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Extract_SNR.py
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Extract_SNR.py
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'''
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
SALT RSS Aperture Extraction (With Minimum Desired Single to Noise Ratio)
Extract regions (outward from the object's centre) for a FITS file
processed by the SALT RSS pipeline.
The target FITS file is typically a 2D flux spectrum of a galaxy.
The SALT RSS Data Reduction procedure is described in:
http://mips.as.arizona.edu/~khainline/salt_redux.html
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
'''
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Import Libraries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
import os # For bash commands
import numpy as np # For array handling
from pyraf import iraf # For IRAF commands
import astropy.io.fits as fits # For FITS file handling
from pathlib import Path # To extract filenames
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Load IRAF Libraries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
iraf.images()
iraf.images.imutil()
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Aperture Extraction
The following methods are quite similar,
with minor differences.
extract_1kpc(): Extract 0-1 kiloparsec regions from the centre.
extract_left(): Extract regions left (-) from the centre of the object,
such that these regions have a signal-to-noise ratio (SNR) above the desired
minimum.
extract_right(): Extract regions right (+) from the centre of the object,
such that these regions have a signal-to-noise ratio (SNR) above the desired
minimum.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
def extract_1kpc_left(path, file, centre, pix_per_kpc):
'''
:param path [String]: File path containing the galaxy's FITS file.
:param file [String]: The galaxy's FITS file.
:param centre [float]: Central pixel of the galaxy's FITS file.
:param pix_per_kpc [float]: Pixel per kiloparsec ratio for the galaxy.
:return:
'''
# Change to file path
os.chdir(path)
print('Changed to path: {}'.format(path))
# Set pixel ranges
pix_end = int(centre)
pix_start = pix_end - 1
# Set operands
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
# Set file names
res = 'result.fits'
temp = 'temp.fits'
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Extract Apertures
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
flag = False;
while flag is False:
# Set kpc
kpc = (((pix_start + pix_end) / 2.0) - centre) / pix_per_kpc
print('pix_start = {}'.format(pix_start))
print('pix_end = {}'.format(pix_end))
iraf.images.imutil.imarith(operand1=op1, op='+', operand2=op2, result=res, verbose='No', mode='ql')
if kpc > -0.5:
iraf.images.imutil.imcopy(input=res, output=temp)
iraf.images.imutil.imdelete(images=res)
pix_start = pix_start - 1
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[0]'.format(temp)
else:
out_file = '{}_-0.5kpcL.fits'.format(file)
iraf.images.imutil.imcopy(input=res, output=out_file)
iraf.images.imutil.imdelete(images=res)
# Update Header Information
iraf.imutil.hedit(images=out_file, fields='ymin_pixel', value=pix_start)
iraf.imutil.hedit(images=out_file, fields='ymax_pixel', value=pix_end)
pix_end = pix_start - 1
pix_start = pix_end - 1
flag = True
iraf.images.imutil.imdelete(images=temp)
break
return None
def extract_1kpc_right(path, file, centre, pix_per_kpc):
'''
:param path [String]: File path containing the galaxy's FITS file.
:param file [String]: The galaxy's FITS file.
:param centre [float]: Central pixel of the galaxy's FITS file.
:param pix_per_kpc [float]: Pixel per kiloparsec ratio for the galaxy.
:return:
'''
# Change to file path
os.chdir(path)
print('Changed to path: {}'.format(path))
# Set pixel ranges
pix_start = int(centre)
pix_end = int(centre + 1)
# Set operands
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
# Set file names
res = 'result.fits'
temp = 'temp.fits'
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Extract Apertures
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
flag = False;
while flag is False:
# Set kpc
kpc = (((pix_start + pix_end) / 2.0) - centre) / pix_per_kpc
print('pix_start = {}'.format(pix_start))
print('pix_end = {}'.format(pix_end))
iraf.images.imutil.imarith(operand1=op1, op='+', operand2=op2, result=res, verbose='No', mode='ql')
if kpc < 0.5:
iraf.images.imutil.imcopy(input = res, output = temp)
iraf.images.imutil.imdelete(images = res)
pix_end = pix_end + 1
op1 = '{}[0]'.format(temp)
op2 = '{}[*,{}]'.format(file, pix_end)
else:
out_file = '{}_0.5kpcR.fits'.format(file)
iraf.images.imutil.imcopy(input=res, output=out_file)
iraf.images.imutil.imdelete(images=res)
# Update Header Information
iraf.imutil.hedit(images=out_file, fields='ymin_pixel', value=pix_start)
iraf.imutil.hedit(images=out_file, fields='ymax_pixel', value=pix_end)
pix_start = pix_end + 1
pix_end = pix_start + 1
flag = True
iraf.images.imutil.imdelete(images=temp)
break
return None
def extract_left(path, file, desired_SNR, centre, pix_per_kpc):
'''
:param path [String]: File path containing the galaxy's FITS file.
:param file [String]: The galaxy's FITS file.
:param desired_SNR [float]: Desired *minimum* signal-to-noise ratio for aperture extraction.
:param centre [float]: Central pixel of the galaxy's FITS file.
:param pix_per_kpc [float]: Pixel per kiloparsec ratio for the galaxy.
:return:
'''
# Change to file path
os.chdir(path)
print('Changed to path: {}'.format(path))
# Set pixel ranges
pix_end = int(centre)
pix_start = pix_end - 1
# Set operands
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
# Set file names
res = 'result.fits'
temp = 'temp.fits'
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Extract Apertures
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
flag = False;
while flag is False:
# Set kpc
kpc = (((pix_start + pix_end) / 2.0) - centre) / pix_per_kpc
kpc = np.round(kpc, 2)
if pix_end - pix_start > 50:
print('Maximum aperture size of 50 exceeded.')
try:
iraf.images.imutil.imdelete(images=temp)
except:
pass
try:
iraf.images.imutil.imdelete(images=res)
except:
pass
flag = True;
break;
print('pix_start = {}'.format(pix_start))
print('pix_end = {}'.format(pix_end))
iraf.images.imutil.imarith(operand1=op1, op='+', operand2=op2, result=res, verbose='No', mode='ql')
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Open FITS File
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
hdu = fits.open(res)
galaxy = hdu[0].data
try:
if len(galaxy[0] > 1):
galaxy = galaxy[0]
except:
pass
print('galaxy = {}'.format(galaxy))
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Calculate Signal-To-Noise Ratio
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
signal = np.median(galaxy)
n = len(galaxy)
noise = 0.6052697 * np.median(np.abs(2.0 * galaxy[2:n - 2] - galaxy[0:n - 4] - galaxy[4:n]))
SNR = signal / noise
print('Singal-To-Noise Ratio = {}'.format(SNR))
# Delete aperture if Signal-To-Noise Ratio is too low
# Then further increase aperture size
# Else, keep FITS file and adjust starting pixel
if SNR < desired_SNR:
iraf.images.imutil.imcopy(input=res, output=temp)
iraf.images.imutil.imdelete(images=res)
pix_start = pix_start - 1
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[0]'.format(temp)
else:
out_file = '{}_{}kpcL.fits'.format(file, kpc)
iraf.images.imutil.imcopy(input=res, output=out_file)
iraf.images.imutil.imdelete(images=res)
# Update Header Information
iraf.imutil.hedit(images=out_file, fields='SNR', value=SNR)
iraf.imutil.hedit(images=out_file, fields='ymin_pixel', value=pix_start)
iraf.imutil.hedit(images=out_file, fields='ymax_pixel', value=pix_end)
pix_end = pix_start - 1
pix_start = pix_end - 1
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
return None
def extract_right(path, file, desired_SNR, centre, pix_per_kpc):
'''
:param path [String]: File path containing the galaxy's FITS file.
:param file [String]: The galaxy's FITS file.
:param desired_SNR [float]: Desired *minimum* signal-to-noise ratio for aperture extraction.
:param centre [float]: Central pixel of the galaxy's FITS file.
:param pix_per_kpc [float]: Pixel per kiloparsec ratio for the galaxy.
:return:
'''
# Change to file path
os.chdir(path)
print('Changed to path: {}'.format(path))
# Set pixel ranges
pix_start = int(centre)
pix_end = int(centre + 1)
# Set operands
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
# Set file names
res = 'result.fits'
temp = 'temp.fits'
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Extract Apertures
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
flag = False;
while flag is False:
# Set kpc
kpc = (((pix_start + pix_end) / 2.0) - centre) / pix_per_kpc
kpc = np.round(kpc, 2)
if pix_end - pix_start > 50:
print('Maximum aperture size of 50 exceeded.')
try:
iraf.images.imutil.imdelete(images = temp)
except:
pass
try:
iraf.images.imutil.imdelete(images = res)
except:
pass
flag = True;
break;
print('pix_start = {}'.format(pix_start))
print('pix_end = {}'.format(pix_end))
iraf.images.imutil.imarith(operand1=op1, op='+', operand2=op2, result=res, verbose='No', mode='ql')
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Open FITS File
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
hdu = fits.open(res)
galaxy = hdu[0].data
try:
if len(galaxy[0] > 1):
galaxy = galaxy[0]
except:
pass
print('galaxy = {}'.format(galaxy))
'''
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Calculate Signal-To-Noise Ratio
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
'''
signal = np.median(galaxy)
n = len(galaxy)
noise = 0.6052697 * np.median(np.abs(2.0 * galaxy[2:n - 2] - galaxy[0:n - 4] - galaxy[4:n]))
SNR = signal / noise
print('Singal-To-Noise Ratio = {}'.format(SNR))
# Delete aperture if Signal-To-Noise Ratio is too low
# Then further increase aperture size
# Else, keep FITS file and adjust starting pixel
if SNR < desired_SNR:
iraf.images.imutil.imcopy(input = res, output = temp)
iraf.images.imutil.imdelete(images = res)
pix_end = pix_end + 1
op1 = '{}[0]'.format(temp)
op2 = '{}[*,{}]'.format(file, pix_end)
else:
out_file = '{}_{}kpcR.fits'.format(file, kpc)
iraf.images.imutil.imcopy(input=res, output=out_file)
iraf.images.imutil.imdelete(images=res)
# Update Header Information
iraf.imutil.hedit(images=out_file, fields='SNR', value=SNR)
iraf.imutil.hedit(images=out_file, fields='ymin_pixel', value=pix_start)
iraf.imutil.hedit(images=out_file, fields='ymax_pixel', value=pix_end)
pix_start = pix_end + 1
pix_end = pix_start + 1
op1 = '{}[*,{}]'.format(file, pix_start)
op2 = '{}[*,{}]'.format(file, pix_end)
return None
if __name__ == '__main__':
# Set extraction mode
mode = str(raw_input("Please enter extraction mode. Enter 'B' for Both, 'L' for Left and 'R' for Right: "))
# Set filepath of data
path = raw_input('Please enter file path of the galaxy\'s FITS file: ')
# Set filename
file = raw_input('Please enter file name of the galaxy\'s FITS file (with complete extension): ')
# Set desired signal-to-noise ratio
desired_SNR = float(input('Please enter the desired Signal-To-Noise Ratio: '))
# Set centre pixel number
centre = float(input('Please enter the center pixel of the galaxy: '))
# Set pixel per kiloparsec ratio
pix_per_kpc = float(input('Please enter the pixel per kpc value for this galaxy: '))
# Extract regions
if mode == 'B':
extract_left(path, file, desired_SNR, centre, pix_per_kpc)
extract_1kpc_left(path, file, centre, pix_per_kpc)
extract_right(path, file, desired_SNR, centre, pix_per_kpc)
extract_1kpc_right(path, file, centre, pix_per_kpc)
elif mode == 'L':
extract_left(path, file, desired_SNR, centre, pix_per_kpc)
extract_1kpc_left(path, file, centre, pix_per_kpc)
elif mode == 'R':
extract_right(path, file, desired_SNR, centre, pix_per_kpc)
extract_1kpc_right(path, file, centre, pix_per_kpc)