'''

>>> Rutgers SALT Supernova Spectral Reduction Pipeline <<<

This module contains functions which run a specific PyRAF task

corresponding to one step of the entire reduction process.

Each function sets the parameters for a PyRAF task and then

runs it on the data. These functions are primarily called by

the core module containing the main pipeline functions: tasks.py.

Please refer to the documentation for more information about

how each PyRAF call affects the data.

*** Modifications ***

Sept. 26, 2013: Created module. -Viraj Pandya

'''

import pyfits

import shutil

# PyRAF is the main program used to reduce, extract, and calibrate data.

from pyraf import iraf

from iraf import images

from iraf import imutil

from iraf import immatch

from iraf import noao

from iraf import imred

from iraf import ccdred

from iraf import onedspec

from iraf import twodspec

from iraf import apextract

from iraf import longslit

from iraf import pysalt

from iraf import saltspec

import dicts # These are the pipeline's global dictionaries.

import params # Customizable parameters for the pipeline.

# This function sets the parameters for the pyraf task ccdred.flatcombine and then runs it.

def run_flatcombine(flatstocombine,combflatname,customRun=False):

ccdred.flatcombine(input=flatcombineseq,output=combflatname)

# This function sets the parameters for the pyraf task longslit.response and then runs it.

def run_response(combinedflat,normflatname,customRun=False):

longslit.response(calibration=combinedflat,normalization=combinedflat,response=normflatname)

# This function sets the parameters for the pyraf task immatch.imcombine and then runs it.

def run_imcombine(imagestocombine,combimgname,commongain,customRun=False):

immatch.imcombine(input=imagestocombine,output=combimgname)

# This function sets the parameters for the pyraf task imutil.imarith and then runs it.

def run_imarith(dividend,divisor,quotient,customRun=False):

imutil.imarith(operand1=dividend,op='/',operand2=divisor,result=quotient)

# This function sets the parameters for the pysalt task saltspec.specidentify and then runs it.

def run_specidentify(arcimage,lamplines,idfile,customRun=False):

saltspec.specidentify(images=arcimage,linelist=lamplines,outfile=idfile)

# This function sets the parameters for saltspec.specrectify and runs the task.

# It outputs 2-D wavelength-corrected images (science, arc, and standard star).

def run_specrectify(input,output,idfile,customRun=False):

saltspec.specrectify(images=input,outimages=output,solfile=idfile)

# This function sets the parameters for the pyraf task twodspec.longslit.background and then runs it.

def run_background(twodimage,newimage,customRun=False):

longslit.background(input=twodimage,output=newimage)

# This function sets the parameters for the pyraf task apextract.apall and then runs it.

def run_apall(twodimage,spectrum,saltgain,faint,customRun=False):

apextract.apall(input=twodimage,output=spectrum,nfind=1,trace='yes',fittrace='yes',recenter='yes',resize='yes',edit='yes',extract='yes')

# This function sets the parameters for the pyraf task apextract.apsum and then runs it.

def run_apsum(twodimage,refimage,spectrum,customRun=False):

apextract.apsum(input=twodimage,output=spectrum,references=refimage)

# This function sets the parameters for the pyraf task apextract.apsum and then runs it

def run_apsumSci(inputimage,refimage,spectrum,customRun=False):

apextract.apsum(input=inputimage,output=spectrum,references=refimage)

# This function sets the parameters for and runs identify

def run_identify(arcsci,lamplines,customRun=False):

onedspec.identify(images=arcsci,coordlist=lamplines)

# This function sets the parameters for and runs the pyraf task reidentify.

def run_reidentify(input,ref,lamplines,customRun=False):

onedspec.reidentify(reference=ref,images=input,coordlist=lamplines)

# This function sets the parameters for the pyraf task onedspec.dispcor and then runs it.

def run_dispcor(original,corrected,customRun=False):

onedspec.dispcor(input=original,output=corrected)

# This function sets the parameters for the pyraf task onedspec.standard and then runs it.

# The user has already been alerted by fluxcal function above about the star_name.

def run_standard(standardimage,outputname,exp,air,starName,customRun=False):

onedspec.standard(input=standardimage+'[1]',output=outputname)

# This function sets the parameters for the pyraf task onedspec.sensfunc and then runs it.

def run_sensfunc(stddata,sensname,customRun=False):

onedspec.sensfunc(standards=stddata,sensitivity=sensname)

# This function sets the parameters for the pyraf task onedspec.calibrate and then runs it.

def run_calibrate(scienceimage,fluximage,sensfilename,customRun=False):

onedspec.calibrate(input=scienceimage1,output=fluximage)

# This function sets the parameters for the pyraf task onedspec.odcombine and then runs it.

def run_odcombine(inputlistseq,finalspectrumname,saltgain,customRun=False):

onedspec.odcombine(input=inputlistseq,output=finalspectrumname)

# This function creates a copy of a FITS file and preserves the 2-extension structure.

def run_imcopy(inputname,outputname,numExt=2,customRun=False):

# imcopy seems to cause a weird bug in tasks.scaleFluxScienceSpectra() (not exact copy is created), using shutil instead

shutil.copyfile(inputname,outputname) # careful, this will overwrite outputname if it already exists

print inputname+' ==> copied to ==> '+outputname

# This function deletes a file.

def run_imdel(inputname,customRun=False):

imutil.imdel(inputname)

# This function extracts bands from a spectrum stored in a FITS file.

def run_scopy(inputname,outputname,band,customRun=False):

onedspec.scopy.unlearn()

onedspec.scopy(input=inputname+'[1]',output=outputname,bands=band,format='multispec',clobber='yes',verbose='yes')

# This *generalized* function sets the parameters for the pyraf task imutil.imarith and then runs it.

def run_imarithGeneral(op1,op2,oper,outname,customRun=False):

imutil.imarith(operand1=op1,op=oper,operand2=op2,result=outname)