Image Subtraction Module¶

# Import the relevant packages

import numpy as np
from astropy.io import fits #FITS files handling
import os  #Call commands from outside Python
from astropy.io import ascii  #Read/write ascii files

# Useful to smooth the images with a Gaussian kernel before the subtraction
from scipy.signal import convolve as scipy_convolve
from astropy.convolution import convolve 
from astropy.convolution import Gaussian2DKernel
from astropy.stats import sigma_clipped_stats

from astropy.coordinates import SkyCoord
from astropy import units as u

# Background subtraction
from astropy.stats import SigmaClip
from photutils import Background2D, MedianBackground
from photutils import make_source_mask

# Plot
import matplotlib.pyplot as plt

# Running external programs
import subprocess
import shutil

def test_dependency(dep, alternate_name=None):
    """
    Test external dependency by trying to run it as a subprocess
    """
    try:
        subprocess.check_output(dep, stderr=subprocess.PIPE, shell=True)
        print("%s is installed properly as %s. OK" % (dep, dep))
        return 1
    except subprocess.CalledProcessError:
        try:
            subprocess.check_output(alternate_name, stderr=subprocess.PIPE, shell=True)
            print("%s is installed properly as %s. OK" % (dep, alternate_name))
            return 1
        except subprocess.CalledProcessError:
            print("===%s/%s IS NOT YET INSTALLED PROPERLY===" % (dep, alternate_name))
            return 0
    
dependencies = [('sextractor', 'sex'), ('SWarp', 'swarp'), ('psfex', 'PSFEx'), ('ds9', 'DS9')]
i = 0
for dep_name1, dep_name2 in dependencies:
    i += test_dependency(dep_name1, dep_name2)
print("%i out of %i external dependencies installed properly.\n" % (i, len(dependencies)))
if i != len(dependencies):
    print("Please correctly install these programs before continuing by following the instructions in README.md.")
else:
    print("You are ready to continue.")   

# remove temporary fits files in current working directory
[os.remove(f) for f in os.listdir() if f.endswith('.fits')]

# Set directory structure
cwd = os.getcwd()
proc_dir = os.path.join(cwd, 'processed')
data_dir = os.path.join(cwd, 'data')
out_dir = os.path.join(proc_dir, 'out')
if os.path.isdir(proc_dir): 
    shutil.rmtree(proc_dir)
os.mkdir(proc_dir)

for f in os.listdir(data_dir):
    shutil.copy2(os.path.join(data_dir, f), os.path.join(proc_dir, f))
os.chdir(proc_dir)