Add Spatial Collapsed Spectrum selection to Line Analysis

CHANGES.rst

@@ -11,6 +11,8 @@ Cubeviz
 
 - Image viewers now have linked pan/zoom and linked box zoom. [#1596]
 
+- Added ability to select spatial subset collasped spectrum for Line Analysis [#1583]
+
 Imviz
 ^^^^^
 

jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py

@@ -66,6 +66,9 @@ class LineAnalysis(PluginTemplateMixin, DatasetSelectMixin, SpectralSubsetSelect
     dialog = Bool(False).tag(sync=True)
     template_file = __file__, "line_analysis.vue"
 
+    spatial_subset_items = List().tag(sync=True)
+    collapsed_spectrum_selected = Unicode().tag(sync=True)
+
     continuum_subset_items = List().tag(sync=True)
     continuum_subset_selected = Unicode().tag(sync=True)
 
@@ -97,6 +100,15 @@ def __init__(self, *args, **kwargs):
         # require entries to be in spectrum-viewer (not other cubeviz images, etc)
         self.dataset.add_filter('layer_in_spectrum_viewer')
 
+        if self.app.state.settings.get("configuration") == "cubeviz":
+            self.spatial_subset = SubsetSelect(self,
+                                               'spatial_subset_items',
+                                               'collapsed_spectrum_selected',
+                                               default_text='Entire Cube Spectrum',
+                                               allowed_type='spatial')
+        else:
+            self.spatial_subset = None
+
         self.hub.subscribe(self, AddDataMessage,
                            handler=self._on_viewer_data_changed)
         self.hub.subscribe(self, RemoveDataMessage,
@@ -139,7 +151,9 @@ def _on_viewer_subsets_changed(self, msg):
         msg : `glue.core.Message`
             The glue message passed to this callback method.
         """
-        if (msg.subset.label in [self.spectral_subset_selected, self.continuum_subset_selected]
+        if (msg.subset.label in [self.spectral_subset_selected,
+                                 self.collapsed_spectrum_selected,
+                                 self.continuum_subset_selected]
                 and self.plugin_opened):
             self._calculate_statistics()
 
@@ -210,7 +224,8 @@ def _on_identified_line_changed(self, msg):
             # in which case we'll default to the identified line
             self.selected_line = self.identified_line
 
-    @observe("spectral_subset_selected", "dataset_selected", "continuum_subset_selected", "width")
+    @observe("collapsed_spectrum_selected", "spectral_subset_selected", "dataset_selected",
+             "continuum_subset_selected", "width")
     def _calculate_statistics(self, *args, **kwargs):
         """
         Run the line analysis functions on the selected data/subset and
@@ -222,7 +237,16 @@ def _calculate_statistics(self, *args, **kwargs):
         # show spinner with overlay
         self.results_computing = True
 
-        full_spectrum = self.dataset.selected_obj
+        if self.config == 'cubeviz' and self.collapsed_spectrum_selected != 'Entire Cube Spectrum':
+            # then we're acting on the auto-collapsed data in the spectrum-viewer
+            # of a spatial subset.  In the future, we may want to expose on-the-fly
+            # collapse options... but right now these will follow the settings of the
+            # spectrum-viewer itself
+            full_spectrum = self.app.get_data_from_viewer('spectrum-viewer',
+                                                          self.collapsed_spectrum_selected)
+        else:
+            full_spectrum = self.dataset.selected_obj
+
         if full_spectrum is None or self.width == "" or not self.plugin_opened:
             # this can happen DURING a unit conversion change
             self.update_results(None)

jdaviz/configs/specviz/plugins/line_analysis/line_analysis.vue

@@ -20,6 +20,15 @@
       hint="Select the data set to be analysed."
     />
 
+    <plugin-subset-select
+      v-if="config=='cubeviz'"
+      :items="spatial_subset_items"
+      :selected.sync="collapsed_spectrum_selected"
+      :show_if_single_entry="true"
+      label="Collapsed Spectrum"
+      hint="Select collapsed spectrum to analyze."
+    />
+
     <plugin-subset-select 
       :items="spectral_subset_items"
       :selected.sync="spectral_subset_selected"

jdaviz/configs/specviz/plugins/line_analysis/tests/test_line_analysis.py

@@ -1,8 +1,11 @@
 import astropy.units as u
 from astropy.table import QTable
-import numpy as np
-from glue.core.roi import XRangeROI
+from astropy.wcs import WCS
+from glue.core.roi import XRangeROI, RectangularROI
 from glue.core.edit_subset_mode import NewMode
+import numpy as np
+import pytest
+from specutils import Spectrum1D
 
 from jdaviz.configs.specviz.plugins.line_analysis.line_analysis import _coerce_unit
 from jdaviz.core.events import LineIdentifyMessage
@@ -41,6 +44,50 @@ def test_plugin(specviz_helper, spectrum1d):
             assert len(result_dict.get('uncertainty')) > 0
 
 
+@pytest.mark.filterwarnings('ignore:No observer defined on WCS')
+def test_spatial_subset(cubeviz_helper):
+    """
+    Tests that the spatial selection returns any valid result, DOES NOT VALIDATE THE VALUE
+    Not checking the value attempts to circumvent the issue we ran into here:
+    https://github.com/spacetelescope/jdaviz/pull/1564#discussion_r949427663
+    """
+
+    flux = np.arange(250).reshape((5, 5, 10)) * u.Jy
+    wcs_dict = {"CTYPE1": "RA---TAN", "CTYPE2": "DEC--TAN", "CTYPE3": "WAVE-LOG",
+                "CRVAL1": 205, "CRVAL2": 27, "CRVAL3": 4.622e-7,
+                "CDELT1": -0.0001, "CDELT2": 0.0001, "CDELT3": 8e-11,
+                "CRPIX1": 0, "CRPIX2": 0, "CRPIX3": 0}
+    w = WCS(wcs_dict)
+    large_cube = Spectrum1D(flux=flux, wcs=w)
+
+    label = "Test Cube"
+    cubeviz_helper.load_data(large_cube, data_label=label)
+
+    # add a region and rerun stats for that region
+    cubeviz_helper.app.get_viewer('flux-viewer').apply_roi(RectangularROI(-0.5, 0.5, 0.5, 2.5))
+    cubeviz_helper.app.get_viewer('flux-viewer').session.edit_subset_mode._mode = NewMode
+    # The cube only has one slice, so we have to grab the entire viewer's range to create a region
+    cubeviz_helper.app.get_viewer('spectrum-viewer').apply_roi(
+        XRangeROI(cubeviz_helper.app.get_viewer('spectrum-viewer').state.x_min,
+                  cubeviz_helper.app.get_viewer('spectrum-viewer').state.x_max))
+
+    cubeviz_helper.app.state.drawer = True
+
+    plugin = cubeviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
+    plugin.open_in_tray()
+
+    plugin.collapsed_spectrum_selected = "Subset 1"
+    plugin.spectral_subset_selected = 'Subset 2'
+    plugin.continuum_subset_selected = 'Surrounding'
+    plugin.width = 3
+
+    for result in plugin.results:
+        # Check that there exists a value
+        assert not np.isnan(float(result['result']))
+        # Check the unit is not dimensionless
+        assert u.Unit(result['unit']) != u.dimensionless_unscaled
+
+
 def test_line_identify(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
     specviz_helper.load_spectrum(spectrum1d, data_label=label)