Source code for tw_source_finder.get_morphology_images

# script to generate dilated images

import math
import os
import os.path
import sys
import timeit
from optparse import OptionParser

import numpy
from astropy.coordinates import SkyCoord

from tw_source_finder.make_morphology_mask import make_mask
from tw_source_finder.read_input_table import process_input_file


def process_images(
    filename,
    filter_size,
    filter_type,
    offset_flux,
    use_conv,
    double_erode,
    do_batch,
):
    print("processing file ", filename)
    text = open(filename, "r").readlines()
    info = text[0].split()
    print("opening info ", info)
    freq = info[1]
    print("specified freq", freq)

    # not all these parameters are used here
    freq, names, ra_deg, dec_deg = process_input_file(filename, True)
    num_proc = len(ra_deg)
    for i in range(num_proc):
        position = SkyCoord(ra_deg[i], dec_deg[i], unit="deg", frame="icrs")
        print("i, position", i, position)
        ra_dec = position.to_string("hmsdms")
        print("input ra_dec ", ra_dec)
        blank = " "
        underscore = "_"
        out_ra_dec = ra_dec.replace(blank, underscore)
        print("output ra_dec ", out_ra_dec)
        if use_conv:
            field_name = names[i] + "_conv"
        else:
            field_name = names[i]
        print("i, field_name_i ", i, field_name)
        parameter_list = []
        parameter_list.append(" ")
        parameter_list.append(field_name)
        parameter_list.append(offset_flux)
        parameter_list.append(filter_size)
        parameter_list.append(filter_type)
        parameter_list.append(do_batch)
        parameter_list.append(double_erode)
        make_mask(parameter_list)


def main(argv):
    parser = OptionParser(usage="%prog [options] ")
    parser.add_option(
        "-f",
        "--file",
        dest="filename",
        help="Filename with radio source names, positions, redshit etc (default = None)",
        default=None,
    )
    parser.add_option(
        "-s",
        "--filter_size",
        dest="filter_size",
        help="Size of structure element (default = 0)",
        default=0,
    )
    parser.add_option(
        "-t",
        "--filter_type",
        dest="filter_type",
        help="Type of structure element D(isk) or R(ectangle) (default = D)",
        default="D",
    )
    parser.add_option(
        "--th",
        "--threshold",
        dest="threshold",
        help="Threshhold value for mask, in units of noise (default = 6)",
        default=6,
    )
    parser.add_option(
        "--use_conv",
        dest="use_conv",
        help="Select a convolved image (default = F)",
        default=False,
    )
    parser.add_option(
        "--use_batch",
        dest="use_batch",
        help="Run in batch mode (no interactive response) (default = F)",
        default=False,
    )
    parser.add_option(
        "--use_double_e",
        dest="use_double",
        help="Use second erode (no interactive response) (default = T)",
        default=True,
    )
    (options, args) = parser.parse_args()
    print("options", options)
    filename = options.filename
    filter_size = int(options.filter_size)
    filter_type = options.filter_type
    offset_flux = float(options.threshold)
    use_conv = options.use_conv
    if use_conv != False:
        use_conv = True
    use_batch = options.use_batch
    if use_batch != False:
        use_Batch = True
    use_double_erode = options.use_double
    if use_double_erode != True:
        use_double_erode = False

    start_time = timeit.default_timer()
    process_images(
        filename,
        filter_size,
        filter_type,
        offset_flux,
        use_conv,
        use_double_erode,
        use_batch,
    )
    elapsed = timeit.default_timer() - start_time
    print("Run Time:", elapsed, "seconds")


# =============================
#
# e.g. example: run as 'get_morphology_images.py -f abellsouth.csv -t D --th 6'
#
if __name__ == "__main__":
    main(sys.argv)