loading line lists at redshifted wavelength (spacetelescope#2726)

* updating lines so they receive redshift if redshift applied prior to new line being added to viewer

* test: cut/simplied logic and excess data, allclose for asserts; viewer: more readable if; line_list: cut conditional logic of redshift

* added change log

* change log text altered

CHANGES.rst

@@ -122,6 +122,8 @@ Other Changes and Additions
 Bug Fixes
 ---------
 
+- Fix redshifted line lists that were displaying at rest wavelengths, by assuming a global redshift. [#2726]
+
 Cubeviz
 ^^^^^^^
 

jdaviz/configs/default/plugins/line_lists/line_list_mixin.py

@@ -42,17 +42,17 @@ def erase_spectral_lines(self, name=None):
             self._default_spectrum_viewer_reference_name
         ).erase_spectral_lines(name=name)
 
-    def plot_spectral_line(self, line):
+    def plot_spectral_line(self, line, global_redshift=None):
         """Convenience function to get to the viewer function"""
         self.app.get_viewer(
             self._default_spectrum_viewer_reference_name
-        ).plot_spectral_line(line)
+        ).plot_spectral_line(line, global_redshift)
 
-    def plot_spectral_lines(self):
+    def plot_spectral_lines(self, global_redshift=None):
         """Convenience function to get to the viewer function"""
         self.app.get_viewer(
             self._default_spectrum_viewer_reference_name
-        ).plot_spectral_lines()
+        ).plot_spectral_lines(global_redshift)
 
     @property
     def spectral_lines(self):

jdaviz/configs/default/plugins/line_lists/line_lists.py

@@ -524,7 +524,7 @@ def _list_from_notebook(self, msg):
         self.send_state('loaded_lists')
         self.send_state('list_contents')
 
-        self._viewer.plot_spectral_lines(tmp_names_rest)
+        self._viewer.plot_spectral_lines(tmp_names_rest, global_redshift=self._global_redshift)
         self.update_line_mark_dict()
 
         msg_text = ("Spectral lines loaded from notebook. Lines can be hidden"
@@ -664,7 +664,7 @@ def vue_show_all_in_list(self, listname):
         self.list_contents = lc
         self.send_state('list_contents')
 
-        self._viewer.plot_spectral_lines()
+        self._viewer.plot_spectral_lines(global_redshift=self._global_redshift)
         self.update_line_mark_dict()
 
     def vue_hide_all_in_list(self, listname):
@@ -697,7 +697,7 @@ def vue_plot_all_lines(self, event):
 
         self.send_state('list_contents')
 
-        self._viewer.plot_spectral_lines()
+        self._viewer.plot_spectral_lines(global_redshift=self._global_redshift)
         self.update_line_mark_dict()
 
     def vue_erase_all_lines(self, event):
@@ -735,7 +735,7 @@ def vue_change_visible(self, data):
         self.list_contents = list_contents
 
         if show:
-            self._viewer.plot_spectral_line(name_rest)
+            self._viewer.plot_spectral_line(name_rest, global_redshift=self._global_redshift)
         else:
             self._viewer.erase_spectral_lines(name_rest=name_rest)
 

jdaviz/configs/default/plugins/line_lists/tests/test_line_lists.py

@@ -6,6 +6,7 @@
 from astropy.table import QTable
 from specutils import Spectrum1D
 
+from jdaviz.core.marks import SpectralLine
 from jdaviz.core.linelists import get_available_linelists
 
 
@@ -123,8 +124,7 @@ def test_load_available_preset_lists(specviz_helper, spectrum1d):
 
 
 def test_line_identify(specviz_helper, spectrum1d):
-    label = "Test 1D Spectrum"
-    specviz_helper.load_data(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d)
 
     lt = QTable()
     lt['linename'] = ['O III', 'Halpha']
@@ -141,3 +141,52 @@ def test_line_identify(specviz_helper, spectrum1d):
     ll_plugin.vue_change_visible(('Test List', line, 0))
     assert line.get('show') is False
     assert line.get('identify', False) is False
+
+
+def test_global_redshift_applied(specviz_helper, spectrum1d):
+    specviz_helper.load_data(spectrum1d)
+
+    # Create a table with redshift included
+    lt = QTable({'linename': ['O III', 'Halpha'],
+                 'rest': [5007, 6563] * u.AA,
+                 'redshift': u.Quantity([0, 0])})
+
+    with pytest.warns(UserWarning, match='per line/list redshifts not supported, use viz.set_redshift'):  # noqa
+        specviz_helper.load_line_list(lt)
+
+    # Load a line, and apply redshift globally
+    specviz_helper.plot_spectral_line("Halpha")
+    specviz_helper.set_redshift(0.01)
+    # Load second line, redshift should also be applied to it
+    specviz_helper.plot_spectral_line("O III")
+
+    viewer_lines = [mark for mark in specviz_helper.app.get_viewer(
+        specviz_helper._default_spectrum_viewer_reference_name).figure.marks
+        if isinstance(mark, SpectralLine)]
+
+    assert np.allclose([line.redshift for line in viewer_lines], 0.01)
+
+
+def test_global_redshift_applied_to_all(specviz_helper, spectrum1d):
+    specviz_helper.load_data(spectrum1d)
+
+    # Create a table with redshift included
+    lt = QTable({'linename': ['O III', 'Halpha', 'O I'],
+                 'rest': [5007, 6563, 6300] * u.AA,
+                 'redshift': u.Quantity([0, 0, 0])})
+
+    with pytest.warns(UserWarning, match='per line/list redshifts not supported, use viz.set_redshift'):  # noqa
+        specviz_helper.load_line_list(lt)
+
+    # Load a line, so we can apply redshift
+    specviz_helper.plot_spectral_line("Halpha")
+    global_redshift = 0.01
+    specviz_helper.set_redshift(global_redshift)
+    # Load remaining lines
+    specviz_helper.plot_spectral_lines(global_redshift)
+
+    viewer_lines = [mark for mark in specviz_helper.app.get_viewer(
+        specviz_helper._default_spectrum_viewer_reference_name).figure.marks
+        if isinstance(mark, SpectralLine)]
+
+    assert np.allclose([line.redshift for line in viewer_lines], 0.01)

jdaviz/configs/specviz/plugins/viewers.py

@@ -261,7 +261,7 @@ def get_scales(self):
             self.toolbar.active_tool = None
         return {'x': fig.interaction.x_scale, 'y': fig.interaction.y_scale}
 
-    def plot_spectral_line(self, line, plot_units=None, **kwargs):
+    def plot_spectral_line(self, line, global_redshift=None, plot_units=None, **kwargs):
         if isinstance(line, str):
             # Try the full index first (for backend calls), otherwise name only
             try:
@@ -271,9 +271,14 @@ def plot_spectral_line(self, line, plot_units=None, **kwargs):
         if plot_units is None:
             plot_units = self.data()[0].spectral_axis.unit
 
+        if global_redshift is None:
+            redshift = self.redshift
+        else:
+            redshift = global_redshift
+
         line_mark = SpectralLine(self,
                                  line['rest'].to_value(plot_units),
-                                 self.redshift,
+                                 redshift,
                                  name=line["linename"],
                                  table_index=line["name_rest"],
                                  colors=[line["colors"]], **kwargs)
@@ -285,7 +290,7 @@ def plot_spectral_line(self, line, plot_units=None, **kwargs):
         line["show"] = True
         self._broadcast_plotted_lines()
 
-    def plot_spectral_lines(self, colors=["blue"], **kwargs):
+    def plot_spectral_lines(self, colors=["blue"], global_redshift=None, **kwargs):
         """
         Plots a user-provided astropy table of spectral lines in the viewer.
         """
@@ -301,13 +306,18 @@ def plot_spectral_lines(self, colors=["blue"], **kwargs):
         lines = self.spectral_lines
         plot_units = self.data()[0].spectral_axis.unit
 
+        if global_redshift is None:
+            redshift = self.redshift
+        else:
+            redshift = global_redshift
+
         marks = []
         for line, color in zip(lines, colors):
             if not line["show"]:
                 continue
             line = SpectralLine(self,
                                 line['rest'].to_value(plot_units),
-                                redshift=self.redshift,
+                                redshift,
                                 name=line["linename"],
                                 table_index=line["name_rest"],
                                 colors=[color], **kwargs)