deprecate conf-specific helper methods in specviz, specviz2d, cubeviz (…

…spacetelescope#3388)

* deprecate helper-specific methods in specviz/2d
* re-implement get_spectra
* fix RTD warning
* fix aper phot doc ref to export table
* update tests
* update notebooks

CHANGES.rst

@@ -53,9 +53,13 @@ Mosviz
 Specviz
 ^^^^^^^
 
+- Specviz-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [#3388]
+
 Specviz2d
 ^^^^^^^^^
 
+- Specviz2d-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [#3388]
+
 Bug Fixes
 ---------
 
@@ -64,9 +68,13 @@ Cubeviz
 
 - Fixed copious warnings from spaxel tool when data has INF. [#3368]
 
+- Cubeviz-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [#3388]
+
 Imviz
 ^^^^^
 
+- ``get_aperture_photometry_results`` helper-level method is deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [#3388]
+
 Mosviz
 ^^^^^^
 

docs/cubeviz/export_data.rst

@@ -86,20 +86,20 @@ For a list of model labels:
 
 .. code-block:: python
 
-    models = cubeviz.get_models()
+    models = cubeviz.plugins['Model Fitting'].get_models()
     models
 
 Once you know the model labels, to get a specific model:
 
 .. code-block:: python
 
-    mymodel = cubeviz.get_models(model_label="ModelLabel", x=10)
+    mymodel = cubeviz.plugins['Model Fitting'].get_models(model_label="ModelLabel", x=10)
 
 To extract all of the model parameters:
 
 .. code-block:: python
 
-    myparams = cubeviz.get_model_parameters(model_label="ModelLabel", x=x, y=y)
+    myparams = cubeviz.plugins['Model Fitting'].get_model_parameters(model_label="ModelLabel", x=x, y=y)
     myparams
 
 where the ``model_label`` parameter identifies which model should be returned and

docs/specviz/export_data.rst

@@ -84,20 +84,20 @@ For a list of model labels:
 
 .. code-block:: python
 
-    models = specviz.get_models()
+    models = specviz.plugins['Model Fitting'].get_models()
     models
 
 Once you know the model labels, to get a specific model:
 
 .. code-block:: python
 
-    mymodel = specviz.get_models(model_label="ModelLabel")
+    mymodel = specviz.plugins['Model Fitting'].get_models(model_label="ModelLabel")
 
 To extract all of the model parameters:
 
 .. code-block:: python
 
-    myparams = specviz.get_model_parameters(model_label="ModelLabel")
+    myparams = specviz.plugins['Model Fitting'].get_model_parameters(model_label="ModelLabel")
     myparams
 
 where the ``model_label`` parameter identifies which model should be returned.

jdaviz/app.py

@@ -366,9 +366,6 @@ def __init__(self, configuration=None, *args, **kwargs):
         self.hub.subscribe(self, SnackbarMessage,
                            handler=self._on_snackbar_message)
 
-        # Add a fitted_models dictionary that the helpers (or user) can access
-        self.fitted_models = {}
-
         # Internal cache so we don't have to keep calling get_object for the same Data.
         # Key should be (data_label, statistic) and value the translated object.
         self._get_object_cache = {}

jdaviz/configs/cubeviz/helper.py

@@ -1,3 +1,5 @@
+from astropy.utils.decorators import deprecated
+
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
 from jdaviz.configs.specviz import Specviz
 from jdaviz.core.events import AddDataMessage, SnackbarMessage
@@ -97,6 +99,7 @@ def load_data(self, data, data_label=None, override_cube_limit=False, **kwargs):
                     color='warning', sender=self, timeout=10000)
             self.app.hub.broadcast(msg)
 
+    @deprecated(since="4.2", alternative="plugins['Slice'].value")
     def select_wavelength(self, wavelength):
         """
         Select the slice closest to the provided wavelength.
@@ -149,8 +152,7 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
                               spectral_subset=spectral_subset,
                               cls=cls, use_display_units=use_display_units)
 
-    # Need this method for Imviz Aperture Photometry plugin.
-
+    @deprecated(since="4.2", alternative="plugins['Aperture Photometry'].export_table()")
     def get_aperture_photometry_results(self):
         """Return aperture photometry results, if any.
         Results are calculated using :ref:`cubeviz-aper-phot` plugin.
@@ -161,4 +163,4 @@ def get_aperture_photometry_results(self):
             Photometry results if available or `None` otherwise.
 
         """
-        return self.plugins['Aperture Photometry']._obj.export_table()
+        return self.plugins['Aperture Photometry'].export_table()

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

@@ -36,11 +36,11 @@ def test_slice(cubeviz_helper, spectrum1d_cube):
     assert cubeviz_helper.app.get_viewer("flux-viewer").slice == 1
     assert cubeviz_helper.app.get_viewer("flux-viewer").state.slices[-1] == 1
     assert cubeviz_helper.app.get_viewer("uncert-viewer").state.slices[-1] == 1
-    cubeviz_helper.select_wavelength(slice_values[0])
+    sl.value = slice_values[0]
     assert cubeviz_helper.app.get_viewer("flux-viewer").slice == 0
     assert sl.value == slice_values[0]
 
-    cubeviz_helper.select_wavelength(slice_values[1])
+    sl.value = slice_values[1]
     assert sl.value == slice_values[1]
 
     # test setting a static 2d image to the "watched" flux viewer to make sure it disconnects
@@ -57,14 +57,14 @@ def test_slice(cubeviz_helper, spectrum1d_cube):
     sv.state.layers[0].as_steps = True
     new_len = len(sv.native_marks[0].x)
     assert new_len == 2*orig_len
-    cubeviz_helper.select_wavelength(4.62360028e-07)
+    sl.value = 4.62360028e-07
     assert sl.value == slice_values[1]
 
     # Add test for unit conversion
     uc_plugin = cubeviz_helper.plugins['Unit Conversion']._obj
     uc_plugin.spectral_unit.selected = 'Angstrom'
     assert sl.value_unit == 'Angstrom'
-    cubeviz_helper.select_wavelength(4623.60028)
+    sl.value = 4623.60028
     assert sl.value == 4623.600276968349
 
     # Retrieve updated slice_values

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

@@ -31,7 +31,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     plg.dataset_selected = "test[FLUX]"
     plg.aperture_selected = "Subset 1"
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[0]
+    row = plg.export_table()[0]
 
     # Basically, we should recover the input rectangle here.
     assert_allclose(row["xcenter"], 1 * u.pix)
@@ -51,7 +51,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     cube_slice_plg = cubeviz_helper.plugins["Slice"]._obj
     cube_slice_plg.vue_goto_first()
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[1]
+    row = plg.export_table()[1]
 
     # Same rectangle but different slice value.
     assert_allclose(row["xcenter"], 1 * u.pix)
@@ -79,7 +79,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     plg.dataset_selected = "test[FLUX] collapsed"
     plg.aperture_selected = "Subset 1"
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[2]
+    row = plg.export_table()[2]
 
     # Basically, we should recover the input rectangle here.
     assert_allclose(row["xcenter"], 1 * u.pix)
@@ -121,7 +121,7 @@ def test_cubeviz_aperphot_generated_3d_gaussian_smooth(cubeviz_helper, image_cub
     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]
+    row = cubeviz_helper.plugins['Aperture Photometry'].export_table()[0]
 
     # Basically, we should recover the input rectangle here.
     assert_allclose(row["xcenter"], 1 * u.pix)
@@ -182,7 +182,7 @@ def test_cubeviz_aperphot_cube_sr_and_pix2(cubeviz_helper,
         cube_unit = u.MJy / solid_angle_unit  # cube unit in app is now per pix2
 
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[0]
+    row = cubeviz_helper.plugins['Aperture Photometry'].export_table()[0]
 
     # Basically, we should recover the input rectangle here, minus background.
     assert_allclose(row["xcenter"], 3 * u.pix)
@@ -227,7 +227,7 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper,
     assert_allclose(plg.flux_scaling, 0.003631)
 
     plg.vue_do_aper_phot()
-    row = cubeviz_helper.get_aperture_photometry_results()[0]
+    row = cubeviz_helper.plugins['Aperture Photometry'].export_table()[0]
 
     # Basically, we should recover the input rectangle here, minus background.
     assert_allclose(row["xcenter"], 3 * u.pix)

jdaviz/configs/default/plugins/data_quality/data_quality.py

@@ -53,8 +53,6 @@ class DataQuality(PluginTemplateMixin, ViewerSelectMixin):
     """
     template_file = __file__, "data_quality.vue"
 
-    irrelevant_msg = Unicode("").tag(sync=True)
-
     # `layer` is the science data layer
     science_layer_multiselect = Bool(False).tag(sync=True)
     science_layer_items = List().tag(sync=True)