Source code for pypeit.spectrographs.wht_isis

"""
Module for WHT/ISIS specific methods.

.. include:: ../include/links.rst
"""
from pathlib import Path

import numpy as np
from astropy.io import fits
from astropy.table import Table

from pypeit import log
from pypeit import PypeItError
from pypeit import telescopes
from pypeit.core import framematch
from pypeit.spectrographs import spectrograph
from pypeit.core import parse
from pypeit.images import detector_container
from pypeit.par import parset




class WHTISISSpectrograph(spectrograph.Spectrograph):
    """
    Child to handle WHT/ISIS specific code
    """
    ndet = 1
    telescope = telescopes.WHTTelescopePar()
    url = 'https://www.ing.iac.es/astronomy/instruments/isis/'



    def init_meta(self):
        """
        Define how metadata are derived from the spectrograph files.

        That is, this associates the PypeIt-specific metadata keywords
        with the instrument-specific header cards using :attr:`meta`.
        """
        self.meta = {}
        # Required (core)
        self.meta['ra'] = dict(ext=0, card='RA')
        self.meta['dec'] = dict(ext=0, card='DEC')
        self.meta['target'] = dict(ext=0, card='OBJECT')
        self.meta['decker'] = dict(card=None, compound=True)
        self.meta['binning'] = dict(card=None, compound=True)

        self.meta['mjd'] = dict(ext=0, card='MJD-OBS')
        self.meta['exptime'] = dict(ext=0, card='EXPTIME')
        self.meta['airmass'] = dict(ext=0, card='AIRMASS')
        self.meta['decker'] = dict(ext=0, card='ISISLITU')
        # Extras for config and frametyping
        self.meta['dispname'] = dict(ext=0, card='ISIGRAT')
        self.meta['dichroic'] = dict(ext=0, card='ISIDICHR')
        self.meta['dispangle'] = dict(ext=0, card='CENWAVE', rtol=1e-3)
        self.meta['slitwid'] = dict(ext=0, card='ISISLITW')
        self.meta['idname'] = dict(ext=0, card='IMAGETYP')
        # Lamps
        self.meta['lampstat01'] = dict(ext=0, card='CAGLAMPS')




    def compound_meta(self, headarr, meta_key):
        """
        Methods to generate metadata requiring interpretation of the header
        data, instead of simply reading the value of a header card.

        Args:
            headarr (:obj:`list`):
                List of `astropy.io.fits.Header`_ objects.
            meta_key (:obj:`str`):
                Metadata keyword to construct.

        Returns:
            object: Metadata value read from the header(s).
        """
        if meta_key == 'binning':
            binspatial = headarr[0]['CCDXBIN']
            binspec = headarr[0]['CCDYBIN']
            return parse.binning2string(binspec, binspatial)
        raise PypeItError("Not ready for this compound meta")




    def configuration_keys(self):
        """
        Return the metadata keys that define a unique instrument
        configuration.

        This list is used by :class:`~pypeit.metadata.PypeItMetaData` to
        identify the unique configurations among the list of frames read
        for a given reduction.

        Returns:
            :obj:`list`: List of keywords of data pulled from file headers
            and used to constuct the :class:`~pypeit.metadata.PypeItMetaData`
            object.
        """
        return ['dispname', 'decker', 'binning', 'dispangle', 'dichroic']




    def raw_header_cards(self):
        """
        Return additional raw header cards to be propagated in
        downstream output files for configuration identification.

        The list of raw data FITS keywords should be those used to populate
        the :meth:`~pypeit.spectrographs.spectrograph.Spectrograph.configuration_keys`
        or are used in :meth:`~pypeit.spectrographs.spectrograph.Spectrograph.config_specific_par`
        for a particular spectrograph, if different from the name of the
        PypeIt metadata keyword.

        This list is used by :meth:`~pypeit.spectrographs.spectrograph.Spectrograph.subheader_for_spec`
        to include additional FITS keywords in downstream output files.

        Returns:
            :obj:`list`: List of keywords from the raw data files that should
            be propagated in output files.
        """
        return ['ISIGRAT', 'ISISLITU', 'CCDXBIN', 'CCDYBIN', 'CENWAVE', 'ISIDICHR']




    def pypeit_file_keys(self):
        """
        Define the list of keys to be output into a standard PypeIt file.

        Returns:
            :obj:`list`: The list of keywords in the relevant
            :class:`~pypeit.metadata.PypeItMetaData` instance to print to the
            :ref:`pypeit_file`.
        """
        return super().pypeit_file_keys() + ['slitwid']






class WHTISISBlueSpectrograph(WHTISISSpectrograph):
    """
    Child to handle WHT/ISIS blue specific code
    """

    name = 'wht_isis_blue'
    camera = 'ISISb'
    comment = 'Blue camera'
    allowed_extensions = ['.fit', '.fit.gz']
    


    def get_detector_par(self, det, hdu=None):
        """
        Return metadata for the selected detector.

        Args:
            det (:obj:`int`):
                1-indexed detector number.
            hdu (`astropy.io.fits.HDUList`_, optional):
                The open fits file with the raw image of interest.  If not
                provided, frame-dependent parameters are set to a default.

        Returns:
            :class:`~pypeit.images.detector_container.DetectorContainer`:
            Object with the detector metadata.
        """
        # Binning
        # TODO: Could this be detector dependent??
        binning = '1,1' if hdu is None else self.get_meta_value(self.get_headarr(hdu), 'binning')

        # Detector 1
        detector_dict = dict(
            binning         = binning,
            det             = 1,
            dataext         = 1,
            specaxis        = 0,
            specflip        = False,
            spatflip        = False,
            platescale      = 0.20,
            darkcurr        = 0.0,  # e-/pixel/hour
            saturation      = 65535.,
            nonlinear       = 0.76,
            mincounts       = -1e10,
            numamplifiers   = 1,
            gain            = np.atleast_1d(1.2),
            ronoise         = np.atleast_1d(5.0),
            datasec         = np.atleast_1d('[:,2:4030]'),
            )
        return detector_container.DetectorContainer(**detector_dict)




    @classmethod
    def default_pypeit_par(cls):
        """
        Return the default parameters to use for this instrument.
        
        Returns:
            :class:`~pypeit.par.pypeitpar.PypeItPar`: Parameters required by
            all of PypeIt methods.
        """
        par = super().default_pypeit_par()

        # Ignore PCA
        par['calibrations']['slitedges']['sync_predict'] = 'nearest'

        # JFH Is this correct?
        # Processing steps
        par.reset_all_processimages_par(use_overscan=False)
        # Make a bad pixel mask
        par['calibrations']['bpm_usebias'] = True
        # Set pixel flat combination method
        par['calibrations']['pixelflatframe']['process']['combine'] = 'median'
        # Change the wavelength calibration method
        par['calibrations']['wavelengths']['method'] = 'full_template'
        par['calibrations']['wavelengths']['lamps'] = ['NeI', 'ArI', 'ArII', 'CuI']
        par['calibrations']['wavelengths']['n_first'] = 3
        par['calibrations']['wavelengths']['n_final'] = 5
        par['calibrations']['wavelengths']['sigdetect'] = 10.0
        # Do not flux calibrate
        par['fluxcalib'] = None
        # Set the default exposure time ranges for the frame typing
        par['calibrations']['biasframe']['exprng'] = [None, 0.001]
        par['calibrations']['darkframe']['exprng'] = [999999, None]     # No dark frames
        par['calibrations']['pinholeframe']['exprng'] = [999999, None]  # No pinhole frames
        par['calibrations']['arcframe']['exprng'] = [None, 120]
        par['calibrations']['standardframe']['exprng'] = [None, 120]
        par['scienceframe']['exprng'] = [90, None]

        return par




    def config_specific_par(
            self,
            inp:str|list|Path|fits.Header|Table,
            inp_par:parset.ParSet|None=None
        ) -> parset.ParSet:
        """
        Modify the PypeIt parameters to hard-wired values used for
        specific instrument configurations.

        Args:
            inp (:obj:`str`, :obj:`list`, `Path`_, `astropy.io.fits.Header`_, `astropy.table.Table`_):
                Input filename, an `astropy.io.fits.Header`_ object, or a list
                of `astropy.io.fits.Header`_ objects.  Or a row from the
                metadata table.
            inp_par (:class:`~pypeit.par.parset.ParSet`, optional):
                Parameter set used for the full run of PypeIt.  If None,
                use :func:`default_pypeit_par`.

        Returns:
            :class:`~pypeit.par.parset.ParSet`: The PypeIt parameter set
            adjusted for configuration specific parameter values.
        """
        # Start with instrument-wide parameters
        par = super().config_specific_par(inp, inp_par=inp_par)

        # Adjust parameters based on grating used
        grating = self.get_meta_value(inp, 'dispname')

        # Wavelength calibrations
        if grating == 'R1200B':
            par['calibrations']['wavelengths']['reid_arxiv'] = 'wht_isis_blue_1200_4800.fits'

        return par




    def check_frame_type(self, ftype, fitstbl, exprng=None):
        """
        Check for frames of the provided type.

        Args:
            ftype (:obj:`str`):
                Type of frame to check. Must be a valid frame type; see
                frame-type :ref:`frame_type_defs`.
            fitstbl (`astropy.table.Table`_):
                The table with the metadata for one or more frames to check.
            exprng (:obj:`list`, optional):
                Range in the allowed exposure time for a frame of type
                ``ftype``. See
                :func:`pypeit.core.framematch.check_frame_exptime`.

        Returns:
            `numpy.ndarray`_: Boolean array with the flags selecting the
            exposures in ``fitstbl`` that are ``ftype`` type frames.
        """
        good_exp = framematch.check_frame_exptime(fitstbl['exptime'], exprng)
        if ftype in ['science', 'standard']:
            return good_exp & (fitstbl['lampstat01'] == 'Off') & (fitstbl['idname'] == 'object')
        if ftype == 'bias':
            return good_exp & (fitstbl['idname'] == 'zero')
        if ftype in ['pixelflat', 'trace']:
            return good_exp & (fitstbl['lampstat01'] == 'W') & (fitstbl['idname'] == 'flat')
        if ftype in ['pinhole', 'dark']:
            # Don't type pinhole or dark frames
            return np.zeros(len(fitstbl), dtype=bool)
        if ftype in ['arc', 'tilt']:
            return good_exp & (fitstbl['lampstat01'] == 'CuNe+CuAr') & (fitstbl['idname'] == 'arc')
        log.debug('Cannot determine if frames are of type {0}.'.format(ftype))
        return np.zeros(len(fitstbl), dtype=bool)






class WHTISISRedSpectrograph(WHTISISSpectrograph):
    """
    Child to handle WHT/ISISr red specific code
    """

    name = 'wht_isis_red'
    camera = 'ISISr'
    comment = 'Red camera'



    def get_detector_par(self, det, hdu=None):
        """
        Return metadata for the selected detector.

        Args:
            det (:obj:`int`):
                1-indexed detector number.
            hdu (`astropy.io.fits.HDUList`_, optional):
                The open fits file with the raw image of interest.  If not
                provided, frame-dependent parameters are set to a default.

        Returns:
            :class:`~pypeit.images.detector_container.DetectorContainer`:
            Object with the detector metadata.
        """
        # Binning
        # TODO: Could this be detector dependent??
        binning = '1,1' if hdu is None else self.get_meta_value(self.get_headarr(hdu), 'binning')

        # Detector 1
        detector_dict = dict(
            binning=binning,
            det=1,
            dataext=1,
            specaxis=0,
            specflip=False,
            spatflip=False,
            platescale=0.22,
            darkcurr=0.0,  # e-/pixel/hour
            saturation=65535.,
            nonlinear=0.76,
            mincounts=-1e10,
            numamplifiers=1,
            gain=np.atleast_1d(0.98),
            ronoise=np.atleast_1d(4.0),
            datasec=np.atleast_1d('[:,:]'),
        )
        return detector_container.DetectorContainer(**detector_dict)




    @classmethod
    def default_pypeit_par(cls):
        """
        Return the default parameters to use for this instrument.
        
        Returns:
            :class:`~pypeit.par.pypeitpar.PypeItPar`: Parameters required by
            all of PypeIt methods.
        """
        par = super().default_pypeit_par()

        # Ignore PCA
        par['calibrations']['slitedges']['sync_predict'] = 'nearest'

        # Turn off the overscan
        par.reset_all_processimages_par(use_overscan=False)
        # Make a bad pixel mask
        par['calibrations']['bpm_usebias'] = True
        # Set pixel flat combination method
        par['calibrations']['pixelflatframe']['process']['combine'] = 'median'
        # Change the wavelength calibration method
        par['calibrations']['wavelengths']['method'] = 'full_template'
        par['calibrations']['wavelengths']['lamps'] = ['NeI', 'ArI', 'ArII', 'CuI']
        par['calibrations']['wavelengths']['sigdetect'] = 10.0
        # Do not flux calibrate
        par['fluxcalib'] = None
        # Set the default exposure time ranges for the frame typing
        par['calibrations']['biasframe']['exprng'] = [None, 0.001]
        par['calibrations']['darkframe']['exprng'] = [999999, None]     # No dark frames
        par['calibrations']['pinholeframe']['exprng'] = [999999, None]  # No pinhole frames
        par['calibrations']['arcframe']['exprng'] = [None, 120]
        par['calibrations']['standardframe']['exprng'] = [None, 120]
        par['scienceframe']['exprng'] = [90, None]

        return par




    def config_specific_par(
            self,
            inp:str|list|Path|fits.Header|Table,
            inp_par:parset.ParSet|None=None
        ) -> parset.ParSet:
        """
        Modify the PypeIt parameters to hard-wired values used for
        specific instrument configurations.

        Args:
            inp (:obj:`str`, :obj:`list`, `Path`_, `astropy.io.fits.Header`_, `astropy.table.Table`_):
                Input filename, an `astropy.io.fits.Header`_ object, or a list
                of `astropy.io.fits.Header`_ objects.  Or a row from the
                metadata table.
            inp_par (:class:`~pypeit.par.parset.ParSet`, optional):
                Parameter set used for the full run of PypeIt.  If None,
                use :func:`default_pypeit_par`.

        Returns:
            :class:`~pypeit.par.parset.ParSet`: The PypeIt parameter set
            adjusted for configuration specific parameter values.
        """
        # Start with instrument-wide parameters
        par = super().config_specific_par(inp, inp_par=inp_par)

        # Adjust parameters based on grating used
        grating = self.get_meta_value(inp, 'dispname')

        # Wavelength calibrations
        if grating == 'R1200R':
            par['calibrations']['wavelengths']['reid_arxiv'] = 'wht_isis_red_1200_6000.fits'

        # Return
        return par




    def check_frame_type(self, ftype, fitstbl, exprng=None):
        """
        Check for frames of the provided type.

        Args:
            ftype (:obj:`str`):
                Type of frame to check. Must be a valid frame type; see
                frame-type :ref:`frame_type_defs`.
            fitstbl (`astropy.table.Table`_):
                The table with the metadata for one or more frames to check.
            exprng (:obj:`list`, optional):
                Range in the allowed exposure time for a frame of type
                ``ftype``. See
                :func:`pypeit.core.framematch.check_frame_exptime`.

        Returns:
            `numpy.ndarray`_: Boolean array with the flags selecting the
            exposures in ``fitstbl`` that are ``ftype`` type frames.
        """
        good_exp = framematch.check_frame_exptime(fitstbl['exptime'], exprng)
        if ftype in ['science', 'standard']:
            return good_exp & (fitstbl['lampstat01'] == 'Off') & (fitstbl['idname'] == 'object')
        if ftype == 'bias':
            return good_exp & (fitstbl['idname'] == 'zero')
        if ftype in ['pixelflat', 'trace']:
            return good_exp & (fitstbl['lampstat01'] == 'W') & (fitstbl['idname'] == 'flat')
        if ftype in ['pinhole', 'dark']:
            # Don't type pinhole or dark frames
            return np.zeros(len(fitstbl), dtype=bool)
        if ftype in ['arc', 'tilt']:
            return good_exp & (fitstbl['lampstat01'] == 'CuNe+CuAr') & (fitstbl['idname'] == 'arc')
        log.debug('Cannot determine if frames are of type {0}.'.format(ftype))
        return np.zeros(len(fitstbl), dtype=bool)