def main():
for workdir in curr_work_dirs:
work_path = 'observations/' + workdir
if not os.path.exists(work_path):
os.makedirs(work_path)
if not os.path.exists(work_path+'/database'):
os.makedirs(work_path+'/database')
if not os.path.exists(work_path+'/cosmics'):
os.makedirs(work_path+'/cosmics')
# don't ask, we just need this
os.system("touch %s/blank.txt" % work_path)
# enter working folder, all the way to the end
iraf.cd(work_path)
# maybe useful, maybe not, not sure
iraf.prcacheOff()
# main steps, should work individually
#check_spectra(workdir, '.ec.vh')
create_masterbias(workdir)
create_masterflat(workdir)
#do_ref_apall(workdir)
#normalize_masterflat(workdir)
clean_folder_write_header(workdir)
bias_correct(workdir)
#flat_correct(workdir)
#remove_cosmics(workdir)
do_apall_for_real(workdir)
apply_apall(workdir)
wavelength_solution(workdir)
#check_wav_solution(workdir)
apply_wav_solution(workdir)
vhelio_correct(workdir)
#check_spectra(workdir, '.ec.vh')
combine_normalize_images(workdir, combine=False)
get_RV(workdir, multi_ref=False, multi_sample=False)
# export_spectrum_to_txt(workdir, suffix='.ec_wvl', export_cal=True)
# export_spectrum_to_txt(workdir, suffix='_vh_norm')
#check_spectra(workdir)
#new_flatfield_lens_problems(workdir)
# back to mother folder
iraf.cd('../')
iraf.cd('../')
def init_iraf():
"""Initializes the pyraf environment. """
# The display of graphics is not used, so skips Pyraf graphics
# initialization and run in terminal-only mode to avoid warning messages.
os.environ['PYRAF_NO_DISPLAY'] = '1'
# Set PyRAF process caching off to avoid errors if spawning multiple
# processes.
iraf.prcacheOff()
# Load iraf packages and does not show any output of the tasks.
iraf.digiphot(_doprint = 0)
iraf.apphot(_doprint = 0)
iraf.images(_doprint = 0)
# Set the iraf.phot routine to scripting mode.
iraf.phot.interactive = "no"
iraf.phot.verify = "no"
def init_iraf():
"""Initializes the pyraf environment. """
# The display of graphics is not used, so skips Pyraf graphics
# initialization and run in terminal-only mode to avoid warning messages.
os.environ['PYRAF_NO_DISPLAY'] = '1'
# Set PyRAF process caching off to avoid errors if spawning multiple
# processes.
iraf.prcacheOff()
# Load iraf packages and does not show any output of the tasks.
iraf.digiphot(_doprint=0)
iraf.apphot(_doprint=0)
iraf.images(_doprint=0)
# Set the iraf.phot routine to scripting mode.
iraf.phot.interactive = "no"
iraf.phot.verify = "no"
def setiraf(self):
"""
Set IRAF global parameters and load DAOPHOT package for aperture
photometry.
Parameters
----------
Returns
-------
None
"""
iraf.prcacheOff()
iraf.set(writepars=0)
# Load IRAF packages
iraf.noao(_doprint = 0)
iraf.noao.digiphot(_doprint = 0)
iraf.noao.digiphot.daophot(_doprint = 0)
return
def setiraf(self):
"""
Set IRAF global parameters and load DAOPHOT package for aperture
photometry.
Parameters
----------
Returns
-------
None
"""
iraf.prcacheOff()
iraf.set(writepars=0)
# Load IRAF packages
iraf.noao(_doprint = 0)
iraf.noao.digiphot(_doprint = 0)
iraf.noao.digiphot.daophot(_doprint = 0)
return
#!/scisoft/bin/python
'''
pyraf equivalents of speedup.cl, processccd.cl, combflat.cl, CCDsort.cl, and IRsort.cl
these functions mirror their iraf counterparts pretty closesly, and function in the same way
the pyraf wrapper prevents caching problems and lets us easily change directories, execute functions etc
some projects have special places to pick up data, like the blazar group
the photometric standards, xrb group, and bethany. specific checks are made for those data
'''
import pyfits, os, fnmatch, glob, subprocess
from pyraf import iraf
iraf.prcacheOff()
def cpCals(date, fwheel=['sky', 'V', 'R', 'I'], outdir='.'):
'''
copy the calibration frames from the date specified by "date" to the directory specefied by "outdir"
input:
date: YYYYMMDD of the date directory you want to get data from. program will look under
/data/yalo180/yalo/SMARTS13m/date/ccd/processed/ for calibrations
fwheel: python list specifying the filters of the calibrations you want to copy. by default includes all of them
outdir: string specifying the path you want to copy the calibrations to. by default set to "."
output:
None
'''
date = str(date)
if len(glob.glob('/data/yalo180/yalo/SMARTS13m/' + date)) == 1:
for f in fwheel:
try:
subprocess.check_output('cp -v /data/yalo180/yalo/SMARTS13m/' +
from astropy import wcs
# Importing pyraf -- note that this requires IRAF to be installed
# and the "iraf" and "IRAFARCH" environment variables to be set
with warnings.catch_warnings():
# Ignore the ImportWarning we often get when importing pyraf, because pyraf
# likes to create working dirs with its name in the local dir.
warnings.filterwarnings("ignore", message="(.*)Not importing dir(.*)")
# Disable pyraf graphics:
from stsci.tools import capable
capable.OF_GRAPHICS = False
from pyraf import iraf
from iraf import noao, digiphot, daophot
# Turn cache off to enable multiprocessing to be used;
# cf. http://www.stsci.edu/institute/software_hardware/pyraf/pyraf_faq#3.5
iraf.prcacheOff()
iraf.set(writepars=0)
from .utils import timed
class DaophotError(Exception):
"""Raised if Daophot failed to perform an operation."""
pass
class Daophot(object):
"""DAOPHOT wrapper class.
The constructor of this class expects to receive
ALL the non-default configuration parameters because IRAF is very stateful.
defaults. Set shift=0 in calls to ecreidenfity.
2014-12-17 14:17 IJMC: Added new troubleshooting & alternative
flat-normalization approaches, since PyRAF's
apnormalize continues to give me trouble.
2016-10-15 02:09 IJMC: Trying it for ARIES. This script has been
around for a little while!
2016-10-18 13:50 IJMC: Now apply ARIES quad-detector crosstalk correction
2017-10-11 16:41 IJMC: Handing this off to Nicholas Mehrle. Good luck!
2017-10-25 ????? NM : Moved version control to Git
"""
import os, sys, shutil
from pyraf import iraf as ir
ir.prcacheOff()
# Might be necessary for some iraf tasks with multiprocessing, unsure
ir.set(writepars=0)
from scipy import interpolate, isnan, isinf
try:
from astropy.io import fits as pyfits
except:
import pyfits
import lib.nsdata as ns
import lib.spec as spec
import numpy as ny
from pylab import find
import pdb