Fixing errors after rebase to main

jdaviz/app.py

@@ -758,9 +758,7 @@ def _link_new_data(self, reference_data=None, data_to_be_linked=None):
             spectral_axis_index = dc[0].meta['spectral_axis_index']
             ref_wavelength_component = dc[0].components[spectral_axis_index]
             # May need to update this for specutils 2
-            ref_flux_component = dc[0].components[6]
             linked_wavelength_component = dc[-1].components[1]
-            linked_flux_component = dc[-1].components[-1]
 
             dc.add_link(LinkSame(ref_wavelength_component, linked_wavelength_component))
             return
@@ -1089,7 +1087,7 @@ def _get_range_subset_bounds(self, subset_state,
             if ndim == 2:
                 units = u.pix
             else:
-                handler, _ = data_translator.get_handler_for(Spectrum1D)
+                handler, _ = data_translator.get_handler_for(Spectrum)
                 spec = handler.to_object(data)
                 units = spec.spectral_axis.unit
 

jdaviz/configs/cubeviz/helper.py

@@ -1,5 +1,3 @@
-from jdaviz.core.events import SnackbarMessage
-from jdaviz.core.helpers import ImageConfigHelper
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
 from jdaviz.configs.specviz import Specviz
 from jdaviz.core.events import AddDataMessage, SnackbarMessage

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -75,7 +75,7 @@ def parse_data(app, file_obj, data_type=None, data_label=None,
     if isinstance(file_obj, fits.hdu.hdulist.HDUList):
         try:
             _parse_spectrum1d_3d(
-                app, Spectrum1D.read(file_obj), data_label=data_label,
+                app, Spectrum.read(file_obj), data_label=data_label,
                 flux_viewer_reference_name=flux_viewer_reference_name,
                 uncert_viewer_reference_name=uncert_viewer_reference_name
             )
@@ -128,7 +128,7 @@ def parse_data(app, file_obj, data_type=None, data_label=None,
             else:
                 try:
                     _parse_spectrum1d_3d(
-                        app, Spectrum1D.read(hdulist), data_label=data_label or file_name,
+                        app, Spectrum.read(hdulist), data_label=data_label or file_name,
                         flux_viewer_reference_name=flux_viewer_reference_name,
                         uncert_viewer_reference_name=uncert_viewer_reference_name
                     )

jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py

@@ -611,7 +611,7 @@ def test_spectral_extraction_scientific_validation(
     calspec_fitsrec = fits.getdata(calspec_url)
     column_units = [u.AA] + 2 * [u.Unit('erg s-1 cm-2 AA-1')]
     spectra_table = QTable(calspec_fitsrec, units=column_units)
-    model_spectrum = Spectrum1D(
+    model_spectrum = Spectrum(
         flux=spectra_table['FLUX'],
         spectral_axis=spectra_table['WAVELENGTH']
     )

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

@@ -405,7 +405,7 @@ def test_incompatible_units(specviz_helper, spectrum1d):
 def test_cube_fit_with_nans(cubeviz_helper):
     flux = np.ones((7, 8, 9)) * u.nJy
     flux[:, :, 0] = np.nan
-    spec = Spectrum1D(flux=flux)
+    spec = Spectrum(flux=flux)
     cubeviz_helper.load_data(spec, data_label="test")
 
     mf = cubeviz_helper.plugins["Model Fitting"]
@@ -426,7 +426,7 @@ def test_cube_fit_with_subset_and_nans(cubeviz_helper):
     # Also test with existing mask
     flux = np.ones((7, 8, 9)) * u.nJy
     flux[:, :, 0] = np.nan
-    spec = Spectrum1D(flux=flux)
+    spec = Spectrum(flux=flux)
     spec.flux[5, 5, 7] = 10 * u.nJy
     cubeviz_helper.load_data(spec, data_label="test")
 
@@ -448,7 +448,7 @@ def test_fit_with_count_units(cubeviz_helper):
     flux = np.random.random((7, 8, 9)) * u.count
     spectral_axis = np.linspace(4000, 5000, flux.shape[-1]) * u.AA
 
-    spec = Spectrum1D(flux=flux, spectral_axis=spectral_axis)
+    spec = Spectrum(flux=flux, spectral_axis=spectral_axis)
     cubeviz_helper.load_data(spec, data_label="test")
 
     mf = cubeviz_helper.plugins["Model Fitting"]

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

@@ -189,7 +189,7 @@ def test_fit_cube_no_wcs(cubeviz_helper):
 
 
 def test_toggle_cube_fit_subset(cubeviz_helper):
-    sp = Spectrum1D(flux=np.ones((7, 8, 9)) * u.nJy)  # ny, nx, nz
+    sp = Spectrum(flux=np.ones((7, 8, 9)) * u.nJy)  # ny, nx, nz
     cubeviz_helper.load_data(sp, data_label="test_cube")
     mf = cubeviz_helper.plugins['Model Fitting']
 

jdaviz/configs/specviz/plugins/parsers.py

@@ -97,7 +97,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
                                  "returned an empty list")
         elif path.is_file():
             try:
-                data = Spectrum1D.read(str(path), format=format)
+                data = Spectrum.read(str(path), format=format)
                 if data.flux.ndim == 2:
                     data = split_spectrum_with_2D_flux_array(data)
                 else:
@@ -293,7 +293,7 @@ def split_spectrum_with_2D_flux_array(data):
             unc = data.uncertainty[i, :]
         if data.mask is not None:
             mask = data.mask[i, :]
-        new_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
-                                   uncertainty=unc, mask=mask, meta=data.meta))
+        new_data.append(Spectrum(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
+                                 uncertainty=unc, mask=mask, meta=data.meta))
 
     return new_data

jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py

@@ -36,7 +36,7 @@ def test_value_error_exception(specviz_helper, spectrum1d, new_spectral_axis, ne
 
 
 def test_initialize_specviz_sb(specviz_helper, spectrum1d):
-    spec_sb = Spectrum1D(spectrum1d.flux/u.sr, spectrum1d.spectral_axis)
+    spec_sb = Spectrum(spectrum1d.flux/u.sr, spectrum1d.spectral_axis)
     specviz_helper.load_data(spec_sb, data_label="Test 1D Spectrum")
     plg = specviz_helper.plugins["Unit Conversion"]
     assert plg._obj.flux_unit == "Jy"

jdaviz/configs/specviz/tests/test_helper.py

@@ -410,15 +410,15 @@ def test_load_spectrum_list_directory_concat(tmpdir, specviz_helper):
 def test_load_2d_flux(specviz_helper):
     # Test loading a spectrum with a 2D flux, which should be split into separate
     # 1D Spectrum1D objects to load in Specviz.
-    spec = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
-                      flux=np.ones((4, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+    spec = Spectrum(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
+                    flux=np.ones((4, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
     specviz_helper.load_data(spec, data_label="test")
 
     assert len(specviz_helper.app.data_collection) == 4
     assert specviz_helper.app.data_collection[0].label == "test [0]"
 
-    spec2 = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
-                       flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+    spec2 = Spectrum(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
+                     flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
 
     # Make sure 2D spectra in a SpectrumList also get split properly.
     spec_list = SpectrumList([spec, spec2])

jdaviz/configs/specviz2d/plugins/spectral_extraction/tests/test_spectral_extraction.py

@@ -207,9 +207,9 @@ def test_horne_extract_self_profile(specviz2d_helper):
         spec2d[:, ii] = gaus
 
     wave = np.arange(0, spec2d.shape[1], 1)
-    objectspec = Spectrum1D(spectral_axis=wave*u.m,
-                            flux=spec2d*u.Jy,
-                            uncertainty=VarianceUncertainty(spec2dvar*u.Jy*u.Jy))
+    objectspec = Spectrum(spectral_axis=wave*u.m,
+                          flux=spec2d*u.Jy,
+                          uncertainty=VarianceUncertainty(spec2dvar*u.Jy*u.Jy))
 
     specviz2d_helper.load_data(objectspec)
     pext = specviz2d_helper.app.get_tray_item_from_name('spectral-extraction')

jdaviz/core/helpers.py

@@ -511,10 +511,10 @@ def _handle_display_units(self, data, use_display_units=True):
                             * u.Unit(spectral_unit))
 
                 data = Spectrum(spectral_axis=new_spec,
-                                  flux=new_y,
-                                  uncertainty=new_uncert,
-                                  mask=data.mask,
-                                  spectral_axis_index=data.meta['spectral_axis_index'])
+                                flux=new_y,
+                                uncertainty=new_uncert,
+                                mask=data.mask,
+                                spectral_axis_index=data.meta['spectral_axis_index'])
             else:  # pragma: nocover
                 raise NotImplementedError(f"converting {data.__class__.__name__} to display units is not supported")  # noqa
         return data

jdaviz/core/template_mixin.py

@@ -3240,7 +3240,7 @@ def _get_continuum(self, dataset, spectral_subset, update_marks=False, per_pixel
         min_x = min(spectral_axis.value)
         if per_pixel:
             # full_spectrum.flux is a cube, so we want to act on all spaxels independently
-            continuum_y = np.take(full_spectrum.flux, continuum_mask, axis=spectral_axis_index).value
+            continuum_y = np.take(full_spectrum.flux, continuum_mask, axis=spectral_axis_index).value  # noqa
 
             def fit_continuum(continuum_y_spaxel):
                 return np.polyfit(continuum_x-min_x, continuum_y_spaxel, deg=1)