add toggle feature between surface brightness and flux, currently inc…

…omplete

jdaviz/app.py

@@ -72,7 +72,7 @@ def equivalent_units(self, data, cid, units):
             eqv = u.spectral_density(1 * u.m)  # Value does not matter here.
             list_of_units = set(list(map(str, u.Unit(units).find_equivalent_units(
                 include_prefix_units=True, equivalencies=eqv))) + [
-                    'Jy', 'mJy', 'uJy',
+                    'Jy', 'mJy', 'uJy', 'MJy',
                     'W / (m2 Hz)', 'W / (Hz m2)',  # Order is different in astropy v5.3
                     'eV / (s m2 Hz)', 'eV / (Hz s m2)',
                     'erg / (s cm2)',
@@ -95,13 +95,50 @@ def to_unit(self, data, cid, values, original_units, target_units):
         # gives the units of the values array, which might not be the same
         # as the original native units of the component in the data.
         if cid.label == "flux":
+            # to debug
+            print('orginal_units : ', original_units, "target_units : ", target_units)
+
             spec = data.get_object(cls=Spectrum1D)
             if len(values) == 2:
                 # Need this for setting the y-limits
                 spec_limits = [spec.spectral_axis[0].value, spec.spectral_axis[-1].value]
                 eqv = u.spectral_density(spec_limits*spec.spectral_axis.unit)
+
+            elif '_pixel_scale_factor' in spec.meta:
+                if (u.sr in u.Unit(original_units).bases) and \
+                   (u.sr not in u.Unit(target_units).bases):
+                    # sb -> flux
+
+                    # to debug
+                    print('first if')
+                    print('values before')
+                    print(values)
+
+                    converted_values = values * spec.meta['_pixel_scale_factor']
+
+                    # to debug
+                    print(converted_values)
+
+                    return converted_values
+                else:
+                    # elif (u.sr in u.Unit(target_units).bases) and \
+                    # (u.sr not in u.Unit(original_units).bases):
+                    # flux -> sb
+
+                    # to debug
+                    print('second elif')
+                    print('values before')
+                    print(values)
+
+                    converted_values = values / spec.meta['_pixel_scale_factor']
+                    # to debug
+                    print(converted_values)
+
+                    return converted_values
+
             else:
                 eqv = u.spectral_density(spec.spectral_axis)
+
         else:  # spectral axis
             eqv = u.spectral()
 

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -23,6 +23,7 @@ tray:
   - g-subset-plugin
   - g-markers
   - cubeviz-slice
+  - g-unit-conversion
   - g-gaussian-smooth
   - g-collapse
   - g-model-fitting

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

@@ -3,7 +3,6 @@
 
 import numpy as np
 import astropy
-from astropy import units as u
 from astropy.utils.decorators import deprecated
 from astropy.nddata import (
     NDDataArray, StdDevUncertainty
@@ -524,13 +523,3 @@ def _live_update(self, event={}):
         for mark in self.marks.values():
             mark.update_xy(sp.spectral_axis.value, sp.flux.value)
             mark.visible = True
-
-    def translate_units(self, collapsed_spec):
-        # remove sr
-        if u.sr in collapsed_spec._unit.bases:
-            collapsed_spec._data *= collapsed_spec.meta['_pixel_scale_factor']
-            collapsed_spec._unit *= u.sr
-        # add sr
-        elif u.sr not in collapsed_spec._unit.bases:
-            collapsed_spec._data /= collapsed_spec.meta['_pixel_scale_factor']
-            collapsed_spec._unit /= u.sr

jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.vue

@@ -135,6 +135,17 @@
       </div>
     </div>
 
+    <div>
+      <v-row>
+      <v-switch
+        v-model="translate_unit"
+        label="Translate units"
+        hint="Toggle between surface brightness and flux units"
+        persistent-hint
+      ></v-switch>
+    </v-row>
+  </div>
+
     <div @mouseover="() => active_step='ext'">
       <j-plugin-section-header :active="active_step==='ext'">Extract</j-plugin-section-header>
 
@@ -262,6 +273,5 @@
         </v-overlay>
       </div>
     </div>
-
   </j-tray-plugin>
 </template>

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

@@ -373,6 +373,7 @@ def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
     assert_allclose(sp_subset.flux.value, 12)  # (4 x 4) - 4
 
 
+# this test will have to move
 def test_unit_translation(cubeviz_helper):
     # custom cube so we have PIXAR_SR in metadata, and flux units = Jy/pix
     wcs_dict = {"CTYPE1": "WAVE-LOG", "CTYPE2": "DEC--TAN", "CTYPE3": "RA---TAN",

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

@@ -1,10 +1,11 @@
 import numpy as np
 from astropy import units as u
-from traitlets import List, Unicode, observe
+from traitlets import List, Unicode, observe, Bool
 
 from jdaviz.core.events import GlobalDisplayUnitChanged
 from jdaviz.core.registries import tray_registry
-from jdaviz.core.template_mixin import PluginTemplateMixin, UnitSelectPluginComponent, PluginUserApi
+from jdaviz.core.template_mixin import (PluginTemplateMixin, UnitSelectPluginComponent,
+                                        PluginUserApi)
 from jdaviz.core.validunits import (create_spectral_equivalencies_list,
                                     create_flux_equivalencies_list)
 
@@ -51,6 +52,7 @@ class UnitConversion(PluginTemplateMixin):
     spectral_unit_selected = Unicode().tag(sync=True)
     flux_unit_items = List().tag(sync=True)
     flux_unit_selected = Unicode().tag(sync=True)
+    translate_unit = Bool(False).tag(sync=True)
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -125,6 +127,20 @@ def _on_glue_y_display_unit_changed(self, y_unit):
             self.flux_unit.choices = choices
             self.flux_unit.selected = y_unit
 
+    def translate_units(self):
+        spec_units = u.Unit(self.spectrum_viewer.state.y_display_unit)
+        # remove sr
+        if u.sr in spec_units.bases:
+            spec_units *= u.sr
+            # update display units
+            self.spectrum_viewer.state.y_display_unit = str(spec_units)
+
+        # add sr
+        elif u.sr not in spec_units.bases:
+            spec_units /= u.sr
+            # update display units
+            self.spectrum_viewer.state.y_display_unit = str(spec_units)
+
     @observe('spectral_unit_selected')
     def _on_spectral_unit_changed(self, *args):
         self.hub.broadcast(GlobalDisplayUnitChanged('spectral',
@@ -136,9 +152,25 @@ def _on_spectral_unit_changed(self, *args):
 
     @observe('flux_unit_selected')
     def _on_flux_unit_changed(self, *args):
-        self.hub.broadcast(GlobalDisplayUnitChanged('flux',
-                                                    self.flux_unit.selected,
-                                                    sender=self))
+        # self.hub.broadcast(GlobalDisplayUnitChanged('flux',
+        #                                                self.flux_unit.selected,
+        #                                                sender=self))
         yunit = _valid_glue_display_unit(self.flux_unit.selected, self.spectrum_viewer, 'y')
+        print('y_unit = ', yunit)
         if self.spectrum_viewer.state.y_display_unit != yunit:
             self.spectrum_viewer.state.y_display_unit = yunit
+            self.hub.broadcast(GlobalDisplayUnitChanged('flux',
+                                                        self.flux_unit.selected,
+                                                        sender=self))
+
+    @observe('translate_unit')
+    def _translate(self, *args):
+        # make sure we have a scale factor
+        specs_w_factor = [spec for spec in self.app.data_collection
+                          if "_pixel_scale_factor" in spec.meta]
+
+        if specs_w_factor:
+            self.translate_units()
+        else:
+            raise ValueError("No collapse spectra in data collection, \
+                              please collapse a spectrum first.")

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

@@ -25,10 +25,20 @@
         attach
         :items="flux_unit_items.map(i => i.label)"
         v-model="flux_unit_selected"
-        label="Flux Unit"
-        hint="Global display unit for flux."
+        :label="translate_unit ? 'Flux Unit' : 'Surface Brightness'"
+        :hint="translate_unit ? 'Global display unit for flux.' : 'Global display unit for surface brightness.'"
         persistent-hint
       ></v-select>
     </v-row>
+
+    <v-row v-if="config == 'cubeviz'">
+      <v-switch
+        v-model="translate_unit"
+        label="Translate units"
+        hint="Toggle between surface brightness and flux units"
+        persistent-hint
+        :disabled="config === 'specviz'"
+      ></v-switch>
+    </v-row>
   </j-tray-plugin>
 </template>

jdaviz/configs/specviz/plugins/viewers.py

@@ -559,9 +559,25 @@ def set_plot_axes(self):
         y_display_unit = self.state.y_display_unit
         y_unit = u.Unit(y_display_unit) if y_display_unit else u.dimensionless_unscaled
 
-        if y_unit.is_equivalent(u.Jy / u.sr):
-            flux_unit_type = "Surface brightness"
-        elif y_unit.is_equivalent(u.erg / (u.s * u.cm**2)):
+        # Get local units.
+        locally_defined_flux_units = [
+            u.Jy, u.mJy, u.uJy, u.MJy,
+            u.W / (u.m**2 * u.Hz),
+            u.eV / (u.s * u.m**2 * u.Hz),
+            u.erg / (u.s * u.cm**2),
+            u.erg / (u.s * u.cm**2 * u.Angstrom),
+            u.erg / (u.s * u.cm**2 * u.Hz),
+            u.ph / (u.s * u.cm**2 * u.Angstrom),
+            u.ph / (u.s * u.cm**2 * u.Hz)
+        ]
+
+        locally_defined_sb_units = [
+            unit / u.sr for unit in locally_defined_flux_units
+            ]
+
+        if any(y_unit.is_equivalent(unit) for unit in locally_defined_sb_units):
+            flux_unit_type = "Surface Brightness"
+        elif any(y_unit.is_equivalent(unit) for unit in locally_defined_flux_units):
             flux_unit_type = 'Flux'
         elif y_unit.is_equivalent(u.electron / u.s) or y_unit.physical_type == 'dimensionless':
             # electron / s or 'dimensionless_unscaled' should be labeled counts

jdaviz/core/validunits.py

@@ -67,7 +67,7 @@ def create_flux_equivalencies_list(flux_unit, spectral_axis_unit):
         return []
 
     # Get local units.
-    locally_defined_flux_units = ['Jy', 'mJy', 'uJy',
+    locally_defined_flux_units = ['Jy', 'mJy', 'uJy', 'MJy',
                                   'W / (m2 Hz)',
                                   'eV / (s m2 Hz)',
                                   'erg / (s cm2)',