Compatibility with specutils 2.0

Author: pllim

CHANGES.rst

@@ -15,6 +15,7 @@ Bug Fixes
 Other changes
 ^^^^^^^^^^^^^
 
+- Compatibility with specutils 2.0. [#260]
 
 1.5.1 (2024-03-08)
 ------------------

MANIFEST.in

@@ -1,6 +1,7 @@
 include README.rst
 include CHANGES.rst
 include pyproject.toml
+include conftest.py
 
 recursive-include docs *
 recursive-include licenses *

conftest.py

@@ -6,7 +6,9 @@
 from astropy.io import fits
 from astropy.nddata import CCDData, NDData, VarianceUncertainty
 from astropy.utils.data import get_pkg_data_filename
-from specutils import Spectrum1D, SpectralAxis
+from specutils import SpectralAxis
+
+from specreduce.compat import SPECUTILS_LT_2, Spectrum
 
 try:
     from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
@@ -31,9 +33,13 @@ def _mk_test_data(imgtype, nrows=30, ncols=10):
         flux = image * u.DN
         uncert = VarianceUncertainty(image_ones)
         if imgtype == "spec_no_axis":
-            image = Spectrum1D(flux, uncertainty=uncert)
+            if SPECUTILS_LT_2:
+                kwargs = {}
+            else:
+                kwargs = {"spectral_axis_index": image.ndim - 1}
+            image = Spectrum(flux, uncertainty=uncert, **kwargs)
         else:  # "spec"
-            image = Spectrum1D(flux, spectral_axis=np.arange(ncols) * u.um, uncertainty=uncert)
+            image = Spectrum(flux, spectral_axis=np.arange(ncols) * u.um, uncertainty=uncert)
     return image
 
 
@@ -71,10 +77,15 @@ def all_images():
     sax = SpectralAxis(np.linspace(14.377, 3.677, flux.shape[-1]) * u.um)
     unc = VarianceUncertainty(np.random.rand(*flux.shape))
 
+    if SPECUTILS_LT_2:
+        kwargs = {}
+    else:
+        kwargs = {"spectral_axis_index": img.ndim - 1}
+
     all_images = {}
     all_images['arr'] = img
-    all_images['s1d'] = Spectrum1D(flux, spectral_axis=sax, uncertainty=unc)
-    all_images['s1d_pix'] = Spectrum1D(flux, uncertainty=unc)
+    all_images['s1d'] = Spectrum(flux, spectral_axis=sax, uncertainty=unc)
+    all_images['s1d_pix'] = Spectrum(flux, uncertainty=unc, **kwargs)
     all_images['ccd'] = CCDData(img, uncertainty=unc, unit=flux.unit)
     all_images['ndd'] = NDData(img, uncertainty=unc, unit=flux.unit)
     all_images['qnt'] = img * flux.unit
@@ -86,7 +97,7 @@ def spec1d():
     np.random.seed(7)
     flux = np.random.random(50)*u.Jy
     sa = np.arange(0, 50)*u.pix
-    spec = Spectrum1D(flux, spectral_axis=sa)
+    spec = Spectrum(flux, spectral_axis=sa)
     return spec
 
 
@@ -97,7 +108,7 @@ def spec1d_with_emission_line():
     flux = (np.random.randn(200) +
             10*np.exp(-0.01*((sa.value-130)**2)) +
             sa.value/100) * u.Jy
-    spec = Spectrum1D(flux, spectral_axis=sa)
+    spec = Spectrum(flux, spectral_axis=sa)
     return spec
 
 
@@ -108,7 +119,7 @@ def spec1d_with_absorption_line():
     flux = (np.random.randn(200) -
             10*np.exp(-0.01*((sa.value-130)**2)) +
             sa.value/100) * u.Jy
-    spec = Spectrum1D(flux, spectral_axis=sa)
+    spec = Spectrum(flux, spectral_axis=sa)
     return spec
 
 

notebook_sandbox/apo05.ipynb

@@ -24,7 +24,7 @@
     "from astropy import units as u\n",
     "\n",
     "from astropy.nddata import CCDData, StdDevUncertainty\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from ccdproc import trim_image, Combiner\n",
     "\n",
     "# need to get import to work in notebook w/o global package install\n",

notebook_sandbox/fluxcal_demo.ipynb

@@ -14,7 +14,7 @@
     "from ccdproc import trim_image\n",
     "from astropy import units as u\n",
     "\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from astropy.nddata import StdDevUncertainty\n",
     "\n",
     "# need to get import to work in notebook w/o global package install\n",

notebook_sandbox/wavecal_demo.ipynb

@@ -17,7 +17,7 @@
     "from astropy.nddata import StdDevUncertainty\n",
     "import astropy.units as u\n",
     "\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from specutils.fitting import fit_generic_continuum\n",
     "\n",
     "from specreduce.calibration_data import load_pypeit_calibration_lines\n",

specreduce/background.py

@@ -6,8 +6,8 @@
 import numpy as np
 from astropy import units as u
 from astropy.utils.decorators import deprecated_attribute
-from specutils import Spectrum1D
 
+from specreduce.compat import SPECUTILS_LT_2, Spectrum
 from specreduce.core import _ImageParser, MaskingOption, ImageLike
 from specreduce.extract import _ap_weight_image
 from specreduce.tracing import Trace, FlatTrace
@@ -84,7 +84,7 @@ class Background(_ImageParser):
         "apply_nan_only",
     )
 
-    # TO-DO: update bkg_array with Spectrum1D alternative (is bkg_image enough?)
+    # TO-DO: update bkg_array with Spectrum alternative (is bkg_image enough?)
     bkg_array = deprecated_attribute("bkg_array", "1.3")
 
     def __post_init__(self):
@@ -303,12 +303,18 @@ def bkg_image(self, image=None):
 
         Returns
         -------
-        `~specutils.Spectrum1D` object with same shape as ``image``.
+        spec : `~specutils.Spectrum1D`
+            Spectrum object with same shape as ``image``.
         """
         image = self._parse_image(image)
-        return Spectrum1D(
-            np.tile(self._bkg_array, (image.shape[0], 1)) * image.unit,
-            spectral_axis=image.spectral_axis,
+        arr = np.tile(self._bkg_array, (image.shape[0], 1))
+        if SPECUTILS_LT_2:
+            kwargs = {}
+        else:
+            kwargs = {"spectral_axis_index": arr.ndim - 1}
+        return Spectrum(
+            arr * image.unit,
+            spectral_axis=image.spectral_axis, **kwargs
         )
 
     def bkg_spectrum(self, image=None, bkg_statistic="sum"):
@@ -355,7 +361,7 @@ def bkg_spectrum(self, image=None, bkg_statistic="sum"):
             # can't collapse with a spectral axis in pixels because
             # SpectralCoord only allows frequency/wavelength equivalent units...
             ext1d = statistic_function(bkg_image.flux, axis=self.crossdisp_axis)
-            return Spectrum1D(ext1d, bkg_image.spectral_axis)
+            return Spectrum(ext1d, bkg_image.spectral_axis)
 
     def sub_image(self, image=None):
         """
@@ -369,15 +375,17 @@ def sub_image(self, image=None):
 
         Returns
         -------
-        `~specutils.Spectrum1D` object with same shape as ``image``.
+        spec : `~specutils.Spectrum1D`
+            Spectrum object with same shape as ``image``.
         """
         image = self._parse_image(image)
 
-        # a compare_wcs argument is needed for Spectrum1D.subtract() in order to
+        # a compare_wcs argument is needed for Spectrum.subtract() in order to
         # avoid a TypeError from SpectralCoord when image's spectral axis is in
         # pixels. it is not needed when image's spectral axis has physical units
         kwargs = {"compare_wcs": None} if image.spectral_axis.unit == u.pix else {}
-
+        if not SPECUTILS_LT_2:
+            kwargs["spectral_axis_index"] = image.flux.ndim - 1
         # https://docs.astropy.org/en/stable/nddata/mixins/ndarithmetic.html
         return image.subtract(self.bkg_image(image), **kwargs)
 
@@ -406,7 +414,7 @@ def sub_spectrum(self, image=None):
             # can't collapse with a spectral axis in pixels because
             # SpectralCoord only allows frequency/wavelength equivalent units...
             ext1d = np.nansum(sub_image.flux, axis=self.crossdisp_axis)
-            return Spectrum1D(ext1d, spectral_axis=sub_image.spectral_axis)
+            return Spectrum(ext1d, spectral_axis=sub_image.spectral_axis)
 
     def __rsub__(self, image):
         """

specreduce/calibration_data.py

@@ -12,10 +12,10 @@
 from astropy.utils.data import download_file
 from astropy.utils.exceptions import AstropyUserWarning
 from astropy.coordinates import SpectralCoord
-
-from specutils import Spectrum1D
 from specutils.utils.wcs_utils import vac_to_air
 
+from specreduce.compat import Spectrum
+
 __all__ = [
     'get_available_line_catalogs',
     'load_pypeit_calibration_lines',
@@ -187,7 +187,7 @@ def load_MAST_calspec(
         filename: str | Path,
         cache: bool | Literal['update'] = True,
         show_progress: bool = False
-) -> Spectrum1D | None:
+) -> Spectrum | None:
     """
     Load a standard star spectrum from the ``calspec`` database at MAST. These spectra are provided
     in FITS format and are described in detail at:
@@ -238,7 +238,7 @@ def load_MAST_calspec(
         # supported directly by astropy.units. mJy is chosen since it's the JWST
         # standard and can easily be converted to/from AB magnitudes.
         flux_mjy = synphot.units.convert_flux(wave, flux, u.mJy)
-        spectrum = Spectrum1D(spectral_axis=wave, flux=flux_mjy)
+        spectrum = Spectrum(spectral_axis=wave, flux=flux_mjy)
         return spectrum
 
 
@@ -247,7 +247,7 @@ def load_onedstds(
         specfile: str = "EG131.dat",
         cache: bool | Literal['update'] = True,
         show_progress: bool = False
-) -> Spectrum1D | None:
+) -> Spectrum | None:
     """
     This is a convenience function for loading a standard star spectrum from the 'onedstds'
     dataset in the ``specreduce_data`` package. They will be downloaded from the
@@ -290,11 +290,11 @@ def load_onedstds(
     # the specreduce_data standard star spectra all provide fluxes in AB mag
     flux = t['ABmag'].data * u.ABmag
     flux = flux.to(u.mJy)  # convert to linear flux units
-    spectrum = Spectrum1D(spectral_axis=spectral_axis, flux=flux)
+    spectrum = Spectrum(spectral_axis=spectral_axis, flux=flux)
     return spectrum
 
 
-class AtmosphericExtinction(Spectrum1D):
+class AtmosphericExtinction(Spectrum):
     """
     Spectrum container for atmospheric extinction in magnitudes as a function of wavelength.
     If extinction and spectral_axis are provided, this will use them to build a custom model.
@@ -353,7 +353,7 @@ def __init__(
                 extinction = u.Magnitude(
                     extinction,
                     u.MagUnit(u.dimensionless_unscaled)
-                ).to(u.dimensionless_unscaled)  # Spectrum1D wants this to be linear
+                ).to(u.dimensionless_unscaled)  # Spectrum wants this to be linear
             elif isinstance(extinction, (u.LogUnit, u.Magnitude)) or extinction.unit == u.mag:
                 # if in log or magnitudes, recast into Magnitude with dimensionless physical units
                 extinction = u.Magnitude(

specreduce/compat.py

@@ -0,0 +1,11 @@
+import specutils
+from astropy.utils import minversion
+
+__all__ = []
+
+SPECUTILS_LT_2 = not minversion(specutils, "2.0.dev")
+
+if SPECUTILS_LT_2:
+    from specutils import Spectrum1D as Spectrum
+else:
+    from specutils import Spectrum

specreduce/core.py

@@ -1,14 +1,15 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
-from copy import deepcopy
 import inspect
+from copy import deepcopy
 from dataclasses import dataclass
 from typing import Literal
 
 import numpy as np
 from astropy import units as u
 from astropy.nddata import VarianceUncertainty, NDData
-from specutils import Spectrum1D
+
+from specreduce.compat import SPECUTILS_LT_2, Spectrum
 
 __all__ = ["SpecreduceOperation"]
 
@@ -21,14 +22,14 @@
 
 class _ImageParser:
     """
-    Coerces images from accepted formats to Spectrum1D objects for
+    Coerces images from accepted formats to Spectrum objects for
     internal use in specreduce's operation classes.
 
     Fills any and all of uncertainty, mask, units, and spectral axis
     that are missing in the provided image with generic values.
     Accepted image types are:
 
-        - `~specutils.spectra.spectrum1d.Spectrum1D` (preferred)
+        - `~specutils.Spectrum1D` (preferred)
         - `~astropy.nddata.ccddata.CCDData`
         - `~astropy.nddata.ndddata.NDDData`
         - `~astropy.units.quantity.Quantity`
@@ -49,9 +50,9 @@ class _ImageParser:
 
     def _parse_image(
         self, image: ImageLike, disp_axis: int = 1, mask_treatment: MaskingOption = "apply"
-    ) -> Spectrum1D:
+    ) -> Spectrum:
         """
-        Convert all accepted image types to a consistently formatted Spectrum1D object.
+        Convert all accepted image types to a consistently formatted Spectrum object.
 
         Parameters
         ----------
@@ -81,7 +82,7 @@ def _parse_image(
 
         Returns
         -------
-        Spectrum1D
+        Spectrum
         """
         # would be nice to handle (cross)disp_axis consistently across
         # operations (public attribute? private attribute? argument only?) so
@@ -96,7 +97,7 @@ def _parse_image(
     @staticmethod
     def _get_data_from_image(
         image: ImageLike, disp_axis: int = 1, mask_treatment: MaskingOption = "apply"
-    ) -> Spectrum1D:
+    ) -> Spectrum:
         """
         Extract data array from various input types for `image`.
 
@@ -112,13 +113,13 @@ def _get_data_from_image(
 
         Returns
         -------
-        Spectrum1D
+        Spectrum
         """
         if isinstance(image, u.quantity.Quantity):
             img = image.value
         elif isinstance(image, np.ndarray):
             img = image
-        else:  # NDData, including CCDData and Spectrum1D
+        else:  # NDData, including CCDData and Spectrum
             img = image.data
 
         mask = getattr(image, "mask", None)
@@ -136,7 +137,7 @@ def _get_data_from_image(
         )
 
         # mask (handled above) and uncertainty are set as None when they aren't
-        # specified upon creating a Spectrum1D object, so we must check whether
+        # specified upon creating a Spectrum object, so we must check whether
         # these attributes are absent *and* whether they are present but set as None
         if hasattr(image, "uncertainty"):
             uncertainty = image.uncertainty
@@ -147,8 +148,13 @@ def _get_data_from_image(
 
         spectral_axis = getattr(image, "spectral_axis", np.arange(img.shape[disp_axis]) * u.pix)
 
-        img = Spectrum1D(
-            img * unit, spectral_axis=spectral_axis, uncertainty=uncertainty, mask=mask
+        if SPECUTILS_LT_2:
+            kwargs = {}
+        else:
+            kwargs = {"spectral_axis_index": img.ndim - 1}
+        img = Spectrum(
+            img * unit, spectral_axis=spectral_axis, uncertainty=uncertainty, mask=mask,
+            **kwargs
         )
         return img