utils: Merge fits.py into io.py

Functions "{read,write}_fits_healpix()" merged into io.py

Signed-off-by: Aaron LI <aly@aaronly.me>

1 files changed, 0 insertions, 152 deletions

diff --git a/fg21sim/utils/fits.py b/fg21sim/utils/fits.py
deleted file mode 100644
index 4991cd0..0000000
--- a/fg21sim/utils/fits.py
+++ /dev/null
@@ -1,152 +0,0 @@
-# Copyright (c) 2016 Weitian LI <liweitianux@live.com>
-# MIT license
-
-"""
-FITS utilities
---------------
-
-read_fits_healpix:
-    Read the HEALPix map from a FITS file or a BinTableHDU to 1D array
-    in *RING* ordering.
-
-write_fits_healpix:
-    Write the HEALPix map to a FITS file with proper header as well
-    as the user-provided header.
-"""
-
-from datetime import datetime, timezone
-
-import numpy as np
-from astropy.io import fits
-import healpy as hp
-
-
-# Column formats for FITS binary table
-# Reference:
-# http://docs.astropy.org/en/stable/io/fits/usage/table.html#column-creation
-FITS_COLUMN_FORMATS = {
-    np.dtype("bool"):       "L",
-    np.dtype("uint8"):      "B",
-    np.dtype("int16"):      "I",
-    np.dtype("int32"):      "J",
-    np.dtype("int64"):      "K",
-    np.dtype("float32"):    "E",
-    np.dtype("float64"):    "D",
-    np.dtype("complex64"):  "C",
-    np.dtype("complex128"): "M",
-}
-
-
-def read_fits_healpix(filename):
-    """Read the HEALPix map from a FITS file or a BinTableHDU to 1D array
-    in *RING* ordering.
-
-    Parameters
-    ----------
-    filename : str or `~astropy.io.fits.BinTableHDU`
-        Filename of the HEALPix FITS file,
-        or an `~astropy.io.fits.BinTableHDU` instance.
-
-    Returns
-    -------
-    data : 1D `~numpy.ndarray`
-        HEALPix data in *RING* ordering with same dtype as input
-    header : `~astropy.io.fits.Header`
-        Header of the input FITS file
-
-    NOTE
-    ----
-    This function wraps on `healpy.read_map()`, but set the data type of
-    data array to its original value as in FITS file, as well as return
-    FITS header as `~astropy.io.fits.Header` instance.
-    """
-    if isinstance(filename, fits.BinTableHDU):
-        hdu = filename
-    else:
-        # Read the first extended table
-        hdu = fits.open(filename)[1]
-    # Hack to ignore the dtype byteorder, use native endianness
-    dtype = np.dtype(hdu.data.field(0).dtype.type)
-    header = hdu.header
-    data = hp.read_map(hdu, nest=False, verbose=False)
-    return (data.astype(dtype), header)
-
-
-def write_fits_healpix(filename, hpmap, header=None, clobber=False,
-                       checksum=False):
-    """Write the HEALPix map to a FITS file with proper header as well
-    as the user-provided header.
-
-    This function currently only support one style of HEALPix with the
-    following specification:
-    - Only one column: I (intensity)
-    - ORDERING: RING
-    - COORDSYS: G (Galactic)
-    - OBJECT: FULLSKY
-    - INDXSCHM: IMPLICIT
-
-    Parameters
-    ----------
-    filename : str
-        Filename of the output file to write the HEALPix map data
-    hpmap : 1D `~numpy.ndarray`
-        1D array containing the HEALPix map data, and the ordering
-        scheme should be "RING";
-        The data type is preserved in the output FITS file.
-    header : `~astropy.io.fits.Header`, optional
-        Extra header to be appended to the output FITS
-    clobber : bool, optional
-        Whether overwrite the existing file?
-    checksum : bool, optional
-        Whether calculate the checksum for the output file, which is
-        recorded as the "CHECKSUM" header keyword.
-
-    NOTE
-    ----
-    - This function is intended to replace the most common case of
-      `healpy.write_map()`, which still uses some deprecated functions of
-      `numpy` and `astropy`, meanwhile, it interface/arguments is not very
-      handy.
-    - This function (currently) only implement the very basic feature of
-      the `healpy.write_map()`.
-    """
-    hpmap = np.asarray(hpmap)
-    if hpmap.ndim != 1:
-        raise ValueError("Invalid HEALPix data: only support 1D array")
-    # Hack to ignore the dtype byteorder, use native endianness
-    dtype = np.dtype(hpmap.dtype.type)
-    hpmap = hpmap.astype(dtype)
-    #
-    npix = hpmap.size
-    nside = int((npix / 12) ** 0.5)
-    colfmt = FITS_COLUMN_FORMATS.get(hpmap.dtype)
-    if hpmap.size > 1024:
-        hpmap = hpmap.reshape(int(hpmap.size/1024), 1024)
-        colfmt = "1024" + colfmt
-    #
-    hdr = fits.Header()
-    # set HEALPix parameters
-    hdr["PIXTYPE"] = ("HEALPIX", "HEALPix pixelization")
-    hdr["ORDERING"] = ("RING",
-                       "Pixel ordering scheme, either RING or NESTED")
-    hdr["COORDSYS"] = ("G", "Ecliptic, Galactic or Celestial (equatorial)")
-    hdr["NSIDE"] = (nside, "HEALPix resolution parameter")
-    hdr["NPIX"] = (npix, "Total number of pixels")
-    hdr["FIRSTPIX"] = (0, "First pixel # (0 based)")
-    hdr["LASTPIX"] = (npix-1, "Last pixel # (0 based)")
-    hdr["INDXSCHM"] = ("IMPLICIT", "Indexing: IMPLICIT or EXPLICIT")
-    hdr["OBJECT"] = ("FULLSKY", "Sky coverage, either FULLSKY or PARTIAL")
-    #
-    hdr["EXTNAME"] = ("HEALPIX", "Name of the binary table extension")
-    hdr["CREATOR"] = (__name__, "File creator")
-    hdr["DATE"] = (datetime.now(timezone.utc).astimezone().isoformat(),
-                   "File creation date")
-    # Merge user-provided header
-    # NOTE: use the `.extend()` method instead of `.update()` method
-    if header is not None:
-        hdr.extend(fits.Header(header))
-    #
-    hdu = fits.BinTableHDU.from_columns([
-        fits.Column(name="I", array=hpmap, format=colfmt)
-    ], header=hdr)
-    hdu.writeto(filename, clobber=clobber, checksum=checksum)