Merge pull request #2242 from duytnguyendtn/depsubsets

Deprecate subset getters

CHANGES.rst

@@ -39,6 +39,13 @@ Specviz2d
 API Changes
 -----------
 
+- ``viz.app.get_data_from_viewer()`` is deprecated; use ``viz.get_data()``. [#2242]
+
+- ``viz.app.get_subsets_from_viewer()`` is deprecated; use ``viz.app.get_subsets()``. [#2242]
+
+- ``viz.get_data()`` now takes optional ``**kwargs``; e.g., you could pass in
+  ``function="sum"`` to collapse a cube in Cubeviz. [#2242]
+
 Cubeviz
 ^^^^^^^
 
@@ -48,10 +55,13 @@ Imviz
 Mosviz
 ^^^^^^
 
+- Added new ``statistic`` keyword to ``mosviz.get_viewer("spectrum-2d-viewer").data()``
+  to allow user to collapse 2D spectrum to 1D. [#2242]
+
 Specviz
 ^^^^^^^
 
-* Re-enabled unit conversion support. [#2127]
+- Re-enabled unit conversion support. [#2127]
 
 Specviz2d
 ^^^^^^^^^
@@ -61,6 +71,8 @@ Bug Fixes
 
 - Fixed wrong elliptical region translation in ``app.get_subsets()``. [#2244]
 
+- Fixed ``cls`` input being ignored in ``viz.get_data()``. [#2242]
+
 Cubeviz
 ^^^^^^^
 

docs/cubeviz/export_data.rst

@@ -22,7 +22,7 @@ can be used to extract the *spectrum* of a spatial subset named "Subset 1":
 
 .. code-block:: python
 
-    subset1_spec1d = cubeviz.specviz.get_spectra(subset_to_apply="Subset 1")
+    subset1_spec1d = cubeviz.specviz.get_spectra(spectral_subset="Subset 1")
 
 An example without accessing Specviz:
 
@@ -41,7 +41,7 @@ To get all subsets from the spectrum viewer:
 
 .. code-block:: python
 
-    subset1_spec1d = cubeviz.app.get_subsets_from_viewer("spectrum-viewer")
+    subset1_spec1d = cubeviz.specviz.app.get_subsets()
 
 To access the spatial regions themselves:
 

jdaviz/app.py

@@ -14,6 +14,7 @@
 from astropy.io import fits
 from astropy.coordinates import Angle
 from astropy.time import Time
+from astropy.utils.decorators import deprecated
 from regions import PixCoord, CirclePixelRegion, RectanglePixelRegion, EllipsePixelRegion
 
 from echo import CallbackProperty, DictCallbackProperty, ListCallbackProperty
@@ -662,6 +663,7 @@ def get_viewer_by_id(self, vid):
         """
         return self._viewer_store.get(vid)
 
+    @deprecated(since="3.6", alternative="viz_helper.get_data")
     def get_data_from_viewer(self, viewer_reference, data_label=None,
                              cls='default', include_subsets=True):
         """
@@ -769,6 +771,7 @@ def get_data_from_viewer(self, viewer_reference, data_label=None,
         # If a data label was provided, return only the corresponding data, otherwise return all:
         return data.get(data_label, data)
 
+    @deprecated(since="3.6", alternative="get_subsets")
     def get_subsets_from_viewer(self, viewer_reference, data_label=None, subset_type=None):
         """
         Returns the subsets of a specified viewer converted to astropy regions
@@ -803,9 +806,11 @@ def get_subsets_from_viewer(self, viewer_reference, data_label=None, subset_type
             objects.
         """
         viewer = self.get_viewer(viewer_reference)
-        data = self.get_data_from_viewer(viewer_reference,
-                                         data_label,
-                                         cls=None)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            data = self.get_data_from_viewer(viewer_reference,
+                                             data_label,
+                                             cls=None)
         regions = {}
 
         if data_label is not None:
@@ -845,7 +850,9 @@ def get_subsets_from_viewer(self, viewer_reference, data_label=None, subset_type
                     regions[key] = self.get_subsets(key)
                     continue
 
-                temp_data = self.get_data_from_viewer(viewer_reference, value.label)
+                with warnings.catch_warnings():
+                    warnings.simplefilter("ignore")
+                    temp_data = self.get_data_from_viewer(viewer_reference, value.label)
                 if isinstance(temp_data, Spectrum1D):
                     regions[key] = self.get_subsets(key)
                     continue

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

@@ -1,16 +1,17 @@
+import warnings
+
 import pytest
 import numpy as np
 
 from astropy.utils.data import download_file
 
 
-@pytest.mark.filterwarnings('ignore')
 @pytest.mark.remote_data
 def test_data_retrieval(cubeviz_helper):
     """The purpose of this test is to check that both methods:
 
     - app.get_viewer('spectrum-viewer').data()
-    - app.get_data_from_viewer("spectrum-viewer")
+    - cubeviz_helper.get_data()
 
     return the same spectrum values.
     """
@@ -20,14 +21,16 @@ def test_data_retrieval(cubeviz_helper):
 
     spectrum_viewer_reference_name = "spectrum-viewer"
     fn = download_file(URL, cache=True)
-    cubeviz_helper.load_data(fn)
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore")
+        cubeviz_helper.load_data(fn)
 
     # two ways of retrieving data from the viewer.
     # They should return the same spectral values
     a1 = cubeviz_helper.app.get_viewer(spectrum_viewer_reference_name).data()
-    a2 = cubeviz_helper.app.get_data_from_viewer(spectrum_viewer_reference_name)
+    a2 = cubeviz_helper.get_data("contents[FLUX]", function="sum")
 
     test_value_1 = a1[0].data
-    test_value_2 = list(a2.values())[0].data
+    test_value_2 = a2.flux.value
 
     assert np.allclose(test_value_1, test_value_2, atol=1e-5)

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

@@ -73,7 +73,7 @@ def test_spectrum1d_with_fake_fixed_units(spectrum1d, cubeviz_helper):
     cubeviz_helper.app.add_data_to_viewer('spectrum-viewer', 'test')
     cubeviz_helper.app.get_viewer('spectrum-viewer').apply_roi(XRangeROI(6600, 7400))
 
-    subsets = cubeviz_helper.app.get_subsets_from_viewer("spectrum-viewer")
+    subsets = cubeviz_helper.app.get_subsets()
     reg = subsets.get('Subset 1')
 
     assert len(subsets) == 1

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

@@ -25,8 +25,8 @@ def test_spectrum_at_spaxel(cubeviz_helper, spectrum1d_cube):
     assert len(spectrum_viewer.data()) == 2
 
     # Check that a new subset was created
-    subsets = cubeviz_helper.app.get_subsets_from_viewer('flux-viewer')
-    reg = subsets.get('Subset 1')
+    subsets = cubeviz_helper.app.get_subsets()
+    reg = subsets.get('Subset 1')[0]['region']
     assert len(subsets) == 1
     assert isinstance(reg, RectanglePixelRegion)
 
@@ -64,8 +64,8 @@ def test_spectrum_at_spaxel_altkey_true(cubeviz_helper, spectrum1d_cube):
     assert len(spectrum_viewer.data()) == 2
 
     # Check that subset was created
-    subsets = cubeviz_helper.app.get_subsets_from_viewer('flux-viewer')
-    reg = subsets.get('Subset 1')
+    subsets = cubeviz_helper.app.get_subsets()
+    reg = subsets.get('Subset 1')[0]['region']
     assert len(subsets) == 1
     assert isinstance(reg, RectanglePixelRegion)
 
@@ -77,8 +77,8 @@ def test_spectrum_at_spaxel_altkey_true(cubeviz_helper, spectrum1d_cube):
     assert len(flux_viewer.figure.marks) == 4
     assert len(spectrum_viewer.data()) == 3
 
-    subsets = cubeviz_helper.app.get_subsets_from_viewer('flux-viewer')
-    reg2 = subsets.get('Subset 2')
+    subsets = cubeviz_helper.app.get_subsets()
+    reg2 = subsets.get('Subset 2')[0]['region']
     assert len(subsets) == 2
     assert isinstance(reg2, RectanglePixelRegion)
 

jdaviz/configs/imviz/tests/test_helper.py

@@ -25,12 +25,12 @@ def test_create_new_viewer(imviz_helper, image_2d_wcs):
     assert len(imviz_helper.app.get_viewer_ids()) == 2
 
     # there should be no data in the new viewer
-    assert len(imviz_helper.app.get_data_from_viewer(viewer_name)) == 0
+    assert len(imviz_helper.app.get_viewer(viewer_name).data()) == 0
 
     # then add data, and check that data were added to the new viewer
     imviz_helper.app.add_data_to_viewer(viewer_name, data_label)
-    assert len(imviz_helper.app.get_data_from_viewer(viewer_name)) == 1
+    assert len(imviz_helper.app.get_viewer(viewer_name).data()) == 1
 
     # remove data from the new viewer, check that it was removed
     imviz_helper.app.remove_data_from_viewer(viewer_name, data_label)
-    assert len(imviz_helper.app.get_data_from_viewer(viewer_name)) == 0
+    assert len(imviz_helper.app.get_viewer(viewer_name).data()) == 0

jdaviz/configs/mosviz/plugins/viewers.py

@@ -43,7 +43,7 @@ def __init__(self, *args, **kwargs):
         self.figure.fig_margin = {'left': 0, 'bottom': 0, 'top': 0, 'right': 0}
 
     def data(self, cls=None):
-        return [layer_state.layer  # .get_object(cls=cls or self.default_class)
+        return [layer_state.layer.get_object(cls=cls or self.default_class)
                 for layer_state in self.state.layers
                 if hasattr(layer_state, 'layer') and
                 isinstance(layer_state.layer, BaseData)]
@@ -207,8 +207,9 @@ def _handle_x_axis_orientation(self, *args):
             x_scales.min = max(limits) if self.inverted_x_axis else min(limits)
             x_scales.max = min(limits) if self.inverted_x_axis else max(limits)
 
-    def data(self, cls=None):
-        return [layer_state.layer.get_object(cls=cls or self.default_class)
+    def data(self, cls=None, statistic=None):
+        return [layer_state.layer.get_object(statistic=statistic,
+                                             cls=cls or self.default_class)
                 for layer_state in self.state.layers
                 if hasattr(layer_state, 'layer') and
                 isinstance(layer_state.layer, BaseData)]

jdaviz/configs/mosviz/tests/test_data_loading.py

@@ -2,9 +2,9 @@
 
 from zipfile import ZipFile
 
-from astropy.nddata import CCDData
 import numpy as np
 import pytest
+from astropy.nddata import CCDData
 from specutils import Spectrum1D
 
 from jdaviz.utils import PRIHDR_KEY
@@ -20,12 +20,14 @@ def test_load_spectrum1d(mosviz_helper, spectrum1d):
     assert dc_1.label == label
     assert dc_1.meta['uncertainty_type'] == 'std'
 
-    table = mosviz_helper.app.get_viewer('table-viewer')
+    table = mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name)
     table.widget_table.vue_on_row_clicked(0)
 
-    data = mosviz_helper.app.get_data_from_viewer('spectrum-viewer')
+    data = mosviz_helper.app.get_viewer(mosviz_helper._default_spectrum_viewer_reference_name
+                                        ).data()
 
-    assert isinstance(data[label], Spectrum1D)
+    assert len(data) == 1
+    assert isinstance(data[0], Spectrum1D)
 
     with pytest.raises(AttributeError):
         mosviz_helper.load_1d_spectra([1, 2, 3])
@@ -42,12 +44,14 @@ def test_load_image(mosviz_helper, mos_image):
     assert PRIHDR_KEY not in dc_1.meta
     assert dc_1.meta['RADESYS'] == 'ICRS'
 
-    table = mosviz_helper.app.get_viewer('table-viewer')
+    table = mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name)
     table.widget_table.vue_on_row_clicked(0)
 
-    data = mosviz_helper.app.get_data_from_viewer('image-viewer')
+    data = mosviz_helper.app.get_viewer(mosviz_helper._default_image_viewer_reference_name
+                                        ).data(cls=CCDData)
 
-    dataval = data[f"{label} 0"]
+    assert len(data) == 1
+    dataval = data[0]
     assert isinstance(dataval, CCDData)
     assert dataval.shape == (55, 55)
 
@@ -63,12 +67,14 @@ def test_load_spectrum_collection(mosviz_helper, spectrum_collection):
     assert dc_1.label == labels[0]
     assert dc_1.meta['uncertainty_type'] == 'std'
 
-    table = mosviz_helper.app.get_viewer('table-viewer')
+    table = mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name)
     table.select_row(0)
 
-    data = mosviz_helper.app.get_data_from_viewer('spectrum-viewer')
+    data = mosviz_helper.app.get_viewer(mosviz_helper._default_spectrum_viewer_reference_name
+                                        ).data()
 
-    assert isinstance(data[labels[0]], Spectrum1D)
+    assert len(data) == 1
+    assert isinstance(data[0], Spectrum1D)
 
 
 def test_load_list_of_spectrum1d(mosviz_helper, spectrum1d):
@@ -83,12 +89,14 @@ def test_load_list_of_spectrum1d(mosviz_helper, spectrum1d):
     assert dc_1.label == labels[0]
     assert dc_1.meta['uncertainty_type'] == 'std'
 
-    table = mosviz_helper.app.get_viewer('table-viewer')
+    table = mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name)
     table.widget_table.vue_on_row_clicked(0)
 
-    data = mosviz_helper.app.get_data_from_viewer('spectrum-viewer')
+    data = mosviz_helper.app.get_viewer(mosviz_helper._default_spectrum_viewer_reference_name
+                                        ).data()
 
-    assert isinstance(data[labels[0]], Spectrum1D)
+    assert len(data) == 1
+    assert isinstance(data[0], Spectrum1D)
 
 
 def test_load_mos_spectrum2d(mosviz_helper, mos_spectrum2d):
@@ -102,12 +110,14 @@ def test_load_mos_spectrum2d(mosviz_helper, mos_spectrum2d):
     assert dc_1.label == label
     assert dc_1.meta['INSTRUME'] == 'nirspec'
 
-    table = mosviz_helper.app.get_viewer('table-viewer')
+    table = mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name)
     table.widget_table.vue_on_row_clicked(0)
 
-    data = mosviz_helper.app.get_data_from_viewer('spectrum-2d-viewer')
+    data = mosviz_helper.app.get_viewer(mosviz_helper._default_spectrum_2d_viewer_reference_name
+                                        ).data()
 
-    assert data[label].shape == (1024, 15)
+    assert len(data) == 1
+    assert data[0].shape == (1024, 15)
 
 
 @pytest.mark.parametrize('label', [None, "Test Label"])
@@ -118,7 +128,8 @@ def test_load_multi_image_spec(mosviz_helper, mos_image, spectrum1d, mos_spectru
 
     mosviz_helper.load_data(spectra1d, spectra2d, images=images, images_label=label)
 
-    assert mosviz_helper.app.get_viewer("table-viewer").figure_widget.highlighted == 0
+    assert mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name
+                                        ).figure_widget.highlighted == 0
     assert len(mosviz_helper.app.data_collection) == 10
 
     qtable = mosviz_helper.to_table()
@@ -134,7 +145,8 @@ def test_load_multi_image_and_spec1d_only(mosviz_helper, mos_image, spectrum1d):
 
     mosviz_helper.load_data(spectra_1d=spectra1d, images=images)
 
-    assert mosviz_helper.app.get_viewer("table-viewer").figure_widget.highlighted == 0
+    assert mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name
+                                        ).figure_widget.highlighted == 0
     assert len(mosviz_helper.app.data_collection) == 7
 
 
@@ -144,7 +156,8 @@ def test_load_multi_image_and_spec2d_only(mosviz_helper, mos_image, mos_spectrum
 
     mosviz_helper.load_data(spectra_2d=spectra2d, images=images)
 
-    assert mosviz_helper.app.get_viewer("table-viewer").figure_widget.highlighted == 0
+    assert mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name
+                                        ).figure_widget.highlighted == 0
     assert len(mosviz_helper.app.data_collection) == 7
 
 
@@ -170,7 +183,8 @@ def test_load_single_image_multi_spec(mosviz_helper, mos_image, spectrum1d, mos_
 
     mosviz_helper.load_data(spectra1d, spectra2d, images=mos_image, images_label=label)
 
-    assert mosviz_helper.app.get_viewer("table-viewer").figure_widget.highlighted == 0
+    assert mosviz_helper.app.get_viewer(mosviz_helper._default_table_viewer_reference_name
+                                        ).figure_widget.highlighted == 0
     assert len(mosviz_helper.app.data_collection) == 8
 
     qtable = mosviz_helper.to_table()