Merge branch 'main' into uc_var_names

CHANGES.rst

@@ -6,7 +6,7 @@ New Features
 
 - Added flux/surface brightness translation and surface brightness
   unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113, #3129,
-                                           #3139, #3149, #3155, #3178, #3187]
+                                           #3139, #3149, #3155, #3178, #3185, #3187]
 
 - Plugin tray is now open by default. [#2892]
 

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

@@ -570,6 +570,24 @@ def test_default_spectral_extraction(cubeviz_helper, spectrum1d_cube_fluxunit_jy
     )
 
 
+def test_spectral_extraction_unit_conv_one_spec(
+    cubeviz_helper, spectrum1d_cube_fluxunit_jy_per_steradian
+):
+    cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian)
+    spectrum_viewer = cubeviz_helper.app.get_viewer(
+        cubeviz_helper._default_spectrum_viewer_reference_name)
+    uc = cubeviz_helper.plugins["Unit Conversion"]
+    assert uc.flux_unit == "Jy"
+    uc.flux_unit.selected = "MJy"
+    spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']
+    # Overwrite the one and only default extraction.
+    collapsed = spec_extr_plugin.extract()
+    # Actual values not in display unit but should not affect display unit.
+    assert collapsed.flux.unit == u.Jy
+    assert uc.flux_unit.selected == "MJy"
+    assert spectrum_viewer.state.y_display_unit == "MJy"
+
+
 @pytest.mark.usefixtures('_jail')
 @pytest.mark.remote_data
 @pytest.mark.parametrize(

jdaviz/configs/specviz/plugins/parsers.py

@@ -11,6 +11,7 @@
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.registries import data_parser_registry
 from jdaviz.utils import standardize_metadata, download_uri_to_path
+from jdaviz.core.validunits import check_if_unit_is_per_solid_angle
 
 
 __all__ = ["specviz_spectrum1d_parser"]
@@ -159,6 +160,15 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             # Make metadata layout conform with other viz.
             spec.meta = standardize_metadata(spec.meta)
 
+            # If this is the first loaded data, we want to set spectral y unit type to Flux or
+            # Surface Brightness as appropriate
+            if len(app.data_collection) == 0 and "Unit Conversion" in app._jdaviz_helper.plugins:
+                uc = app._jdaviz_helper.plugins["Unit Conversion"]
+                if check_if_unit_is_per_solid_angle(flux_units):
+                    uc._obj.spectral_y_type = "Surface Brightness"
+                else:
+                    uc._obj.spectral_y_type = "Flux"
+
             app.add_data(spec, data_label[i])
 
             # handle display, with the SpectrumList special case in mind.

jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py

@@ -35,6 +35,15 @@ def test_value_error_exception(specviz_helper, spectrum1d, new_spectral_axis, ne
     assert u.Unit(viewer.state.y_display_unit) == u.Unit(expected_flux)
 
 
+def test_initialize_specviz_sb(specviz_helper, spectrum1d):
+    spec_sb = Spectrum1D(spectrum1d.flux/u.sr, spectrum1d.spectral_axis)
+    specviz_helper.load_data(spec_sb, data_label="Test 1D Spectrum")
+    plg = specviz_helper.plugins["Unit Conversion"]
+    assert plg._obj.flux_unit == "Jy"
+    assert plg._obj.spectral_y_type == "Surface Brightness"
+    assert plg._obj.angle_unit == "sr"
+
+
 @pytest.mark.parametrize('uncert', (False, True))
 def test_conv_wave_only(specviz_helper, spectrum1d, uncert):
     if uncert is False:

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py

@@ -56,17 +56,25 @@ class UnitConversion(PluginTemplateMixin):
     """
     template_file = __file__, "unit_conversion.vue"
 
+    has_spectral = Bool(False).tag(sync=True)
     spectral_unit_items = List().tag(sync=True)
     spectral_unit_selected = Unicode().tag(sync=True)
 
+    has_flux = Bool(False).tag(sync=True)
     flux_unit_items = List().tag(sync=True)
     flux_unit_selected = Unicode().tag(sync=True)
 
-    sb_unit_selected = Unicode().tag(sync=True)
-
+    has_angle = Bool(False).tag(sync=True)
     angle_unit_items = List().tag(sync=True)
     angle_unit_selected = Unicode().tag(sync=True)
 
+    has_sb = Bool(False).tag(sync=True)
+    sb_unit_selected = Unicode().tag(sync=True)
+
+    has_time = Bool(False).tag(sync=True)
+    time_unit_items = List().tag(sync=True)
+    time_unit_selected = Unicode().tag(sync=True)
+
     spectral_y_type_items = List().tag(sync=True)
     spectral_y_type_selected = Unicode().tag(sync=True)
 
@@ -97,30 +105,51 @@ def __init__(self, *args, **kwargs):
         self.session.hub.subscribe(self, AddDataToViewerMessage,
                                    handler=self._find_and_convert_contour_units)
 
+        self.has_spectral = self.config in ('specviz', 'cubeviz', 'specviz2d', 'mosviz')
         self.spectral_unit = UnitSelectPluginComponent(self,
                                                        items='spectral_unit_items',
                                                        selected='spectral_unit_selected')
 
-        self.spectral_y_type = SelectPluginComponent(self,
-                                                     items='spectral_y_type_items',
-                                                     selected='spectral_y_type_selected',
-                                                     manual_options=['Surface Brightness', 'Flux'])
-
+        self.has_flux = self.config in ('specviz', 'cubeviz', 'specviz2d', 'mosviz')
         self.flux_unit = UnitSelectPluginComponent(self,
                                                    items='flux_unit_items',
                                                    selected='flux_unit_selected')
 
+        self.has_angle = self.config in ('cubeviz', 'specviz', 'mosviz')
         self.angle_unit = UnitSelectPluginComponent(self,
                                                     items='angle_unit_items',
                                                     selected='angle_unit_selected')
 
+        self.has_sb = self.has_angle or self.config in ('imviz',)
+        # NOTE: always read_only, exposed through sb_unit property
+
+        self.has_time = False
+        self.time_unit = UnitSelectPluginComponent(self,
+                                                   items='time_unit_items',
+                                                   selected='time_unit_selected')
+
+        self.spectral_y_type = SelectPluginComponent(self,
+                                                     items='spectral_y_type_items',
+                                                     selected='spectral_y_type_selected',
+                                                     manual_options=['Surface Brightness', 'Flux'])
+
     @property
     def user_api(self):
-        if self.app.config == 'cubeviz':
-            expose = ('spectral_unit', 'spectral_y_type', 'flux_unit', 'angle_unit', 'sb_unit')
-        else:
-            expose = ('spectral_unit', 'flux_unit', 'angle_unit')
-        return PluginUserApi(self, expose=expose)
+        expose = []
+        readonly = []
+        if self.has_spectral:
+            expose += ['spectral_unit']
+        if self.has_flux:
+            expose += ['flux_unit']
+        if self.has_angle:
+            expose += ['angle_unit']
+        if self.has_sb:
+            readonly = ['sb_unit']
+        if self.has_time:
+            expose += ['time_unit']
+        if self.config == 'cubeviz':
+            expose += ['spectral_y_type']
+        return PluginUserApi(self, expose=expose, readonly=readonly)
 
     @property
     def sb_unit(self):
@@ -144,7 +173,7 @@ def _on_glue_x_display_unit_changed(self, x_unit_str):
             self.spectral_unit.selected = x_unit_str
             if not len(self.flux_unit.choices) or not len(self.angle_unit.choices):
                 # in case flux_unit was triggered first (but could not be set because there
-                # as no spectral_unit to determine valid equivalencies)
+                # was no spectral_unit to determine valid equivalencies)
                 self._on_glue_y_display_unit_changed(self.spectrum_viewer.state.y_display_unit)
 
     def _on_glue_y_display_unit_changed(self, y_unit_str):
@@ -175,6 +204,14 @@ def _on_glue_y_display_unit_changed(self, y_unit_str):
         if check_if_unit_is_per_solid_angle(y_unit_str):
             flux_choices = create_flux_equivalencies_list(y_unit * u.sr, x_unit)
             self.flux_unit.choices = flux_choices
+            flux_unit = str(y_unit * u.sr)
+            # We need to set the angle_unit before triggering _on_flux_unit_changed via
+            # setting self.flux_unit.selected below, or the lack of angle unit will make it think
+            # we're in Flux units.
+            self.angle_unit.choices = create_angle_equivalencies_list(y_unit)
+            self.angle_unit.selected = self.angle_unit.choices[0]
+            if flux_unit in self.flux_unit.choices and flux_unit != self.flux_unit.selected:
+                self.flux_unit.selected = flux_unit
 
         # sets the angle unit drop down and the surface brightness read-only text
         if self.app.data_collection[0]:

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.vue

@@ -9,7 +9,7 @@
     :popout_button="popout_button"
     :scroll_to.sync="scroll_to">
 
-    <v-row>
+    <v-row v-if="has_spectral">
       <v-select
         :menu-props="{ left: true }"
         attach
@@ -22,7 +22,20 @@
       ></v-select>
     </v-row>
 
-    <v-row>
+    <v-row v-if="has_time">
+      <v-select
+        :menu-props="{ left: true }"
+        attach
+        :items="time_unit_items.map(i => i.label)"
+        v-model="time_unit_selected"
+        :label="api_hints_enabled ? 'plg.time_unit =' : 'Time Unit'"
+        :class="api_hints_enabled ? 'api-hint' : null"
+        hint="Global display unit for time axis."
+        persistent-hint
+      ></v-select>
+    </v-row>
+
+    <v-row v-if="has_flux">
       <v-select
         :menu-props="{ left: true }"
         attach
@@ -34,8 +47,8 @@
         persistent-hint
       ></v-select>
     </v-row>
-
-    <v-row v-if="config in ['cubeviz', 'imviz', 'mosviz']">
+  
+    <v-row v-if="has_angle">
       <v-select
         :menu-props="{ left: true }"
         attach
@@ -49,7 +62,7 @@
       ></v-select>
     </v-row>
 
-    <v-row>
+    <v-row v-if="has_spectral">
       <v-text-field
         v-model="sb_unit_selected"
         :label="api_hints_enabled ? 'plg.sb_unit' : 'Surface Brightness Unit'"
@@ -60,27 +73,29 @@
       ></v-text-field>
     </v-row>
 
-    <v-row v-if="config == 'cubeviz'">
-      <v-divider></v-divider>
-    </v-row>
+    <div v-if="config == 'cubeviz'">
+      <v-row>
+        <v-divider></v-divider>
+      </v-row>
 
-    <v-row  v-if="config == 'cubeviz'">
-      <v-select
-        :menu-props="{ left: true }"
-        attach
-        :items="spectral_y_type_items.map(i => i.label)"
-        v-model="spectral_y_type_selected"
-        :label="api_hints_enabled ? 'plg.spectral_y_type =' : 'Spectral y-axis Type'"
-        :class="api_hints_enabled ? 'api-hint' : null"
-        hint="Select the y-axis physical type for the spectrum-viewer."
-        persistent-hint
-      ></v-select>
-    </v-row>
+      <v-row>
+        <v-select
+          :menu-props="{ left: true }"
+          attach
+          :items="spectral_y_type_items.map(i => i.label)"
+          v-model="spectral_y_type_selected"
+          :label="api_hints_enabled ? 'plg.spectral_y_type =' : 'Spectral y-axis Type'"
+          :class="api_hints_enabled ? 'api-hint' : null"
+          hint="Select the y-axis physical type for the spectrum-viewer."
+          persistent-hint
+        ></v-select>
+      </v-row>
 
-    <v-alert type="warning" v-if="!pixar_sr_exists && config == 'cubeviz'">
-          PIXAR_SR FITS header keyword not found when parsing spectral cube.
-          Flux/Surface Brightness will use default PIXAR_SR value of 1.
-    </v-alert>
+      <v-alert type="warning" v-if="!pixar_sr_exists">
+            PIXAR_SR FITS header keyword not found when parsing spectral cube.
+            Flux/Surface Brightness will use default PIXAR_SR value of 1.
+      </v-alert>
+    </div>
 
   </j-tray-plugin>
 </template>

jdaviz/configs/specviz/tests/test_viewers.py

@@ -26,6 +26,21 @@ def test_spectrum_viewer_axis_labels(specviz_helper, input_unit, y_axis_label):
     assert (y_axis_label in label)
 
 
+@pytest.mark.xfail(reason="FIXME: Some callback magic needs to happen somewhere.")
+def test_spectrum_viewer_keep_unit_when_removed(specviz_helper, spectrum1d):
+    specviz_helper.load_data(spectrum1d, data_label="Test")
+    uc = specviz_helper.plugins["Unit Conversion"]
+    assert uc.flux_unit == "Jy"
+    uc.flux_unit = "MJy"
+    specviz_helper.app.remove_data_from_viewer("spectrum-viewer", "Test")
+    specviz_helper.app.add_data_to_viewer("spectrum-viewer", "Test")
+    # Actual values not in display unit but should not affect display unit.
+    spec = specviz_helper.get_spectra(data_label="Test", apply_slider_redshift=False)
+    assert spec.flux.unit == u.Jy
+    assert uc.flux_unit.selected == "MJy"
+    assert specviz_helper.app._get_display_unit('spectral_y') == "MJy"
+
+
 class TestResetLimitsTwoTests:
     """See https://github.com/spacetelescope/lcviz/pull/93"""
 

jdaviz/core/template_mixin.py

@@ -3910,7 +3910,13 @@ def add_results_from_plugin(self, data_item, replace=None, label=None):
                 add_to_viewer_vis = [True]
                 preserved_attributes = [{}]
 
+        enforce_flux_unit = None
         if label in self.app.data_collection:
+            if self.app.config == "cubeviz":
+                sv = self.app.get_viewer(
+                    self.app._jdaviz_helper._default_spectrum_viewer_reference_name)
+                if len(sv.state.layers) == 1:
+                    enforce_flux_unit = self.app._get_display_unit('spectral_y')
             for viewer_ref in add_to_viewer_refs:
                 self.app.remove_data_from_viewer(viewer_ref, label)
             self.app.data_collection.remove(self.app.data_collection[label])
@@ -3943,6 +3949,9 @@ def add_results_from_plugin(self, data_item, replace=None, label=None):
                                         label,
                                         visible=visible, clear_other_data=this_replace)
 
+            if enforce_flux_unit:
+                sv.state.y_display_unit = enforce_flux_unit
+
             if preserved != {}:
                 layer_state = [layer.state for layer in this_viewer.layers if
                                layer.layer.label == label][0]