Create import_region method for loading region objects (#3104)

* Create import_region method for loading region objects

* Remove call to load_regions

* Add deprecated fixture to load_regions methods

* Update combination_mode to listen to UI

* Update import_region to switch from new to replace mode correctly

* Remove unused pytest fixture

* Add docs and fix rampviz test

* Replace load_regions calls with import_region in notebooks

* Replace applpy_roi with import_region in tests

* Add new parameter to set combination mode to new after subset creation

* Update tests to use subset_plugin._obj

* Replace mode and create_as_new with combination_mode

docs/cubeviz/import_data.rst

@@ -197,15 +197,15 @@ can load the regions into Cubeviz as follows:
 
 .. code-block:: python
 
-    cubeviz.load_regions_from_file("/path/to/data/myregions.reg")
+    cubeviz.plugins['Subset Tools']._obj.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.load_regions_from_file("/path/to/data/myregions.reg", return_bad_regions=True)
+    bad_regions = cubeviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg", return_bad_regions=True)
 
 .. note:: Sky regions are currently unsupported in Cubeviz, unlike Imviz.
 

docs/imviz/import_data.rst

@@ -215,15 +215,15 @@ can load the regions into Imviz as follows:
 
 .. code-block:: python
 
-    imviz.load_regions_from_file("/path/to/data/myregions.reg")
+    imviz.plugins['Subset Tools']._obj.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.load_regions_from_file("/path/to/data/myregions.reg", return_bad_regions=True)
+    bad_regions = imviz.plugins['Subset Tools']._obj.import_region("/path/to/data/myregions.reg", return_bad_regions=True)
 
 You could also define :ref:`regions:shapes` programmatically and load them; e.g.:
 

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

@@ -8,8 +8,8 @@
 from astropy.io import fits
 from astropy.nddata import CCDData
 from astropy.wcs import WCS
-from glue.core.roi import XRangeROI
 from numpy.testing import assert_allclose
+from specutils import SpectralRegion
 
 
 @pytest.mark.parametrize("cube_type", ["Surface Brightness", "Flux"])
@@ -233,8 +233,10 @@ def test_moment_frequency_unit_conversion(cubeviz_helper, spectrum1d_cube_larger
 
     uc = cubeviz_helper.plugins['Unit Conversion']
     mm = cubeviz_helper.plugins['Moment Maps']
-    viewer = cubeviz_helper.app.get_viewer('spectrum-viewer')
-    viewer.apply_roi(XRangeROI(4.624e-07, 4.627e-07))
+
+    unit = u.Unit(uc.spectral_unit.selected)
+    cubeviz_helper.plugins['Subset Tools']._obj.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

@@ -10,7 +10,6 @@
 from astropy.utils.exceptions import AstropyUserWarning
 
 from glue.core.roi import CircularROI, RectangularROI
-from glue.core.edit_subset_mode import ReplaceMode, AndNotMode, NewMode
 from numpy.testing import assert_allclose, assert_array_equal
 from regions import (CirclePixelRegion, CircleAnnulusPixelRegion, EllipsePixelRegion,
                      RectanglePixelRegion, PixCoord)
@@ -84,7 +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.load_regions(regions)
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(regions, combination_mode='new')
 
     extract_plugin = cubeviz_helper.plugins['Spectral Extraction']
     extract_plugin.function = "Sum"
@@ -124,7 +123,7 @@ def test_subset(
     ]
 
     cubeviz_helper.load_data(spectrum1d_cube_with_uncerts)
-    cubeviz_helper.load_regions(regions)
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(regions, combination_mode='new')
 
     plg = cubeviz_helper.plugins['Spectral Extraction']
     plg.function = function
@@ -199,7 +198,8 @@ def test_save_collapsed_to_fits(cubeviz_helper, spectrum1d_cube_with_uncerts, tm
 def test_aperture_markers(cubeviz_helper, spectrum1d_cube):
 
     cubeviz_helper.load_data(spectrum1d_cube)
-    cubeviz_helper.load_regions([CirclePixelRegion(PixCoord(0.5, 0), radius=1.2)])
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        [CirclePixelRegion(PixCoord(0.5, 0), radius=1.2)])
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
     slice_plg = cubeviz_helper.plugins['Slice']
@@ -251,9 +251,10 @@ 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.load_regions([
-        CirclePixelRegion(center, radius=2.5),
-        EllipsePixelRegion(center, width=5, height=5)])
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        CirclePixelRegion(center, radius=2.5), combination_mode='new')
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        EllipsePixelRegion(center, width=5, height=5), combination_mode='new')
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
 
@@ -283,9 +284,9 @@ 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.load_regions([
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
         CirclePixelRegion(center, radius=2.5),
-        EllipsePixelRegion(center, width=5, height=5)])
+        EllipsePixelRegion(center, width=5, height=5)], combination_mode='new')
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
 
@@ -307,7 +308,8 @@ 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.load_regions(RectanglePixelRegion(PixCoord(5, 10), width=4, height=4))
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        RectanglePixelRegion(PixCoord(5, 10), width=4, height=4))
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
 
@@ -334,9 +336,9 @@ 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.load_regions([
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
         CirclePixelRegion(PixCoord(5, 10), radius=2.5),
-        EllipsePixelRegion(PixCoord(13, 10), width=3, height=5)])
+        EllipsePixelRegion(PixCoord(13, 10), width=3, height=5)], combination_mode='new')
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
     with extract_plg.as_active():
@@ -387,9 +389,9 @@ 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.load_regions([
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region([
         CirclePixelRegion(center, radius=2.5),
-        CircleAnnulusPixelRegion(center, inner_radius=2.5, outer_radius=4)])
+        CircleAnnulusPixelRegion(center, inner_radius=2.5, outer_radius=4)], combination_mode='new')
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
 
@@ -414,7 +416,8 @@ 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.load_regions([CirclePixelRegion(PixCoord(14, 15), radius=2.5)])
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        [CirclePixelRegion(PixCoord(14, 15), radius=2.5)])
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
 
@@ -434,16 +437,17 @@ 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.load_regions(RectanglePixelRegion(PixCoord(1.5, 1.5), width=4, height=4))
+    cubeviz_helper.plugins['Subset Tools']._obj.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
     assert_allclose(sp_subset.flux.value, 1.2E-16)  # (4 x 4) - 4
 
 
 def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
-    fv = cubeviz_helper.viewers['flux-viewer']._obj
-    fv.apply_roi(CircularROI(xc=5, yc=5, radius=2))
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(
+        CircularROI(xc=5, yc=5, radius=2))
 
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
     extract_plg.aperture = 'Subset 1'
@@ -454,8 +458,8 @@ 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.app.session.edit_subset_mode.mode = ReplaceMode
-    fv.apply_roi(CircularROI(xc=5, yc=5, radius=3))
+    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))
 
     # update should take place automatically, but since its async, we'll call manually to ensure
     # the update is complete before comparing results
@@ -469,26 +473,22 @@ def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
 
 def test_aperture_composite_detection(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper.load_data(spectrum1d_cube)
-    flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
     subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
     spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']._obj
 
     # create a rectangular subset with all spaxels:
     rectangle = RectangularROI(-0.5, 1.5, -0.5, 3.5)
-    flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:rectangle']
-    flux_viewer.apply_roi(rectangle)
+    subset_plugin.import_region(rectangle)
 
     # select subset 1, ensure it's not a composite subset:
     spec_extr_plugin.aperture_selected = 'Subset 1'
     assert not spec_extr_plugin.aperture.is_composite
 
     # now remove from this subset a circular region in the center:
-    flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:truecircle']
-    subset_plugin.subset_selected = 'Subset 1'
-    cubeviz_helper.app.session.edit_subset_mode.mode = AndNotMode
-
     circle = CircularROI(0.5, 1.5, 1)
-    flux_viewer.apply_roi(circle)
+
+    subset_plugin.combination_mode.selected = 'andnot'
+    subset_plugin.import_region(circle)
 
     # now the subset is composite:
     assert spec_extr_plugin.aperture.is_composite
@@ -497,35 +497,32 @@ def test_aperture_composite_detection(cubeviz_helper, spectrum1d_cube):
 def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper.load_data(spectrum1d_cube)
 
-    flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
     subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
     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)
 
-    flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:rectangle']
-    flux_viewer.apply_roi(lower_aperture)
-
-    cubeviz_helper.app.session.edit_subset_mode.mode = NewMode
-    flux_viewer.apply_roi(upper_aperture)
+    subset_plugin.import_region(lower_aperture)
+    subset_plugin.combination_mode.selected = 'new'
+    subset_plugin.import_region(upper_aperture)
 
     spec_extr_plugin.aperture_selected = 'Subset 1'
     spectrum_1 = spec_extr_plugin.extract()
 
     spec_extr_plugin.aperture_selected = 'Subset 2'
     spectrum_2 = spec_extr_plugin.extract()
 
-    subset_plugin.subset_selected = 'Create New'
     rectangle = RectangularROI(-0.5, 3.5, -0.5, 1.5)
-    flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:rectangle']
-    flux_viewer.apply_roi(rectangle)
 
-    flux_viewer.toolbar.active_tool = flux_viewer.toolbar.tools['bqplot:truecircle']
+    subset_plugin.combination_mode.selected = 'new'
+    subset_plugin.import_region(rectangle)
+
     subset_plugin.subset_selected = 'Subset 3'
-    cubeviz_helper.app.session.edit_subset_mode.mode = AndNotMode
     circle = CircularROI(1.5, 0.5, 1.1)
-    flux_viewer.apply_roi(circle)
+
+    subset_plugin.combination_mode.selected = 'andnot'
+    subset_plugin.import_region(circle)
 
     spec_extr_plugin.aperture_selected = 'Subset 3'
 
@@ -559,10 +556,10 @@ def test_default_spectral_extraction(cubeviz_helper, spectrum1d_cube_fluxunit_jy
     # regression tests make sure that doesn't happen anymore by accounting
     # for non-science pixels in the sums:
     cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian)
-    flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
 
-    # create a spatial subset that spans all spaxels:
-    flux_viewer.apply_roi(CircularROI(1.5, 2, 5))
+    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+
+    subset_plugin.import_region(CircularROI(1.5, 2, 5))
 
     # the first and second spectra correspond to the default extraction
     # and the subset extraction. the fluxes in these extractions should agree:
@@ -646,8 +643,8 @@ def test_spectral_extraction_scientific_validation(
         cubeviz_helper.load_data(uri, cache=True)
 
     # add a subset with an aperture centered on each source
-    flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
-    flux_viewer.apply_roi(CircularROI(*aperture))
+    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    subset_plugin.import_region(CircularROI(*aperture))
 
     # set the slice to the blue end of MIRI CH1
     slice_plugin = cubeviz_helper.plugins['Slice']

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

@@ -14,7 +14,7 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr
     solid_angle_unit = u.pix * u.pix
 
     aper = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=3, height=5)
-    cubeviz_helper.load_regions(aper)
+    cubeviz_helper.plugins['Subset Tools']._obj.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)
@@ -110,7 +110,7 @@ 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.load_regions(aper)
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(aper)
 
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
     plg.dataset_selected = "test[FLUX] spatial-smooth stddev-1.0"
@@ -208,7 +208,7 @@ 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.load_regions([aper, bg])
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region([aper, bg], combination_mode='new')
 
     plg = cubeviz_helper.plugins["Aperture Photometry"]._obj
     plg.dataset_selected = "test[FLUX]"
@@ -275,7 +275,7 @@ 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.load_regions([aper, bg])
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region([aper, bg], combination_mode='new')
 
     ap = cubeviz_helper.plugins['Aperture Photometry']._obj
 

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

@@ -1,4 +1,4 @@
-from glue.core.roi import XRangeROI
+from specutils import SpectralRegion
 
 from jdaviz import Cubeviz
 from jdaviz.app import Application
@@ -43,8 +43,9 @@ 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)
-    spec_viewer = cubeviz_helper.app.get_viewer(cubeviz_helper._default_spectrum_viewer_reference_name) # noqa
-    spec_viewer.apply_roi(XRangeROI(4.62440061e-07, 4.62520112e-07))
+    subset_plugin = cubeviz_helper.plugins['Subset Tools']._obj
+    unit = spectrum1d_cube_larger.spectral_axis.unit
+    subset_plugin.import_region(SpectralRegion(4.62440061e-07 * unit, 4.62520112e-07 * unit))
 
     spatial_with_spec = cubeviz_helper.get_data(data_label="Spectrum (Subset 1, sum)",
                                                 spectral_subset="Subset 2")

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

@@ -2,8 +2,7 @@
 import pytest
 from astropy import units as u
 from astropy.wcs import WCS
-from specutils import Spectrum1D
-from glue.core.roi import XRangeROI
+from specutils import Spectrum1D, SpectralRegion
 from glue_astronomy.translators.spectrum1d import PaddedSpectrumWCS
 from numpy.testing import assert_allclose, assert_array_equal
 
@@ -71,7 +70,9 @@ def test_spectrum1d_with_fake_fixed_units(spectrum1d, cubeviz_helper):
     dc[0].meta["_orig_spec"] = spectrum1d
 
     cubeviz_helper.app.add_data_to_viewer('spectrum-viewer', 'test')
-    cubeviz_helper.app.get_viewer('spectrum-viewer').apply_roi(XRangeROI(6600, 7400))
+    unit = u.Unit(cubeviz_helper.plugins['Unit Conversion'].spectral_unit.selected)
+    cubeviz_helper.plugins['Subset Tools']._obj.import_region(SpectralRegion(6600 * unit,
+                                                                             7400 * unit))
 
     subsets = cubeviz_helper.app.get_subsets()
     reg = subsets.get('Subset 1')