Source code for pypeit.onespec

Provides a simple datamodel for a single spectrum.

.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
import inspect

from IPython import embed

import numpy as np

from pypeit import utils
from pypeit import datamodel
from pypeit import io
from pypeit.spectrographs.util import load_spectrograph

[docs]class OneSpec(datamodel.DataContainer): """ DataContainer to hold single spectra, e.g., from :class:`~pypeit.coadd1d.CoAdd1D`. The datamodel attributes are: .. include:: ../include/class_datamodel_onespec.rst Args: wave wave_grid_mid flux PYP_SPEC ivar mask telluric obj_model ext_mode fluxed Attributes: head0 (``): Primary header spect_meta (:obj:`dict`): Parsed meta from the header spectrograph (:class:`pypeit.spectrographs.spectrograph.Spectrograph`): Build from PYP_SPEC """ version = '1.0.2' datamodel = {'wave': dict(otype=np.ndarray, atype=np.floating, # TODO: The "weighted by pixel contributions" part # should be better explained. descr='Wavelength array (angstroms in vacuum), weighted by pixel ' 'contributions'), 'wave_grid_mid': dict(otype=np.ndarray, atype=np.floating, descr='Wavelength (angstroms in vacuum) evaluated at the ' 'bin centers of a grid that is uniformly spaced ' 'in either lambda or log10-lambda/velocity'), 'flux': dict(otype=np.ndarray, atype=np.floating, descr='Flux array in units of counts/s or 10^-17 erg/s/cm^2/Ang; ' 'see ``fluxed``'), 'ivar': dict(otype=np.ndarray, atype=np.floating, descr='Inverse variance array (matches units of flux)'), 'sigma': dict(otype=np.ndarray, atype=np.floating, descr='One sigma noise array, equivalent to 1/sqrt(ivar) (matches units of flux)'), 'mask': dict(otype=np.ndarray, atype=np.integer, descr='Mask array (1=Good,0=Bad)'), 'telluric': dict(otype=np.ndarray, atype=np.floating, descr='Telluric model'), 'PYP_SPEC': dict(otype=str, descr='``PypeIt`` spectrograph designation'), 'obj_model': dict(otype=np.ndarray, atype=np.floating, descr='Object model for tellurics'), 'ext_mode': dict(otype=str, descr='Extraction mode (options: BOX, OPT)'), 'fluxed': dict(otype=bool, descr='Boolean indicating if the spectrum is fluxed.'), # TODO: Needs a better description. What's in the dictionary? # Why isn't this dictionary expanded into its elements? I.e., # shouldn't each element of this dictionary be a component of # the datamodel? 'spect_meta': dict(otype=dict, descr='header dict')} internals = ['head0', 'filename', 'spectrograph', 'spect_meta', 'history']
[docs] @classmethod def from_file(cls, ifile, verbose=True, chk_version=True, **kwargs): """ Instantiate the object from an extension in the specified fits file. Over-load :func:`~pypeit.datamodel.DataContainer.from_file` to deal with the header Args: ifile (:obj:`str`, `Path`_): Fits file with the data to read verbose (:obj:`bool`, optional): Print informational messages (not currently used) chk_version (:obj:`bool`, optional): Passed to :func:`from_hdu`. kwargs (:obj:`dict`, optional): Arguments passed directly to :func:`from_hdu`. """ with io.fits_open(ifile) as hdu: self = cls.from_hdu(hdu, chk_version=chk_version, **kwargs) self.filename = ifile self.head0 = hdu[0].header self.spectrograph = load_spectrograph(self.PYP_SPEC) self.spect_meta = self.spectrograph.parse_spec_header(self.head0) return self
def __init__(self, wave, wave_grid_mid, flux, PYP_SPEC=None, ivar=None, sigma=None, mask=None, telluric=None, obj_model=None, ext_mode=None, fluxed=None): args, _, _, values = inspect.getargvalues(inspect.currentframe()) _d = dict([(k,values[k]) for k in args[1:]]) # Setup the DataContainer datamodel.DataContainer.__init__(self, d=_d)
[docs] def _bundle(self): """ Override the base class method simply to set the HDU extension name. """ return super()._bundle(ext='SPECTRUM')
[docs] def to_file(self, ofile, primary_hdr=None, history=None, **kwargs): """ Over-load :func:`pypeit.datamodel.DataContainer.to_file` to deal with the header Args: ofile (:obj:`str`): Filename primary_hdr (``_, optional): **kwargs: Passed to super.to_file() """ if primary_hdr is None: primary_hdr = io.initialize_header() # Build the header if self.head0 is not None and self.PYP_SPEC is not None: spectrograph = load_spectrograph(self.PYP_SPEC) subheader = spectrograph.subheader_for_spec(self.head0, self.head0, extra_header_cards = ['RA_OBJ', 'DEC_OBJ']) else: subheader = {} # Add em in for key in subheader: primary_hdr[key] = subheader[key] # Add history if history is not None: history.write_to_header(primary_hdr) # Do it super().to_file(ofile, primary_hdr=primary_hdr, **kwargs)