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toolbox.py
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toolbox.py
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"""
Toolbox for the Photometry Pipeline
2016-03-09, [email protected]
"""
from __future__ import print_function
from __future__ import division
# Photometry Pipeline
# Copyright (C) 2016-2018 Michael Mommert, [email protected]
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see
# <http://www.gnu.org/licenses/>.
import sys
try:
from past.utils import old_div
except ImportError:
print('Module future not found. Please install with: pip install future')
sys.exit()
import math
import numpy as np
# only import if Python3 is used
if sys.version_info > (3, 0):
from future import standard_library
standard_library.install_aliases()
from builtins import range
# TIME AND DATE
def jd_to_gregorian(jd, is_mjd=False):
""" convert a julian date into a gregorian data """
if is_mjd:
mjd = jd
else:
mjd = jd - 2400000.5
MJD0 = 2400000.5 # 1858 November 17, 00:00:00 hours
modf = math.modf
a = int(mjd+MJD0+0.5)
b = int(old_div((a-1867216.25), 36524.25))
c = a + b - int(modf(old_div(b, 4))[1]) + 1525
d = int(old_div((c-122.1), 365.25))
e = 365*d + int(modf(old_div(d, 4))[1])
f = int(old_div((c-e), 30.6001))
day = int(c - e - int(30.6001*f))
month = int(f - 1 - 12*int(modf(old_div(f, 14))[1]))
year = int(d - 4715 - int(modf(old_div((7+month), 10))[1]))
fracofday = mjd - math.floor(mjd)
hour = int(math.floor(fracofday * 24.0))
minute = int(math.floor(((fracofday*24.0)-hour)*60.))
second = int(math.floor(((((fracofday*24.0)-hour)*60.)-minute)*60.))
return (year, month, day, hour, minute, second)
def dateobs_to_jd(date):
"""convert a string of the format YYYY-MM-DDTHH:MM:SS into a julian
date; 'T' is used as a separator between date and time
"""
if 'T' in date:
date = date.split('T')
if ' ' in date:
date = date.split(' ')
time = date[1].split(':')
date = date[0].split('-')
# check if date is yyyy-mm-dd or dd-mm-yyyy
if len(date[2]) == 4 and len(date[0]) < 3:
date = date[::-1]
a = (14 - float(date[1]))//12
y = float(date[0]) + 4800 - a
m = float(date[1]) + 12*a - 3
return float(date[2]) + ((153*m + 2)//5) + 365*y + y//4 - y//100 \
+ y//400 - 32045.5 + old_div(float(time[0]), 24.) + old_div(float(time[1]), 1440.) \
+ old_div(float(time[2]), 86400.)
def jd_to_fractionalyear(jd, is_mjd=False):
""" convert a julian date into a fractional year, e.g., 2000.123456 """
if is_mjd:
jd += 2400000.5
date = jd_to_gregorian(jd)
year = date[0]+old_div(date[1], 12.)+old_div(date[2], 365.) + \
old_div(date[3], 8760.)+old_div(date[4], 525600.)
return year
def fractionalyear_to_jd(date):
""" convert a fractional year into a julian date """
jd_jan1 = dateobs_to_jd('%4d-01-01T00:00:00' % math.floor(date))
return jd_jan1 + 365*(date-math.floor(date))
# ASTROMATIC tools
def read_scamp_output():
""" routine to read in the 'scamp.xml' file """
raw = open('scamp_output.xml', 'r').readlines()
headers, hdr_idx, data = {}, 0, []
read_this, idx = False, 0
while idx < len(raw):
# read header
if read_this and raw[idx].find('<FIELD name=') > -1:
headers[raw[idx][raw[idx].find('<FIELD name')+13:
raw[idx].find('" datatype')]] = hdr_idx
hdr_idx += 1
# read data
# new data line
if read_this and raw[idx].find('<TR>') > -1:
this_data = []
# flush data line
if read_this and raw[idx].find('</TR>') > -1:
data.append(np.hstack(this_data))
# actually read data line
if read_this and raw[idx].find('<TD>') > -1:
line = raw[idx].replace('</TD>', '<TD>').split('<TD>')
for item in line:
if len(item.strip()) > 0 and item.find('\n') == -1:
this_data.append(item)
# control reading
# activate reading
if not read_this and \
raw[idx].find('<TABLE ID="Fields" name="Fields">') > -1:
read_this = True
# deactivate reading
if read_this and raw[idx].find('</TABLEDATA></DATA>') > -1:
read_this = False
idx += 1
# check if data rows have same length as header
for i in range(len(data)):
if len(headers) != len(data[i]):
raise (RuntimeError,
('data and header lists from SCAMP output file have '
'different lengths for image %s; do the FITS files have the '
'OBJECT keyword populated?') % data[i][headers['Catalog_Name']])
return (headers, data)
# PP tools
def get_binning(header, obsparam):
""" derive binning from image header
use obsparam['binning'] keywords, unless both keywords are set to 1
return: tuple (binning_x, binning_y)"""
if (isinstance(obsparam['binning'][0], int) and
isinstance(obsparam['binning'][1], int)):
binning_x = obsparam['binning'][0]
binning_y = obsparam['binning'][1]
elif '#' in obsparam['binning'][0]:
if '#blank' in obsparam['binning'][0]:
binning_x = float(header[obsparam['binning'][0].
split('#')[0]].split()[0])
binning_y = float(header[obsparam['binning'][1].
split('#')[0]].split()[1])
elif '#x' in obsparam['binning'][0]:
binning_x = float(header[obsparam['binning'][0].
split('#')[0]].split('x')[0])
binning_y = float(header[obsparam['binning'][1].
split('#')[0]].split('x')[1])
elif '#_' in obsparam['binning'][0]:
binning_x = float(header[obsparam['binning'][0].
split('#')[0]].split('_')[0])
binning_y = float(header[obsparam['binning'][1].
split('#')[0]].split('_')[1])
elif '#CH#' in obsparam['binning'][0]:
# only for RATIR
channel = header['INSTRUME'].strip()[1]
binning_x = float(header[obsparam['binning'][0].
replace('#CH#', channel)])
binning_y = float(header[obsparam['binning'][1].
replace('#CH#', channel)])
else:
binning_x = header[obsparam['binning'][0]]
binning_y = header[obsparam['binning'][1]]
return (binning_x, binning_y)
def skycenter(catalogs, ra_key='ra_deg', dec_key='dec_deg'):
"""derive center position and radius from catalogs"""
from astropy.coordinates import SkyCoord
from astropy import units as u
# using percentiles instead of min/max to get better handle
# on outliers
min_ra = min([np.percentile(cat[ra_key], 1)
for cat in catalogs])
max_ra = max([np.percentile(cat[ra_key], 99)
for cat in catalogs])
min_dec = min([np.percentile(cat[dec_key], 1)
for cat in catalogs])
max_dec = max([np.percentile(cat[dec_key], 99)
for cat in catalogs])
ra, dec = (np.rad2deg(np.angle(np.exp(1j*np.deg2rad(min_ra)) +
np.exp(1j*np.deg2rad(max_ra)))),
np.rad2deg(np.angle(np.exp(1j*np.deg2rad(min_dec)) +
np.exp(1j*np.deg2rad(max_dec)))))
lower_left = SkyCoord(ra=min_ra, dec=min_dec, frame='icrs', unit='deg')
upper_right = SkyCoord(ra=max_ra, dec=max_dec, frame='icrs', unit='deg')
rad = lower_left.separation(upper_right).deg/2
return ra, dec, rad
# miscellaneous tools
def if_val_in_dict(target_val, dic):
"""check if a value appears in a nested dict structure"""
result = False
for key, val in dic.items():
if type(val) is dict:
if if_val_in_dict(target_val, val):
result = True
elif type(val) is list:
if target_val in val:
result = True
else:
if target_val == val:
result = True
return result