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, 142 insertions, 2 deletions

diff --git a/fg21sim/utils/io.py b/fg21sim/utils/io.py
index 050574c..49fa3c1 100644
--- a/fg21sim/utils/io.py
+++ b/fg21sim/utils/io.py
@@ -2,22 +2,47 @@
 # MIT license
 
 """
-Input/output utilities.
+Input/output 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.
 """
 
 import os
 import logging
 import pickle
-from datetime import datetime
+from datetime import datetime, timezone
 
 import numpy as np
 import pandas as pd
 from astropy.io import fits
+import healpy as hp
 
 
 logger = logging.getLogger(__name__)
 
 
+# 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 _create_dir(filepath):
     """
     Check the existence of the target directory, and create it if necessary.
@@ -169,3 +194,118 @@ def write_fits_image(outfile, image, header=None, float32=True,
     hdu = fits.PrimaryHDU(data=image, header=header)
     hdu.writeto(outfile, checksum=checksum)
     logger.info("Wrote image to FITS file: %s" % outfile)
+
+
+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)