Implement slice in output table

and do not display slice for cubeviz 2D data,
as requested.

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

@@ -220,6 +220,7 @@ def _on_slider_updated(self, event):
 
         self.hub.broadcast(SliceWavelengthUpdatedMessage(slice=value,
                                                          wavelength=self.wavelength,
+                                                         wavelength_unit=self.wavelength_unit,
                                                          sender=self))
 
     def vue_goto_first(self, *args):

jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py

@@ -1,5 +1,7 @@
+import numpy as np
 import pytest
 from astropy import units as u
+from astropy.tests.helper import assert_quantity_allclose
 from astropy.utils.exceptions import AstropyUserWarning
 from numpy.testing import assert_allclose
 from regions import RectanglePixelRegion, PixCoord
@@ -33,7 +35,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     assert_allclose(row["sum"], 75 * flux_unit)  # 3 (w) x 5 (h) x 5 (v)
     assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix))  # 3 (w) x 5 (h)
     assert_allclose(row["mean"], 5 * flux_unit)
-    assert row["slice"] == 4
+    assert_quantity_allclose(row["slice"], 4.894499866699333 * u.um)
 
     # Move slider and make sure it recomputes for a new slice automatically.
     cube_slice_plg = cubeviz_helper.plugins["Slice"]._obj
@@ -50,27 +52,21 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     assert_allclose(row["sum"], 15 * flux_unit)  # 3 (w) x 5 (h) x 1 (v)
     assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix))  # 3 (w) x 5 (h)
     assert_allclose(row["mean"], 1 * flux_unit)
-    assert row["slice"] == 0
-
-
-def test_cubeviz_aperphot_generated_2d_collapse(cubeviz_helper, image_cube_hdu_obj_microns):
-    cubeviz_helper.load_data(image_cube_hdu_obj_microns, data_label="test")
-    flux_unit = u.Unit("1E-17 erg*s^-1*cm^-2*Angstrom^-1")
+    assert_quantity_allclose(row["slice"], 4.8904998665093435 * u.um)
 
+    # We continue on with test_cubeviz_aperphot_generated_2d_collapse here
+    # because we want to make sure the result would append properly between 3D and 2D.
     collapse_plg = cubeviz_helper.plugins["Collapse"]._obj
     collapse_plg.vue_collapse()
 
     # Need this to make it available for photometry data drop-down.
     cubeviz_helper.app.add_data_to_viewer("uncert-viewer", "test[FLUX] collapsed")
 
-    aper = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=3, height=5)
-    cubeviz_helper.load_regions(aper)
-
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
     plg.dataset_selected = "test[FLUX] collapsed"
     plg.aperture_selected = "Subset 1"
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[0]
+    row = cubeviz_helper.get_aperture_photometry_results()[2]
 
     # Basically, we should recover the input rectangle here.
     assert_allclose(row["xcenter"], 1 * u.pix)
@@ -81,6 +77,7 @@ def test_cubeviz_aperphot_generated_2d_collapse(cubeviz_helper, image_cube_hdu_o
     assert_allclose(row["sum"], 540 * flux_unit)  # 3 (w) x 5 (h) x 36 (v)
     assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix))  # 3 (w) x 5 (h)
     assert_allclose(row["mean"], 36 * flux_unit)
+    assert np.isnan(row["slice"])
 
 
 def test_cubeviz_aperphot_generated_2d_moment(cubeviz_helper, image_cube_hdu_obj_microns):
@@ -111,6 +108,7 @@ def test_cubeviz_aperphot_generated_2d_moment(cubeviz_helper, image_cube_hdu_obj
     assert_allclose(row["sum"], 540 * flux_unit)  # 3 (w) x 5 (h) x 36 (v)
     assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix))  # 3 (w) x 5 (h)
     assert_allclose(row["mean"], 36 * flux_unit)
+    assert np.isnan(row["slice"])
 
     # Moment 1 has no compatible unit, so should not be available for photometry.
     moment_plg.n_moment = 1
@@ -152,6 +150,7 @@ def test_cubeviz_aperphot_generated_3d_gaussian_smooth(cubeviz_helper, image_cub
     assert_allclose(row["sum"], 48.54973 * flux_unit)  # 3 (w) x 5 (h) x <5 (v)
     assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix))  # 3 (w) x 5 (h)
     assert_allclose(row["mean"], 3.236648941040039 * flux_unit)
+    assert_quantity_allclose(row["slice"], 4.894499866699333 * u.um)
 
 
 def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_custom_fluxunit):
@@ -182,3 +181,4 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_c
     assert_allclose(row["pixarea_tot"], 2.350443053909789e-13 * u.sr)
     assert_allclose(row["aperture_sum_mag"], 23.72476627732448 * u.mag)
     assert_allclose(row["mean"], 5 * (u.MJy / u.sr))
+    assert_quantity_allclose(row["slice"], 0.46236 * u.um)

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py

@@ -70,7 +70,9 @@ class SimpleAperturePhotometry(PluginTemplateMixin, ApertureSubsetSelectMixin,
     fit_radial_profile = Bool(False).tag(sync=True)
     fit_results = List().tag(sync=True)
 
-    cube_slice = Any(0).tag(sync=True)  # Cubeviz only
+    # Cubeviz only
+    cube_slice = Any(0).tag(sync=True)
+    is_cube = Bool(False).tag(sync=True)
 
     icon_radialtocheck = Unicode(read_icon(os.path.join(ICON_DIR, 'radialtocheck.svg'), 'svg+xml')).tag(sync=True)  # noqa
     icon_checktoradial = Unicode(read_icon(os.path.join(ICON_DIR, 'checktoradial.svg'), 'svg+xml')).tag(sync=True)  # noqa
@@ -139,6 +141,17 @@ def _on_slice_changed(self, msg):
         if self.config != "cubeviz":
             return
         self.cube_slice = msg.slice
+        self._cube_wave = u.Quantity(msg.wavelength, msg.wavelength_unit)
+
+    @observe("dataset_selected")
+    def _on_dataset_selected_changed(self, event={}):
+        if self.config != "cubeviz":
+            return
+        # self.dataset might not exist when app is setting itself up.
+        if hasattr(self, "dataset") and self.dataset.selected_dc_item.ndim > 2:
+            self.is_cube = True
+        else:
+            self.is_cube = False
 
     def _get_defaults_from_metadata(self, dataset=None):
         defaults = {}
@@ -439,9 +452,7 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,
         if hasattr(reg, 'to_pixel'):
             sky_center = reg.center
             if self.config == "cubeviz" and data.ndim > 2:
-                cube_slice_plg = self.app._jdaviz_helper.plugins["Slice"]._obj
-                ycenter, xcenter = w.world_to_pixel(
-                    u.Quantity(cube_slice_plg.wavelength, cube_slice_plg.wavelength_unit), sky_center)[1]  # noqa: E501
+                ycenter, xcenter = w.world_to_pixel(self._cube_wave, sky_center)[1]
             else:  # "imviz"
                 xcenter, ycenter = w.world_to_pixel(sky_center)
         else:
@@ -528,7 +539,11 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,
             indexes=[1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 18, 18, 18])
 
         if self.config == "cubeviz":
-            phot_table.add_column(int(self.cube_slice), name="slice", index=29)
+            if data.ndim > 2:
+                slice_val = self._cube_wave
+            else:
+                slice_val = u.Quantity(np.nan, self._cube_wave.unit)
+            phot_table.add_column(slice_val, name="slice", index=29)
 
         if add_to_table:
             try:

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue

@@ -32,7 +32,7 @@
       hint="Select the data for photometry."
     />
 
-    <div v-if='config == "cubeviz"'>
+    <div v-if='config == "cubeviz" && is_cube'>
       <v-row class="row-no-outside-padding row-min-bottom-padding">
         <v-col>
           <v-text-field

jdaviz/core/events.py

@@ -317,10 +317,11 @@ def slice(self):
 
 class SliceWavelengthUpdatedMessage(Message):
     '''Message generated by the slice plugin when the selected slice and wavelength are updated'''
-    def __init__(self, slice, wavelength, *args, **kwargs):
+    def __init__(self, slice, wavelength, wavelength_unit, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.slice = slice
         self.wavelength = wavelength
+        self.wavelength_unit = wavelength_unit
 
 
 class SliceToolStateMessage(Message):