Fix aperture weight mask with loaded mask cube

CHANGES.rst

@@ -114,7 +114,7 @@ Cubeviz
 
 - Fixed initializing a Gaussian1D model component when ``Cube Fit`` is toggled on. [#3295]
 
-- Spectral extraction now correctly respects the loaded mask cube. [#3319]
+- Spectral extraction now correctly respects the loaded mask cube. [#3319, #3358]
 
 Imviz
 ^^^^^

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

@@ -386,14 +386,14 @@ def slice_display_unit(self):
         return astropy.units.Unit(self.app._get_display_unit(self.slice_display_unit_name))
 
     @property
-    def mask_non_science(self):
+    def inverted_mask_non_science(self):
         # Aperture masks begin by removing from consideration any pixel
         # set to NaN, which corresponds to a pixel on the "non-science" portions
         # of the detector. For JWST spectral cubes, these pixels are also marked in
-        # the DQ array with flag `513`.
-        return np.logical_not(
-            np.isnan(self.dataset.selected_obj.flux.value)
-        ).astype(float)
+        # the DQ array with flag `513`. Also respect the loaded mask, if it exists
+        nan_mask = np.isnan(self.dataset.selected_obj.flux.value)
+        return np.logical_not(np.logical_or(self.mask_cube.get_component('flux').data,
+                                            nan_mask)).astype(float)
 
     @property
     def aperture_weight_mask(self):
@@ -402,10 +402,10 @@ def aperture_weight_mask(self):
         # wavelength, on the range [0, 1].
         if self.aperture.selected == self.aperture.default_text:
             # Entire Cube
-            return self.mask_non_science
+            return self.inverted_mask_non_science
 
         return (
-            self.mask_non_science *
+            self.inverted_mask_non_science *
             self.aperture.get_mask(
                 self.dataset.selected_obj,
                 self.aperture_method_selected,

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

@@ -209,8 +209,29 @@ def test_numpy_cube(cubeviz_helper):
     assert flux.units == 'ct / pix2'
 
 
+def test_loading_with_mask(cubeviz_helper):
+    # This also tests that spaxel is converted to pix**2
+    custom_spec = Spectrum1D(flux=[[[20, 1], [9, 1]], [[3, 1], [6, 5]]] * u.Unit("erg / Angstrom s cm**2 spaxel"),  # noqa
+                             spectral_axis=[1, 2]*u.AA,
+                             mask=[[[1, 0], [0, 0]], [[0, 0], [0, 0]]])
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore")
+        cubeviz_helper.load_data(custom_spec)
+        #cubeviz_helper.load_data("https://stsci.box.com/shared/static/gts87zqt5265msuwi4w5u003b6typ6h0.gz", cache=True)  # noqa
+
+    uc = cubeviz_helper.plugins['Unit Conversion']
+    uc.spectral_y_type = "Surface Brightness"
+
+    se = cubeviz_helper.plugins['Spectral Extraction']
+    se.function = "Mean"
+    se.extract()
+    extracted = cubeviz_helper.get_data("Spectrum (mean)")
+    assert_allclose(extracted.flux.value, [6, 2])
+    assert extracted.unit == u.Unit("erg / Angstrom s cm**2 pix**2")
+
+
 @pytest.mark.remote_data
-def test_manga_cube(cubeviz_helper):
+def test_manga_with_mask(cubeviz_helper):
     # Remote data test of loading and extracting an up-to-date (as of 11/19/2024) MaNGA cube
     # This also tests that spaxel is converted to pix**2
     with warnings.catch_warnings():
@@ -224,7 +245,7 @@ def test_manga_cube(cubeviz_helper):
     se.function = "Mean"
     se.extract()
     extracted_max = cubeviz_helper.get_data("Spectrum (mean)").max()
-    assert_allclose(extracted_max.value, 2.836957E-18)
+    assert_allclose(extracted_max.value, 5.566169e-18)
     assert extracted_max.unit == u.Unit("erg / Angstrom s cm**2 pix**2")