def run_fxcor(lstl, lstu, tpl, tpu, chip):
if chip == 'l':
templ = tpl
lst = lstl
else:
templ = tpu
lst = lstu
lista = '@' + lst
chip_par = 'rvout_' + chip
iraf.noao()
iraf.rv()
iraf.fxcor(lista,
templ,
output=chip_par,
verbose='txtonly',
interac='no',
observa='paranal')
rv = []
rvlist = open(chip_par + '.txt', "r")
for cols in (raw.strip().split() for raw in rvlist):
vobs_index = len(cols) - 3
if cols[0][0] != '#':
rv.append(float(cols[vobs_index]))
rvlist.close()
return rv
def ImportPackages():
iraf.noao(_doprint=0)
iraf.rv(_doprint=0)
iraf.imred(_doprint=0)
iraf.kpnoslit(_doprint=0)
iraf.ccdred(_doprint=0)
iraf.astutil(_doprint=0)
iraf.keywpars.setParam('ra','CAT-RA')
iraf.keywpars.setParam('dec','CAT-DEC')
iraf.keywpars.setParam('ut','UT')
iraf.keywpars.setParam('utmiddl','UT-M_E')
iraf.keywpars.setParam('exptime','EXPTIME')
iraf.keywpars.setParam('epoch','CAT-EPOC')
iraf.keywpars.setParam('date_ob','DATE-OBS')
iraf.keywpars.setParam('hjd','HJD')
iraf.keywpars.setParam('mjd_obs','MJD-OBS')
iraf.keywpars.setParam('vobs','VOBS')
iraf.keywpars.setParam('vrel','VREL')
iraf.keywpars.setParam('vhelio','VHELIO')
iraf.keywpars.setParam('vlsr','VLSR')
iraf.keywpars.setParam('vsun','VSUN')
iraf.keywpars.setParam('mode','ql')
iraf.fxcor.setParam('continu','both')
iraf.fxcor.setParam('filter','none')
iraf.fxcor.setParam('rebin','smallest')
iraf.fxcor.setParam('pixcorr','no')
iraf.fxcor.setParam('apodize','0.2')
iraf.fxcor.setParam('function','gaussian')
iraf.fxcor.setParam('width','INDEF')
iraf.fxcor.setParam('height','0.')
iraf.fxcor.setParam('peak','no')
iraf.fxcor.setParam('minwidt','3.')
iraf.fxcor.setParam('maxwidt','21.')
iraf.fxcor.setParam('weights','1.')
iraf.fxcor.setParam('backgro','0.')
iraf.fxcor.setParam('window','INDEF')
iraf.fxcor.setParam('wincent','INDEF')
iraf.fxcor.setParam('verbose','long')
iraf.fxcor.setParam('imupdat','no')
iraf.fxcor.setParam('graphic','stdgraph')
iraf.fxcor.setParam('interac','yes')
iraf.fxcor.setParam('autowri','yes')
iraf.fxcor.setParam('autodra','yes')
iraf.fxcor.setParam('ccftype','image')
iraf.fxcor.setParam('observa','lapalma')
iraf.fxcor.setParam('mode','ql')
return 0
def fxcor(spec, task, template_spec, spec_list_file, fxcor_output_file, fxcor_range="4173-5447", interactive='no'):
"""
Run fxcor on the binned spectra to determine the relative velocity (with respect to the template spectra)
INPUT: BIN_SCI, FXCOR_TEMPLATE
OUTPUT: FXCOR_BIN_LIST, FXCOR_FILE(s)
Note: make sure you select the parameters for your desired use. Refer to the IRAF rv package help for description
of what each parameter is/does
"""
if os.path.exists(fxcor_output_file + '.txt'):
print('File {} already exists'.format(fxcor_output_file + '.txt'))
return
assert task == "abs" or task == "ems", "'task' is neight 'ab' or 'ems'"
spec_list = []
for i in range(len(glob.glob(spec.format('*')))):
spec_list.append(spec.format(i))
assert len(spec_list) > 0, 'Input files {} do not exist'.format(spec.format('*'))
np.array(spec_list).tofile(spec_list_file, sep='\n')
from pyraf import iraf
iraf.noao()
iraf.rv()
if task == 'ems':
iraf.fxcor('@{}'.format(spec_list_file), spec.format(template_spec), output=fxcor_output_file, continuum="both",
interactive=interactive, order=1, high_rej=2, low_rej=2, osample=fxcor_range, rsample=fxcor_range,
rebin="smallest", imupdate="no", pixcorr="no", filter="both", f_type="welch", cuton=20, cutoff=1000,
fullon=30, fulloff=800, ra="RA", dec="DEC", ut="UTSTART", epoch="EQUINOX", verbose="txtonly")
elif task == 'abs':
# Run interactively to make sure not fitting noise features, adapet osample/rsample to avoid such noise
iraf.fxcor('@{}'.format(spec_list_file), spec.format(template_spec), output=fxcor_output_file, continuum="both",
interactive=interactive, order=1, high_rej=2, low_rej=2, osample=fxcor_range, rsample=fxcor_range,
rebin="smallest", imupdate="no", pixcorr="no", filter="both", f_type="welch", cuton=20, cutoff=800,
fullon=30, fulloff=800, ra="RA", dec="DEC", ut="UTSTART", epoch="EQUINOX", verbose="txtonly")
assert os.path.exists(fxcor_output_file + '.txt'), 'Error in iraf.fxcor: File {} was not created'.format(
fxcor_output_file + '.txt')
def run_fxcor(st_names, templ, setup):
arq = open(setup + '/' + 'speclist', 'w')
for i in range(len(st_names)):
arq.write(st_names[i] + '.fits\n')
arq.close()
lista = '@' + setup + '/' + 'speclist'
clean_cr(lista)
outname = setup + '/' + 'rvout_' + setup
iraf.noao()
iraf.rv()
iraf.fxcor(lista,
templ,
output=outname,
verbose='txtonly',
interac='no',
observa='paranal')
rv = []
rvlist = open(outname + '.txt', "r")
for cols in (raw.strip().split() for raw in rvlist):
vobs_index = len(cols) - 3
if cols[0][0] != '#':
rv.append(float(cols[vobs_index]))
rvlist.close()
return rv
def ImportPackages():
iraf.noao(_doprint=0)
iraf.rv(_doprint=0)
iraf.keywpars.setParam("ra", "CAT-RA")
iraf.keywpars.setParam("dec", "CAT-DEC")
# must use UT as UT mid exposure for RV correct or it
# messes up the HJD values by a lot
iraf.keywpars.setParam("ut", "UT-M_E")
iraf.keywpars.setParam("utmiddl", "")
iraf.keywpars.setParam("exptime", "EXPTIME")
iraf.keywpars.setParam("epoch", "CAT-EPOC")
iraf.keywpars.setParam("date_ob", "DATE-OBS")
iraf.keywpars.setParam("hjd", "HJD")
iraf.keywpars.setParam("mjd_obs", "MJD-OBS")
iraf.keywpars.setParam("vobs", "VOBS")
iraf.keywpars.setParam("vrel", "VREL")
iraf.keywpars.setParam("vhelio", "VHELIO")
iraf.keywpars.setParam("vlsr", "VLSR")
iraf.keywpars.setParam("vsun", "VSUN")
iraf.keywpars.setParam("mode", "ql")
iraf.rvcorrect.setParam("imupdat", "yes")
iraf.rvcorrect.setParam("observa", "lapalma")
return 0
import glob import pyfits from pyraf import iraf import shutil import numpy as np import matplotlib.pyplot as plt from datetime import date import operator import time import traceback from lmfit import minimize, Parameters, report_fit #import cosmics iraf.noao(_doprint=0,Stdout="/dev/null") iraf.rv(_doprint=0,Stdout="/dev/null") iraf.imred(_doprint=0,Stdout="/dev/null") iraf.ccdred(_doprint=0,Stdout="/dev/null") iraf.images(_doprint=0,Stdout="/dev/null") iraf.immatch(_doprint=0,Stdout="/dev/null") iraf.onedspec(_doprint=0,Stdout="/dev/null") iraf.twodspec(_doprint=0,Stdout="/dev/null") iraf.apextract(_doprint=0,Stdout="/dev/null") iraf.imutil(_doprint=0,Stdout="/dev/null") iraf.echelle(_doprint=0,Stdout="/dev/null") iraf.astutil(_doprint=0,Stdout="/dev/null") iraf.apextract.dispaxi=1 iraf.echelle.dispaxi=1 #fixes a bug with latest versions of iraf iraf.ccdred.instrum='blank.txt'
Created on 25/03/16
@author: Carlos Eduardo Barbosa
Using pyraf to calculate VHELIO correction
"""
import os
import pyfits as pf
from pyraf import iraf
from config import *
iraf.rv(_doprint=0)
if __name__ == "__main__":
os.chdir(data_dir)
fits = sorted([x for x in os.listdir(".") if x.endswith(".fits")])
table = "VHELIO"
for img in fits:
h = pf.getheader(img)
print img,
if "VHELIO" not in h.keys():
print
continue
# try:
# iraf.hedit (images=img, fields="EPOCH", value=2000., add=True,
# delete=False, verify=False, show=False,
# update=True)
from astropy.io import fits
import numpy as np
from astropy.io import ascii
from astroplan import Observer
import astropy.coordinates
from pytz import timezone
from astropy.time import Time
from astropy import units as u
from pyraf import iraf
from astropy.table import Table
import time
import pandas as pd
iraf.noao()
iraf.rv()
iraf.oned()
LaSilla=Observer.at_site("lasilla", timezone="America/Santiago")
def info_s1d(s1d):
with fits.open(s1d) as image:
t_MJD=Time(image[0].header['MJD-OBS'], format='mjd')
info = pd.DataFrame({"NAME_S1D":[s1d[s1d.find('untar/')+6:len(s1d)]],
"MJD":[image[0].header['MJD-OBS']],
"EXPTIME":[image[0].header['EXPTIME']],
"RA":[image[0].header['RA']],
"DEC":[image[0].header['DEC']],
"RADVEL":[image[0].header['HIERARCH ESO TEL TARG RADVEL']],
"NAME":[image[0].header['HIERARCH ESO OBS TARG NAME']],
"PROG_ID":[image[0].header['HIERARCH ESO OBS PROG ID']],
def fxcor(spectrum, template, wl_start, wl_end):
try:
# [TODO] Destroy IRAF
from pyraf import iraf
except NameError:
iraf.noao()
iraf.noao.onedspec()
iraf.rv()
if not os.path.exists(spectrum):
raise IOError('Spectrum file "%s" does not exist.' % (spectrum, ))
if not os.path.exists(template):
raise IOError('Template file "%s" does not exist.' % (template, ))
# Check whether the spectrum and template are ASCII files. If they are we
# need them into FITS to continue.
to_remove = [] # for cleaning up later
spectrum_base, spectrum_ext = os.path.splitext(spectrum)
spectrum_ext = spectrum_ext[1:]
if spectrum_ext not in ('txt', 'ascii', 'fits'):
logging.warn("Don't know what format the spectrum provided is in. Assuming ASCII..")
if spectrum_ext != 'fits':
wave = np.loadtxt(spectrum, usecols=(0, ))
spectrum_fits = '.'.join([spectrum_base, '_tmp.fits'])
iraf.onedspec.rspectext(input = spectrum,
output = spectrum_fits,
dtype = 'linear',
crval1 = np.min(wave),
cdelt1 = np.median(np.diff(wave)))
to_remove.append(spectrum_fits)
else: spectrum_fits = spectrum
template_base, template_ext = os.path.splitext(template)
template_ext = template_ext[1:]
if template_ext not in ('txt', 'ascii', 'fits'):
logging.warn("Don't know what format the template provided is in. Assuming ASCII..")
if template_ext != 'fits':
wave = np.loadtxt(spectrum, usecols=(0, ))
template_fits = '.'.join([template_base, '_tmp.fits'])
iraf.onedspec.rspectext(input = template,
output = template_fits,
dtype = 'linear',
crval1 = np.min(wave),
cdelt1 = np.median(np.diff(wave)))
to_remove.append(template_fits)
else: template_fits = template
sample = ':'.join(map(str, [wl_start, wl_end]))
output_filename = 'fxcor'
try:
iraf.rv.fxcor(objects=spectrum_fits, templates=template_fits, rebin='template',
osample=sample, rsample=sample, output=output_filename, verbose='long', interactive=0, Stdout=1)
except:
raise
else:
fxcor_log = []
with open(output_filename + '.log', 'r') as output:
fxcor_log.extend(output.readlines())
fxcor_out = []
with open(output_filename + '.txt', 'r') as output:
fxcor_out.extend(output.readlines())
fxcor_log = ''.join(fxcor_log)
fxcor_out = ''.join(fxcor_out)
fxcor_output = np.loadtxt(output_filename + '.txt', comments='#', dtype=str)
fxcor_hght, fxcor_fwhm, fxcor_tdr, fxcor_obs, fxcor_rel, fxcor_helio, fxcor_err = fxcor_output[-7::]
# Translate
if 'INDEF' in [fxcor_hght, fxcor_rel, fxcor_err]:
v_rad = fxcor_rel.replace('INDEF', '0')
correlation = fxcor_hght.replace('INDEF', '0')
v_err = fxcor_rel.replace('INDEF', '-999')
v_rad, correlation, v_err = map(float, [fxcor_rel, fxcor_hght, fxcor_err])
os.system('rm -f %s fxcor.txt fxcor.log fxcor.gki' % (' '.join(to_remove), ))
return (v_rad, v_err, correlation, )
import sys import os import string from numpy import * import functions import spectype_functions import spectype_numerical_functions import matplotlib import matplotlib.pyplot as plt import pyfits from pyraf import iraf from scipy import interpolate iraf.kpnoslit() iraf.noao() iraf.rv() ################### ### Description ### ################### ### Take input spectrum ### Find chisq in logg - teff space for every reddenining ### Add over reddening ### Find min chisq ### usage: python spectype_main.py file_path file_name ### Takes input params from config_file #################