FEAT: Load annulus from file, load reg files from IMPORT DATA

CHANGES.rst

@@ -12,6 +12,11 @@ Cubeviz
 Imviz
 ^^^^^
 
+- Added the ability to load DS9 region files (``.reg``) using the ``IMPORT DATA``
+  button. However, this only works after loading at least one image into Imviz. [#2201]
+
+- Added support for new ``CircularAnnulusROI`` subset from glue. [#2201]
+
 Mosviz
 ^^^^^^
 

docs/imviz/import_data.rst

@@ -43,6 +43,9 @@ application. A notification will appear to let users know if the data import
 was successful. Afterward, the new data set can be found in the :guilabel:`Data`
 tab of each viewer's options menu as described in :ref:`cubeviz-selecting-data`.
 
+Once data is loaded, you may use the :guilabel:`Import Data` button again
+to load regions from a ``.reg`` file; also see :ref:`imviz-import-regions-api`.
+
 .. _imviz-import-api:
 
 Importing data via the API

jdaviz/configs/imviz/plugins/parsers.py

@@ -82,6 +82,11 @@ def parse_data(app, file_obj, ext=None, data_label=None):
                 )
             with rdd.open(file_obj) as pf:
                 _parse_image(app, pf, data_label, ext=ext)
+
+        elif file_obj_lower.endswith('.reg'):
+            # This will load DS9 regions as Subset but only if there is already data.
+            app._jdaviz_helper.load_regions_from_file(file_obj)
+
         else:  # Assume FITS
             with fits.open(file_obj) as pf:
                 _parse_image(app, pf, data_label, ext=ext)

jdaviz/configs/imviz/tests/data/ds9_annulus_01.reg

@@ -0,0 +1,4 @@
+# Region file format: DS9 version 4.1
+global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
+icrs
+annulus(197.8929,-1.36599,1.9820003",3.9640007",5.946001") # color=magenta font="helvetica 10 bold roman" text={Annulus}

jdaviz/configs/imviz/tests/test_regions.py

@@ -1,18 +1,15 @@
-import glue_astronomy
 import numpy as np
+import pytest
 from astropy import units as u
 from astropy.coordinates import SkyCoord, Angle
 from astropy.utils.data import get_pkg_data_filename
-from packaging.version import Version
 from photutils.aperture import CircularAperture, SkyCircularAperture
 from regions import (PixCoord, CircleSkyRegion, RectanglePixelRegion, CirclePixelRegion,
                      EllipsePixelRegion, PointSkyRegion, PolygonPixelRegion,
                      CircleAnnulusPixelRegion, CircleAnnulusSkyRegion, Regions)
 
 from jdaviz.configs.imviz.tests.utils import BaseImviz_WCS_NoWCS
 
-GLUE_ASTRONOMY_LT_0_7_1 = not (Version(glue_astronomy.__version__) >= Version("0.7.1.dev"))
-
 
 class BaseRegionHandler:
     """Test to see if region is loaded.
@@ -122,13 +119,15 @@ def test_regions_sky_has_wcs(self):
         self.imviz._apply_interactive_region('bqplot:circle', (1.5, 2.5), (3.6, 4.6))
 
         sky = SkyCoord(ra=337.5202808, dec=-20.833333059999998, unit='deg')
-        # This will become indistinguishable from normal Subset.
+        # These will become indistinguishable from normal Subset.
         my_reg_sky_1 = CircleSkyRegion(sky, Angle(0.5, u.arcsec))
-        # Masked subset.
         my_reg_sky_2 = CircleAnnulusSkyRegion(center=sky, inner_radius=0.0004 * u.deg,
                                               outer_radius=0.0005 * u.deg)
-        # Add them both.
-        bad_regions = self.imviz.load_regions([my_reg_sky_1, my_reg_sky_2], return_bad_regions=True)
+        # Masked subset.
+        my_reg_sky_3 = PolygonPixelRegion(vertices=PixCoord(x=[1, 1, 3, 3, 1], y=[1, 3, 3, 1, 1]))
+        # Add them all.
+        bad_regions = self.imviz.load_regions([my_reg_sky_1, my_reg_sky_2, my_reg_sky_3],
+                                              return_bad_regions=True)
         assert len(bad_regions) == 0
 
         # Mimic interactive regions (after)
@@ -139,15 +138,28 @@ def test_regions_sky_has_wcs(self):
         # that check hopefully is already done in glue-astronomy.
         # Apparently, static region ate up one number...
         subsets = self.imviz.get_interactive_regions()
-        assert list(subsets.keys()) == ['Subset 1', 'Subset 2', 'Subset 4', 'Subset 5'], subsets
+        assert list(subsets.keys()) == ['Subset 1', 'Subset 2', 'Subset 3', 'Subset 5', 'Subset 6'], subsets  # noqa: E501
         assert isinstance(subsets['Subset 1'], CirclePixelRegion)
         assert isinstance(subsets['Subset 2'], CirclePixelRegion)
-        assert isinstance(subsets['Subset 4'], EllipsePixelRegion)
-        assert isinstance(subsets['Subset 5'], RectanglePixelRegion)
+        assert isinstance(subsets['Subset 3'], CircleAnnulusPixelRegion)
+        assert isinstance(subsets['Subset 5'], EllipsePixelRegion)
+        assert isinstance(subsets['Subset 6'], RectanglePixelRegion)
 
         # Check static region
         self.verify_region_loaded('MaskedSubset 1')
 
+    def test_regions_annulus_from_load_data(self):
+        # This file actually will load 2 annuli
+        regfile = get_pkg_data_filename('data/ds9_annulus_01.reg')
+        self.imviz.load_data(regfile)
+        assert len(self.imviz.app.data_collection) == 2  # Make sure not loaded as data
+
+        subsets = self.imviz.get_interactive_regions()
+        subset_names = list(subsets.keys())
+        assert subset_names == ['Subset 1', 'Subset 2']
+        for n in subset_names:
+            assert isinstance(subsets[n], CircleAnnulusPixelRegion)
+
     def test_photutils_pixel(self):
         my_aper = CircularAperture((5, 5), r=2)
         bad_regions = self.imviz.load_regions([my_aper], return_bad_regions=True)
@@ -173,18 +185,21 @@ def setup_class(self):
         self.raw_regions = Regions.read(self.region_file, format='ds9')
 
     def test_ds9_load_all(self, imviz_helper):
+        with pytest.raises(ValueError, match="Cannot load regions without data"):
+            imviz_helper.load_data(self.region_file)
+
         self.viewer = imviz_helper.default_viewer
         imviz_helper.load_data(self.arr, data_label='my_image')
         bad_regions = imviz_helper.load_regions_from_file(self.region_file, return_bad_regions=True)
         assert len(bad_regions) == 1
 
-        # Will load 8/9 and 6 of that become ROIs.
+        # Will load 8/9 and 7 of that become ROIs.
         subsets = imviz_helper.get_interactive_regions()
         assert list(subsets.keys()) == ['Subset 1', 'Subset 2', 'Subset 3',
-                                        'Subset 4', 'Subset 5', 'Subset 6'], subsets
+                                        'Subset 4', 'Subset 5', 'Subset 6', 'Subset 7'], subsets
 
-        for i in (1, 2):  # The other 2 are MaskedSubset
-            self.verify_region_loaded(f'MaskedSubset {i}', count=1)
+        # The other 1 is MaskedSubset
+        self.verify_region_loaded('MaskedSubset 1', count=1)
 
     def test_ds9_load_two_good(self, imviz_helper):
         self.viewer = imviz_helper.default_viewer
@@ -234,18 +249,12 @@ def test_annulus(self):
         new_subset = subset_groups[0].subset_state & ~subset_groups[1].subset_state
         self.viewer.apply_subset_state(new_subset)
 
-        # In older glue-astronomy, annulus is no longer accessible by API
-        # but also should not crash Imviz.
         subsets = self.imviz.get_interactive_regions()
         assert len(self.imviz.app.data_collection.subset_groups) == 3
-        if GLUE_ASTRONOMY_LT_0_7_1:
-            expected_subset_keys = ['Subset 1', 'Subset 2']
-        else:
-            expected_subset_keys = ['Subset 1', 'Subset 2', 'Subset 3']
-            assert isinstance(subsets['Subset 3'], CircleAnnulusPixelRegion)
-        assert list(subsets.keys()) == expected_subset_keys, subsets
+        assert list(subsets.keys()) == ['Subset 1', 'Subset 2', 'Subset 3'], subsets
         assert isinstance(subsets['Subset 1'], CirclePixelRegion)
         assert isinstance(subsets['Subset 2'], CirclePixelRegion)
+        assert isinstance(subsets['Subset 3'], CircleAnnulusPixelRegion)
 
         # Clear the regions for next test.
         self.imviz._delete_all_regions()

jdaviz/core/helpers.py

@@ -658,12 +658,17 @@ def load_regions(self, regions, max_num_regions=None, refdata_label=None,
             If not requested, return `None`.
 
         """
+        if len(self.app.data_collection) == 0:
+            raise ValueError('Cannot load regions without data.')
+
         from photutils.aperture import (CircularAperture, SkyCircularAperture,
                                         EllipticalAperture, SkyEllipticalAperture,
-                                        RectangularAperture, SkyRectangularAperture)
+                                        RectangularAperture, SkyRectangularAperture,
+                                        CircularAnnulus, SkyCircularAnnulus)
         from regions import (Regions, CirclePixelRegion, CircleSkyRegion,
                              EllipsePixelRegion, EllipseSkyRegion,
-                             RectanglePixelRegion, RectangleSkyRegion)
+                             RectanglePixelRegion, RectangleSkyRegion,
+                             CircleAnnulusPixelRegion, CircleAnnulusSkyRegion)
         from jdaviz.core.region_translators import regions2roi, aperture2regions
 
         # If user passes in one region obj instead of list, try to be smart.
@@ -688,23 +693,27 @@ def load_regions(self, regions, max_num_regions=None, refdata_label=None,
         has_wcs = data_has_valid_wcs(data, ndim=2)
 
         for region in regions:
-            if isinstance(region, (SkyCircularAperture, SkyEllipticalAperture,
-                                   SkyRectangularAperture, CircleSkyRegion,
-                                   EllipseSkyRegion, RectangleSkyRegion)) and not has_wcs:
+            if (isinstance(region, (SkyCircularAperture, SkyEllipticalAperture,
+                                    SkyRectangularAperture, SkyCircularAnnulus,
+                                    CircleSkyRegion, EllipseSkyRegion,
+                                    RectangleSkyRegion, CircleAnnulusSkyRegion))
+                    and not has_wcs):
                 bad_regions.append((region, 'Sky region provided but data has no valid WCS'))
                 continue
 
             # photutils: Convert to regions shape first
             if isinstance(region, (CircularAperture, SkyCircularAperture,
                                    EllipticalAperture, SkyEllipticalAperture,
-                                   RectangularAperture, SkyRectangularAperture)):
+                                   RectangularAperture, SkyRectangularAperture,
+                                   CircularAnnulus, SkyCircularAnnulus)):
                 region = aperture2regions(region)
 
             # regions: Convert to ROI.
             # NOTE: Out-of-bounds ROI will succeed; this is native glue behavior.
             if isinstance(region, (CirclePixelRegion, CircleSkyRegion,
                                    EllipsePixelRegion, EllipseSkyRegion,
-                                   RectanglePixelRegion, RectangleSkyRegion)):
+                                   RectanglePixelRegion, RectangleSkyRegion,
+                                   CircleAnnulusPixelRegion, CircleAnnulusSkyRegion)):
                 state = regions2roi(region, wcs=data.coords)
 
                 # TODO: Do we want user to specify viewer? Does it matter?

jdaviz/core/region_translators.py

@@ -3,7 +3,7 @@
 """
 from astropy import units as u
 from astropy.coordinates import Angle
-from glue.core.roi import CircularROI, EllipticalROI, RectangularROI
+from glue.core.roi import CircularROI, EllipticalROI, RectangularROI, CircularAnnulusROI
 from photutils.aperture import (CircularAperture, SkyCircularAperture,
                                 EllipticalAperture, SkyEllipticalAperture,
                                 RectangularAperture, SkyRectangularAperture,
@@ -115,7 +115,8 @@ def regions2roi(region_shape, wcs=None):
     <glue.core.roi.CircularROI object at ...>
 
     """
-    if isinstance(region_shape, (CircleSkyRegion, EllipseSkyRegion, RectangleSkyRegion)):
+    if isinstance(region_shape, (CircleSkyRegion, EllipseSkyRegion, RectangleSkyRegion,
+                                 CircleAnnulusSkyRegion)):
         if wcs is None:
             raise ValueError(f'WCS must be provided for {region_shape}')
 
@@ -140,6 +141,10 @@ def regions2roi(region_shape, wcs=None):
         roi = RectangularROI(
             xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
             theta=region_shape.angle.to_value(u.radian))
+    elif isinstance(region_shape, CircleAnnulusPixelRegion):
+        roi = CircularAnnulusROI(
+            xc=region_shape.center.x, yc=region_shape.center.y,
+            inner_radius=region_shape.inner_radius, outer_radius=region_shape.outer_radius)
     else:
         raise NotImplementedError(f'{region_shape.__class__.__name__} is not supported')
 

pyproject.toml

@@ -12,7 +12,7 @@ dependencies = [
     "traitlets>=5.0.5",
     "bqplot>=0.12.37",
     "bqplot-image-gl>=1.4.11",
-    "glue-core>=1.6.0,!=1.9.0,!=1.10",
+    "glue-core>=1.11",
     "glue-jupyter>=0.15.0",
     "echo>=0.5.0",
     "ipykernel>=6.19.4",
@@ -26,7 +26,7 @@ dependencies = [
     "specutils>=1.9",
     "specreduce>=1.3.0,<1.4.0",
     "photutils>=1.4",
-    "glue-astronomy>=0.7",
+    "glue-astronomy>=0.9",
     "asteval>=0.9.23",
     "idna",
     "vispy>=0.6.5",