Rename Subset Tools Plugin (#3293)

* Rename Subset Tools plugin

* Continue with renaming subset tools

* Fix codestyle and update docstring

* Add a change log

* Fix failing test

* Remove direct use of _obj in notebooks

* Remove _obj from tests

* Remove remaining _obj reference

* Continue with removing of redundant _obj

* Remove .selected from tests

* Clean up remaining redundant calls

* Revert removal _obj calls on unexposed api.s

* Fix tests

* Revert latest changes

* Fix tests enforcing non exposed apis with _obj

* Fix code syle

* Update CHANGES.rst

Co-authored-by: Kyle Conroy <[email protected]>

* Fix typo in notebooks

* Codestyle

* Suppress output

CHANGES.rst

@@ -26,6 +26,8 @@ Specviz2d
 API Changes
 -----------
 - Removed API access to plugins that have passed the deprecation period: Links Control, Canvas Rotation, Export Plot. [#3270]
+
+- Renamed the ``Subset Tools`` plugin to ``Subsets`` which now exposes the ``subset``, ``combination_mode``, ``get_center``, and ``set_center`` in the user API. [#3293]
 
 Cubeviz
 ^^^^^^^

docs/cubeviz/import_data.rst

@@ -197,15 +197,15 @@ can load the regions into Cubeviz as follows:
 
 .. code-block:: python
 
-    cubeviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg")
+    cubeviz.plugins['Subsets'].import_region("/path/to/data/myregions.reg")
 
 Unsupported regions will be skipped and trigger a warning. Those that
 failed to load, if any, can be returned as a list of tuples of the
 form ``(region, reason)``:
 
 .. code-block:: python
 
-    bad_regions = cubeviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg", return_bad_regions=True)
+    bad_regions = cubeviz.plugins['Subsets'].import_region("/path/to/data/myregions.reg", return_bad_regions=True)
 
 .. note:: Sky regions are currently unsupported in Cubeviz, unlike Imviz.
 

docs/cubeviz/plugins.rst

@@ -61,12 +61,12 @@ Visualize data quality arrays for spectral cubes from JWST.
 
 .. _cubeviz-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 .. seealso::
 
-    :ref:`Subset Tools <imviz-subset-plugin>`
+    :ref:`Subsets <imviz-subset-plugin>`
         Imviz documentation describing the concept of subsets in Jdaviz.
 
 

docs/imviz/import_data.rst

@@ -218,15 +218,15 @@ can load the regions into Imviz as follows:
 
 .. code-block:: python
 
-    imviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg")
+    imviz.plugins['Subsets'].import_region("/path/to/data/myregions.reg")
 
 Unsupported regions will be skipped and trigger a warning. Those that
 failed to load, if any, can be returned as a list of tuples of the
 form ``(region, reason)``:
 
 .. code-block:: python
 
-    bad_regions = imviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg", return_bad_regions=True)
+    bad_regions = imviz.plugins['Subsets'].import_region("/path/to/data/myregions.reg", return_bad_regions=True)
 
 You could also define :ref:`regions:shapes` programmatically and load them; e.g.:
 

docs/imviz/plugins.rst

@@ -94,8 +94,8 @@ in the "Filter by bits" dropdown, or from the API we could:
 
 .. _imviz-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 This plugin allows you to select an existing subset to modify, or to select
 :guilabel:`Create new` to create a new subset by selecting and using the region selector

docs/mosviz/plugins.rst

@@ -36,12 +36,12 @@ This plugin gives access to per-viewer and per-layer plotting options.
 
 .. _mosviz-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 .. seealso::
 
-    :ref:`Subset Tools <imviz-subset-plugin>`
+    :ref:`Subsets <imviz-subset-plugin>`
         Imviz documentation describing the concept of subsets in Jdaviz.
 
 .. _imviz_export_markers:

docs/rampviz/plugins.rst

@@ -30,12 +30,12 @@ To show axes on image viewers, toggle on the "Show axes" option at the bottom of
 
 .. _rampviz-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 .. seealso::
 
-    :ref:`Subset Tools <imviz-subset-plugin>`
+    :ref:`Subsets <imviz-subset-plugin>`
         Imviz documentation describing the concept of subsets in Jdaviz.
 
 

docs/specviz/plugins.rst

@@ -42,12 +42,12 @@ Plot Options
 
 .. _specviz-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 .. seealso::
 
-    :ref:`Subset Tools <imviz-subset-plugin>`
+    :ref:`Subsets <imviz-subset-plugin>`
         Imviz documentation describing the concept of subsets in Jdaviz. Subsets
         in Specviz are strictly spectral subsets and do not support rotation or
         recentering.

docs/specviz2d/plugins.rst

@@ -30,12 +30,12 @@ Plot Options
 
 .. _specviz2d-subset-plugin:
 
-Subset Tools
-============
+Subsets
+=======
 
 .. seealso::
 
-    :ref:`Subset Tools <imviz-subset-plugin>`
+    :ref:`Subsets <imviz-subset-plugin>`
         Imviz documentation describing the concept of subsets in Jdaviz.
 
 Markers

jdaviz/components/data_menu_subset_edit.vue

@@ -25,7 +25,7 @@
     <v-list dense style="width: 300px">
       <v-list-item>
         <v-list-item-content>
-          <j-tooltip :tooltipcontent="'Open '+subset_selected+' in Subset Tools plugin'">
+          <j-tooltip :tooltipcontent="'Open '+subset_selected+' in Subsets plugin'">
             <span
               style="cursor: pointer; width: 100%"
               @click="() => {$emit('view-info')}"

jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py

@@ -229,8 +229,8 @@ def test_moment_frequency_unit_conversion(cubeviz_helper, spectrum1d_cube_larger
     mm = cubeviz_helper.plugins['Moment Maps']
 
     unit = u.Unit(uc.spectral_unit.selected)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(SpectralRegion(4.624e-07 * unit,
-                                                                             4.627e-07 * unit))
+    cubeviz_helper.plugins['Subsets'].import_region(SpectralRegion(4.624e-07 * unit,
+                                                                   4.627e-07 * unit))
 
     uc.spectral_unit = 'Hz'
     mm.spectral_subset = 'Subset 1'

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

@@ -83,7 +83,7 @@ def test_gauss_smooth_before_spec_extract(cubeviz_helper, spectrum1d_cube_with_u
         # two-pixel region:
         CirclePixelRegion(PixCoord(0.5, 0), radius=1.2)
     ]
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(regions, combination_mode='new')
+    cubeviz_helper.plugins['Subsets'].import_region(regions, combination_mode='new')
 
     extract_plugin = cubeviz_helper.plugins['Spectral Extraction']
     extract_plugin.function = "Sum"
@@ -123,7 +123,7 @@ def test_subset(
     ]
 
     cubeviz_helper.load_data(spectrum1d_cube_with_uncerts)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(regions, combination_mode='new')
+    cubeviz_helper.plugins['Subsets'].import_region(regions, combination_mode='new')
 
     plg = cubeviz_helper.plugins['Spectral Extraction']
     plg.function = function
@@ -174,7 +174,7 @@ def test_extracted_file_in_export_plugin(cubeviz_helper, spectrum1d_cube_with_un
 def test_aperture_markers(cubeviz_helper, spectrum1d_cube):
 
     cubeviz_helper.load_data(spectrum1d_cube)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         [CirclePixelRegion(PixCoord(0.5, 0), radius=1.2)])
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
@@ -227,9 +227,9 @@ def test_cone_aperture_with_different_methods(cubeviz_helper, spectrum1d_cube_la
                                               expected_flux_2400):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
     center = PixCoord(5, 10)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         CirclePixelRegion(center, radius=2.5), combination_mode='new')
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         EllipsePixelRegion(center, width=5, height=5), combination_mode='new')
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
@@ -260,7 +260,7 @@ def test_cylindrical_aperture_with_different_methods(cubeviz_helper, spectrum1d_
                                                      subset, aperture_method, expected_flux_wav):
     cubeviz_helper.load_data(spectrum1d_cube_largest, data_label="test")
     center = PixCoord(5, 10)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
+    cubeviz_helper.plugins['Subsets'].import_region([
         CirclePixelRegion(center, radius=2.5),
         EllipsePixelRegion(center, width=5, height=5)], combination_mode='new')
 
@@ -284,7 +284,7 @@ def test_cylindrical_aperture_with_different_methods(cubeviz_helper, spectrum1d_
 # NOTE: Not as thorough as circle and ellipse above but good enough.
 def test_rectangle_aperture_with_exact(cubeviz_helper, spectrum1d_cube_largest):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         RectanglePixelRegion(PixCoord(5, 10), width=4, height=4))
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
@@ -312,7 +312,7 @@ def test_background_subtraction(cubeviz_helper, spectrum1d_cube_largest):
     spectrum1d_cube_largest = spectrum1d_cube_largest + 1 * u.Jy
 
     cubeviz_helper.load_data(spectrum1d_cube_largest)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
+    cubeviz_helper.plugins['Subsets'].import_region([
         CirclePixelRegion(PixCoord(5, 10), radius=2.5),
         EllipsePixelRegion(PixCoord(13, 10), width=3, height=5)], combination_mode='new')
 
@@ -365,7 +365,7 @@ def test_background_subtraction(cubeviz_helper, spectrum1d_cube_largest):
 def test_cone_and_cylinder_errors(cubeviz_helper, spectrum1d_cube_largest):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
     center = PixCoord(5, 10)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
+    cubeviz_helper.plugins['Subsets'].import_region([
         CirclePixelRegion(center, radius=2.5),
         CircleAnnulusPixelRegion(center, inner_radius=2.5, outer_radius=4)], combination_mode='new')
 
@@ -392,7 +392,7 @@ def test_cone_and_cylinder_errors(cubeviz_helper, spectrum1d_cube_largest):
 def test_cone_aperture_with_frequency_units(cubeviz_helper, spectral_cube_wcs):
     data = Spectrum1D(flux=np.ones((128, 129, 256)) * u.nJy, wcs=spectral_cube_wcs)
     cubeviz_helper.load_data(data, data_label="Test Flux")
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         [CirclePixelRegion(PixCoord(14, 15), radius=2.5)])
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
@@ -413,7 +413,7 @@ def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
     sp = extract_plg.extract()  # Default settings (sum)
     assert_allclose(sp.flux.value, 9.6E-16)  # (10 x 10) - 4
 
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         RectanglePixelRegion(PixCoord(1.5, 1.5), width=4, height=4))
     extract_plg.aperture = 'Subset 1'
     sp_subset = extract_plg.extract()  # Default settings but on Subset
@@ -422,7 +422,7 @@ def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
 
 def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+    cubeviz_helper.plugins['Subsets'].import_region(
         CircularROI(xc=5, yc=5, radius=2))
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
@@ -434,8 +434,8 @@ def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
 #    orig_med_flux = np.median(cubeviz_helper.get_data('extracted').flux)
 
     # replace Subset 1 with a larger subset, resulting fluxes should increase
-    cubeviz_helper.plugins['Subset Tools']._obj.combination_mode.selected = 'replace'
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(CircularROI(xc=5, yc=5, radius=3))
+    cubeviz_helper.plugins['Subsets'].combination_mode = 'replace'
+    cubeviz_helper.plugins['Subsets'].import_region(CircularROI(xc=5, yc=5, radius=3))
 
     # update should take place automatically, but since its async, we'll call manually to ensure
     # the update is complete before comparing results
@@ -449,7 +449,7 @@ def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
 
 def test_aperture_composite_detection(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper.load_data(spectrum1d_cube)
-    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin = cubeviz_helper.plugins['Subsets']
     spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']._obj
 
     # create a rectangular subset with all spaxels:
@@ -463,7 +463,7 @@ def test_aperture_composite_detection(cubeviz_helper, spectrum1d_cube):
     # now remove from this subset a circular region in the center:
     circle = CircularROI(0.5, 1.5, 1)
 
-    subset_plugin.combination_mode.selected = 'andnot'
+    subset_plugin.combination_mode = 'andnot'
     subset_plugin.import_region(circle)
 
     # now the subset is composite:
@@ -473,14 +473,14 @@ def test_aperture_composite_detection(cubeviz_helper, spectrum1d_cube):
 def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper.load_data(spectrum1d_cube)
 
-    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin = cubeviz_helper.plugins['Subsets']
     spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']._obj
 
     lower_aperture = RectangularROI(-0.5, 0.5, -0.5, 1.5)
     upper_aperture = RectangularROI(2.5, 3.5, -0.5, 1.5)
 
     subset_plugin.import_region(lower_aperture)
-    subset_plugin.combination_mode.selected = 'new'
+    subset_plugin.combination_mode = 'new'
     subset_plugin.import_region(upper_aperture)
 
     spec_extr_plugin.aperture_selected = 'Subset 1'
@@ -491,13 +491,13 @@ def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
 
     rectangle = RectangularROI(-0.5, 3.5, -0.5, 1.5)
 
-    subset_plugin.combination_mode.selected = 'new'
+    subset_plugin.combination_mode = 'new'
     subset_plugin.import_region(rectangle)
 
-    subset_plugin.subset_selected = 'Subset 3'
+    subset_plugin._obj.subset_selected = 'Subset 3'
     circle = CircularROI(1.5, 0.5, 1.1)
 
-    subset_plugin.combination_mode.selected = 'andnot'
+    subset_plugin.combination_mode = 'andnot'
     subset_plugin.import_region(circle)
 
     spec_extr_plugin.aperture_selected = 'Subset 3'
@@ -533,7 +533,7 @@ def test_default_spectral_extraction(cubeviz_helper, spectrum1d_cube_fluxunit_jy
     # for non-science pixels in the sums:
     cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian)
 
-    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin = cubeviz_helper.plugins['Subsets']
 
     subset_plugin.import_region(CircularROI(1.5, 2, 5))
 
@@ -619,7 +619,7 @@ def test_spectral_extraction_scientific_validation(
         cubeviz_helper.load_data(uri, cache=True)
 
     # add a subset with an aperture centered on each source
-    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin = cubeviz_helper.plugins['Subsets']
     subset_plugin.import_region(CircularROI(*aperture))
 
     # set the slice to the blue end of MIRI CH1

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

@@ -16,7 +16,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     solid_angle_unit = PIX2
 
     aper = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=3, height=5)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(aper)
+    cubeviz_helper.plugins['Subsets'].import_region(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)
@@ -112,7 +112,7 @@ def test_cubeviz_aperphot_generated_3d_gaussian_smooth(cubeviz_helper, image_cub
     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.plugins['Subset Tools']._obj.import_region(aper)
+    cubeviz_helper.plugins['Subsets'].import_region(aper)
 
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
     plg.dataset_selected = "test[FLUX] spatial-smooth stddev-1.0"
@@ -210,7 +210,7 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_c
 
     aper = RectanglePixelRegion(center=PixCoord(x=3, y=1), width=1, height=1)
     bg = RectanglePixelRegion(center=PixCoord(x=2, y=0), width=1, height=1)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region([aper, bg], combination_mode='new')
+    cubeviz_helper.plugins['Subsets'].import_region([aper, bg], combination_mode='new')
 
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
     plg.dataset_selected = "test[FLUX]"
@@ -277,7 +277,7 @@ def test_cubeviz_aperphot_unit_conversion(cubeviz_helper, spectrum1d_cube_custom
     bg = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=1, height=1)
 
     cubeviz_helper.load_data(mjy_sr_cube, data_label="test")
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region([aper, bg], combination_mode='new')
+    cubeviz_helper.plugins['Subsets'].import_region([aper, bg], combination_mode='new')
 
     ap = cubeviz_helper.plugins['Aperture Photometry']._obj
 

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

@@ -43,7 +43,7 @@ def test_get_data_spatial_and_spectral(cubeviz_helper, spectrum1d_cube_larger):
     cubeviz_helper._apply_interactive_region('bqplot:ellipse', (0, 0), (9, 8))
 
     # Subset 2 (spectral)
-    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin = cubeviz_helper.plugins['Subsets']
     unit = spectrum1d_cube_larger.spectral_axis.unit
     subset_plugin.import_region(SpectralRegion(4.62440061e-07 * unit, 4.62520112e-07 * unit))
 

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

@@ -72,8 +72,8 @@ def test_spectrum1d_with_fake_fixed_units(spectrum1d, cubeviz_helper):
 
     cubeviz_helper.app.add_data_to_viewer('spectrum-viewer', 'test')
     unit = u.Unit(cubeviz_helper.plugins['Unit Conversion'].spectral_unit.selected)
-    cubeviz_helper.plugins['Subset Tools']._obj.import_region(SpectralRegion(6600 * unit,
-                                                                             7400 * unit))
+    cubeviz_helper.plugins['Subsets'].import_region(SpectralRegion(6600 * unit,
+                                                                   7400 * unit))
 
     subsets = cubeviz_helper.app.get_subsets()
     reg = subsets.get('Subset 1')