# Copyright (c) 2017,2019 Weitian LI # MIT License """ Generic simulation sky supporting both sky patch and HEALPix all-sky maps. References ---------- * Python - 3. Data Model https://docs.python.org/3/reference/datamodel.html#special-method-names """ import logging import copy from datetime import datetime import numpy as np from scipy import ndimage from astropy.io import fits import astropy.units as au from astropy.coordinates import SkyCoord from regions import PixCoord, RectanglePixelRegion from reproject import reproject_interp, reproject_to_healpix import healpy as hp from .utils.wcs import make_wcs from .utils.io import (read_fits_healpix, write_fits_healpix, write_fits_image) from .utils.random import spherical_uniform from .utils.units import UnitConversions as AUC logger = logging.getLogger(__name__) class SkyBase: """ The base class for both the sky patch and HEALPix all-sky map classes. Attributes ---------- type_ : str The type of the sky image Values: ``patch`` or ``healpix`` data : `~numpy.ndarray` The data array read from input sky image, or to be written into output FITS file. frequency_ : float The frequency of the input/output sky image. Unit: [MHz] pixelsize_ : float The pixel size of the sky image. Unit: [arcsec] creator_ : str The creator of the (output) sky image. Default: ``__name__`` header_ : `~astropy.io.fits.Header` The FITS header information of the input/output file. float32_ : bool Whether to use single/float32 data type to save the sky image? Default: True clobber_ : bool, optional Whether to overwrite the existing output file. Default: False checksum_ : bool, optional Whether to calculate the checksum data for the output FITS file, which may cost some time. Default: False """ def __init__(self, float32=True, clobber=False, checksum=False): self.type_ = None self.data = None self.frequency_ = None # [MHz] self.pixelsize_ = None # [arcsec] self.creator_ = __name__ self.header_ = fits.Header() self.float32_ = float32 self.clobber_ = clobber self.checksum_ = checksum def __add__(self, other): """Binary arithmetic operation: ``+``.""" if isinstance(other, self.__class__): return self.data + other.data elif isinstance(other, (int, float, np.ndarray)): return self.data + other else: raise NotImplementedError def __sub__(self, other): """Binary arithmetic operation: ``-``.""" if isinstance(other, self.__class__): return self.data - other.data elif isinstance(other, (int, float, np.ndarray)): return self.data - other else: raise NotImplementedError def __mul__(self, other): """Binary arithmetic operation: ``*``.""" if isinstance(other, self.__class__): return self.data * other.data elif isinstance(other, (int, float, np.ndarray)): return self.data * other else: raise NotImplementedError def __truediv__(self, other): """Binary arithmetic operation: ``/``.""" if isinstance(other, self.__class__): return self.data / other.data elif isinstance(other, (int, float, np.ndarray)): return self.data / other else: raise NotImplementedError def __pow__(self, other): """Binary arithmetic operation: ``**``.""" if isinstance(other, self.__class__): return self.data ** other.data elif isinstance(other, (int, float, np.ndarray)): return self.data ** other else: raise NotImplementedError def __iadd__(self, other): """ Augmented arithmetic assignment: ``+=``. NOTE ---- These augmented arithmetic assignment methods should attempt to do the operation in-place (modifying ``self``) and return the result (which could be, but does not have to be, ``self``). """ if isinstance(other, self.__class__): self.data += other.data return self elif isinstance(other, (int, float, np.ndarray)): self.data += other return self else: raise NotImplementedError def __isub__(self, other): """Augmented arithmetic assignment: ``-=``.""" if isinstance(other, self.__class__): self.data -= other.data return self elif isinstance(other, (int, float, np.ndarray)): self.data -= other return self else: raise NotImplementedError def __imul__(self, other): """Augmented arithmetic assignment: ``*=``.""" if isinstance(other, self.__class__): self.data *= other.data return self elif isinstance(other, (int, float, np.ndarray)): self.data *= other return self else: raise NotImplementedError def __itruediv__(self, other): """Augmented arithmetic assignment: ``/=``.""" if isinstance(other, self.__class__): self.data /= other.data return self elif isinstance(other, (int, float, np.ndarray)): self.data /= other return self else: raise NotImplementedError def __neg__(self): """Unary arithmetic operation: ``-``.""" return -self.data def __abs__(self): """Unary arithmetic operation: ``abs()``.""" return np.abs(self.data) def add(self, obj, *args, **kwargs): """ Add/superimpose an object to the sky image. """ raise NotImplementedError @property def shape(self): """ Numpy array shape of the (current/output) sky data. """ return self.data.shape @property def frequency(self): """ The frequency of the sky image. Unit: [MHz] """ if self.frequency_ is not None: return self.frequency_ else: return self.header_.get("FREQ", None) @frequency.setter def frequency(self, value): """ Set the frequency of the sky image. Unit: [MHz] """ self.frequency_ = value @property def pixelsize(self): """ Pixel size of the sky image. Unit: [arcsec] """ return self.pixelsize_ @property def creator(self): """ The creator of the sky image. """ if self.creator_ is not None: return self.creator_ else: return self.header_.get("CREATOR", None) @creator.setter def creator(self, value): """ Set the creator of the sky image. """ self.creator_ = value @property def header(self): """ The FITS header of the current sky. """ hdr = self.header_.copy() hdr["SkyType"] = (self.type_, "Patch / HEALPix") hdr["PixSize"] = (self.pixelsize, "Pixel size [arcsec]") hdr["CREATOR"] = (self.creator, "Sky Creator") hdr["FREQ"] = (self.frequency, "Sky frequency [MHz]") hdr["DATE"] = (datetime.utcnow().isoformat()+"Z", "File creation date") return hdr def merge_header(self, header, update=False): """ Merge the supplied header to the instance's FITS header. Do not overwrite the original keywords by default (``update=False``). """ self.header_.extend(header, update=update) def add_header(self, key, value, comment=None): """ Add/update a key to the FITS header. """ if comment is None: self.header_[key] = value else: self.header_[key] = (value, comment) def add_history(self, history): """ Add history to the FITS header. """ self.header_.add_history(history) def copy(self): """ Return a (deep) copy of this instance. """ return copy.deepcopy(self) def load(self, infile, frequency=None): """ Load the given sky image into this instance. Parameters ---------- infile : str The path to the given input sky image. frequency : float, optional The frequency of the given sky image if applicable. Unit: [MHz] """ raise NotImplementedError def open(self, infile, frequency=None): """ Open the given input file as a *new* instance. The current instance is *copied*, load the given sky image, and then returned. Returns ------- sky : a *new* instance with given sky image loaded. """ sky = self.copy() sky.load(infile=infile, frequency=frequency) return sky def write(self, outfile, clobber=None): """ Write the sky image (with current data) into a FITS file. Parameters ---------- outfile : str The path/filename to the output FITS file. clobber : bool, optional If not ``None``, then overwrite the default ``self.clobber_`` from the configuration file, to determine whether to overwrite the existing output file. """ raise NotImplementedError @property def area(self): """ Sky coverage of the sky. Unit: [deg^2] """ raise NotImplementedError def random_points(self, n=1): """ Generate uniformly distributed random points within the sky image (coverage). Parameters ---------- n : int, optional The number of random points required. Default: 1 Returns ------- lon, lat : float, or 1D `~numpy.ndarray` The longitudes and latitudes (in world coordinate) generated. Unit: [deg] """ raise NotImplementedError class SkyPatch(SkyBase): """ Support reading & writing FITS file of sky patches. NOTE/XXX -------- Currently just use ``CAR`` (Cartesian) sky projection, i.e., assuming a flat sky!! NOTE ---- X: FITS width / sky R.A. <-> data array rows Y: FITS height / sky Dec. <-> data array columns Parameters ---------- size : (xsize, ysize) tuple The (pixel) dimensions of the (output) sky patch. If the input sky has a different size, then it will be *scaled* to match this output size. pixelsize : float The pixel size of the sky patch, will be used to determine the sky coordinates. Unit: [arcsec] center : (ra, dec) tuple, optional The (R.A., Dec.) coordinate of the sky patch center. Unit: [deg] infile : str, optional The path to the input sky patch frequency : float, optional The frequency of the input sky path Unit: [MHz] Attributes ---------- type_ : ``patch`` This is a sky patch. data : 2D `~numpy.ndarray` The 2D data array of sky image, with shape (self.ysize, self.xsize). (HEALPix map stores data in an 1D array.) """ def __init__(self, size, pixelsize, center=(0.0, 0.0), infile=None, frequency=None, **kwargs): super().__init__(**kwargs) self.type_ = "patch" self.xsize, self.ysize = size # Initialize an empty image self.data = np.zeros(shape=(self.ysize, self.xsize)) self.pixelsize_ = pixelsize self.xcenter, self.ycenter = center if infile is not None: self.load(infile, frequency) @property def area(self): """ The sky coverage of this patch. Unit: [deg^2] XXX/FIXME --------- Assumed a flat sky, without WCS projection!! """ lonsize, latsize = self.size return (lonsize * latsize) @property def size(self): """ The sky patch size along X/longitude and Y/latitude axes. Returns ------- (lonsize, latsize) : float tuple Longitudinal and latitudinal sizes Unit: [deg] """ return (self.xsize * self.pixelsize * AUC.arcsec2deg, self.ysize * self.pixelsize * AUC.arcsec2deg) @property def center(self): return (self.xcenter, self.ycenter) @property def lon_limit(self): """ The longitudinal (X axis) limits. Returns ------- (lon_min, lon_max) : float tuple The minimum and maximum longitudes (X axis). Unit: [deg] """ lonsize, latsize = self.size return (self.xcenter - 0.5*lonsize, self.xcenter + 0.5*lonsize) @property def lat_limit(self): """ The latitudinal (Y axis) limits. Returns ------- (lat_min, lat_max) : float tuple The minimum and maximum latitudes (Y axis). Unit: [deg] """ lonsize, latsize = self.size return (self.ycenter - 0.5*latsize, self.ycenter + 0.5*latsize) def add(self, obj, center): """ Add/superimpose the object image into this sky patch. XXX/FIXME ---------- Assumed a flat sky!! Parameters ---------- obj : 2D `~numpy.ndarray` The object image to be added into the sky. NOTE: Should have same pixel size as the sky patch. center : (ra, dec) tuple The central coordinate (R.A., Dec.) of the given object. """ obj = np.asarray(obj) nrow, ncol = obj.shape xc, yc = center ric, cic = self.world2pix(xc, yc) # Index ranges (inclusive at both ends) for the supplied object # image on the sky array rimin0, rimax0 = ric - nrow//2, ric + (nrow-1)//2 cimin0, cimax0 = cic - ncol//2, cic + (ncol-1)//2 # Index ranges for the supplied object image rimin1, rimax1 = 0, nrow-1 cimin1, cimax1 = 0, ncol-1 # Check the object boundaries if ((rimin0 >= self.ysize) or (rimax0 < 0) or (cimin0 >= self.xsize) or (cimax0 < 0)): logger.warning("The given object is beyond the sky coverage") return if rimin0 < 0: rimin1 = -rimin0 rimin0 = 0 if rimax0 >= self.ysize: rimax1 = nrow - (rimax0-self.ysize) - 2 rimax0 = self.ysize-1 if cimin0 < 0: cimin1 = -cimin0 cimin0 = 0 if cimax0 >= self.xsize: cimax1 = nrow - (cimax0-self.xsize) - 2 cimax0 = self.xsize-1 self.data[rimin0:(rimax0+1), cimin0:(cimax0+1)] += obj[rimin1:(rimax1+1), cimin1:(cimax1+1)] def world2pix(self, x, y): """ Convert the world coordinates (R.A., Dec.) into the pixel coordinates (indexes) within the sky data array. Parameters ---------- x, y : float, `~numpy.ndarray` The R.A., Dec. world coordinates Unit: [deg] Returns ------- ri, ci : int, `~numpy.ndarray` The row, column indexes within the sky data array. """ pixelsize = self.pixelsize * AUC.arcsec2deg # [deg] x, y = np.asarray(x), np.asarray(y) # [deg] ri0, ci0 = self.ysize//2, self.xsize//2 ri = np.round((y - self.ycenter) / pixelsize + ri0).astype(int) ci = np.round((x - self.xcenter) / pixelsize + ci0).astype(int) return (ri, ci) def load(self, infile, frequency=None): """ Load input sky image from file into this instance. Parameters ---------- infile : str The path to the input sky patch frequency : float, optional The frequency of the sky patch; Unit: [MHz] """ self.infile = infile if frequency is not None: self.frequency = frequency with fits.open(infile) as f: self.data = f[0].data header = f[0].header.copy(strip=True) self.header_.extend(header, update=True) self.ysize_in, self.xsize_in = self.data.shape logger.info("Loaded sky patch from: %s (%dx%d)" % (infile, self.xsize_in, self.ysize_in)) if (self.xsize_in != self.xsize) or (self.ysize_in != self.ysize): logger.warning("Scale input sky patch to size %dx%d" % (self.xsize, self.ysize)) zoom = ((self.ysize+0.1)/self.ysize_in, (self.xsize+0.1)/self.xsize_in) self.data = ndimage.zoom(self.data, zoom=zoom, order=1) def write(self, outfile, clobber=None): """ Write current data to file. """ if clobber is None: clobber = self.clobber_ write_fits_image(outfile, image=self.data, header=self.header, float32=self.float32_, clobber=clobber, checksum=self.checksum_) @property def header(self): """ FITS header of the sky for storing information in the output file. """ hdr = super().header hdr.extend(self.wcs.to_header(), update=True) hdr["OBJECT"] = "Sky Patch" hdr["EXTNAME"] = "IMAGE" hdr["RA0"] = (self.center[0], "R.A. of patch center [deg]") hdr["DEC0"] = (self.center[1], "Dec. of patch center [deg]") return hdr @property def wcs(self): """ The WCS header with sky projection information, for sky <-> pixel coordinate(s) conversion. NOTE/XXX -------- Currently just use the `CAR` (Cartesian) projection, i.e., assuming a flat sky. """ w = make_wcs(center=(self.xcenter, self.ycenter), size=(self.xsize, self.ysize), pixelsize=self.pixelsize, frame="ICRS", projection="CAR") return w def contains(self, skycoord): """ Check whether the given (list of) sky coordinate(s) falls inside this sky patch (region). Parameters ---------- skycoord : `~astropy.coordinate.SkyCoord` or (lon, lat) tuple The (list of) sky coordinate(s) to check, or the (list of) longitudes and latitudes of sky coordinates [ deg ] Returns ------- inside : bool (list of) boolean values indicating whether the given sky coordinate(s) is inside this sky patch. """ if not isinstance(skycoord, SkyCoord): lon, lat = skycoord skycoord = SkyCoord(lon, lat, unit=au.deg) wcs = self.wcs pixcoord = PixCoord.from_sky(skycoord, wcs=wcs) center = PixCoord(x=self.xcenter, y=self.ycenter) region = RectanglePixelRegion(center=center, width=self.xsize, height=self.ysize) return region.contains(pixcoord) def reproject_from(self, data, wcs, squeeze=False, eps=1e-5): """ Reproject the given image/data together with WCS information onto the grid of this sky. Parameters ---------- data : 2D float `~numpy.ndarray` The input data/image to be reprojected wcs : `~astropy.wcs.WCS` The WCS information of the input data/image (naxis=2) squeeze : bool, optional Whether to squeeze the reprojected data to only keep the pixels greater than a small positive value specified by parameter ``eps``. Default: False eps : float, optional The small positive value to specify the squeeze threshold. Default: 1e-5 Returns ------- If ``squeeze=True``, then returns tuple of ``(indexes, values)``, otherwise, returns the reprojected image/data array. indexes : 1D int `~numpy.ndarray` The indexes of the pixels with positive values. values : 1D float `~numpy.ndarray` The values of the above pixels. reprojected : 1D `~numpy.ndarray` The reprojected data/image with same shape of this sky, i.e., ``self.data``. """ wcs_out = self.wcs shape_out = (self.ysize, self.xsize) reprojected, __ = reproject_interp( input_data=(data, wcs), output_projection=wcs_out, shape_out=shape_out) reprojected = reprojected.flatten() if squeeze: with np.errstate(invalid="ignore"): indexes = reprojected > eps values = reprojected[indexes] return (indexes, values) else: return reprojected def random_points(self, n=1): """ Generate uniformly distributed random points within the sky patch. Returns ------- lon : float, or 1D `~numpy.ndarray` Longitudes (Galactic/equatorial); Unit: [deg] lat : float, or 1D `~numpy.ndarray` Latitudes (Galactic/equatorial); Unit: [deg] """ lon_min, lon_max = self.lon_limit lat_min, lat_max = self.lat_limit lon = np.random.uniform(low=lon_min, high=lon_max, size=n) lat = np.random.uniform(low=lat_min, high=lat_max, size=n) return (lon, lat) class SkyHealpix(SkyBase): """ Support the HEALPix all-sky map. Parameters ---------- nside : int The pixel resolution of HEALPix (must be power of 2) infile : str, optional The path to the input sky patch frequency : float, optional The frequency of the input sky path Unit: [MHz] Attributes ---------- shape : int tuple, (npix,) The shape (i.e., length) of the HEALPix array pixelsize : float The pixel size of the HEALPix map Unit: [arcsec] """ def __init__(self, nside, infile=None, frequency=None, **kwargs): super().__init__(**kwargs) self.type_ = "healpix" self.nside = nside self.pixelsize_ = (hp.nside2resol(self.nside, arcmin=True) * AUC.arcmin2arcsec) self.data = np.zeros(shape=hp.nside2npix(self.nside)) if infile is not None: self.load(infile, frequency) @property def area(self): """ The sky coverage of this HEALPix map, i.e., all sky = 4π, Unit: [deg^2] """ return 4*np.pi * AUC.rad2deg**2 def load(self, infile, frequency=None): """ Load input HEALPix all-sky map into this instance. Parameters ---------- infile : str The path to the input HEALPix all-sky map. frequency : float, optional The frequency of the sky patch; Unit: [MHz] """ self.infile = infile if frequency is not None: self.frequency = frequency self.data, header = read_fits_healpix(infile) self.header_.extend(header, update=True) self.nside_in = header["NSIDE"] logger.info("Loaded HEALPix sky map from: {0} (Nside={1})".format( infile, self.nside_in)) if self.nside_in != self.nside: self.data = hp.ud_grade(self.data, nside_out=self.nside) logger.warning("Upgrade/downgrade sky map from Nside " + "{0} to {1}".format(self.nside_in, self.nside)) def write(self, outfile, clobber=None): """ Write current data to file. """ if clobber is None: clobber = self.clobber_ write_fits_healpix(outfile, hpmap=self.data, header=self.header, float32=self.float32_, clobber=self.clobber_, checksum=self.checksum_) def contains(self, skycoord): """ Shim method to be consistent with ``SkyPatch``. Always returns ``True``, since the HEALPix map covers all sky. """ if skycoord.isscalar: return True else: return np.ones(shape=len(skycoord), dtype=np.bool) def reproject_from(self, data, wcs, squeeze=False): """ Reproject the given image/data together with WCS information onto the grid of this sky. Parameters ---------- data : 2D float `~numpy.ndarray` The input data/image to be reprojected wcs : `~astropy.wcs.WCS` The WCS information of the input data/image (naxis=2) squeeze : bool, optional Whether to squeeze the reprojected data to only keep the positive pixels. Returns ------- If ``squeeze=True``, then returns tuple of ``(indexes, values)``, otherwise, returns the reprojected image/data array. indexes : 1D int `~numpy.ndarray` The indexes of the pixels with positive values. values : 1D float `~numpy.ndarray` The values of the above pixels. reprojected : 1D `~numpy.ndarray` The reprojected data/image with same shape of this sky, i.e., ``self.data.shape``. """ eps = 1e-5 reprojected, __ = reproject_to_healpix( input_data=(data, wcs), coord_system_out="galactic", nested=False, nside=self.nside) if squeeze: with np.errstate(invalid="ignore"): indexes = reprojected > eps values = reprojected[indexes] return (indexes, values) else: return reprojected def random_points(self, n=1): """ Generate uniformly distributed random points within the sky (i.e., all sky; on an unit sphere). Returns ------- lon : float, or 1D `~numpy.ndarray` Longitudes (Galactic/equatorial), [0, 360) [deg]. lat : float, or 1D `~numpy.ndarray` Latitudes (Galactic/equatorial), [-90, 90] [deg]. """ theta, phi = spherical_uniform(n) lon = np.degrees(phi) lat = 90.0 - np.degrees(theta) return (lon, lat) ########################################################################## def get_sky(configs): """ Sky class factory function to support both the sky patch and HEALPix all-sky map. Parameters ---------- configs : ConfigManager object An `ConfigManager` object contains default and user configurations. For more details, see the example config specification. """ # Parameters for the base sky class kwargs = { "float32": configs.getn("output/float32"), "clobber": configs.getn("output/clobber"), "checksum": configs.getn("output/checksum"), } skytype = configs.getn("sky/type") if skytype == "patch": sec = "sky/patch" xsize = configs.getn(sec+"/xsize") ysize = configs.getn(sec+"/ysize") xcenter = configs.getn(sec+"/xcenter") ycenter = configs.getn(sec+"/ycenter") pixelsize = configs.getn(sec+"/pixelsize") return SkyPatch(size=(xsize, ysize), pixelsize=pixelsize, center=(xcenter, ycenter), **kwargs) elif skytype == "healpix": sec = "sky/healpix" nside = configs.getn(sec+"/nside") return SkyHealpix(nside=nside, **kwargs) else: raise ValueError("unknown sky type: %s" % skytype)