Merge pull request #1823 from pllim/pong

Imviz: Allow Subset recentering via centroiding

CHANGES.rst

@@ -18,6 +18,8 @@ Imviz
 
 - Warnings in aperture photometry plugin when using raw profile with large subsets. [#1801]
 
+- Subset Tools plugin now allows recentering of editable spatial subset. [#1823]
+
 Mosviz
 ^^^^^^
 

docs/imviz/plugins.rst

@@ -44,14 +44,21 @@ This plugin allows you to select an existing subset to modify, or to select
 :guilabel:`Create new` to create a new subset by selecting and using the region selector
 in the spectrum viewer toolbar. You can also choose the operation that will be
 applied by the selector tool. Note that these are synched with the subset tools
-in the app-level toolbar. It does not show static regions loaded
+in the app-level toolbar. It might not show some static regions loaded
 via the API unless an interactive region is drawn after.
 
 If an existing subset is selected, the parameters of the subset will also be
 shown. Note that while parameters for compound regions (e.g., a subset with
 multiple disjoint regions) are displayed, the logical operations joining them
 (``OR``, ``AND``, etc.) are not shown.
 
+For a simple subset in Imviz only, you can choose to recenter it based
+on the selected Data. The centroid is calculated by
+:attr:`photutils.aperture.ApertureStats.centroid`, which is the
+center-of-mass of the data within the aperture.
+No background subtraction is performed. Click :guilabel:`Recenter`
+to change its parameters and move it to the calculated centroid.
+
 For a simple subset, you can edit its parameters by changing the values
 in the corresponding editable text fields. Once you have entered the new
 value(s), click :guilabel:`Update` to apply. You should see the subset

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

@@ -5,11 +5,11 @@
 from glue.core.roi import CircularROI, EllipticalROI, RectangularROI
 from glue.core.subset import RoiSubsetState, RangeSubsetState, CompositeSubsetState
 from glue_jupyter.widgets.subset_mode_vuetify import SelectionModeMenu
-from traitlets import List, Unicode, Bool, observe
+from traitlets import Any, List, Unicode, Bool, observe
 
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.registries import tray_registry
-from jdaviz.core.template_mixin import PluginTemplateMixin, SubsetSelect
+from jdaviz.core.template_mixin import PluginTemplateMixin, DatasetSelectMixin, SubsetSelect
 
 __all__ = ['SubsetPlugin']
 
@@ -23,7 +23,7 @@
 
 
 @tray_registry('g-subset-plugin', label="Subset Tools")
-class SubsetPlugin(PluginTemplateMixin):
+class SubsetPlugin(PluginTemplateMixin, DatasetSelectMixin):
     template_file = __file__, "subset_plugin.vue"
     select = List([]).tag(sync=True)
     subset_items = List([]).tag(sync=True)
@@ -34,6 +34,8 @@ class SubsetPlugin(PluginTemplateMixin):
     subset_definitions = List([]).tag(sync=True)
     has_subset_details = Bool(False).tag(sync=True)
 
+    subplugins_opened = Any().tag(sync=True)
+
     is_editable = Bool(False).tag(sync=True)
 
     def __init__(self, *args, **kwargs):
@@ -226,6 +228,141 @@ def vue_update_subset(self, *args):
             self.hub.broadcast(SnackbarMessage(
                 f"Failed to update Subset: {repr(err)}", color='error', sender=self))
 
+    def vue_recenter_subset(self, *args):
+        # Composite region cannot be edited. This only works for Imviz.
+        if not self.is_editable or self.config != 'imviz':  # no-op
+            raise NotImplementedError(
+                f'Cannot recenter: is_editable={self.is_editable}, config={self.config}')
+
+        from photutils.aperture import ApertureStats
+        from jdaviz.core.region_translators import regions2aperture, _get_region_from_spatial_subset
+
+        try:
+            reg = _get_region_from_spatial_subset(self, self.subset_selected)
+            aperture = regions2aperture(reg)
+            data = self.dataset.selected_dc_item
+            comp = data.get_component(data.main_components[0])
+            comp_data = comp.data
+            phot_aperstats = ApertureStats(comp_data, aperture)
+
+            # Centroid was calculated in selected data, which might or might not be
+            # the reference data. However, Subset is always defined w.r.t.
+            # the reference data, so we need to convert back.
+            viewer = self.app._jdaviz_helper.default_viewer
+            x, y, _ = viewer._get_real_xy(
+                data, phot_aperstats.xcentroid, phot_aperstats.ycentroid, reverse=True)
+            if not np.all(np.isfinite((x, y))):
+                raise ValueError(f'Invalid centroid ({x}, {y})')
+        except Exception as err:
+            self.set_center(self.get_center(), update=False)
+            self.hub.broadcast(SnackbarMessage(
+                f"Failed to calculate centroid: {repr(err)}", color='error', sender=self))
+        else:
+            self.set_center((x, y), update=True)
+
+    def get_center(self):
+        """Return the center of the Subset.
+        This may or may not be the centroid obtain from data.
+
+        Returns
+        -------
+        cen : number, tuple of numbers, or `None`
+            The center of the Subset in ``x`` or ``(x, y)``,
+            depending on the Subset type, if applicable.
+            If Subset is not editable, this returns `None`.
+
+        Raises
+        ------
+        NotImplementedError
+            Subset type is not supported.
+
+        """
+        # Composite region cannot be edited.
+        if not self.is_editable:  # no-op
+            return
+
+        subset_state = self.subset_select.selected_subset_state
+
+        if isinstance(subset_state, RoiSubsetState):
+            sbst_obj = subset_state.roi
+            if isinstance(sbst_obj, (CircularROI, EllipticalROI)):
+                cen = sbst_obj.get_center()
+            elif isinstance(sbst_obj, RectangularROI):
+                cen = sbst_obj.center()
+            else:  # pragma: no cover
+                raise NotImplementedError(
+                    f'Getting center of {sbst_obj.__class__} is not supported')
+
+        elif isinstance(subset_state, RangeSubsetState):
+            cen = (subset_state.hi - subset_state.lo) * 0.5 + subset_state.lo
+
+        else:  # pragma: no cover
+            raise NotImplementedError(
+                f'Getting center of {subset_state.__class__} is not supported')
+
+        return cen
+
+    def set_center(self, new_cen, update=False):
+        """Set the desired center for the selected Subset, if applicable.
+        If Subset is not editable, nothing is done.
+
+        Parameters
+        ----------
+        new_cen : number or tuple of numbers
+            The new center defined either as ``x`` or ``(x, y)``,
+            depending on the Subset type.
+
+        update : bool
+            If `True`, the Subset is also moved to the new center.
+            Otherwise, only the relevant editable fields are updated but the
+            Subset is not moved.
+
+        Raises
+        ------
+        NotImplementedError
+            Subset type is not supported.
+
+        """
+        # Composite region cannot be edited, so just grab first element.
+        if not self.is_editable:  # no-op
+            return
+
+        subset_state = self.subset_select.selected_subset_state
+
+        if isinstance(subset_state, RoiSubsetState):
+            x, y = new_cen
+            sbst_obj = subset_state.roi
+            if isinstance(sbst_obj, (CircularROI, EllipticalROI)):
+                self._set_value_in_subset_definition(0, "X Center", "value", x)
+                self._set_value_in_subset_definition(0, "Y Center", "value", y)
+            elif isinstance(sbst_obj, RectangularROI):
+                cx, cy = sbst_obj.center()
+                dx = x - cx
+                dy = y - cy
+                self._set_value_in_subset_definition(0, "Xmin", "value", sbst_obj.xmin + dx)
+                self._set_value_in_subset_definition(0, "Xmax", "value", sbst_obj.xmax + dx)
+                self._set_value_in_subset_definition(0, "Ymin", "value", sbst_obj.ymin + dy)
+                self._set_value_in_subset_definition(0, "Ymax", "value", sbst_obj.ymax + dy)
+            else:  # pragma: no cover
+                raise NotImplementedError(f'Recentering of {sbst_obj.__class__} is not supported')
+
+        elif isinstance(subset_state, RangeSubsetState):
+            dx = new_cen - ((subset_state.hi - subset_state.lo) * 0.5 + subset_state.lo)
+            self._set_value_in_subset_definition(0, "Lower bound", "value", subset_state.lo + dx)
+            self._set_value_in_subset_definition(0, "Upper bound", "value", subset_state.hi + dx)
+
+        else:  # pragma: no cover
+            raise NotImplementedError(
+                f'Getting center of {subset_state.__class__} is not supported')
+
+        if update:
+            self.vue_update_subset()
+        else:
+            # Force UI to update on browser without changing the subset.
+            tmp = self.subset_definitions
+            self.subset_definitions = []
+            self.subset_definitions = tmp
+
     # List of JSON-like dict is nice for front-end but a pain to look up,
     # so we use these helper functions.
 

jdaviz/configs/default/plugins/subset_plugin/subset_plugin.vue

@@ -22,6 +22,29 @@
       </v-col>
     </v-row>
 
+    <!-- Sub-plugin for recentering of spatial subset (Imviz only) -->
+    <v-row v-if="config=='imviz' && is_editable">
+      <v-expansion-panels accordion v-model="subplugins_opened">
+        <v-expansion-panel>
+          <v-expansion-panel-header >
+            <span style="padding: 6px">Recenter</span>
+          </v-expansion-panel-header>
+          <v-expansion-panel-content>
+            <plugin-dataset-select
+             :items="dataset_items"
+             :selected.sync="dataset_selected"
+             :show_if_single_entry="true"
+             label="Data"
+             hint="Select the data for centroiding."
+            />
+            <v-row justify="end" no-gutters>
+              <v-btn color="primary" text @click="recenter_subset">Recenter</v-btn>
+            </v-row>
+          </v-expansion-panel-content>
+        </v-expansion-panel>
+      </v-expansion-panels>
+    </v-row>
+
     <!-- Composite region cannot be edited, so just grab first element. -->
     <div v-if="is_editable">
       <v-row v-for="(item, index2) in subset_definitions[0]"

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

@@ -22,7 +22,7 @@
 
 from jdaviz.core.custom_traitlets import FloatHandleEmpty
 from jdaviz.core.events import SnackbarMessage, LinkUpdatedMessage
-from jdaviz.core.region_translators import regions2aperture
+from jdaviz.core.region_translators import regions2aperture, _get_region_from_spatial_subset
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import PluginTemplateMixin, DatasetSelectMixin, SubsetSelect
 from jdaviz.utils import bqplot_clear_figure, PRIHDR_KEY
@@ -142,28 +142,6 @@ def _dataset_selected_changed(self, event={}):
         # and auto-populate background, if applicable.
         self._subset_selected_changed()
 
-    def _get_region_from_subset(self, subset):
-        for subset_grp in self.app.data_collection.subset_groups:
-            if subset_grp.label == subset:
-                for sbst in subset_grp.subsets:
-                    if sbst.data.label == self.dataset_selected:
-                        reg = sbst.data.get_selection_definition(
-                            subset_id=subset, 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.
-                        viewer = self.app._jdaviz_helper.default_viewer
-
-                        x, y, _ = viewer._get_real_xy(
-                            self.app.data_collection[self.dataset_selected],
-                            reg.center.x, reg.center.y)
-                        reg.center.x = x
-                        reg.center.y = y
-                        return reg
-        else:
-            raise ValueError(f'Subset "{subset}" not found')
-
     def _on_subset_update(self, msg):
         if self.dataset_selected == '' or self.subset_selected == '':
             return
@@ -189,7 +167,7 @@ def _subset_selected_changed(self, event={}):
             return
 
         try:
-            self._selected_subset = self._get_region_from_subset(subset_selected)
+            self._selected_subset = _get_region_from_spatial_subset(self, subset_selected)
             self._selected_subset.meta['label'] = subset_selected
 
             if isinstance(self._selected_subset, CirclePixelRegion):
@@ -251,7 +229,7 @@ def _bg_subset_selected_changed(self, event={}):
             return
 
         try:
-            reg = self._get_region_from_subset(bg_subset_selected)
+            reg = _get_region_from_spatial_subset(self, bg_subset_selected)
             self.background_value = self._calc_bg_subset_median(reg)
         except Exception as e:
             self.background_value = 0

jdaviz/configs/imviz/plugins/viewers.py

@@ -220,12 +220,15 @@ def on_limits_change(self, *args):
             return
         self.set_compass(self.state.layers[i].layer)
 
-    def _get_real_xy(self, image, x, y):
+    def _get_real_xy(self, image, x, y, reverse=False):
         """Return real (X, Y) position and status in case of dithering.
 
         ``coords_status`` is for ``self.label_mouseover`` coords handling only.
         When `True`, it sets the coords, otherwise it resets.
 
+        ``reverse=True`` is only for internal roundtripping (e.g., centroiding
+        in Subset Tools plugin). Never use this for coordinates display panel.
+
         """
         if data_has_valid_wcs(image):
             # Convert these to a SkyCoord via WCS - note that for other datasets
@@ -235,8 +238,12 @@ def _get_real_xy(self, image, x, y):
                 # Convert X,Y from reference data to the one we are actually seeing.
                 # world_to_pixel return scalar ndarray that we need to convert to float.
                 if self.get_link_type(image.label) == 'wcs':
-                    x, y = list(map(float, image.coords.world_to_pixel(
-                        self.state.reference_data.coords.pixel_to_world(x, y))))
+                    if not reverse:
+                        x, y = list(map(float, image.coords.world_to_pixel(
+                            self.state.reference_data.coords.pixel_to_world(x, y))))
+                    else:
+                        x, y = list(map(float, self.state.reference_data.coords.world_to_pixel(
+                            image.coords.pixel_to_world(x, y))))
                 coords_status = True
             except Exception:
                 coords_status = False

jdaviz/configs/imviz/tests/test_subset_centroid.py

@@ -0,0 +1,64 @@
+from regions import PixCoord, CirclePixelRegion
+
+from jdaviz.configs.imviz.tests.utils import BaseImviz_WCS_GWCS
+
+
+class TestImvizSpatialSubsetCentroid(BaseImviz_WCS_GWCS):
+    def test_centroiding(self):
+        reg = CirclePixelRegion(PixCoord(2, 2), 3)
+        self.imviz.load_regions(reg)
+
+        plg = self.imviz.plugins['Subset Tools']
+        plg._obj.subset_selected = 'Subset 1'
+
+        # Since they are linked by pixels, the bright corner pixel aligns
+        # and nothing should change.
+        for data_label in ('fits_wcs[DATA]', 'gwcs[DATA]', 'no_wcs'):
+            plg._obj.dataset_selected = data_label
+            plg._obj.set_center((2, 2), update=True)  # Move the Subset back first.
+            plg._obj.vue_recenter_subset()
+
+            # Calculate and move to centroid.
+            for key in ("X Center", "Y Center"):
+                assert plg._obj._get_value_from_subset_definition(0, key, "value") == -1
+                assert plg._obj._get_value_from_subset_definition(0, key, "orig") == -1
+
+            # Radius will not be touched.
+            for key in ("value", "orig"):
+                assert plg._obj._get_value_from_subset_definition(0, "Radius", key) == 3
+
+        assert plg._obj.get_center() == (-1, -1)
+
+        # FITS WCS and GWCS are rotated from each other.
+        # Plain array always by pixel wrt FITS WCS.
+        self.imviz.link_data(link_type='wcs')
+
+        plg._obj.dataset_selected = 'fits_wcs[DATA]'
+        plg._obj.set_center((2, 2), update=True)  # Move the Subset back first.
+        plg._obj.vue_recenter_subset()
+        for key in ("X Center", "Y Center"):
+            assert plg._obj._get_value_from_subset_definition(0, key, "value") == -1
+            assert plg._obj._get_value_from_subset_definition(0, key, "orig") == -1
+
+        # GWCS does not extrapolate and this Subset is out of bounds,
+        # so will get NaNs and enter the exception handling logic.
+        plg._obj.dataset_selected = 'gwcs[DATA]'
+        plg._obj.set_center((2, 2), update=True)  # Move the Subset back first.
+        plg._obj.vue_recenter_subset()
+        for key in ("X Center", "Y Center"):
+            assert plg._obj._get_value_from_subset_definition(0, key, "value") == 2
+            assert plg._obj._get_value_from_subset_definition(0, key, "orig") == 2
+
+        # No WCS case will be same as FITS WCS.
+        plg._obj.dataset_selected = 'no_wcs'
+        plg._obj.vue_recenter_subset()
+        for key in ("X Center", "Y Center"):
+            assert plg._obj._get_value_from_subset_definition(0, key, "value") == -1
+            assert plg._obj._get_value_from_subset_definition(0, key, "orig") == -1
+
+        # This ends up not getting used in production but just in case we need it
+        # back in the future.
+        plg._obj.set_center((2, 2), update=False)
+        for key in ("X Center", "Y Center"):
+            assert plg._obj._get_value_from_subset_definition(0, key, "value") == 2
+            assert plg._obj._get_value_from_subset_definition(0, key, "orig") == -1