Add methods for querying NASA Exoplanet Archive for ephemeris

CHANGES.rst

@@ -3,6 +3,8 @@
 
 * Prevent duplicate sub-intervals (quarter/sector/campaign) in data labels. [#120]
 
+* Add feature to query the NASA Exoplanet Archive for exoplanet ephemerides. [#127]
+
 0.4.3 (unreleased)
 ------------------
 

lcviz/conftest.py

@@ -37,8 +37,15 @@ def light_curve_like_kepler_quarter(seed=42):
     )
     lc['flux_alt'] = flux + 1
     lc['flux_alt_err'] = flux_err
-    lc.meta['MISSION'] = 'KEPLER'
-    lc.meta['QUARTER'] = 10
+    lc.meta.update(
+        {
+            'MISSION': 'KEPLER',
+            'QUARTER': 10,
+            'OBJECT': 'HAT-P-11',
+            'RA': 297.7101763,
+            'DEC': 48.0818635,
+        }
+    )
 
     return lc
 

lcviz/plugins/ephemeris/ephemeris.py

@@ -1,5 +1,9 @@
 import numpy as np
+from astropy.coordinates import SkyCoord
 from astropy.time import Time
+import astropy.units as u
+from astroquery.ipac.nexsci.nasa_exoplanet_archive import NasaExoplanetArchive
+
 from traitlets import Bool, Float, List, Unicode, observe
 
 from glue.core.link_helpers import LinkSame
@@ -8,8 +12,10 @@
 from jdaviz.core.events import (NewViewerMessage, ViewerAddedMessage, ViewerRemovedMessage)
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import (PluginTemplateMixin, DatasetSelectMixin,
-                                        SelectPluginComponent, EditableSelectPluginComponent)
+                                        SelectPluginComponent, EditableSelectPluginComponent,
+                                        with_spinner)
 from jdaviz.core.user_api import PluginUserApi
+from jdaviz.core.events import SnackbarMessage
 
 from lightkurve import periodogram, FoldedLightCurve
 
@@ -24,6 +30,8 @@
 _default_dpdt = 0.0
 _default_wrap_at = 1.0
 
+_default_query_radius = 2  # [arcsec]
+
 
 @tray_registry('ephemeris', label="Ephemeris")
 class Ephemeris(PluginTemplateMixin, DatasetSelectMixin):
@@ -87,13 +95,26 @@
 
     period_at_max_power = Float().tag(sync=True)
 
+    # QUERIES
+    query_name = Unicode().tag(sync=True)
+    query_ra = FloatHandleEmpty().tag(sync=True)
+    query_dec = FloatHandleEmpty().tag(sync=True)
+    query_radius = FloatHandleEmpty(_default_query_radius).tag(sync=True)
+    query_result_items = List().tag(sync=True)
+    query_result_selected = Unicode().tag(sync=True)
+    ra_dec_step = Float(0.01).tag(sync=True)
+    period_from_catalog = FloatHandleEmpty().tag(sync=True)
+    t0_from_catalog = FloatHandleEmpty().tag(sync=True)
+    query_spinner = Bool().tag(sync=True)
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         self._default_initialized = False
         self._ignore_ephem_change = False
         self._ephemerides = {}
         self._prev_wrap_at = _default_wrap_at
+        self._nasa_exoplanet_archive = None
 
         self.dataset.add_filter(is_not_tpf)
 
@@ -117,6 +138,10 @@
                                             selected='method_selected',
                                             manual_options=['Lomb-Scargle', 'Box Least Squares'])
 
+        self.query_result = SelectPluginComponent(self,
+                                                  items='query_result_items',
+                                                  selected='query_result_selected')
+
         # TODO: could optimize by only updating for the new data entry only
         # (would require some refactoring and probably wouldn't have significant gains)
         self.hub.subscribe(self, DataCollectionAddMessage, handler=self._update_all_phase_arrays)
@@ -125,12 +150,16 @@
 
     @property
     def user_api(self):
-        expose = ['component', 'period', 'dpdt', 't0', 'wrap_at',
-                  'ephemeris', 'ephemerides',
-                  'update_ephemeris', 'create_phase_viewer',
-                  'add_component', 'remove_component', 'rename_component',
-                  'times_to_phases', 'phases_to_times', 'get_data',
-                  'dataset', 'method', 'period_at_max_power', 'adopt_period_at_max_power']
+        expose = [
+            'component', 'period', 'dpdt', 't0', 'wrap_at',
+            'ephemeris', 'ephemerides',
+            'update_ephemeris', 'create_phase_viewer',
+            'add_component', 'remove_component', 'rename_component',
+            'times_to_phases', 'phases_to_times', 'get_data',
+            'dataset', 'method', 'period_at_max_power',
+            'adopt_period_at_max_power', 'query_for_ephemeris',
+            'query_result', 'adopt_from_catalog', 'adopt_from_catalog_in_new_viewer'
+        ]
         return PluginUserApi(self, expose=expose)
 
     def _phase_comp_lbl(self, component=None):
@@ -578,3 +607,109 @@
         phlc.sort("time")
 
         return phlc
+
+    @property
+    def nasa_exoplanet_archive(self):
+        if self._nasa_exoplanet_archive is None:
+            self._nasa_exoplanet_archive = NasaExoplanetArchive()
+
+        return self._nasa_exoplanet_archive
+
+    @observe('dataset_selected')
+    def _query_params_from_metadata(self, *args):
+        self.query_name = self.dataset.selected_obj.meta.get('OBJECT', '')
+        self.query_ra = self.dataset.selected_obj.meta.get('RA')
+        self.query_dec = self.dataset.selected_obj.meta.get('DEC')
+
+    def query_for_ephemeris(self):
+        query_result = None
+
+        if self.query_name:
+            # first query by object name:
+            query_result = self.nasa_exoplanet_archive.query_object(
+                object_name=self.query_name,
+                table='pscomppars'
+            )
+
+        if (
+            (query_result is None or len(query_result) == 0) and
+            (None not in (self.query_ra, self.query_dec))
+        ):
+            # next query by coordinates:
+            coord = SkyCoord(ra=self.query_ra, dec=self.query_dec, unit=u.deg)
+            query_result = self.nasa_exoplanet_archive.query_region(
+                table='pscomppars',
+                coordinates=coord,
+                radius=self.query_radius * u.arcsec,
+            )
+
+        if query_result is None or len(query_result) == 0:
+            # no metadata found for RA, Dec, or object name
+            return None
+
+        else:
+            query_result.sort('pl_name')
+            self.astroquery_result = query_result
+            self.astroquery_result.add_index('pl_name')
+            self.query_result_items = [
+                {
+                    'label': name,  # required key for SelectPluginComponent
+                    'period': period,
+                    'epoch': epoch if not np.isnan(epoch) else 0
+                }
+                for name, period, epoch in zip(
+                    list(self.astroquery_result['pl_name']),
+                    np.array(self.astroquery_result['pl_orbper'].to_value(u.day)),
+                    np.array(self.astroquery_result['pl_tranmid'].to_value(u.day))
+                )
+            ]
+
+    @observe('query_result_selected')
+    def _select_query_result(self, *args):
+        selected_query_result = self.astroquery_result.loc[self.query_result_selected]
+        self.period_from_catalog = selected_query_result['pl_orbper'].base.to_value(u.day)
+        ref_time = self.app.data_collection[0].coords.reference_time.jd
+        if np.isnan(selected_query_result['pl_tranmid'].base.to_value(u.day)):
+            self.t0_from_catalog = 0
+        else:
+            self.t0_from_catalog = (
+                selected_query_result['pl_tranmid'].base.to_value(u.day) - ref_time
+            ) % self.period_from_catalog
+
+    @with_spinner('query_spinner')
+    def vue_query_for_ephemeris(self, *args):
+        self.query_for_ephemeris()
+
+    def adopt_from_catalog(self, *args):
+        if len(self._get_phase_viewers()):
+            # if a phase viewer is available, adopt the ephemeris in the phase viewer:
+            if not np.any(np.isnan([self.period_from_catalog, self.t0_from_catalog])):
+                self.period = self.period_from_catalog
+                self.t0 = self.t0_from_catalog
+
+                # reset the phase axis wrap to feature the primary transit:
+                self.wrap_at = 0.5
+                viewer = self._get_phase_viewers()[0]
+                viewer.reset_limits()
+        else:
+            # otherwise, adopt the ephemeris in a new phase viewer:
+            self.adopt_from_catalog_in_new_viewer()
+
+    def adopt_from_catalog_in_new_viewer(self, *args):
+        new_component_label = self.query_result_selected.replace(' ', '')
+        if new_component_label in self.component.choices:
+            # warn the user that an ephemeris component already exists with this label,
+            # a second won't be added:
+            self.hub.broadcast(
+                SnackbarMessage(
+                    f"Ephemeris component {new_component_label} already exists, skipping.",
+                    sender=self, color="warning"
+                )
+            )
+        else:
+            self.add_component(new_component_label)
+            self.create_phase_viewer()
+            self.adopt_from_catalog()
+
+    def vue_adopt_from_catalog_in_new_viewer(self, *args):
+        self.adopt_from_catalog_in_new_viewer()

lcviz/plugins/ephemeris/ephemeris.vue

@@ -67,7 +67,6 @@
           label="Period derivative"
           v-model.number="dpdt"
           :step="dpdt_step"
-          type="number"
           hint="The first time-derivative of the period of the ephemeris."
           persistent-hint
           :rules="[() => dpdt!=='' || 'This field is required']"
@@ -81,7 +80,6 @@
           label="Wrapping phase"
           v-model.number="wrap_at"
           :step="0.1"
-          type="number"
           :hint="'Phased data will encompass the range '+wrap_at_range+'.'"
           persistent-hint
           :rules="[() => wrap_at!=='' || 'This field is required']"
@@ -110,8 +108,6 @@
         ></v-select>
       </v-row>
 
-
-
       <div style="display: grid"> <!-- overlay container -->
         <div style="grid-area: 1/1">
 
@@ -120,7 +116,7 @@
           </v-row>
           <v-row v-else>
             <j-tooltip :tooltipcontent="'adopt period into '+component_selected+' ephemeris.'">
-              <v-btn text color='primary '@click='adopt_period_at_max_power' style="padding: 0px">
+              <v-btn text color='primary' @click='adopt_period_at_max_power' style="padding: 0px">
                 period: {{period_at_max_power}}
               </v-btn>
             </j-tooltip>
@@ -144,7 +140,120 @@
         </div>
       </div>
 
+      <j-plugin-section-header>Query NASA Exoplanet Archive</j-plugin-section-header>
+      <v-row>
+        <span class="v-messages v-messages__message text--secondary">
+          Query the
+          <a href="https://exoplanetarchive.ipac.caltech.edu/docs/pscp_about.html" target="_blank">
+          Planetary Systems Composite Data</a> table from
+          <a href="https://exoplanetarchive.ipac.caltech.edu/" target="_blank">
+          NASA Exoplanet Archive</a>. Queries first by name, then falls back on
+          coordinates if the object name is not recognized.
+        </span>
+      </v-row>
 
+      <v-row>
+        <v-text-field
+          ref="query_name"
+          type="string"
+          label="Object name"
+          v-model.number="query_name"
+          hint="Object name."
+          persistent-hint
+        ></v-text-field>
+      </v-row>
+      <v-row>
+        <v-text-field
+          ref="query_ra"
+          type="number"
+          label="RA (degrees)"
+          v-model.number="query_ra"
+          :step="ra_dec_step"
+          hint="Object right ascension."
+          persistent-hint
+        ></v-text-field>
+      </v-row>
+      <v-row>
+        <v-text-field
+          ref="query_dec"
+          type="number"
+          label="Dec (degrees)"
+          v-model.number="query_dec"
+          :step="ra_dec_step"
+          hint="Object declination."
+          persistent-hint
+        ></v-text-field>
+      </v-row>
+      <v-row>
+        <v-text-field
+          ref="query_radius"
+          type="number"
+          label="Radius (arcseconds)"
+          v-model.number="query_radius"
+          :step="1"
+          hint="Radius around the query coordinate."
+          persistent-hint
+        ></v-text-field>
+      </v-row>
+
+      <v-row justify="end">
+        <j-tooltip tooltipcontent="Query for this object.">
+          <plugin-action-button
+            :spinner="query_spinner"
+            :results_isolated_to_plugin="false"
+            @click="query_for_ephemeris">
+              Query
+          </plugin-action-button>
+        </j-tooltip>
+      </v-row>
+      <div v-if="query_result_items.length > 0">
+        <v-row>
+          <v-select
+            :menu-props="{ left: true }"
+            attach
+            :items="query_result_items"
+            :item-value="item => item.label"
+            v-model="query_result_selected"
+            label="Ephemerides available"
+            :hint="'Ephemeris parameters from ' + query_result_items.length + ' available query result(s)'"
+            persistent-hint
+            dense
+          >
+
+          <template v-slot:selection="{ item }">
+            <span>
+              {{ item.label }}
+            </span>
+          </template>
+          <template v-slot:item="{ item }">
+            <span style="margin-top: 8px; margin-bottom: 0px">
+                {{ item.label }}
+              <v-row style="line-height: 1.0; margin: 0px; opacity: 0.85; font-size: 8pt">
+                Period: {{ item.period }} d, Epoch: {{ item.epoch }} d
+              </v-row>
+            </span>
+          </template>
+
+          </v-select>
+        </v-row>
+
+        <v-row v-if="query_result_selected !== ''">
+          <span class="v-messages v-messages__message text--secondary">
+            Period: {{period_from_catalog}} d, Epoch: {{t0_from_catalog}} d
+          </span>
+          <j-tooltip :tooltipcontent="'Adopt period and epoch into '+component_selected+' ephemeris.'">
+            <v-row justify="end">
+            <v-col>
+              <plugin-action-button
+                @click="adopt_from_catalog_in_new_viewer"
+                :disabled="component_items.map(item => item.label).includes(query_result_selected.replace(/\s/g, ''))">
+                  Create new component
+              </plugin-action-button>
+            </v-col>
+            </v-row>
+          </j-tooltip>
+        </v-row>
+      </div>
     </div>
 
   </j-tray-plugin>

lcviz/tests/test_parser.py

@@ -124,7 +124,8 @@ def test_apply_yrangerois(helper, light_curve_like_kepler_quarter):
 def test_data_label(helper, light_curve_like_kepler_quarter):
     # add data without specifying data label:
     helper.load_data(light_curve_like_kepler_quarter)
-    assert helper.app.data_collection[-1].label == 'Light curve [Q10]'
+    object_name = helper.app.data_collection[-1].meta['OBJECT']
+    assert helper.app.data_collection[-1].label == f'{object_name} [Q10]'
 
     # specify label, check that quarter isn't appended:
     data_label = 'Cool target'