background spectrum: live-preview and export

docs/specviz2d/plugins.rst

@@ -94,9 +94,11 @@ The background step of the plugin allows for creating background and background-
 images via `specreduce.background <https://specreduce.readthedocs.io/en/latest/#module-specreduce.background>`_.
 
 Once you interact with any of the inputs in the background step or hover over that area
-of the plugin, the live visualization will change to show the center (dotted line) and edges
-(solid lines) of the background region(s).  Choose between creating the background
-around the trace defined in the Trace section, or around a "Manual" flat trace.
+of the plugin, the live visualization in the 2d spectrum viewer will change to show the center 
+(dotted line) and edges (solid lines) of the background region(s).  The 1D representation of the
+background will also be visualized in the 1D spectrum viewer (dotted line).
+
+Choose between creating the background around the trace defined in the Trace section, or around a "Manual" flat trace.
 
 To visualize the resulting background or background-subtracted image, click on the respective panel,
 and choose a label for the new data entry.  The exported images will now appear in the data dropdown
@@ -108,7 +110,10 @@ To export and access the specreduce Background object defined in the plugin, cal
 
   bg = sp_ext.export_bg()
 
-To access the background image or background-subtracted image as a :class:`~specutils.Spectrum1D` object, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_img` or :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_img`, respectively.
+To access the background image, background spectrum, or background-subtracted image as a :class:`~specutils.Spectrum1D` object,
+call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_img`,
+:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_spectrum`,
+or :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_sub`, respectively.
 
 To import the parameters from a specreduce Background object into the plugin, whether it's new or was exported and modified in the notebook, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_bg`::
 

jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py

@@ -80,6 +80,14 @@ class SpectralExtraction(PluginTemplateMixin):
     bg_add_to_viewer_items = List().tag(sync=True)
     bg_add_to_viewer_selected = Unicode().tag(sync=True)
 
+    bg_spec_results_label = Unicode().tag(sync=True)
+    bg_spec_results_label_default = Unicode().tag(sync=True)
+    bg_spec_results_label_auto = Bool(True).tag(sync=True)
+    bg_spec_results_label_invalid_msg = Unicode('').tag(sync=True)
+    bg_spec_results_label_overwrite = Bool().tag(sync=True)
+    bg_spec_add_to_viewer_items = List().tag(sync=True)
+    bg_spec_add_to_viewer_selected = Unicode().tag(sync=True)
+
     bg_sub_results_label = Unicode().tag(sync=True)
     bg_sub_results_label_default = Unicode().tag(sync=True)
     bg_sub_results_label_auto = Bool(True).tag(sync=True)
@@ -175,6 +183,16 @@ def __init__(self, *args, **kwargs):
         self.bg_add_results.viewer.filters = ['is_spectrum_2d_viewer']
         self.bg_results_label_default = 'background'
 
+        self.bg_spec_add_results = AddResults(self, 'bg_spec_results_label',
+                                              'bg_spec_results_label_default',
+                                              'bg_spec_results_label_auto',
+                                              'bg_spec_results_label_invalid_msg',
+                                              'bg_spec_results_label_overwrite',
+                                              'bg_spec_add_to_viewer_items',
+                                              'bg_spec_add_to_viewer_selected')
+        self.bg_spec_add_results.viewer.filters = ['is_spectrum_viewer']
+        self.bg_spec_results_label_default = 'background-spectrum'
+
         self.bg_sub_add_results = AddResults(self, 'bg_sub_results_label',
                                              'bg_sub_results_label_default',
                                              'bg_sub_results_label_auto',
@@ -312,7 +330,7 @@ def _update_plugin_marks(self, *args):
                          'bg': ['trace',
                                 'bg1_center', 'bg1_lower', 'bg1_upper',
                                 'bg2_center', 'bg2_lower', 'bg2_upper',
-                                'extract'],
+                                'bg_spec', 'extract'],
                          'ext': ['trace',
                                  'ext_upper', 'ext_lower',
                                  'extract']}
@@ -353,11 +371,12 @@ def marks(self):
         # NOTE: += won't trigger the figure to notice new marks
         viewer2d.figure.marks = viewer2d.figure.marks + list(self._marks.values())
 
-        mark1d = PluginLine(viewer1d, visible=self.plugin_opened)
-        self._marks['extract'] = mark1d
+        self._marks['extract'] = PluginLine(viewer1d, visible=self.plugin_opened)
+        self._marks['bg_spec'] = PluginLine(viewer1d, visible=self.plugin_opened, line_style='dotted')  # noqa
 
         # NOTE: += won't trigger the figure to notice new marks
-        viewer1d.figure.marks = viewer1d.figure.marks + [mark1d]
+        viewer1d.figure.marks = viewer1d.figure.marks + [self._marks['extract'],
+                                                         self._marks['bg_spec']]
 
         return self._marks
 
@@ -397,7 +416,7 @@ def _interaction_in_bg_step(self, event={}):
         except Exception:
             # NOTE: ignore error, but will be raised when clicking ANY of the export buttons
             for mark in ['trace', 'bg1_center', 'bg1_lower', 'bg1_upper',
-                         'bg2_center', 'bg2_lower', 'bg2_upper']:
+                         'bg2_center', 'bg2_lower', 'bg2_upper', 'bg_spec']:
                 self.marks[mark].clear()
         else:
             xs = range(len(trace.trace))
@@ -430,6 +449,13 @@ def _interaction_in_bg_step(self, event={}):
                 for mark in ['bg2_center', 'bg2_lower', 'bg2_upper']:
                     self.marks[mark].clear()
 
+        try:
+            spec = self.export_bg_spectrum()
+        except Exception:
+            self.marks['bg_spec'].clear()
+        else:
+            self.marks['bg_spec'].update_xy(spec.spectral_axis, spec.flux)
+
         self.active_step = 'bg'
         self._update_plugin_marks()
 
@@ -664,6 +690,28 @@ def vue_create_bg_img(self, *args):
                                 color='error', sender=self)
             )
 
+    def export_bg_spectrum(self, add_data=False, **kwargs):
+        """
+        Create a background 1D spectrum from the input parameters defined in the plugin.
+
+        Parameters
+        ----------
+        add_data : bool
+            Whether to add the resulting spectrum to the application, according to the options
+            defined in the plugin.
+        """
+        bg = self.export_bg(**kwargs)
+        spec = bg.bkg_spectrum()
+
+        if add_data:
+            # TODO: implement new add_results
+            self.bg_spec_add_results.add_results_from_plugin(spec, replace=False)
+
+        return spec
+
+    def vue_create_bg_spec(self, *args):
+        self.export_bg_spectrum(add_data=True)
+
     def export_bg_sub(self, add_data=False, **kwargs):
         """
         Create a background-subtracted 2D spectrum from the input parameters defined in the plugin.

jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.vue

@@ -227,7 +227,7 @@
         <v-expansion-panels popout>
           <v-expansion-panel>
             <v-expansion-panel-header v-slot="{ open }">
-              <span style="padding: 6px">Export Background</span>
+              <span style="padding: 6px">Export Background Image</span>
             </v-expansion-panel-header>
             <v-expansion-panel-content>
               <plugin-add-results
@@ -251,7 +251,31 @@
         <v-expansion-panels popout>
           <v-expansion-panel>
             <v-expansion-panel-header v-slot="{ open }">
-              <span style="padding: 6px">Export Subtracted</span>
+              <span style="padding: 6px">Export Background Spectrum</span>
+            </v-expansion-panel-header>
+            <v-expansion-panel-content>
+              <plugin-add-results
+                :label.sync="bg_spec_results_label"
+                :label_default="bg_spec_results_label_default"
+                :label_auto.sync="bg_spec_results_label_auto"
+                :label_invalid_msg="bg_spec_results_label_invalid_msg"
+                :label_overwrite="bg_spec_results_label_overwrite"
+                label_hint="Label for the background spectrum"
+                :add_to_viewer_items="bg_spec_add_to_viewer_items"
+                :add_to_viewer_selected.sync="bg_spec_add_to_viewer_selected"
+                action_label="Export"
+                action_tooltip="Create Background Spectrum"
+                @click:action="create_bg_spec"
+              ></plugin-add-results>
+            </v-expansion-panel-content>
+          </v-expansion-panel>
+        </v-expansion-panels>
+      </v-row>
+      <v-row>
+        <v-expansion-panels popout>
+          <v-expansion-panel>
+            <v-expansion-panel-header v-slot="{ open }">
+              <span style="padding: 6px">Export Background-Subtracted Image</span>
             </v-expansion-panel-header>
             <v-expansion-panel-content>
               <plugin-add-results

jdaviz/configs/specviz2d/plugins/spectral_extraction/tests/test_spectral_extraction.py

@@ -97,6 +97,8 @@ def test_plugin(specviz2d_helper):
     assert pext.bg_width == 4
     bg_img = pext.export_bg_img()
     assert isinstance(bg_img, Spectrum1D)
+    bg_spec = pext.export_bg_spectrum()
+    assert isinstance(bg_spec, Spectrum1D)
     bg_sub = pext.export_bg_sub()
     assert isinstance(bg_sub, Spectrum1D)