Source code for lezargus.container.cube

"""Spectral data cube container.

This module and class primarily deals with spectral data cubes containing both
spatial and spectral information.
"""

import numpy as np

from lezargus.container import LezargusContainerArithmetic
from lezargus.library import hint
from lezargus.library import logging


[docs]class LezargusCube(LezargusContainerArithmetic): """Container to hold spectral cube data and perform operations on it. Attributes ---------- wavelength : ndarray The wavelength of the spectra. The unit of wavelength is typically in microns; but, check the `wavelength_unit` value. data : ndarray The flux of the spectra cube. The unit of the flux is typically in flam; but, check the `flux_unit` value. uncertainty : ndarray The uncertainty in the flux of the spectra. The unit of the uncertainty is the same as the flux value; per `uncertainty_unit`. wavelength_unit : Astropy Unit The unit of the wavelength array. flux_unit : Astropy Unit The unit of the flux array. uncertainty_unit : Astropy Unit The unit of the uncertainty array. This unit is the same as the flux unit. mask : ndarray A mask of the flux data, used to remove problematic areas. Where True, the values of the flux is considered mask. flags : ndarray Flags of the flux data. These flags store metadata about the flux. header : Header The header information, or metadata in general, about the data. """
[docs] def __init__( self: hint.Self, wavelength: hint.ndarray, data: hint.ndarray, uncertainty: hint.ndarray = None, wavelength_unit: str | hint.Unit | None = None, data_unit: str | hint.Unit | None = None, mask: hint.ndarray | None = None, flags: hint.ndarray | None = None, header: hint.Header | None = None, ) -> None: """Instantiate the spectra class. Parameters ---------- wavelength : ndarray The wavelength of the spectra. data : ndarray The flux of the spectra. uncertainty : ndarray, default = None The uncertainty of the spectra. By default, it is None and the uncertainty value is 0. wavelength_unit : Astropy-Unit like, default = None The wavelength unit of the spectra. It must be interpretable by the Astropy Units package. If None, the the unit is dimensionless. data_unit : Astropy-Unit like, default = None The data unit of the spectra. It must be interpretable by the Astropy Units package. If None, the the unit is dimensionless. mask : ndarray, default = None A mask which should be applied to the spectra, if needed. flags : ndarray, default = None A set of flags which describe specific points of data in the spectra. header : Header, default = None A set of header data describing the data. Note that when saving, this header is written to disk with minimal processing. We highly suggest writing of the metadata to conform to the FITS Header specification as much as possible. """ # The data must be three dimensional. container_dimensions = 3 if len(data.shape) != container_dimensions: logging.error( error_type=logging.InputError, message=( "The input data for a LezargusCube instantiation has a" " shape {sh}, which is not the expected three dimensions." .format( sh=data.shape, ) ), ) # The wavelength and the flux data must be parallel, and thus the same # shape. wavelength = np.array(wavelength, dtype=float) data = np.array(data, dtype=float) if wavelength.shape[0] != data.shape[2]: logging.critical( critical_type=logging.InputError, message=( "Wavelength array shape: {wv_s}; flux cube array shape:" " {dt_s}. The cube wavelength dimension length {dt_s_w} is" " not compatible with the wavelength length {wv_s_w}." .format( wv_s=wavelength.shape, dt_s=data.shape, dt_s_w=data.shape[2], wv_s_w=wavelength.shape[2], ) ), ) # Constructing the original class. We do not deal with WCS here because # the base class does not support it. We do not involve units here as # well for speed concerns. Both are handled during reading and writing. super().__init__( wavelength=wavelength, data=data, uncertainty=uncertainty, wavelength_unit=wavelength_unit, data_unit=data_unit, mask=mask, flags=flags, header=header, )
[docs] @classmethod def read_fits_file( cls: hint.Type["LezargusCube"], filename: str, ) -> hint.Self: """Read a Lezargus cube FITS file. We load a Lezargus FITS file from disk. Note that this should only be used for 3-D cube files. Parameters ---------- filename : str The filename to load. Returns ------- cube : Self-like The LezargusCube class instance. """ # Any pre-processing is done here. # Loading the file. spectra = cls._read_fits_file(filename=filename) # Any post-processing is done here. # All done. return spectra
[docs] def write_fits_file( self: hint.Self, filename: str, overwrite: bool = False, ) -> hint.Self: """Write a Lezargus cube FITS file. We write a Lezargus FITS file to disk. Parameters ---------- filename : str The filename to write to. overwrite : bool, default = False If True, overwrite file conflicts. Returns ------- None """ # Any pre-processing is done here. # Saving the file. self._write_fits_file(filename=filename, overwrite=overwrite)
# Any post-processing is done here. # All done.