#! /usr/bin/env python
# S.Rodney
# 2014.03.04
"""Process a set of flt files to produce wcs- and pixel-registered
images across all filters and epochs, following the Drizzlepac
tweakreg/astrodrizzle/tweakback registration sequence as described in
section 7.5 of the drizzlepac handbook:

- Sort the flts by epoch, visit and filter
- [ Use tweakreg for intra-visit alignment ]
- Use astrodrizzle to combine each single-visit set into a drz_sci.fits product
- Define a wcs reference frame using one of the images
- Improve the wcs-alignment between all single-visit drizzled images and the
  ref image, using tweakreg.
- Using tweakback, propagate the new tweaked solutions back to the original
  flt.fits images.
- Drizzle-combine the updated flt.fits images to make single-epoch,
  single-filter registered drz products.
- Subtract a template epoch.

"""

import glob
import os
import shutil
import stat
import numpy as np
from sndrizpipe import register
from sndrizpipe import exposures
from sndrizpipe import drizzle
from sndrizpipe import badpix
from sndrizpipe import imarith
from astropy.io import fits as pyfits
from drizzlepac.tweakback import tweakback
from sndrizpipe import pseudodiff

# file permissions for chmod ug+rw o+r
PERMISSIONS = (
            stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IROTH)


def multipipe():
    """ 
    Run the pipeline for all <rootname>.flt directories found
    within the current directory
    """
    # TODO : use parallel processing
    # look for flt/flc/flm files in directories called <rootname>.flt
    fltdirlist = glob.glob("*.flt")
    if not len(fltdirlist):
        raise RuntimeError("There is no <rootname>.flt directory!")
    for fltdir in fltdirlist:
        runpipe(fltdir)


# TODO : write a log file, recording user settings and results
def runpipe(outroot, onlyfilters=[], onlyepochs=[],
            # combine together multiple bands
            combinefilterdict={'method': None}, # Run all the processing steps
            doall=False, # Setup : copy flts into sub-directories
            dosetup=False, epochlistfile=None, # construct a ref image
            dorefim=False, # Single Visit tweakreg/drizzle pass :
            dodriz1=False, drizcr=1, intravisitreg=False,
            # Register to a given image or  epoch, visit and filter
            doreg=False, singlestar=False, refim=None, refepoch=None,
            refvisit=None, reffilter=None,
            # Drizzle registered flts by epoch and filter
            dodriz2=False, singlesci=False, # make diff images
            dodiff=False, tempepoch=0, tempfilters=None, singlesubs=False,
            # make multi-epoch stack images
            dostack=False, # source detection and matching
            interactive=False, threshold=5, nbright=None, peakmin=None,
            peakmax=None,  # fluxmin=None, fluxmax=None,
            searchrad=1.5, minobj=10, mjdmin=0, mjdmax=0, epochspan=5,
            refcat=None, rfluxmax=None, rfluxmin=None, refnbright=None,
            nclip=3, sigmaclip=3.0, drizcrsnr='5,4.5', shiftonly=False,
            ra=None, dec=None, rot=0, imsize_arcsec=None, naxis12=None,
            pixscale=None, pixfrac=None, wht_type='IVM', stackepochs=None,
            stacktemplate=False, stackpixscale=None, stackpixfrac=None,
            clean=False, clobber=False, verbose=True, debug=False):
    """ 
    Primary pipeline function.  Executes all the intermediate steps: 
       register, sort, drizzle, subtract, mask
    """

    # Check for logically incompatible parameters
    if nbright and minobj and (nbright < minobj - 1):
        raise RuntimeError(' nbright < minobj \n'
                           'You have nbright=%i and minobj=%i\n' % (
                           nbright, minobj) + "That doesn't work.")
    if shiftonly:
        fitgeometry = 'shift'
    else:
        fitgeometry = 'rscale'
    if fitgeometry == 'rscale' and ((nbright and nbright < 3) or minobj < 3):
        raise RuntimeError(
            ' Not requiring enough stars for rotation+scale fit.\n'
            'You have nbright=%i and minobj=%i\n' % (
            nbright, minobj) + "and you also have fitgeometry='rscale'."
                               "Try again with --shiftonly")
    if onlyfilters:
        if type(onlyfilters) == str:
            onlyfilters = onlyfilters.lower().split(',')
        onlyfilters = [filt[:5].lower() for filt in onlyfilters]
        if combinefilterdict['method'] == 'driz':
            onlyfilters += combinefilterdict['name']

    if type(onlyepochs) in [str, int, float]:
        onlyepochs = [int(ep) for ep in str(onlyepochs).split(',')]
    if tempfilters is not None and len(onlyfilters) != 1:
        raise RuntimeError(
            'You specified filter(s) to combine/scale for the template epoch'
            'but you did not limit the processing to a single filter.'
            "If you use --tempfilters then you must also specify a "
            "single filter for processing with '--filters X'")
    if singlestar and ((ra is None) or (dec is None)):
        raise RuntimeError(
            'If you set the --singlestar flag for processing a single '
            '(standard) star then you MUST also provide a target RA and '
            'DEC with the --ra and --dec options.')
    drizcrsnr = drizcrsnr.replace(',', ' ')

    topdir = os.path.abspath('.')
    fltdir = outroot + '.flt'

    if doall:
        dosetup = True
        dorefim = True
        dodriz1 = True
        doreg   = True
        dodriz2 = True
        dodiff  = True
        # Note: we don't set dostack = True with doall, so you have to use
        #  --dostack to get a stacked image

    # For single-star registrations, set some useful defaults for the user
    if singlestar:
        if not searchrad:
            searchrad = 10
        if threshold > 0.5:
            # this becomes threshmin, so we only allow
            # the user to decrease from 0.5
            threshold = 0.5
        if wht_type == 'ERR':
            print("WARNING :forcing the final_wht_type to EXP instead of ERR"
                  ' (best for bright sources dominated by poisson noise)')
            wht_type = 'EXP'
        if drizcr == 1:
            print("WARNING :forcing a re-run of driz_cr for multi-visit stacks"
                  ' (important to to avoid suppressing flux in bright stars)')
            drizcr = 2

    # STAGE 0 : (always runs)
    # get a list of exposures and epochs, sorting flt files into epochs
    if not epochlistfile:
        epochlistfile = "%s_epochs.txt" % outroot
    fltlist = glob.glob("%s/*fl?.fits" % fltdir)
    if not len(fltlist):
        print ('\n\n')
        print ('fltlist')
        print (fltlist)
        raise RuntimeError("There are no flt/flc/flm files in %s !!" % fltdir)

    if os.path.exists(epochlistfile):
        print ('epochlistfile', epochlistfile)
        explist_all = exposures.read_explist(epochlistfile,
            combinefilterdict=combinefilterdict)
        if verbose:
            print("%s exists. Adopting existing exposure list and "
                  "epoch sorting." % epochlistfile)
            exposures.print_epochs(explist_all, outfile=None, verbose=verbose,
                                   clobber=False, onlyfilters=None,
                                   onlyepochs=None)
    else:
        if verbose:
            print("Generating exposure list and epoch sorting "
                  "from %s/*fl?.fits." % fltdir)
        explist_all = exposures.get_explist(fltlist, outroot=outroot,
            targetradec=[ra, dec], combinefilterdict=combinefilterdict)
        exposures.define_epochs(explist_all, epochspan=epochspan,
                                mjdmin=mjdmin, mjdmax=mjdmax)
        exposures.print_epochs(explist_all, outfile=epochlistfile,
                               verbose=verbose, clobber=False,
                               onlyfilters=None, onlyepochs=None)
    if clobber > 1 or len(explist_all) < len(fltlist):
        print("New flt files detected in %s." % fltdir)
        if not clobber:
            print("Turn on --clobber to rewrite the epochs list %s" % (
                epochlistfile))
        else:
            print("Updating %s with new flt files detected in %s" % (
                epochlistfile, fltdir))
            explist_all = exposures.update_epochs(explist_all, fltlist,
                epochspan=epochspan, mjdmin=mjdmin, mjdmax=mjdmax,
                targetradec=[ra, dec], combinefilterdict=combinefilterdict)
            exposures.print_epochs(explist_all, outfile=epochlistfile,
                                   verbose=verbose, clobber=clobber,
                                   onlyfilters=None, onlyepochs=None)

    if refim and not os.path.exists(refim):
        raise RuntimeError('Ref image %s does not exist.' % refim)
    if not refim:
        # No refimage has been specified, so set the default refimage name
        refdrzdir = '%s.refim' % outroot
        refimbasename = '%s_wcsref_drz_sci.fits' % outroot
        refim = os.path.abspath(os.path.join(refdrzdir, refimbasename))
        if os.path.exists(refim.replace('_drz_sci', '_drc_sci')):
            refim = refim.replace('_drz_sci', '_drc_sci')

    if refcat:
        refcat = os.path.abspath(refcat)

    # reduce the working exposure list to contain only those exposures
    # that we actually want to process
    explist = []
    for exp in explist_all:
        if exp.epoch < 0 or not exp.ontarget:
            continue
        if onlyfilters and exp.filter not in onlyfilters:
            continue
        elif onlyepochs and exp.epoch not in onlyepochs:
            continue
        else:
            explist.append(exp)

    # STAGE 1 :
    # copy pristine flt files into epoch sub-directories
    if dosetup:
        if verbose:
            print("sndrizpipe : (1) SETUP : copying flt files into subdirs")
        exposures.copy_to_epochdirs(explist, onlyfilters=onlyfilters,
                                    onlyepochs=onlyepochs, verbose=verbose,
                                    clobber=clobber)

    FEVgrouplist = sorted(np.unique([exp.FEVgroup for exp in explist]))
    FEgrouplist = sorted(np.unique([exp.FEgroup for exp in explist]))
    epochlist = sorted(np.unique([exp.epoch for exp in explist]))
    filterlist = sorted(np.unique([exp.filter for exp in explist]))
    if combinefilterdict['method'] is not None:
        combinefilterdict['diffimfiles'] = {}
        combinefilterdict['diffwhtfiles'] = {}
        for epoch in epochlist:
            combinefilterdict['diffimfiles'][epoch] = {}
            combinefilterdict['diffwhtfiles'][epoch] = {}
        if combinefilterdict['method'] == 'driz':
            filterlist = combinefilterdict['name']

    # STAGE 2 :
    # Construct the WCS reference image
    if dorefim and not singlestar:
        refimclobber = clobber and (reffilter or refepoch or refvisit)
        if verbose:
            print("sndrizpipe : (2) REFIM : Constructing WCS ref image.")
        if os.path.exists(refim) and refimclobber:
            os.remove(refim)
        if os.path.exists(refim):
            print("%s already exists.  Not clobbering." % refim)
            if clobber:
                print("To clobber and remake the ref image, you must provide "
                      "at least one of --reffilter, --refepoch, --refvisit")
        else:
            refdrzdir = os.path.dirname(refim)
            if verbose:
                print(" Constructing reference image %s in %s" % (
                    os.path.basename(refim), refdrzdir))

            # Collect the necessary flt files for constructing the ref image
            if not refepoch:
                refepoch = np.min(epochlist)
            if not reffilter:
                reffilter = sorted(
                    [exp.filter for exp in explist if exp.epoch == refepoch])[
                    0]
            reffilter = reffilter.lower()

            # if refvisit is not set, use the visit with the most exposures
            if not refvisit:
                # visits, exp_times, visit_depth = np.array( ([], [], []) )
                explistRIvisfind = [exp for exp in explist_all if (
                            exp.epoch == refepoch and exp.filter == reffilter)]
                pidvisits = [exp.pidvisit for exp in explistRIvisfind]
                unique_visits = np.unique(pidvisits)
                if len(unique_visits) == 1:
                    refvisit = unique_visits[0]
                elif len(unique_visits) < 1:
                    raise RuntimeError(
                        "No visits satisfy the refimage requirements:\n" + "  filter = %s     epoch = %s" % (
                        reffilter, refepoch))
                else:
                    Nexp_per_visit = [
                        len(np.where(np.char.equal(pidvisits, vis))[0]) for vis
                        in unique_visits]
                    ideepest = np.argmax(Nexp_per_visit)
                    refvisit = unique_visits[ideepest]
            refvisit = refvisit.upper()
            if refvisit.find('.') > 0:
                refvisit = refvisit.replace('.', '_')

            explistRI = sorted([exp for exp in explist_all if
                                exp.epoch == refepoch and exp.filter == reffilter and exp.pidvisit == refvisit])
            if len(explistRI) < 1:
                raise RuntimeError(
                    "Error : not enough exposures for refim with"
                    "epoch %i  ;  filter %s  ;  visit %s  " % (
                        refepoch, reffilter, refvisit))
            refdrzdir = os.path.dirname(refim)
            if not os.path.isdir(refdrzdir):
                os.makedirs(refdrzdir)
            for exp in explistRI:
                fltfile = os.path.basename(exp.filename)
                refsrcdir = os.path.abspath(fltdir)
                shutil.copy(os.path.join(refsrcdir, fltfile), refdrzdir)
                os.chmod(os.path.join(refdrzdir, fltfile), PERMISSIONS)
            fltlistRI = [exp.filename for exp in explistRI]

            refimbasename = os.path.basename(refim)
            drzpt = max(refimbasename.find('_drz_sci.fits'),
                        refimbasename.find('_drc_sci.fits'))
            refimroot = refimbasename[:drzpt]
            os.chdir(refdrzdir)

            # drizzle the ref image using firstDrizzle :
            # (full frame, native rotation, auto-selecting the optimal
            # pixscale and pixfrac based on number of flts)
            refdrzsci, refimwht = drizzle.firstDrizzle(fltlistRI, refimroot,
                driz_cr=drizcr, driz_cr_snr=drizcrsnr, clean=clean)
            refim = os.path.join(os.path.abspath(refdrzdir),
                                 os.path.basename(refdrzsci))

            if refcat:
                # Update the WCS header info in the ref image to match the
                # given reference catalog
                if verbose:
                    print(" Registering reference image"
                          " %s to ref catalog %s" % (refdrzsci, refcat))
                wcsname = register.RunTweakReg(refdrzsci, refim=refim,
                    refcat=refcat,
                    wcsname='REFCAT:%s' % os.path.basename(refcat),
                    searchrad=searchrad, refnbright=refnbright,
                    rmaxflux=rfluxmax, rminflux=rfluxmin, peakmin=peakmin,
                    peakmax=peakmax, # fluxmin=fluxmin, fluxmax=fluxmax,
                    fitgeometry=fitgeometry, threshold=threshold,
                    minobj=minobj, nbright=nbright, nclip=nclip,
                    sigmaclip=sigmaclip, clean=clean, verbose=verbose,
                    interactive=interactive, clobber=clobber, debug=debug)

            if clean:
                for fltfile in fltlistRI:
                    if os.path.isfile(fltfile):
                        os.remove(fltfile)
                    if os.path.isfile('OrIg_files/%s' % fltfile):
                        os.remove('OrIg_files/%s' % fltfile)
                if os.path.isdir('OrIg_files'):
                    os.rmdir('OrIg_files')
                refimwht = refdrzsci.replace('sci.fits', 'wht.fits')
                if os.path.isfile(refimwht):
                    os.remove(refimwht)
                refimctx = refdrzsci.replace('sci.fits', 'ctx.fits')
                if os.path.isfile(refimctx):
                    os.remove(refimctx)

            os.chdir(topdir)

    # If refnbright was provided, then we must make an RA,Dec reference
    # catalog when one does not already exist
    if refnbright and not refcat and not singlestar:
        assert (os.path.exists(refim))
        refdrzdir = os.path.dirname(refim)
        os.chdir(refdrzdir)
        refcatfile = \
        register.mkSourceCatalog(os.path.basename(refim), threshold=threshold,
            peakmin=peakmin, peakmax=peakmax)[0]
        os.chdir(topdir)
        refcat = os.path.abspath(os.path.join(refdrzdir, refcatfile))

    # STAGE 3 :
    # Drizzle together each drizzle group (same epoch, visit and
    # filter), using almost-default parameters, doing CR rejection
    # and applying intravisit registrations if requested.  The output
    # is a drz_sci.fits file in the native rotation.
    if dodriz1:
        if verbose:
            print("sndrizpipe : (3) DRIZ1 : first astrodrizzle pass.")
        for FEVgroup in FEVgrouplist:
            explistFEV = [exp for exp in explist if exp.FEVgroup == FEVgroup]
            thisepoch = explistFEV[0].epoch
            thisfilter = explistFEV[0].filter
            if onlyepochs and thisepoch not in onlyepochs:
                continue
            if onlyfilters and thisfilter not in onlyfilters:
                continue

            epochdir = explistFEV[0].epochdir
            fltlistFEV = [exp.filename for exp in explistFEV]
            outrootFEV = '%s_%s_nat' % (outroot, FEVgroup)

            os.chdir(epochdir)
            outsciFEV = '%s_%s_sci.fits' % (
                outrootFEV, explistFEV[0].drzsuffix)
            if os.path.exists(outsciFEV) and clobber:
                os.remove(outsciFEV)
            if os.path.exists(outsciFEV):
                if verbose:
                    print("%s exists.  Not clobbering." % outsciFEV)
                os.chdir(topdir)
                continue
            if intravisitreg:
                # run tweakreg for intravisit registration tweaks
                wcsname = register.RunTweakReg(fltlistFEV, wcsname='INTRAVIS',
                    refcat=refcat, searchrad=searchrad, threshold=threshold,
                    minobj=minobj, peakmin=peakmin, peakmax=peakmax,
                    # fluxmin=fluxmin, fluxmax=fluxmax,
                    fitgeometry=fitgeometry, nbright=nbright, clean=clean,
                    refnbright=refnbright, nclip=nclip, sigmaclip=sigmaclip,
                    rminflux=rfluxmin, rmaxflux=rfluxmax, verbose=verbose,
                    interactive=interactive, clobber=clobber, debug=debug)
            drizzle.firstDrizzle(fltlistFEV, outrootFEV, driz_cr=drizcr,
                driz_cr_snr=drizcrsnr,
                wcskey=((intravisitreg and 'INTRAVIS') or ''), clobber=clobber,
                verbose=verbose, clean=clean)
            # Be extra careful with CR flags when we only have 2 IR exposures
            # the hotpix function below will remove any CR flags that don't
            # appear in both exposures, leaving only those that are very
            # likely hot pix, b/c the same pixel is flagged in both exposures.
            if 'camera' in explistFEV[0].__dict__.keys():
                camera = explistFEV[0].camera
            elif explistFEV[0].rootname.startswith('i'):
                if explistFEV[0].filename.endswith('flc.fits'):
                    camera = 'WFC3-UVIS'
                elif explistFEV[0].filter.lower().startswith('f1'):
                    camera = 'WFC3-IR'
                else:
                    camera = 'WFC3-UVIS'
            elif explistFEV[0].rootname.startswith('j'):
                camera = 'ACS-WFC'
            if drizcr and len(fltlistFEV) == 2 and camera == 'WFC3-IR':
                drizzle.hotpixPostargClean(fltlistFEV[0], fltlistFEV[1],
                                           verbose=verbose)

            os.chdir(topdir)
            continue

    # STAGE 4 :
    # Run tweakreg to register all the single-visit drz images
    # to a common WCS defined by the refcat/refim, updating the drz file hdrs.
    # Then use tweakback to propagate that back into the flt files
    if doreg:
        if verbose:
            print("sndrizpipe : (4) REG : registering images.")

        if not singlestar:
            refim = os.path.abspath(refim)
            if not os.path.exists(refim):
                raise RuntimeError(
                    "No refim file %s!  Maybe you should re-run with "
                    "dorefim=True." % refim)

            # Fix the output ra,dec center point if not provided by the user.
            if not ra and not dec:
                ra = pyfits.getval(refim, "CRVAL1")
                dec = pyfits.getval(refim, "CRVAL2")

        for FEVgroup in FEVgrouplist:
            explistFEV = [exp for exp in explist if exp.FEVgroup == FEVgroup]
            thisepoch = explistFEV[0].epoch
            thisfilter = explistFEV[0].filter
            if onlyepochs and thisepoch not in onlyepochs:
                continue
            if onlyfilters and thisfilter not in onlyfilters:
                continue

            epochdir = explistFEV[0].epochdir
            fltlistFEV = [exp.filename for exp in explistFEV]
            outrootFEV = '%s_%s_nat' % (outroot, FEVgroup)
            outsciFEV = '%s_%s_sci.fits' % (
                outrootFEV, explistFEV[0].drzsuffix)

            os.chdir(epochdir)

            if not os.path.exists(outsciFEV):
                RuntimeError("Missing %s." % outsciFEV)
            origwcs = pyfits.getval(outsciFEV, 'WCSNAME').strip()

            if singlestar:
                # Special case for handling standard star images:
                wcsname = register.SingleStarReg(outsciFEV, ra, dec,
                    refim=None, threshmin=threshold, peakmin=peakmin,
                    peakmax=peakmax, searchrad=searchrad,
                    wcsname='SINGLESTAR:%.6f,%.6f' % (ra, dec),
                    verbose=verbose)

            else:
                # register to the ref image and ref catalog
                wcsname = register.RunTweakReg(outsciFEV,
                    wcsname='REFIM:%s' % os.path.basename(refim), refim=refim,
                    refcat=refcat, searchrad=searchrad, threshold=threshold,
                    minobj=minobj, peakmin=peakmin, peakmax=peakmax,
                    # fluxmin=fluxmin, fluxmax=fluxmax,
                    fitgeometry=fitgeometry, nbright=nbright, clean=clean,
                    refnbright=refnbright, rminflux=rfluxmin,
                    rmaxflux=rfluxmax, nclip=nclip, sigmaclip=sigmaclip,
                    verbose=verbose, interactive=interactive, clobber=clobber,
                    debug=debug)

            # Run tweakback to update the constituent flts
            try:
                tweakback(outsciFEV, input=fltlistFEV, origwcs=origwcs,
                          wcsname=wcsname, newname=wcsname, verbose=verbose, force=clobber)
            except KeyError as e:
                import pdb
                pdb.set_trace()
                print("Key Error %s" % e)
            os.chdir(topdir)

    # STAGE 5:
    # Second astrodrizzle pass, wherein we rerun
    # astrodrizzle to get wcs- and pixel-registered drz images
    # combining all flt files with the same filter and epoch.
    if dodriz2:
        if verbose:
            print("sndrizpipe : (5) DRIZ2 : second astrodrizzle pass.")
        for FEgroup in FEgrouplist:
            explistFE = [exp for exp in explist if exp.FEgroup == FEgroup]
            thisepoch = explistFE[0].epoch
            thisfilter = explistFE[0].filter
            if onlyepochs and thisepoch not in onlyepochs:
                continue
            if onlyfilters and thisfilter not in onlyfilters:
                continue

            epochdir = explistFE[0].epochdir
            fltlistFE = [exp.filename for exp in explistFE]
            outrootFE = '%s_%s_reg' % (outroot, FEgroup)

            err = None
            os.chdir(epochdir)
            outsciFE = '%s_%s_sci.fits' % (outrootFE, explistFE[0].drzsuffix)
            if os.path.exists(outsciFE) and clobber:
                os.remove(outsciFE)
            if os.path.exists(outsciFE):
                if verbose:
                    print("%s exists.  Not clobbering." % outsciFE)
                os.chdir(topdir)
                continue

            # Always use imedian combination for WFC3-IR.  For ACS or UVIS,
            # use imedian combination for bright stars (where high poisson
            # noise leads to flux suppression for iminmed) and for cases where
            # we  have a large number of input flts.  Otherwise, iminmed is
            # safer and does not introduce a bias.
            combine_type = 'imedian'
            if explistFE[0].camera != 'WFC3-IR' and not singlestar and len(
                    fltlistFE) < 7:
                combine_type = 'iminmed'

            outscilist, outwhtlist, outbpxlist = drizzle.secondDrizzle(
                fltlistFE, outrootFE, refimage=None, ra=ra, dec=dec, rot=rot,
                imsize_arcsec=imsize_arcsec, naxis12=naxis12,
                wht_type=wht_type, pixscale=pixscale, pixfrac=pixfrac,
                combine_type=combine_type, driz_cr=(drizcr > 1),
                driz_cr_snr=drizcrsnr, singlesci=(singlesubs or singlesci),
                clean=clean, clobber=clobber, verbose=verbose, debug=debug)

            # As above, be extra careful with CR flagging when we
            # only have 2 IR exposures
            if (drizcr > 1 and len(fltlistFE) == 2 and explistFE[
                0].camera == 'WFC3-IR'):
                drizzle.hotpixPostargClean(fltlistFE[0], fltlistFE[1],
                                           verbose=verbose)
                outscilist, outwhtlist, outbpxlist = drizzle.secondDrizzle(
                    fltlistFE, outrootFE, refimage=None, ra=ra, dec=dec,
                    rot=rot, imsize_arcsec=imsize_arcsec, naxis12=naxis12,
                    wht_type=wht_type, pixscale=pixscale, pixfrac=pixfrac,
                    combine_type=combine_type, driz_cr=False,
                    driz_cr_snr=drizcrsnr, singlesci=(singlesubs or singlesci),
                    clean=clean, clobber=True, verbose=verbose, debug=debug)

            os.chdir(topdir)

    # STAGE 6
    # Define a template epoch for each filter and subtract it
    # from the other epochs
    if dodiff:
        if verbose:
            print("sndrizpipe : (6) DIFF : subtracting template images.")
        for filter in filterlist:
            if onlyfilters and filter not in onlyfilters:
                continue
            topdir = os.path.abspath('.')
            for epoch in epochlist:
                if onlyepochs and epoch not in onlyepochs:
                    continue
                if epoch == tempepoch:
                    continue
                if ((combinefilterdict['method'] == 'driz') and (
                        filter in combinefilterdict['filterlist'])):
                    explistFE = [exp for exp in explist if
                                 filter in combinefilterdict[
                                     'filterlist'] and exp.epoch == epoch]
                else:
                    explistFE = [exp for exp in explist if
                                 exp.filter == filter and exp.epoch == epoch]
                if len(explistFE) == 0:
                    continue
                epochdirFE = explistFE[0].epochdir
                outrootFE = "%s_%s" % (outroot, explistFE[0].FEgroup)
                drzsuffix = explistFE[0].drzsuffix
                regsci = "%s_reg_%s_sci.fits" % (outrootFE, drzsuffix)

                os.chdir(epochdirFE)
                if not os.path.isfile(regsci):
                    os.chdir(topdir)
                    continue

                # Locate and/or construct templates
                tempdir = os.path.join(os.path.abspath(topdir),
                                       outroot + '.e%02i' % tempepoch)
                if tempfilters is not None:
                    tempsci = os.path.join(tempdir,
                                           '%s_~%s_e%02i_reg_%s_sci.fits' % (
                                               outroot, filter, tempepoch,
                                               drzsuffix))
                else:
                    tempsci = os.path.join(tempdir,
                                           '%s_%s_e%02i_reg_%s_sci.fits' % (
                                               outroot, filter, tempepoch,
                                               drzsuffix))
                if tempfilters and not os.path.exists(tempsci):
                    # Combine multiple filters from the template epoch to make
                    # a pseudo-template with ~filtername in the filename.
                    tempfilter1 = tempfilters.split(',')[0]
                    tempsci1 = os.path.join(tempdir,
                                            '%s_%s_e%02i_reg_%s_sci.fits' % (
                                                outroot, tempfilter1,
                                                tempepoch, drzsuffix))
                    if ',' in tempfilters:
                        tempfilter2 = tempfilters.split(',')[1]
                        tempsci2 = os.path.join(tempdir,
                            '%s_%s_e%02i_reg_%s_sci.fits' % (
                                outroot, tempfilter2, tempepoch, drzsuffix))
                    else:
                        tempfilter2, tempsci2 = None, None
                    targetfilter = pseudodiff.camfiltername(regsci)
                    tempsci, tempwht, tempbpx = pseudodiff.mkscaledtemplate(
                        targetfilter, tempsci1, tempsci2, outfile=tempsci,
                        filtdir='HSTFILTERS', verbose=verbose, clobber=clobber)
                tempwht = tempsci.replace('sci.fits', 'wht.fits')
                tempbpx = tempsci.replace('sci.fits', 'bpx.fits')

                regscilist = [regsci]
                subscilist = [outrootFE + "-e%02i_sub_sci.fits" % tempepoch]

                if singlesubs or singlesci:
                    for exp in explistFE:
                        singlesci = '%s_reg_%s_single_sci.fits' % (
                            outrootFE, exp.rootname)
                        subsci = '%s-e%02i_%s_single_sub_sci.fits' % (
                            outrootFE, tempepoch, exp.rootname)
                        regscilist.append(singlesci)
                        subscilist.append(subsci)
                for regsci, subsci in zip(regscilist, subscilist):
                    if not os.path.isfile(tempsci) or not os.path.isfile(
                            regsci):
                        print("Can't create diff image %s" % subsci)
                        print("  missing either  %s" % tempsci)
                        print("    or  %s" % regsci)
                        continue

                    regwht = regsci.replace('_sci.fits', '_wht.fits')
                    regbpx = regsci.replace('_sci.fits', '_bpx.fits')

                    diffim = imarith.imsubtract(tempsci, regsci,
                                                outfile=subsci,
                                                clobber=clobber,
                                                verbose=verbose, debug=debug)
                    diffwht = imarith.combine_ivm_maps(regwht, tempwht,
                                                       diffim.replace(
                                                           'sci.fits',
                                                           'wht.fits'),
                                                       clobber=clobber,
                                                       verbose=verbose)
                    diffbpx = badpix.unionmask(tempbpx, regbpx,
                                               diffim.replace('sci.fits',
                                                              'bpx.fits'),
                                               clobber=clobber,
                                               verbose=verbose)
                    diffim_masked = badpix.applymask(diffim, diffbpx,
                                                     clobber=clobber,
                                                     verbose=verbose)
                    if clean:
                        # delete the sub_sci.fits, b/c it is superseded
                        os.remove(diffim)
                    print("Created diff image %s using reg_sci image %s, "
                          "template %s, wht map %s, and bpx mask %s" % (
                              diffim_masked, regsci, tempsci, diffwht,
                              diffbpx))
                    if ((combinefilterdict['method'] == 'avg') and (
                            filter in combinefilterdict['filterlist'])):
                        diffimfile = os.path.abspath(diffim_masked)
                        diffwhtfile = os.path.abspath(diffwht)
                        combinefilterdict['diffimfiles'][epoch][
                            filter] = diffimfile
                        combinefilterdict['diffwhtfiles'][epoch][
                            filter] = diffwhtfile
                os.chdir(topdir)
            pass  # end for epoch in epochlist
        pass  # end for filter in filterlist

    # STAGE 6.5
    # add together difference image products from multiple filters
    if combinefilterdict['method'] == 'avg':
        for epoch in epochlist:
            if epoch == tempepoch:
                continue
            filterkeylist = combinefilterdict['diffimfiles'][epoch].keys()
            if len(filterkeylist) == 0:
                print("No suitable diff images for combination.")
                continue
            difflist = [combinefilterdict['diffimfiles'][epoch][f] for f in
                        filterkeylist]
            whtlist = [combinefilterdict['diffwhtfiles'][epoch][f] for f in
                       filterkeylist]
            outfile = difflist[0].replace(combinefilterdict['filterlist'][0],
                                          combinefilterdict['name'])
            outwht = whtlist[0].replace(combinefilterdict['filterlist'][0],
                                        combinefilterdict['name'])
            imarith.imweightedaverage(difflist, whtlist, outfile, outwht,
                                      clobber=clobber, verbose=verbose)
            print("Created composite diff image %s by adding together "
                  "filters %s in epoch %02i" % (
                      outfile, ','.join(combinefilterdict['filterlist']),
                      epoch))

    # STAGE 7
    # Drizzle together all specified non-template epochs into a single stack
    # e.g. for use in defining the source position
    if dostack:
        if verbose:
            print("sndrizpipe : (7) STACK : stack together source images.")
        topdir = os.path.abspath('.')
        stackdir = '%s.stack' % outroot
        if stackepochs is not None:
            if type(stackepochs) in [str, int, float]:
                stackepochs = [int(ep) for ep in str(stackepochs).split(',')]
            if tempepoch in stackepochs:
                stacktemplate = True
        else:
            stackepochs = onlyepochs
        if not os.path.isdir(stackdir):
            os.mkdir(stackdir)
        for filter in filterlist:
            if onlyfilters and filter not in onlyfilters:
                continue
            fltlistStack = []
            for epoch in epochlist:
                if stackepochs and epoch not in stackepochs:
                    continue
                if epoch == tempepoch and not stacktemplate:
                    continue
                explistFE = [exp for exp in explist if
                             exp.filter == filter and exp.epoch == epoch]
                if len(explistFE) == 0:
                    continue
                epochdirFE = explistFE[0].epochdir
                fltlistStack += [os.path.join(epochdirFE, exp.filename) for exp
                                 in explistFE]

            if len(fltlistStack) == 0:
                print("Cannot create a stack for filter %s : "
                      "no non-template images available." % filter)
                if verbose:
                    print("Use --stacktemplate to allow template images "
                          "to be included, or specify"
                          "particular epochs with --stackepochs X,Y,Z")
                continue

            for flt in fltlistStack:
                if not os.path.exists(
                        os.path.join(stackdir, os.path.basename(flt))):
                    shutil.copy(flt, stackdir)
            fltlistStack = [os.path.basename(flt) for flt in fltlistStack]
            outrootStack = outroot + '_%s_stack' % filter.lower()
            outsciStack = os.path.join(stackdir,
                                       outrootStack + '_drz_sci.fits')
            if os.path.isfile(outsciStack):
                print(" Stacked image %s already exists " % outsciStack)
                if not clobber:
                    print(" Not clobbering. ")
                    continue
            if verbose:
                if stackepochs:
                    epochstr = ','.join(
                        [str(ep) for ep in stackepochs]).rstrip(',')
                else:
                    epochstr = 'ALL'
                print(" Constructing stacked image %s_drz_sci.fits "
                      "from epochs %s" % (outrootStack, epochstr))

            # set the combine type carefully, as above for the driz2 stage.
            combine_type = 'iminmed'
            if singlestar or len(fltlistStack) > 7:
                combine_type = 'imedian'

            if stackpixscale is None:
                stackpixscale = pixscale
            if stackpixfrac is None:
                stackpixfrac = pixfrac
            os.chdir(stackdir)
            outscilist, outwhtlist, outbpxlist = drizzle.secondDrizzle(
                fltlistStack, outrootStack, refimage=None, ra=ra, dec=dec,
                rot=rot, imsize_arcsec=imsize_arcsec, wht_type=wht_type,
                pixscale=stackpixscale, pixfrac=stackpixfrac, driz_cr=drizcr,
                driz_cr_snr=drizcrsnr, singlesci=False, clean=clean,
                combine_type=combine_type, clobber=clobber, verbose=verbose,
                debug=debug)

            os.chdir(topdir)
            # make a stacked diff image (for locating SN center)
            drzsuffix = explistFE[0].drzsuffix
            tempdir = os.path.join(os.path.abspath(topdir),
                                   outroot + '.e%02i' % tempepoch)
            tempsci = os.path.join(tempdir, '%s_%s_e%02i_reg_%s_sci.fits' % (
                outroot, filter, tempepoch, drzsuffix))
            subsciStack = os.path.join(os.path.abspath(stackdir), (
                        outrootStack + "-e%02i_sub_sci.fits" % tempepoch))
            if os.path.isfile(tempsci):
                print(" Making diff image from the stack %s" % outrootStack)
                diffim = imarith.imsubtract(tempsci, outsciStack,
                                            outfile=subsciStack,
                                            clobber=clobber, verbose=verbose,
                                            debug=debug)
            pass  # end for filter in filterlist

    if clean > 1:
        topdir = os.path.abspath('.')
        if verbose:
            print("sndrizpipe : (7) CLEAN level 2 : remove OrIg flt files.")
            if clean > 2:
                print("Clean level 3 : remove last-drizzle flt files")
        for filter in filterlist:
            if onlyfilters and filter not in onlyfilters:
                continue
            for epoch in epochlist:
                if onlyepochs and epoch not in onlyepochs:
                    continue
                explistFE = [exp for exp in explist if
                             exp.filter == filter and exp.epoch == epoch]
                if len(explistFE) == 0:
                    continue
                epochdirFE = explistFE[0].epochdir
                if not os.path.isdir(epochdirFE):
                    continue
                os.chdir(epochdirFE)
                for exp in explistFE:
                    fltfile = exp.filename
                    fltfileOrIg = os.path.join('OrIg_files', fltfile)
                    if os.path.isfile(fltfileOrIg):
                        os.remove(fltfileOrIg)
                    if clean > 2 and os.path.isfile(fltfile):
                        os.remove(fltfile)
                os.chdir(topdir)

    if clean > 3:
        if verbose:
            print("Clean level 4 : remove single-visit 'nat' "
                  "drizzle and tweakreg products")
            if clean > 4:
                print("Clean level 5 : remove all temporary files "
                      "(race condition possible when processing multiple "
                      "filters in the same epoch simultaneously)")
        for FEVgroup in FEVgrouplist:
            explistFEV = [exp for exp in explist if exp.FEVgroup == FEVgroup]
            if len(explistFEV) == 0:
                continue
            thisepoch = explistFEV[0].epoch
            thisfilter = explistFEV[0].filter
            if onlyepochs and thisepoch not in onlyepochs:
                continue
            if onlyfilters and thisfilter not in onlyfilters:
                continue
            epochdir = explistFEV[0].epochdir
            outrootFEV = '%s_%s_nat' % (outroot, FEVgroup)

            if not os.path.isdir(epochdir):
                continue
            os.chdir(epochdir)
            drzsuffix = explistFEV[0].drzsuffix
            natsci = "%s_%s_sci.fits" % (outrootFEV, drzsuffix)
            if clean > 3 and os.path.isfile(natsci):
                os.remove(natsci)
            natwht = natsci.replace('sci.fits', 'wht.fits')
            if clean > 3 and os.path.isfile(natwht):
                os.remove(natwht)
            natctx = natsci.replace('sci.fits', 'ctx.fits')
            if clean > 3 and os.path.isfile(natctx):
                os.remove(natctx)
            if clean > 3:
                natroot = natsci.replace('.fits', '')
                natcoolist = glob.glob(natroot + '_*.coo') + glob.glob(
                    natroot + '_*.match') + glob.glob(natroot + '_*.list')
                for natcoo in natcoolist:
                    os.remove(natcoo)
            if clean > 4:
                # Nuclear option : causes a race condition when processing
                # with separate filters in the same epoch on separate processes
                tmpmasklist = glob.glob('tmp*staticMask.fits')
                for tmpmask in tmpmasklist:
                    if os.path.exists(tmpmask):
                        os.remove(tmpmask)
                if os.path.exists('OrIg_files'):
                    shutil.rmtree('OrIg_files')

            os.chdir(topdir)

    return 0


def mkparser():
    from textwrap import dedent
    import argparse

    class SmartFormatter(argparse.HelpFormatter):
        def _split_lines(self, text, width):
            # this is the RawTextHelpFormatter._split_lines
            if text.startswith('R|'):
                return text[2:].splitlines()
            return argparse.HelpFormatter._split_lines(self, text, width)

    parser = argparse.ArgumentParser(
        description='Run astrodrizzle and tweakreg on a set of flt, flc or flm'
                    'images, building single-epoch drizzled images '
                    'and diff images.', formatter_class=SmartFormatter)

    # Required positional argument
    parser.add_argument('rootname', help='Root name for the input flt dir'
                                         '(<rootname>.flt), also used for the output '
                                         '_drz products. ')

    # optional arguments :
    parser.add_argument('--filters', metavar='X,Y,Z',
                        help='Process only these filters '
                             '(comma-separated list)', default='')
    parser.add_argument('--epochs', metavar='X,Y,Z',
                        help='Process only these epochs '
                             '(comma-separated list)', default='')

    parser.add_argument('--combinefilterlist', type=str, metavar='X,Y,Z',
                        help='Combine these filters into a single image'
                             ' (comma-seperated list)', default=None)
    parser.add_argument('--combinefiltermethod', type=str,
                        choices=['avg', 'driz'],
                        help='Use a weighted average or drizzling to combine '
                             'multiple filters together', default=None)
    parser.add_argument('--combinefiltername', type=str, metavar='A',
                        help='Name for combined filter ', default=None)

    parser.add_argument('--clobber', action='store_true',
                        help='Turn on clobber mode. [False]', default=False)
    parser.add_argument('--clobberlevel', type=int, dest='clobber',
                        help='Turn up the clobber level (0-10)', default=1)
    parser.add_argument('--verbose', dest='verbose', action='store_true',
                        help='Turn on verbosity. [default is ON]',
                        default=True)
    parser.add_argument('--verboselevel', type=int, dest='verbose',
                        help='Turn up the verbosity (0-10).', default=1)
    parser.add_argument('--quiet', dest='verbose', action='store_false',
                        help='Turn off verbosity. [default is ON]',
                        default=True)
    parser.add_argument('--clean', type=int, choices=[0, 1, 2, 3, 4, 5],
                        default=1, help=dedent("""\
                        R|Clean up cruft:
                        [0] Keep all intermediate files.
                        [1] Remove intermediate drizzle and diff files, '
                            including ctx.fits and sub_sci.fits (the default);
                        [2] and clear out OrIg_files/*fl?.fits;
                        [3] and remove last-drizzle flts in epoch sub-dirs;
                        [4] and delete nat_drz products and tweakreg catalogs;
                        [5] and remove any tmp*staticMask.fits files
                            (Warning: race conditions possible)."""))
    parser.add_argument('--debug', action='store_true',
                        help='Enter debug mode. [False]', default=False)
    parser.add_argument('--dotest', action='store_true',
                        help='Process the SN Stone test data (all other'
                             'options ignored)', default=False)

    parser.add_argument('--singlestar', action='store_true',
                        help='Special case for registering images with only '
                             'a single bright source, e.g. standard stars.',
                        default=False)

    proc = parser.add_argument_group("Processing stages")
    proc.add_argument('--dosetup', action='store_true',
                      help='(1) copy flt files into epoch subdirs',
                      default=False)
    proc.add_argument('--dorefim', action='store_true',
                      help='(2) build the WCS ref image', default=False)
    proc.add_argument('--dodriz1', action='store_true',
                      help='(3) first astrodrizzle pass (pre-registration)',
                      default=False)
    proc.add_argument('--doreg', action='store_true',
                      help='(4) run tweakreg to align with refimage',
                      default=False)
    proc.add_argument('--dodriz2', action='store_true',
                      help='(5) second astrodrizzle pass (registered)',
                      default=False)
    proc.add_argument('--dodiff', action='store_true',
                      help='(6) subtract and mask to make diff images',
                      default=False)
    proc.add_argument('--dostack', action='store_true',
                      help='(7) construct a multi-epoch stack image',
                      default=False)
    proc.add_argument('--doall', action='store_true',
                      help='Run all necessary processing stages',
                      default=False)

    sortpar = parser.add_argument_group("(1) Settings for epoch sorting stage")
    sortpar.add_argument('--mjdmin', metavar='0', type=float,
                         help='All observations prior to this date are put '
                              'into epoch 0.', default=0)
    sortpar.add_argument('--mjdmax', metavar='inf', type=float,
                         help='All observations after this date are put into '
                              'the last epoch.', default=0)
    sortpar.add_argument('--epochspan', metavar='5', type=float,
                         help='Max number of days spanning a single epoch.',
                         default=5)

    refpar = parser.add_argument_group(
        '(2) Settings for constructing the TweakReg '
        'WCS reference image')
    refpar.add_argument('--refimage', metavar='Z.fits',
                        help='Existing tweakreg refimage. Full path required',
                        default='')
    refpar.add_argument('--refepoch', metavar='X', type=int,
                        help='Use this epoch to define the tweakreg refimage',
                        default=0)
    refpar.add_argument('--reffilter', metavar='X',
                        help='Use this filter to define the tweakreg refimage',
                        default='')
    refpar.add_argument('--refvisit', metavar='PID.vis',
                        help='Use this PID.visit to define the tweakreg '
                             'refimage [e.g. 12099.A1]', default='')

    driz1par = parser.add_argument_group(
        "(3) Settings for astrodrizzle stage(s)")
    driz1par.add_argument('--drizcr', type=int, default=1,
                          choices=[-1, 0, 1, 2], help=dedent("""\
R|Astrodrizzle cosmic ray rejection stage:
[-1] remove CR flags and don't add any more;
[0] Keep existing CR flags and don't do any new CR rejection;
[1] Remove CR flags and run CR rejection only within the visit (the default);
[2] Re-run CR flagging at the multi-visit drizzle and stack stages."""))
    driz1par.add_argument('--drizcrsnr', metavar='5,4.5', type=str,
                          help='Sigma values for CR rejection thresholds.',
                          default='5,4.5')

    regpar = parser.add_argument_group('(4) Settings for tweakreg source '
                                       'detection and WCS registration stage')
    regpar.add_argument('--threshold', metavar='5', type=float,
                        help='Detection threshold in sigmas for tweakreg '
                             'object detection.', default=5)
    regpar.add_argument('--peakmin', metavar='X', type=float,
                        help='Require peak flux above this value for tweakreg '
                             'object detection.', default=None)
    regpar.add_argument('--peakmax', metavar='X', type=float,
                        help='Require peak flux below this value for tweakreg '
                             'object detection.', default=None)
    regpar.add_argument('--interactive', action='store_true',
                        help='Run tweakreg interactively (showing plots)',
                        default=False)
    regpar.add_argument('--intravisitreg', action='store_true',
                        help='Run tweakreg before first drizzle stage to do '
                             'intra-visit registration.', default=False)
    regpar.add_argument('--searchrad', metavar='X', type=float,
                        help='Search radius in arcsec for tweakreg '
                             'catalog matching.', default=1.5)
    regpar.add_argument('--minobj', metavar='N', type=int,
                        help='Minimum number matched objects for '
                             'tweakreg registration.', default=10)
    regpar.add_argument('--refcat', metavar='X.cat',
                        help='Existing source catalog for limiting '
                             'tweakreg matches.', default='')
    regpar.add_argument('--rfluxmin', metavar='X', type=float,
                        help='Limit the tweakreg reference catalog to objects '
                             'brighter than this magnitude.', default=None)
    regpar.add_argument('--rfluxmax', metavar='X', type=float,
                        help='Limit the tweakreg reference catalog to objects '
                             'fainter than this magnitude.', default=None)
    regpar.add_argument('--refnbright', metavar='N', type=int,
                        help='Number of brightest objects to use from the '
                             'tweakreg reference catalog.', default=None)
    regpar.add_argument('--shiftonly', action='store_true',
                        help='Only allow a shift for image alignment. '
                             'No rotation or scale.', default=False)
    regpar.add_argument('--nbright', metavar='N', type=int,
                        help='Number of brightest objects to use from each '
                             'single-exposure source catalog.', default=None)
    regpar.add_argument('--nclip', metavar='3', type=int,
                        help='Number of sigma-clipping iterations for '
                             'catalog matching.', default=3)
    regpar.add_argument('--sigmaclip', metavar='3.0', type=float,
                        help='Clipping limit in sigmas, for catalog matching',
                        default=3.0)

    driz2par = parser.add_argument_group(
        "(5) Settings for final astrodrizzle stage")
    driz2par.add_argument('--radec', metavar='X,Y', type=str,
                          help='R.A.,Dec for center of output image '
                               '(decimal degrees)', default=None)
    driz2par.add_argument('--ra', metavar='X', type=float,
                          help='R.A. for center of output image', default=None)
    driz2par.add_argument('--dec', metavar='X', type=float,
                          help='Decl. for center of output image',
                          default=None)
    driz2par.add_argument('--rot', metavar='0', type=float,
                          help='Rotation (deg E of N) for output image',
                          default=0.0)
    driz2par.add_argument('--imsize', metavar='X', type=float,
                          help='Size of output image [arcsec]', default=None)
    driz2par.add_argument('--naxis12', metavar='X,Y', type=str,
                          help='Size of output image [X,Y pixels]',
                          default=None)
    driz2par.add_argument('--pixscale', metavar='X', type=float,
                          help='Pixel scale to use for astrodrizzle.',
                          default=None)
    driz2par.add_argument('--pixfrac', metavar='X', type=float,
                          help='Pixfrac to use for astrodrizzle.',
                          default=None)
    driz2par.add_argument('--wht_type', type=str,
                          help='Type of the weight image.',
                          choices=['IVM', 'EXP'], default='IVM')
    driz2par.add_argument('--singlesci', action='store_true',
                          help='Make individual-exposure _single_sci.fits '
                               'images. (also set by --singlesubs)',
                          default=False)

    diffpar = parser.add_argument_group("(6) Settings for subtraction stage")
    diffpar.add_argument('--singlesubs', action='store_true',
                         help='Make diff images from the individual-exposure '
                              '_single_sci.fits images. Also sets --singlesci',
                         default=False)
    diffpar.add_argument('--tempepoch', metavar='0', type=int,
                         help='Template epoch.', default=0)
    diffpar.add_argument('--tempfilters', metavar='X,Y', type=str,
                         help='Make a composite template by combining '
                              'images in these filters.', default=None)

    stackpar = parser.add_argument_group(
        "(7) Settings for multi-epoch stack stage")
    stackpar.add_argument('--stacktemplate', action='store_true',
                          help='Include the template epoch in the '
                               'multi-epoch stack.', default=False)
    stackpar.add_argument('--stackpixscale', metavar='X', type=float,
                          help='Set the pixel scale for the '
                               'multi-epoch stack.', default=None)
    stackpar.add_argument('--stackpixfrac', metavar='X', type=float,
                          help='Set the pixfrac for the '
                               'multi-epoch stack.', default=None)
    stackpar.add_argument('--stackepochs', metavar='X,Y,Z', type=str,
                          help='Specify the epochs to combine for the '
                               'multi-epoch stack.', default=None)

    return parser


def main():
    parser = mkparser()
    argv = parser.parse_args()

    if argv.dotest:
        from sndrizpipe import testpipe
        testpipe.doalltest()
        return 0

    ra, dec = None, None
    if argv.ra is not None and argv.dec is not None:
        ra, dec = argv.ra, argv.dec
    elif argv.radec is not None:
        ra, dec = [float(x) for x in argv.radec.split(',')]

    combinefilterdict = {'method': None, 'name': None, 'filterlist': None}
    if argv.combinefilterlist:
        if not argv.combinefiltername or not argv.combinefiltermethod:
            raise SyntaxError(
                "When specifying a set of bands to be combined (using "
                "--combinefilterlist), you must also specify "
                "a name for the combination using --combinebandname and "
                "a method (driz or add) e.g., "
                "--combinefilterlist F125W,F160W  --combinefiltername JH "
                "--combinefiltermethod add")
        combinefilterdict['name'] = argv.combinefiltername
        combinefilterdict['filterlist'] = argv.combinefilterlist.lower().split(
            ',')
        combinefilterdict['method'] = argv.combinefiltermethod.lower()

    # Run the pipeline :
    runpipe(argv.rootname, onlyfilters=(argv.filters or []),
            onlyepochs=(argv.epochs or []),
            combinefilterdict=combinefilterdict, doall=argv.doall,
            dosetup=argv.dosetup, dorefim=argv.dorefim, dodriz1=argv.dodriz1,
            doreg=argv.doreg, dodriz2=argv.dodriz2, dodiff=argv.dodiff,
            dostack=argv.dostack, drizcr=argv.drizcr, drizcrsnr=argv.drizcrsnr,
            intravisitreg=argv.intravisitreg, refim=argv.refimage,
            refepoch=argv.refepoch, refvisit=argv.refvisit,
            reffilter=argv.reffilter, tempepoch=argv.tempepoch,
            tempfilters=argv.tempfilters, refcat=argv.refcat,
            interactive=argv.interactive, peakmin=argv.peakmin,
            peakmax=argv.peakmax, rfluxmax=argv.rfluxmin,
            rfluxmin=argv.rfluxmax, refnbright=argv.refnbright,
            nbright=argv.nbright, searchrad=argv.searchrad,
            threshold=argv.threshold, nclip=argv.nclip,
            sigmaclip=argv.sigmaclip, minobj=argv.minobj,
            shiftonly=argv.shiftonly, singlestar=argv.singlestar,
            mjdmin=argv.mjdmin, mjdmax=argv.mjdmax, epochspan=argv.epochspan,
            ra=ra, dec=dec, rot=argv.rot, imsize_arcsec=argv.imsize,
            naxis12=argv.naxis12, pixscale=argv.pixscale, pixfrac=argv.pixfrac,
            wht_type=argv.wht_type, clean=argv.clean,
            singlesubs=argv.singlesubs,
            singlesci=(argv.singlesci or argv.singlesubs),
            stackepochs=argv.stackepochs, stackpixscale=argv.stackpixscale,
            stackpixfrac=argv.stackpixfrac, clobber=argv.clobber,
            verbose=argv.verbose, debug=argv.debug)
    return 0


#if __name__ == "__main__":
#    main()
