Merge pull request #2034 from duytnguyendtn/auto-backport-of-pr-2023-…

…on-v3.3.x

Manual Backport PR #2023 on branch v3.3.x (Fix 2D smooth visibility bug by utilizing SpectralExtraction linking logic)

CHANGES.rst

@@ -9,6 +9,8 @@ Bug Fixes
 
 * Loading valid data no longer emits JSON serialization warnings. [#2011]
 
+* Fixed linking issue preventing smoothed spectrum from showing in Specviz2D. [#2023]
+
 Cubeviz
 ^^^^^^^
 

jdaviz/app.py

@@ -424,7 +424,11 @@ def _link_new_data(self, reference_data=None, data_to_be_linked=None):
                      LinkSame(linked_data.components[0], ref_data.components[1])]
             dc.add_link(links)
             return
-        elif linked_data.meta.get('Plugin', None) == 'SpectralExtraction':
+        elif (linked_data.meta.get('Plugin', None) == 'SpectralExtraction' or
+                (linked_data.meta.get('Plugin', None) == ('GaussianSmooth') and
+                 linked_data.ndim < 3 and  # Cube linking requires special logic. See below
+                 ref_data.ndim < 3)
+              ):
             links = [LinkSame(linked_data.components[0], ref_data.components[0]),
                      LinkSame(linked_data.components[1], ref_data.components[1])]
             dc.add_link(links)

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

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 from astropy.utils.exceptions import AstropyUserWarning
 from specutils import Spectrum1D
@@ -168,3 +169,30 @@ def test_spectrum1d_smooth(specviz_helper, spectrum1d):
     assert spec_viewer.label_mouseover.world_ra_deg == ''
     assert spec_viewer.label_mouseover.world_dec_deg == ''
     assert spec_viewer.label_mouseover.icon == ''
+
+
+def test_spectrum2d_smooth(specviz2d_helper, spectrum2d):
+    data_label = 'test'
+    dc = specviz2d_helper.app.data_collection
+    specviz2d_helper.load_data(spectrum_2d=spectrum2d, spectrum_2d_label=data_label)
+
+    gs_plugin = specviz2d_helper.plugins['Gaussian Smooth']
+
+    # The Autocollapsed spectrum is given the label of "Spectrum 1D by default"
+    smooth_source_dataset = "Spectrum 1D"
+    gs_plugin.dataset = smooth_source_dataset
+    test_stddev_level = 100.0
+    gs_plugin.stddev = test_stddev_level
+    gs_plugin.smooth()
+
+    assert len(dc) == 3
+    assert dc[2].label == f'{smooth_source_dataset} smooth stddev-{test_stddev_level}'
+
+    # Ensure all marks were created properly (i.e. not in their initialized state)
+    # [0,1] is the default (initialization) value for the marks
+    marks = specviz2d_helper.app.get_viewer('spectrum-viewer').native_marks
+
+    assert len(marks) == 2
+    for mark in marks:
+        np.testing.assert_allclose(mark.x, spectrum2d.spectral_axis.value)
+        assert not np.array_equal(mark.y, [0, 1])

jdaviz/conftest.py

@@ -226,6 +226,18 @@ def mos_spectrum1d():
     return Spectrum1D(spectral_axis=spec_axis, flux=flux)
 
 
+@pytest.fixture
+def spectrum2d():
+    '''
+    A simple 2D Spectrum1D with a center "trace" array rising from 0 to 10
+    with two "zero array" buffers above and below
+    '''
+    data = np.zeros((5, 10))
+    data[3] = np.arange(10)
+
+    return Spectrum1D(flux=data*u.MJy, spectral_axis=data[3]*u.um)
+
+
 @pytest.fixture
 def mos_spectrum2d():
     '''