From e1e30e7c1999c4a2538c6da7ca1f39d7fe67b0f5 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 12 May 2023 10:09:01 -0400
Subject: [PATCH 01/21] Add option to get_data to apply spectral subset to
 collapse spatial

---
 jdaviz/configs/cubeviz/helper.py |  9 +++++++--
 jdaviz/configs/specviz/helper.py |  7 +++++--
 jdaviz/core/helpers.py           | 17 ++++++++++++++---
 3 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index dc102af7e0..85b0e2dfa9 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -120,7 +120,8 @@ def specviz(self):
             self._specviz = Specviz(app=self.app)
         return self._specviz
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None):
+    def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
+                 spectral_to_spatial=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -138,6 +139,9 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=Non
             If True, will collapse according to the current collapse function defined in the
             spectrum viewer.  If provided as a string, the cube will be collapsed with the provided
             function.  If False, None, or not passed, the entire cube will be returned.
+        spectral_to_spatial : str, optional
+            Spectral subset to be applied to spatial subset. Only possible if function is
+            set to True.
 
         Returns
         -------
@@ -147,7 +151,8 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=Non
         """
         if function is True:
             return self.specviz.get_data(data_label=data_label, cls=cls,
-                                         subset_to_apply=subset_to_apply)
+                                         subset_to_apply=subset_to_apply,
+                                         spectral_to_spatial=spectral_to_spatial)
         elif function is False:
             function = None
         return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 04db731d89..396986ee42 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -271,7 +271,7 @@ def set_spectrum_tick_format(self, fmt, axis=None):
             self._default_spectrum_viewer_reference_name
         ).figure.axes[axis].tick_format = fmt
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None):
+    def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -284,6 +284,9 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None):
             The type that data will be returned as.
         subset_to_apply : str, optional
             Subset that is to be applied to data before it is returned.
+        spectral_to_spatial : str, optional
+            Spectral subset to be applied to spatial subset. Only possible if this is
+            a specviz instance inside cubeviz.
 
         Returns
         -------
@@ -302,4 +305,4 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None):
             function = None
 
         return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-                              function=function)
+                              function=function, spectral_to_spatial=spectral_to_spatial)
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index d9a415768d..e8695dc956 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -22,6 +22,7 @@
 from glue.config import data_translator
 from ipywidgets.widgets import widget_serialization
 from specutils import Spectrum1D
+from specutils.manipulation import extract_region
 
 
 from jdaviz.app import Application
@@ -410,7 +411,8 @@ def show_in_new_tab(self, title=None):  # pragma: no cover
                       DeprecationWarning)
         return self.show(loc="sidecar:tab-after", title=title)
 
-    def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None):
+    def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
+                  spectral_to_spatial=None):
         list_of_valid_function_values = ('minimum', 'maximum', 'mean',
                                          'median', 'sum')
         if function and function not in list_of_valid_function_values:
@@ -480,9 +482,15 @@ def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=No
                             warnings.warn(f"Not able to get {data_label} returned with"
                                           f" subset {subsets.label} applied of type {cls}."
                                           f" Exception: {e}")
+        # Apply spectral subset to spatial subset if applicable
+        if spectral_to_spatial:
+            sr = self.app.get_subsets(spectral_to_spatial)
+            if sr:
+                data = extract_region(data, sr, return_single_spectrum=True)
+
         return data
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None):
+    def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -495,6 +503,8 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None):
             The type that data will be returned as.
         subset_to_apply : str, optional
             Subset that is to be applied to data before it is returned.
+        spectral_to_spatial : str, optional
+            Spectral subset to be applied to spatial subset.
 
         Returns
         -------
@@ -502,7 +512,8 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None):
             Data is returned as type cls with subsets applied.
 
         """
-        return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply)
+        return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
+                              spectral_to_spatial=spectral_to_spatial)
 
 
 class ImageConfigHelper(ConfigHelper):

From 797096eda43b77f561c5434b3d4b2d6324486b2a Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 10:09:04 -0400
Subject: [PATCH 02/21] Fix tests that use get_data

---
 jdaviz/configs/cubeviz/helper.py              | 17 ++++----
 .../plugins/tests/test_cubeviz_helper.py      | 12 +++---
 jdaviz/configs/specviz/helper.py              | 21 ++++++----
 .../plugins/line_analysis/line_analysis.py    |  2 +-
 jdaviz/core/helpers.py                        | 40 +++++++++++++------
 jdaviz/core/template_mixin.py                 | 10 +++--
 jdaviz/core/tests/test_helpers.py             |  4 +-
 7 files changed, 66 insertions(+), 40 deletions(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index 85b0e2dfa9..cccc521f0b 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -120,8 +120,8 @@ def specviz(self):
             self._specviz = Specviz(app=self.app)
         return self._specviz
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
-                 spectral_to_spatial=None):
+    def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, function=None,
+                 cls=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -149,14 +149,15 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None, function=Non
             Data is returned as type cls with subsets applied.
 
         """
-        if function is True:
-            return self.specviz.get_data(data_label=data_label, cls=cls,
-                                         subset_to_apply=subset_to_apply,
-                                         spectral_to_spatial=spectral_to_spatial)
+        if function:
+            return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
+                                         cls=cls, spatial_subset=spatial_subset, function=function)
+        elif function is None and spectral_subset and spatial_subset:
+            function = True
         elif function is False:
             function = None
-        return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-                              function=function)
+        return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
+                              spectral_subset=spectral_subset, function=function, cls=cls)
 
 
 def layer_is_cube_image_data(layer):
diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 2e9b0422a1..c958535eba 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -29,7 +29,7 @@ def test_invalid_function(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
 
     with pytest.raises(ValueError, match='function 42 not in list of valid '):
-        cubeviz_helper.get_data(data_label="test[FLUX]", subset_to_apply='Subset 1', function=42)
+        cubeviz_helper.get_data(data_label="test[FLUX]", spatial_subset='Subset 1', function=42)
 
     # Also make sure specviz redshift slider warning does not show up.
     # https://github.com/spacetelescope/jdaviz/issues/2029
@@ -41,20 +41,20 @@ def test_valid_function(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
 
     results_cube = cubeviz_helper.get_data(data_label="test[FLUX]",
-                                           subset_to_apply='Subset 1')
+                                           spatial_subset='Subset 1')
     assert results_cube.flux.ndim == 3
     results_false = cubeviz_helper.get_data(data_label="test[FLUX]",
-                                            subset_to_apply='Subset 1', function=False)
+                                            spatial_subset='Subset 1', function=False)
     assert results_false.flux.ndim == 3
 
     results_def = cubeviz_helper.get_data(data_label="test[FLUX]",
-                                          subset_to_apply='Subset 1', function=True)
+                                          spatial_subset='Subset 1', function=True)
     assert results_def.flux.ndim == 1
 
     results_min = cubeviz_helper.get_data(data_label="test[FLUX]",
-                                          subset_to_apply='Subset 1', function="minimum")
+                                          spatial_subset='Subset 1', function="minimum")
     results_max = cubeviz_helper.get_data(data_label="test[FLUX]",
-                                          subset_to_apply='Subset 1', function="maximum")
+                                          spatial_subset='Subset 1', function="maximum")
     assert isinstance(results_min, Spectrum1D)
     assert_quantity_allclose(results_min.flux,
                              [6., 14.] * u.Jy, atol=1e-5 * u.Jy)
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 396986ee42..2d104f0975 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -79,7 +79,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
 
         if data_label is not None:
             spectrum = get_data_method(data_label=data_label,
-                                       subset_to_apply=subset_to_apply,
+                                       spectral_subset=subset_to_apply,
                                        cls=Spectrum1D)
             spectra[data_label] = spectrum
         else:
@@ -88,7 +88,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
                 if subset_to_apply is not None:
                     if lyr.label == subset_to_apply:
                         spectrum = get_data_method(data_label=lyr.data.label,
-                                                   subset_to_apply=subset_to_apply,
+                                                   spectral_subset=subset_to_apply,
                                                    cls=Spectrum1D,
                                                    **function_kwargs)
                         spectra[lyr.data.label] = spectrum
@@ -97,7 +97,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
                 else:
                     if isinstance(lyr, GroupedSubset):
                         spectrum = get_data_method(data_label=lyr.data.label,
-                                                   subset_to_apply=lyr.label,
+                                                   spectral_subset=lyr.label,
                                                    cls=Spectrum1D,
                                                    **function_kwargs)
                         spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
@@ -271,7 +271,7 @@ def set_spectrum_tick_format(self, fmt, axis=None):
             self._default_spectrum_viewer_reference_name
         ).figure.axes[axis].tick_format = fmt
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
+    def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -294,15 +294,22 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_
             Data is returned as type cls with subsets applied.
 
         """
+        spatial_subset = kwargs.pop("spatial_subset", None)
+        function = kwargs.pop("function", None)
         if self.app.config == 'cubeviz':
             # then this is a specviz instance inside cubeviz and we want to default to the
             # viewer's collapse function
             default_sp_viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
-            function = getattr(default_sp_viewer.state, 'function', None)
+            if function is True or function is None:
+                function = getattr(default_sp_viewer.state, 'function', None)
+
             if cls is None:
                 cls = Spectrum1D
         else:
             function = None
 
-        return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-                              function=function, spectral_to_spatial=spectral_to_spatial)
+        # return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
+        #                       function=function, spectral_to_spatial=spectral_to_spatial)
+        # print(function)
+        return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
+                              spectral_subset=spectral_subset, function=function, cls=cls)
diff --git a/jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py b/jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py
index 134a9b917d..e19b115b1d 100644
--- a/jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py
+++ b/jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py
@@ -383,7 +383,7 @@ def _calculate_statistics(self, *args, **kwargs):
             # cube, but still apply that to the spatially-collapsed spectrum.
             continuum_mask = ~self._specviz_helper.get_data(
                 self.dataset.selected,
-                subset_to_apply=self.continuum_subset_selected).mask
+                spectral_subset=self.continuum_subset_selected).mask
             spectral_axis_nanmasked = spectral_axis.value.copy()
             spectral_axis_nanmasked[~continuum_mask] = np.nan
             if self.spectral_subset_selected == "Entire Spectrum":
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index e8695dc956..79b1dc5f55 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -411,8 +411,10 @@ def show_in_new_tab(self, title=None):  # pragma: no cover
                       DeprecationWarning)
         return self.show(loc="sidecar:tab-after", title=title)
 
-    def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
-                  spectral_to_spatial=None):
+    # def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
+    #               spectral_to_spatial=None):
+    def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
+                  function=None, cls=None):
         list_of_valid_function_values = ('minimum', 'maximum', 'mean',
                                          'median', 'sum')
         if function and function not in list_of_valid_function_values:
@@ -420,9 +422,14 @@ def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=No
                              f" function values {list_of_valid_function_values}")
 
         list_of_valid_subset_names = [x.label for x in self.app.data_collection.subset_groups]
-        if subset_to_apply and subset_to_apply not in list_of_valid_subset_names:
-            raise ValueError(f"Subset {subset_to_apply} not in list of valid"
+        if spatial_subset and spatial_subset not in list_of_valid_subset_names:
+            raise ValueError(f"Subset {spatial_subset} not in list of valid"
                              f" subset names {list_of_valid_subset_names}")
+        elif spectral_subset and spectral_subset not in list_of_valid_subset_names:
+            raise ValueError(f"Subset {spectral_subset} not in list of valid"
+                             f" subset names {list_of_valid_subset_names}")
+
+        # TODO: check if spectral is spectral and spatial is spatial
 
         if data_label and data_label not in self.app.data_collection.labels:
             raise ValueError(f'{data_label} not in {self.app.data_collection.labels}.')
@@ -451,7 +458,7 @@ def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=No
         if cls == Spectrum1D:
             object_kwargs['statistic'] = function
 
-        if not subset_to_apply:
+        if not spatial_subset and not spectral_subset:
             if 'Trace' in data.meta:
                 if cls is not None:  # pragma: no cover
                     raise ValueError("cls not supported for Trace object")
@@ -461,11 +468,15 @@ def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=No
 
             return data
 
-        if not cls and subset_to_apply:
+        if not cls and spatial_subset:
             raise AttributeError(f"A valid cls must be provided to"
-                                 f" apply subset {subset_to_apply} to data. "
+                                 f" apply subset {spatial_subset} to data. "
                                  f"Instead, {cls} was given.")
-
+        elif not cls and spectral_subset:
+            raise AttributeError(f"A valid cls must be provided to"
+                                 f" apply subset {spectral_subset} to data. "
+                                 f"Instead, {cls} was given.")
+        subset_to_apply = spatial_subset if spatial_subset else spectral_subset if spectral_subset else None
         # Loop through each subset
         for subsets in self.app.data_collection.subset_groups:
             # If name matches the name in subsets_to_apply, continue
@@ -483,14 +494,15 @@ def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=No
                                           f" subset {subsets.label} applied of type {cls}."
                                           f" Exception: {e}")
         # Apply spectral subset to spatial subset if applicable
-        if spectral_to_spatial:
-            sr = self.app.get_subsets(spectral_to_spatial)
+        if spatial_subset and spectral_subset:
+            sr = self.app.get_subsets(spectral_subset)
             if sr:
                 data = extract_region(data, sr, return_single_spectrum=True)
 
         return data
 
-    def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
+    # def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
+    def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, cls=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         subset_to_apply.
@@ -512,8 +524,10 @@ def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_
             Data is returned as type cls with subsets applied.
 
         """
-        return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-                              spectral_to_spatial=spectral_to_spatial)
+        # return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
+        #                       spectral_to_spatial=spectral_to_spatial)
+        return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
+                              spectral_subset=spectral_subset, function=None, cls=None)
 
 
 class ImageConfigHelper(ConfigHelper):
diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
index fb094d6f5e..28f2f89d8a 100644
--- a/jdaviz/core/template_mixin.py
+++ b/jdaviz/core/template_mixin.py
@@ -1031,8 +1031,12 @@ def selected_subset_state(self):
 
     @property
     def selected_subset_mask(self):
-        get_data_kwargs = {'data_label': self.plugin.dataset.selected,
-                           'subset_to_apply': self.selected}
+        if self._allowed_type == 'spatial':
+            get_data_kwargs = {'data_label': self.plugin.dataset.selected,
+                               'spatial_subset': self.selected}
+        elif self._allowed_type == 'spectral':
+            get_data_kwargs = {'data_label': self.plugin.dataset.selected,
+                               'spectral_subset': self.selected}
 
         if self.app.config == 'cubeviz' and self._allowed_type == 'spectral':
             viewer_ref = getattr(self.plugin,
@@ -1487,7 +1491,7 @@ def selected_spectrum_for_spatial_subset(self, spatial_subset=SPATIAL_DEFAULT_TE
         if spatial_subset == SPATIAL_DEFAULT_TEXT:
             spatial_subset = None
         return self.plugin._specviz_helper.get_data(data_label=self.selected,
-                                                    subset_to_apply=spatial_subset)
+                                                    spatial_subset=spatial_subset)
 
     def _is_valid_item(self, data):
         def not_from_plugin(data):
diff --git a/jdaviz/core/tests/test_helpers.py b/jdaviz/core/tests/test_helpers.py
index 5340bd5f21..6b32860f30 100644
--- a/jdaviz/core/tests/test_helpers.py
+++ b/jdaviz/core/tests/test_helpers.py
@@ -64,7 +64,7 @@ def setup_class(self, specviz_helper, spectrum1d, multi_order_spectrum_list):
     def test_get_data_with_one_subset_per_data(self, specviz_helper, label, subset_name, answer):
 
         results = specviz_helper.get_data(data_label=label,
-                                          subset_to_apply=subset_name)
+                                          spectral_subset=subset_name)
         assert list(results.mask) == answer
 
     def test_get_data_no_label_multiple_in_dc(self, specviz_helper):
@@ -88,4 +88,4 @@ def test_get_data_invald_cls_class(self, specviz_helper):
 
     def test_get_data_invald_subset_name(self, specviz_helper):
         with pytest.raises(ValueError, match="not in list of valid subset names"):
-            specviz_helper.get_data('Test 1D Spectrum', subset_to_apply="Fail")
+            specviz_helper.get_data('Test 1D Spectrum', spectral_subset="Fail")

From b9cd460a559eb5f41c3fb580936090e47f8fdb4c Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 15:03:06 -0400
Subject: [PATCH 03/21] Implement review comments

---
 jdaviz/configs/specviz/helper.py | 6 +++---
 jdaviz/core/helpers.py           | 6 ++----
 jdaviz/core/template_mixin.py    | 9 +++------
 3 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 2d104f0975..0df9094c4c 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -296,6 +296,9 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
         """
         spatial_subset = kwargs.pop("spatial_subset", None)
         function = kwargs.pop("function", None)
+        if len(kwargs) > 0:
+            raise ValueError(f'kwargs {[x for x in kwargs.keys()]} are not valid')
+
         if self.app.config == 'cubeviz':
             # then this is a specviz instance inside cubeviz and we want to default to the
             # viewer's collapse function
@@ -308,8 +311,5 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
         else:
             function = None
 
-        # return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-        #                       function=function, spectral_to_spatial=spectral_to_spatial)
-        # print(function)
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
                               spectral_subset=spectral_subset, function=function, cls=cls)
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 79b1dc5f55..00457046d2 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -411,8 +411,6 @@ def show_in_new_tab(self, title=None):  # pragma: no cover
                       DeprecationWarning)
         return self.show(loc="sidecar:tab-after", title=title)
 
-    # def _get_data(self, data_label=None, cls=None, subset_to_apply=None, function=None,
-    #               spectral_to_spatial=None):
     def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                   function=None, cls=None):
         list_of_valid_function_values = ('minimum', 'maximum', 'mean',
@@ -476,7 +474,8 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
             raise AttributeError(f"A valid cls must be provided to"
                                  f" apply subset {spectral_subset} to data. "
                                  f"Instead, {cls} was given.")
-        subset_to_apply = spatial_subset if spatial_subset else spectral_subset if spectral_subset else None
+        subset_to_apply = (spatial_subset if spatial_subset
+                           else spectral_subset if spectral_subset else None)
         # Loop through each subset
         for subsets in self.app.data_collection.subset_groups:
             # If name matches the name in subsets_to_apply, continue
@@ -501,7 +500,6 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
 
         return data
 
-    # def get_data(self, data_label=None, cls=None, subset_to_apply=None, spectral_to_spatial=None):
     def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, cls=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
index 28f2f89d8a..82b2670cba 100644
--- a/jdaviz/core/template_mixin.py
+++ b/jdaviz/core/template_mixin.py
@@ -1031,12 +1031,9 @@ def selected_subset_state(self):
 
     @property
     def selected_subset_mask(self):
-        if self._allowed_type == 'spatial':
-            get_data_kwargs = {'data_label': self.plugin.dataset.selected,
-                               'spatial_subset': self.selected}
-        elif self._allowed_type == 'spectral':
-            get_data_kwargs = {'data_label': self.plugin.dataset.selected,
-                               'spectral_subset': self.selected}
+        get_data_kwargs = {'data_label': self.plugin.dataset.selected}
+        if self._allowed_type:
+            get_data_kwargs[f'{self._allowed_type}_subset'] = self.selected
 
         if self.app.config == 'cubeviz' and self._allowed_type == 'spectral':
             viewer_ref = getattr(self.plugin,

From b2f3f791e85689e2839935c373e18069d9d071dc Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 15:41:14 -0400
Subject: [PATCH 04/21] Apply spectral subset mask to collapsed spatial subset

---
 jdaviz/core/helpers.py | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 00457046d2..e0ecb81b66 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -476,6 +476,7 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                                  f"Instead, {cls} was given.")
         subset_to_apply = (spatial_subset if spatial_subset
                            else spectral_subset if spectral_subset else None)
+        spec_sub = None
         # Loop through each subset
         for subsets in self.app.data_collection.subset_groups:
             # If name matches the name in subsets_to_apply, continue
@@ -492,11 +493,22 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                             warnings.warn(f"Not able to get {data_label} returned with"
                                           f" subset {subsets.label} applied of type {cls}."
                                           f" Exception: {e}")
+            elif (spatial_subset and spectral_subset and
+                  subsets.label.lower() == spectral_subset.lower()):
+                # Same logic as if statement
+                spec_sub = [spec_sub_data for spec_sub_data in subsets.subsets if
+                            spec_sub_data.data.label == data_label][0]
         # Apply spectral subset to spatial subset if applicable
         if spatial_subset and spectral_subset:
-            sr = self.app.get_subsets(spectral_subset)
-            if sr:
-                data = extract_region(data, sr, return_single_spectrum=True)
+            handler, _ = data_translator.get_handler_for(cls)
+            try:
+                spec_subset = handler.to_object(spec_sub, **object_kwargs)
+            except Exception as e:
+                warnings.warn(f"Not able to get {data_label} returned with"
+                              f" subset {subsets.label} applied of type {cls}."
+                              f" Exception: {e}")
+            # Return collapsed Spectrum1D object with spectral subset mask applied
+            data.mask = ~spec_subset.mask
 
         return data
 

From edd3b55e09601983b52296bea9df791c0bab5850 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 15:49:47 -0400
Subject: [PATCH 05/21] Update docstrings

---
 jdaviz/configs/cubeviz/helper.py | 16 ++++++++--------
 jdaviz/configs/specviz/helper.py |  7 ++-----
 jdaviz/core/helpers.py           | 11 ++++-------
 3 files changed, 14 insertions(+), 20 deletions(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index cccc521f0b..171109fb74 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -130,18 +130,18 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
         ----------
         data_label : str, optional
             Provide a label to retrieve a specific data set from data_collection.
-        cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
-            The type that data will be returned as.
-        subset_to_apply : str, optional
-            Subset that is to be applied to data before it is returned.
+        spatial_subset : str, optional
+            Spatial subset applied to data.
+        spectral_subset : str, optional
+            Spectral subset applied to data.
         function : {True, False, 'minimum', 'maximum', 'mean', 'median', 'sum'}, optional
             Ignored if ``data_label`` does not point to cube-like data.
             If True, will collapse according to the current collapse function defined in the
             spectrum viewer.  If provided as a string, the cube will be collapsed with the provided
-            function.  If False, None, or not passed, the entire cube will be returned.
-        spectral_to_spatial : str, optional
-            Spectral subset to be applied to spatial subset. Only possible if function is
-            set to True.
+            function.  If False, None, or not passed, the entire cube will be returned (unless there
+            are values for ``spatial_subset`` and ``spectral_subset``).
+        cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
+            The type that data will be returned as.
 
         Returns
         -------
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 0df9094c4c..7e2efa0c38 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -280,13 +280,10 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
         ----------
         data_label : str, optional
             Provide a label to retrieve a specific data set from data_collection.
+        spectral_subset : str, optional
+            Spectral subset applied to data.
         cls : `~specutils.Spectrum1D`, optional
             The type that data will be returned as.
-        subset_to_apply : str, optional
-            Subset that is to be applied to data before it is returned.
-        spectral_to_spatial : str, optional
-            Spectral subset to be applied to spatial subset. Only possible if this is
-            a specviz instance inside cubeviz.
 
         Returns
         -------
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index e0ecb81b66..c141b12b85 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -22,7 +22,6 @@
 from glue.config import data_translator
 from ipywidgets.widgets import widget_serialization
 from specutils import Spectrum1D
-from specutils.manipulation import extract_region
 
 
 from jdaviz.app import Application
@@ -521,12 +520,12 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, c
         ----------
         data_label : str, optional
             Provide a label to retrieve a specific data set from data_collection.
+        spatial_subset : str, optional
+            Spatial subset applied to data.
+        spectral_subset : str, optional
+            Spectral subset applied to data.
         cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
             The type that data will be returned as.
-        subset_to_apply : str, optional
-            Subset that is to be applied to data before it is returned.
-        spectral_to_spatial : str, optional
-            Spectral subset to be applied to spatial subset.
 
         Returns
         -------
@@ -534,8 +533,6 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, c
             Data is returned as type cls with subsets applied.
 
         """
-        # return self._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply,
-        #                       spectral_to_spatial=spectral_to_spatial)
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
                               spectral_subset=spectral_subset, function=None, cls=None)
 

From dd13038439508a970ba8051d2af7793a45307cbc Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 16:16:06 -0400
Subject: [PATCH 06/21] Add tests

---
 jdaviz/configs/cubeviz/helper.py              |  4 +--
 .../plugins/tests/test_cubeviz_helper.py      | 30 +++++++++++++++++++
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index 171109fb74..16361cc44d 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -149,11 +149,9 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
-        if function:
+        if function or (spectral_subset and spatial_subset):
             return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                          cls=cls, spatial_subset=spatial_subset, function=function)
-        elif function is None and spectral_subset and spatial_subset:
-            function = True
         elif function is False:
             function = None
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index c958535eba..8cb634c94c 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -4,6 +4,8 @@
 from astropy.tests.helper import assert_quantity_allclose
 from specutils import Spectrum1D
 
+from glue.core.roi import XRangeROI
+
 
 def test_nested_helper(cubeviz_helper):
     '''Ensures the Cubeviz helper is always returned, even after the Specviz helper is called'''
@@ -65,3 +67,31 @@ def test_valid_function(cubeviz_helper, spectrum1d_cube):
     assert cubeviz_helper.get_data(data_label="test[FLUX]").flux.ndim == 3
     # but calling through specviz automatically collapses
     assert cubeviz_helper.specviz.get_data(data_label="test[FLUX]").flux.ndim == 1
+
+
+def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
+    data_label = "test"
+    cubeviz_helper.load_data(spectrum1d_cube_larger, data_label)
+    cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
+
+    spec_viewer = cubeviz_helper.app.get_viewer(cubeviz_helper._default_spectrum_viewer_reference_name)
+    spec_viewer.apply_roi(XRangeROI(4.62440061e-07, 4.62520112e-07))
+
+    data_label = data_label + "[FLUX]"
+    # This will be the same if function is None or True
+    spatial_with_spec = cubeviz_helper.get_data(data_label=data_label,
+                                                spatial_subset="Subset 1",
+                                                spectral_subset="Subset 2")
+    assert spatial_with_spec.flux.ndim == 1
+    assert list(spatial_with_spec.mask) == [False, False, True, True, False,
+                                            False, False, False, False, False]
+    assert max(list(spatial_with_spec.flux.value)) == 157.
+    assert min(list(spatial_with_spec.flux.value)) == 13.
+
+    spatial_with_spec = cubeviz_helper.get_data(data_label=data_label,
+                                                spatial_subset="Subset 1",
+                                                spectral_subset="Subset 2",
+                                                function='minimum')
+    assert max(list(spatial_with_spec.flux.value)) == 78.
+    assert min(list(spatial_with_spec.flux.value)) == 6.
+

From dfd7d60e8372f74cc018e1e54a8e4a64a69006da Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 16:19:48 -0400
Subject: [PATCH 07/21] Fix style checks

---
 jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 8cb634c94c..223501d69d 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -74,7 +74,7 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     cubeviz_helper.load_data(spectrum1d_cube_larger, data_label)
     cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
 
-    spec_viewer = cubeviz_helper.app.get_viewer(cubeviz_helper._default_spectrum_viewer_reference_name)
+    spec_viewer = cubeviz_helper.app.get_viewer(cubeviz_helper._default_spectrum_viewer_reference_name) # noqa
     spec_viewer.apply_roi(XRangeROI(4.62440061e-07, 4.62520112e-07))
 
     data_label = data_label + "[FLUX]"
@@ -94,4 +94,3 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
                                                 function='minimum')
     assert max(list(spatial_with_spec.flux.value)) == 78.
     assert min(list(spatial_with_spec.flux.value)) == 6.
-

From ff0ecb6da0a898d34a0f9c2fa3169f759a2da6cf Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 19 May 2023 16:45:35 -0400
Subject: [PATCH 08/21] Change error message

---
 jdaviz/core/helpers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index c141b12b85..07122e5ff8 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -504,7 +504,7 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                 spec_subset = handler.to_object(spec_sub, **object_kwargs)
             except Exception as e:
                 warnings.warn(f"Not able to get {data_label} returned with"
-                              f" subset {subsets.label} applied of type {cls}."
+                              f" subset {spectral_subset} applied of type {cls}."
                               f" Exception: {e}")
             # Return collapsed Spectrum1D object with spectral subset mask applied
             data.mask = ~spec_subset.mask

From da88b3b2b81db44f45c5c05f7bcf931a29c964c7 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 08:40:51 -0400
Subject: [PATCH 09/21] Add explicit get_data to imviz

---
 jdaviz/configs/imviz/helper.py | 22 ++++++++++++++++++++++
 jdaviz/core/helpers.py         |  2 +-
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/jdaviz/configs/imviz/helper.py b/jdaviz/configs/imviz/helper.py
index ed5fe8cf8c..5d09c9a045 100644
--- a/jdaviz/configs/imviz/helper.py
+++ b/jdaviz/configs/imviz/helper.py
@@ -239,6 +239,28 @@ def get_catalog_source_results(self):
         """
         return getattr(self.app, '_catalog_source_table', None)
 
+    def get_data(self, data_label=None, spatial_subset=None, cls=None):
+        """
+        Returns data with name equal to data_label of type cls with subsets applied from
+        spatial_subset.
+
+        Parameters
+        ----------
+        data_label : str, optional
+            Provide a label to retrieve a specific data set from data_collection.
+        spatial_subset : str, optional
+            Spatial subset applied to data.
+        cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
+            The type that data will be returned as.
+
+        Returns
+        -------
+        data : cls
+            Data is returned as type cls with subsets applied.
+
+        """
+        return self._get_data(data_label=data_label, spatial_subset=spatial_subset, cls=cls)
+
 
 def split_filename_with_fits_ext(filename):
     """Split a ``filename[ext]`` input into filename and FITS extension.
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 07122e5ff8..8f72191633 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -514,7 +514,7 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
     def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, cls=None):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
-        subset_to_apply.
+        spatial_subsets and/or spectral_subsets.
 
         Parameters
         ----------

From 1831afde7164ecd6ff488f4da0368079cf1acbbc Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 08:51:21 -0400
Subject: [PATCH 10/21] Raise error when cubeviz kwargs are used in specviz
 get_data

---
 jdaviz/configs/specviz/helper.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 7e2efa0c38..1b558ca25a 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -305,6 +305,8 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
 
             if cls is None:
                 cls = Spectrum1D
+        elif spatial_subset or function:
+            raise ValueError('kwargs spatial subset and function are not valid in specviz')
         else:
             function = None
 

From 01207fd6738daa20894672070a77143c96f2c5dd Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 09:03:18 -0400
Subject: [PATCH 11/21] Implement review requests

---
 jdaviz/configs/specviz/helper.py |  1 +
 jdaviz/core/helpers.py           | 15 +++++----------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 1b558ca25a..8f44c4f99a 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -308,6 +308,7 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None, **kwargs):
         elif spatial_subset or function:
             raise ValueError('kwargs spatial subset and function are not valid in specviz')
         else:
+            spatial_subset = None
             function = None
 
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 8f72191633..4418551b49 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -511,30 +511,25 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
 
         return data
 
-    def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, cls=None):
+    def get_data(self, data_label=None, cls=None):
         """
-        Returns data with name equal to data_label of type cls with subsets applied from
-        spatial_subsets and/or spectral_subsets.
+        Returns data with name equal to data_label of type cls.
 
         Parameters
         ----------
         data_label : str, optional
             Provide a label to retrieve a specific data set from data_collection.
-        spatial_subset : str, optional
-            Spatial subset applied to data.
-        spectral_subset : str, optional
-            Spectral subset applied to data.
         cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
             The type that data will be returned as.
 
         Returns
         -------
         data : cls
-            Data is returned as type cls with subsets applied.
+            Data is returned as type cls.
 
         """
-        return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
-                              spectral_subset=spectral_subset, function=None, cls=None)
+        return self._get_data(data_label=data_label, spatial_subset=None,
+                              spectral_subset=None, function=None, cls=None)
 
 
 class ImageConfigHelper(ConfigHelper):

From b9203d7bf131429c32077a26c6670a3af92bf27b Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 10:17:12 -0400
Subject: [PATCH 12/21] Add get_data to specviz2d

---
 jdaviz/configs/cubeviz/helper.py   |  5 ++++-
 jdaviz/configs/specviz2d/helper.py | 22 ++++++++++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index 16361cc44d..b207569faa 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -149,9 +149,12 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
-        if function or (spectral_subset and spatial_subset):
+        if function and spectral_subset and spatial_subset:
             return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                          cls=cls, spatial_subset=spatial_subset, function=function)
+        elif function is False and (spectral_subset and spatial_subset):
+            raise ValueError("function cannot be False if spectral_subset"
+                             " and spatial_subset have values")
         elif function is False:
             function = None
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
diff --git a/jdaviz/configs/specviz2d/helper.py b/jdaviz/configs/specviz2d/helper.py
index c2a50a7888..c41be5df54 100644
--- a/jdaviz/configs/specviz2d/helper.py
+++ b/jdaviz/configs/specviz2d/helper.py
@@ -238,3 +238,25 @@ def load_trace(self, trace, data_label, show_in_viewer=True):
             self.app.add_data_to_viewer(
                 self._default_spectrum_2d_viewer_reference_name, data_label
             )
+
+    def get_data(self, data_label=None, spectral_subset=None, cls=None):
+        """
+        Returns data with name equal to data_label of type cls with subsets applied from
+        spectral_subset.
+
+        Parameters
+        ----------
+        data_label : str, optional
+            Provide a label to retrieve a specific data set from data_collection.
+        spectral_subset : str, optional
+            Spectral subset applied to data.
+        cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
+            The type that data will be returned as.
+
+        Returns
+        -------
+        data : cls
+            Data is returned as type cls with subsets applied.
+
+        """
+        return self._get_data(data_label=data_label, spectral_subset=spectral_subset, cls=cls)

From 8389ee4c5be4449c878369f8f5610c1d0e0efe51 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 10:48:40 -0400
Subject: [PATCH 13/21] Add line to fix CI

---
 jdaviz/configs/cubeviz/helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index b207569faa..0bf4625974 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -149,7 +149,7 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
-        if function and spectral_subset and spatial_subset:
+        if (function or function is None) and spectral_subset and spatial_subset:
             return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                          cls=cls, spatial_subset=spatial_subset, function=function)
         elif function is False and (spectral_subset and spatial_subset):

From afca9a9587946d0c64cfcce714a9480b8838da02 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 22 May 2023 11:21:15 -0400
Subject: [PATCH 14/21] Make sure function is respected with just spatial
 subset

---
 jdaviz/configs/cubeviz/helper.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index 0bf4625974..1e918fda10 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -149,7 +149,10 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
-        if (function or function is None) and spectral_subset and spatial_subset:
+        if function is not False and spectral_subset and spatial_subset:
+            return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
+                                         cls=cls, spatial_subset=spatial_subset, function=function)
+        elif function and spatial_subset:
             return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                          cls=cls, spatial_subset=spatial_subset, function=function)
         elif function is False and (spectral_subset and spatial_subset):

From dea9920d647f45ba2c9081c67c150dd7f448cebe Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 23 May 2023 13:55:34 -0400
Subject: [PATCH 15/21] Add more catches for incorrect or invalid parameters

---
 jdaviz/configs/cubeviz/helper.py              | 13 +++++-----
 .../plugins/tests/test_cubeviz_helper.py      | 26 ++++++++++++++++---
 jdaviz/core/helpers.py                        | 15 ++++++++---
 3 files changed, 40 insertions(+), 14 deletions(-)

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
index 1e918fda10..bb7a23e2e5 100644
--- a/jdaviz/configs/cubeviz/helper.py
+++ b/jdaviz/configs/cubeviz/helper.py
@@ -149,15 +149,16 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
-        if function is not False and spectral_subset and spatial_subset:
+        # If function is a value ('sum' or 'minimum') or True and spatial and spectral
+        # are set, then we collapse the cube along the spatial subset using the function, then
+        # we apply the mask from the spectral subset.
+        # If function is any value other than False, we use specviz
+        if (function is not False and spectral_subset and spatial_subset) or function:
             return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                          cls=cls, spatial_subset=spatial_subset, function=function)
-        elif function and spatial_subset:
-            return self.specviz.get_data(data_label=data_label, spectral_subset=spectral_subset,
-                                         cls=cls, spatial_subset=spatial_subset, function=function)
-        elif function is False and (spectral_subset and spatial_subset):
+        elif function is False and spectral_subset:
             raise ValueError("function cannot be False if spectral_subset"
-                             " and spatial_subset have values")
+                             " is set")
         elif function is False:
             function = None
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 223501d69d..6429d3ca7c 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -71,6 +71,8 @@ def test_valid_function(cubeviz_helper, spectrum1d_cube):
 
 def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     data_label = "test"
+    spatial_subset = "Subset 1"
+    spectral_subset = "Subset 2"
     cubeviz_helper.load_data(spectrum1d_cube_larger, data_label)
     cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
 
@@ -80,8 +82,8 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     data_label = data_label + "[FLUX]"
     # This will be the same if function is None or True
     spatial_with_spec = cubeviz_helper.get_data(data_label=data_label,
-                                                spatial_subset="Subset 1",
-                                                spectral_subset="Subset 2")
+                                                spatial_subset=spatial_subset,
+                                                spectral_subset=spectral_subset)
     assert spatial_with_spec.flux.ndim == 1
     assert list(spatial_with_spec.mask) == [False, False, True, True, False,
                                             False, False, False, False, False]
@@ -89,8 +91,24 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     assert min(list(spatial_with_spec.flux.value)) == 13.
 
     spatial_with_spec = cubeviz_helper.get_data(data_label=data_label,
-                                                spatial_subset="Subset 1",
-                                                spectral_subset="Subset 2",
+                                                spatial_subset=spatial_subset,
+                                                spectral_subset=spectral_subset,
                                                 function='minimum')
     assert max(list(spatial_with_spec.flux.value)) == 78.
     assert min(list(spatial_with_spec.flux.value)) == 6.
+
+    collapse_with_spectral = cubeviz_helper.get_data(data_label=data_label,
+                                                     spectral_subset=spectral_subset,
+                                                     function=True)
+
+    with pytest.raises(ValueError, match=f'{spectral_subset} is not a spatial subset.'):
+        cubeviz_helper.get_data(data_label=data_label, spatial_subset=spectral_subset, function=True)
+    with pytest.raises(ValueError, match=f'{spatial_subset} is not a spectral subset.'):
+        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spatial_subset, function=True)
+    with pytest.raises(ValueError, match='function cannot be False if spectral_subset'):
+        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spectral_subset, function=False)
+
+    collapse_with_spectral2 = cubeviz_helper.get_data(data_label=data_label,
+                                                      function=True)
+
+    assert list(collapse_with_spectral.flux) == list(collapse_with_spectral2.flux)
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 4418551b49..15e9f63a19 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -15,13 +15,14 @@
 import astropy.units as u
 from astropy.wcs.wcsapi import BaseHighLevelWCS
 from astropy.nddata import CCDData
+from regions.core.core import Region
 from glue.core import HubListener
 from glue.core.edit_subset_mode import NewMode
 from glue.core.message import SubsetCreateMessage, SubsetDeleteMessage
 from glue.core.subset import Subset, MaskSubsetState
 from glue.config import data_translator
 from ipywidgets.widgets import widget_serialization
-from specutils import Spectrum1D
+from specutils import Spectrum1D, SpectralRegion
 
 
 from jdaviz.app import Application
@@ -426,8 +427,6 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
             raise ValueError(f"Subset {spectral_subset} not in list of valid"
                              f" subset names {list_of_valid_subset_names}")
 
-        # TODO: check if spectral is spectral and spatial is spatial
-
         if data_label and data_label not in self.app.data_collection.labels:
             raise ValueError(f'{data_label} not in {self.app.data_collection.labels}.')
         elif not data_label and len(self.app.data_collection) > 1:
@@ -439,7 +438,16 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
         if cls is not None and not isclass(cls):
             raise TypeError(
                 "cls in get_data must be a class or None.")
+
+        # Check if spectral is spectral and spatial is spatial
+        all_subsets = self.app.get_subsets(object_only=True)
         data = self.app.data_collection[data_label]
+        if spatial_subset and not isinstance(all_subsets[spatial_subset][0],
+                                             Region):
+            raise ValueError(f"{spatial_subset} is not a spatial subset.")
+        if spectral_subset and not isinstance(all_subsets[spectral_subset],
+                                              SpectralRegion):
+            raise ValueError(f"{spectral_subset} is not a spectral subset.")
 
         if not cls:
             if 'Trace' in data.meta:
@@ -484,7 +492,6 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                 for subset in subsets.subsets:
                     # If the subset applies to data with the same name as data_label, continue
                     if subset.data.label == data_label:
-
                         handler, _ = data_translator.get_handler_for(cls)
                         try:
                             data = handler.to_object(subset, **object_kwargs)

From 3b22c46572d07055f8b6de9ef9840039b2d91237 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 23 May 2023 13:58:46 -0400
Subject: [PATCH 16/21] Fix style check

---
 .../configs/cubeviz/plugins/tests/test_cubeviz_helper.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 6429d3ca7c..037d837e96 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -102,11 +102,14 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
                                                      function=True)
 
     with pytest.raises(ValueError, match=f'{spectral_subset} is not a spatial subset.'):
-        cubeviz_helper.get_data(data_label=data_label, spatial_subset=spectral_subset, function=True)
+        cubeviz_helper.get_data(data_label=data_label, spatial_subset=spectral_subset,
+                                function=True)
     with pytest.raises(ValueError, match=f'{spatial_subset} is not a spectral subset.'):
-        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spatial_subset, function=True)
+        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spatial_subset,
+                                function=True)
     with pytest.raises(ValueError, match='function cannot be False if spectral_subset'):
-        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spectral_subset, function=False)
+        cubeviz_helper.get_data(data_label=data_label, spectral_subset=spectral_subset,
+                                function=False)
 
     collapse_with_spectral2 = cubeviz_helper.get_data(data_label=data_label,
                                                       function=True)

From d4fe3fa0238d5b27a86847585ceedb9e55a7d3c6 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 23 May 2023 15:38:16 -0400
Subject: [PATCH 17/21] Cover case where cubeviz.get_data uses spectral subset
 and function

---
 .../plugins/tests/test_cubeviz_helper.py      |  9 +--
 jdaviz/configs/specviz/helper.py              |  3 +-
 jdaviz/core/helpers.py                        | 77 ++++++++++---------
 3 files changed, 47 insertions(+), 42 deletions(-)

diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 037d837e96..d3a4363d0f 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -100,6 +100,10 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     collapse_with_spectral = cubeviz_helper.get_data(data_label=data_label,
                                                      spectral_subset=spectral_subset,
                                                      function=True)
+    collapse_with_spectral2 = cubeviz_helper.get_data(data_label=data_label,
+                                                      function=True)
+
+    assert list(collapse_with_spectral.flux) == list(collapse_with_spectral2.flux)
 
     with pytest.raises(ValueError, match=f'{spectral_subset} is not a spatial subset.'):
         cubeviz_helper.get_data(data_label=data_label, spatial_subset=spectral_subset,
@@ -110,8 +114,3 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     with pytest.raises(ValueError, match='function cannot be False if spectral_subset'):
         cubeviz_helper.get_data(data_label=data_label, spectral_subset=spectral_subset,
                                 function=False)
-
-    collapse_with_spectral2 = cubeviz_helper.get_data(data_label=data_label,
-                                                      function=True)
-
-    assert list(collapse_with_spectral.flux) == list(collapse_with_spectral2.flux)
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 8f44c4f99a..2adde425c3 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -85,6 +85,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
         else:
             for layer_state in viewer.state.layers:
                 lyr = layer_state.layer
+                print(lyr.label, type(lyr))
                 if subset_to_apply is not None:
                     if lyr.label == subset_to_apply:
                         spectrum = get_data_method(data_label=lyr.data.label,
@@ -97,7 +98,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
                 else:
                     if isinstance(lyr, GroupedSubset):
                         spectrum = get_data_method(data_label=lyr.data.label,
-                                                   spectral_subset=lyr.label,
+                                                   spatial_subset=lyr.label,
                                                    cls=Spectrum1D,
                                                    **function_kwargs)
                         spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 15e9f63a19..2a0485fc1a 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -413,6 +413,7 @@ def show_in_new_tab(self, title=None):  # pragma: no cover
 
     def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                   function=None, cls=None):
+        # Start validity checks
         list_of_valid_function_values = ('minimum', 'maximum', 'mean',
                                          'median', 'sum')
         if function and function not in list_of_valid_function_values:
@@ -439,15 +440,8 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
             raise TypeError(
                 "cls in get_data must be a class or None.")
 
-        # Check if spectral is spectral and spatial is spatial
-        all_subsets = self.app.get_subsets(object_only=True)
+        # End validity checks and start data retrieval
         data = self.app.data_collection[data_label]
-        if spatial_subset and not isinstance(all_subsets[spatial_subset][0],
-                                             Region):
-            raise ValueError(f"{spatial_subset} is not a spatial subset.")
-        if spectral_subset and not isinstance(all_subsets[spectral_subset],
-                                              SpectralRegion):
-            raise ValueError(f"{spectral_subset} is not a spectral subset.")
 
         if not cls:
             if 'Trace' in data.meta:
@@ -481,40 +475,51 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
             raise AttributeError(f"A valid cls must be provided to"
                                  f" apply subset {spectral_subset} to data. "
                                  f"Instead, {cls} was given.")
-        subset_to_apply = (spatial_subset if spatial_subset
-                           else spectral_subset if spectral_subset else None)
-        spec_sub = None
-        # Loop through each subset
-        for subsets in self.app.data_collection.subset_groups:
-            # If name matches the name in subsets_to_apply, continue
-            if subsets.label.lower() == subset_to_apply.lower():
-                # Loop through each data a subset applies to
-                for subset in subsets.subsets:
-                    # If the subset applies to data with the same name as data_label, continue
-                    if subset.data.label == data_label:
-                        handler, _ = data_translator.get_handler_for(cls)
-                        try:
-                            data = handler.to_object(subset, **object_kwargs)
-                        except Exception as e:
-                            warnings.warn(f"Not able to get {data_label} returned with"
-                                          f" subset {subsets.label} applied of type {cls}."
-                                          f" Exception: {e}")
-            elif (spatial_subset and spectral_subset and
-                  subsets.label.lower() == spectral_subset.lower()):
-                # Same logic as if statement
-                spec_sub = [spec_sub_data for spec_sub_data in subsets.subsets if
-                            spec_sub_data.data.label == data_label][0]
-        # Apply spectral subset to spatial subset if applicable
-        if spatial_subset and spectral_subset:
+
+        # Now we work on applying subsets to the data
+        all_subsets = self.app.get_subsets(object_only=True)
+
+        # Handle spatial subset
+        if spatial_subset and not isinstance(all_subsets[spatial_subset][0],
+                                             Region):
+            raise ValueError(f"{spatial_subset} is not a spatial subset.")
+        elif spatial_subset:
+            real_spatial = [sub for subsets in self.app.data_collection.subset_groups
+                            for sub in subsets.subsets
+                            if sub.data.label == data_label and subsets.label == spatial_subset][0]
+            handler, _ = data_translator.get_handler_for(cls)
+            try:
+                data = handler.to_object(real_spatial, **object_kwargs)
+            except Exception as e:
+                warnings.warn(f"Not able to get {data_label} returned with"
+                              f" subset {spatial_subset} applied of type {cls}."
+                              f" Exception: {e}")
+        elif function:
+            # This covers the case where cubeviz.get_data is called using a spectral_subset
+            # with function set.
+            data = data.get_object(cls=cls, **object_kwargs)
+
+        # Handle spectral subset, including case where spatial subset is also set
+        if spectral_subset and not isinstance(all_subsets[spectral_subset],
+                                              SpectralRegion):
+            raise ValueError(f"{spectral_subset} is not a spectral subset.")
+        elif spectral_subset:
+            real_spectral = [sub for subsets in self.app.data_collection.subset_groups
+                             for sub in subsets.subsets
+                             if sub.data.label == data_label and subsets.label == spectral_subset][0] # noqa
+
             handler, _ = data_translator.get_handler_for(cls)
             try:
-                spec_subset = handler.to_object(spec_sub, **object_kwargs)
+                spec_subset = handler.to_object(real_spectral, **object_kwargs)
             except Exception as e:
                 warnings.warn(f"Not able to get {data_label} returned with"
                               f" subset {spectral_subset} applied of type {cls}."
                               f" Exception: {e}")
-            # Return collapsed Spectrum1D object with spectral subset mask applied
-            data.mask = ~spec_subset.mask
+            if spatial_subset or function:
+                # Return collapsed Spectrum1D object with spectral subset mask applied
+                data.mask = ~spec_subset.mask
+            else:
+                data = spec_subset
 
         return data
 

From e49baabe0289909a629665a1a1509bd79100d853 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 23 May 2023 15:55:05 -0400
Subject: [PATCH 18/21] Fix bug with get_spectra

---
 jdaviz/configs/specviz/helper.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 2adde425c3..c2a918b681 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -1,6 +1,7 @@
 import warnings
 
 from astropy import units as u
+from regions.core.core import Region
 from glue.core.subset_group import GroupedSubset
 from specutils import SpectralRegion, Spectrum1D
 
@@ -76,6 +77,7 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
         get_data_method = self.app._jdaviz_helper.get_data
         viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
         function_kwargs = {'function': getattr(viewer.state, "function")} if self.app.config == 'cubeviz' else {}  # noqa
+        all_subsets = self.app.get_subsets(object_only=True)
 
         if data_label is not None:
             spectrum = get_data_method(data_label=data_label,
@@ -85,7 +87,6 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
         else:
             for layer_state in viewer.state.layers:
                 lyr = layer_state.layer
-                print(lyr.label, type(lyr))
                 if subset_to_apply is not None:
                     if lyr.label == subset_to_apply:
                         spectrum = get_data_method(data_label=lyr.data.label,
@@ -96,12 +97,20 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
                     else:
                         continue
                 else:
-                    if isinstance(lyr, GroupedSubset):
+                    if (isinstance(lyr, GroupedSubset) and lyr.label in all_subsets.keys() and
+                            isinstance(all_subsets[lyr.label][0], Region)):
                         spectrum = get_data_method(data_label=lyr.data.label,
                                                    spatial_subset=lyr.label,
                                                    cls=Spectrum1D,
                                                    **function_kwargs)
                         spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
+                    elif (isinstance(lyr, GroupedSubset) and lyr.label in all_subsets.keys() and
+                            isinstance(all_subsets[lyr.label], SpectralRegion)):
+                        spectrum = get_data_method(data_label=lyr.data.label,
+                                                   spectral_subset=lyr.label,
+                                                   cls=Spectrum1D,
+                                                   **function_kwargs)
+                        spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
                     else:
                         spectrum = get_data_method(data_label=lyr.label,
                                                    cls=Spectrum1D,

From 43a342ff957e889800ab04e01379e1f75aad77c6 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 23 May 2023 16:51:47 -0400
Subject: [PATCH 19/21] Switch mask to be False where spectral subset is
 applied

---
 jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py | 4 ++--
 jdaviz/core/helpers.py                                      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index d3a4363d0f..c4229448a2 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -85,8 +85,8 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
                                                 spatial_subset=spatial_subset,
                                                 spectral_subset=spectral_subset)
     assert spatial_with_spec.flux.ndim == 1
-    assert list(spatial_with_spec.mask) == [False, False, True, True, False,
-                                            False, False, False, False, False]
+    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.
 
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 2a0485fc1a..c6759786c9 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -517,7 +517,7 @@ def _get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                               f" Exception: {e}")
             if spatial_subset or function:
                 # Return collapsed Spectrum1D object with spectral subset mask applied
-                data.mask = ~spec_subset.mask
+                data.mask = spec_subset.mask
             else:
                 data = spec_subset
 

From e84a308c9d3f5e18c9b0b1091af33b841006de42 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Wed, 24 May 2023 09:48:10 -0400
Subject: [PATCH 20/21] Add get_data to mosviz

---
 jdaviz/configs/mosviz/helper.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index eefc35a968..8d16f085a7 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -1076,3 +1076,25 @@ def get_spectrum_2d(self, row=None, apply_slider_redshift="Warn"):
         `~specutils.Spectrum1D`
         """
         return self._get_spectrum('2D Spectra', row, apply_slider_redshift)
+
+    def get_data(self, data_label=None, spectral_subset=None, cls=None):
+        """
+        Returns data with name equal to data_label of type cls with subsets applied from
+        spectral_subset.
+
+        Parameters
+        ----------
+        data_label : str, optional
+            Provide a label to retrieve a specific data set from data_collection.
+        spectral_subset : str, optional
+            Spectral subset applied to data.
+        cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
+            The type that data will be returned as.
+
+        Returns
+        -------
+        data : cls
+            Data is returned as type cls with subsets applied.
+
+        """
+        return self._get_data(data_label=data_label, spectral_subset=spectral_subset, cls=cls)

From 155bc857eda3ad0584374b8dbfd7db9d52e38b80 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Wed, 24 May 2023 13:30:51 -0400
Subject: [PATCH 21/21] Update change file

---
 CHANGES.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGES.rst b/CHANGES.rst
index 91b8ccdc1a..be85848478 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -20,6 +20,9 @@ Cubeviz
 - ``get_data`` now supports ``function=True`` to adopt the collapse-function from the spectrum viewer.
   [#2117]
 
+- ``get_data`` now supports applying a spectral mask to a collapse spatial subset. [#2199]
+
+
 Imviz
 ^^^^^