utils: Merge fits.py into io.py

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

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

7 files changed, 149 insertions, 159 deletions

diff --git a/bin/get-healpix-patch b/bin/get-healpix-patch
index b1245e8..879067d 100755
--- a/bin/get-healpix-patch
+++ b/bin/get-healpix-patch
@@ -21,7 +21,7 @@ from reproject import reproject_from_healpix
 from fg21sim.share import CONFIGS
 from fg21sim.sky import SkyPatch
 from fg21sim.utils import setup_logging
-from fg21sim.utils.fits import read_fits_healpix
+from fg21sim.utils.io import read_fits_healpix
 from fg21sim.utils.units import UnitConversions as AUC
 
 
diff --git a/bin/hpx2healpix b/bin/hpx2healpix
index b5de5e6..8fc8777 100755
--- a/bin/hpx2healpix
+++ b/bin/hpx2healpix
@@ -66,7 +66,7 @@ def main():
 
     logger.info("Importing modules + Numba JIT, waiting ...")
     from fg21sim.utils.healpix import hpx2healpix
-    from fg21sim.utils.fits import write_fits_healpix
+    from fg21sim.utils.io import write_fits_healpix
     hp_data, hp_header = hpx2healpix(args.infile,
                                      append_history=history,
                                      append_comment=comments)
diff --git a/bin/zea2healpix b/bin/zea2healpix
index 4e3242b..9f6f154 100755
--- a/bin/zea2healpix
+++ b/bin/zea2healpix
@@ -82,7 +82,7 @@ def main():
 
     logger.info("Importing modules + Numba JIT, waiting ...")
     from fg21sim.utils.reproject import zea2healpix
-    from fg21sim.utils.fits import write_fits_healpix
+    from fg21sim.utils.io import write_fits_healpix
     hp_data, hp_header, __ = zea2healpix(args.infile1, args.infile2,
                                          nside=args.nside,
                                          order=args.interp_order,
diff --git a/fg21sim/sky.py b/fg21sim/sky.py
index 2e5d4a8..eb9f824 100644
--- a/fg21sim/sky.py
+++ b/fg21sim/sky.py
@@ -20,7 +20,9 @@ from reproject import reproject_interp, reproject_to_healpix
 import healpy as hp
 
 from .utils.wcs import make_wcs
-from .utils.fits import read_fits_healpix, write_fits_healpix
+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
 
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)
diff --git a/fg21sim/utils/healpix.py b/fg21sim/utils/healpix.py
index 9db8d0d..9ec210b 100644
--- a/fg21sim/utils/healpix.py
+++ b/fg21sim/utils/healpix.py
@@ -33,7 +33,7 @@ import numba as nb
 import healpy as hp
 from astropy.io import fits
 
-from .fits import read_fits_healpix
+from .io import read_fits_healpix
 
 
 logger = logging.getLogger(__name__)
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)