271 lines
12 KiB
Python
271 lines
12 KiB
Python
from ..lib.helpers import error, isLambda
|
|
from scipy.interpolate import interp1d
|
|
import astropy.units as u
|
|
import math
|
|
from typing import Union, Callable
|
|
import logging
|
|
from astropy.io import ascii
|
|
import re
|
|
|
|
|
|
# noinspection PyUnresolvedReferences
|
|
class SpectralQty:
|
|
"""
|
|
A class to hold and work with spectral quantities
|
|
"""
|
|
|
|
def __init__(self, wl: u.Quantity, qty: u.Quantity, extrapolate: bool = False):
|
|
"""
|
|
Initialize a new spectral quantity
|
|
|
|
Parameters
|
|
----------
|
|
wl : Quantity
|
|
The binned wavelengths
|
|
qty : Quantity
|
|
The quantity values corresponding to the binned wavelengths. If the values are supplied without a unit,
|
|
they are assumed to be dimensionless.
|
|
extrapolate : bool
|
|
Whether extrapolation should be allowed. If disabled, the spectrum will be truncated and a warning given.
|
|
Returns
|
|
-------
|
|
sqty : SpectralQty
|
|
The created spectral quantity.
|
|
"""
|
|
# Check if both lengths are equal
|
|
if len(wl) == len(qty):
|
|
# check if units are given. If not, add a dimensionless unit
|
|
if hasattr(wl, "unit"):
|
|
self.wl = wl
|
|
else:
|
|
self.wl = wl * u.dimensionless_unscaled
|
|
if hasattr(qty, "unit"):
|
|
self.qty = qty
|
|
else:
|
|
self.qty = qty * u.dimensionless_unscaled
|
|
else:
|
|
error("Lengths not matching")
|
|
self._extrapolate = extrapolate
|
|
|
|
@classmethod
|
|
def fromFile(cls, file: str, wl_unit_default: u.Quantity = None, qty_unit_default: u.Quantity = None,
|
|
extrapolate: bool = False) -> "SpectralQty":
|
|
"""
|
|
Initialize a new spectral quantity and read the values from a file
|
|
|
|
Parameters
|
|
----------
|
|
file : str
|
|
Path to the file to read the values from. The file needs to provide two columns: wavelength
|
|
and the corresponding spectral quantity. The format of the file will be guessed by
|
|
`astropy.io.ascii.read()`. If the file doesn't provide units via astropy's enhanced CSV format, the units
|
|
will be read from the column headers or otherwise assumed to be *wl_unit_default* and *qty_unit_default*.
|
|
wl_unit_default : Quantity
|
|
Default unit to be used for the wavelength column if no units are provided by the file.
|
|
qty_unit_default : Quantity
|
|
Default unit to be used for the quantity column if no units are provided by the file.
|
|
extrapolate : bool
|
|
Whether extrapolation should be allowed. If disabled, the spectrum will be truncated and a warning given.
|
|
Returns
|
|
-------
|
|
sqty : SpectralQty
|
|
The created spectral quantity.
|
|
"""
|
|
# Read the file
|
|
data = ascii.read(file)
|
|
# Check if units are given
|
|
if data[data.colnames[0]].unit is None:
|
|
# Convert values to float
|
|
data[data.colnames[0]] = list(map(float, data[data.colnames[0]]))
|
|
data[data.colnames[1]] = list(map(float, data[data.colnames[1]]))
|
|
# Check if units are given in column headers
|
|
if all([re.search("\\[.+\\]", x) for x in data.colnames]):
|
|
# Extract units from headers and apply them on the columns
|
|
# noinspection PyArgumentList
|
|
units = [u.Unit(re.findall("(?<=\\[).+(?=\\])", x)[0]) for x in data.colnames]
|
|
data[data.colnames[0]].unit = units[0]
|
|
data[data.colnames[1]].unit = units[1]
|
|
# Use default units
|
|
elif wl_unit_default is not None and qty_unit_default is not None:
|
|
data[data.colnames[0]].unit = wl_unit_default
|
|
data[data.colnames[1]].unit = qty_unit_default
|
|
return cls(data[data.colnames[0]].quantity, data[data.colnames[1]].quantity, extrapolate=extrapolate)
|
|
|
|
def __eq__(self, other) -> bool:
|
|
"""
|
|
Check if this object is equal to another object
|
|
|
|
Parameters
|
|
----------
|
|
other : SpectralQty
|
|
Object to compare with
|
|
|
|
Returns
|
|
-------
|
|
res : bool
|
|
Result of the comparison
|
|
"""
|
|
return self.wl.unit == other.wl.unit and self.qty.unit == other.qty.unit and \
|
|
len(self.wl) == len(other.wl) and len(self.qty) == len(other.qty) and \
|
|
all([math.isclose(x, y, rel_tol=1e-5) for x, y in zip(self.wl.value, other.wl.value)]) and \
|
|
all([math.isclose(x, y, rel_tol=1e-5) for x, y in zip(self.qty.value, other.qty.value)])
|
|
|
|
def __add__(self, other: Union[int, float, u.Quantity, "SpectralQty", Callable]) -> "SpectralQty":
|
|
"""
|
|
Calculate the sum with another object
|
|
|
|
Parameters
|
|
----------
|
|
other : Union[int, float, u.Quantity, "SpectralQty", Callable]
|
|
Addend to be added to this object. If the binning of the object on the right hand side differs
|
|
from the binning of the left object, the object on the right hand side will be rebinned.
|
|
|
|
Returns
|
|
-------
|
|
sum : SpectralQty
|
|
The sum of both objects
|
|
"""
|
|
# Summand is of type int or float, use same unit
|
|
if isinstance(other, int) or isinstance(other, float):
|
|
return SpectralQty(self.wl, self.qty + other * self.qty.unit)
|
|
# Summand is of type Quantity
|
|
elif isinstance(other, u.Quantity):
|
|
if other.unit == self.qty.unit:
|
|
return SpectralQty(self.wl, self.qty + other)
|
|
else:
|
|
raise TypeError("Units are not matching for addition.")
|
|
# Summand is of type lambda
|
|
elif isLambda(other):
|
|
return SpectralQty(self.wl, self.qty + [other(wl).value for wl in self.wl] * other(self.wl[0]).unit)
|
|
# Summand is of type SpectralQty
|
|
else:
|
|
if other.wl.unit.is_equivalent(self.wl.unit) and other.qty.unit.is_equivalent(self.qty.unit):
|
|
# Wavelengths are matching, just add the quantities
|
|
if len(self.wl) == len(other.wl) and (self.wl == other.wl).all():
|
|
return SpectralQty(self.wl, self.qty + other.qty)
|
|
# Wavelengths are not matching, rebinning needed
|
|
else:
|
|
# Rebin addend
|
|
other_rebinned = other.rebin(self.wl)
|
|
if len(self.wl) == len(other_rebinned.wl) and (self.wl == other_rebinned.wl).all():
|
|
return SpectralQty(self.wl, self.qty + other_rebinned.qty)
|
|
else:
|
|
# Wavelengths are still not matching as extrapolation is disabled, rebin this spectral quantity
|
|
return SpectralQty(other_rebinned.wl, self.rebin(other_rebinned.wl).qty + other_rebinned.qty)
|
|
else:
|
|
error("Units are not matching for addition.")
|
|
|
|
__radd__ = __add__
|
|
|
|
def __sub__(self, other: Union[int, float, u.Quantity, "SpectralQty", Callable]) -> "SpectralQty":
|
|
"""
|
|
Calculate the difference to another object
|
|
|
|
Parameters
|
|
----------
|
|
other : Union[int, float, u.Quantity, "SpectralQty", Callable]
|
|
Subtrahend to be subtracted from this object. If the binning of the object on the right hand side differs
|
|
from the binning of the left object, the object on the right hand side will be rebinned.
|
|
|
|
Returns
|
|
-------
|
|
sum : SpectralQty
|
|
The difference of both objects
|
|
"""
|
|
# Subtrahend is of type int or float, use same unit
|
|
if isinstance(other, int) or isinstance(other, float):
|
|
return SpectralQty(self.wl, self.qty - other * self.qty.unit)
|
|
# Subtrahend is of type Quantity
|
|
elif isinstance(other, u.Quantity):
|
|
if other.unit == self.qty.unit:
|
|
return SpectralQty(self.wl, self.qty - other)
|
|
else:
|
|
raise TypeError('Units are not matching for subtraction.')
|
|
# Subtrahend is of type lambda
|
|
elif isLambda(other):
|
|
return SpectralQty(self.wl, self.qty - [other(wl).value for wl in self.wl] * other(self.wl[0]).unit)
|
|
# Subtrahend is of type SpectralQty
|
|
else:
|
|
if other.wl.unit.is_equivalent(self.wl.unit) and other.qty.unit.is_equivalent(self.qty.unit):
|
|
# Wavelengths are matching, just subtract the quantities
|
|
if len(self.wl) == len(other.wl) and (self.wl == other.wl).all():
|
|
return SpectralQty(self.wl, self.qty - other.qty)
|
|
# Wavelengths are not matching, rebinning needed
|
|
else:
|
|
# Rebin subtrahend
|
|
other_rebinned = other.rebin(self.wl)
|
|
if len(self.wl) == len(other_rebinned.wl) and (self.wl == other_rebinned.wl).all():
|
|
return SpectralQty(self.wl, self.qty - other_rebinned.qty)
|
|
else:
|
|
# Wavelengths are still not matching as extrapolation is disabled, rebin this spectral quantity
|
|
return SpectralQty(other_rebinned.wl, self.rebin(other_rebinned.wl).qty - other_rebinned.qty)
|
|
else:
|
|
error("Units are not matching for substraction.")
|
|
|
|
def __mul__(self, other: Union[int, float, u.Quantity, "SpectralQty", Callable]) -> "SpectralQty":
|
|
"""
|
|
Calculate the product with another object
|
|
|
|
Parameters
|
|
----------
|
|
other : Union[int, float, u.Quantity, "SpectralQty", Callable]
|
|
Factor to be multiplied with this object. If the binning of the object on the right hand side differs
|
|
from the binning of the left object, the object on the right hand side will be rebinned.
|
|
|
|
Returns
|
|
-------
|
|
sum : SpectralQty
|
|
The product of both objects
|
|
"""
|
|
# Factor is of type int, float or Quantity, just multiply
|
|
if isinstance(other, int) or isinstance(other, float) or isinstance(other, u.Quantity):
|
|
return SpectralQty(self.wl, self.qty * other)
|
|
# Factor is of type lambda
|
|
elif isLambda(other):
|
|
return SpectralQty(self.wl, self.qty * [other(wl).value for wl in self.wl] * other(self.wl[0]).unit)
|
|
# Factor is of type SpectralQty
|
|
else:
|
|
if other.wl.unit.is_equivalent(self.wl.unit):
|
|
# Wavelengths are matching, just multiply the quantities
|
|
if len(self.wl) == len(other.wl) and (self.wl == other.wl).all():
|
|
return SpectralQty(self.wl, self.qty * other.qty)
|
|
# Wavelengths are not matching, rebinning needed
|
|
else:
|
|
# Rebin factor
|
|
other_rebinned = other.rebin(self.wl)
|
|
if len(self.wl) == len(other_rebinned.wl) and (self.wl == other_rebinned.wl).all():
|
|
return SpectralQty(self.wl, self.qty * other_rebinned.qty)
|
|
else:
|
|
# Wavelengths are still not matching as extrapolation is disabled, rebin this spectral quantity
|
|
return SpectralQty(other_rebinned.wl, self.rebin(other_rebinned.wl).qty * other_rebinned.qty)
|
|
else:
|
|
error("Units are not matching for multiplication.")
|
|
|
|
__rmul__ = __mul__
|
|
|
|
def rebin(self, wl: u.Quantity) -> "SpectralQty":
|
|
"""
|
|
Resample the spectral quantity sqty(wl) over the new grid wl, rebinning if necessary, otherwise interpolates.
|
|
Copied from ExoSim (https://github.com/ExoSim/ExoSimPublic).
|
|
|
|
Parameters
|
|
----------
|
|
wl : Quantity
|
|
new binned wavelengths
|
|
|
|
Returns
|
|
-------
|
|
sqty : SpectralQty
|
|
The rebinned spectral quantity
|
|
"""
|
|
|
|
if not wl.unit.is_equivalent(self.wl.unit):
|
|
error("Mismatching units for rebinning: " + wl.unit + ", " + self.wl.unit)
|
|
if not self._extrapolate:
|
|
if min(wl) < min(self.wl) or max(wl) > max(self.wl):
|
|
logging.warning("Extrapolation disabled, bandwidth will be reduced.")
|
|
# Remove new wavelengths where extrapolation would have been necessary
|
|
wl = [x.value for x in wl if min(self.wl) <= x <= max(self.wl)] * wl.unit
|
|
f = interp1d(self.wl, self.qty.value, fill_value="extrapolate")
|
|
return SpectralQty(wl, f(wl.to(self.wl.unit)) * self.qty.unit)
|