"""Spectrum data container, holding spectral data.
This module and class primarily deals with spectral data.
"""
# isort: split
# Import required to remove circular dependencies from type checking.
from __future__ import annotations
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from lezargus.library import hint
# isort: split
import copy
import numpy as np
import lezargus
from lezargus.container import LezargusContainerArithmetic
from lezargus.library import logging
[docs]
class LezargusSpectrum(LezargusContainerArithmetic):
"""Container to hold spectral data and perform operations on it.
Attributes
----------
For all available attributes, see :py:class:`LezargusContainerArithmetic`.
"""
[docs]
def __init__(
self: LezargusSpectrum,
wavelength: hint.ndarray,
data: hint.ndarray,
uncertainty: hint.ndarray | None = None,
wavelength_unit: str | hint.Unit | None = None,
data_unit: str | hint.Unit | None = None,
spectral_scale: float | None = None,
pixel_scale: float | None = None,
slice_scale: float | None = None,
mask: hint.ndarray | None = None,
flags: hint.ndarray | None = None,
header: hint.Header | None = None,
) -> None:
"""Instantiate the spectrum class.
Parameters
----------
wavelength : ndarray
The wavelength axis of the spectral component of the data, if any.
The unit of wavelength is typically in meters; but, check the
:py:attr:`wavelength_unit` value.
data : ndarray
The data stored in this container. The unit of the flux is typically
in W m^-2 m^-1; but, check the :py:attr:`data_unit` value.
uncertainty : ndarray
The uncertainty in the data of the spectrum. The unit of the
uncertainty is the same as the data value; per
:py:attr:`uncertainty_unit`.
wavelength_unit : Astropy Unit
The unit of the wavelength array. If None, we assume unit-less.
data_unit : Astropy Unit
The unit of the data array. If None, we assume unit-less.
spectral_scale : float, default = None
The spectral scale, or spectral resolution, of the spectral
component, if any. Must be in meters per pixel. Scale is None if
none is provided.
pixel_scale : float, default = None
The E-W, "x" dimension, pixel plate scale of the spatial component,
if any. Must be in radians per pixel. Scale is None if none
is provided.
slice_scale : float, default = None
The N-S, "y" dimension, pixel slice scale of the spatial component,
if any. Must be in radians per slice/pixel. Scale is None if none
is provided.
mask : ndarray, default = None
A mask of the data, used to remove problematic areas. Where True,
the values of the data is considered masked. If None, we assume
the mask is all clear.
flags : ndarray, default = None
Flags of the data. These flags store metadata about the data. If
None, we assume that there are no harmful flags.
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. If None, we just use an
empty header.
Returns
-------
None
"""
# The data must be one dimensional.
container_dimensions = 1
if len(data.shape) != container_dimensions:
logging.error(
error_type=logging.InputError,
message=(
"The input data for a LezargusSpectrum instantiation has a"
f" shape {data.shape}, which is not the expected one"
" dimension."
),
)
# The wavelength and the data must be parallel, and thus the same
# shape.
wavelength = np.array(wavelength, dtype=float)
data = np.array(data, dtype=float)
if wavelength.shape != data.shape:
logging.critical(
critical_type=logging.InputError,
message=(
f"Wavelength array shape: {wavelength.shape}; data array"
f" shape: {data.shape}. The arrays need to be the same"
" shape or cast-able to such."
),
)
# 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,
spectral_scale=spectral_scale,
pixel_scale=pixel_scale,
slice_scale=slice_scale,
mask=mask,
flags=flags,
header=header,
)
[docs]
@classmethod
def read_fits_file(
cls: hint.Type[hint.Self],
filename: str,
) -> hint.Self:
"""Read a Lezargus spectrum FITS file.
We load a Lezargus FITS file from disk. Note that this should only
be used for a 1-D spectrum file.
Parameters
----------
filename : str
The filename to load.
Returns
-------
spectrum : Self-like
The LezargusSpectrum class instance.
"""
# Any pre-processing is done here.
# Loading the file.
spectrum = cls._read_fits_file(filename=filename)
# Any post-processing is done here.
# All done.
return spectrum
[docs]
@classmethod
def stitch(
cls: hint.Type[hint.Self],
*spectra: hint.LezargusSpectrum,
weights: list[hint.ndarray] | str = "uniform",
average_routine: hint.Callable[
[hint.ndarray, hint.ndarray, hint.ndarray],
tuple[float, float],
] = None,
) -> hint.Self:
"""Stitch spectra together to make a single spectrum.
We stitch all of the input spectra. If the spectrum are not already
to the same scale however, this will result in wildly incorrect
results. The header information is preserved, though we take what we
can from the other objects.
Parameters
----------
*spectra : LezargusSpectrum
The set of Lezargus spectra which we will stitch together.
weights : list[ndarray] or str, default = None
A list of the weights in the data for stitching. Each entry in
the list must have a corresponding entry in the wavelength and
data list, or None. For convenience, we provide short-cut inputs
for the following:
- `uniform` : Uniform weights.
- `invar` : Inverse variance weights.
average_routine : Callable, str, default = None
The function used to average all of the spectra together.
It must also be able to accept weights and propagate uncertainties.
If None, we default to the weighted mean. Namely, it must be of the
form f(val, uncert, weight) = avg, uncert.
Returns
-------
stitch_spectrum : LezargusSpectrum
The spectrum after stitching.
"""
# If there are no spectra to stitch, then we do nothing.
if len(spectra) == 0:
# We still warn just in case.
logging.warning(
warning_type=logging.InputWarning,
message="No spectra supplied to stitch.",
)
return spectra
# We need to make sure these are all Lezargus spectrum.
lz_spectra = []
for spectrumdex in spectra:
if not isinstance(spectrumdex, LezargusSpectrum):
logging.critical(
critical_type=logging.InputError,
message=(
f"Input type {type(spectrumdex)} is not a"
" LezargusSpectrum, we cannot use it to stitch."
),
)
lz_spectra.append(spectrumdex)
# We need to translate the weight input.
if isinstance(weights, str):
weights = weights.casefold()
if weights == "uniform":
# We compute uniform weights.
using_weights = [
np.ones_like(spectrumdex.wavelength)
for spectrumdex in lz_spectra
]
elif weights == "invar":
# We compute weights which are the inverse of the variance
# in the data.
using_weights = [
1 / spectrumdex.uncertainty**2 for spectrumdex in lz_spectra
]
else:
using_weights = None
# A valid shortcut string has not been provided.
accepted_options = ["uniform", "invar"]
logging.critical(
critical_type=logging.InputError,
message=(
f"The weight shortcut option {weights} is not valid; it"
f" must be one of: {accepted_options}"
),
)
else:
using_weights = weights
# Next, we stitch together the data for the spectrum.
(
stitch_wavelength,
stitch_data,
stitch_uncertainty,
) = lezargus.library.stitch.stitch_spectra_discrete(
wavelength_arrays=[
spectrumdex.wavelength for spectrumdex in lz_spectra
],
data_arrays=[spectrumdex.data for spectrumdex in lz_spectra],
uncertainty_arrays=[
spectrumdex.uncertainty for spectrumdex in lz_spectra
],
weight_arrays=using_weights,
average_routine=average_routine,
interpolate_routine=None,
)
# We also stitch together the flags and the mask. They are handled
# with a different function.
logging.error(
error_type=logging.ToDoError,
message="Flag and mask stitching not yet supported.",
)
stitch_mask = None
stitch_flags = None
# We merge the header.
logging.error(
error_type=logging.ToDoError,
message="Header stitching not yet supported.",
)
stitch_header = None
# We compile the new spectrum. We do not expect a subclass but we
# try and allow it.
stitch_spectrum = cls(
wavelength=stitch_wavelength,
data=stitch_data,
uncertainty=stitch_uncertainty,
wavelength_unit=lz_spectra[0].wavelength_unit,
data_unit=lz_spectra[0].data_unit,
mask=stitch_mask,
flags=stitch_flags,
header=stitch_header,
)
# All done.
return stitch_spectrum
[docs]
def write_fits_file(
self: hint.Self,
filename: str,
overwrite: bool = False,
) -> hint.Self:
"""Write a Lezargus spectrum 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.
[docs]
def convolve(
self: hint.Self,
kernel: hint.ndarray | None = None,
kernel_stack: hint.ndarray | None = None,
kernel_function: hint.Callable | None = None,
) -> hint.Self:
"""Convolve the spectrum with a spectral kernel.
See py:func:`convolve_spectrum_by_spectral_kernel` for full
documentation.
Parameters
----------
kernel : ndarray, default = None
The static 2D kernel.
kernel_stack : ndarray, default = None
The variable 2D kernel stack.
kernel_function : Callable, default = None
The dynamic 2D kernel function.
Returns
-------
convolved_cube : ndarray
A near copy of the data cube after convolution.
"""
return lezargus.container.function.convolve_spectrum_by_spectral_kernel(
spectrum=self,
kernel=kernel,
kernel_stack=kernel_stack,
kernel_function=kernel_function,
)
[docs]
def interpolate(
self: hint.Self,
wavelength: hint.ndarray,
extrapolate: bool = False,
skip_mask: bool = True,
skip_flags: bool = True,
) -> tuple[
hint.ndarray,
hint.ndarray,
hint.ndarray | None,
hint.ndarray | None,
]:
"""Interpolation calling function for spectrum.
Each entry is considered a single point to interpolate over.
Parameters
----------
wavelength : ndarray
The wavelength values which we are going to interpolate to. The
units of the data of this array should be the same as the
wavelength unit stored.
extrapolate : bool, default = False
If True, we extrapolate. Otherwise, the edges are NaNs.
skip_mask : bool, default = True
If provided, the propagation of data mask through the
interpolation is skipped. It is computationally a little expensive
otherwise.
skip_flags : bool, default = True
If provided, the propagation of data flags through the
interpolation is skipped. It is computationally a little expensive
otherwise.
Returns
-------
interp_data : ndarray
The interpolated data.
interp_uncertainty : ndarray
The interpolated uncertainty.
interp_mask : ndarray or None
A best guess attempt at finding the appropriate mask for the
interpolated data. If skip_mask=True, then we skip the computation
and return None instead.
interp_flags : ndarray or None
A best guess attempt at finding the appropriate flags for the
interpolated data. If skip_flags=True, then we skip the computation
and return None instead.
"""
# Interpolation cannot deal with NaNs, so we exclude any set of data
# which includes them.
(
clean_wavelength,
clean_data,
clean_uncertainty,
) = lezargus.library.sanitize.clean_finite_arrays(
self.wavelength,
self.data,
self.uncertainty,
)
# If the wavelengths we are using to interpolate to are not all
# numbers, it is a good idea to warn. It is not a good idea to change
# the input the user provided.
if not np.all(np.isfinite(wavelength)):
logging.warning(
warning_type=logging.AccuracyWarning,
message=(
"The input wavelength for interpolation are not all finite."
),
)
# As a sanity check, we check if we are trying to interpolate outside
# of our data range.
overlap = lezargus.library.wrapper.wavelength_overlap_fraction(
base=clean_wavelength,
contain=wavelength,
)
if overlap < 1:
logging.warning(
warning_type=logging.AccuracyWarning,
message=(
"Interpolation is attempted at a wavelength beyond the"
" domain of wavelengths of this spectrum. The overlap"
f" fraction is {overlap}."
),
)
# The interpolated data for both the data itself and uncertainty.
# We use gaps to remove any unwanted data, assuming the cleaned
# wavelength is perfect.
gap_size = lezargus.library.interpolate.get_smallest_gap(
wavelength=clean_wavelength,
)
interp_data = lezargus.library.interpolate.Spline1DInterpolate(
x=clean_wavelength,
v=clean_data,
extrapolate=extrapolate,
extrapolate_fill=np.nan,
gap=gap_size,
)(wavelength)
interp_uncertainty = lezargus.library.interpolate.Spline1DInterpolate(
x=clean_wavelength,
v=clean_uncertainty,
extrapolate=extrapolate,
extrapolate_fill=np.nan,
gap=gap_size,
)(wavelength)
# Checking if we need to compute the interpolation of a mask.
if skip_mask:
interp_mask = None
else:
interp_mask = np.full_like(interp_data, False)
logging.error(
error_type=logging.ToDoError,
message=(
"The interpolation of a mask for a spectrum is not yet"
" implemented."
),
)
# Checking if we need to compute the interpolation of flag array.
if skip_flags:
interp_flags = None
else:
interp_flags = np.full_like(interp_data, 1)
logging.error(
error_type=logging.ToDoError,
message=(
"The interpolation of flags for a spectrum is not yet"
" implemented."
),
)
# All done.
return interp_data, interp_uncertainty, interp_mask, interp_flags
[docs]
def stitch_on(
self: hint.Self,
*spectra: hint.LezargusSpectrum,
**kwargs: object,
) -> hint.Self:
"""Stitch this spectrum with other input spectra.
We stitch spectra onto this spectra. This function is basically
a compatibility wrapper around the class method :py:meth:`stitch`.
Parameters
----------
*spectra : LezargusSpectrum
A set of Lezargus spectra which we will stitch to this one.
**kwargs : object
Arguments passed to :py:meth:`stitch`.
Returns
-------
stitch_spectrum : LezargusSpectrum
The spectrum after stitching.
"""
# We just add ourselves to the rest of the spectra to stitch together.
self_copy = copy.deepcopy(self)
all_spectra = [self_copy, *spectra]
return self.stitch(*all_spectra, **kwargs)