EXP: Build test case for

advanced aperture photometry.

Add tests that will fail without fix

WIP: How to actually fix this mess

Remove warning from doc

[ci skip] [rtd skip]

CHANGES.rst

@@ -81,6 +81,10 @@ Cubeviz
 Imviz
 ^^^^^
 
+- Fixed inaccurate results when aperture photometry is performed on non-reference data
+  that are of a different pixel scale or are rotated w.r.t. the reference data when
+  linked by WCS. [#2154]
+
 Mosviz
 ^^^^^^
 

docs/imviz/plugins.rst

@@ -165,10 +165,6 @@ Simple Aperture Photometry
 
     Regardless of your workflow, any WCS distortion in an image is ignored.
 
-    When you have multiple images linked by WCS and they have different
-    pixel scales or sky orientation, the selected aperture may be incorrectly defined
-    for images that are not the reference image (usually the first loaded one).
-
 This plugin performs simple aperture photometry
 and plots a radial profile for one object within
 an interactively selected region. A typical workflow is as follows:

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

@@ -370,7 +370,7 @@ def vue_recenter_subset(self, *args):
             data = self.dataset.selected_dc_item
             comp = data.get_component(data.main_components[0])
             comp_data = comp.data
-            phot_aperstats = ApertureStats(comp_data, aperture)
+            phot_aperstats = ApertureStats(comp_data, aperture, wcs=data.coords)
 
             # Centroid was calculated in selected data, which might or might not be
             # the reference data. However, Subset is always defined w.r.t.

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py

@@ -25,6 +25,10 @@
 
 __all__ = ['SimpleAperturePhotometry']
 
+# TODO: This plugin needs to show params wrt ref data because that is how glue
+#       defined it, but then it needs to do internal calculation using region
+#       that took account of the dither.
+
 
 @tray_registry('imviz-aper-phot-simple', label="Imviz Simple Aperture Photometry")
 class SimpleAperturePhotometry(PluginTemplateMixin, DatasetSelectMixin, TableMixin, PlotMixin):

jdaviz/configs/imviz/tests/test_simple_aper_phot.py

@@ -1,11 +1,13 @@
 import pytest
 import numpy as np
 from astropy import units as u
+from astropy.io import fits
 from astropy.tests.helper import assert_quantity_allclose
+from astropy.utils.data import get_pkg_data_filename
 from numpy.testing import assert_allclose, assert_array_equal
 from photutils.aperture import (ApertureStats, CircularAperture, EllipticalAperture,
                                 RectangularAperture, EllipticalAnnulus)
-from regions import CircleAnnulusPixelRegion, PixCoord
+from regions import CircleAnnulusPixelRegion, CirclePixelRegion, RectanglePixelRegion, PixCoord
 
 from jdaviz.configs.imviz.plugins.aper_phot_simple.aper_phot_simple import (
     _curve_of_growth, _radial_profile)
@@ -184,6 +186,59 @@ def test_plugin_no_wcs(self):
         assert_array_equal(tbl['sky_center'], None)
 
 
+class TestAdvancedAperPhot:
+    @pytest.fixture(autouse=True)
+    def setup_class(self, imviz_helper):
+        # Reference image
+        fn_1 = get_pkg_data_filename('data/gauss100_fits_wcs.fits')
+        imviz_helper.load_data(fn_1)
+        # Different pixel scale
+        imviz_helper.load_data(get_pkg_data_filename('data/gauss100_fits_wcs_block_reduced.fits'))
+        # Different pixel scale + rotated
+        imviz_helper.load_data(get_pkg_data_filename('data/gauss100_fits_wcs_block_reduced_rotated.fits'))  # noqa: E501
+
+        # Reference image again but without any WCS
+        data = fits.getdata(fn_1, ext=0)
+        imviz_helper.load_data(data, data_label='no_wcs')
+
+        # Link them by WCS
+        imviz_helper.link_data(link_type='wcs')
+
+        # Regions to be used for aperture photometry
+        regions = []
+        positions = [(145.1, 168.3), (84.7, 224.1), (48.3, 200.3)]
+        for x, y in positions:
+            regions.append(CirclePixelRegion(center=PixCoord(x=x, y=y), radius=5))
+        regions.append(RectanglePixelRegion(center=PixCoord(x=229, y=152), width=17, height=5))
+        imviz_helper.load_regions(regions)
+
+        self.imviz = imviz_helper
+        self.viewer = imviz_helper.default_viewer
+        self.phot_plugin = imviz_helper.plugins["Imviz Simple Aperture Photometry"]._obj
+
+        # Data has a mean background of 5.
+        self.phot_plugin.bg_subset_selected = 'Manual'
+        self.phot_plugin.background_value = 5.0
+
+    @pytest.mark.parametrize('data_label', [
+        'gauss100_fits_wcs[PRIMARY,1]',
+        'gauss100_fits_wcs_block_reduced[PRIMARY,1]',
+        'gauss100_fits_wcs_block_reduced_rotated[PRIMARY,1]',
+        'no_wcs'])
+    @pytest.mark.parametrize(('subset_label', 'expected_sum'), [
+        ('Subset 1', 738.8803424408962),
+        ('Subset 2', 348.33262363800094),
+        ('Subset 3', 857.5194857987592),
+        ('Subset 4', 762.3263959884644)])
+    def test_aperphot(self, data_label, subset_label, expected_sum):
+        """All data should give similar result for the same Subset."""
+        self.phot_plugin.dataset_selected = data_label
+        self.phot_plugin.subset_selected = subset_label
+        self.phot_plugin.vue_do_aper_phot()
+        tbl = self.imviz.get_aperture_photometry_results()
+        assert_allclose(tbl['sum'][-1], expected_sum)
+
+
 def test_annulus_background(imviz_helper):
     from photutils.datasets import make_4gaussians_image
 

jdaviz/core/region_translators.py

@@ -32,7 +32,7 @@ def _get_region_from_spatial_subset(plugin_obj, subset_label):
         The plugin is assumed to have a special setup that gives
         it access to these attributes: ``app`` and ``dataset_selected``.
         The ``app._jdaviz_helper.default_viewer`` attribute must also
-        exist and point to an image viewer that has a ``_get_real_xy``
+        exist and point to an image viewer that has a ``get_link_type``
         method.
 
     subset_label : str
@@ -41,7 +41,8 @@ def _get_region_from_spatial_subset(plugin_obj, subset_label):
     Returns
     -------
     reg : `regions.Region`
-        An equivalent ``regions`` shape.
+        An equivalent ``regions`` shape. This can be a pixel or sky
+        region, so the plugin needs to be able to deal with both.
 
     Raises
     ------
@@ -59,18 +60,19 @@ def _get_region_from_spatial_subset(plugin_obj, subset_label):
                 if sbst.data.label == plugin_obj.dataset_selected:
                     reg = sbst.data.get_selection_definition(
                         subset_id=subset_label, format='astropy-regions')
+
                     # Works around https://github.com/glue-viz/glue-astronomy/issues/52
-                    # Assume it is always pixel region, not sky region. Even with multiple
-                    # viewers, they all seem to share the same reference image even when it is
-                    # not loaded in all the viewers, so use default viewer.
+                    # Even with multiple viewers, they all seem to share the same
+                    # reference image even when it is not loaded in all the viewers,
+                    # so use default viewer.
                     viewer = plugin_obj.app._jdaviz_helper.default_viewer
+                    link_type = viewer.get_link_type(plugin_obj.dataset_selected)
 
-                    x, y, _, _ = viewer._get_real_xy(
-                        plugin_obj.app.data_collection[plugin_obj.dataset_selected],
-                        reg.center.x, reg.center.y)
-                    reg.center.x = x
-                    reg.center.y = y
-                    return reg
+                    if link_type == 'wcs':
+                        return reg.to_sky(
+                            plugin_obj.app.data_collection[plugin_obj.dataset_selected].coords)
+                    else:  # pixels or self
+                        return reg
     else:
         raise ValueError(f'Subset "{subset_label}" not found')