import os
from copy import deepcopy
import logging

from stsci.tools import wcsutil

from hstaxe.axeerror import aXeError
from hstaxe.config import (getCONF, getDATA,
                          getOUTPUT, get_ext_info)

from . import configfile
from . import axeiol


# make sure there is a logger
_log = logging.getLogger(__name__)

class Sex2GolPy:
    """This task generates a Grism Object List file using an Input Object List."""

    def __init__(self, grisim, config,
                 in_sex=None,
                 dirname=None,
                 out_sex=None,
                 spec_hdu=None,
                 dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """

        # store some parameters
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None

        # determine the grism image extensions
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)

        # determine the grism image extensions
        self.dirname, self.dirname_extinfo = self._get_dirname_information(dirname,
                                                                           config,
                                                                           grisim,
                                                                           self.grism_extinfo,
                                                                           dir_hdu)

        # get information on the input and output lists
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
                                                             self.dirname_extinfo,
                                                             self.grisim,
                                                             self.grism_extinfo,
                                                             in_sex, out_sex)

        # save a name for stdout
        self.stdout = getOUTPUT("pysex2gol.stdout")

    def __str__(self):
        """String method for the class"""
        # define the prefix
        prefix = "py_SEX2GOL: "

        # compose the feedback
        big_str = "{0:s}  Setup:\n".format(prefix)
        big_str += "{0:s}  Input g/prism image:      {0:s} \n".format(prefix, self.grisim)
        big_str += "{0:s}  Configuration file name:  {0:s} \n".format(prefix, self.config)
        big_str += "{0:s}  Direct image:             {0:s} \n".format(prefix, self.dirname)
        big_str += "{0:s}  G/Prism extension:        {0:s} \n".format(prefix, self.grism_extinfo['axe_ext'])
        big_str += "{0:s}  Direct image extension:   {0:s} \n".format(prefix, self.dirname_extinfo['axe_ext'])
        big_str += "{0:s}  Input catalog name:       {0:s} \n".format(prefix, self.in_sex)
        big_str += "{0:s}  Output catalog name:      {0:s}   ".format(prefix, self.out_sex)

        # return the string
        return big_str

    def _cleanup(self):
        """Clean up files created for stdout

        This is a cleaning procedure in case nothing bad happened.
        """
        # delete stdout/stderr
        if os.path.isfile(self.stdout):
            os.unlink(self.stdout)

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """

        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)

        else:
            # make by hand the extension information
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu-1}

        # return the extension info
        return ext_info

    def _get_dirname_information(self,
                                 dirname=None,
                                 config="",
                                 grisim="",
                                 grism_extinfo=None,
                                 dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        # check whether ANY direct image information exists
        if ((dirname is None) and (dir_hdu is None)):
            # set the grism image as direct image
            dirname = grisim
            dirname_extinfo = grism_extinfo

        elif ((dirname is not None) and (dir_hdu is None)):
            # load the configuration file;
            # determine the extension information
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf

        elif ((dirname is not None) and (dir_hdu is not None)):
            # make by hand the extension information
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu-1}

        else:
            # error and out
            err_msg = ("Specifying NO direct image but a direct image HDU: "
                       "{0:d} makrs NO sense!".format(dir_hdu))
            raise aXeError(err_msg)

        # return the name and the extension info
        return dirname, dirname_extinfo

    def _resolve_list_names(self, dirname='',
                            dirname_extinfo=None,
                            grisim='',
                            grism_extinfo=None,
                            in_sex=None,
                            out_sex=None):
        """Determine the lists for input and output.

        Parameters
        ----------
        dirname : str
            The direct image name
        dirname_extinfo : dict
            A dictionary that contains the direct
            header and data information
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            A dictionary that contains the grism
            header and data information
        in_sex : str
            The name of the source extractor catalog
            that goes with the direct image
        out_sex : str
            The name of the output grism object list
            that is created using the input catalog

        Returns
        -------
        A tuple of the names of the input and output catalog names
        """
        # compose the default name
        if in_sex is None:
            # compose the filename from the direct image name
            in_sex = dirname.replace(".fits", "_{0:d}.cat"
                                     .format(dirname_extinfo['axe_ext']))

        # check whether the explicitly given filename exists
        if not os.path.isfile(in_sex):
            err_msg = ("The Input Object List: {0:s}  does not exist!"
                       .format(in_sex))
            raise aXeError(err_msg)

        if out_sex is None:
            # compose the name for the output GOL
            out_sex = os.path.basename(grisim).replace(".fits", "_{0:d}.cat".format(grism_extinfo['axe_ext']))

        # return the IOL and the GOL names
        return in_sex, out_sex

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""

        # load the IOL into an astropy table
        # the table is in iol.catalog
        self.iol = axeiol.InputObjectList(self.in_sex)

        # check for an empty table
        if len(self.iol.catalog) < 1:
            _log.info("Empty catalog found\n")
            return None

        # create a new GOL that's a copy of the input list
        self.gol = deepcopy(self.iol.catalog) # just make a copy

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        # compose the WCS-term for the direct and grism images
        dir_term = getDATA("{0:s} [{1:d}]".format(self.dirname, self.dirname_extinfo['fits_ext']))
        gri_term = getDATA("{0:s} [{1:d}]".format(self.grisim, self.grism_extinfo['fits_ext']))

        # generate the WCS objects
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)

        # go over each row in the catalog
        for row in self.gol:

            # make a position tuple
            try:
                xy_direct = (row['X_IMAGE'], row['Y_IMAGE'])
            except KeyError:          
                # self._treat_NULL_table
                raise aXeError("No coordinate columns in catalog, empty?")

            # convert to RADEC using the direct image
            radec_pos = dir_wcs.xy2rd(xy_direct)

            # convert to XY on grism image
            xy_grism = gri_wcs.rd2xy(radec_pos)

            # store projected vals in the GOL
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])

    # def _treat_NULL_table(self, out_name):
    #     """Transfer an empty table.

    #     Parameters
    #     ----------
    #     out_name : str
    #         The name of the output file


    #     The header of the empty table is written to the
    #     GOL file.
    #     """
    #     catalog = Table.read(self.in_sex, format='ascii.sextractor')
    #     new_catalog = deepcopy(catalog)
    #     if os.access(out_name, os.F_OK):
    #         os.remove(out_name)
    #     of = open(out_name, 'w')
    #     for num, name in zip(range(len(new_catalog.colnames)), new_catalog.colnames):
    #         of.write("# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n".format(num+1,
    #                                                               name,
    #                                                               new_catalog[name].description,
    #                                                               str(new_catalog[name].unit))
    #                                                              )
    #     new_catalog.write(of, format='ascii.no_header', overwrite=False)
    #     of.close()

    def run(self, silent=False):
        """Make the SEX2GOL transformations"""
        if not silent:
            _log.info("py_SEX2GOL:  Start processing ...\n",)
        else:
            sout = open(self.stdout, 'w+')
            sout.write(str(self)+"\n")
            sout.write("py_SEX2GOL:  Start processing ...")

        # copy the relevant data to the GOL catalog
        self._copy_catalog()

        # check whether something can be done
        if (self.iol and self.gol):
            # transfer the coordinates
            self._transfer_coos()

            # store the GOL
            # This needs to be stored in the same way as SEXTRACTOR
            outfile = getOUTPUT(self.out_sex)
            if os.access(outfile, os.F_OK):
                os.remove(outfile)
            _log.info("Saving {} objects to {}".format(len(self.gol),outfile))
            of = open(outfile, 'w')
            for num, name in zip(range(len(self.gol.colnames)), self.gol.colnames):
                of.write("# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n".format(num+1, name,
                                                     self.gol[name].description,
                                                     str(self.gol[name].unit)))
            self.gol.write(of, format='ascii.no_header', overwrite=False)
            of.close()

        else:
            # if there are no objects, just copy the empty table
            # header to the GOL
            #self._treat_NULL_table(getOUTPUT(self.out_sex))

            # give feedback
            if not silent:
                _log.info("\npy_SEX2GOL:  Warning! Empty table copied to GOL")
            else:
                # open stdout/stderr
                sout.write("pysex2gol:  Warning! Empty table copied to GOL")

        # give feedback
        if not silent:
            _log.info("     Done")
        else:
            sout.write("     Done\n")
            sout.close()

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        # run the executable
        retcode = self.run(silent=silent)

        # check whether the run was good
        if silent:
            # do the cleaning
            self._cleanup()

        return retcode

95a800f7d13acdde0238376828e9a0beb5eb5f60
<mask token>


class Sex2GolPy:
    <mask token>

    def __init__(self, grisim, config, in_sex=None, dirname=None, out_sex=
        None, spec_hdu=None, dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)
        self.dirname, self.dirname_extinfo = self._get_dirname_information(
            dirname, config, grisim, self.grism_extinfo, dir_hdu)
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
            self.dirname_extinfo, self.grisim, self.grism_extinfo, in_sex,
            out_sex)
        self.stdout = getOUTPUT('pysex2gol.stdout')

    def __str__(self):
        """String method for the class"""
        prefix = 'py_SEX2GOL: '
        big_str = '{0:s}  Setup:\n'.format(prefix)
        big_str += '{0:s}  Input g/prism image:      {0:s} \n'.format(prefix,
            self.grisim)
        big_str += '{0:s}  Configuration file name:  {0:s} \n'.format(prefix,
            self.config)
        big_str += '{0:s}  Direct image:             {0:s} \n'.format(prefix,
            self.dirname)
        big_str += '{0:s}  G/Prism extension:        {0:s} \n'.format(prefix,
            self.grism_extinfo['axe_ext'])
        big_str += '{0:s}  Direct image extension:   {0:s} \n'.format(prefix,
            self.dirname_extinfo['axe_ext'])
        big_str += '{0:s}  Input catalog name:       {0:s} \n'.format(prefix,
            self.in_sex)
        big_str += '{0:s}  Output catalog name:      {0:s}   '.format(prefix,
            self.out_sex)
        return big_str
    <mask token>

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """
        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)
        else:
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu - 1}
        return ext_info

    def _get_dirname_information(self, dirname=None, config='', grisim='',
        grism_extinfo=None, dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        if dirname is None and dir_hdu is None:
            dirname = grisim
            dirname_extinfo = grism_extinfo
        elif dirname is not None and dir_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf
        elif dirname is not None and dir_hdu is not None:
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu - 1}
        else:
            err_msg = (
                'Specifying NO direct image but a direct image HDU: {0:d} makrs NO sense!'
                .format(dir_hdu))
            raise aXeError(err_msg)
        return dirname, dirname_extinfo
    <mask token>

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""
        self.iol = axeiol.InputObjectList(self.in_sex)
        if len(self.iol.catalog) < 1:
            _log.info('Empty catalog found\n')
            return None
        self.gol = deepcopy(self.iol.catalog)

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        dir_term = getDATA('{0:s} [{1:d}]'.format(self.dirname, self.
            dirname_extinfo['fits_ext']))
        gri_term = getDATA('{0:s} [{1:d}]'.format(self.grisim, self.
            grism_extinfo['fits_ext']))
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)
        for row in self.gol:
            try:
                xy_direct = row['X_IMAGE'], row['Y_IMAGE']
            except KeyError:
                raise aXeError('No coordinate columns in catalog, empty?')
            radec_pos = dir_wcs.xy2rd(xy_direct)
            xy_grism = gri_wcs.rd2xy(radec_pos)
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])
    <mask token>

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        retcode = self.run(silent=silent)
        if silent:
            self._cleanup()
        return retcode

<mask token>


class Sex2GolPy:
    <mask token>

    def __init__(self, grisim, config, in_sex=None, dirname=None, out_sex=
        None, spec_hdu=None, dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)
        self.dirname, self.dirname_extinfo = self._get_dirname_information(
            dirname, config, grisim, self.grism_extinfo, dir_hdu)
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
            self.dirname_extinfo, self.grisim, self.grism_extinfo, in_sex,
            out_sex)
        self.stdout = getOUTPUT('pysex2gol.stdout')

    def __str__(self):
        """String method for the class"""
        prefix = 'py_SEX2GOL: '
        big_str = '{0:s}  Setup:\n'.format(prefix)
        big_str += '{0:s}  Input g/prism image:      {0:s} \n'.format(prefix,
            self.grisim)
        big_str += '{0:s}  Configuration file name:  {0:s} \n'.format(prefix,
            self.config)
        big_str += '{0:s}  Direct image:             {0:s} \n'.format(prefix,
            self.dirname)
        big_str += '{0:s}  G/Prism extension:        {0:s} \n'.format(prefix,
            self.grism_extinfo['axe_ext'])
        big_str += '{0:s}  Direct image extension:   {0:s} \n'.format(prefix,
            self.dirname_extinfo['axe_ext'])
        big_str += '{0:s}  Input catalog name:       {0:s} \n'.format(prefix,
            self.in_sex)
        big_str += '{0:s}  Output catalog name:      {0:s}   '.format(prefix,
            self.out_sex)
        return big_str

    def _cleanup(self):
        """Clean up files created for stdout

        This is a cleaning procedure in case nothing bad happened.
        """
        if os.path.isfile(self.stdout):
            os.unlink(self.stdout)

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """
        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)
        else:
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu - 1}
        return ext_info

    def _get_dirname_information(self, dirname=None, config='', grisim='',
        grism_extinfo=None, dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        if dirname is None and dir_hdu is None:
            dirname = grisim
            dirname_extinfo = grism_extinfo
        elif dirname is not None and dir_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf
        elif dirname is not None and dir_hdu is not None:
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu - 1}
        else:
            err_msg = (
                'Specifying NO direct image but a direct image HDU: {0:d} makrs NO sense!'
                .format(dir_hdu))
            raise aXeError(err_msg)
        return dirname, dirname_extinfo

    def _resolve_list_names(self, dirname='', dirname_extinfo=None, grisim=
        '', grism_extinfo=None, in_sex=None, out_sex=None):
        """Determine the lists for input and output.

        Parameters
        ----------
        dirname : str
            The direct image name
        dirname_extinfo : dict
            A dictionary that contains the direct
            header and data information
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            A dictionary that contains the grism
            header and data information
        in_sex : str
            The name of the source extractor catalog
            that goes with the direct image
        out_sex : str
            The name of the output grism object list
            that is created using the input catalog

        Returns
        -------
        A tuple of the names of the input and output catalog names
        """
        if in_sex is None:
            in_sex = dirname.replace('.fits', '_{0:d}.cat'.format(
                dirname_extinfo['axe_ext']))
        if not os.path.isfile(in_sex):
            err_msg = 'The Input Object List: {0:s}  does not exist!'.format(
                in_sex)
            raise aXeError(err_msg)
        if out_sex is None:
            out_sex = os.path.basename(grisim).replace('.fits',
                '_{0:d}.cat'.format(grism_extinfo['axe_ext']))
        return in_sex, out_sex

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""
        self.iol = axeiol.InputObjectList(self.in_sex)
        if len(self.iol.catalog) < 1:
            _log.info('Empty catalog found\n')
            return None
        self.gol = deepcopy(self.iol.catalog)

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        dir_term = getDATA('{0:s} [{1:d}]'.format(self.dirname, self.
            dirname_extinfo['fits_ext']))
        gri_term = getDATA('{0:s} [{1:d}]'.format(self.grisim, self.
            grism_extinfo['fits_ext']))
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)
        for row in self.gol:
            try:
                xy_direct = row['X_IMAGE'], row['Y_IMAGE']
            except KeyError:
                raise aXeError('No coordinate columns in catalog, empty?')
            radec_pos = dir_wcs.xy2rd(xy_direct)
            xy_grism = gri_wcs.rd2xy(radec_pos)
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])

    def run(self, silent=False):
        """Make the SEX2GOL transformations"""
        if not silent:
            _log.info('py_SEX2GOL:  Start processing ...\n')
        else:
            sout = open(self.stdout, 'w+')
            sout.write(str(self) + '\n')
            sout.write('py_SEX2GOL:  Start processing ...')
        self._copy_catalog()
        if self.iol and self.gol:
            self._transfer_coos()
            outfile = getOUTPUT(self.out_sex)
            if os.access(outfile, os.F_OK):
                os.remove(outfile)
            _log.info('Saving {} objects to {}'.format(len(self.gol), outfile))
            of = open(outfile, 'w')
            for num, name in zip(range(len(self.gol.colnames)), self.gol.
                colnames):
                of.write('# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n'.format(num +
                    1, name, self.gol[name].description, str(self.gol[name]
                    .unit)))
            self.gol.write(of, format='ascii.no_header', overwrite=False)
            of.close()
        elif not silent:
            _log.info('\npy_SEX2GOL:  Warning! Empty table copied to GOL')
        else:
            sout.write('pysex2gol:  Warning! Empty table copied to GOL')
        if not silent:
            _log.info('     Done')
        else:
            sout.write('     Done\n')
            sout.close()

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        retcode = self.run(silent=silent)
        if silent:
            self._cleanup()
        return retcode

<mask token>


class Sex2GolPy:
    """This task generates a Grism Object List file using an Input Object List."""

    def __init__(self, grisim, config, in_sex=None, dirname=None, out_sex=
        None, spec_hdu=None, dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)
        self.dirname, self.dirname_extinfo = self._get_dirname_information(
            dirname, config, grisim, self.grism_extinfo, dir_hdu)
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
            self.dirname_extinfo, self.grisim, self.grism_extinfo, in_sex,
            out_sex)
        self.stdout = getOUTPUT('pysex2gol.stdout')

    def __str__(self):
        """String method for the class"""
        prefix = 'py_SEX2GOL: '
        big_str = '{0:s}  Setup:\n'.format(prefix)
        big_str += '{0:s}  Input g/prism image:      {0:s} \n'.format(prefix,
            self.grisim)
        big_str += '{0:s}  Configuration file name:  {0:s} \n'.format(prefix,
            self.config)
        big_str += '{0:s}  Direct image:             {0:s} \n'.format(prefix,
            self.dirname)
        big_str += '{0:s}  G/Prism extension:        {0:s} \n'.format(prefix,
            self.grism_extinfo['axe_ext'])
        big_str += '{0:s}  Direct image extension:   {0:s} \n'.format(prefix,
            self.dirname_extinfo['axe_ext'])
        big_str += '{0:s}  Input catalog name:       {0:s} \n'.format(prefix,
            self.in_sex)
        big_str += '{0:s}  Output catalog name:      {0:s}   '.format(prefix,
            self.out_sex)
        return big_str

    def _cleanup(self):
        """Clean up files created for stdout

        This is a cleaning procedure in case nothing bad happened.
        """
        if os.path.isfile(self.stdout):
            os.unlink(self.stdout)

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """
        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)
        else:
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu - 1}
        return ext_info

    def _get_dirname_information(self, dirname=None, config='', grisim='',
        grism_extinfo=None, dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        if dirname is None and dir_hdu is None:
            dirname = grisim
            dirname_extinfo = grism_extinfo
        elif dirname is not None and dir_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf
        elif dirname is not None and dir_hdu is not None:
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu - 1}
        else:
            err_msg = (
                'Specifying NO direct image but a direct image HDU: {0:d} makrs NO sense!'
                .format(dir_hdu))
            raise aXeError(err_msg)
        return dirname, dirname_extinfo

    def _resolve_list_names(self, dirname='', dirname_extinfo=None, grisim=
        '', grism_extinfo=None, in_sex=None, out_sex=None):
        """Determine the lists for input and output.

        Parameters
        ----------
        dirname : str
            The direct image name
        dirname_extinfo : dict
            A dictionary that contains the direct
            header and data information
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            A dictionary that contains the grism
            header and data information
        in_sex : str
            The name of the source extractor catalog
            that goes with the direct image
        out_sex : str
            The name of the output grism object list
            that is created using the input catalog

        Returns
        -------
        A tuple of the names of the input and output catalog names
        """
        if in_sex is None:
            in_sex = dirname.replace('.fits', '_{0:d}.cat'.format(
                dirname_extinfo['axe_ext']))
        if not os.path.isfile(in_sex):
            err_msg = 'The Input Object List: {0:s}  does not exist!'.format(
                in_sex)
            raise aXeError(err_msg)
        if out_sex is None:
            out_sex = os.path.basename(grisim).replace('.fits',
                '_{0:d}.cat'.format(grism_extinfo['axe_ext']))
        return in_sex, out_sex

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""
        self.iol = axeiol.InputObjectList(self.in_sex)
        if len(self.iol.catalog) < 1:
            _log.info('Empty catalog found\n')
            return None
        self.gol = deepcopy(self.iol.catalog)

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        dir_term = getDATA('{0:s} [{1:d}]'.format(self.dirname, self.
            dirname_extinfo['fits_ext']))
        gri_term = getDATA('{0:s} [{1:d}]'.format(self.grisim, self.
            grism_extinfo['fits_ext']))
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)
        for row in self.gol:
            try:
                xy_direct = row['X_IMAGE'], row['Y_IMAGE']
            except KeyError:
                raise aXeError('No coordinate columns in catalog, empty?')
            radec_pos = dir_wcs.xy2rd(xy_direct)
            xy_grism = gri_wcs.rd2xy(radec_pos)
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])

    def run(self, silent=False):
        """Make the SEX2GOL transformations"""
        if not silent:
            _log.info('py_SEX2GOL:  Start processing ...\n')
        else:
            sout = open(self.stdout, 'w+')
            sout.write(str(self) + '\n')
            sout.write('py_SEX2GOL:  Start processing ...')
        self._copy_catalog()
        if self.iol and self.gol:
            self._transfer_coos()
            outfile = getOUTPUT(self.out_sex)
            if os.access(outfile, os.F_OK):
                os.remove(outfile)
            _log.info('Saving {} objects to {}'.format(len(self.gol), outfile))
            of = open(outfile, 'w')
            for num, name in zip(range(len(self.gol.colnames)), self.gol.
                colnames):
                of.write('# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n'.format(num +
                    1, name, self.gol[name].description, str(self.gol[name]
                    .unit)))
            self.gol.write(of, format='ascii.no_header', overwrite=False)
            of.close()
        elif not silent:
            _log.info('\npy_SEX2GOL:  Warning! Empty table copied to GOL')
        else:
            sout.write('pysex2gol:  Warning! Empty table copied to GOL')
        if not silent:
            _log.info('     Done')
        else:
            sout.write('     Done\n')
            sout.close()

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        retcode = self.run(silent=silent)
        if silent:
            self._cleanup()
        return retcode

import os
from copy import deepcopy
import logging
from stsci.tools import wcsutil
from hstaxe.axeerror import aXeError
from hstaxe.config import getCONF, getDATA, getOUTPUT, get_ext_info
from . import configfile
from . import axeiol
_log = logging.getLogger(__name__)


class Sex2GolPy:
    """This task generates a Grism Object List file using an Input Object List."""

    def __init__(self, grisim, config, in_sex=None, dirname=None, out_sex=
        None, spec_hdu=None, dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)
        self.dirname, self.dirname_extinfo = self._get_dirname_information(
            dirname, config, grisim, self.grism_extinfo, dir_hdu)
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
            self.dirname_extinfo, self.grisim, self.grism_extinfo, in_sex,
            out_sex)
        self.stdout = getOUTPUT('pysex2gol.stdout')

    def __str__(self):
        """String method for the class"""
        prefix = 'py_SEX2GOL: '
        big_str = '{0:s}  Setup:\n'.format(prefix)
        big_str += '{0:s}  Input g/prism image:      {0:s} \n'.format(prefix,
            self.grisim)
        big_str += '{0:s}  Configuration file name:  {0:s} \n'.format(prefix,
            self.config)
        big_str += '{0:s}  Direct image:             {0:s} \n'.format(prefix,
            self.dirname)
        big_str += '{0:s}  G/Prism extension:        {0:s} \n'.format(prefix,
            self.grism_extinfo['axe_ext'])
        big_str += '{0:s}  Direct image extension:   {0:s} \n'.format(prefix,
            self.dirname_extinfo['axe_ext'])
        big_str += '{0:s}  Input catalog name:       {0:s} \n'.format(prefix,
            self.in_sex)
        big_str += '{0:s}  Output catalog name:      {0:s}   '.format(prefix,
            self.out_sex)
        return big_str

    def _cleanup(self):
        """Clean up files created for stdout

        This is a cleaning procedure in case nothing bad happened.
        """
        if os.path.isfile(self.stdout):
            os.unlink(self.stdout)

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """
        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)
        else:
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu - 1}
        return ext_info

    def _get_dirname_information(self, dirname=None, config='', grisim='',
        grism_extinfo=None, dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        if dirname is None and dir_hdu is None:
            dirname = grisim
            dirname_extinfo = grism_extinfo
        elif dirname is not None and dir_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf
        elif dirname is not None and dir_hdu is not None:
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu - 1}
        else:
            err_msg = (
                'Specifying NO direct image but a direct image HDU: {0:d} makrs NO sense!'
                .format(dir_hdu))
            raise aXeError(err_msg)
        return dirname, dirname_extinfo

    def _resolve_list_names(self, dirname='', dirname_extinfo=None, grisim=
        '', grism_extinfo=None, in_sex=None, out_sex=None):
        """Determine the lists for input and output.

        Parameters
        ----------
        dirname : str
            The direct image name
        dirname_extinfo : dict
            A dictionary that contains the direct
            header and data information
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            A dictionary that contains the grism
            header and data information
        in_sex : str
            The name of the source extractor catalog
            that goes with the direct image
        out_sex : str
            The name of the output grism object list
            that is created using the input catalog

        Returns
        -------
        A tuple of the names of the input and output catalog names
        """
        if in_sex is None:
            in_sex = dirname.replace('.fits', '_{0:d}.cat'.format(
                dirname_extinfo['axe_ext']))
        if not os.path.isfile(in_sex):
            err_msg = 'The Input Object List: {0:s}  does not exist!'.format(
                in_sex)
            raise aXeError(err_msg)
        if out_sex is None:
            out_sex = os.path.basename(grisim).replace('.fits',
                '_{0:d}.cat'.format(grism_extinfo['axe_ext']))
        return in_sex, out_sex

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""
        self.iol = axeiol.InputObjectList(self.in_sex)
        if len(self.iol.catalog) < 1:
            _log.info('Empty catalog found\n')
            return None
        self.gol = deepcopy(self.iol.catalog)

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        dir_term = getDATA('{0:s} [{1:d}]'.format(self.dirname, self.
            dirname_extinfo['fits_ext']))
        gri_term = getDATA('{0:s} [{1:d}]'.format(self.grisim, self.
            grism_extinfo['fits_ext']))
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)
        for row in self.gol:
            try:
                xy_direct = row['X_IMAGE'], row['Y_IMAGE']
            except KeyError:
                raise aXeError('No coordinate columns in catalog, empty?')
            radec_pos = dir_wcs.xy2rd(xy_direct)
            xy_grism = gri_wcs.rd2xy(radec_pos)
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])

    def run(self, silent=False):
        """Make the SEX2GOL transformations"""
        if not silent:
            _log.info('py_SEX2GOL:  Start processing ...\n')
        else:
            sout = open(self.stdout, 'w+')
            sout.write(str(self) + '\n')
            sout.write('py_SEX2GOL:  Start processing ...')
        self._copy_catalog()
        if self.iol and self.gol:
            self._transfer_coos()
            outfile = getOUTPUT(self.out_sex)
            if os.access(outfile, os.F_OK):
                os.remove(outfile)
            _log.info('Saving {} objects to {}'.format(len(self.gol), outfile))
            of = open(outfile, 'w')
            for num, name in zip(range(len(self.gol.colnames)), self.gol.
                colnames):
                of.write('# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n'.format(num +
                    1, name, self.gol[name].description, str(self.gol[name]
                    .unit)))
            self.gol.write(of, format='ascii.no_header', overwrite=False)
            of.close()
        elif not silent:
            _log.info('\npy_SEX2GOL:  Warning! Empty table copied to GOL')
        else:
            sout.write('pysex2gol:  Warning! Empty table copied to GOL')
        if not silent:
            _log.info('     Done')
        else:
            sout.write('     Done\n')
            sout.close()

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        retcode = self.run(silent=silent)
        if silent:
            self._cleanup()
        return retcode

import os
from copy import deepcopy
import logging

from stsci.tools import wcsutil

from hstaxe.axeerror import aXeError
from hstaxe.config import (getCONF, getDATA,
                          getOUTPUT, get_ext_info)

from . import configfile
from . import axeiol


# make sure there is a logger
_log = logging.getLogger(__name__)

class Sex2GolPy:
    """This task generates a Grism Object List file using an Input Object List."""

    def __init__(self, grisim, config,
                 in_sex=None,
                 dirname=None,
                 out_sex=None,
                 spec_hdu=None,
                 dir_hdu=None):
        """
        Parameters
        ----------
        grisim : str
            input grism/prism image
        config : str
            axe configuration filename
        in_sex : str
            name of the object file
        dirname : str
            direct image name
        out_sex : str
            overwrites the default output object catalog name
        spec_hdu : int
            grism/prism image extension to be used
        dir_hdu :  int
            direct image extension to be used

        Returns
        -------
        Creates output catalog files in source extractor format

        Notes
        -----
        There are three different kinds of Input Object List that
        can be fed into aXe:

        * an Input Object List (in SExtractor format) of objects on a
          direct image covering (roughly) the same field as the grism image
        * an Input Object List in SExtractor format, which gives the objects
          on the grism image in world coordinates (RA, Dec and theta_sky)

        The image coordinates of the objects on the grism image will be
        recomputed using the WCS information of the grism image and the
        direct image. This approach therefore relies on the accuracy of
        the WCS information given in those images.

        """

        # store some parameters
        self.grisim = grisim
        self.config = config
        self.in_sex = None
        self.out_sex = None
        self.dirname = dirname
        self.iol = None
        self.gol = None

        # determine the grism image extensions
        self.grism_extinfo = self._get_grism_ext_info(grisim, config, spec_hdu)

        # determine the grism image extensions
        self.dirname, self.dirname_extinfo = self._get_dirname_information(dirname,
                                                                           config,
                                                                           grisim,
                                                                           self.grism_extinfo,
                                                                           dir_hdu)

        # get information on the input and output lists
        self.in_sex, self.out_sex = self._resolve_list_names(self.dirname,
                                                             self.dirname_extinfo,
                                                             self.grisim,
                                                             self.grism_extinfo,
                                                             in_sex, out_sex)

        # save a name for stdout
        self.stdout = getOUTPUT("pysex2gol.stdout")

    def __str__(self):
        """String method for the class"""
        # define the prefix
        prefix = "py_SEX2GOL: "

        # compose the feedback
        big_str = "{0:s}  Setup:\n".format(prefix)
        big_str += "{0:s}  Input g/prism image:      {0:s} \n".format(prefix, self.grisim)
        big_str += "{0:s}  Configuration file name:  {0:s} \n".format(prefix, self.config)
        big_str += "{0:s}  Direct image:             {0:s} \n".format(prefix, self.dirname)
        big_str += "{0:s}  G/Prism extension:        {0:s} \n".format(prefix, self.grism_extinfo['axe_ext'])
        big_str += "{0:s}  Direct image extension:   {0:s} \n".format(prefix, self.dirname_extinfo['axe_ext'])
        big_str += "{0:s}  Input catalog name:       {0:s} \n".format(prefix, self.in_sex)
        big_str += "{0:s}  Output catalog name:      {0:s}   ".format(prefix, self.out_sex)

        # return the string
        return big_str

    def _cleanup(self):
        """Clean up files created for stdout

        This is a cleaning procedure in case nothing bad happened.
        """
        # delete stdout/stderr
        if os.path.isfile(self.stdout):
            os.unlink(self.stdout)

    def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
        """Determine the extension information on the grism image.

        Parameters
        ----------
        grisim : str
            The name of the grism images
        config : str
            The name of the configuration file
        spec_hdu : int, None
            The extention number of the spectra data

        Returns
        -------
        ext_info : dict
            A dictionary that contains the header extension
            and the data extension
        """

        if spec_hdu is None:
            conf = configfile.ConfigFile(getCONF(config))
            ext_info = get_ext_info(getDATA(grisim), conf)

        else:
            # make by hand the extension information
            ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu-1}

        # return the extension info
        return ext_info

    def _get_dirname_information(self,
                                 dirname=None,
                                 config="",
                                 grisim="",
                                 grism_extinfo=None,
                                 dir_hdu=None):
        """Determine the direct image information.

        Parameters
        ----------
        dirname : str
            Diretory name
        config : str
            The name of the config file
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            Dictionary of header information
        dir_hdu :  fits.HDU
            FITS header data unit

        Returns
        -------
        A tuple of the direct image name and a dictionary of
        extension information

        """
        # check whether ANY direct image information exists
        if ((dirname is None) and (dir_hdu is None)):
            # set the grism image as direct image
            dirname = grisim
            dirname_extinfo = grism_extinfo

        elif ((dirname is not None) and (dir_hdu is None)):
            # load the configuration file;
            # determine the extension information
            conf = configfile.ConfigFile(getCONF(config))
            dirname_extinfo = get_ext_info(getDATA(grisim), conf)
            del conf

        elif ((dirname is not None) and (dir_hdu is not None)):
            # make by hand the extension information
            dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu-1}

        else:
            # error and out
            err_msg = ("Specifying NO direct image but a direct image HDU: "
                       "{0:d} makrs NO sense!".format(dir_hdu))
            raise aXeError(err_msg)

        # return the name and the extension info
        return dirname, dirname_extinfo

    def _resolve_list_names(self, dirname='',
                            dirname_extinfo=None,
                            grisim='',
                            grism_extinfo=None,
                            in_sex=None,
                            out_sex=None):
        """Determine the lists for input and output.

        Parameters
        ----------
        dirname : str
            The direct image name
        dirname_extinfo : dict
            A dictionary that contains the direct
            header and data information
        grisim : str
            The name of the grisim image
        grism_extinfo : dict
            A dictionary that contains the grism
            header and data information
        in_sex : str
            The name of the source extractor catalog
            that goes with the direct image
        out_sex : str
            The name of the output grism object list
            that is created using the input catalog

        Returns
        -------
        A tuple of the names of the input and output catalog names
        """
        # compose the default name
        if in_sex is None:
            # compose the filename from the direct image name
            in_sex = dirname.replace(".fits", "_{0:d}.cat"
                                     .format(dirname_extinfo['axe_ext']))

        # check whether the explicitly given filename exists
        if not os.path.isfile(in_sex):
            err_msg = ("The Input Object List: {0:s}  does not exist!"
                       .format(in_sex))
            raise aXeError(err_msg)

        if out_sex is None:
            # compose the name for the output GOL
            out_sex = os.path.basename(grisim).replace(".fits", "_{0:d}.cat".format(grism_extinfo['axe_ext']))

        # return the IOL and the GOL names
        return in_sex, out_sex

    def _copy_catalog(self):
        """Copies relevant data from IOL to GOL"""

        # load the IOL into an astropy table
        # the table is in iol.catalog
        self.iol = axeiol.InputObjectList(self.in_sex)

        # check for an empty table
        if len(self.iol.catalog) < 1:
            _log.info("Empty catalog found\n")
            return None

        # create a new GOL that's a copy of the input list
        self.gol = deepcopy(self.iol.catalog) # just make a copy

    def _transfer_coos(self):
        """Transfer coordinates from the IOL to the GOL"""
        # compose the WCS-term for the direct and grism images
        dir_term = getDATA("{0:s} [{1:d}]".format(self.dirname, self.dirname_extinfo['fits_ext']))
        gri_term = getDATA("{0:s} [{1:d}]".format(self.grisim, self.grism_extinfo['fits_ext']))

        # generate the WCS objects
        dir_wcs = wcsutil.WCSObject(dir_term)
        gri_wcs = wcsutil.WCSObject(gri_term)

        # go over each row in the catalog
        for row in self.gol:

            # make a position tuple
            try:
                xy_direct = (row['X_IMAGE'], row['Y_IMAGE'])
            except KeyError:          
                # self._treat_NULL_table
                raise aXeError("No coordinate columns in catalog, empty?")

            # convert to RADEC using the direct image
            radec_pos = dir_wcs.xy2rd(xy_direct)

            # convert to XY on grism image
            xy_grism = gri_wcs.rd2xy(radec_pos)

            # store projected vals in the GOL
            row['X_IMAGE'] = float(xy_grism[0])
            row['Y_IMAGE'] = float(xy_grism[1])

    # def _treat_NULL_table(self, out_name):
    #     """Transfer an empty table.

    #     Parameters
    #     ----------
    #     out_name : str
    #         The name of the output file


    #     The header of the empty table is written to the
    #     GOL file.
    #     """
    #     catalog = Table.read(self.in_sex, format='ascii.sextractor')
    #     new_catalog = deepcopy(catalog)
    #     if os.access(out_name, os.F_OK):
    #         os.remove(out_name)
    #     of = open(out_name, 'w')
    #     for num, name in zip(range(len(new_catalog.colnames)), new_catalog.colnames):
    #         of.write("# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n".format(num+1,
    #                                                               name,
    #                                                               new_catalog[name].description,
    #                                                               str(new_catalog[name].unit))
    #                                                              )
    #     new_catalog.write(of, format='ascii.no_header', overwrite=False)
    #     of.close()

    def run(self, silent=False):
        """Make the SEX2GOL transformations"""
        if not silent:
            _log.info("py_SEX2GOL:  Start processing ...\n",)
        else:
            sout = open(self.stdout, 'w+')
            sout.write(str(self)+"\n")
            sout.write("py_SEX2GOL:  Start processing ...")

        # copy the relevant data to the GOL catalog
        self._copy_catalog()

        # check whether something can be done
        if (self.iol and self.gol):
            # transfer the coordinates
            self._transfer_coos()

            # store the GOL
            # This needs to be stored in the same way as SEXTRACTOR
            outfile = getOUTPUT(self.out_sex)
            if os.access(outfile, os.F_OK):
                os.remove(outfile)
            _log.info("Saving {} objects to {}".format(len(self.gol),outfile))
            of = open(outfile, 'w')
            for num, name in zip(range(len(self.gol.colnames)), self.gol.colnames):
                of.write("# {0:d} {1:s}\t\t{2:s}\t\t[{3:s}]\n".format(num+1, name,
                                                     self.gol[name].description,
                                                     str(self.gol[name].unit)))
            self.gol.write(of, format='ascii.no_header', overwrite=False)
            of.close()

        else:
            # if there are no objects, just copy the empty table
            # header to the GOL
            #self._treat_NULL_table(getOUTPUT(self.out_sex))

            # give feedback
            if not silent:
                _log.info("\npy_SEX2GOL:  Warning! Empty table copied to GOL")
            else:
                # open stdout/stderr
                sout.write("pysex2gol:  Warning! Empty table copied to GOL")

        # give feedback
        if not silent:
            _log.info("     Done")
        else:
            sout.write("     Done\n")
            sout.close()

    def runall(self, silent=False):
        """Run the wrapped task

        The method executes the associated C-executable. The return code given
        by the C-executable is returned. In silent mode stdout and stderr
        are writtren to a file, in non-silent mode to the screen.

        @param silent: boolean for silent mode
        @type silent: boolean

        @return: the return code of the C-executable
        @rtype: int
        """
        # run the executable
        retcode = self.run(silent=silent)

        # check whether the run was good
        if silent:
            # do the cleaning
            self._cleanup()

        return retcode
