available for this '
'aperture.'.format(method))
use_exact, subpixels = _translate_mask_method(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 position, _slice, _geom_slice in zip(self.positions, self._slices,
self._geom_slices):
px_min, px_max = _geom_slice[1].start, _geom_slice[1].stop
py_min, py_max = _geom_slice[0].start, _geom_slice[0].stop
dx = px_max - px_min
dy = py_max - py_min
mask = elliptical_overlap_grid(px_min, px_max, py_min, py_max,
dx, dy, a, b, self.theta,
use_exact, subpixels)
if hasattr(self, 'a_in'): # annulus
mask -= elliptical_overlap_grid(px_min, px_max, py_min,
py_max, dx, dy, self.a_in,
b_in, self.theta, use_exact,
subpixels)
masks.append(ApertureMask(mask, _slice))
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):
try:
self.a = float(a)
self.b = float(b)
self.theta = float(theta)
except TypeError:
raise TypeError("'a' and 'b' and 'theta' must be numeric, "
"received {0} and {1} and {2}."
.format((type(a), type(b), type(theta))))
if a < 0 or b < 0:
raise ValueError("'a' and 'b' must be non-negative.")
self.positions = _sanitize_pixel_positions(positions)
@property
def _slices(self):
# TODO: use an actual minimal bounding box
radius = max(self.a, self.b)
x_min = np.floor(self.positions[:, 0] - radius + 0.5).astype(int)
x_max = np.floor(self.positions[:, 0] + radius + 1.5).astype(int)
y_min = np.floor(self.positions[:, 1] - radius + 0.5).astype(int)
y_max = np.floor(self.positions[:, 1] + radius + 1.5).astype(int)
return [(slice(ymin, ymax), slice(xmin, xmax))
for xmin, xmax, ymin, ymax in zip(x_min, x_max, y_min, y_max)]
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)
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):
try:
self.a_in = float(a_in)
self.a_out = float(a_out)
self.b_out = float(b_out)
self.theta = float(theta)
except TypeError:
raise TypeError("'a_in' and 'a_out' and 'b_out' and 'theta' must "
"be numeric, received {0} and {1} and {2} and "
"{3}.".format((type(a_in), type(a_out),
type(b_out), type(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.b_in = b_out * a_in / a_out
self.positions = _sanitize_pixel_positions(positions)
@property
def _slices(self):
# TODO: use an actual minimal bounding box
radius = max(self.a_out, self.b_out)
x_min = np.floor(self.positions[:, 0] - radius + 0.5).astype(int)
x_max = np.floor(self.positions[:, 0] + radius + 1.5).astype(int)
y_min = np.floor(self.positions[:, 1] - radius + 0.5).astype(int)
y_max = np.floor(self.positions[:, 1] + radius + 1.5).astype(int)
return [(slice(ymin, ymax), slice(xmin, xmax))
for xmin, xmax, ymin, ymax in zip(x_min, x_max, y_min, y_max)]
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 = _make_annulus_path(patch_inner, patch_outer)
patch = mpatches.PathPatch(path, **kwargs)
ax.add_patch(patch)
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 should 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
def to_pixel(self, wcs, mode='all'):
"""
Convert the aperture to an `EllipticalAperture` instance in
pixel coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The 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.
"""
x, y = skycoord_to_pixel(self.positions, wcs, mode=mode)
central_pos = SkyCoord([wcs.wcs.crval], frame=self.positions.name,
unit=wcs.wcs.cunit)
xc, yc, scale, angle = skycoord_to_pixel_scale_angle(central_pos, wcs)
if self.a.unit.physical_type == 'angle':
a = (scale * self.a).to(u.pixel).value
b = (scale * self.b).to(u.pixel).value
else: # pixel
a = self.a.value
b = self.b.value
theta = (angle + self.theta).to(u.radian).value
pixel_positions = np.array([x, y]).transpose()
return EllipticalAperture(pixel_positions, a, b, theta)
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 should 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
def to_pixel(self, wcs, mode='all'):
"""
Convert the aperture to an `EllipticalAnnulus` instance in pixel
coordinates.
Parameters
----------
wcs : `~astropy.wcs.WCS`
The 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.
"""
x, y = skycoord_to_pixel(self.positions, wcs, mode=mode)
central_pos = SkyCoord([wcs.wcs.crval], frame=self.positions.name,
unit=wcs.wcs.cunit)
xc, yc, scale, angle = skycoord_to_pixel_scale_angle(central_pos, wcs)
if self.a_in.unit.physical_type == 'angle':
a_in = (scale * self.a_in).to(u.pixel).value
a_out = (scale * self.a_out).to(u.pixel).value
b_out = (scale * self.b_out).to(u.pixel).value
else:
a_in = self.a_in.value
a_out = self.a_out.value
b_out = self.b_out.value
theta = (angle + self.theta).to(u.radian).value
pixel_positions = np.array([x, y]).transpose()
return EllipticalAnnulus(pixel_positions, a_in, a_out, b_out, theta)
|