Example #1
0
    def Setup(self):

        # Sort the data
        msgs.bug("Files and folders should not be deleted -- there should be an option to overwrite files automatically if they already exist, or choose to rename them if necessary")
        self._filesort = arsort.sort_data(self)
        # Write out the details of the sorted files
        if self._argflag['out']['sorted'] is not None: arsort.sort_write(self)
        # Match Science frames to calibration frames
        arsort.match_science(self)
        # If the user is only debugging, then exit now
        if self._argflag['run']['calcheck']:
            msgs.info("Calibration check complete. Change the 'calcheck' flag to continue with data reduction")
            sys.exit()
        # Make directory structure for different objects
        self._sci_targs = arsort.make_dirs(self)
        return
Example #2
0
def SetupScience(argflag, spect, fitsdict):
    """ Create an exposure class for every science frame
    Also links to standard star frames

    Parameters
    ----------
    argflag : dict
      Arguments and flags used for reduction
    spect : dict
      Properties of the spectrograph.
    fitsdict : dict
      Contains relevant information from fits header files

    Returns
    -------
    sciexp : list
      A list containing all science exposure classes
    """
    # Sort the data
    msgs.bug(
        "Files and folders should not be deleted -- there should be an option to overwrite files automatically if they already exist, or choose to rename them if necessary"
    )
    filesort = arsort.sort_data(argflag, spect, fitsdict)
    # Write out the details of the sorted files
    if argflag['out']['sorted'] is not None:
        arsort.sort_write(argflag['out']['sorted'], spect, fitsdict, filesort)
    # Match calibration frames to science frames
    spect = arsort.match_science(argflag, spect, fitsdict, filesort)
    # If the user is only debugging, then exit now
    if argflag['run']['calcheck']:
        msgs.info(
            "Calibration check complete. Change the 'calcheck' flag to continue with data reduction"
        )
        sys.exit()
    # Make directory structure for different objects
    sci_targs = arsort.make_dirs(argflag, fitsdict, filesort)
    # Create the list of science exposures
    numsci = np.size(filesort['science'])
    sciexp = []
    for i in xrange(numsci):
        sciexp.append(arsciexp.ScienceExposure(i, argflag, spect, fitsdict))
    return sciexp
Example #3
0
def SetupScience(argflag, spect, fitsdict):
    """ Create an exposure class for every science frame
    Also links to standard star frames

    Parameters
    ----------
    argflag : dict
      Arguments and flags used for reduction
    spect : dict
      Properties of the spectrograph.
    fitsdict : dict
      Contains relevant information from fits header files

    Returns
    -------
    sciexp : list
      A list containing all science exposure classes
    """
    # Sort the data
    msgs.bug("Files and folders should not be deleted -- there should be an option to overwrite files automatically if they already exist, or choose to rename them if necessary")
    filesort = arsort.sort_data(argflag, spect, fitsdict)
    # Write out the details of the sorted files
    if argflag['out']['sorted'] is not None:
        arsort.sort_write(argflag['out']['sorted'], spect, fitsdict, filesort)
    # Match calibration frames to science frames
    spect = arsort.match_science(argflag, spect, fitsdict, filesort)
    # If the user is only debugging, then exit now
    if argflag['run']['calcheck']:
        msgs.info("Calibration check complete. Change the 'calcheck' flag to continue with data reduction")
        sys.exit()
    # Make directory structure for different objects
    sci_targs = arsort.make_dirs(argflag, fitsdict, filesort)
    # Create the list of science exposures
    numsci = np.size(filesort['science'])
    sciexp = []
    for i in range(numsci):
        sciexp.append(arsciexp.ScienceExposure(i, argflag, spect, fitsdict))
    return sciexp
Example #4
0
def SetupScience(fitsdict):
    """ Create an exposure class for every science frame
    Also links to standard star frames and calibrations

    Parameters
    ----------
    fitsdict : dict
      Contains relevant information from fits header files

    Returns
    -------
    sciexp : list
      A list containing all science exposure classes
    """
    # Init
    if settings.argflag['run']['calcheck'] or settings.argflag['run']['setup']:
        do_qa = False
        bad_to_unknown = True
    else:
        do_qa = True
        bad_to_unknown = False
    if settings.argflag['run']['setup']:
        skip_cset = True
    else:
        skip_cset = False
    # Sort the data
    msgs.bug(
        "Files and folders should not be deleted -- there should be an option to overwrite files automatically if they already exist, or choose to rename them if necessary"
    )
    filesort = arsort.sort_data(fitsdict, flag_unknown=bad_to_unknown)
    # Write out the details of the sorted files into a .lst file
    if settings.argflag['output']['sorted'] is not None:
        srt_tbl = arsort.sort_write(fitsdict, filesort)
    # Match calibration frames to science frames
    arsort.match_science(fitsdict, filesort)
    # Make directory structure for different objects
    if do_qa:
        sci_targs = arsort.make_dirs(fitsdict, filesort)
    # Create the list of science exposures
    numsci = np.size(settings.spect['science']['index'])
    sciexp = []
    for i in range(numsci):
        sciexp.append(arsciexp.ScienceExposure(i, fitsdict, do_qa=do_qa))

    # Generate setup and group dicts
    setup_dict = {}
    if settings.argflag['reduce']['masters']['force']:
        # Check that setup was input
        if len(settings.argflag['reduce']['masters']['setup']) == 0:
            msgs.error(
                "Need to specify   reduce masters setup   in your PYPIT file!")
        # setup_dict
        setup = settings.argflag['reduce']['masters']['setup']
        setup_dict = {}
        setup_dict[setup[0]] = {}
        for ii in range(1, 20):  # Dummy detectors
            setup_dict[setup[0]][arparse.get_dnum(ii)] = dict(binning='1x1')
        setup_dict[setup[0]][setup[-2:]] = {}
        iSCI = filesort['science']
        setup_dict[setup[0]][setup[-2:]]['sci'] = [
            fitsdict['filename'][i] for i in iSCI
        ]
        # Write
        calib_file = arsort.write_calib(setup_dict)
        return sciexp, setup_dict
    # Run through the setups to fill setup_dict
    setupIDs = []
    for sc in range(numsci):
        for kk in range(settings.spect['mosaic']['ndet']):
            # Use user-supplied setup name (useful for some book-keeping)?
            try:
                cname = settings.argflag['setup']['name']
            except KeyError:
                cname = None
            setupID = arsort.instr_setup(sciexp[sc],
                                         kk + 1,
                                         fitsdict,
                                         setup_dict,
                                         skip_cset=skip_cset,
                                         config_name=cname)
            if kk == 0:  # Only save the first detector for run setup
                setupIDs.append(setupID)

    # Calib IDs
    group_dict = {}
    if settings.argflag['run']['setup']:  # Collate all matching files
        for sc, setupID in enumerate(setupIDs):
            scidx = sciexp[sc]._idx_sci[0]
            # Set group_key
            config_key = setupID[0]
            # Plan init
            if config_key not in group_dict.keys():
                group_dict[config_key] = {}
                for key in filesort.keys():
                    if key not in ['unknown', 'dark']:
                        group_dict[config_key][key] = []
                    group_dict[config_key]['sciobj'] = []
                    group_dict[config_key]['stdobj'] = []
            # Fill group_dict too
            for key in filesort.keys():
                if key in ['unknown', 'dark', 'failures']:
                    continue
                for idx in settings.spect[key]['index'][sc]:
                    # Only add if new
                    if fitsdict['filename'][idx] not in group_dict[config_key][
                            key]:
                        group_dict[config_key][key].append(
                            fitsdict['filename'][idx])
                        if key == 'standard':  # Add target name
                            group_dict[config_key]['stdobj'].append(
                                fitsdict['target'][idx])
                    if key == 'science':  # Add target name
                        group_dict[config_key]['sciobj'].append(
                            fitsdict['target'][scidx])
            #debugger.set_trace()
        # Write .sorted file
        if len(group_dict) > 0:
            arsort.write_sorted(srt_tbl, group_dict, setup_dict)
        else:
            msgs.warn("No group dict entries and therefore no .sorted file")

    # Write setup -- only if not present
    setup_file, nexist = arsort.get_setup_file()
    # Write calib file (if not in setup mode)
    if not settings.argflag['run']['setup']:
        calib_file = arsort.write_calib(setup_dict)
    else:
        arsort.write_setup(setup_dict)
    # Finish calcheck or setup
    if settings.argflag['run']['calcheck'] or settings.argflag['run']['setup']:
        if settings.argflag['run']['calcheck']:
            msgs.info("Inspect the .calib file: {:s}".format(calib_file))
            msgs.info(
                "*********************************************************")
            msgs.info("Calibration check complete and successful!")
            msgs.info(
                "Set 'run calcheck False' to continue with data reduction")
            msgs.info(
                "*********************************************************")
            # Instrument specific (might push into a separate file)
            if settings.argflag['run']['spectrograph'] in ['keck_lris_blue']:
                if settings.argflag['reduce']['flatfield']['useframe'] in [
                        'pixelflat'
                ]:
                    msgs.warn(
                        "We recommend a slitless flat for your instrument.")
            return 'calcheck', None
        elif settings.argflag['run']['setup']:
            for idx in filesort['failures']:
                msgs.warn(
                    "No Arc found: Skipping object {:s} with file {:s}".format(
                        fitsdict['target'][idx], fitsdict['filename'][idx]))
            msgs.info("Setup is complete.")
            msgs.info("Inspect the .setups file: {:s}".format(setup_file))
            return 'setup', None
        else:
            msgs.error("Should not get here")
    return sciexp, setup_dict