Remove annulus from aperture photometry plugin (#2276)

* Remove annulus from aperture
photometry plugin. Use the draw tool.

[ci skip] [rtd skip]

* Add change log

CHANGES.rst

@@ -60,6 +60,11 @@ Cubeviz
 Imviz
 ^^^^^
 
+- Simple Aperture Photometry plugin: Custom annulus background options are removed.
+  Please draw/load annulus as you would with other region shapes, then select it
+  in the plugin from Subset dropdown for the background. Using annulus region as
+  aperture is not supported. [#2276]
+
 Mosviz
 ^^^^^^
 

docs/imviz/plugins.rst

@@ -181,15 +181,18 @@ an interactively selected region. A typical workflow is as follows:
    object of interest using its center of mass, if you wish.
    Depending on the object, it may take several iterations for re-centering
    to converge, or it may never converge at all.
+
+   .. note::
+
+       You cannot use annulus region as aperture (an exception will be thrown)
+       but you may use it for background (see below).
+
 5. If you want to subtract background before performing photometry,
    you have the following 3 options. Otherwise if your image is already
    background subtracted, choose "Manual" and leave the background set at 0:
 
   * Manual: Enter the background value in the :guilabel:`Background value` field.
     This value must be in the same unit as display data, if applicable.
-  * Annulus: Enter its inner radius and width in the :guilabel:`Annulus inner radius`
-    and :guilabel:`Annulus width`, respectively. Median of the pixels within
-    the annulus region will be used but the annulus shape will not be shown on display.
   * Subset: Define a region for background calculation (median) using Subset draw tool
     and select that region using the :guilabel:`Background` dropdown menu. Only regions
     created with the :guilabel:`replace` option are acceptable as background regions

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

@@ -14,11 +14,8 @@
 from packaging.version import Version
 from photutils.aperture import (ApertureStats, CircularAperture, EllipticalAperture,
                                 RectangularAperture)
-from regions import (CircleAnnulusPixelRegion, CirclePixelRegion, EllipsePixelRegion,
-                     RectanglePixelRegion)
 from traitlets import Any, Bool, Integer, List, Unicode, observe
 
-from jdaviz.core.custom_traitlets import FloatHandleEmpty
 from jdaviz.core.events import SnackbarMessage, LinkUpdatedMessage
 from jdaviz.core.region_translators import regions2aperture, _get_region_from_spatial_subset
 from jdaviz.core.registries import tray_registry
@@ -38,8 +35,6 @@ class SimpleAperturePhotometry(PluginTemplateMixin, DatasetSelectMixin, TableMix
     bg_subset_items = List().tag(sync=True)
     bg_subset_selected = Unicode("").tag(sync=True)
     background_value = Any(0).tag(sync=True)
-    bg_annulus_inner_r = FloatHandleEmpty(0).tag(sync=True)
-    bg_annulus_width = FloatHandleEmpty(10).tag(sync=True)
     pixel_area = Any(0).tag(sync=True)
     counts_factor = Any(0).tag(sync=True)
     flux_scaling = Any(0).tag(sync=True)
@@ -66,7 +61,7 @@ def __init__(self, *args, **kwargs):
                                       'bg_subset_items',
                                       'bg_subset_selected',
                                       default_text='Manual',
-                                      manual_options=['Manual', 'Annulus'],
+                                      manual_options=['Manual'],
                                       allowed_type='spatial')
 
         headers = ['xcenter', 'ycenter', 'sky_center',
@@ -161,7 +156,7 @@ def _on_link_update(self, msg):
         if self.dataset_selected == '' or self.subset_selected == '':
             return
 
-        # Force background auto-calculation (including annulus) to update when linking has changed.
+        # Force background auto-calculation to update when linking has changed.
         self._subset_selected_changed()
 
     @observe('subset_selected')
@@ -173,18 +168,6 @@ def _subset_selected_changed(self, event={}):
         try:
             self._selected_subset = _get_region_from_spatial_subset(self, subset_selected)
             self._selected_subset.meta['label'] = subset_selected
-
-            if isinstance(self._selected_subset, CirclePixelRegion):
-                self.bg_annulus_inner_r = self._selected_subset.radius
-            elif isinstance(self._selected_subset, EllipsePixelRegion):
-                self.bg_annulus_inner_r = max(self._selected_subset.width,
-                                              self._selected_subset.height) * 0.5
-            elif isinstance(self._selected_subset, RectanglePixelRegion):
-                self.bg_annulus_inner_r = np.sqrt(self._selected_subset.width ** 2 +
-                                                  self._selected_subset.height ** 2) * 0.5
-            else:  # pragma: no cover
-                raise TypeError(f'Unsupported region shape: {self._selected_subset.__class__}')
-
             self.subset_area = int(np.ceil(self._selected_subset.area))
 
         except Exception as e:
@@ -206,30 +189,12 @@ def _calc_bg_subset_median(self, reg):
         # photutils/background/_utils.py --> nanmedian()
         return np.nanmedian(img_stat)  # Naturally in data unit
 
-    @observe('bg_annulus_inner_r', 'bg_annulus_width')
-    def _bg_annulus_updated(self, *args):
-        if self.bg_subset_selected != 'Annulus':
-            return
-
-        try:
-            inner_r = float(self.bg_annulus_inner_r)
-            reg = CircleAnnulusPixelRegion(
-                self._selected_subset.center, inner_radius=inner_r,
-                outer_radius=inner_r + float(self.bg_annulus_width))
-            self.background_value = self._calc_bg_subset_median(reg)
-
-        except Exception:  # Error snackbar suppressed to prevent excessive queue.
-            self.background_value = 0
-
     @observe('bg_subset_selected')
     def _bg_subset_selected_changed(self, event={}):
         bg_subset_selected = event.get('new', self.bg_subset_selected)
         if bg_subset_selected == 'Manual':
             # we'll later access the user's self.background_value directly
             return
-        if bg_subset_selected == 'Annulus':
-            self._bg_annulus_updated()
-            return
 
         try:
             reg = _get_region_from_spatial_subset(self, bg_subset_selected)

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue

@@ -36,30 +36,6 @@
           </span>
         </v-row>
 
-        <v-row v-if="bg_subset_selected=='Annulus'">
-          <v-text-field
-            label="Annulus inner radius"
-            v-model.number="bg_annulus_inner_r"
-            type="number"
-            :rules="[() => bg_annulus_inner_r>0 || 'Must be positive.']"
-            hint="Background annulus inner radius in pixels"
-            persistent-hint
-          >
-          </v-text-field>
-        </v-row>
-
-        <v-row v-if="bg_subset_selected=='Annulus'">
-          <v-text-field
-            label="Annulus width"
-            v-model.number="bg_annulus_width"
-            type="number"
-            :rules="[() => bg_annulus_width>0 || 'Must be positive.']"
-            hint="Background annulus width in pixels (inner radius + width = outer radius)"
-            persistent-hint
-          >
-          </v-text-field>
-        </v-row>
-
         <v-row>
           <v-text-field
             label="Background value"

jdaviz/configs/imviz/tests/test_simple_aper_phot.py

@@ -2,10 +2,10 @@
 import numpy as np
 from astropy import units as u
 from astropy.tests.helper import assert_quantity_allclose
-from glue.core.edit_subset_mode import ReplaceMode
 from numpy.testing import assert_allclose, assert_array_equal
 from photutils.aperture import (ApertureStats, CircularAperture, EllipticalAperture,
                                 RectangularAperture, EllipticalAnnulus)
+from regions import CircleAnnulusPixelRegion, PixCoord
 
 from jdaviz.configs.imviz.plugins.aper_phot_simple.aper_phot_simple import (
     _curve_of_growth, _radial_profile)
@@ -52,7 +52,7 @@ def test_plugin_wcs_dithered(self):
         phot_plugin.current_plot_type = 'Radial Profile (Raw)'
         assert phot_plugin._selected_data is not None
         assert phot_plugin._selected_subset is not None
-        assert phot_plugin.bg_subset.labels == ['Manual', 'Annulus', 'Subset 1']
+        assert phot_plugin.bg_subset.labels == ['Manual', 'Subset 1']
         assert_allclose(phot_plugin.background_value, 0)
         assert_allclose(phot_plugin.counts_factor, 0)
         assert_allclose(phot_plugin.pixel_area, 0)
@@ -159,12 +159,6 @@ def test_plugin_wcs_dithered(self):
         phot_plugin.dataset_selected = 'twos'
         assert_allclose(phot_plugin.background_value, 2)  # Recalculate based on new Data
 
-        # Check rectangle annulus math
-        phot_plugin.bg_subset_selected = 'Annulus'
-        phot_plugin.subset_selected = 'Subset 3'
-        assert_allclose(phot_plugin.bg_annulus_inner_r, 6.363961030678928)  # half-width = 4.5
-        assert_allclose(phot_plugin.bg_annulus_width, 10)
-
         # Curve of growth
         phot_plugin.current_plot_type = 'Curve of Growth'
         phot_plugin.vue_do_aper_phot()
@@ -203,28 +197,37 @@ def test_annulus_background(imviz_helper):
     phot_plugin.dataset_selected = 'ones'
 
     # Mark an object of interest
+    # CirclePixelRegion(center=PixCoord(x=150, y=25), radius=7)
     imviz_helper._apply_interactive_region('bqplot:circle', (143, 18), (157, 32))
+
+    # Load annulus (this used to be part of the plugin but no longer)
+    annulus_1 = CircleAnnulusPixelRegion(
+        PixCoord(x=150, y=25), inner_radius=7, outer_radius=17)
+    imviz_helper.load_regions([annulus_1])
+
     phot_plugin.subset_selected = 'Subset 1'
-    phot_plugin.bg_subset_selected = 'Annulus'
+    phot_plugin.bg_subset_selected = 'Subset 2'
 
     # Check annulus for ones
-    assert_allclose(phot_plugin.bg_annulus_inner_r, 7)  # From circle
-    assert_allclose(phot_plugin.bg_annulus_width, 10)  # Default
     assert_allclose(phot_plugin.background_value, 1)
 
     # Switch data
     phot_plugin.dataset_selected = 'four_gaussians'
-    assert_allclose(phot_plugin.bg_annulus_inner_r, 7)  # Unchanged
-    assert_allclose(phot_plugin.bg_annulus_width, 10)
     assert_allclose(phot_plugin.background_value, 5.745596129482831)  # Changed
 
     # Draw ellipse on another object
+    # EllipsePixelRegion(center=PixCoord(x=20.5, y=37.5), width=41, height=15)
     imviz_helper._apply_interactive_region('bqplot:ellipse', (0, 30), (41, 45))
-    phot_plugin.subset_selected = 'Subset 2'
+
+    # Load annulus (this used to be part of the plugin but no longer)
+    annulus_2 = CircleAnnulusPixelRegion(
+        PixCoord(x=20.5, y=37.5), inner_radius=20.5, outer_radius=30.5)
+    imviz_helper.load_regions([annulus_2])
+
+    phot_plugin.subset_selected = 'Subset 3'
+    phot_plugin.bg_subset_selected = 'Subset 4'
 
     # Check new annulus for four_gaussians
-    assert_allclose(phot_plugin.bg_annulus_inner_r, 20.5)  # From ellipse half-width
-    assert_allclose(phot_plugin.bg_annulus_width, 10)  # Unchanged
     assert_allclose(phot_plugin.background_value, 5.13918435824334)  # Changed
 
     # Switch to manual, should not change
@@ -236,29 +239,18 @@ def test_annulus_background(imviz_helper):
     assert_allclose(phot_plugin.background_value, 44.72559981461203)
 
     # Switch back to annulus, should be same as before in same mode
-    phot_plugin.bg_subset_selected = 'Annulus'
-    assert_allclose(phot_plugin.bg_annulus_inner_r, 20.5)
-    assert_allclose(phot_plugin.bg_annulus_width, 10)
+    phot_plugin.bg_subset_selected = 'Subset 4'
     assert_allclose(phot_plugin.background_value, 5.13918435824334)
 
-    # Manually change inner_r
-    phot_plugin.bg_annulus_inner_r = 40
-    assert_allclose(phot_plugin.background_value, 4.783765940615679)
-
-    # Manually change width
-    phot_plugin.bg_annulus_width = 5
-    assert_allclose(phot_plugin.background_value, 4.894003242594493)
-
-    # Move the last created Subset (ellipse) and make sure background updates
-    imviz_helper.app.session.edit_subset_mode.mode = ReplaceMode
-    imviz_helper._apply_interactive_region('bqplot:ellipse', (0, 30), (51, 55))
-    assert_allclose(phot_plugin.bg_annulus_inner_r, 40)
-    assert_allclose(phot_plugin.bg_annulus_width, 5)
-    assert_allclose(phot_plugin.background_value, 4.894003)
-
-    # Bad annulus should not crash plugin
-    phot_plugin.bg_annulus_inner_r = -1
-    assert_allclose(phot_plugin.background_value, 0)
+    # Edit the annulus and make sure background updates
+    subset_plugin = imviz_helper.plugins["Subset Tools"]._obj
+    subset_plugin.subset_selected = "Subset 4"
+    subset_plugin._set_value_in_subset_definition(0, "X Center", "value", 25.5)
+    subset_plugin._set_value_in_subset_definition(0, "Y Center", "value", 42.5)
+    subset_plugin._set_value_in_subset_definition(0, "Inner radius", "value", 40)
+    subset_plugin._set_value_in_subset_definition(0, "Outer radius", "value", 45)
+    subset_plugin.vue_update_subset()
+    assert_allclose(phot_plugin.background_value, 4.89189)
 
 
 # NOTE: Extracting the cutout for radial profile is aperture