WIP: Fix astrowidgets API

More safeguards

fix multi viewer linked pan/zoom (or breaking it, not sure)

Fix CI
mainly by using more conventional ways to adjust the tests
take give back same result as main, so also undo the result changes.
Deleted unnecessary functions.

Better change log, add basic doc.
It bothers me that there is no user doc at all. I will add some basic info here.
Better doc is already a future ticket.

I do not need get_bottom_layer is needed

GWCS is also BaseHighLevelWCS, no need to check separately.

imviz.link_data API should error out sooner when subsets need to be cleared first.

Remove unnecessary check for viewer.data() especially since that might waste memory.

More code simplification. And clarify behavior more in doc.

Docstring nitpick

Nope did not work out as I hoped

I think I fixed aper phot

CHANGES.rst

@@ -27,6 +27,9 @@ Cubeviz
 Imviz
 ^^^^^
 
+- There is now option for image rotation in Links Control plugin.
+  This feature requires WCS linking. [#2179]
+
 - Aperture photometry (previously "Imviz Simple Aperture Photometry") now supports batch mode. [#2465]
 
 - Aperture photometry sum is now presented in scientific notation consistently. [#2530]
@@ -51,6 +54,12 @@ Cubeviz
 Imviz
 ^^^^^
 
+- Linking by WCS will now always generate a hidden reference data layer
+  without distortion. As a result, when WCS linked, the first loaded data
+  is no longer the reference data. Additionally, if data is distorted,
+  its distortion will show when linked by WCS. If there is also data without WCS,
+  it can no longer be displayed when WCS linked. [#2179]
+
 Mosviz
 ^^^^^^
 
@@ -188,8 +197,6 @@ Cubeviz
 Imviz
 ^^^^^
 
-- Added viewer rotation support via Glue linking [#2179]
-
 - The stretch histogram within plot options can now be popped-out into its own window. [#2314]
 
 - vmin/vmax step size in the plot options plugin is now dynamic based on the full range of the

docs/imviz/plugins.rst

@@ -106,7 +106,7 @@ Orientation
 
 .. note::
 
-  This plugin was previous called "Links Control"
+    This plugin was previous called "Links Control".
 
 This plugin is used to align image layers by pixels or sky (WCS) using
 :func:`~jdaviz.configs.imviz.helper.link_image_data`.
@@ -119,6 +119,13 @@ performant at the cost of accuracy but should be accurate to within a pixel
 for most cases. If approximation fails, WCS linking still automatically
 falls back to full transformation.
 
+Since Jdaviz v3.9, when linking by WCS, a hidden reference data layer
+without distortion will be created and all the data would be linked to
+it instead of the first loaded data. As a result, working in pixel
+space when linked by WCS is not recommended. Additionally, any data
+with distorted WCS would show as distorted on the display. Furthermore,
+any data without WCS can no longer be shown in WCS linking mode.
+
 For the best experience, it is recommended that you decide what kind of
 link you want and set it at the beginning of your Imviz session,
 rather than later.
@@ -134,6 +141,21 @@ From the API within the Jupyter notebook (if linking by WCS):
 
     imviz.link_data(link_type='wcs')
 
+.. _imviz-orientation-rotation:
+
+Orientation: Image Rotation
+===========================
+
+When linked by WCS, sky rotation is also possible. You can choose from
+presets (N-up, E-left/right) or provide your own sky angle.
+
+.. warning::
+
+    Each rotation request created a new reference data layer in the background.
+    Just as in :ref:`imviz-import-data`, the performance would be impacted by
+    the number of active rotation layers you have; Only keep the desired rotation layer.
+    Note that the "default orientation" layer cannot be removed.
+
 .. _imviz-compass:
 
 Compass

jdaviz/app.py

@@ -556,7 +556,7 @@ def _change_reference_data(self, new_refdata_label, viewer_id=None):
             # adjust zoom to account for new refdata if both the
             # old and new refdata are WCS-only layers
             # (which also ensures zoom_level is already determined):
-            fov_sky_final = viewer._get_fov(new_refdata)
+            fov_sky_final = viewer._get_fov()
             viewer.zoom(
                 float(fov_sky_final / fov_sky_init)
             )

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

@@ -422,7 +422,7 @@ def vue_recenter_subset(self, *args):
 
         def _do_recentering(subset, subset_state):
             try:
-                reg = _get_region_from_spatial_subset(self, subset_state) # noqa
+                reg = _get_region_from_spatial_subset(self, subset_state)
                 aperture = regions2aperture(reg)
                 data = self.dataset.selected_dc_item
                 comp = data.get_component(data.main_components[0])

jdaviz/configs/imviz/helper.py

@@ -7,7 +7,6 @@
 import astropy.units as u
 from astropy.utils.exceptions import AstropyDeprecationWarning
 from astropy.wcs.wcsapi import BaseHighLevelWCS
-from gwcs.wcs import WCS as GWCS
 from glue.core import BaseData
 from glue.core.link_helpers import LinkSame
 from glue.plugins.wcs_autolinking.wcs_autolinking import WCSLink, NoAffineApproximation
@@ -410,17 +409,6 @@ def layer_is_table_data(layer):
     return isinstance(layer, BaseData) and layer.ndim == 1
 
 
-def get_bottom_layer(viewer):
-    """
-    Get the first-loaded image layer in Imviz.
-    """
-    image_layers = [lyr.layer for lyr in viewer.layers
-                    if lyr.visible and layer_is_image_data(lyr.layer)]
-    if not len(image_layers):
-        return None
-    return image_layers[0]
-
-
 def get_wcs_only_layer_labels(app):
     return [data.label for data in app.data_collection
             if layer_is_wcs_only(data)]
@@ -519,7 +507,7 @@ def link_image_data(app, link_type='pixels', wcs_fallback_scheme=None, wcs_use_a
                          f"got {wcs_fallback_scheme}")
     if link_type == 'wcs':
         at_least_one_data_have_wcs = len([
-            hasattr(d, 'coords') and isinstance(d.coords, (BaseHighLevelWCS, GWCS))
+            hasattr(d, 'coords') and isinstance(d.coords, BaseHighLevelWCS)
             for d in app.data_collection
         ]) > 0
         if not at_least_one_data_have_wcs:
@@ -557,9 +545,7 @@ def link_image_data(app, link_type='pixels', wcs_fallback_scheme=None, wcs_use_a
     old_link_type = getattr(app, '_link_type', None)
     refdata, iref = get_reference_image_data(app)
     # default reference layer is the first-loaded image:
-    default_reference_layer = get_bottom_layer(app._jdaviz_helper.default_viewer)
-    if default_reference_layer is None:
-        default_reference_layer = refdata
+    default_reference_layer = app.data_collection[0]
 
     # if linking via WCS, add WCS-only reference data layer:
     insert_base_wcs_layer = (
@@ -612,6 +598,10 @@ def link_image_data(app, link_type='pixels', wcs_fallback_scheme=None, wcs_use_a
             # links already exist for this entry and we're not changing the type
             continue
 
+        # We are not touching fake WCS layers in pixel linking.
+        if link_type == 'pixels' and data.meta.get('_WCS_ONLY'):
+            continue
+
         ids1 = data.pixel_component_ids
         new_links = []
         try:

jdaviz/configs/imviz/plugins/orientation/orientation.py

@@ -8,7 +8,7 @@
 
 import astropy.units as u
 from jdaviz.configs.imviz.helper import (
-    link_image_data, get_bottom_layer
+    link_image_data
 )
 from jdaviz.configs.imviz.wcs_utils import (
     get_compass_info, _get_rotated_nddata_from_label
@@ -243,6 +243,10 @@ def _update_link(self, msg={}):
         self.linking_in_progress = False
         self._update_layer_label_default()
 
+        # Clear previous zoom limits because they no longer mean anything.
+        for v in self.app._viewer_store.values():
+            v._prev_limits = None
+
     def _on_subset_change(self, msg):
         self.need_clear_subsets = len(self.app.data_collection.subset_groups) > 0
 
@@ -259,8 +263,7 @@ def vue_reset_astrowidget_markers(self, *args):
             viewer.reset_markers()
 
     def _get_wcs_angles(self):
-        viewer = self.app.get_viewer(self.viewer.selected)
-        first_loaded_image = get_bottom_layer(viewer)
+        first_loaded_image = self.app.data_collection[0]
         degn, dege, flip = get_compass_info(
             first_loaded_image.coords, first_loaded_image.shape
         )[-3:]
@@ -302,8 +305,7 @@ def add_orientation(self, rotation_angle=None, east_left=None, label=None,
         if wrt_data is None:
             # if not specified, use first-loaded image layer as the
             # default rotation:
-            viewer = self.app.get_viewer(self.viewer.selected)
-            wrt_data = get_bottom_layer(viewer)
+            wrt_data = self.app.data_collection[0]
 
         # Default rotation is the same orientation as the original reference data:
         degn = self._get_wcs_angles()[0]
@@ -383,7 +385,7 @@ def _refdata_change_available(self):
         else:
             is_subset = False
         return (
-            ref_data is not None and len(viewer.data()) and
+            ref_data is not None and
             len(self.orientation.selected) and len(self.viewer.selected) and
             not is_subset
         )

jdaviz/configs/imviz/plugins/tools.py

@@ -19,9 +19,22 @@ class _ImvizMatchedZoomMixin(_MatchedZoomMixin):
     disable_matched_zoom_in_other_viewer = False
 
     def _is_matched_viewer(self, viewer):
-        # only match zooms in viewers that share reference data
         return isinstance(viewer, BqplotImageView)
 
+    def _post_activate(self):
+        # NOTE: For Imviz only.
+        # Set the reference data in other viewers to be the same as the current viewer.
+        # If adding the data to the viewer, make sure it is not actually shown since the
+        # user didn't request it.
+        for viewer in self._iter_matched_viewers(include_self=False):
+            if self.viewer.state.reference_data not in viewer.state.layers_data:
+                viewer.add_data(self.viewer.state.reference_data)
+                for layer in viewer.state.layers:
+                    if layer.layer is self.viewer.state.reference_data:
+                        layer.visible = False
+                        break
+            viewer.state.reference_data = self.viewer.state.reference_data
+
 
 @viewer_tool
 class ImagePanZoom(PanZoom):

jdaviz/configs/imviz/plugins/viewers.py

@@ -305,43 +305,38 @@ def get_link_type(self, data_label):
 
         return link_type
 
-    def _get_fov(self, data):
+    def _get_fov(self):
+        data = self.state.reference_data
+        if self.jdaviz_app._link_type != "wcs" or data.coords is None:
+            return
+
         # compute the mean of the height and width of the
         # viewer's FOV on ``data`` in world units:
         x_corners = [
             self.state.x_min,
             self.state.x_max,
-            self.state.x_min,
-            self.state.x_max
+            self.state.x_min
         ]
         y_corners = [
             self.state.y_min,
             self.state.y_min,
-            self.state.y_max,
             self.state.y_max
         ]
 
-        y_corners, x_corners = self._get_real_xy(
-            data, x_corners, y_corners
-        )[:2]
-        sky_corners = data.coords.pixel_to_world(x_corners * u.pix, y_corners * u.pix)
+        sky_corners = data.coords.pixel_to_world(x_corners, y_corners)
         height_sky = abs(sky_corners[0].separation(sky_corners[2]))
         width_sky = abs(sky_corners[0].separation(sky_corners[1]))
         fov_sky = u.Quantity([height_sky, width_sky]).mean()
         return fov_sky
 
     def _get_center_skycoord(self, data=None):
-        if data is None:
-            data = self.state.reference_data
         # get SkyCoord for the center of ``data`` in this viewer:
-        width = self.state.x_max - self.state.x_min
-        height = self.state.y_max - self.state.y_min
-        x_cen = self.state.x_min + (width * 0.5)
-        y_cen = self.state.y_min + (height * 0.5)
-        x_cen, y_cen = self._get_real_xy(
-            data, x_cen, y_cen
-        )[:2]
-        sky_cen = data.coords.pixel_to_world(
-            x_cen * u.pix, y_cen * u.pix
-        )
-        return sky_cen
+        x_cen = (self.state.x_min + self.state.x_max) * 0.5
+        y_cen = (self.state.y_min + self.state.y_max) * 0.5
+
+        if (self.jdaviz_app._link_type == "wcs" or data is None
+                or data.label == self.state.reference_data.label):
+            return self.state.reference_data.coords.pixel_to_world(x_cen, y_cen)
+
+        if data.coords is not None:
+            return data.coords.pixel_to_world(x_cen, y_cen)

jdaviz/configs/imviz/tests/test_astrowidgets_api.py

@@ -111,8 +111,7 @@ def test_center_on_pix(self):
         self.viewer.center_on((0, 0))
         assert_allclose((self.viewer.state.x_min, self.viewer.state.x_max,
                          self.viewer.state.y_min, self.viewer.state.y_max),
-                        [lim if i > 1 else lim + 1
-                         for i, lim in enumerate(expected_position)], rtol=rtol)
+                        [-5.75, 5.25, -5.75, 5.25], rtol=rtol)
 
         # Centering by sky on second data.
         self.viewer.blink_once()

jdaviz/configs/imviz/tests/test_delete_data.py

@@ -26,10 +26,10 @@ def test_delete_with_subset_wcs(self):
         self.imviz.link_data(link_type='wcs', wcs_fallback_scheme=None, error_on_fail=True)
 
         # Add a subset
-        reg = CirclePixelRegion(PixCoord(2, 2), 3)
+        reg = CirclePixelRegion(PixCoord(2, 2), 3).to_sky(self.wcs_1)
         self.imviz.load_regions(reg)
 
-        reg = RectanglePixelRegion(PixCoord(1, 1), 2, 2)
+        reg = RectanglePixelRegion(PixCoord(1, 1), 2, 2).to_sky(self.wcs_1)
         self.imviz.load_regions(reg)
 
         assert len(self.imviz.app.data_collection.subset_groups) == 2
@@ -47,13 +47,13 @@ def test_delete_with_subset_wcs(self):
         subset1 = self.imviz.app.data_collection.subset_groups[0]
         subset2 = self.imviz.app.data_collection.subset_groups[1]
         assert subset1.subset_state.xatt.parent.label == "has_wcs_1[SCI,1]"
-        assert_allclose(subset1.subset_state.center(), (2.25, 2.25))
+        assert_allclose(subset1.subset_state.center(), (2, 2))
 
         assert subset2.subset_state.xatt.parent.label == "has_wcs_1[SCI,1]"
-        assert_allclose(subset2.subset_state.roi.xmin, 0.25)
-        assert_allclose(subset2.subset_state.roi.ymin, 0.25)
-        assert_allclose(subset2.subset_state.roi.xmax, 2.25)
-        assert_allclose(subset2.subset_state.roi.ymax, 2.25)
+        assert_allclose(subset2.subset_state.roi.xmin, 0, atol=1e-6)
+        assert_allclose(subset2.subset_state.roi.ymin, 0, atol=1e-6)
+        assert_allclose(subset2.subset_state.roi.xmax, 2)
+        assert_allclose(subset2.subset_state.roi.ymax, 2)
 
         # We have to remove the data from the viewer before deleting the data from the app.
         self.imviz.app.remove_data_from_viewer("imviz-0", "has_wcs_1[SCI,1]")
@@ -64,10 +64,10 @@ def test_delete_with_subset_wcs(self):
 
         # Check that the reparenting and coordinate recalculations happened
         assert subset1.subset_state.xatt.parent.label == "has_wcs_2[SCI,1]"
-        assert_allclose(subset1.subset_state.center(), (3.25, 2.25))
+        assert_allclose(subset1.subset_state.center(), (3, 2))
 
         assert subset2.subset_state.xatt.parent.label == "has_wcs_2[SCI,1]"
-        assert_allclose(subset2.subset_state.roi.xmin, 1.25, atol=1e-6)
-        assert_allclose(subset2.subset_state.roi.ymin, 0.25, atol=1e-6)
-        assert_allclose(subset2.subset_state.roi.xmax, 3.25, atol=1e-6)
-        assert_allclose(subset2.subset_state.roi.ymax, 2.25, atol=1e-6)
+        assert_allclose(subset2.subset_state.roi.xmin, 1)
+        assert_allclose(subset2.subset_state.roi.ymin, 0, atol=1e-6)
+        assert_allclose(subset2.subset_state.roi.xmax, 3)
+        assert_allclose(subset2.subset_state.roi.ymax, 2)