Merge pull request #2273 from duytnguyendtn/specload

Replace load_spectrum with load_data

CHANGES.rst

@@ -11,6 +11,8 @@ New Features
 
 - Plots within plugins can now be popped-out into their own windows. [#2254]
 
+- The ``specviz.load_spectrum`` method is deprecated; use ``specviz.load_data`` instead. [#2273]
+
 Cubeviz
 ^^^^^^^
 

docs/cubeviz/import_data.rst

@@ -74,7 +74,7 @@ Importing data via the API
 
 Alternatively, users who work in a coding environment like a Jupyter
 notebook can access the Cubeviz helper class API. Using this API, users can
-load data into the application through code with the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
+load data into the application through code with the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data`
 method, which takes as input a :class:`~specutils.Spectrum1D` object.
 
 FITS Files
@@ -162,7 +162,7 @@ object, you can load it into Cubeviz as follows:
     # Create your spectrum1
     spec3d = Spectrum1D(data, wcs=my_wcs)
     cubeviz = Cubeviz()
-    cubeviz.load_spectrum(spec3d, data_label='My Cube')
+    cubeviz.load_data(spec3d, data_label='My Cube')
     cubeviz.show()
 
 There is no plan to natively load such objects until ``datamodels``

docs/specviz/export_data.rst

@@ -45,7 +45,7 @@ spectrum containing only your subset by running:
     spec = specviz.get_data(spectral_subset='Subset 1')
     subset_spec = Spectrum1D(flux=spec.flux[~spec.mask],
                              spectral_axis=spec.spectral_axis[~spec.mask])
-    specviz.load_spectrum(subset_spec)
+    specviz.load_data(subset_spec)
 
 .. seealso::
 

docs/specviz/import_data.rst

@@ -51,7 +51,7 @@ Importing data via the API
 Alternatively, users who work in a coding environment like a Jupyter
 notebook can access the Specviz helper class API. Using this API, users can
 load data into the application through code with the
-:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data`
 method, which takes as input a :class:`~specutils.Spectrum1D` object.
 
 FITS Files
@@ -64,15 +64,15 @@ The example below loads a FITS file into Specviz:
     from specutils import Spectrum1D
     spec1d = Spectrum1D.read("/path/to/data/file")
     specviz = Specviz()
-    specviz.load_spectrum(spec1d, data_label="my_spec")
+    specviz.load_data(spec1d, data_label="my_spec")
     specviz.show()
 
 You can also pass the path to a file that `~specutils.Spectrum1D` understands directly to the
-:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` method:
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data` method:
 
 .. code-block:: python
 
-    specviz.load_spectrum("path/to/data/file")
+    specviz.load_data("path/to/data/file")
 
 Creating Your Own Array
 -----------------------
@@ -90,7 +90,7 @@ You can create your own array to load into Specviz:
     wavelength = np.arange(5100, 5300) * u.AA
     spec1d = Spectrum1D(spectral_axis=wavelength, flux=flux)
     specviz = Specviz()
-    specviz.load_spectrum(spec1d, data_label="my_spec")
+    specviz.load_data(spec1d, data_label="my_spec")
     specviz.show()
 
 JWST datamodels
@@ -111,7 +111,7 @@ object, you can load it into Specviz as follows:
 
     spec1d = Spectrum1D(flux=flux, spectral_axis=wave)
     specviz = Specviz()
-    specviz.load_spectrum(spec1d, data_label="MultiSpecModel")
+    specviz.load_data(spec1d, data_label="MultiSpecModel")
     specviz.show()
 
 There is no plan to natively load such objects until ``datamodels``
@@ -122,7 +122,7 @@ is separated from the ``jwst`` pipeline package.
 Importing a SpectrumList
 ------------------------
 
-The :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` also accepts
+The :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data` also accepts
 a `~specutils.SpectrumList` object, in which case it will both load the
 individual `~specutils.Spectrum1D` objects in the list and additionally attempt
 to stitch together the spectra into a single data object so that
@@ -132,7 +132,7 @@ they can be manipulated and analyzed in the application as a single entity:
 
     from specutils import SpectrumList
     spec_list = SpectrumList([spec1d_1, spec1d_2])
-    specviz.load_spectrum(spec_list)
+    specviz.load_data(spec_list)
     specviz.show()
 
 In the screenshot below, the combined spectrum is plotted in gray, and one of
@@ -145,13 +145,13 @@ end of the red region in the screenshot below:
 .. image:: img/spectrumlist_combined.png
 
 This functionality is also available in limited instances by providing a directory path
-to the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` method. Note
+to the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data` method. Note
 that the ``read`` method of :class:`~specutils.SpectrumList` is only set up to handle
 directory input in limited cases, for example JWST MIRI MRS data, and will throw an error
 in other cases. In cases that it does work, only files in the directory level specified
 will be read, with no recursion into deeper folders.
 
-The :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` method also takes
+The :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_data` method also takes
 an optional keyword argument ``concat_by_file``. When set to ``True``, the spectra
 loaded in the :class:`~specutils.SpectrumList` will be concatenated together into one
 combined spectrum per loaded file, which may be useful for MIRI observations, for example.

jdaviz/configs/default/plugins/line_lists/tests/test_line_lists.py

@@ -12,7 +12,7 @@
 def test_line_lists(specviz_helper):
     spec = Spectrum1D(flux=np.random.rand(100)*u.Jy,
                       spectral_axis=np.arange(6000, 7000, 10)*u.AA)
-    specviz_helper.load_spectrum(spec)
+    specviz_helper.load_data(spec)
 
     lt = QTable()
     lt['linename'] = ['O III', 'Halpha']
@@ -51,7 +51,7 @@ def test_redshift(specviz_helper, spectrum1d):
     assert plg._obj.disabled_msg
 
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     assert not plg._obj.disabled_msg
 
@@ -102,7 +102,7 @@ def test_redshift(specviz_helper, spectrum1d):
 def test_load_available_preset_lists(specviz_helper, spectrum1d):
     """ Loads all available line lists and checks the medium requirement """
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     # Check to make sure we got our line lists
     available_linelists = get_available_linelists()
@@ -125,7 +125,7 @@ def test_load_available_preset_lists(specviz_helper, spectrum1d):
 
 def test_line_identify(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     lt = QTable()
     lt['linename'] = ['O III', 'Halpha']

jdaviz/configs/default/plugins/model_fitting/tests/test_plugin.py

@@ -20,7 +20,7 @@
 
 
 def test_default_model_labels(specviz_helper, spectrum1d):
-    specviz_helper.load_spectrum(spectrum1d)
+    specviz_helper.load_data(spectrum1d)
     modelfit_plugin = specviz_helper.plugins['Model Fitting']
     # By default, the spectral region should be the entire spectrum
     assert modelfit_plugin._obj.spectral_subset_selected == "Entire Spectrum"
@@ -46,7 +46,7 @@ def test_default_model_labels(specviz_helper, spectrum1d):
 
 
 def test_custom_model_labels(specviz_helper, spectrum1d):
-    specviz_helper.load_spectrum(spectrum1d)
+    specviz_helper.load_data(spectrum1d)
     modelfit_plugin = specviz_helper.plugins['Model Fitting']
 
     for i, model in enumerate(MODELS):
@@ -68,7 +68,7 @@ def test_register_model_with_uncertainty_weighting(specviz_helper, spectrum1d):
     spectrum1d.uncertainty = StdDevUncertainty(spectrum1d.flux * 0.1)
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
-        specviz_helper.load_spectrum(spectrum1d)
+        specviz_helper.load_data(spectrum1d)
     modelfit_plugin = specviz_helper.plugins['Model Fitting']
 
     # Test registering a simple linear fit
@@ -105,7 +105,7 @@ def test_register_model_uncertainty_is_none(specviz_helper, spectrum1d):
     spectrum1d.uncertainty = None
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
-        specviz_helper.load_spectrum(spectrum1d)
+        specviz_helper.load_data(spectrum1d)
     modelfit_plugin = specviz_helper.plugins['Model Fitting']
 
     # Test registering a simple linear fit
@@ -157,7 +157,7 @@ def test_register_cube_model(cubeviz_helper, spectrum1d_cube):
 def test_user_api(specviz_helper, spectrum1d):
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
-        specviz_helper.load_spectrum(spectrum1d)
+        specviz_helper.load_data(spectrum1d)
     p = specviz_helper.plugins['Model Fitting']
 
     # even though the default label is set to C, adding Linear1D should default to its automatic
@@ -195,7 +195,7 @@ def test_user_api(specviz_helper, spectrum1d):
 def test_fit_gaussian_with_fixed_mean(specviz_helper, spectrum1d):
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
-        specviz_helper.load_spectrum(spectrum1d)
+        specviz_helper.load_data(spectrum1d)
     modelfit_plugin = specviz_helper.plugins['Model Fitting']
 
     modelfit_plugin.create_model_component('Gaussian1D', 'G')
@@ -217,7 +217,7 @@ def test_fit_gaussian_with_fixed_mean(specviz_helper, spectrum1d):
 def test_reestimate_parameters(specviz_helper, spectrum1d):
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
-        specviz_helper.load_spectrum(spectrum1d)
+        specviz_helper.load_data(spectrum1d)
     mf = specviz_helper.plugins['Model Fitting']
 
     mf.create_model_component('Gaussian1D', 'G')
@@ -327,12 +327,12 @@ def test_subset_masks(cubeviz_helper, spectrum1d_cube_larger):
 
 def test_invalid_subset(specviz_helper, spectrum1d):
     # 6000-8000
-    specviz_helper.load_spectrum(spectrum1d, data_label="right_spectrum")
+    specviz_helper.load_data(spectrum1d, data_label="right_spectrum")
 
     # 5000-7000
     sp2 = Spectrum1D(spectral_axis=spectrum1d.spectral_axis - 1000*spectrum1d.spectral_axis.unit,
                      flux=spectrum1d.flux * 1.25)
-    specviz_helper.load_spectrum(sp2, data_label="left_spectrum")
+    specviz_helper.load_data(sp2, data_label="left_spectrum")
 
     # apply subset that overlaps on left_spectrum, but not right_spectrum
     # NOTE: using a subset that overlaps the right_spectrum (reference) results in errors when

jdaviz/configs/default/plugins/subset_plugin/tests/test_subset_plugin.py

@@ -6,7 +6,7 @@
 
 @pytest.mark.filterwarnings('ignore')
 def test_plugin(specviz_helper, spectrum1d):
-    specviz_helper.load_spectrum(spectrum1d)
+    specviz_helper.load_data(spectrum1d)
     p = specviz_helper.plugins['Subset Tools']
 
     # regression test for https://github.com/spacetelescope/jdaviz/issues/1693

jdaviz/configs/specviz/helper.py

@@ -1,7 +1,7 @@
 import warnings
 
 from astropy import units as u
-from astropy.utils.decorators import deprecated_renamed_argument
+from astropy.utils.decorators import deprecated_renamed_argument, deprecated
 from regions.core.core import Region
 from glue.core.subset_group import GroupedSubset
 from specutils import SpectralRegion, Spectrum1D
@@ -41,11 +41,35 @@ def __init__(self, *args, **kwargs):
         self.app.hub.subscribe(self, RedshiftMessage,
                                handler=self._redshift_listener)
 
+    @deprecated(since="3.6", alternative="load_data")
     def load_spectrum(self, data, data_label=None, format=None, show_in_viewer=True,
                       concat_by_file=False):
         """
         Loads a data file or `~specutils.Spectrum1D` object into Specviz.
 
+        Parameters
+        ----------
+        data : str, `~specutils.Spectrum1D`, or `~specutils.SpectrumList`
+            Spectrum1D, SpectrumList, or path to compatible data file.
+        data_label : str
+            The Glue data label found in the ``DataCollection``.
+        format : str
+            Loader format specification used to indicate data format in
+            `~specutils.Spectrum1D.read` io method.
+        show_in_viewer : bool
+            Show data in viewer(s).
+        concat_by_file : bool
+            If True and there is more than one available extension, concatenate
+            the extensions within each spectrum file passed to the parser and
+            add a concatenated spectrum to the data collection.
+        """
+        self.load_data(data, data_label, format, show_in_viewer, concat_by_file)
+
+    def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
+                  concat_by_file=False):
+        """
+        Load data into Specviz.
+
         Parameters
         ----------
         data : str, `~specutils.Spectrum1D`, or `~specutils.SpectrumList`

jdaviz/configs/specviz/plugins/line_analysis/tests/test_line_analysis.py

@@ -14,7 +14,7 @@
 
 def test_plugin(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -79,7 +79,7 @@ def test_spatial_subset(cubeviz_helper, image_cube_hdu_obj):
 
 def test_user_api(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     sv = specviz_helper.app.get_viewer('spectrum-viewer')
     sv.apply_roi(XRangeROI(6500, 7400))
@@ -109,7 +109,7 @@ def test_user_api(specviz_helper, spectrum1d):
 
 def test_line_identify(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     lt = QTable()
     lt['linename'] = ['O III', 'Halpha']
@@ -180,7 +180,7 @@ def test_coerce_unit():
 
 def test_continuum_surrounding_spectral_subset(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -207,7 +207,7 @@ def test_continuum_surrounding_spectral_subset(specviz_helper, spectrum1d):
 
 def test_continuum_spectral_same_value(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -234,7 +234,7 @@ def test_continuum_spectral_same_value(specviz_helper, spectrum1d):
 
 def test_continuum_surrounding_invalid_width(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -259,7 +259,7 @@ def test_continuum_surrounding_invalid_width(specviz_helper, spectrum1d):
 
 def test_continuum_subset_spectral_entire(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -286,7 +286,7 @@ def test_continuum_subset_spectral_entire(specviz_helper, spectrum1d):
 
 def test_continuum_subset_spectral_subset2(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -319,7 +319,7 @@ def test_continuum_subset_spectral_subset2(specviz_helper, spectrum1d):
 
 def test_continuum_surrounding_no_right(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -347,7 +347,7 @@ def test_continuum_surrounding_no_right(specviz_helper, spectrum1d):
 
 def test_continuum_surrounding_no_left(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -375,7 +375,7 @@ def test_continuum_surrounding_no_left(specviz_helper, spectrum1d):
 
 def test_subset_changed(specviz_helper, spectrum1d):
     label = "Test 1D Spectrum"
-    specviz_helper.load_spectrum(spectrum1d, data_label=label)
+    specviz_helper.load_data(spectrum1d, data_label=label)
 
     plugin = specviz_helper.app.get_tray_item_from_name('specviz-line-analysis')
     plugin.open_in_tray()
@@ -406,12 +406,12 @@ def test_subset_changed(specviz_helper, spectrum1d):
 
 def test_invalid_subset(specviz_helper, spectrum1d):
     # 6000-8000
-    specviz_helper.load_spectrum(spectrum1d, data_label="right_spectrum")
+    specviz_helper.load_data(spectrum1d, data_label="right_spectrum")
 
     # 5000-7000
     sp2 = Spectrum1D(spectral_axis=spectrum1d.spectral_axis - 1000*spectrum1d.spectral_axis.unit,
                      flux=spectrum1d.flux * 1.25)
-    specviz_helper.load_spectrum(sp2, data_label="left_spectrum")
+    specviz_helper.load_data(sp2, data_label="left_spectrum")
 
     # apply subset that overlaps on left_spectrum, but not right_spectrum
     # NOTE: using a subset that overlaps the right_spectrum (reference) results in errors when