make_catalogs.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Two simple functions to convert some of the sextractor output catalogs
into more readable file formats

Created on Tue Feb  8 14:42:53 2022

Copyright (c) 2022 Maurizio D'Addona <mauritiusdadd@gmail.com>

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.
"""

import os
import sys
from astropy.table import Table
from astropy.io import ascii


def makeCatalogsFromLDAC(input_fit, out_formats=['ascii', 'fits'], hdu=2):
    base_inp_dir = os.path.dirname(input_fit)
    base_inp_name = os.path.basename(input_fit)
    base_inp_name = os.path.splitext(base_inp_name)[0]

    orig_table = Table.read(input_fit, format='fits', hdu=hdu)

    # Transform columns containing vectors in multiple columns
    new_table = Table()
    for colname in orig_table.columns:
        col = orig_table[colname]
        # If there is a colum that contains a vector
        if len(col.shape) > 1:
            # then split the column in multiple columns
            for i in range(col.shape[1]):
                sub_col = col[..., i]
                sub_col.name = f"{col.name}_{i+1}"
                new_table.add_column(sub_col)
        else:
            # otherwise just use the column as it is
            new_table.add_column(col)

    for fmt in out_formats:
        out_name = base_inp_name.replace('_ldac', '') + f"_cat.{fmt}"
        out_name = os.path.join(base_inp_dir, out_name)
        new_table.write(out_name, format=fmt, overwrite=True)


def makeCatalogsFromSexASCII(input_ascii, out_formats=['ascii', 'fits'],
                             comment_header='#'):
    base_inp_dir = os.path.dirname(input_ascii)
    base_inp_name = os.path.basename(input_ascii)
    base_inp_name = os.path.splitext(base_inp_name)[0]

    with open(input_ascii, 'r') as f:
        ascii_lines = f.readlines()

    myt = ascii.read(ascii_lines)

    for fmt in out_formats:
        out_name = base_inp_name.replace('_ldac', '') + f"_cat.{fmt}"
        out_name = os.path.join(base_inp_dir, out_name)
        myt.write(out_name, format=fmt, overwrite=True)


if __name__ == '__main__':
    for inp_cat in sys.argv[1:]:
        print(f"reading '{inp_cat}'")
        try:
            makeCatalogsFromLDAC(inp_cat)
        except Exception:
            makeCatalogsFromSexASCII(inp_cat)