Cubeviz spectral regions fixes

CHANGES.rst

@@ -22,6 +22,11 @@ API Changes
 - Viewers now can access the calling Jdaviz application using
   ``viewer.session.jdaviz_app``. [#1051]
 
+Cubeviz
+^^^^^^^
+
+- Subsets from the spectrum viewer are now returned as SpectralRegion objects. [#1046]
+
 Bug Fixes
 ---------
 
@@ -34,6 +39,8 @@ Bug Fixes
 Cubeviz
 ^^^^^^^
 
+- Spectral region retrieval now properly handles the case of multiple subregions. [#1046]
+
 Imviz
 ^^^^^
 

jdaviz/app.py

@@ -26,6 +26,7 @@
 from glue.core.subset import Subset, RangeSubsetState, RoiSubsetState
 from glue_jupyter.app import JupyterApplication
 from glue_jupyter.state_traitlets_helpers import GlueState
+from glue_jupyter.bqplot.profile import BqplotProfileView
 from ipyvuetify import VuetifyTemplate
 
 from jdaviz.core.config import read_configuration, get_configuration
@@ -617,10 +618,12 @@ def _get_all_subregions(mask, spec_axis_data):
                     this_type = type(value.subset_state)
 
                 # Skip spatial or spectral subsets if only the other is wanted
-                if subset_type == "spectral" and this_type == RoiSubsetState:
-                    continue
-                elif subset_type == "spatial" and this_type == RangeSubsetState:
-                    continue
+                if subset_type == "spectral" or isinstance(viewer, BqplotProfileView):
+                    if this_type == RoiSubsetState:
+                        continue
+                elif subset_type == "spatial" or not isinstance(viewer, BqplotProfileView):
+                    if this_type == RangeSubsetState:
+                        continue
 
                 # Range selection on a profile is currently not supported in
                 #  the glue translation machinery for astropy regions, so we
@@ -648,6 +651,16 @@ def _get_all_subregions(mask, spec_axis_data):
                     regions[key] = subregions_in_subset
                     continue
 
+                temp_data = self.get_data_from_viewer(viewer_reference, value.label)
+                if isinstance(temp_data, Spectrum1D):
+                    # Note that we look for mask == False here, rather than True above,
+                    # because specutils masks are the reverse of Glue (of course)
+                    subregions_in_subset = _get_all_subregions(
+                             np.where(~temp_data.mask)[0], # noqa
+                             temp_data.spectral_axis)
+                    regions[key] = subregions_in_subset
+                    continue
+
                 # Get the pixel coordinate [z] of the 3D data, repeating the
                 #  wavelength axis. This doesn't seem strictly necessary as it
                 #  returns the same data if the pixel axis is [y] or [x]

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

@@ -6,8 +6,7 @@
 from glue.core.message import (DataCollectionAddMessage,
                                DataCollectionDeleteMessage)
 from traitlets import List, Unicode, Any, Bool, observe
-from specutils import Spectrum1D, manipulation, SpectralRegion, analysis
-from regions import RectanglePixelRegion
+from specutils import Spectrum1D, manipulation, analysis
 
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.registries import tray_registry
@@ -33,8 +32,8 @@ class MomentMap(TemplateMixin):
     spectral_min = Any().tag(sync=True)
     spectral_max = Any().tag(sync=True)
     spectral_unit = Unicode().tag(sync=True)
-    spectral_subset_items = List(["None"]).tag(sync=True)
-    selected_subset = Unicode("None").tag(sync=True)
+    spectral_subset_items = List(["Entire Spectrum"]).tag(sync=True)
+    selected_subset = Unicode("Entire Spectrum").tag(sync=True)
 
     # NOTE: this is currently cubeviz-specific so will need to be updated
     # to be config-specific if using within other viewer configurations.
@@ -95,34 +94,23 @@ def _on_data_selected(self, event):
     def _on_subset_selected(self, event):
         # If "None" selected, reset based on bounds of selected data
         self._selected_subset = self.selected_subset
-        if self._selected_subset == "None":
+        if self._selected_subset == "Entire Spectrum":
             cube = self._selected_data.get_object(cls=Spectrum1D, statistic=None)
             self.spectral_min = cube.spectral_axis[0].value
             self.spectral_max = cube.spectral_axis[-1].value
         else:
             spec_sub = self._spectral_subsets[self._selected_subset]
-            unit = u.Unit(self.spectral_unit)
-            spec_reg = SpectralRegion.from_center(spec_sub.center.x * unit,
-                                                  spec_sub.width * unit)
-            self.spectral_min = spec_reg.lower.value
-            self.spectral_max = spec_reg.upper.value
+            self.spectral_min = spec_sub.lower.value
+            self.spectral_max = spec_sub.upper.value
 
     @observe("filename")
     def _on_filename_changed(self, event):
         self._filename = self.filename
 
     def vue_list_subsets(self, event):
         """Populate the spectral subset selection dropdown"""
-        temp_subsets = self.app.get_subsets_from_viewer("spectrum-viewer")
-        temp_list = ["None"]
-        temp_dict = {}
-        # Attempt to filter out spatial subsets
-        for key, region in temp_subsets.items():
-            if type(region) == RectanglePixelRegion:
-                temp_dict[key] = region
-                temp_list.append(key)
-        self._spectral_subsets = temp_dict
-        self.spectral_subset_items = temp_list
+        self._spectral_subsets = self.app.get_subsets_from_viewer("spectrum-viewer")
+        self.spectral_subset_items = ["Entire Spectrum"] + sorted(self._spectral_subsets.keys())
 
     def vue_calculate_moment(self, *args):
         # Retrieve the data cube and slice out desired region, if specified

jdaviz/tests/test_subsets.py

@@ -1,8 +1,12 @@
+import astropy.units as u
+from astropy.tests.helper import assert_quantity_allclose
 import numpy as np
 import pytest
 from glue.core import Data
 from glue.core.roi import RectangularROI, XRangeROI
+from glue.core.edit_subset_mode import OrMode
 from numpy.testing import assert_allclose
+from specutils import SpectralRegion
 from regions import RectanglePixelRegion
 
 from jdaviz.app import Application
@@ -61,18 +65,18 @@ def test_region_from_subset_profile(jdaviz_app, spectral_cube_wcs):
 
     jdaviz_app.add_data_to_viewer('spectrum-viewer', 'Test 1D Flux')
 
-    jdaviz_app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(1, 3.5))
+    jdaviz_app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(5, 15.5))
 
     subsets = jdaviz_app.get_subsets_from_viewer('spectrum-viewer', subset_type='spectral')
     reg = subsets.get('Subset 1')
 
+    print(reg)
+
     assert len(subsets) == 1
-    assert isinstance(reg, RectanglePixelRegion)
+    assert isinstance(reg, SpectralRegion)
 
-    assert_allclose(reg.center.x, 2.25)
-    assert_allclose(reg.center.y, 128)
-    assert_allclose(reg.width, 2.5)
-    assert_allclose(reg.height, 256)
+    assert_quantity_allclose(reg.lower, 5.0 * u.Hz)
+    assert_quantity_allclose(reg.upper, 14.0 * u.Hz)
 
 
 def test_region_spectral_spatial(jdaviz_app, spectral_cube_wcs):
@@ -82,7 +86,7 @@ def test_region_spectral_spatial(jdaviz_app, spectral_cube_wcs):
     jdaviz_app.add_data_to_viewer('spectrum-viewer', 'Test Flux')
     jdaviz_app.add_data_to_viewer('flux-viewer', 'Test Flux')
 
-    jdaviz_app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(1, 3.5))
+    jdaviz_app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(5, 15.5))
 
     flux_viewer = jdaviz_app.get_viewer("flux-viewer")
     # We set the active tool here to trigger a reset of the Subset state to "Create new"
@@ -92,13 +96,13 @@ def test_region_spectral_spatial(jdaviz_app, spectral_cube_wcs):
     subsets = jdaviz_app.get_subsets_from_viewer('spectrum-viewer', subset_type='spectral')
     reg = subsets.get('Subset 1')
 
+    print(reg)
+
     assert len(subsets) == 1
-    assert isinstance(reg, RectanglePixelRegion)
+    assert isinstance(reg, SpectralRegion)
 
-    assert_allclose(reg.center.x, 2.25)
-    assert_allclose(reg.center.y, 128)
-    assert_allclose(reg.width, 2.5)
-    assert_allclose(reg.height, 256)
+    assert_quantity_allclose(reg.lower, 5.0 * u.Hz)
+    assert_quantity_allclose(reg.upper, 14 * u.Hz)
 
     subsets = jdaviz_app.get_subsets_from_viewer('flux-viewer', subset_type='spatial')
     reg = subsets.get('Subset 2')
@@ -110,3 +114,28 @@ def test_region_spectral_spatial(jdaviz_app, spectral_cube_wcs):
     assert_allclose(reg.center.y, 1.55)
     assert_allclose(reg.width, 2.5)
     assert_allclose(reg.height, 3.5)
+
+
+def test_disjoint_spectral_subset(jdaviz_app, spectral_cube_wcs):
+    data = Data(flux=np.ones((256, 128, 128)), label='Test Flux', coords=spectral_cube_wcs)
+    jdaviz_app.data_collection.append(data)
+
+    jdaviz_app.add_data_to_viewer('spectrum-viewer', 'Test Flux')
+    jdaviz_app.add_data_to_viewer('flux-viewer', 'Test Flux')
+
+    spec_viewer = jdaviz_app.get_viewer("spectrum-viewer")
+    spec_viewer.apply_roi(XRangeROI(5, 15.5))
+
+    # Add second region to Subset 1
+    jdaviz_app.session.edit_subset_mode.mode = OrMode
+    spec_viewer.apply_roi(XRangeROI(30, 35))
+
+    subsets = jdaviz_app.get_subsets_from_viewer('spectrum-viewer')
+    reg = subsets.get('Subset 1')
+
+    assert len(reg) == 2
+    assert isinstance(reg, SpectralRegion)
+    assert_quantity_allclose(reg[0].lower, 5.0*u.Hz)
+    assert_quantity_allclose(reg[0].upper, 15.0*u.Hz)
+    assert_quantity_allclose(reg[1].lower, 30.0*u.Hz)
+    assert_quantity_allclose(reg[1].upper, 34.0*u.Hz)

setup.cfg

@@ -31,7 +31,7 @@ install_requires =
     ipygoldenlayout>=0.3.0
     voila>=0.2.4
     pyyaml>=5.4.1
-    specutils>=1.5.0
+    specutils>=1.6.0
     glue-astronomy>=0.3.2
     click>=7.1.2
     spectral-cube>=0.5