Example #1
0
def apall_config(
    config_file,
    config_default='/Users/ando/andry/research/Make_software/saltrss/apall_conf.yml'
):
    config = yaml.safe_load(open(config_default))
    custom_config = {}
    if os.path.exists(config_file):
        custom_config = yaml.safe_load(open(config_file))

    config = config_merge(custom_config, config)

    sections = [
        'iraf.apall',
    ]
    iraf.noao(_doprint=0)
    iraf.twodspec(_doprint=0)
    iraf.onedspec(_doprint=0)
    iraf.apextract(_doprint=0)
    iraf.apextract.unlearn()
    iraf.apall.unlearn()
    iraf.apsum.unlearn()
    iraf.apextract.setParam('dispaxis', 1)

    for section_name in sections:
        params = config[section_name].items()
        for param_id in params:
            eval(section_name).setParam(param_id[0], param_id[1])
    return config
Example #2
0
def apall(lstfile):
    iraf.noao()
    iraf.twodspec()
    iraf.apextract(dispaxis = 2, database = 'database')
    f = open(lstfile)
    l = f.readlines()
    f.close()
    l = [tmp.split('\n')[0] for tmp in l]
    path = os.getcwd()
    for i in l:
        infile = 'wftbo' + i
        outfile = 'awftbo' + i
        while True:
            if os.path.isfile(outfile):
                print('remove ' + outfile)
                os.remove(outfile)
            delfile = path + os.sep + 'database/ap' + infile[0:-5]
            if os.path.isfile(delfile):
                print('remove ' + delfile)
                os.remove(delfile)
            iraf.apall(input = infile
                , output = outfile, apertures = 2, format = 'multispec'
                , references = '', profiles = '', interactive = True
                , find = True, recenter = True, resize = False
                , edit = True, trace = True, fittrace = True
                , extract = True, extras = True, review = True
                , line = 'INDEF', nsum = 10, lower = -15.0
                , upper = 15.0, apidtable = '', b_function = 'chebyshev'
                , b_order = 2, b_sample = '-50:-26,26:50', b_naverage = -25
                , b_niterate = 1, b_low_reject = 3.0, b_high_reject = 3.0
                , b_grow = 0.0, width = 5.0, radius = 10.0
                , threshold = 0.0, nfind = 2, minsep = 5.0
                , maxsep = 100000.0, order = 'increasing', aprecenter = ''
                , npeaks = 'INDEF', shift = True, llimit ='INDEF'
                , ulimit = 'INDEF', ylevel = 0.1, peak = True
                , bkg = True, r_grow = 0.0, avglimits = False
                , t_nsum = 20, t_step = 10, t_nlost = 3, t_function = 'legendre'
                , t_order = 7, t_sample = '*', t_naverage = 1
                , t_niterate = 1, t_low_reject = 3.0, t_high_reject = 3.0
                , t_grow = 0.0, background = 'fit', skybox = 1
                , weights = 'variance', pfit = 'fit1d', clean = True
                , saturation = 'INDEF', readnoise = 9.4, gain = 0.35
                , lsigma = 4.0, usigma = 4.0, nsubaps = 1)
            iraf.flpr()
            sspecplot.sspecplot(outfile)
            getval = raw_input('Are you need repeat apall,may be clean should be close(r/n)')
            if getval != 'r':
                break
Example #3
0
def apall(ilst, olst):
    iraf.noao()
    iraf.twodspec()
    iraf.apextract(dispaxis=1, database='database')
    for i, infile in enumerate(ilst):
        outfile = olst[i]
        laper, raper, back_samp = -7, 7, '-30:-15,15:30'
        while True:
            if os.path.isfile(outfile):
                print('remove ' + outfile)
                os.remove(outfile)

            delfile = os.getcwd()+os.sep+'database/ap'+infile[0:-5]
            if os.path.isfile(delfile):
                print('remove ' + delfile)
                os.remove(delfile)
            iraf.apall(input=infile, output=outfile, apertures=2,
                       format='multispec', references='', profiles='',
                       interactive=True, find=True, recenter=True,
                       resize=False, edit=True, trace=True, fittrace=True,
                       extract=True, extras=True, review=True, line='INDEF',
                       nsum=10, lower=laper, upper=raper, apidtable='',
                       b_function='chebyshev', b_order=2, b_sample=back_samp,
                       b_naverage=-25, b_niterate=1, b_low_reject=3.0,
                       b_high_reject=3.0, b_grow=0.0, width=5.0, radius=10.0,
                       threshold=0.0, nfind=2, minsep=5.0, maxsep=100000.0,
                       order='increasing', aprecenter='', npeaks='INDEF',
                       shift=True, llimit='INDEF', ulimit='INDEF', ylevel=0.1,
                       peak=True, bkg=True, r_grow=0.0, avglimits=False,
                       t_nsum=20, t_step=10, t_nlost=3, t_function='legendre',
                       t_order=12, t_sample='*', t_naverage=1, t_niterate=1,
                       t_low_reject=3.0, t_high_reject=3.0, t_grow=0.0,
                       background='median', skybox=1, weights='none',
                       pfit='fit1d', clean=True, saturation='INDEF',
                       readnoise='CCDRON', gain='CCDGAIN', lsigma=4.0, usigma=4.0,
                       nsubaps=1)

            iraf.flpr()
            getval = raw_input(('Are you need repeat apall,'
                                'may be clean should be close(r/n)'))
            if getval != 'r':
                break
Example #4
0
    def ApallTask(self, InputFile, OutputFile, Fits_Folder, line, nsum = None, lower_lim = None, upper_lim = None, extras = 'yes', Suffix = 'bg'):
        
        iraf.noao(_doprint=0)
        iraf.twodspec(_doprint=0)         
        iraf.apextract(_doprint=0)
        
        #Incase no output name is given, we generate one with the provided "preffix" (The defaul format is a_std_wolf.dat)
        if OutputFile == None:
            OutputFile = self.outputNameGenerator(InputFile + '[1]', Suffix)  
            
        ApallConf = self.ApallAttributes(InputFile, OutputFile, Fits_Folder, line, nsum, lower_lim, upper_lim, extras)  
      
        #Display the equivalent command in IRAF
        Command = self.printIrafCommand('apall', ApallConf)
        print '--- Using the command'
        print Command
      
#         p = Popen(iraf.twodspec.apextract.apall(**ApallConf), shell=True, stdout=PIPE, stderr=STDOUT)
        
        #Run the task        
        iraf.twodspec.apextract.apall(**ApallConf)
      
        return OutputFile
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'


os.environ['PYRAF_BETA_STATUS'] = '1'

# REFS NEW: ecEC59550 ecEC59758 ecEC59795 ecEC59842 ecEC59844 ecEC59864 ecEC59866 ecEC59881 ecEC59883 ecEC59885

observations = {
  'cemp_cand': {'ORIG_DIR':'/home/nandir/IRAF_Echelle_Asiago/CEMP_obs/201712/',
Example #6
0
def load_modules():
    # Define a function to load all of the modules so that they don't' import 
    # unless we need them
    global iraf
    from pyraf import iraf
    iraf.pysalt()
    iraf.saltspec()
    iraf.saltred()
    iraf.set(clobber='YES')
    
    global sys
    import sys

    global os
    import os

    global shutil
    import shutil

    global glob
    from glob import glob
    
    global pyfits
    import pyfits

    global np
    import numpy as np
    
    global lacosmicx
    import lacosmicx
    
    global interp
    from scipy import interp
    
    global signal
    from scipy import signal
    
    global ndimage
    from scipy import ndimage
    
    global interpolate
    from scipy import interpolate
    
    global WCS
    from astropy.wcs import WCS
    
    global optimize
    from scipy import optimize
    
    global ds9
    import pyds9 as ds9
    
    global GaussianProcess
    from sklearn.gaussian_process import GaussianProcess
    
    global pandas
    import pandas
    
    iraf.onedspec()
    iraf.twodspec()
    iraf.longslit()
    iraf.apextract()
    iraf.imutil()
    iraf.rvsao(motd='no')
Example #7
0
'''
from glob import glob
from pyraf import iraf
iraf.stsdas()
iraf.hst_calib()
iraf.stis()
import pyfits
from numpy import isnan, min, logical_and, bitwise_and, linspace, median, arange, correlate, exp, average
from scipy.interpolate import interp1d
from scipy.integrate import trapz
import os
from scipy.optimize import curve_fit

import stistools
iraf.twodspec()
iraf.apextract()
iraf.set(clobber='yes')


def gauss(x, a, x0, sigma, sky):
    return a * exp(-(x - x0)**2 / (2 * sigma**2) + sky)


def tofits(filename, data, hdr=None, clobber=False):
    """simple pyfits wrapper to make saving fits files easier."""
    from pyfits import PrimaryHDU, HDUList
    hdu = PrimaryHDU(data)
    if hdr is not None:
        hdu.header = hdr
    hdulist = HDUList([hdu])
    hdulist.writeto(filename, clobber=clobber, output_verify='ignore')
Example #8
0
#   SALT/RSS longslit reduction                                                         #
#                                                                                       #		
#########################################################################################
'''

import os
from pyraf import iraf
from astropy.io import fits
from shutil import copy2
import rsstools as rt
import numpy as np

iraf.noao(_doprint=0)
iraf.twodspec(_doprint=0)
iraf.longslit(_doprint=0)
iraf.apextract(dispaxis='1')
iraf.stsdas(_doprint=0)
iraf.analysis(_doprint=0)
iraf.fitting(_doprint=0)


class arc(object):
    def __init__(self, name):
        self.name = name 
        self.noext = os.path.splitext(self.name)[0]
        self.idname = rt.makesetups(self.name,"arc")
        self.idfits = self.idname+'.fits'
        self.linelist = self.idname.split('_')[0].lower()+'.dat'
        self.header = self.read_header()
    def read_header(self):
        return fits.getheader(self.name)  
Example #9
0
def extract_spectrum(targetdir,
                     trace,
                     arcspec,
                     refspec,
                     t_nsum,
                     t_step,
                     line,
                     ylevel,
                     interactive):

    """
    Extract spectrum

    Must be in target directory.

    """

    iraf.noao(_doprint=0)
    iraf.onedspec(_doprint=0)
    iraf.twodspec(_doprint=0)
    iraf.apextract(_doprint=0)

    basedir = '/data/lc585/WHT_20150331/OBS/'
    targetdir = os.path.join(basedir,targetdir,'Reduced')

    print 'Target directory is ' + targetdir
    print 'Extracting spectrum...'


    if os.path.exists( os.path.join(targetdir, 'imcomb.ms.fits') ):
        os.remove( os.path.join( targetdir, 'imcomb.ms.fits') )
        print 'Removing file ' + os.path.join( targetdir, 'imcomb.ms.fits')

    # If can't fit trace use trace from nearby object

    if trace == 'no':

        dest = os.path.join(targetdir,'database')

        if not os.path.exists(dest):
            os.makedirs(dest)

        db = os.path.join(basedir,refspec,'Reduced','database','ap_data_lc585_WHT_20150331_OBS_'+refspec+'_Reduced_imcomb')

        shutil.copy(db,dest)

        iraf.apall.setParam('references',os.path.join(basedir,refspec,'Reduced','imcomb.fit')) # List of aperture reference images

        print 'Using trace from reference spectra ' + refspec

    # Since frame is averaged I think we need to scale down read nosie but gain will stay the same.
    names = []
    for n in os.listdir(targetdir):
        if (n.endswith('.fit')) & (n.startswith('r')):
            names.append(n)

    nframes = float(len(names))

    # Doesn't seem to work if I give it absolute path to input!
    iraf.apall.setParam('input','imcomb.fit') # List of input images
    iraf.apall.setParam('output','') # List of output spectra
    iraf.apall.setParam('apertur','') # Apertures
    iraf.apall.setParam('format','multispec') # Extracted spectra format
    iraf.apall.setParam('referen','') # List of aperture reference images
    iraf.apall.setParam('profile','') # List of aperture profile images

    iraf.apall.setParam('interac',interactive) # Run task interactively?
    iraf.apall.setParam('find','no') # Find apertures?
    iraf.apall.setParam('recente','no') # Recenter apertures?
    iraf.apall.setParam('resize','no') # Resize apertures?
    iraf.apall.setParam('edit','yes') # Edit apertures?
    iraf.apall.setParam('trace',trace) # Trace apertures?
    iraf.apall.setParam('fittrac',interactive) # Fit the traced points interactively?
    iraf.apall.setParam('extract','yes') # Extract spectra?
    iraf.apall.setParam('extras','yes') # Extract sky, sigma, etc.?
    iraf.apall.setParam('review',interactive) # Review extractions?

    iraf.apall.setParam('line',line) # Dispersion line
    iraf.apall.setParam('nsum',20) # Number of dispersion lines to sum or median

                                # DEFAULT APERTURE PARAMETERS

    iraf.apall.setParam('lower',-5.) # Lower aperture limit relative to center
    iraf.apall.setParam('upper',5.) # Upper aperture limit relative to center
    iraf.apall.setParam('apidtab','') # Aperture ID table (optional)

                                # DEFAULT BACKGROUND PARAMETERS
    # Background is now a constant at each wavelength
    iraf.apall.setParam('b_funct','chebyshev') # Background function
    iraf.apall.setParam('b_order',1) # Background function order
    iraf.apall.setParam('b_sampl','-10:-6,6:10') # Background sample regions
    iraf.apall.setParam('b_naver',-3) # Background average or median
    iraf.apall.setParam('b_niter',2) # Background rejection iterations
    iraf.apall.setParam('b_low_r',3.) # Background lower rejection sigma
    iraf.apall.setParam('b_high_',3.) # Background upper rejection sigma
    iraf.apall.setParam('b_grow',0.) # Background rejection growing radius

                                # APERTURE CENTERING PARAMETERS

    iraf.apall.setParam('width',5.) # Profile centering width
    iraf.apall.setParam('radius',10.) # Profile centering radius
    iraf.apall.setParam('thresho',0.) # Detection threshold for profile centering

                                # AUTOMATIC FINDING AND ORDERING PARAMETERS

    iraf.apall.setParam('nfind','') # Number of apertures to be found automatically
    iraf.apall.setParam('minsep',5.) # Minimum separation between spectra
    iraf.apall.setParam('maxsep',100000.) # Maximum separation between spectra
    iraf.apall.setParam('order','increasing') # Order of apertures

                                # RECENTERING PARAMETERS

    iraf.apall.setParam('aprecen','') # Apertures for recentering calculation
    iraf.apall.setParam('npeaks','INDEF') # Select brightest peaks
    iraf.apall.setParam('shift','yes') # Use average shift instead of recentering?

                                # RESIZING PARAMETERS

    iraf.apall.setParam('llimit','INDEF') # Lower aperture limit relative to center
    iraf.apall.setParam('ulimit','INDEF') # Upper aperture limit relative to center
    iraf.apall.setParam('ylevel',0.2) # Fraction of peak or intensity for automatic widt
    iraf.apall.setParam('peak','yes') # Is ylevel a fraction of the peak?
    iraf.apall.setParam('bkg','yes') # Subtract background in automatic width?
    iraf.apall.setParam('r_grow',0.) # Grow limits by this factor
    iraf.apall.setParam('avglimi','no') # Average limits over all apertures?

                                # TRACING PARAMETERS

    iraf.apall.setParam('t_nsum',20) # Number of dispersion lines to sum
    iraf.apall.setParam('t_step', 20) # Tracing step
    iraf.apall.setParam('t_nlost',3) # Number of consecutive times profile is lost befo
    iraf.apall.setParam('t_funct','spline3') # Trace fitting function
    iraf.apall.setParam('t_order',2) # Trace fitting function order
    iraf.apall.setParam('t_sampl','*') # Trace sample regions
    iraf.apall.setParam('t_naver',1) # Trace average or median
    iraf.apall.setParam('t_niter',2) # Trace rejection iterations
    iraf.apall.setParam('t_low_r',3.) # Trace lower rejection sigma
    iraf.apall.setParam('t_high_',3.) # Trace upper rejection sigma
    iraf.apall.setParam('t_grow',0.) # Trace rejection growing radius

                                # EXTRACTION PARAMETERS

    iraf.apall.setParam('backgro','none') # Background to subtract
    iraf.apall.setParam('skybox',1) # Box car smoothing length for sky
    iraf.apall.setParam('weights','variance') # Extraction weights (none|variance)
    iraf.apall.setParam('pfit','fit1d') # Profile fitting type (fit1d|fit2d)
    iraf.apall.setParam('clean','yes') # Detect and replace bad pixels?
    iraf.apall.setParam('saturat',300000.) # Saturation level
    # iraf.apall.setParam('readnoi',17.0)
    iraf.apall.setParam('readnoi',17./np.sqrt(nframes)) # Read out noise sigma (photons)
    iraf.apall.setParam('gain',4.) # Photon gain (photons/data number)
    iraf.apall.setParam('lsigma',4.) # Lower rejection threshold
    iraf.apall.setParam('usigma',4.) # Upper rejection threshold
    iraf.apall.setParam('nsubaps',1) # Number of subapertures per aperture
    iraf.apall.setParam('mode','q') # h = hidden, q = query, l = learn

    iraf.apall()

    # Now extract arc through same aperture for wavelength calibration

    print '\n' '\n' '\n'
    print 'Extracting Arc through same aperture...'

    if os.path.exists( os.path.join(targetdir,'aimcomb.fits')):
        os.remove( os.path.join(targetdir, 'aimcomb.fits') )
        print 'Removing file ' + os.path.join(targetdir, 'aimcomb.fits')


    arcspec = os.path.join(basedir,arcspec)

    iraf.apall.setParam('input', arcspec)
    iraf.apall.setParam('output', 'aimcomb')
    iraf.apall.setParam('references', 'imcomb.fit' )
    iraf.apall.setParam('recenter','no')
    iraf.apall.setParam('trace','no')
    iraf.apall.setParam('background','no')
    iraf.apall.setParam('interactive','no')

    iraf.apall()


    if os.path.exists( os.path.join(targetdir, 'imcomb+bkgd.ms.fits') ):
        os.remove( os.path.join( targetdir, 'imcomb+bkgd.ms.fits') )
        print 'Removing file ' + os.path.join( targetdir, 'imcomb+bkgd.ms.fits')


    iraf.apall.setParam('input','imcomb+bkgd.fit') # List of input images
    iraf.apall.setParam('output','') # List of output spectra
    iraf.apall.setParam('referen','imcomb.fit') # List of aperture reference images

    iraf.apall.setParam('interac','yes') # Run task interactively?
    iraf.apall.setParam('find','yes') # Find apertures?
    iraf.apall.setParam('recenter','no') # Recenter apertures?
    iraf.apall.setParam('resize','no') # Resize apertures?
    iraf.apall.setParam('edit','yes') # Edit apertures?
    iraf.apall.setParam('trace','no') # Trace apertures?
    iraf.apall.setParam('fittrac',interactive) # Fit the traced points interactively?
    iraf.apall.setParam('extract','yes') # Extract spectra?
    iraf.apall.setParam('extras','yes') # Extract sky, sigma, etc.?
    iraf.apall.setParam('review','yes') # Review extractions?

                                # DEFAULT BACKGROUND PARAMETERS
    # Background is now a constant at each wavelength
    iraf.apall.setParam('b_funct','chebyshev') # Background function
    iraf.apall.setParam('b_order',1) # Background function order
    iraf.apall.setParam('b_sampl','-10:-6,6:10') # Background sample regions
    iraf.apall.setParam('b_naver',-3) # Background average or median
    iraf.apall.setParam('b_niter',2) # Background rejection iterations
    iraf.apall.setParam('b_low_r',3.) # Background lower rejection sigma
    iraf.apall.setParam('b_high_',3.) # Background upper rejection sigma
    iraf.apall.setParam('b_grow',0.) # Background rejection growing radius

                                # EXTRACTION PARAMETERS

    # before i wasn't dividing by the square root of the frames, but surely this must be true if I'm taking the average

    iraf.apall.setParam('backgro','median') # Background to subtract
    iraf.apall.setParam('skybox',1) # Box car smoothing length for sky
    iraf.apall.setParam('weights','variance') # Extraction weights (none|variance)
    iraf.apall.setParam('pfit','fit1d') # Profile fitting type (fit1d|fit2d)
    iraf.apall.setParam('clean','yes') # Detect and replace bad pixels?
    iraf.apall.setParam('saturat',300000.) # Saturation level
    # iraf.apall.setParam('readnoi',17.0)
    iraf.apall.setParam('readnoi',17.0/np.sqrt(nframes)) # Read out noise sigma (photons)
    iraf.apall.setParam('gain',4.) # Photon gain (photons/data number)
    iraf.apall.setParam('lsigma',4.) # Lower rejection threshold
    iraf.apall.setParam('usigma',4.) # Upper rejection threshold
    iraf.apall.setParam('nsubaps',1) # Number of subapertures per aperture

    iraf.apall()

    hdulist = fits.open(os.path.join(targetdir, 'imcomb+bkgd.ms.fits'))
    sigma = hdulist[0].data[3,0,:]
    hdulist.close()

    hdulist = fits.open(os.path.join(targetdir, 'imcomb.ms.fits'), mode='update')
    hdulist[0].data[2,0,:] = sigma
    hdulist.flush()
    hdulist.close()

    return None
Example #10
0
from numpy import *
from scipy.optimize import leastsq,fsolve#,fmin_slsqp
from scipy.integrate import quad
from scipy.stats import *
from datetime import datetime, date, time
import matplotlib.pyplot as plt
from datetime import timedelta
from numpy.random import randint
import pyfits
iraf.tables()
iraf.noao()
iraf.imred()
iraf.twodspec()
iraf.onedspec()
iraf.ccdred()
iraf.apextract()
iraf.longslit()
iraf.plot()
iraf.stsdas()
iraf.nebular()
from time import strftime


#############################################################
########Setup a list of lines and fitting regions
#############################################################

#the list of lines
linenames=[3727,4102,4340,4363,4686,4861,4959,5007,5755,5876,6548,6562,6584,6717,6731]
elines=array([.5*(3727.092+3729.875),4102.89,4341.68,4364.436,4686,4862.68,4960.295,5008.240,5754.59,5876,6549.86,6564.61,6585.27,6718.29,6732.67])
#define a preferred background region width
Example #11
0
def load_modules():
    # Define a function to load all of the modules so that they don't' import 
    # unless we need them
    global iraf
    from pyraf import iraf
    iraf.pysalt()
    iraf.saltspec()
    iraf.saltred()
    iraf.set(clobber='YES')
    
    global sys
    import sys

    global os
    import os

    global shutil
    import shutil

    global glob
    from glob import glob
    
    global pyfits
    import pyfits

    global np
    import numpy as np
    
    global lacosmicx
    import lacosmicx
    
    global interp
    from scipy import interp
    
    global signal
    from scipy import signal
    
    global ndimage
    from scipy import ndimage
    
    global interpolate
    from scipy import interpolate
    
    global WCS
    from astropy.wcs import WCS
    
    global optimize
    from scipy import optimize
    
    global ds9
    import ds9
    
    global GaussianProcess
    from sklearn.gaussian_process import GaussianProcess
    
    global pandas
    import pandas
    
    iraf.onedspec()
    iraf.twodspec()
    iraf.longslit()
    iraf.apextract()
    iraf.imutil()
Example #12
0
def main():
    iraf.noao()
    iraf.imred()
    iraf.ccdred()
    iraf.crutil()
    iraf.twodspec()
    iraf.apextract()
    name = os.popen('ls object*.lst').readlines()
    name = [i.split('\n')[0] for i in name]
    if len(name) == 0:
        print 'no object, the script end'
    for i in name:
        print 'open file ' + i + '...'
        f = open(i)
        l = f.readlines()
        f.close()
        l = [i2.split('\n')[0] for i2 in l]
        for i2 in l:
            print i2
        objs = []
        calibs = []
        standards = []
        fno = l.index('object') + 1
        while fno < len(l):
            if '.fits' not in l[fno]:
                break
            objs.append('ftbo' + l[fno])
            fno += 1
        fno = l.index('calibration') + 1
        while fno < len(l):
            if '.fits' not in l[fno]:
                break
            calibs.append('ftbo' + l[fno])
            fno += 1
        fno = l.index('standard') + 1
        while fno < len(l):
            if '.fits' not in l[fno]:
                break
            standards.append('ftbo' + l[fno])
            fno += 1
        print '=' * 20, 'reject cosmic ray', '=' * 20
        #cobj = shift_align(objs)
        #cstandard = shift_align(standards)
        cobjs = []
        cstandards = []
        for eobj in objs:
            cobjs.append(cos_clear([eobj]))
        for eobj in standards:
            cstandards.append(cos_clear([eobj]))
        print 'The fits having rejected cosmic ray is: '
        print cobjs
        print cstandards
        print '=' * 20, 'get spectrum line', '=' * 20
        acobjs = []
        acstandards = []
        for cobj in cobjs:
            acobjs.append(get_spec_line(cobj))
        for cobj in cstandards:
            acstandards.append(get_spec_line(cobj))
        acalibs = []
        for i3 in calibs:
            acalibs.append(get_cal_spec_line(i3, cobj))
        print '=' * 20, 'wavelength identify', '=' * 20
        iacalibs = wl_identy(acalibs)
        print '=' * 20, 'wavelength calibrate', '=' * 20
        inamepart = i.replace('.','_').split('_')
        objnames = []
        stdobjnames = []
        for numb in xrange(len(acobjs)):
            objnames.append( 'iac' + inamepart[1] + '_' + inamepart[2] + '_' + inamepart[3] +
                    '_' + str(numb) + '.fits')
        for numb in xrange(len(acstandards)):
            stdobjnames.append('iacstd' + inamepart[1] + '_' + inamepart[2] + '_' + inamepart[3] +
                    '_' + str(numb) + '.fits')
        for numb in xrange(len(objnames)):
            wl_cal(acobjs[numb], objnames[numb], iacalibs)
        for numb in xrange(len(stdobjnames)):
            wl_cal(acstandards[numb], stdobjnames[numb], iacalibs)
        print '=' * 20, 'flux calibrate', '=' * 20
        for objname in objnames:
            final_objname = flux_cal_new(objname, stdobjnames)
        print 'the final object name is', final_objname
for j in range(len(file_list)):
    if sensfile not in file_list[j]:
        if arcfile not in file_list[j]:
            if '.ms.fits' not in file_list[j]:
                if '.w.fits' not in file_list[j]:
                    final.append(file_list[j])

### Define the object name
obj = name(final[0])

### Save the list of spectra
np.savetxt('./speclist', final, fmt="%s")

### apall on arc
iraf.twodspec()
iraf.apextract(dispaxis=1)

if extract_arc != 'n':
    print('\n' + 'Extracting arc file')
    iraf.apall(input=arcfile,
               output='arc.ms',
               apertur=1,
               interac='yes',
               find='yes',
               nfind=1,
               recente='yes',
               resize='yes',
               background='none')

    ## identify lines
    print('\n' + 'Identify arc lines')
Example #14
0
iraf.noao(_doprint=0,Stdout="/dev/null")
iraf.imred(_doprint=0,Stdout="/dev/null")
iraf.ccdred(_doprint=0,Stdout="/dev/null")

# <codecell>

#bias subtract
iraf.ccdproc(images=flat, ccdtype='', fixpix='no', oversca='no', trim='no', zerocor='yes', darkcor='no', flatcor='no', zero='masterbias',Stdout="/dev/null")

# <codecell>

#apall on a flat field
print " + Extract masterflat"
iraf.noao(_doprint=0,Stdout="/dev/null")
iraf.twodspec(_doprint=0,Stdout="/dev/null")
iraf.apextract(_doprint=0,Stdout="/dev/null")

# <codecell>

#adds DISPAXIS=1 to the header
iraf.hedit(images=flat, fields='DISPAXIS', value=1, add='yes', verify='no', update='yes',Stdout="/dev/null")

# <codecell>

iraf.unlearn('apall') #restores initial paramenters to apall

# <codecell>

shift_master(ap_ref[ccd], "database/ap%s" % ap_ref[ccd][:-5])

# <codecell>
def oned_extract(object_b_fn, object_b_fn_ec, order_def, colour):
# Import IRAF modules:
  iraf.noao(_doprint=0)
  iraf.twodspec(_doprint=0)
  iraf.apextract(_doprint=0)
# Check input file and reference extraction exist before proceeding:
  if os.path.isfile(object_b_fn) == True:
    if os.path.isfile(order_def) == True:
# Extract one dimensional spectrum from bias- and background scatter-subtracted
# normalized flat-fielded red object frame using IRAF task apall:
      if colour == 'red':
        parList = "r_oned_extraction_apall.par"
        if os.path.isfile(parList) == True:
          iraf.apall.setParList(ParList = "r_oned_extraction_apall.par")
          iraf.apall(input=object_b_fn, output=object_b_fn_ec, references=order_def)
          print ' '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print 'One dimensional spectral extraction of bias- and   '
          print 'background-subtracted, normalized flat-fielded     '
          print 'red object ' + object_b_fn
          print 'to create ' + object_b_fn_ec + '.'
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print ' '
        else:
          print ' '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print 'One dimensional extraction IRAF .par file          ' 
          print str(parList)
          print 'does not exist. Exiting script.                    '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print ' '
          print ' '
          sys.exit()
# Extract one dimensional spectrum from bias- and background scatter-subtracted
# normalized flat-fielded blue object frame using IRAF task apall:
      if colour == 'blue':
        parList = "b_oned_extraction_apall.par"
        if os.path.isfile(parList) == True:
          iraf.apall.setParList(ParList = "b_oned_extraction_apall.par")
          iraf.apall(input=object_b_fn, output=object_b_fn_ec, references=order_def)
          print ' '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print 'One dimensional spectral extraction of bias- and   '
          print 'background-subtracted, normalized flat-fielded     '
          print 'blue object ' + object_b_fn
          print 'to create ' + object_b_fn_s + '.'
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print ' '
        else:
          print ' '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print 'One dimensional extraction IRAF .par file          ' 
          print str(parList)
          print 'does not exist. Exiting script.                    '
          print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
          print ' '
          print ' '
          sys.exit()
    else:
      print ' '
      print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
      print 'Order definition frame                             ' 
      print str(order_def)
      print 'does not exist. Exiting script.                    '
      print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
      print ' '
      print ' '
      sys.exit()
  else:
    print ' '
    print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
    print 'Input frame                                        ' 
    print str(object_b_fn)
    print 'does not exist. Exiting script.                    '
    print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
    print ' '
    print ' '
    sys.exit()
Example #16
0
lowerclip_gr7 = 3500
upperclip_gr7 = 7720
lowerclip_gr8 = 5900
upperclip_gr8 = 9150

combclip_gr7 = 7065
combclip_gr8 = 6965
# ------------------------------------------------------------------------------------------------------------------- #

# ------------------------------------------------------------------------------------------------------------------- #
# Load IRAF Packages
# ------------------------------------------------------------------------------------------------------------------- #
iraf.noao(_doprint=0)
iraf.images(_doprint=0)
iraf.twodspec(_doprint=0)
iraf.apextract(_doprint=0)
iraf.onedspec(_doprint=0)
# ------------------------------------------------------------------------------------------------------------------- #

# ------------------------------------------------------------------------------------------------------------------- #
# Functions For File Handling
# ------------------------------------------------------------------------------------------------------------------- #


def remove_file(file_name):
    """
    Removes the file "file_name" in the constituent directory.
    Args:
         file_name  : Name of the file to be removed from the current directory
    Returns:
        None
# Delete some directories/files from previous runs.

os.system("rm -rf login.cl pyraf database uparm")
os.system("mkiraf")

# Now load IRAF

import pyraf.iraf as iraf

# Load the packages we might need.

iraf.noao(_doprint=0)
iraf.onedspec(_doprint=0)
iraf.twodspec(_doprint=0)
iraf.apextract(_doprint=0)
iraf.unlearn(iraf.apall)

# The name of the science file.

filename = 'vega_9.3narrow.fit'
extracted_filename = 'vega_9.3narrow.ms.fits'
calibrated_filename = 'vega_9.3narrow.calib.fits'

# Delete previous results.

os.system("rm "+extracted_filename+" "+calibrated_filename)

# Make sure that the dispersion axis is in the header.

iraf.hedit(images=[filename], fields=["DISPAXIS"], value=["1"], add="Yes")
Example #18
0
def apall(imlist_name, reference=''):
    """
    Extract 1d spectrum by tracing column of 2d data.
    Interactive mode is turned on by default.

    On the interactive mode;
    (1) Aperture selection
    :w -> e1, e2 : Zoom in
    :w -> a      : Zoom out
    :m           : Select aperture
    :l -> Click left of the aper. : Set lower limit of the aperture.
    :u -> Click right of the aper. : Set upper limit of the aperture.

    (2) Background selection
    :z  : Delete previously-selected background region.
    :b  : Enter the background mode
    :s1, s2 (on the left part of bkg) : Set the region of left bkg.
    :s3, s4 (on the right part of bkg) : Set the region of right bkg.
    And then enter q --> Yes, Yes

    (3) Fitting mode
    :d : Exclude a point
    :function : Change the fitting function. ("legendre" by default) 
    :order=15 : Change the function order into 15.
    :niterate : Cliping iteration (3 times by default)
    :f        : Go fitting
    :q        : Confirm
    And the enter q --> Yes, Yes

    Output image will be saved as "XXX.ms.fits"
    reference='' : Not using specified aperture used.
    reference='??.ms' : Use the same aperture of ??.ms. Do copy of database of the reference into the same location of input image***
    """
    import glob
    import os, sys
    from pyraf import iraf
    iraf.noao()
    iraf.twodspec()
    iraf.apextract()
    imlist = glob.glob(imlist_name)
    imlist.sort()
    for i in range(len(imlist)):
        inim = imlist[i]
        print('1d extraction for ' + inim + '...')
        if reference == '':
            iraf.apall(input=inim,
                       apertures='',
                       interactive='yes',
                       find='no',
                       t_function="legendre",
                       t_order=15,
                       t_niterate=3,
                       t_low_reject=3,
                       t_high_reject=3.)
        elif reference != '':
            iraf.apall(input=inim,
                       apertures='',
                       reference=reference,
                       interactive='no',
                       find='no',
                       recenter='no',
                       trace='no',
                       t_function="legendre",
                       t_order=15,
                       t_niterate=3,
                       t_low_reject=3,
                       t_high_reject=3.)
    print('Done.')