Generalize units in slice plugin

CHANGES.rst

@@ -60,6 +60,9 @@ Cubeviz
 - ``spatial_subset`` in the spectral extraction plugin is now renamed to ``aperture`` and the deprecated name will
   be removed in a future release. [#2664]
 
+- Slice plugin's ``wavelength``, ``wavelength_unit``, and ``show_wavelength`` are deprecated in favor
+  of ``value``, ``value_unit``, and ``show_value``, respectively. [#2706]
+
 Imviz
 ^^^^^
 

jdaviz/configs/cubeviz/helper.py

@@ -104,14 +104,8 @@ def select_wavelength(self, wavelength):
         """
         if not isinstance(wavelength, (int, float)):
             raise TypeError("wavelength must be a float or int")
-        # Retrieve the x slices from the spectrum viewer's marks
-        sv = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
-        x_all = sv.native_marks[0].x
-        if sv.state.layers[0].as_steps:
-            # then the marks have been doubled in length (each point duplicated)
-            x_all = x_all[::2]
-        index = np.argmin(abs(x_all - wavelength))
-        return self.select_slice(int(index))
+        msg = SliceSelectSliceMessage(value=wavelength, sender=self)
+        self.app.hub.broadcast(msg)
 
     @property
     def specviz(self):

jdaviz/configs/cubeviz/plugins/slice/slice.py

@@ -5,13 +5,14 @@
 import numpy as np
 import astropy.units as u
 from astropy.units import UnitsWarning
+from astropy.utils.decorators import deprecated
 from glue_jupyter.bqplot.image import BqplotImageView
 from glue_jupyter.bqplot.profile import BqplotProfileView
-from traitlets import Bool, observe, Any, Int
+from traitlets import Any, Bool, Int, Unicode, observe
 from specutils.spectra.spectrum1d import Spectrum1D
 
 from jdaviz.core.events import (AddDataMessage, SliceToolStateMessage,
-                                SliceSelectSliceMessage, SliceWavelengthUpdatedMessage,
+                                SliceSelectSliceMessage, SliceValueUpdatedMessage,
                                 GlobalDisplayUnitChanged)
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import PluginTemplateMixin
@@ -33,24 +34,26 @@
     * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.close_in_tray`
     * ``slice``
       Current slice number.
-    * ``wavelength``
-      Wavelength of the current slice.  When setting this directly, it will update automatically to
-      the wavelength corresponding to the nearest slice.
+    * ``value``
+      Value (wavelength or frequency) of the current slice.  When setting this directly, it will
+      update automatically to the value corresponding to the nearest slice.
     * ``show_indicator``
       Whether to show indicator in spectral viewer when slice tool is inactive.
-    * ``show_wavelength``
-      Whether to show slice wavelength in label to right of indicator.
+    * ``show_value``
+      Whether to show slice value in label to right of indicator.
     """
     template_file = __file__, "slice.vue"
     slice = Any(0).tag(sync=True)
-    wavelength = Any(-1).tag(sync=True)
-    wavelength_unit = Any("").tag(sync=True)
-    min_value = Int(0).tag(sync=True)
-    max_value = Int(100).tag(sync=True)
+    value = Any(-1).tag(sync=True)
+    value_label = Unicode("Wavelength").tag(sync=True)
+    value_unit = Any("").tag(sync=True)
+
+    min_slice = Int(0).tag(sync=True)
+    max_slice = Int(100).tag(sync=True)
     wait = Int(200).tag(sync=True)
 
     show_indicator = Bool(True).tag(sync=True)
-    show_wavelength = Bool(True).tag(sync=True)
+    show_value = Bool(True).tag(sync=True)
 
     is_playing = Bool(False).tag(sync=True)
     play_interval = Int(200).tag(sync=True)  # milliseconds
@@ -81,22 +84,30 @@
         self.session.hub.subscribe(self, AddDataMessage,
                                    handler=self._on_data_added)
 
-        # update internal wavelength when x display unit is changed (preserving slice)
+        # update internal value (wavelength/frequency) when x display unit is changed
+        # so that the current slice number is preserved
         self.session.hub.subscribe(self, GlobalDisplayUnitChanged,
                                    handler=self._on_global_display_unit_changed)
 
     @property
-    def _default_spectrum_viewer_reference_name(self):
-        return self.app._jdaviz_helper_default_spectrum_viewer_reference_name
+    @deprecated(since="3.9", alternative="value")
+    def wavelength(self):
+        return self.user_api.value
+
+    @property
+    @deprecated(since="3.9", alternative="value_unit")
+    def wavelength_unit(self):
+        return self.user_api.value_unit
 
     @property
-    def _default_image_viewer_reference_name(self):
-        return self.app._jdaviz_helper._default_image_viewer_reference_name
+    @deprecated(since="3.9", alternative="show_value")
+    def show_wavelength(self):
+        return self.user_api.show_value
 
     @property
     def user_api(self):
-        return PluginUserApi(self, expose=('slice', 'wavelength',
-                                           'show_indicator', 'show_wavelength'))
+        return PluginUserApi(self, expose=('slice', 'wavelength', 'value',
+                                           'show_indicator', 'show_wavelength', 'show_value'))
 
     @property
     def slice_indicator(self):
@@ -114,7 +125,7 @@
                 self._watched_viewers.remove(viewer)
         elif isinstance(viewer, BqplotProfileView) and watch:
             if self._x_all is None and len(viewer.data()):
-                # cache wavelengths so that wavelength <> slice conversion can be done efficiently
+                # cache values (wavelengths/freqs) so that value <> slice conversion is efficient
                 self._update_data(viewer.data()[0].spectral_axis)
 
             if viewer not in self._indicator_viewers:
@@ -126,9 +137,9 @@
     def _on_data_added(self, msg):
         if isinstance(msg.viewer, BqplotImageView):
             if len(msg.data.shape) == 3:
-                self.max_value = msg.data.shape[-1] - 1  # Same as i_end in Export Plot plugin
+                self.max_slice = msg.data.shape[-1] - 1  # Same as i_end in Export Plot plugin
                 self._watch_viewer(msg.viewer, True)
-                msg.viewer.state.slices = (0, 0, int(self.slice))
+                self._set_viewer_to_slice(msg.viewer, int(self.slice))
 
         elif isinstance(msg.viewer, BqplotProfileView):
             self._watch_viewer(msg.viewer, True)
@@ -141,18 +152,18 @@
     def _update_data(self, x_all):
         self._x_all = x_all.value
 
-        if self.wavelength == -1:
+        if self.value == -1:
             if len(x_all):
                 # initialize at middle of cube
                 self.slice = int(len(x_all)/2)
             else:
-                # leave in the pre-init state and don't update the wavelength/slice
+                # leave in the pre-init state and don't update the value/slice
                 return
 
         # Also update unit when data is updated
-        self.wavelength_unit = x_all.unit.to_string()
+        self.value_unit = x_all.unit.to_string()
 
-        # force wavelength to update from the current slider value
+        # force value (wavelength/frequency) to update from the current slider slice
         self._on_slider_updated({'new': self.slice})
 
         # update data held inside slice indicator and force reverting to original active status
@@ -168,70 +179,81 @@
 
     def _on_select_slice_message(self, msg):
         # NOTE: by setting the slice index, the observer (_on_slider_updated)
-        # will sync across all viewers and update the wavelength
+        # will sync across all viewers and update the value (wavelength/frequency)
         with warnings.catch_warnings():
             warnings.simplefilter('ignore', category=UnitsWarning)
-            self.slice = msg.slice
+            if msg.slice is not None:
+                self.slice = msg.slice
+            elif msg.value is not None:
+                self.value = msg.value
+
+    @property
+    def slice_axis(self):
+        return 'spectral'
 
     def _on_global_display_unit_changed(self, msg):
-        if msg.axis != 'spectral':
+        if msg.axis != self.slice_axis:
             return
-        prev_unit = self.wavelength_unit
+        prev_unit = self.value_unit
         # original unit during init can be blank or deg (before axis is set correctly)
         if self._x_all is None or prev_unit in ('deg', ''):
             return
         self._update_data((self._x_all * u.Unit(prev_unit)).to(msg.unit, u.spectral()))
 
-    @observe('wavelength')
-    def _on_wavelength_updated(self, event):
+    @observe('value')
+    def _on_value_updated(self, event):
         # convert to float (JS handles stripping any invalid characters)
         try:
             value = float(event.get('new'))
         except ValueError:
             # do not accept changes, we'll revert via the slider
             # since this @change event doesn't have access to
-            # the old value, and self.wavelength already updated
+            # the old value, and self.value already updated
             # via the v-model
             self._on_slider_updated({'new': self.slice})
             return
 
         # NOTE: by setting the index, this should recursively update the
-        # wavelength to the nearest applicable value in _on_slider_updated
+        # value (wavelength/frequency) to the nearest applicable value in _on_slider_updated
         self.slice = int(np.argmin(abs(value - self._x_all)))
 
-    @observe('show_indicator', 'show_wavelength')
+    @observe('show_indicator', 'show_value')
     def _on_setting_changed(self, event):
         msg = SliceToolStateMessage({event['name']: event['new']}, sender=self)
         self.session.hub.broadcast(msg)
 
+    def _set_viewer_to_slice(self, viewer, value):
+        viewer.state.slices = (0, 0, value)
+
     @observe('slice')
     def _on_slider_updated(self, event):
         if self._x_all is None:
             return
 
-        value = int(event.get('new', int(len(self._x_all)/2))) % (int(self.max_value) + 1)
+        value = int(event.get('new', int(len(self._x_all)/2))) % (int(self.max_slice) + 1)
 
-        self.wavelength = self._x_all[value]
+        self.value = self._x_all[value]
 
         for viewer in self._watched_viewers:
-            viewer.state.slices = (0, 0, value)
+            self._set_viewer_to_slice(viewer, value)
         for viewer in self._indicator_viewers:
-            viewer._update_slice_indicator(value)
+            if hasattr(viewer, 'slice_indicator'):
+                viewer.slice_indicator.slice = value
 
-        self.hub.broadcast(SliceWavelengthUpdatedMessage(slice=value,
-                                                         wavelength=self.wavelength,
-                                                         wavelength_unit=self.wavelength_unit,
-                                                         sender=self))
+        self.hub.broadcast(SliceValueUpdatedMessage(slice=value,
+                                                    value=self.value,
+                                                    value_unit=self.value_unit,
+                                                    sender=self))
 
     def vue_goto_first(self, *args):
         if self.is_playing:
             return
-        self._on_slider_updated({'new': self.min_value})
+        self._on_slider_updated({'new': self.min_slice})
 
     def vue_goto_last(self, *args):
         if self.is_playing:
             return
-        self._on_slider_updated({'new': self.max_value})
+        self._on_slider_updated({'new': self.max_slice})
 
     def vue_play_next(self, *args):
         if self.is_playing:

jdaviz/configs/cubeviz/plugins/slice/slice.vue

@@ -1,6 +1,6 @@
 <template>
   <j-tray-plugin
-    description='Select slice (or wavelength) of the cube to show in the image viewers and highlighted in the spectrum viewer.  The slice can also be changed interactively in the spectrum viewer by activating the slice tool.'
+    description='Select slice of the cube to show in the image viewers.  The slice can also be changed interactively in the spectrum viewer by activating the slice tool.'
     :link="docs_link || 'https://jdaviz.readthedocs.io/en/'+vdocs+'/'+config+'/plugins.html#slice'"
     :popout_button="popout_button">
 
@@ -14,16 +14,16 @@
             <v-row>
               <v-switch
                 label="Show Indicator"
-                hint="Show indicator in spectral viewer even when slice tool is inactive."
+                hint="Show slice indicator even when slice tool is inactive."
                 v-model="show_indicator"
                 persistent-hint>
               </v-switch>
             </v-row>
             <v-row>
               <v-switch
-                label="Show Wavelength"
-                hint="Show slice wavelength in label to right of indicator."
-                v-model="show_wavelength"
+                label="Show Value"
+                :hint="'Show slice '+value_label.toLowerCase()+' in label to right of indicator.'"
+                v-model="show_value"
                 persistent-hint>
               </v-switch>
             </v-row>
@@ -37,39 +37,31 @@
         :value="slice"
         @input="throttledSetValue"
         class="align-center"
-        :max="max_value"
-        :min="min_value"
+        :max="max_slice"
+        :min="min_slice"
         hide-details
       />
     </v-row>
 
-    <v-row class="row-no-outside-padding row-min-bottom-padding">
-      <v-col>
-        <v-text-field
-          v-model.number="slice"
-          class="mt-0 pt-0"
-          type="number"
-          label="Slice"
-          hint="Slice number"
-        ></v-text-field>
-      </v-col>
-      <v-col cols=3>
-        <span> / {{ max_value }}</span>
-      </v-col>
+    <v-row>
+      <v-text-field
+        v-model.number="slice"
+        class="mt-0 pt-0"
+        type="number"
+        label="Slice"
+        hint="Slice number"
+        :suffix="'/'+max_slice"
+      ></v-text-field>
     </v-row>
 
-    <v-row class="row-no-outside-padding">
-      <v-col>
-        <v-text-field
-          v-model="wavelength"
-          class="mt-0 pt-0"
-          label="Wavelength"
-          hint="Wavelength corresponding to slice, in units of spectrum"
-        ></v-text-field>
-      </v-col>
-      <v-col cols=3>
-        <span>{{ wavelength_unit }}</span>
-      </v-col>
+    <v-row>
+      <v-text-field
+        v-model="value"
+        class="mt-0 pt-0"
+        :label="value_label"
+        :hint="value_label+' corresponding to slice'"
+        :suffix="value_unit"
+      ></v-text-field>
     </v-row>
 
     <v-row class="row-no-outside-padding row-min-bottom-padding">

jdaviz/configs/cubeviz/plugins/slice/tests/test_slice.py

@@ -43,13 +43,13 @@ def test_slice(cubeviz_helper, spectrum1d_cube):
     assert sl.slice == 1
 
     # from the widget this logic is duplicated (to avoid sending logic through messages)
-    sl._on_wavelength_updated({'new': '4.62e-07'})
+    sl._on_value_updated({'new': '4.62e-07'})
     assert sl.slice == 0
-    assert np.allclose(sl.wavelength, 4.62280007e-07)
+    assert np.allclose(sl.value, 4.62280007e-07)
 
     # make sure that passing an invalid value from the UI would revert to the previous value
     # JS strips invalid characters, but doesn't ensure its float-compatible
-    sl._on_wavelength_updated({'new': '1.2.3'})
+    sl._on_value_updated({'new': '1.2.3'})
     assert sl.slice == 0
 
     assert len(sl._watched_viewers) == 2  # flux-viewer, uncert-viewer
@@ -81,7 +81,7 @@ def test_slice(cubeviz_helper, spectrum1d_cube):
     assert sl.slice == 0
 
     sl.vue_goto_last()
-    assert sl.slice == sl.max_value
+    assert sl.slice == sl.max_slice
 
     sl.vue_play_next()  # Should automatically wrap to beginning
     assert sl.slice == 0
@@ -109,13 +109,13 @@ def test_indicator_settings(cubeviz_helper, spectrum1d_cube):
 
     assert sl.show_indicator is True
     assert indicator._show_if_inactive is True
-    assert sl.show_wavelength is True
+    assert sl.show_value is True
     assert indicator.label.visible is True
 
     sl.show_indicator = False
     assert indicator._show_if_inactive is False
 
-    sl.show_wavelength = False
+    sl.show_value = False
     assert indicator.label.visible is False