Aperture photometry in Cubeviz (#2666)

* Implement Cubeviz aperture photometry. Add tests and documentation. Attach WCS to some Cubeviz 2D products, where it is needed but missing. Minor clean-ups. * Add slice info to aper phot plugin for cubeviz * Clarify slice field in aper phot Co-authored-by: Kyle Conroy <[email protected]> * Fix plugin data menu bug * Implement slice in output table and do not display slice for cubeviz 2D data, as requested. * Add doc for new slice column for Cubeviz phot table. * Fix table GUI for slice wavelength and display slice wavelength instead of index in read-only text field. * Display slice_wave in plot and text results --------- Co-authored-by: Kyle Conroy <[email protected]>
spacetelescope · Feb 2, 2024 · 9373a9e · 9373a9e
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -26,6 +26,8 @@ Cubeviz
 
 - Spectral extraction plugin re-organized into subsections to be more consistent with specviz2d. [#2676]
 
+- New aperture photometry plugin that can perform aperture photometry on selected cube slice. [#2666]
+
 Imviz
 ^^^^^
 

diff --git a/docs/cubeviz/export_data.rst b/docs/cubeviz/export_data.rst
@@ -133,3 +133,26 @@ Markers Table
 All mouseover information in the :ref:`markers plugin <markers-plugin>` can be exported to an
 :ref:`astropy table <astropy:astropy-table>`
 by calling :meth:`~jdaviz.core.template_mixin.TableMixin.export_table` (see :ref:`plugin-apis`).
+
+
+.. _cubeviz_export_photometry:
+
+Aperture Photometry
+===================
+
+Cubeviz can export photometry output table like Imviz:
+
+.. code-block:: python
+
+    results = cubeviz.get_aperture_photometry_results()
+
+.. seealso::
+
+    :ref:`Imviz Aperture Photometry <imviz_export_photometry>`
+        Imviz documentation describing exporting of aperture photometry results in Jdaviz.
+
+In addition to the columns that :ref:`Imviz Aperture Photometry <imviz_export_photometry>`
+would provide, the table from Cubeviz has this extra column after ``data_label``:
+
+* ``slice_wave``: Wavelength value at the selected slice of the cube used for computation.
+  If a 2D data (e.g., collapsed cube) is selected, the value would be NaN instead.
diff --git a/docs/cubeviz/plugins.rst b/docs/cubeviz/plugins.rst
@@ -291,6 +291,19 @@ Click :guilabel:`EXTRACT` to produce a new 1D spectrum dataset
 from the spectral cube, which has uncertainties propagated by
 `astropy.nddata <https://docs.astropy.org/en/stable/nddata/nddata.html>`_.
 
+.. _cubeviz-aper-phot:
+
+Aperture Photometry
+===================
+
+Cubeviz allows aperture photometry on some 3D and 2D data, as long as they
+have valid flux units. For 3D data, the current :ref:`slice` is used.
+
+.. seealso::
+
+    :ref:`Imviz Aperture Photometry <aper-phot-simple>`
+        Imviz documentation describing the concept of aperture photometry in Jdaviz.
+
 .. _cubeviz-export-plot:
 
 Export Plot

diff --git a/jdaviz/components/plugin_dataset_select.vue b/jdaviz/components/plugin_dataset_select.vue
@@ -20,7 +20,7 @@
         <div class="single-line" style="width: 100%">
           <v-chip v-if="multiselect" style="width: calc(100% - 10px)">
             <span>
-              <j-layer-viewer-icon v-if="data.item.icon" span_style="margin-right: 4px" :icon="data.item.icon" :prevent_invert_if_dark="true" :is_wcs_only="isWCSOnlyLayer()"></j-layer-viewer-icon>
+              <j-layer-viewer-icon v-if="data.item.icon" span_style="margin-right: 4px" :icon="data.item.icon" :prevent_invert_if_dark="true"></j-layer-viewer-icon>
               {{ data.item.label }}
             </span>
           </v-chip>
@@ -64,12 +64,6 @@
 <script>
 module.exports = {
   props: ['items', 'selected', 'label', 'hint', 'rules', 'show_if_single_entry', 'multiselect'],
-  methods: {
-    isWCSOnlyLayer(item) {
-      const wcsOnly = Object.keys(this.$props.viewer.wcs_only_layers).includes(item.name)
-      return wcsOnly
-    },
-  }
 };
 </script>
 

diff --git a/jdaviz/configs/cubeviz/cubeviz.yaml b/jdaviz/configs/cubeviz/cubeviz.yaml
@@ -30,6 +30,7 @@ tray:
   - specviz-line-analysis
   - cubeviz-moment-maps
   - cubeviz-spectral-extraction
+  - imviz-aper-phot-simple
   - g-export-plot
 viewer_area:
   - container: col

diff --git a/jdaviz/configs/cubeviz/helper.py b/jdaviz/configs/cubeviz/helper.py
@@ -168,6 +168,20 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
                               spectral_subset=spectral_subset, function=function,
                               cls=cls, use_display_units=use_display_units)
 
+    # Need this method for Imviz Aperture Photometry plugin.
+
+    def get_aperture_photometry_results(self):
+        """Return aperture photometry results, if any.
+        Results are calculated using :ref:`cubeviz-aper-phot` plugin.
+
+        Returns
+        -------
+        results : `~astropy.table.QTable` or `None`
+            Photometry results if available or `None` otherwise.
+
+        """
+        return self.plugins['Aperture Photometry']._obj.export_table()
+
 
 def layer_is_cube_image_data(layer):
     return isinstance(layer, BaseData) and layer.ndim in (2, 3)

diff --git a/jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py b/jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py
@@ -239,7 +239,15 @@ def calculate_moment(self, add_data=True):
         # Need transpose to align JWST mirror shape: This is because specutils
         # arrange the array shape to be (nx, ny, nz) but 2D visualization
         # assumes (ny, nx) as per row-major convention.
-        data_wcs = getattr(cube.wcs, 'celestial', None)
+
+        # Extract 2D WCS from input cube.
+        data = self.dataset.selected_dc_item
+        # Similar to coords_info logic.
+        if '_orig_spec' in getattr(data, 'meta', {}):
+            w = data.meta['_orig_spec'].wcs
+        else:
+            w = data.coords
+        data_wcs = getattr(w, 'celestial', None)
         if data_wcs:
             data_wcs = data_wcs.swapaxes(0, 1)  # We also transpose WCS to match.
 

diff --git a/jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py b/jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py
@@ -30,6 +30,7 @@ def test_user_api(cubeviz_helper, spectrum1d_cube):
         assert len(mm._obj.continuum_marks['center'].x) > 0
 
         mom_sub = mm.calculate_moment()
+        assert isinstance(mom_sub.wcs, WCS)
 
         assert mom != mom_sub
 
@@ -45,7 +46,7 @@ def test_user_api(cubeviz_helper, spectrum1d_cube):
             mm.calculate_moment()
 
 
-def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmpdir):
+def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmp_path):
     dc = cubeviz_helper.app.data_collection
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", message="No observer defined on WCS.*")
@@ -110,7 +111,7 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmpdir):
                                          "204.9998877673 27.0001000000 (deg)")
 
     assert mm._obj.filename == 'moment0_test_FLUX.fits'  # Auto-populated on calculate.
-    mm._obj.filename = str(tmpdir.join(mm._obj.filename))  # But we want it in tmpdir for testing.
+    mm._obj.filename = str(tmp_path / mm._obj.filename)  # But we want it in tmp_path for testing.
     mm._obj.vue_save_as_fits()
     assert os.path.isfile(mm._obj.filename)
 
@@ -134,7 +135,7 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmpdir):
                                          "204.9998877673 27.0001000000 (deg)")
 
 
-def test_moment_velocity_calculation(cubeviz_helper, spectrum1d_cube, tmpdir):
+def test_moment_velocity_calculation(cubeviz_helper, spectrum1d_cube):
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", message="No observer defined on WCS.*")
         cubeviz_helper.load_data(spectrum1d_cube, data_label='test')

diff --git a/jdaviz/configs/cubeviz/plugins/slice/slice.py b/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):

diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py
@@ -0,0 +1,184 @@
+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
+
+
+def test_cubeviz_aperphot_cube_orig_flux(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")
+
+    aper = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=3, height=5)
+    cubeviz_helper.load_regions(aper)
+
+    # Make sure MASK is not an option even when shown in viewer.
+    cubeviz_helper.app.add_data_to_viewer("flux-viewer", "test[MASK]", visible=True)
+
+    plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
+    assert plg.dataset.labels == ["test[FLUX]", "test[ERR]"]
+    assert plg.cube_slice == "4.894e+00 um"
+
+    plg.dataset_selected = "test[FLUX]"
+    plg.aperture_selected = "Subset 1"
+    plg.vue_do_aper_phot()
+    row = cubeviz_helper.get_aperture_photometry_results()[0]
+
+    # Basically, we should recover the input rectangle here.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 2 * u.pix)
+    sky = row["sky_center"]
+    assert_allclose(sky.ra.deg, 205.43985906934287)
+    assert_allclose(sky.dec.deg, 27.003490103642033)
+    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_quantity_allclose(row["slice_wave"], 4.894499866699333 * u.um)
+
+    # Move slider and make sure it recomputes for a new slice automatically.
+    cube_slice_plg = cubeviz_helper.plugins["Slice"]._obj
+    cube_slice_plg.slice = 0
+    plg.vue_do_aper_phot()
+    row = cubeviz_helper.get_aperture_photometry_results()[1]
+
+    # Same rectangle but different slice value.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 2 * u.pix)
+    sky = row["sky_center"]
+    assert_allclose(sky.ra.deg, 205.43985906934287)
+    assert_allclose(sky.dec.deg, 27.003490103642033)
+    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_quantity_allclose(row["slice_wave"], 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")
+
+    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()[2]
+
+    # Basically, we should recover the input rectangle here.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 2 * u.pix)
+    sky = row["sky_center"]
+    assert_allclose(sky.ra.deg, 205.43985906934287)
+    assert_allclose(sky.dec.deg, 27.003490103642033)
+    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_wave"])
+
+
+def test_cubeviz_aperphot_generated_2d_moment(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")
+
+    moment_plg = cubeviz_helper.plugins["Moment Maps"]
+    _ = moment_plg.calculate_moment()
+
+    # Need this to make it available for photometry data drop-down.
+    cubeviz_helper.app.add_data_to_viewer("uncert-viewer", "test[FLUX] moment 0")
+
+    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] moment 0"
+    plg.aperture_selected = "Subset 1"
+    plg.vue_do_aper_phot()
+    row = cubeviz_helper.get_aperture_photometry_results()[0]
+
+    # Basically, we should recover the input rectangle here.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 2 * u.pix)
+    sky = row["sky_center"]
+    assert_allclose(sky.ra.deg, 205.43985906934287)
+    assert_allclose(sky.dec.deg, 27.003490103642033)
+    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_wave"])
+
+    # Moment 1 has no compatible unit, so should not be available for photometry.
+    moment_plg.n_moment = 1
+    moment_plg.reference_wavelength = 5
+    _ = moment_plg.calculate_moment()
+    m1_lbl = "test[FLUX] moment 1"
+    cubeviz_helper.app.add_data_to_viewer("uncert-viewer", m1_lbl)
+    assert (m1_lbl in cubeviz_helper.app.data_collection.labels and
+            m1_lbl not in plg.dataset.choices)
+
+
+def test_cubeviz_aperphot_generated_3d_gaussian_smooth(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")
+
+    gauss_plg = cubeviz_helper.plugins["Gaussian Smooth"]._obj
+    gauss_plg.mode_selected = "Spatial"
+    with pytest.warns(AstropyUserWarning, match="The following attributes were set on the data"):
+        _ = gauss_plg.smooth()
+
+    # Need this to make it available for photometry data drop-down.
+    cubeviz_helper.app.add_data_to_viewer("uncert-viewer", "test[FLUX] spatial-smooth stddev-1.0")
+
+    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] spatial-smooth stddev-1.0"
+    plg.aperture_selected = "Subset 1"
+    plg.vue_do_aper_phot()
+    row = cubeviz_helper.get_aperture_photometry_results()[0]
+
+    # Basically, we should recover the input rectangle here.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 2 * u.pix)
+    sky = row["sky_center"]
+    assert_allclose(sky.ra.deg, 205.43985906934287)
+    assert_allclose(sky.dec.deg, 27.003490103642033)
+    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_wave"], 4.894499866699333 * u.um)
+
+
+def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_custom_fluxunit):
+    cube = spectrum1d_cube_custom_fluxunit(fluxunit=u.MJy / u.sr)
+    cubeviz_helper.load_data(cube, data_label="test")
+
+    aper = RectanglePixelRegion(center=PixCoord(x=1, y=3), width=1, height=1)
+    bg = RectanglePixelRegion(center=PixCoord(x=0, y=2), width=1, height=1)
+    cubeviz_helper.load_regions([aper, bg])
+
+    plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
+    plg.dataset_selected = "test[FLUX]"
+    plg.aperture_selected = "Subset 1"
+    plg.background_selected = "Subset 2"
+
+    # Make sure per steradian is handled properly.
+    assert_allclose(plg.pixel_area, 0.01)
+    assert_allclose(plg.flux_scaling, 0.003631)
+
+    plg.vue_do_aper_phot()
+    row = cubeviz_helper.get_aperture_photometry_results()[0]
+
+    # Basically, we should recover the input rectangle here, minus background.
+    assert_allclose(row["xcenter"], 1 * u.pix)
+    assert_allclose(row["ycenter"], 3 * u.pix)
+    assert_allclose(row["sum"], 1.1752215e-12 * u.MJy)  # (15 - 10) MJy/sr x 2.3504431e-13 sr
+    assert_allclose(row["sum_aper_area"], 1 * (u.pix * u.pix))
+    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_wave"], 0.46236 * u.um)
diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_parsers.py b/jdaviz/configs/cubeviz/plugins/tests/test_parsers.py
@@ -53,7 +53,7 @@ def test_fits_image_hdu_with_microns(image_cube_hdu_obj_microns, cubeviz_helper)
         flux_unit_str = "erg / (Angstrom cm2 s)"
     else:
         flux_unit_str = "erg / (Angstrom s cm2)"
-    assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +1.00000e+00 1e-17 {flux_unit_str}',  # noqa
+    assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +5.00000e+00 1e-17 {flux_unit_str}',  # noqa
                                          'World 13h41m45.5759s +27d00m12.3044s (ICRS)',
                                          '205.4398995981 27.0034178810 (deg)')  # noqa
     unc_viewer = cubeviz_helper.app.get_viewer('uncert-viewer')
-Original file line number
+Diff line change
@@ Expand Up / @@ -26,6 +26,8 @@ Cubeviz @@
     - Spectral extraction plugin re-organized into subsections to be more consistent with specviz2d. [#2676]
+    - New aperture photometry plugin that can perform aperture photometry on selected cube slice. [#2666]
     Imviz
     ^^^^^
@@ Expand Down @@