class LofarBlock(EarthBoundInstrumentGeometryBlock):
"""
`LOw-Frequency ARray (LOFAR) <http://www.lofar.org/>`_ located in Europe.
This LOFAR model consists of 62 stations, each containing between 17 to 24 HBA dipole antennas.
"""
@chk.check('N_station', chk.allow_None(chk.is_integer))
def __init__(self, N_station=None):
"""
Parameters
----------
N_station : int
Number of stations to use. (Default = all)
Sometimes only a subset of an instrument’s stations are desired.
Setting `N_station` limits the number of stations to those that appear first in `XYZ` when sorted by STATION_ID.
"""
XYZ = self._get_geometry()
super().__init__(XYZ, N_station)
def _get_geometry(self):
"""
Load instrument geometry.
Returns
-------
:py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
ITRS instrument geometry.
"""
rel_path = pathlib.Path('data', 'phased_array', 'instrument',
'LOFAR.csv')
abs_path = pkg.resource_filename('pypeline', str(rel_path))
itrs_geom = (pd.read_csv(abs_path).set_index(
['STATION_ID', 'ANTENNA_ID']))
XYZ = _as_InstrumentGeometry(itrs_geom)
return XYZ
class MwaBlock(EarthBoundInstrumentGeometryBlock):
"""
`Murchison Widefield Array (MWA) <http://www.mwatelescope.org/>`_ located in Australia.
MWA consists of 128 stations, each containing 16 dipole antennas.
"""
@chk.check(
dict(N_station=chk.allow_None(chk.is_integer),
station_only=chk.is_boolean))
def __init__(self, N_station=None, station_only=False):
"""
Parameters
----------
N_station : int
Number of stations to use. (Default = all)
Sometimes only a subset of an instrument’s stations are desired.
Setting `N_station` limits the number of stations to those that appear first in `XYZ` when sorted by STATION_ID.
station_only : bool
If :py:obj:`True`, model MWA stations as single-element antennas. (Default = False)
"""
XYZ = self._get_geometry(station_only)
super().__init__(XYZ, N_station)
def _get_geometry(self, station_only):
"""
Load instrument geometry.
Parameters
----------
station_only : bool
If :py:obj:`True`, model stations as single-element antennas.
Returns
-------
:py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
ITRS instrument geometry.
"""
rel_path = pathlib.Path('data', 'phased_array', 'instrument',
'MWA.csv')
abs_path = pkg.resource_filename('pypeline', str(rel_path))
itrs_geom = (pd.read_csv(abs_path).set_index('STATION_ID'))
station_id = itrs_geom.index.get_level_values('STATION_ID')
if station_only:
itrs_geom.index = (pd.MultiIndex.from_product(
[station_id, [0]], names=['STATION_ID', 'ANTENNA_ID']))
else:
# Generate flat 4x4 antenna grid pointing towards the Noth pole.
x_lim = y_lim = 1.65
lY, lX = np.meshgrid(np.linspace(-y_lim, y_lim, 4),
np.linspace(-x_lim, x_lim, 4),
indexing='ij')
l = np.stack((lX, lY, np.zeros((4, 4))), axis=0)
# For each station: rotate 4x4 array to lie on the sphere's surface.
xyz_station = itrs_geom.loc[:, ['X', 'Y', 'Z']].values
df_stations = []
for st_id, st_cog in zip(station_id, xyz_station):
_, st_colat, st_lon = sph.cart2pol(*st_cog)
st_cog_unit = np.array(sph.pol2cart(1, st_colat, st_lon))
R_1 = pylinalg.rot([0, 0, 1], st_lon)
R_2 = pylinalg.rot(axis=np.cross([0, 0, 1], st_cog_unit),
angle=st_colat)
R = R_2 @ R_1
st_layout = np.reshape(
st_cog.reshape(3, 1, 1) + np.tensordot(R, l, axes=1),
(3, -1))
idx = (pd.MultiIndex.from_product(
[[st_id], range(16)], names=['STATION_ID', 'ANTENNA_ID']))
df_stations += [
pd.DataFrame(data=st_layout.T,
index=idx,
columns=['X', 'Y', 'Z'])
]
itrs_geom = pd.concat(df_stations)
XYZ = _as_InstrumentGeometry(itrs_geom)
return XYZ
class EarthBoundInstrumentGeometryBlock(InstrumentGeometryBlock):
"""
Sub-class specialized in instruments that move with the Earth, such as radio telescopes.
"""
@chk.check(
dict(XYZ=chk.is_instance(InstrumentGeometry),
N_station=chk.allow_None(chk.is_integer)))
def __init__(self, XYZ, N_station=None):
"""
Parameters
----------
XYZ : :py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
ITRS instrument geometry.
N_station : int
Number of stations to use. (Default = all)
Sometimes only a subset of an instrument’s stations are desired.
Setting `N_station` limits the number of stations to those that appear first in `XYZ` when sorted by STATION_ID.
"""
super().__init__(XYZ, N_station)
@chk.check('time', chk.is_instance(time.Time))
def __call__(self, time):
"""
Determine instrument antenna positions in ICRS.
Parameters
----------
time : :py:class:`~astropy.time.Time`
Moment at which the coordinates are wanted.
Returns
-------
:py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
(N_antenna, 3) ICRS instrument geometry.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import LofarBlock
import astropy.time as atime
import astropy.units as u
.. doctest::
>>> instr = LofarBlock()
>>> time = atime.Time('J2000')
>>> xyz = instr(time)
>>> np.around(xyz.data[:5], 2)
array([[ 1148711.63, -3679538.21, 5064569. ],
[ 1148716.62, -3679538.41, 5064567.74],
[ 1148705.76, -3679542.23, 5064567.43],
[ 1148710.75, -3679542.42, 5064566.16],
[ 1148715.74, -3679542.61, 5064564.9 ]])
>>> xyz = instr(time + 30 * u.min)
>>> np.around(xyz.data[:5], 2)
array([[ 1620400.85, -3497579.41, 5064547.21],
[ 1620405.82, -3497578.94, 5064545.95],
[ 1620395.56, -3497584.15, 5064545.63],
[ 1620400.53, -3497583.69, 5064544.37],
[ 1620405.5 , -3497583.23, 5064543.11]])
"""
layout = self._layout.loc[:, ['X', 'Y', 'Z']].values.T
r = linalg.norm(layout, axis=0)
itrs_layout = coord.CartesianRepresentation(layout)
itrs_position = coord.SkyCoord(itrs_layout, obstime=time, frame='itrs')
icrs_position = r * (itrs_position.transform_to('icrs').cartesian.xyz)
icrs_layout = pd.DataFrame(data=icrs_position.T,
index=self._layout.index,
columns=('X', 'Y', 'Z'))
return _as_InstrumentGeometry(icrs_layout)
@chk.check(
dict(obs_start=chk.is_instance(time.Time),
obs_end=chk.is_instance(time.Time)))
def icrs2bfsf_rot(self, obs_start, obs_end):
"""
Rotation matrix from ICRS to the local *Bluebild FastSynthesis Frame* (BFSF).
Parameters
----------
obs_start : :py:class:`~astropy.time.Time`
Start of the observation period.
obs_end : :py:class:`~astropy.time.Time`
End of the observation period.
Returns
-------
R : :py:class:`~numpy.ndarray`
(3, 3) ICRS -> BFSF rotation matrix.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import LofarBlock
import astropy.time as atime
import astropy.units as u
.. doctest::
>>> instr = LofarBlock()
>>> obs_start = atime.Time('J2000')
>>> obs_end = obs_start + 4 * u.h
>>> R = instr.icrs2bfsf_rot(obs_start, obs_end)
>>> np.around(R, 3)
array([[ 0.963, -0.27 , -0. ],
[ 0.27 , 0.963, 0. ],
[-0. , 0. , -1. ]])
"""
if obs_start > obs_end:
raise ValueError('Parameter[obs_start] must precede '
'Parameter[obs_end].')
# Find the position of the antennas at several time-instants
# during `period`.
N_interval = 20
sampling_times = (obs_start +
((obs_end - obs_start) /
(N_interval - 1)) * np.arange(N_interval))
icrs_layouts = [self.__call__(t).data for t in sampling_times]
icrs_layouts = np.stack(icrs_layouts, axis=1) # (N_antenna, N_time, 3)
# For each antenna `i`, find a normal vector `n_{i}` to the
# rotation plane.
N_antenna = len(icrs_layouts)
abc = np.zeros((N_antenna, 3))
for i, xyz in enumerate(icrs_layouts):
a = np.concatenate([xyz[:, :2], np.ones((len(xyz), 1))], axis=-1)
b = xyz[:, 2]
coeffs, *_ = linalg.lstsq(a, b)
abc[i] = coeffs
# Average vectors `n_{i}` to obtain the global normal vector `n`.
# Construct rotation matrix R using 3 basis vectors Ex, Ey, Ez.
# Ez must be co-linear to the plane's normal vector.
a, b, c = np.mean(abc, axis=0)
z_ax = np.r_[a, b, -1]
y_ax = np.r_[b, -a, 0]
x_ax = np.cross(z_ax, y_ax)
R = np.stack([x_ax, y_ax, z_ax], axis=0)
R /= linalg.norm(R, axis=1, keepdims=True)
return R
@chk.check(
dict(wl=chk.is_real,
obs_start=chk.is_instance(time.Time),
obs_end=chk.is_instance(time.Time)))
def bfsf_kernel_bandwidth(self, wl, obs_start, obs_end):
"""
Bandwidth of :math:`2 \pi`-periodic complex plane-wave kernel in BFSF coordinates.
Parameters
----------
wl : float
Wave-length [m] of observations.
obs_start : :py:class:`~astropy.time.Time`
Start of the observation period.
obs_end : :py:class:`~astropy.time.Time`
End of the observation period.
Returns
-------
N_FS : int
Kernel bandwidth when evaluated in the BFSF reference frame.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import LofarBlock
import astropy.time as atime
import astropy.units as u
from scipy.constants import speed_of_light
.. doctest::
>>> instr = LofarBlock(N_station=48)
>>> freq = 145e6
>>> wl = speed_of_light / freq
>>> obs_start = atime.Time('J2000')
>>> obs_end = obs_start + 4 * u.h
>>> instr.bfsf_kernel_bandwidth(wl, obs_start, obs_end)
21783
"""
if wl <= 0:
raise ValueError('Parameter[wl] must be positive.')
R = self.icrs2bfsf_rot(obs_start, obs_end)
obs_mid = obs_start + (obs_end - obs_start) / 2
icrs_XYZ = self.__call__(obs_mid).data
bfsf_XYZ = icrs_XYZ @ R.T
bfsf_XYZ -= np.mean(bfsf_XYZ, axis=0)
bfsf_XY = bfsf_XYZ[:, :2]
XY_baseline = linalg.norm(bfsf_XY[:, np.newaxis, :] -
bfsf_XY[np.newaxis, :, :],
axis=-1)
N = sp.jv_series_threshold((2 * np.pi / wl) * XY_baseline.max())
return 2 * N + 1
class StationaryInstrumentGeometryBlock(InstrumentGeometryBlock):
"""
Sub-class specialized in instruments that are stationary, i.e. that do not move with time.
"""
@chk.check(
dict(XYZ=chk.is_instance(InstrumentGeometry),
N_station=chk.allow_None(chk.is_integer)))
def __init__(self, XYZ, N_station=None):
"""
Parameters
----------
XYZ : :py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
Instrument geometry.
N_station : int
Number of stations to use. (Default = all)
Sometimes only a subset of an instrument's stations are desired.
Setting `N_station` limits the number of stations to those that appear first in `XYZ` when sorted by STATION_ID.
"""
super().__init__(XYZ, N_station)
def __call__(self):
"""
Determine instrument antenna positions.
As the instrument's geometry does not change through time, :py:func:`~pypeline.phased_array.instrument.StationaryInstrumentGeometryBlock.__call__` always returns the same object.
Returns
-------
:py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
(N_antenna, 3) instrument geometry.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import PyramicBlock
.. doctest::
>>> instr = PyramicBlock()
>>> xyz = instr().data[:5]
>>> np.around(xyz, 3)
array([[-0.014, -0.025, 0.01 ],
[-0.026, -0.045, 0.043],
[-0.038, -0.065, 0.075],
[-0.042, -0.073, 0.088],
[-0.044, -0.077, 0.095]])
"""
return _as_InstrumentGeometry(self._layout)
@chk.check('wl', chk.is_real)
def bfsf_kernel_bandwidth(self, wl):
"""
Bandwidth of :math:`2 \pi`-periodic complex plane-wave kernel in BFSF coordinates.
Parameters
----------
wl : float
Wave-length [m] of observations.
Returns
-------
N_FS : int
Kernel bandwidth when evaluated in the BFSF reference frame.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import PyramicBlock
from scipy.constants import speed_of_sound
.. doctest::
>>> instr = PyramicBlock()
>>> freq = 3500
>>> wl = speed_of_sound / freq
>>> instr.bfsf_kernel_bandwidth(wl)
67
"""
if wl <= 0:
raise ValueError('Parameter[wl] must be positive.')
R = np.eye(
3) # Stationary instruments have (BFSF basis) = (Canonical basis)
icrs_XYZ = self.__call__().data
bfsf_XYZ = icrs_XYZ @ R.T
bfsf_XYZ -= np.mean(bfsf_XYZ, axis=0)
bfsf_XY = bfsf_XYZ[:, :2]
XY_baseline = linalg.norm(bfsf_XY[:, np.newaxis, :] -
bfsf_XY[np.newaxis, :, :],
axis=-1)
N = sp.jv_series_threshold((2 * np.pi / wl) * XY_baseline.max())
return 2 * N + 1
class InstrumentGeometryBlock(core.Block):
"""
Compute antenna positions.
"""
@chk.check(
dict(XYZ=chk.is_instance(InstrumentGeometry),
N_station=chk.allow_None(chk.is_integer)))
def __init__(self, XYZ, N_station=None):
"""
Parameters
----------
XYZ : :py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
Instrument geometry.
N_station : int
Number of stations to use. (Default = all)
Sometimes only a subset of an instrument's stations are desired.
Setting `N_station` limits the number of stations to those that appear first in `XYZ` when sorted by STATION_ID.
"""
super().__init__()
if N_station is not None:
if N_station < 1:
raise ValueError('Parameter[N_station] must be positive.')
self._layout = XYZ.as_frame()
if N_station is not None:
stations = np.unique(
XYZ.index[0].get_level_values('STATION_ID'))[:N_station]
self._layout = self._layout.loc[stations]
def __call__(self, *args, **kwargs):
"""
Determine instrument antenna positions.
Parameters
----------
*args
Positional arguments.
**kwargs
Keyword arguments.
Returns
-------
:py:class:`~pypeline.phased_array.instrument.InstrumentGeometry`
(N_antenna, 3) instrument geometry.
"""
raise NotImplementedError
@chk.check('wl', chk.is_real)
def nyquist_rate(self, wl):
"""
Order of imageable complex plane-waves.
Parameters
----------
wl : float
Wave-length [m] of observations.
Returns
-------
N : int
Maximum order of complex plane waves that can be imaged by the instrument.
Examples
--------
.. testsetup::
from pypeline.phased_array.instrument import MwaBlock
from scipy.constants import speed_of_light
.. doctest::
>>> instr = MwaBlock()
>>> freq = 145e6
>>> wl = speed_of_light / freq
>>> instr.nyquist_rate(wl)
8753
"""
if wl <= 0:
raise ValueError('Parameter[wl] must be positive.')
XYZ = self._layout.values
baseline = linalg.norm(XYZ[:, np.newaxis, :] - XYZ[np.newaxis, :, :],
axis=-1)
N = sp.spherical_jn_series_threshold((2 * np.pi / wl) * baseline.max())
return N
class SphericalImage:
"""
Wrapper around :py:class:`SphericalImageContainer_float32` and
:py:class:`SphericalImageContainer_float64` to enable advanced functionality.
Main features:
* import images from FITS format;
* export images to FITS format;
* advanced 2D plotting based on `Matplotlib <https://matplotlib.org/>`_;
* view exported images with `DS9 <http://ds9.si.edu/site/Home.html>`_.
Examples
--------
.. doctest::
import numpy as np
import pypeline.phased_array.util.grid as grid
import pypeline.phased_array.util.io.image as image
import pypeline.util.math.sphere as sph
import pypeline.util.math.stat as stat
# grid settings =======================
direction = np.array(sph.eq2cart(1,
lat=np.radians(30),
lon=np.radians(20)))
FoV = np.radians(60)
N_height, N_width = 256, 384
px_grid = grid.uniform_grid(direction, FoV, size=[N_height, N_width])
# data settings =======================
beta0, a0 = 0.7, [1, 1, 1]
beta1, a1 = 0.9, [0, 0, 1]
kent0 = stat.Kent(k=stat.Kent.min_scale(FoV, beta0) * 2,
beta=beta0,
g1=direction,
a=a0)
kent1 = stat.Kent(k=stat.Kent.min_scale(FoV, beta1) * 2,
beta=beta1,
g1=direction,
a=a1)
data0 = (kent0
.pdf(px_grid.reshape(3, N_height * N_width).T)
.reshape(N_height, N_width))
data1 = (kent1
.pdf(px_grid.reshape(3, N_height * N_width).T)
.reshape(N_height, N_width))
data = np.stack([data0, data1], axis=0)
# Image creation ======================
I_container = image.SphericalImageContainer_float64(data, px_grid)
I = image.SphericalImage(I_container)
Data IO:
.. doctest::
I.to_fits('test.fits') # save to FITS
I2 = image.from_fits('test.fits') # load from FITS
Interactive plotting:
.. doctest::
I.draw() # AEQD projection by default, all layers.
.. image:: _img/sphericalimage_aeqd_example.png
.. doctest::
I.draw(index=0, projection='GNOM') # Only show first data slice.
.. image:: _img/sphericalimage_gnom_example.png
.. doctest::
I.draw(index=1, projection='LCC', data_kwargs=dict(cmap='jet'))
.. image:: _img/sphericalimage_lcc_example.png
"""
@chk.check('container',
chk.is_instance(im_cpp.SphericalImageContainer_float32,
im_cpp.SphericalImageContainer_float64))
def __init__(self, container):
"""
Parameters
----------
container: :py:class:`~pypeline_phased_array_util_io_image_pybind11.SphericalImageContainer_float32` or :py:class:`~pypeline_phased_array_util_io_image_pybind11.SphericalImageContainer_float64`
Bare container holding spherical image data.
"""
self._container = container
@property
def image(self):
"""
Returns
-------
:py:class:`~numpy.ndarray`
(N_image, ...) data cube.
"""
return self._container.image
@property
def grid(self):
"""
Returns
-------
:py:class:`~numpy.ndarray`
(3, ...) Cartesian coordinates of the sky on which the data points are defined.
"""
return self._container.grid
@chk.check('file_name', chk.is_instance(str))
def to_fits(self, file_name):
"""
Save image to FITS file.
Parameters
----------
file_name : str
Name of file.
Notes
-----
* :py:class:`~pypeline.phased_array.util.io.image.SphericalImage` subclasses that write WCS information assume the grid is specified in ICRS.
If this is not the case, rotate the grid accordingly before calling :py:meth:`~pypeline.phased_array.util.io.image.SphericalImage.to_fits`.
* Data cubes are stored in a secondary IMAGE frame and can be viewed with DS9 using::
$ ds9 <FITS_file>.fits[IMAGE]
WCS information is only available in external FITS viewers if using :py:class:`~pypeline.phased_array.util.io.image.EqualAngleImage`.
"""
primary_hdu = self._PrimaryHDU()
image_hdu = self._ImageHDU()
hdulist = fits.HDUList([primary_hdu, image_hdu])
hdulist.writeto(file_name, overwrite=True)
def _PrimaryHDU(self):
"""
Generate primary Header Descriptor Unit (HDU) for FITS export.
Returns
-------
hdu : :py:class:`~astropy.io.fits.PrimaryHDU`
"""
metadata = dict(IMG_TYPE=(self.__class__.__name__,
'SphericalImage subclass'), )
# grid: stored as angles to reduce file size.
_, colat, lon = sph.cart2pol(*self.grid)
coordinates = np.stack([np.degrees(colat), np.degrees(lon)], axis=0)
hdu = fits.PrimaryHDU(data=coordinates)
for k, v in metadata.items():
hdu.header[k] = v
return hdu
def _ImageHDU(self):
"""
Generate image Header Descriptor Unit (HDU) for FITS export.
Returns
-------
hdu : :py:class:`~astropy.io.fits.ImageHDU`
"""
hdu = fits.ImageHDU(data=self.image, name='IMAGE')
return hdu
@classmethod
@chk.check(
dict(primary_hdu=chk.is_instance(fits.PrimaryHDU),
image_hdu=chk.is_instance(fits.ImageHDU)))
def _from_fits(cls, primary_hdu, image_hdu):
"""
Load image from Header Descriptor Units.
Parameters
----------
primary_hdu : :py:class:`~astropy.io.fits.PrimaryHDU`
image_hdu : :py:class:`~astropy.io.fits.ImageHDU`
Returns
-------
I : :py:class:`~pypeline.phased_array.util.io.image.SphericalImage`
"""
# PrimaryHDU: grid specification.
colat, lon = primary_hdu.data
x, y, z = sph.pol2cart(1, np.radians(colat), np.radians(lon))
grid = np.stack([x, y, z], axis=0)
# ImageHDU: extract data cube.
image = image_hdu.data
# Make sure (image, grid) have the same dtype to work with SphericalImageContainer_floatxx().
image = image.astype(grid.dtype)
if grid.dtype == np.dtype(np.float32):
I_container = im_cpp.SphericalImageContainer_float32(image, grid)
else: # float64 mode
I_container = im_cpp.SphericalImageContainer_float64(image, grid)
I = cls(I_container)
return I
@property
def shape(self):
"""
Returns
-------
tuple
Shape of data cube.
"""
return self.image.shape
@chk.check(
dict(index=chk.accept_any(chk.is_integer, chk.has_integers,
chk.is_instance(slice)),
projection=chk.is_instance(str),
catalog=chk.allow_None(chk.is_instance(sky.SkyEmission)),
show_gridlines=chk.is_boolean,
show_colorbar=chk.is_boolean,
ax=chk.allow_None(chk.is_instance(axes.Axes)),
data_kwargs=chk.allow_None(chk.is_instance(dict)),
grid_kwargs=chk.allow_None(chk.is_instance(dict)),
catalog_kwargs=chk.allow_None(chk.is_instance(dict))))
def draw(self,
index=slice(None),
projection='AEQD',
catalog=None,
show_gridlines=True,
show_colorbar=True,
ax=None,
data_kwargs=None,
grid_kwargs=None,
catalog_kwargs=None):
"""
Plot spherical image using a 2D projection.
Parameters
----------
index : int, array-like(int), slice
Slices of the data-cube to show.
If multiple layers are provided, they are summed together.
projection : str
Plot projection.
Must be one of (case-insensitive):
* AEQD: `Azimuthal Equi-Distant <https://en.wikipedia.org/wiki/Azimuthal_equidistant_projection>`_; (default)
* LAEA: `Lambert Equal-Area <https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection>`_;
* LCC: `Lambert Conformal Conic <https://en.wikipedia.org/wiki/Lambert_conformal_conic_projection>`_;
* ROBIN: `Robinson <https://en.wikipedia.org/wiki/Robinson_projection>`_;
* GNOM: `Gnomonic <https://en.wikipedia.org/wiki/Gnomonic_projection>`_;
* HEALPIX: `Hierarchical Equal-Area Pixelisation <https://en.wikipedia.org/wiki/HEALPix>`_.
Notes
-----
* (AEQD, LAEA, LCC, GNOM) are recommended for mapping portions of the sphere.
* LCC breaks down when mapping polar regions.
* GNOM breaks down when mapping large FoVs.
* (ROBIN, HEALPIX) are recommended for mapping the entire sphere.
catalog : :py:class:`~pypeline.phased_array.util.data_gen.sky.SkyEmission`
Source catalog to overlay on top of images. (Default: no overlay)
show_gridlines : bool
Show RA/DEC gridlines. (Default: True)
It is possible for the gridlines to be plotted on the wrong range
when the grid crosses the 180W/E meridian.
show_colorbar : bool
Show colorbar. (Default: True)
ax : :py:class:`~matplotlib.axes.Axes`
Axes to draw on.
If :py:obj:`None`, a new axes is used.
data_kwargs : dict
Keyword arguments related to data-cube visualization.
Accepted keys are:
* :py:meth:`~matplotlib.axes.Axes.contourf` options.
* :py:meth:`~matplotlib.axes.Axes.tricontourf` options.
grid_kwargs : dict
Keyword arguments related to grid visualization.
Accepted keys are:
* N_parallel : int
Number declination lines to show in viewable region. (Default: 3)
* N_meridian : int
Number of right-ascension lines to show in viewable region. (Default: 3)
* polar_plot : bool
Correct RA/DEC gridlines when mapping polar regions. (Default: False)
When mapping polar regions, meridian lines may be doubled at 180W/E, making it seem like a meridian line is missing.
Setting `polar_plot` to :py:obj:`True` redistributes the meridians differently to correct the issue.
This option only makes sense when mapping polar regions, and will produce incorrect gridlines otherwise.
* ticks : bool
Add RA/DEC labels next to gridlines. (Default: False)
TODO: change to True once implemented
catalog_kwargs : dict
Keyword arguments related to catalog visualization.
Accepted keys are:
* :py:meth:`~matplotlib.axes.Axes.scatter` options.
Returns
-------
ax : :py:class:`~matplotlib.axes.Axes`
"""
if ax is None:
fig, ax = plt.subplots()
proj = self._draw_projection(projection)
scm = self._draw_data(index, data_kwargs, proj, ax)
cbar = self._draw_colorbar(show_colorbar, scm, ax) # noqa: F841
self._draw_gridlines(show_gridlines, grid_kwargs, proj, ax)
self._draw_catalog(catalog, catalog_kwargs, proj, ax)
self._draw_beautify(proj, ax)
return ax
@chk.check('projection', chk.is_instance(str))
def _draw_projection(self, projection):
"""
Setup :py:class:`pyproj.Proj` object to do (lon,lat) <-> (x,y) transforms.
Parameters
----------
projection : str
`projection` parameter given to :py:meth:`draw`.
Returns
-------
proj : :py:class:`pyproj.Proj`
"""
# Most projections can be provided a point in space around which distortions are minimized.
# We choose this point to approximately map to the center of the grid when appropriate.
# (approximate since it is not always a spherical cap.)
if self._container.is_gridded: # (3, N_height, N_width) grid
grid_dir = np.mean(self.grid, axis=(1, 2))
else: # (3, N_points) grid
grid_dir = np.mean(self.grid, axis=1)
_, grid_lat, grid_lon = sph.cart2eq(*grid_dir)
grid_lat = coord.Angle(grid_lat * u.rad).to_value(u.deg)
grid_lon = coord.Angle(grid_lon * u.rad).wrap_at(180 * u.deg).to_value(
u.deg)
p_name = projection.lower()
if p_name == 'lcc':
# Lambert Conformal Conic
proj = pyproj.Proj(proj='lcc', lon_0=grid_lon, lat_0=grid_lat, R=1)
elif p_name == 'aeqd':
# Azimuthal Equi-Distant
proj = pyproj.Proj(proj='aeqd',
lon_0=grid_lon,
lat_0=grid_lat,
R=1)
elif p_name == 'laea':
# Lambert Equal-Area
proj = pyproj.Proj(proj='laea',
lon_0=grid_lon,
lat_0=grid_lat,
R=1)
elif p_name == 'robin':
# Robinson
proj = pyproj.Proj(proj='robin', lon_0=grid_lon, R=1)
elif p_name == 'gnom':
# Gnomonic
proj = pyproj.Proj(proj='gnom',
lon_0=grid_lon,
lat_0=grid_lat,
R=1)
elif p_name == 'healpix':
# Hierarchical Equal-Area Pixelisation
proj = pyproj.Proj(proj='healpix',
lon_0=grid_lon,
lat_0=grid_lat,
R=1)
else:
raise ValueError('Parameter[projection] is not a valid projection '
'specifier.')
return proj
@chk.check(
dict(index=chk.accept_any(chk.is_integer, chk.has_integers,
chk.is_instance(slice)),
data_kwargs=chk.allow_None(chk.is_instance(dict)),
projection=chk.is_instance(pyproj.Proj),
ax=chk.is_instance(axes.Axes)))
def _draw_data(self, index, data_kwargs, projection, ax):
"""
Contour plot of data.
Parameters
----------
index : int, array-like(int), slice
`index` parameter given to :py:meth:`draw`.
data_kwargs : dict
`data_kwargs` parameter given to :py:meth:`draw`.
projection : :py:class:`~pyproj.Proj`
PyProj projection object.
ax : :py:class:`~matplotlib.axes.Axes`
Axes to plot on.
Returns
-------
scm : :py:class:`~matplotlib.cm.ScalarMappable`
"""
if data_kwargs is None:
data_kwargs = dict()
N_image = self.shape[0]
if chk.is_integer(index):
index = np.array([index], dtype=int)
elif chk.has_integers(index):
index = np.array(index, dtype=int)
else: # slice()
index = np.arange(N_image, dtype=int)[index]
if index.size == 0:
raise ValueError('No data-cube slice chosen.')
if not np.all((0 <= index) & (index < N_image)):
raise ValueError('Parameter[index] is out of bounds.')
data = np.sum(self.image[index], axis=0)
# Transform (lon,lat) to (x,y).
# Some projections have unmappable regions or exhibit singularities at certain points.
# These regions are colored white in contour plots by replacing their incorrect value (1e30) with NaN.
_, grid_lat, grid_lon = sph.cart2eq(*self.grid)
grid_lat = coord.Angle(grid_lat * u.rad).to_value(u.deg)
grid_lon = coord.Angle(grid_lon * u.rad).wrap_at(180 * u.deg).to_value(
u.deg)
grid_x, grid_y = projection(grid_lon, grid_lat, errcheck=False)
grid_x[np.isclose(grid_x, 1e30)] = np.nan
grid_y[np.isclose(grid_y, 1e30)] = np.nan
# Colormap choice
if 'cmap' in data_kwargs:
obj = data_kwargs.pop('cmap')
if chk.is_instance(str)(obj):
cmap = cm.get_cmap(obj)
else:
cmap = obj
else:
cmap = plot.cmap('matthieu-custom-sky', N=38)
if self._container.is_gridded:
scm = ax.contourf(grid_x,
grid_y,
data,
cmap.N,
cmap=cmap,
**data_kwargs)
else:
triangulation = tri.Triangulation(grid_x, grid_y)
scm = ax.tricontourf(triangulation,
data,
cmap.N,
cmap=cmap,
**data_kwargs)
# Show coordinates in status bar
def sexagesimal_coords(x, y):
lon, lat = projection(x, y, errcheck=False, inverse=True)
lon = (coord.Angle(lon * u.deg).wrap_at(180 * u.deg).to_string(
unit=u.hourangle, sep='hms'))
lat = (coord.Angle(lat * u.deg).to_string(unit=u.degree,
sep='dms'))
msg = f'RA: {lon}, DEC: {lat}'
return msg
ax.format_coord = sexagesimal_coords
return scm
@chk.check(
dict(show_colorbar=chk.is_boolean,
scm=chk.is_instance(cm.ScalarMappable),
ax=chk.is_instance(axes.Axes)))
def _draw_colorbar(self, show_colorbar, scm, ax):
"""
Attach colorbar.
Parameters
----------
show_colorbar : bool
`show_colorbar` parameter given to :py:meth:`draw`.
scm : :py:class:`~matplotlib.cm.ScalarMappable`
Intensity scale.
ax : :py:class:`~matplotlib.axes.Axes`
Axes to plot on.
Returns
-------
cbar : :py:class:`~matplotlib.colorbar.Colorbar`
"""
if show_colorbar:
cbar = plot.colorbar(scm, ax)
else:
cbar = None
return cbar
@chk.check(
dict(show_gridlines=chk.is_boolean,
grid_kwargs=chk.allow_None(chk.is_instance(dict)),
projection=chk.is_instance(pyproj.Proj),
ax=chk.is_instance(axes.Axes)))
def _draw_gridlines(self, show_gridlines, grid_kwargs, projection, ax):
"""
Plot Right-Ascension / Declination lines.
Parameters
----------
show_gridlines : bool
`show_gridlines` parameter given to :py:meth:`draw`.
grid_kwargs : dict
`grid_kwargs` parameter given to :py:meth:`draw`.
projection : :py:class:`pyproj.Proj`
PyProj projection object.
ax : :py:class:`~matplotlib.axes.Axes`
Axes to plot on.
"""
if grid_kwargs is None:
grid_kwargs = dict()
if 'N_parallel' in grid_kwargs:
N_parallel = grid_kwargs.pop('N_parallel')
if not (chk.is_integer(N_parallel) and (N_parallel >= 3)):
raise ValueError('Value[N_parallel] must be at least 3.')
else:
N_parallel = 3
if 'N_meridian' in grid_kwargs:
N_meridian = grid_kwargs.pop('N_meridian')
if not (chk.is_integer(N_meridian) and (N_meridian >= 3)):
raise ValueError('Value[N_meridian] must be at least 3.')
else:
N_meridian = 3
if 'polar_plot' in grid_kwargs:
polar_plot = grid_kwargs.pop('polar_plot')
if not chk.is_boolean(polar_plot):
raise ValueError('Value[polar_plot] must be boolean.')
else:
polar_plot = False
if 'ticks' in grid_kwargs:
show_ticks = grid_kwargs.pop('ticks')
if not chk.is_boolean(show_ticks):
raise ValueError('Value[ticks] must be boolean.')
else:
# TODO: change to True once implemented.
show_ticks = False
plot_style = dict(alpha=0.5, color='k', linewidth=1, linestyle='solid')
plot_style.update(grid_kwargs)
_, grid_lat, grid_lon = sph.cart2eq(*self.grid)
grid_lat = coord.Angle(grid_lat * u.rad).to_value(u.deg)
grid_lon = coord.Angle(grid_lon * u.rad).wrap_at(180 * u.deg).to_value(
u.deg)
# RA curves
meridian = dict()
dec_span = np.linspace(grid_lat.min(), grid_lat.max(), 200)
if polar_plot:
ra = np.linspace(-180, 180, N_meridian, endpoint=False)
else:
ra = np.linspace(grid_lon.min(), grid_lon.max(), N_meridian)
for _ in ra:
ra_span = _ * np.ones_like(dec_span)
# Transform (lon,lat) to (x,y).
# Some projections have unmappable regions or exhibit singularities at certain points.
# These regions are colored white in contour plots by replacing their incorrect value (1e30) with NaN.
grid_x, grid_y = projection(ra_span, dec_span, errcheck=False)
grid_x[np.isclose(grid_x, 1e30)] = np.nan
grid_y[np.isclose(grid_y, 1e30)] = np.nan
if show_gridlines:
mer = ax.plot(grid_x, grid_y, **plot_style)[0]
meridian[_] = mer
# DEC curves
parallel = dict()
ra_span = np.linspace(grid_lon.min(), grid_lon.max(), 200)
if polar_plot:
dec = np.linspace(grid_lat.min(), grid_lat.max(), N_parallel + 1)
else:
dec = np.linspace(grid_lat.min(), grid_lat.max(), N_parallel)
for _ in dec:
dec_span = _ * np.ones_like(ra_span)
# Transform (lon,lat) to (x,y).
# Some projections have unmappable regions or exhibit singularities at certain points.
# These regions are colored white in contour plots by replacing their incorrect value (1e30) with NaN.
grid_x, grid_y = projection(ra_span, dec_span, errcheck=False)
grid_x[np.isclose(grid_x, 1e30)] = np.nan
grid_y[np.isclose(grid_y, 1e30)] = np.nan
if show_gridlines:
par = ax.plot(grid_x, grid_y, **plot_style)[0]
parallel[_] = par
# LAT/LON ticks
if show_gridlines and show_ticks:
raise NotImplementedError('Not yet implemented.')
@chk.check(
dict(catalog=chk.allow_None(chk.is_instance(sky.SkyEmission)),
projection=chk.is_instance(pyproj.Proj),
ax=chk.is_instance(axes.Axes)))
def _draw_catalog(self, catalog, catalog_kwargs, projection, ax):
"""
Overlay catalog on top of map.
Parameters
----------
catalog : :py:class:`~pypeline.phased_array.util.data_gen.sky.SkyEmission`
`catalog` parameter given to :py:meth:`draw`.
catalog_kwargs : dict
`catalog_kwargs` parameter given to :py:meth:`draw`.
projection : :py:class:`pyproj.Proj`
PyProj projection object.
ax : :py:class:`~matplotlib.axes.Axes`
Axes to plot on.
"""
if catalog is not None:
_, c_lat, c_lon = sph.cart2eq(*catalog.xyz.T)
c_lat = coord.Angle(c_lat * u.rad).to_value(u.deg)
c_lon = coord.Angle(c_lon * u.rad).wrap_at(180 * u.deg).to_value(
u.deg)
c_x, c_y = projection(c_lon, c_lat, errcheck=False)
c_x[np.isclose(c_x, 1e30)] = np.nan
c_y[np.isclose(c_y, 1e30)] = np.nan
if catalog_kwargs is None:
catalog_kwargs = dict()
plot_style = dict(s=400, facecolors='none', edgecolors='w')
plot_style.update(catalog_kwargs)
ax.scatter(c_x, c_y, **plot_style)
@chk.check(
dict(projection=chk.is_instance(pyproj.Proj),
ax=chk.is_instance(axes.Axes)))
def _draw_beautify(self, projection, ax):
"""
Format plot.
Parameters
----------
projection : :py:class:`pyproj.Proj`
PyProj projection object.
ax : :py:class:`~matplotlib.axes.Axes`
Axes to draw on.
"""
ax.axis('off')
ax.axis('equal')
# ############################################################################## # _linalg.py # ========== # Author : Sepand KASHANI [[email protected]] # ############################################################################## import numpy as np import scipy.linalg as linalg import pypeline.util.argcheck as chk @chk.check( dict(A=chk.accept_any(chk.has_reals, chk.has_complex), B=chk.allow_None(chk.accept_any(chk.has_reals, chk.has_complex)), tau=chk.is_real, N=chk.allow_None(chk.is_integer))) def eigh(A, B=None, tau=1, N=None): """ Solve a generalized eigenvalue problem. Finds :math:`(D, V)`, solution of the generalized eigenvalue problem .. math:: A V = B V D. This function is a wrapper around :py:func:`scipy.linalg.eigh` that adds energy truncation and extra output formats. Parameters ----------
cb = colorbar(im, ax)
fig.show()
.. image:: _img/colorbar_example.png
"""
fig = ax.get_figure()
divider = ax_grid.make_axes_locatable(ax)
ax_colorbar = divider.append_axes('right', size='5%', pad=0.05,
axes_class=axes.Axes)
colorbar = fig.colorbar(scm, cax=ax_colorbar)
return colorbar
@chk.check(dict(name=chk.is_instance(str),
N=chk.allow_None(chk.is_integer)))
def cmap(name, N=None):
"""
Load one of Pypeline's custom colormaps.
All maps are defined under ``<pypeline_dir>/data/colormap/``.
Parameters
----------
name : str
colormap name.
N : int, optional
Number of color levels. (Default: all).
If `N` is smaller than the number of levels available in the colormap, then the last `N` colors will be used.
