# Source code for drizzlepac.catalogs

    """
    :Authors: Warren Hack

    :License: :doc:`LICENSE`

    """
    from __future__ import absolute_import, division, print_function
    import os, sys
    import copy
    from distutils.version import LooseVersion

    import numpy as np
    #import pywcs
    import astropy
    from astropy import wcs as pywcs
    import astropy.coordinates as coords
    from astropy import units as u
    from stsci.tools import logutil, textutil
    from stsci.skypac.utils import basicFITScheck, get_extver_list

    import stwcs
    from stwcs import wcsutil
    from astropy.io import fits
    import stsci.imagestats as imagestats
    import pyregion

    #import idlphot
    from . import tweakutils, util
    from .mapreg import _AuxSTWCS

    ASTROPY_VER_GE13 = LooseVersion(astropy.__version__) >= LooseVersion('1.3')

    COLNAME_PARS = ['xcol','ycol','fluxcol']
    CATALOG_ARGS = ['sharpcol','roundcol','hmin','fwhm','maxflux','minflux','fluxunits','nbright']+COLNAME_PARS

    REFCOL_PARS = ['refxcol','refycol','rfluxcol']
    REFCAT_ARGS = ['rmaxflux','rminflux','rfluxunits','refnbright']+REFCOL_PARS

    sortKeys = ['minflux','maxflux','nbright','fluxunits']

    log = logutil.create_logger(__name__, level=logutil.logging.NOTSET)

    def generateCatalog(wcs, mode='automatic', catalog=None,
                        src_find_filters=None, **kwargs):
        """ Function which determines what type of catalog object needs to be
            instantiated based on what type of source selection algorithm the user
            specified.

            Parameters
            ----------
            wcs : obj
                WCS object generated by STWCS or PyWCS
            catalog : str or ndarray
                Filename of existing catalog or ndarray of image for generation of source catalog.
            kwargs : dict
                Parameters needed to interpret source catalog from input catalog
                with `findmode` being required.

            Returns
            -------
            catalog : obj
                A Catalog-based class instance for keeping track of WCS and
                associated source catalog
        """
        if not isinstance(catalog,Catalog):
            if mode == 'automatic': # if an array is provided as the source
                # Create a new catalog directly from the image
                catalog = ImageCatalog(wcs,catalog,src_find_filters,**kwargs)
            else: # a catalog file was provided as the catalog source
                catalog = UserCatalog(wcs,catalog,**kwargs)

        return catalog

    class Catalog(object):
        """ Base class for keeping track of a source catalog for an input WCS

            .. warning:: This class should never be instantiated by itself,
                         as necessary methods are not defined yet.
        """
        PAR_PREFIX = ''
        PAR_NBRIGHT_PREFIX = ''

        def __init__(self, wcs, catalog_source, **kwargs):
            """
            This class requires the input of a WCS and a source for the catalog,
            along with any arguments necessary for interpreting the catalog.

            Parameters
            ----------
            wcs : obj
                Input WCS object generated using STWCS or HSTWCS
            catalog_source : str
                Name of the file from which to read the catalog.
            kwargs : dict
                Parameters for interpreting the catalog file or for performing the source
                extraction from the image. These will be set differently depending on
                the type of catalog being instantiated.
            """
            self.wcs = wcs # could be None in case of user-supplied catalog
            self.xypos = None
            self.in_units = 'pixels'
            self.sharp = None
            self.round1 = None
            self.round2 = None
            self.numcols = None

            self.flux_col = True # keep track of whether fluxes were read in
            self.sharp_col = True # keep track of whether sharpness was read in

            self.origin = 1 # X,Y coords will ALWAYS be FITS 1-based, not numpy 0-based
            self.pars = kwargs
            if 'use_sharp_round' in self.pars:
                self.use_sharp_round = self.pars['use_sharp_round']
            else:
                self.use_sharp_round = False

            self.start_id = 0
            if 'start_id' in self.pars:
                self.start_id = self.pars['start_id']

            self.fname = catalog_source
            self.source = catalog_source
            self.catname = None

            self.num_objects = None

            self.radec = None # catalog of sky positions for all sources on this chip/image
            self.set_colnames()

            self._apply_flux_limits = False # used in child class to control
                                            # source filtering on flux

            # parse task parameters to find flux limits:
            self.minflux = self.pars.get(self.PAR_PREFIX + 'minflux')
            self.maxflux = self.pars.get(self.PAR_PREFIX + 'maxflux')
            self.fluxunits = self.pars.get(self.PAR_PREFIX + 'fluxunits')
            self.nbright = self.pars.get(self.PAR_NBRIGHT_PREFIX + 'nbright')

        def generateXY(self, **kwargs):
            """ Method to generate source catalog in XY positions
                Implemented by each subclass
            """
            pass

        def set_colnames(self):
            """ Method to define how to interpret a catalog file
                Only needed when provided a source catalog as input
            """
            pass

        def _readCatalog(self):
            pass

        def generateRaDec(self):
            """ Convert XY positions into sky coordinates using STWCS methods
            """
            self.prefix = self.PAR_PREFIX

            if not isinstance(self.wcs,pywcs.WCS):
                print(
                    textutil.textbox(
                        'WCS not a valid PyWCS object. '
                        'Conversion of RA/Dec not possible...'
                        ),
                    file=sys.stderr
                )
                raise ValueError

            if self.xypos is None or len(self.xypos[0]) == 0:
                self.xypos = None
                warnstr = textutil.textbox(
                    'WARNING: \n'
                    'No objects found for this image...'
                )

                for line in warnstr.split('\n'):
                    log.warning(line)

                print(warnstr)

                return

            if self.radec is None:
                print('     Found {:d} objects.'.format(len(self.xypos[0])))
                if self.wcs is not None:
                    ra, dec = self.wcs.all_pix2world(self.xypos[0], self.xypos[1], self.origin)
                    self.radec = [ra, dec] + copy.deepcopy(self.xypos[2:])
                else:
                    # If we have no WCS, simply pass along the XY input positions
                    # under the assumption they were already sky positions.
                    self.radec = copy.deepcopy(self.xypos)

        def apply_exclusions(self,exclusions):
            """ Trim sky catalog to remove any sources within regions specified by
                exclusions file
            """
            # parse exclusion file into list of positions and distances
            exclusion_coords = tweakutils.parse_exclusions(exclusions)
            if exclusion_coords is None:
                return

            excluded_list = []
            radec_indx = list(range(len(self.radec[0])))
            for ra,dec,indx in zip(self.radec[0],self.radec[1],radec_indx):
                src_pos = coords.SkyCoord(ra=ra,dec=dec,unit=(u.hourangle,u.deg))

                # check to see whether this source is within an exclusion region
                for reg in exclusion_coords:
                    if reg['units'] == 'sky':
                        regpos = reg['pos']
                        regdist = reg['distance'] # units: arcsec
                    else:
                        regradec = self.wcs.all_pix2world([reg['pos']],1)[0]
                        regpos = (regradec[0],regradec[1])
                        regdist = reg['distance']*self.wcs.pscale # units: arcsec

                    epos = coords.SkyCoord(ra=regpos[0],dec=regpos[1],unit=(u.hourangle,u.deg))
                    if float(epos.separation(src_pos).to_string(unit=u.arcsec,decimal=True)) <= regdist:
                        excluded_list.append(indx)
                        break
            # create a list of all 'good' sources outside all exclusion regions
            for e in excluded_list: radec_indx.remove(e)
            radec_indx = np.array(radec_indx,dtype=int)
            num_excluded = len(excluded_list)
            if num_excluded > 0:
                radec_trimmed = []
                xypos_trimmed = []
                for arr in self.radec:
                    radec_trimmed.append(arr[radec_indx])
                for arr in self.xypos:
                    xypos_trimmed.append(arr[radec_indx])
                xypos_trimmed[-1] = np.arange(len(xypos_trimmed[0]))
                self.radec = radec_trimmed
                self.xypos = xypos_trimmed
                log.info('Excluded %d sources from catalog.'%num_excluded)

        def apply_flux_limits(self):
            """ Apply any user-specified limits on source selection
                Limits based on fluxes
            """
            if not self._apply_flux_limits:
                return

            # only if limits are set should they be applied
            if ((self.maxflux is None and self.minflux is None) or
                self.fluxunits is None):
                return

            print("\n     Applying flux limits...")
            print("         minflux = {}".format(self.minflux))
            print("         maxflux = {}".format(self.maxflux))
            print("         fluxunits = '{:s}'".format(self.fluxunits))
            print("         nbright = {}".format(self.nbright))

            # start by checking to see whether fluxes were read in to use for
            # applying the limits
            if not self.flux_col:
                print("    WARNING: Catalog did not contain fluxes for use in trimming...")
                return

            if self.xypos is not None and self.radec is not None:
                if len(self.xypos) < len(self.radec):
                    src_cat = self.radec
                else:
                    src_cat = self.xypos
            else:
                src_cat = self.radec if self.xypos is None else self.xypos

            if src_cat is None:
                raise RuntimeError("No catalogs available for filtering")

            if len(src_cat) < 3:
                print("    WARNING: No fluxes read in for catalog for use in trimming...")
                return

            fluxes = copy.deepcopy(src_cat[2])

            # apply limits equally to all .radec and .xypos entries
            # Start by clipping by any specified flux range
            if self.fluxunits == 'mag':
                if self.minflux is None:
                    flux_mask = fluxes >= self.maxflux
                elif self.maxflux is None:
                    flux_mask = fluxes <= self.minflux
                else:
                    flux_mask = (fluxes <= self.minflux) & (fluxes >= self.maxflux)
            else:
                if self.minflux is None:
                    flux_mask = fluxes <= self.maxflux
                elif self.maxflux is None:
                    flux_mask = fluxes >= self.minflux
                else:
                    flux_mask = (fluxes >= self.minflux) & (fluxes <= self.maxflux)

            if self.radec is None:
                all_radec = None
            else:
                all_radec = [rd[flux_mask].copy() for rd in self.radec]

            if self.xypos is None:
                all_xypos = None
            else:
                all_xypos = [xy[flux_mask].copy() for xy in self.xypos]

            nrem = flux_mask.size - np.count_nonzero(flux_mask)
            print("     Removed {:d} sources based on flux limits.".format(nrem))

            if self.nbright is not None:
                print("Selecting catalog based on {} brightest sources".format(self.nbright))
                fluxes = fluxes[flux_mask]

                # find indices of brightest sources
                idx = np.argsort(fluxes)
                if self.fluxunits == 'mag':
                    idx = idx[:self.nbright]
                else:
                    idx = (idx[::-1])[:self.nbright]

                # pick out only the brightest 'nbright' sources
                if all_radec is not None:
                    all_radec = [rd[idx] for rd in all_radec]
                if all_xypos is not None:
                    all_xypos = [xy[idx] for xy in all_xypos]

            self.radec = all_radec
            self.xypos = all_xypos

            if len(self.radec[0]) == 0:
                print("Trimming of catalog resulted in NO valid sources! ")
                raise ValueError

        def buildCatalogs(self, exclusions=None, **kwargs):
            """ Primary interface to build catalogs based on user inputs.
            """
            self.generateXY(**kwargs)
            self.generateRaDec()
            if exclusions:
                self.apply_exclusions(exclusions)

            # apply selection limits as specified by the user:
            self.apply_flux_limits()

        def plotXYCatalog(self, **kwargs):
            """
            Method which displays the original image and overlays the positions
            of the detected sources from this image's catalog.

            Plotting `kwargs` that can be provided are:

                vmin, vmax, cmap, marker

            Default colormap is `summer`.

            """
            try:
                from matplotlib import pyplot as pl
            except:
                pl = None

            if pl is not None: # If the pyplot package could be loaded...
                pl.clf()
                pars = kwargs.copy()

                if 'marker' not in pars:
                    pars['marker'] = 'b+'

                if 'cmap' in pars:
                    pl_cmap = pars['cmap']
                    del pars['cmap']
                else:
                    pl_cmap = 'summer'
                pl_vmin = None
                pl_vmax = None
                if 'vmin' in pars:
                    pl_vmin = pars['vmin']
                    del pars['vmin']
                if 'vmax' in pars:
                    pl_vmax = pars['vmax']
                    del pars['vmax']

                pl.imshow(self.source,cmap=pl_cmap,vmin=pl_vmin,vmax=pl_vmax)
                pl.plot(self.xypos[0]-1,self.xypos[1]-1,pars['marker'])

        def writeXYCatalog(self,filename):
            """ Write out the X,Y catalog to a file
            """
            if self.xypos is None:
                warnstr = textutil.textbox(
                    'WARNING: \n    No X,Y source catalog to write to file. ')
                for line in warnstr.split('\n'):
                    log.warning(line)
                print(warnstr)
                return

            f = open(filename,'w')
            f.write("# Source catalog derived for %s\n"%self.wcs.filename)
            f.write("# Columns: \n")
            if self.use_sharp_round:
                f.write('#    X      Y         Flux       ID      Sharp       Round1       Round2\n')
            else:
                f.write('#    X      Y         Flux       ID\n')
            f.write('#   (%s)   (%s)\n'%(self.in_units,self.in_units))

            for row in range(len(self.xypos[0])):
                for i in range(len(self.xypos)):
                    f.write("%g  "%(self.xypos[i][row]))
                f.write("\n")

            f.close()

    class ImageCatalog(Catalog):
        """ Class which generates a source catalog from an image using
            Python-based, daofind-like algorithms

            Required input `kwargs` parameters::

                computesig, skysigma, threshold, peakmin, peakmax,
                hmin, conv_width, [roundlim, sharplim]

        """
        def __init__(self, wcs, catalog_source, src_find_filters=None, **kwargs):
            # 'src_find_filters' - None or a dictionary. The dictionary
            # MUST contain keys 'region_file' and 'region_file_mode':
            # - 'region_file': the name of the region file that indicates regions
            #   of the image that should be used for source finding
            #   ("include" regions) or regions of the image that should NOT be used
            #   for source finding ("exclude" regions). If it is None - the entire
            #   image will be used for source finding.
            # - 'region_file_mode': 'exclude only' or 'normal' - if 'exclude only' then regular regions are
            #   interpretted as 'exclude' regions and exclude regions (with '-' in front)
            #   are ignored. If 'region_file_mode' = 'normal' then normal DS9 interpretation
            #   of the regions will be applied.
            self.src_find_filters = src_find_filters
            super(ImageCatalog, self).__init__(wcs, catalog_source, **kwargs)
            extind = self.fname.rfind('[')
            self.fnamenoext = self.fname if extind < 0 else self.fname[:extind]
            if self.wcs.extname == ('',None):
                self.wcs.extname = (0)
            self.source = fits.getdata(self.wcs.filename,ext=self.wcs.extname, memmap=False)
            self.nbright = None # No GUI parameter defined yet for this filtering

        def _combine_exclude_mask(self, mask):
            # create masks from exclude/include regions and combine it with the
            # input DQ mask:
            #
            regmask = None
            if self.src_find_filters is not None and \
               'region_file' in self.src_find_filters:
                reg_file_name = self.src_find_filters['region_file']
                if not os.path.isfile(reg_file_name):
                    raise IOError("The 'exclude' region file '{:s}' does not exist."
                                  .format(reg_file_name))
            else:
                return mask

            # get data image size:
            (img_ny, img_nx) = self.source.shape

            # find out if user provided a region file or a mask FITS file:
            reg_file_ext = os.path.splitext(reg_file_name)[-1]
            if reg_file_ext.lower().strip() in ['.fits', '.fit'] and \
               basicFITScheck(reg_file_name):
                # likely we are dealing with a FITS file.
                # check that the file is a simple with 2 axes:
                hdulist = fits.open(reg_file_name, memmap=False)
                extlist = get_extver_list(hdulist,extname=None)
                for ext in extlist:
                    usermask = hdulist[ext].data
                    if usermask.shape == (img_ny, img_nx):
                        regmask = usermask.astype(np.bool)
                        break
                hdulist.close()
                if regmask is None:
                    raise ValueError("None of the image-like extensions in the "
                                     "user-provided exclusion mask '{}' has a "
                                     "correct shape".format(reg_file_name))

            else:
                # we are dealing with a region file:
                reglist = pyregion.open(reg_file_name)

                ## check that regions are in image-like coordinates:
                ##TODO: remove the code below once 'pyregion' package can correctly
                ##      (DS9-like) convert sky coordinates to image coordinates for all
                ##      supported shapes.
                #if not all([ (x.coord_format == 'image' or \
                #              x.coord_format == 'physical') for x in reglist]):
                #    print("WARNING: Some exclusion regions are in sky coordinates.\n"
                #          "         These regions will be ignored.")
                #    # filter out regions in sky coordinates:
                #    reglist = pyregion.ShapeList(
                #        [x for x in reglist if x.coord_format == 'image' or \
                #         x.coord_format == 'physical']
                #    )

                #TODO: comment out next lines if we do not support region files
                #      in sky coordinates and uncomment previous block:
                # Convert regions from sky coordinates to image coordinates:
                auxwcs    = _AuxSTWCS(self.wcs)
                reglist = reglist.as_imagecoord(auxwcs, rot_wrt_axis=2)

                # if all regions are exclude regions, then assume that the entire image
                # should be included and that exclude regions exclude from this
                # rectangular region representing the entire image:
                if all([x.exclude for x in reglist]):
                    # we slightly widen the box to make sure that
                    # the entire image is covered:
                    imreg = pyregion.parse("image;box({:.1f},{:.1f},{:d},{:d},0)"
                                           .format((img_nx+1)/2.0, (img_ny+1)/2.0,
                                                   img_nx+1, img_ny+1)
                                           )

                    reglist = pyregion.ShapeList(imreg + reglist)

                # create a mask from regions:
                regmask = np.asarray(
                    reglist.get_mask(shape=(img_ny, img_nx)),
                    dtype=np.bool
                )

            if mask is not None and regmask is not None:
                mask = np.logical_and(regmask, mask)
            else:
                mask = regmask

            #DEBUG:
            if mask is not None:
                fn = os.path.splitext(self.fname)[0] + '_srcfind_mask.fits'
                if ASTROPY_VER_GE13:
                    fits.writeto(fn, mask.astype(dtype=np.uint8), overwrite=True)
                else:
                    fits.writeto(fn, mask.astype(dtype=np.uint8), clobber=True)

            return mask

        def generateXY(self, **kwargs):
            """ Generate source catalog from input image using DAOFIND-style algorithm
            """
            #x,y,flux,sharp,round = idlphot.find(array,self.pars['hmin'],self.pars['fwhm'],
            #                    roundlim=self.pars['roundlim'], sharplim=self.pars['sharplim'])
            print("  #  Source finding for '{}', EXT={} started at: {}"
                  .format(self.fnamenoext, self.wcs.extname, util._ptime()[0]))
            if self.pars['computesig']:
                # compute sigma for this image
                sigma = self._compute_sigma()
            else:
                sigma = self.pars['skysigma']
            skymode = sigma**2
            log.info('   Finding sources using sky sigma = %f'%sigma)
            if self.pars['threshold'] in [None,"INDEF",""," "]:
                hmin = skymode
            else:
                hmin = sigma*self.pars['threshold']

            if 'mask' in kwargs and kwargs['mask'] is not None:
                dqmask = np.asarray(kwargs['mask'], dtype=bool)
            else:
                dqmask = None

            # get the mask for source finding:
            mask = self._combine_exclude_mask(dqmask)

            x, y, flux, src_id, sharp, round1, round2 = tweakutils.ndfind(
                self.source,
                hmin,
                self.pars['conv_width'],
                skymode,
                sharplim=[self.pars['sharplo'],self.pars['sharphi']],
                roundlim=[self.pars['roundlo'],self.pars['roundhi']],
                peakmin=self.pars['peakmin'],
                peakmax=self.pars['peakmax'],
                fluxmin=self.pars['fluxmin'],
                fluxmax=self.pars['fluxmax'],
                nsigma=self.pars['nsigma'],
                ratio=self.pars['ratio'],
                theta=self.pars['theta'],
                mask=mask,
                use_sharp_round=self.use_sharp_round,
                nbright=self.nbright
            )

            if len(x) == 0:
                if  not self.pars['computesig']:
                    sigma = self._compute_sigma()
                    hmin = sigma * self.pars['threshold']
                    log.info('No sources found with original thresholds. Trying automatic settings.')
                    x, y, flux, src_id, sharp, round1, round2 = tweakutils.ndfind(
                        self.source,
                        hmin,
                        self.pars['conv_width'],
                        skymode,
                        sharplim=[self.pars['sharplo'],self.pars['sharphi']],
                        roundlim=[self.pars['roundlo'],self.pars['roundhi']],
                        peakmin=self.pars['peakmin'],
                        peakmax=self.pars['peakmax'],
                        fluxmin=self.pars['fluxmin'],
                        fluxmax=self.pars['fluxmax'],
                        nsigma=self.pars['nsigma'],
                        ratio=self.pars['ratio'],
                        theta=self.pars['theta'],
                        mask = mask,
                        use_sharp_round = self.use_sharp_round,
                        nbright=self.limits.get('nbright')
                    )
            if len(x) == 0:
                xypostypes = 3*[float]+[int]+(3 if self.use_sharp_round else 0)*[float]
                self.xypos = [np.empty(0, dtype=i) for i in xypostypes]
                warnstr = textutil.textbox('WARNING: \n'+
                    'No valid sources found with the current parameter values!')
                for line in warnstr.split('\n'):
                    log.warning(line)
                print(warnstr)
            else:
                # convert the positions from numpy 0-based to FITS 1-based
                if self.use_sharp_round:
                    self.xypos = [x+1, y+1, flux, src_id+self.start_id, sharp, round1, round2]
                else:
                    self.xypos = [x+1, y+1, flux, src_id+self.start_id]

            log.info('###Source finding finished at: %s'%(util._ptime()[0]))

            self.in_units = 'pixels' # Not strictly necessary, but documents units when determined
            self.sharp = sharp
            self.round1 = round1
            self.round2 = round2
            self.numcols = 7 if self.use_sharp_round else 4
            self.num_objects = len(x)
            self._apply_flux_limits = False # limits already applied by 'ndfind'

        def _compute_sigma(self):
            src_vals = self.source
            if np.any(np.isnan(self.source)):
                src_vals = self.source[np.where(np.isnan(self.source) == False)]
            istats = imagestats.ImageStats(src_vals, nclip=3,
                                           fields='mode,stddev', binwidth=0.01)
            sigma = np.sqrt(2.0 * np.abs(istats.mode))
            return sigma

    class UserCatalog(Catalog):
        """ Class to manage user-supplied catalogs as inputs.

            Required input `kwargs` parameters::

                xyunits, xcol, ycol[, fluxcol, [idcol]]

        """
        COLNAMES = COLNAME_PARS
        IN_UNITS = None

        def __init__(self, wcs, catalog_source, **kwargs):
            super(UserCatalog, self).__init__(wcs, catalog_source, **kwargs)
            self._apply_flux_limits = True

        def set_colnames(self):
            self.colnames = []

            cnum = 1
            for cname in self.COLNAMES:
                if cname in self.pars and not util.is_blank(self.pars[cname]):
                    self.colnames.append(self.pars[cname])
                else:
                    # Insure that at least x and y columns had default values
                    if 'fluxcol' not in cname:
                        self.colnames.append(str(cnum))
                    cnum += 1

            # count the number of columns
            self.numcols = len(self.colnames)

            if self.IN_UNITS is not None:
                self.in_units = self.IN_UNITS
            else:
                self.in_units = self.pars['xyunits']

        def _readCatalog(self):
            # define what columns will be read
            # The following loops
            #colnums = [self.pars['xcol']-1,self.pars['ycol']-1,self.pars['fluxcol']-1]

            # read the catalog now, one for each chip/mosaic
            # Currently, this only supports ASCII catalog files
            # Support for FITS tables needs to be added
            catcols = tweakutils.readcols(self.source, cols=self.colnames)
            if not util.is_blank(catcols) and len(catcols[0]) == 0:
                catcols = None
            return catcols

        def generateXY(self, **kwargs):
            """
            Method to interpret input catalog file as columns of positions and fluxes.
            """
            self.num_objects = 0
            xycols = self._readCatalog()

            if xycols is not None:
                # convert the catalog into attribute
                self.xypos = xycols[:3]
                # convert optional columns if they are present
                if self.numcols > 3:
                    self.xypos.append(np.asarray(xycols[3], dtype=int)) # source ID
                if self.numcols > 4:
                    self.sharp = xycols[4]
                if self.numcols > 5:
                    self.round1 = xycols[5]
                if self.numcols > 6:
                    self.round2 = xycols[6]
                self.num_objects = len(xycols[0])

            if self.numcols < 3: # account for flux column
                self.xypos.append(np.zeros(self.num_objects, dtype=float))
                self.flux_col = False

            if self.numcols < 4: # add source ID column
                self.xypos.append(np.arange(self.num_objects)+self.start_id)

            if self.use_sharp_round:
                for i in range(len(self.xypos), 7):
                    self.xypos.append(np.zeros(self.num_objects, dtype=float))
                self.sharp_col = False

            if self.pars['xyunits'] == 'degrees':
                self.radec = [x.copy() for x in self.xypos]
                if self.wcs is not None:
                    self.xypos[:2] = list(self.wcs.all_world2pix(np.array(self.xypos[:2]).T, self.origin).T)

        def plotXYCatalog(self, **kwargs):
            """
            Plots the source catalog positions using matplotlib's `pyplot.plot()`

            Plotting `kwargs` that can also be passed include any keywords understood
            by matplotlib's `pyplot.plot()` function such as::

                vmin, vmax, cmap, marker

            """
            try:
                from matplotlib import pyplot as pl
            except:
                pl = None

            if pl is not None:
                pl.clf()
                pl.plot(self.xypos[0],self.xypos[1],**kwargs)

    class RefCatalog(UserCatalog):
        """ Class which manages a reference catalog.

        Notes
        -----
        A *reference catalog* is defined as a catalog of undistorted source positions
        given in RA/Dec which would be used as the master list for subsequent
        matching and fitting.

        """
        COLNAMES = REFCOL_PARS
        IN_UNITS = 'degrees'
        PAR_PREFIX = "r"
        PAR_NBRIGHT_PREFIX = 'ref'

        def __init__(self, wcs, catalog_source, **kwargs):
            super(RefCatalog, self).__init__(wcs, catalog_source, **kwargs)
            self._apply_flux_limits = True

        def generateXY(self, **kwargs):
            return

        def generateRaDec(self):
            self.prefix = self.PAR_PREFIX
            if isinstance(self.source,list):
                self.radec = self.source
            else:
                self.radec = self._readCatalog()

        def buildXY(self,catalogs):
            return