Debug cubeviz spectrum1d parser

CHANGES.rst

@@ -196,6 +196,8 @@ Bug Fixes
 Cubeviz
 ^^^^^^^
 
+- No longer incorrectly swap RA and Dec axes when loading Spectrum1D objects. [#3133]
+
 Imviz
 ^^^^^
 

jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py

@@ -109,7 +109,7 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmp_path):
     )
 
     result = dc[-1].get_object(cls=CCDData)
-    assert result.shape == (4, 2)  # Cube shape is (2, 2, 4)
+    assert result.shape == (2, 4)  # Cube shape is (2, 2, 4), moment transposes
     assert isinstance(dc[-1].coords, WCS)
 
     # Make sure coordinate display now show moment map info (no WCS)

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -423,8 +423,6 @@ def _parse_spectrum1d_3d(app, file_obj, data_label=None,
         else:
             flux = val
 
-        flux = np.moveaxis(flux, 1, 0)
-
         with warnings.catch_warnings():
             warnings.filterwarnings(
                 'ignore', message='Input WCS indicates that the spectral axis is not last',

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

@@ -498,8 +498,8 @@ def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
     subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
     spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']._obj
 
-    lower_aperture = RectangularROI(-0.5, 1.5, -0.5, 0.5)
-    upper_aperture = RectangularROI(-0.5, 1.5, 2.5, 3.5)
+    lower_aperture = RectangularROI(-0.5, 0.5, -0.5, 1.5)
+    upper_aperture = RectangularROI(2.5, 3.5, -0.5, 1.5)
 
     flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:rectangle']
     flux_viewer.apply_roi(lower_aperture)
@@ -514,14 +514,14 @@ def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
     spectrum_2 = spec_extr_plugin.extract()
 
     subset_plugin.subset_selected = 'Create New'
-    rectangle = RectangularROI(-0.5, 1.5, -0.5, 3.5)
+    rectangle = RectangularROI(-0.5, 3.5, -0.5, 1.5)
     flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:rectangle']
     flux_viewer.apply_roi(rectangle)
 
     flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:truecircle']
     subset_plugin.subset_selected = 'Subset 3'
     cubeviz_helper.app.session.edit_subset_mode.mode = AndNotMode
-    circle = CircularROI(0.5, 1.5, 1.1)
+    circle = CircularROI(1.5, 0.5, 1.1)
     flux_viewer.apply_roi(circle)
 
     spec_extr_plugin.aperture_selected = 'Subset 3'

jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py

@@ -166,8 +166,8 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_c
     cube = spectrum1d_cube_custom_fluxunit(fluxunit=u.MJy / u.sr)
     cubeviz_helper.load_data(cube, data_label="test")
 
-    aper = RectanglePixelRegion(center=PixCoord(x=1, y=3), width=1, height=1)
-    bg = RectanglePixelRegion(center=PixCoord(x=0, y=2), width=1, height=1)
+    aper = RectanglePixelRegion(center=PixCoord(x=3, y=1), width=1, height=1)
+    bg = RectanglePixelRegion(center=PixCoord(x=2, y=0), width=1, height=1)
     cubeviz_helper.load_regions([aper, bg])
 
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
@@ -183,8 +183,8 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_c
     row = cubeviz_helper.get_aperture_photometry_results()[0]
 
     # Basically, we should recover the input rectangle here, minus background.
-    assert_allclose(row["xcenter"], 1 * u.pix)
-    assert_allclose(row["ycenter"], 3 * u.pix)
+    assert_allclose(row["xcenter"], 3 * u.pix)
+    assert_allclose(row["ycenter"], 1 * u.pix)
     assert_allclose(row["sum"], 1.1752215e-12 * u.MJy)  # (15 - 10) MJy/sr x 2.3504431e-13 sr
     assert_allclose(row["sum_aper_area"], 1 * (u.pix * u.pix))
     assert_allclose(row["pixarea_tot"], 2.350443053909789e-13 * u.sr)

jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py

@@ -51,5 +51,5 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     assert spatial_with_spec.flux.ndim == 1
     assert list(spatial_with_spec.mask) == [True, True, False, False, True,
                                             True, True, True, True, True]
-    assert max(list(spatial_with_spec.flux.value)) == 157.
-    assert min(list(spatial_with_spec.flux.value)) == 13.
+    assert max(list(spatial_with_spec.flux.value)) == 232.
+    assert min(list(spatial_with_spec.flux.value)) == 16.

jdaviz/configs/cubeviz/plugins/tests/test_parsers.py

@@ -149,7 +149,7 @@ def test_spectrum3d_no_wcs_parse(cubeviz_helper):
     data = cubeviz_helper.app.data_collection[0]
     flux = data.get_component('flux')
     assert data.label.endswith('[FLUX]')
-    assert data.shape == (3, 2, 4)  # y, x, z
+    assert data.shape == (2, 3, 4)  # y, x, z
     assert isinstance(data.coords, PaddedSpectrumWCS)
     assert_array_equal(flux.data, 1)
     assert flux.units == 'nJy'

jdaviz/configs/default/plugins/gaussian_smooth/tests/test_gaussian_smooth.py

@@ -121,10 +121,10 @@ def test_spatial_convolution(cubeviz_helper, spectrum1d_cube):
 
     assert len(dc) == 3
     assert dc[-1].label == f'{data_label}[FLUX] spatial-smooth stddev-3.0'
-    assert dc[-1].shape == (2, 4, 2)  # specutils moved spectral axis to last
+    assert dc[-1].shape == (4, 2, 2)  # specutils moved spectral axis to last
     assert (dc[f'{data_label}[FLUX] spatial-smooth stddev-3.0'].get_object(cls=Spectrum1D,
                                                                            statistic=None).shape
-            == (2, 4, 2))
+            == (4, 2, 2))
 
 
 def test_specviz_smooth(specviz_helper, spectrum1d):

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

@@ -89,10 +89,10 @@ def test_parameter_retrieval(cubeviz_helper, spectral_cube_wcs):
         plugin.calculate_fit()
 
     params = cubeviz_helper.get_model_parameters()
-    slope_res = np.zeros((4, 3))
+    slope_res = np.zeros((3, 4))
     slope_res[2, 2] = 1.0
     slope_res = slope_res * u.nJy / u.Hz
-    intercept_res = np.ones((4, 3))
+    intercept_res = np.ones((3, 4))
     intercept_res[2, 2] = 0
     intercept_res = intercept_res * u.nJy
     assert_quantity_allclose(params['model']['slope'], slope_res,

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

@@ -169,7 +169,7 @@ def test_fit_cube_no_wcs(cubeviz_helper):
     assert len(fitted_model) == 56  # ny * nx
     # Make sure shapes are all self-consistent within Cubeviz instance.
     fitted_data = cubeviz_helper.app.data_collection["model"]
-    assert fitted_data.shape == (8, 7, 9)  # nx, ny, nz
+    assert fitted_data.shape == (7, 8, 9)  # nx, ny, nz
     assert fitted_data.shape == cubeviz_helper.app.data_collection[0].shape
     assert fitted_data.shape == output_cube.shape
 

jdaviz/conftest.py

@@ -246,8 +246,8 @@ def spectrum1d_cube_largest():
                 "CDELT1": 8e-11, "CDELT2": 0.0001, "CDELT3": -0.0001,
                 "CRPIX1": 0, "CRPIX2": 0, "CRPIX3": 0}
     w = WCS(wcs_dict)
-    flux = np.zeros((30, 20, 3001), dtype=np.float32)  # nx=20 ny=30 nz=3001
-    flux[5:15, 1:11, :] = 1  # Bright corner
+    flux = np.zeros((20, 30, 3001), dtype=np.float32)  # nx=20 ny=30 nz=3001
+    flux[1:11, 5:15, :] = 1  # Bright corner
     return Spectrum1D(flux=flux * u.Jy, wcs=w, meta=wcs_dict)