Removing logic for wcs1d-multispec (#107)

* Removing logic for wcs1d-multispec

* Update astrodbkit/spectra.py

Co-authored-by: Kelle Cruz <kellecruz@gmail.com>

---------

Co-authored-by: Kelle Cruz <kellecruz@gmail.com>

Author: dr-rodriguez

.gitignore

@@ -64,3 +64,6 @@ pip-wheel-metadata/
 
 # Mac OSX
 .DS_Store
+
+.cursor
+uv.lock

astrodbkit/spectra.py

@@ -2,14 +2,10 @@
 
 import os
 
-import astropy.units as u
-import numpy as np
 from astropy.io import fits
 from astropy.nddata import StdDevUncertainty
 from astropy.units import Unit
-from astropy.wcs import WCS
 from specutils import Spectrum
-from specutils.io.parsing_utils import read_fileobj_or_hdulist
 from specutils.io.registers import data_loader
 
 # pylint: disable=no-member, unused-argument
@@ -75,112 +71,6 @@ def spex_prism_loader(filename, **kwargs):
     return Spectrum(flux=data, spectral_axis=wave, uncertainty=uncertainty, meta=meta)
 
 
-def identify_wcs1d_multispec(origin, *args, **kwargs):
-    """
-    Identifier for WCS1D multispec
-    """
-    hdu = kwargs.get("hdu", 0)
-
-    # Check if number of axes is one and dimension of WCS is greater than one
-    with read_fileobj_or_hdulist(*args, **kwargs) as hdulist:
-        return (
-            hdulist[hdu].header.get("WCSDIM", 1) > 1
-            and hdulist[hdu].header["NAXIS"] > 1
-            and "WAT0_001" in hdulist[hdu].header
-            and hdulist[hdu].header.get("WCSDIM", 1) == hdulist[hdu].header["NAXIS"]
-            and "LINEAR" in hdulist[hdu].header.get("CTYPE1", "")
-        )
-
-
-@data_loader("wcs1d-multispec", identifier=identify_wcs1d_multispec, extensions=["fits"], dtype=Spectrum, priority=10)
-def wcs1d_multispec_loader(file_obj, flux_unit=None, hdu=0, verbose=False, **kwargs):
-    """
-    Loader for multiextension spectra as wcs1d. Adapted from wcs1d_fits_loader
-
-    Parameters
-    ----------
-    file_obj : str, file-like or HDUList
-        FITS file name, object (provided from name by Astropy I/O Registry),
-        or HDUList (as resulting from astropy.io.fits.open()).
-    flux_unit : :class:`~astropy.units.Unit` or str, optional
-        Units of the flux for this spectrum. If not given (or None), the unit
-        will be inferred from the BUNIT keyword in the header. Note that this
-        unit will attempt to convert from BUNIT if BUNIT is present.
-    hdu : int
-        The index of the HDU to load into this spectrum.
-    verbose : bool
-        Print extra info.
-    **kwargs
-        Extra keywords for :func:`~specutils.io.parsing_utils.read_fileobj_or_hdulist`.
-
-    Returns
-    -------
-    :class:`~specutils.Spectrum`
-    """
-
-    with read_fileobj_or_hdulist(file_obj, **kwargs) as hdulist:
-        header = hdulist[hdu].header
-        wcs = WCS(header)
-
-        # Load data, convert units if BUNIT and flux_unit is provided and not the same
-        if "BUNIT" in header:
-            data = u.Quantity(hdulist[hdu].data, unit=header["BUNIT"])
-            if u.A in data.unit.bases:
-                data = data * u.A / u.AA  # convert ampere to Angroms
-            if flux_unit is not None:
-                data = data.to(flux_unit)
-        else:
-            data = u.Quantity(hdulist[hdu].data, unit=flux_unit)
-
-    if wcs.wcs.cunit[0] == "" and "WAT1_001" in header:
-        # Try to extract from IRAF-style card or use Angstrom as default.
-        wat_dict = dict((rec.split("=") for rec in header["WAT1_001"].split()))
-        unit = wat_dict.get("units", "Angstrom")
-        if hasattr(u, unit):
-            wcs.wcs.cunit[0] = unit
-        else:  # try with unit name stripped of excess plural 's'...
-            wcs.wcs.cunit[0] = unit.rstrip("s")
-        if verbose:
-            print(f"Extracted spectral axis unit '{unit}' from 'WAT1_001'")
-    elif wcs.wcs.cunit[0] == "":
-        wcs.wcs.cunit[0] = "Angstrom"
-
-    # Compatibility attribute for lookup_table (gwcs) WCS
-    wcs.unit = tuple(wcs.wcs.cunit)
-
-    # Identify the correct parts of the data to store
-    if len(data.shape) > 1:
-        flux_data = data[0]
-    else:
-        flux_data = data
-    uncertainty = None
-    if "NAXIS3" in header:
-        for i in range(header["NAXIS3"]):
-            if "spectrum" in header.get(f"BANDID{i+1}", ""):
-                flux_data = data[i]
-            if "sigma" in header.get(f"BANDID{i+1}", ""):
-                uncertainty = data[i]
-
-    # Reshape arrays if needed
-    if len(flux_data) == 1 and len(flux_data.shape) > 1:
-        flux_data = np.reshape(flux_data, -1)
-        if uncertainty is not None:
-            uncertainty = np.reshape(uncertainty, -1)
-
-    # Convert uncertainty to StdDevUncertainty array
-    if uncertainty is not None:
-        uncertainty = StdDevUncertainty(uncertainty)
-
-    # Manually generate spectral axis
-    pixels = [[i] + [0] * (wcs.naxis - 1) for i in range(wcs.pixel_shape[0])]
-    spectral_axis = [i[0] for i in wcs.all_pix2world(pixels, 0)] * wcs.wcs.cunit[0]
-
-    # Store header as metadata information
-    meta = {"header": header}
-
-    return Spectrum(flux=flux_data, spectral_axis=spectral_axis, uncertainty=uncertainty, meta=meta)
-
-
 def load_spectrum(filename: str, spectra_format: str = None, raise_error: bool = False):
     """Attempt to load the filename as a spectrum object
 

astrodbkit/tests/test_spectra.py

@@ -1,5 +1,7 @@
 # Tests for spectra functions
 
+from unittest import mock
+
 import numpy as np
 import pytest
 from astropy.io import fits
@@ -8,17 +10,10 @@
 from astrodbkit.spectra import (
     _identify_spex,
     identify_spex_prism,
-    identify_wcs1d_multispec,
     load_spectrum,
     spex_prism_loader,
-    wcs1d_multispec_loader,
 )
 
-try:
-    import mock
-except ImportError:
-    from unittest import mock
-
 
 @pytest.fixture(scope="module")
 def good_spex_file():
@@ -47,44 +42,6 @@ def bad_spex_file():
     return fits.HDUList([hdu1])
 
 
-@pytest.fixture(scope="module")
-def good_wcs1dmultispec():
-    n = np.empty((2141, 1, 4))
-    hdr = fits.Header()
-    hdr["WCSDIM"] = 3
-    hdr["NAXIS"] = 3
-    hdr["WAT0_001"] = "system=equispec"
-    hdr["WAT1_001"] = "wtype=linear label=Wavelength units=angstroms"
-    hdr["WAT2_001"] = "wtype=linear"
-    hdr["BANDID1"] = "spectrum - background fit, weights variance, clean no"
-    hdr["BANDID2"] = "raw - background fit, weights none, clean no"
-    hdr["BANDID3"] = "background - background fit"
-    hdr["BANDID4"] = "sigma - background fit, weights variance, clean no"
-    hdr["CTYPE1"] = "LINEAR  "
-    hdr["BUNIT"] = "erg/cm2/s/A"
-    hdu1 = fits.PrimaryHDU(n, header=hdr)
-    return fits.HDUList([hdu1])
-
-
-@pytest.fixture(scope="module")
-def alt_wcs1dmultispec():
-    n = np.empty((2141,))
-    hdr = fits.Header()
-    hdr["WCSDIM"] = 1
-    hdr["NAXIS"] = 1
-    hdr["WAT0_001"] = "system=equispec"
-    hdr["WAT1_001"] = "wtype=linear label=Wavelength units=angstroms"
-    hdr["WAT2_001"] = "wtype=linear"
-    hdr["BANDID1"] = "spectrum - background fit, weights variance, clean no"
-    hdr["BANDID2"] = "raw - background fit, weights none, clean no"
-    hdr["BANDID3"] = "background - background fit"
-    hdr["BANDID4"] = "sigma - background fit, weights variance, clean no"
-    hdr["CTYPE1"] = "LINEAR  "
-    hdr["BUNIT"] = "erg/cm2/s/A"
-    hdu1 = fits.PrimaryHDU(n, header=hdr)
-    return fits.HDUList([hdu1])
-
-
 @mock.patch("astrodbkit.spectra.fits.open")
 def test_identify_spex_prism(mock_fits_open, good_spex_file):
     mock_fits_open.return_value = good_spex_file
@@ -115,33 +72,6 @@ def test_load_spex_prism(mock_fits_open, good_spex_file, bad_spex_file):
     assert spectrum.unit == Unit("erg")
 
 
-@mock.patch("astrodbkit.spectra.read_fileobj_or_hdulist")
-def test_identify_wcs1d_multispec(mock_fits_open, good_wcs1dmultispec):
-    mock_fits_open.return_value = good_wcs1dmultispec
-
-    filename = "https://s3.amazonaws.com/bdnyc/optical_spectra/U10929.fits"
-    assert identify_wcs1d_multispec("read", filename)
-
-
-@mock.patch("astrodbkit.spectra.read_fileobj_or_hdulist")
-def test_wcs1d_multispec_loader(mock_fits_open, good_wcs1dmultispec, alt_wcs1dmultispec):
-    mock_fits_open.return_value = good_wcs1dmultispec
-
-    spectrum = wcs1d_multispec_loader("filename")
-    assert spectrum.unit == Unit("erg / (Angstrom cm2 s)")
-    assert spectrum.wavelength.unit == Unit("Angstrom")
-
-    # Check flux_unit is converted correctly
-    spectrum = wcs1d_multispec_loader("filename", flux_unit=Unit("erg / (um cm2 s)"))
-    assert spectrum.unit == Unit("erg / (um cm2 s)")
-
-    # NAXIS=1 example
-    mock_fits_open.return_value = alt_wcs1dmultispec
-    spectrum = wcs1d_multispec_loader("filename")
-    assert spectrum.unit == Unit("erg / (Angstrom cm2 s)")
-    assert spectrum.wavelength.unit == Unit("Angstrom")
-
-
 @mock.patch("astrodbkit.spectra.Spectrum.read")
 def test_load_spectrum(mock_spectrum1d, monkeypatch):
     _ = load_spectrum("fake_file.txt")