Moment map continuum subtraction

CHANGES.rst

@@ -10,6 +10,7 @@ Cubeviz
 
 - Added functionality to Collapse and Spectral Extraction plugins to save results to FITS file. [#2586]
 
+- Moment map plugin now supports linear per-spaxel continuum subtraction. [#2587]
 
 Imviz
 ^^^^^
@@ -26,6 +27,9 @@ Specviz2d
 API Changes
 -----------
 
+- ``width`` argument in Line Analysis plugin is renamed to ``continuum_width`` and ``width``
+  will be removed in a future release. [#2587]
+
 Cubeviz
 ^^^^^^^
 

jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py

@@ -17,6 +17,8 @@
                                         SpectralSubsetSelectMixin,
                                         AddResultsMixin,
                                         SelectPluginComponent,
+                                        SpectralContinuumMixin,
+                                        skip_if_no_updates_since_last_active,
                                         with_spinner)
 from jdaviz.core.user_api import PluginUserApi
 
@@ -30,7 +32,7 @@
 @tray_registry('cubeviz-moment-maps', label="Moment Maps",
                viewer_requirements=['spectrum', 'image'])
 class MomentMap(PluginTemplateMixin, DatasetSelectMixin, SpectralSubsetSelectMixin,
-                AddResultsMixin):
+                SpectralContinuumMixin, AddResultsMixin):
     """
     See the :ref:`Moment Maps Plugin Documentation <moment-maps>` for more details.
 
@@ -44,6 +46,14 @@ class MomentMap(PluginTemplateMixin, DatasetSelectMixin, SpectralSubsetSelectMix
       Dataset to use for computing line statistics.
     * ``spectral_subset`` (:class:`~jdaviz.core.template_mixin.SubsetSelect`):
       Subset to use for the line, or ``Entire Spectrum``.
+    * ``continuum`` (:class:`~jdaviz.core.template_mixin.SubsetSelect`):
+      Subset to use for the continuum, or ``None`` to skip continuum subtraction,
+      or ``Surrounding`` to use a region surrounding the
+      subset set in ``spectral_subset``.
+    * ``continuum_width``:
+      Width, relative to the overall line spectral region, to fit the linear continuum
+      (excluding the region containing the line). If 1, will use endpoints within line region
+      only.
     * ``n_moment``
     * ``output_unit``
       Choice of "Wavelength" or "Velocity", applicable for n_moment >= 1.
@@ -53,6 +63,7 @@ class MomentMap(PluginTemplateMixin, DatasetSelectMixin, SpectralSubsetSelectMix
     * :meth:`calculate_moment`
     """
     template_file = __file__, "moment_maps.vue"
+    uses_active_status = Bool(True).tag(sync=True)
 
     n_moment = IntHandleEmpty(0).tag(sync=True)
     filename = Unicode().tag(sync=True)
@@ -88,20 +99,32 @@ def __init__(self, *args, **kwargs):
 
     @property
     def _default_image_viewer_reference_name(self):
-        return self.jdaviz_helper._default_image_viewer_reference_name
+        return getattr(
+            self.app._jdaviz_helper, '_default_spectrum_viewer_reference_name', 'flux-viewer'
+        )
 
     @property
     def _default_spectrum_viewer_reference_name(self):
-        return self.jdaviz_helper._default_spectrum_viewer_reference_name
+        return getattr(
+            self.app._jdaviz_helper, '_default_spectrum_viewer_reference_name', 'spectrum-viewer'
+        )
 
     @property
     def user_api(self):
         # NOTE: leaving save_as_fits out for now - we may want a more general API to do that
         # accross all plugins at some point
-        return PluginUserApi(self, expose=('dataset', 'spectral_subset', 'n_moment',
+        return PluginUserApi(self, expose=('dataset', 'spectral_subset',
+                                           'continuum', 'continuum_width',
+                                           'n_moment',
                                            'output_unit', 'reference_wavelength',
                                            'add_results', 'calculate_moment'))
 
+    @observe('is_active')
+    def _is_active_changed(self, msg):
+        for pos, mark in self.continuum_marks.items():
+            mark.visible = self.is_active
+        self._calculate_continuum(msg)
+
     @observe("dataset_selected", "dataset_items", "n_moment")
     def _set_default_results_label(self, event={}):
         label_comps = []
@@ -120,6 +143,21 @@ def _set_data_units(self, event={}):
             else:
                 self.dataset_spectral_unit = ""
 
+    @observe("dataset_selected", "spectral_subset_selected",
+             "continuum_subset_selected", "continuum_width")
+    @skip_if_no_updates_since_last_active()
+    def _calculate_continuum(self, msg=None):
+        if not hasattr(self, 'dataset') or self.app._jdaviz_helper is None:  # noqa
+            # during initial init, this can trigger before the component is initialized
+            return
+
+        # NOTE: there is no use in caching this, as the continuum will need to be re-computed
+        # per-spaxel to use within calculating the moment map
+        _ = self._get_continuum(self.dataset,
+                                None,
+                                self.spectral_subset,
+                                update_marks=True)
+
     @with_spinner()
     def calculate_moment(self, add_data=True):
         """
@@ -130,12 +168,19 @@ def calculate_moment(self, add_data=True):
         add_data : bool
             Whether to add the resulting data object to the app according to ``add_results``.
         """
-        # Retrieve the data cube and slice out desired region, if specified
-        if "_orig_spec" in self.dataset.selected_obj.meta:
-            cube = self.dataset.selected_obj.meta["_orig_spec"]
+        if self.continuum.selected == 'None':
+            if "_orig_spec" in self.dataset.selected_obj.meta:
+                cube = self.dataset.selected_obj.meta["_orig_spec"]
+            else:
+                cube = self.dataset.selected_obj
         else:
-            cube = self.dataset.selected_obj
+            _, _, cube = self._get_continuum(self.dataset,
+                                             'per-pixel',
+                                             self.spectral_subset,
+                                             update_marks=False)
 
+        # slice out desired region
+        # TODO: should we add a warning for a composite spectral subset?
         spec_min, spec_max = self.spectral_subset.selected_min_max(cube)
         slab = manipulation.spectral_slab(cube, spec_min, spec_max)
 

jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.vue

@@ -2,8 +2,16 @@
   <j-tray-plugin
     description='Create a 2D image from a data cube.'
     :link="docs_link || 'https://jdaviz.readthedocs.io/en/'+vdocs+'/'+config+'/plugins.html#moment-maps'"
+    :uses_active_status="uses_active_status"
+    @plugin-ping="plugin_ping($event)"
+    :keep_active.sync="keep_active"
     :popout_button="popout_button">
 
+    <j-plugin-section-header>Cube</j-plugin-section-header>
+    <v-row>
+      <j-docs-link>Choose the input cube and spectral subset.</j-docs-link>
+    </v-row>
+
     <plugin-dataset-select
       :items="dataset_items"
       :selected.sync="dataset_selected"
@@ -22,6 +30,50 @@
       hint="Spectral region to compute the moment map."
     />
 
+    <j-plugin-section-header>Continuum Subtraction</j-plugin-section-header>
+    <v-row>
+      <j-docs-link v-if="continuum_subset_selected==='None'">
+        Choose whether and how to compute the continuum for continuum subtraction.
+      </j-docs-link>
+      <j-docs-link v-else>
+        {{continuum_subset_selected=='Surrounding' && spectral_subset_selected=='Entire Spectrum' ? "Since using the entire spectrum, the end points will be used to fit a linear continuum." : "Choose a region to fit a linear line as the underlying continuum."}}  
+        {{continuum_subset_selected=='Surrounding' && spectral_subset_selected!='Entire Spectrum' ? "Choose a width in number of data points to consider on each side of the line region defined above." : null}}
+        When this plugin is opened, a visual indicator will show on the spectrum plot showing the continuum fitted as a thick line, and interpolated into the line region as a thin line.
+        When computing the moment map, these same input options will be used to compute and subtract a linear continuum for each spaxel, independently.
+      </j-docs-link>
+    </v-row>
+
+    <plugin-subset-select 
+      :items="continuum_subset_items"
+      :selected.sync="continuum_subset_selected"
+      :show_if_single_entry="true"
+      :rules="[() => continuum_subset_selected!==spectral_subset_selected || 'Must not match line selection.']"
+      label="Continuum"
+      hint="Select spectral region that defines the continuum."
+    />
+
+    <v-row v-if="continuum_subset_selected=='Surrounding' && spectral_subset_selected!='Entire Spectrum'">
+      <!-- DEV NOTE: if changing the validation rules below, also update the logic to clear the results
+           in line_analysis.py  -->
+      <v-text-field
+        label="Width"
+        type="number"
+        v-model.number="continuum_width"
+        step="0.1"
+        :rules="[() => continuum_width!=='' || 'This field is required.',
+                 () => continuum_width<=10 || 'Width must be <= 10.',
+                 () => continuum_width>=1 || 'Width must be >= 1.']"
+        hint="Width, relative to the overall line spectral region, to fit the linear continuum (excluding the region containing the line).  If 1, will use endpoints within line region only."
+        persistent-hint
+      >
+      </v-text-field>
+    </v-row>
+
+    <j-plugin-section-header>Moment</j-plugin-section-header>
+    <v-row>
+      <j-docs-link>Options for generating the moment map.</j-docs-link>
+    </v-row>
+
     <v-row>
       <v-text-field
         ref="n_moment"

jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py

@@ -12,6 +12,30 @@
 from jdaviz.configs.cubeviz.plugins.moment_maps.moment_maps import MomentMap
 
 
+def test_user_api(cubeviz_helper, spectrum1d_cube):
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", message="No observer defined on WCS.*")
+        cubeviz_helper.load_data(spectrum1d_cube, data_label='test')
+
+    mm = cubeviz_helper.plugins['Moment Maps']
+    assert not mm._obj.continuum_marks['center'].visible
+    with mm.as_active():
+        assert mm._obj.continuum_marks['center'].visible
+        mm.n_moment = 0
+        # no continuum so marks should be empty
+        assert len(mm._obj.continuum_marks['center'].x) == 0
+
+        mom = mm.calculate_moment()
+
+        mm.continuum = 'Surrounding'
+        mm.continuum_width = 10
+        assert len(mm._obj.continuum_marks['center'].x) > 0
+
+        mom_sub = mm.calculate_moment()
+
+        assert mom != mom_sub
+
+
 def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmpdir):
     dc = cubeviz_helper.app.data_collection
     with warnings.catch_warnings():