Merge branch 'main' into manga-logcube-try2

CHANGES.rst

@@ -74,6 +74,9 @@ Cubeviz
 - Generic FITS parsing now goes through ``specutils`` loaders first, if possible.
   If a ``specutils`` loader is used, uncertainty is converted to standard deviation type. [#3119]
 
+- Custom Spectrum1D writer format ``jdaviz-cube`` is removed. Use ``wcs1d-fits`` from
+  ``specutils`` instead. [#2094]
+
 Imviz
 ^^^^^
 

docs/cubeviz/export_data.rst

@@ -74,7 +74,7 @@ where the mask (if available) is as defined in
 
 .. code-block:: python
 
-    mydata.write("mydata.fits", format="jdaviz-cube")
+    mydata.write("mydata.fits", format="wcs1d-fits", hdu=1)
 
 
 .. _cubeviz-export-model:

jdaviz/configs/cubeviz/helper.py

@@ -1,9 +1,3 @@
-import numpy as np
-from astropy.io import fits
-from astropy.io import registry as io_registry
-from specutils import Spectrum1D
-from specutils.io.registers import _astropy_has_priorities
-
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.helpers import ImageConfigHelper
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
@@ -166,63 +160,3 @@ def get_aperture_photometry_results(self):
 
         """
         return self.plugins['Aperture Photometry']._obj.export_table()
-
-
-# TODO: We can remove this when specutils supports it, i.e.,
-#       https://github.com/astropy/specutils/issues/592 and
-#       https://github.com/astropy/specutils/pull/1009
-# NOTE: Cannot use custom_write decorator from specutils because
-#       that involves asking user to manually put something in
-#       their ~/.specutils directory.
-
-def jdaviz_cube_fitswriter(spectrum, file_name, **kwargs):
-    """This is a custom writer for Spectrum1D data cube.
-    This writer is specifically targetting data cube
-    generated from Cubeviz plugins (e.g., cube fitting)
-    with FITS WCS. It writes out data in the following format
-    (with MASK only exist when applicable)::
-
-        No.    Name      Ver    Type
-          0  PRIMARY       1 PrimaryHDU
-          1  SCI           1 ImageHDU (float32)
-          2  MASK          1 ImageHDU (uint16)
-
-    The FITS file generated by this writer does not need a
-    custom reader to be read back into Spectrum1D.
-
-    Examples
-    --------
-    To write out a Spectrum1D cube using this writer:
-
-    >>> spec.write("my_output.fits", format="jdaviz-cube", overwrite=True)  # doctest: +SKIP
-
-    """
-    pri_hdu = fits.PrimaryHDU()
-
-    flux = spectrum.flux
-    sci_hdu = fits.ImageHDU(flux.value.astype(np.float32))
-    sci_hdu.name = "SCI"
-    sci_hdu.header.update(spectrum.meta)
-    sci_hdu.header.update(spectrum.wcs.to_header())
-    sci_hdu.header['BUNIT'] = flux.unit.to_string(format='fits')
-
-    hlist = [pri_hdu, sci_hdu]
-
-    # https://specutils.readthedocs.io/en/latest/spectrum1d.html#including-masks
-    # Good: False or 0
-    # Bad: True or non-zero
-    if spectrum.mask is not None:
-        mask_hdu = fits.ImageHDU(spectrum.mask.astype(np.uint16))
-        mask_hdu.name = "MASK"
-        hlist.append(mask_hdu)
-
-    hdulist = fits.HDUList(hlist)
-    hdulist.writeto(file_name, **kwargs)
-
-
-if _astropy_has_priorities():
-    kwargs = {"priority": 0}
-else:  # pragma: no cover
-    kwargs = {}
-io_registry.register_writer(
-    "jdaviz-cube", Spectrum1D, jdaviz_cube_fitswriter, force=False, **kwargs)

jdaviz/configs/default/plugins/model_fitting/tests/test_fitting.py

@@ -4,7 +4,6 @@
 import pytest
 from astropy import units as u
 from astropy.io import fits
-from astropy.io.registry.base import IORegistryError
 from astropy.modeling import models
 from astropy.nddata import StdDevUncertainty
 from astropy.tests.helper import assert_quantity_allclose
@@ -251,7 +250,7 @@ def test_cube_fitting_backend(cubeviz_helper, unc, tmp_path):
 
     # Check I/O roundtrip.
     out_fn = tmp_path / "fitted_cube.fits"
-    fitted_spectrum.write(out_fn, format="jdaviz-cube", overwrite=True)
+    fitted_spectrum.write(out_fn, format="wcs1d-fits", hdu=1, flux_name="SCI", overwrite=True)
     flux_unit_str = fitted_spectrum.flux.unit.to_string(format="fits")
     coo_expected = fitted_spectrum.wcs.pixel_to_world(1, 0, 2)
     with fits.open(out_fn) as pf:
@@ -268,12 +267,7 @@ def test_cube_fitting_backend(cubeviz_helper, unc, tmp_path):
         assert_allclose([coo[1].ra.deg, coo[1].dec.deg],
                         [coo_expected[1].ra.deg, coo_expected[1].dec.deg])
 
-    # Our custom format is not registered to readers, just writers.
-    # You can read it back in without custom read. See "Cubeviz roundtrip" below.
-    with pytest.raises(IORegistryError, match="No reader defined"):
-        Spectrum1D.read(out_fn, format="jdaviz-cube")
-
-    # Check Cubeviz roundtrip.
+    # Check Cubeviz roundtrip. This should automatically go through wcs1d-fits reader.
     cubeviz_helper.load_data(out_fn)
     assert len(cubeviz_helper.app.data_collection) == 3
     data_sci = cubeviz_helper.app.data_collection["fitted_cube.fits[SCI]"]