Fix matched pan zoom

jdaviz/app.py

@@ -1979,7 +1979,8 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
             layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(self._wcs_only_label, False)
             if layer.layer.data.label == data_label and layer_is_wcs_only:
                 layer.visible = False
-                viewer.state.wcs_only_layers.append(data_label)
+                if data_label not in viewer.state.wcs_only_layers:
+                    viewer.state.wcs_only_layers.append(data_label)
                 selected_items.pop(data_id)
 
         # Sets the plot axes labels to be the units of the most recently
@@ -2254,7 +2255,7 @@ def _create_viewer_item(self, viewer, vid=None, name=None, reference=None):
             'config': self.config,  # give viewer access to app config/layout
             'data_open': False,
             'collapse': True,
-            'reference': reference,
+            'reference': reference or name or vid,
             'linked_by_wcs': linked_by_wcs,
         }
 
@@ -2319,6 +2320,12 @@ def _on_new_viewer(self, msg, vid=None, name=None, add_layers_to_viewer=False):
         ref_data = self._jdaviz_helper.default_viewer._obj.state.reference_data
         new_viewer_item['reference_data_label'] = getattr(ref_data, 'label', None)
 
+        if (
+                getattr(ref_data, 'meta', {}).get('_WCS_ONLY', False) and
+                hasattr(viewer, 'reference') and linked_by_wcs
+        ):
+            viewer.state.reference_data = ref_data
+
         new_stack_item = self._create_stack_item(
             container='gl-stack',
             viewers=[new_viewer_item])
@@ -2333,14 +2340,13 @@ def _on_new_viewer(self, msg, vid=None, name=None, add_layers_to_viewer=False):
 
         self.session.application.viewers.append(viewer)
 
-        # Send out a toast message
-        self.hub.broadcast(ViewerAddedMessage(vid, sender=self))
-
         if add_layers_to_viewer:
             for layer_label in add_layers_to_viewer:
-                self.add_data_to_viewer(viewer.reference, layer_label)
+                if hasattr(viewer, 'reference'):
+                    self.add_data_to_viewer(viewer.reference, layer_label)
 
-            viewer.state.reference_data = ref_data
+        # Send out a toast message
+        self.hub.broadcast(ViewerAddedMessage(vid, sender=self))
 
         return viewer
 

jdaviz/configs/default/plugins/plot_options/plot_options.py

@@ -357,11 +357,7 @@ def supports_line(state):
             return is_profile(state) or is_scatter(state)
 
         def is_image(state):
-            wcs_only = (
-                hasattr(state, 'wcs_only_layers') and
-                self.layer.selected in state.wcs_only_layers
-            )
-            return isinstance(state, BqplotImageLayerState) and not wcs_only
+            return isinstance(state, BqplotImageLayerState)
 
         def not_image(state):
             return not is_image(state)

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

@@ -14,7 +14,7 @@
 from jdaviz.core.events import (
     LinkUpdatedMessage, ExitBatchLoadMessage, ChangeRefDataMessage,
     AstrowidgetMarkersChangedMessage, MarkersPluginUpdate,
-    SnackbarMessage, AddDataToViewerMessage, ViewerAddedMessage
+    SnackbarMessage, ViewerAddedMessage, AddDataMessage
 )
 from jdaviz.core.custom_traitlets import FloatHandleEmpty
 from jdaviz.core.registries import tray_registry
@@ -130,7 +130,7 @@ def __init__(self, *args, **kwargs):
         self.hub.subscribe(self, ViewerAddedMessage,
                            handler=self._on_viewer_added)
 
-        self.hub.subscribe(self, AddDataToViewerMessage,
+        self.hub.subscribe(self, AddDataMessage,
                            handler=self._on_data_add_to_viewer)
 
         self._update_layer_label_default()
@@ -224,7 +224,7 @@ def _update_link(self, msg={}):
         # load data into the viewer that are now compatible with the
         # new link type, remove data from the viewer that are now
         # incompatible:
-        wcs_linked = self.link_type.selected.lower() == 'wcs'
+        wcs_linked = self.link_type.selected == 'WCS'
         viewer_selected = self.app.get_viewer(self.viewer.selected)
 
         data_in_viewer = self.app.get_viewer(viewer_selected.reference).data()
@@ -240,6 +240,9 @@ def _update_link(self, msg={}):
                         f"Data '{data.label}' does not have a valid WCS - removing from viewer.",
                         sender=self, color="warning"))
 
+        if wcs_linked:
+            self._send_wcs_layers_to_all_viewers()
+
         self.linking_in_progress = False
         self._update_layer_label_default()
 
@@ -351,36 +354,54 @@ def add_orientation(self, rotation_angle=None, east_left=None, label=None,
         )
 
         # add orientation layer to all viewers:
-        self._add_data_to_all_viewers(label)
+        for viewer_ref in self.app._viewer_store:
+            self._add_data_to_viewer(label, viewer_ref)
 
         if set_on_create:
-            self.orientation._update_layer_items()
             self.orientation.selected = label
 
-    def _add_data_to_all_viewers(self, data_label):
-        for viewer_ref in self.app.get_viewer_reference_names():
-            layers = [
-                layer.label for layer in
-                self.app.get_viewer(viewer_ref).layers
-            ]
-            if data_label not in layers:
-                self.app.add_data_to_viewer(viewer_ref, data_label)
+    def _add_data_to_viewer(self, data_label, viewer_id):
+        viewer = self.app.get_viewer_by_id(viewer_id)
+
+        wcs_only_layers = viewer.state.wcs_only_layers
+        if data_label not in wcs_only_layers:
+            self.app.add_data_to_viewer(viewer_id, data_label)
 
     def _on_viewer_added(self, msg):
-        for data_label in self.orientation.choices:
-            self._add_data_to_all_viewers(data_label)
+        self._send_wcs_layers_to_all_viewers(viewers_to_update=[msg._viewer_id])
+
+    @observe('viewer_items')
+    def _send_wcs_layers_to_all_viewers(self, *args, **kwargs):
+        if not hasattr(self, 'viewer'):
+            return
+
+        wcs_only_layers = self.app._jdaviz_helper.default_viewer.state.wcs_only_layers
+
+        viewers_to_update = kwargs.get(
+            'viewers_to_update', self.app.get_viewer_reference_names()
+        )
 
-        if hasattr(self, 'orientation') and len(self.orientation.choices):
-            self.viewer.selected = msg._viewer_id
-            self.orientation.selected = self.orientation.choices[0]
+        for viewer_ref in viewers_to_update:
+            for wcs_layer in wcs_only_layers:
+                if wcs_layer not in self.app.get_viewer_by_id(viewer_ref).state.wcs_only_layers:
+                    self.app.add_data_to_viewer(viewer_ref, wcs_layer)
+
+            self.viewer.selected = viewer_ref
+
+            self.orientation.set_wcs_only_filter(wcs_only=self.link_type_selected == 'WCS')
+            # select the default orientation if no data have yet been
+            # added to a newly created viewer:
+            if (
+                    base_wcs_layer_label in self.orientation.choices and
+                    not len(self.viewer.selected_obj.layers)
+            ):
+                self.orientation.selected = base_wcs_layer_label
 
     def _on_data_add_to_viewer(self, msg):
-        if (
-            msg._viewer_reference != 'imviz-0' and
-            self.app.get_viewer_by_id(msg._viewer_reference).state.reference_data is None
-        ):
-            self.viewer.selected = msg._viewer_reference
-            self.orientation.selected = base_wcs_layer_label
+        if msg._viewer_id != 'imviz-0':
+            if len(self.viewer.selected_obj.layers) == 1:
+                # on adding first data layer, reset the limits:
+                self.viewer.selected_obj.state.reset_limits()
 
     def vue_add_orientation(self, *args, **kwargs):
         self.add_orientation(set_on_create=True)
@@ -392,8 +413,8 @@ def _change_reference_data(self, *args, **kwargs):
                 self.orientation.selected, viewer_id=self.viewer.selected
             )
 
-    def _on_refdata_change(self, msg={}):
-        self.orientation.only_wcs_layers = msg.data.meta.get('_WCS_ONLY', False)
+    def _on_refdata_change(self, msg):
+        self.orientation.set_wcs_only_filter(wcs_only=msg.data.meta.get('_WCS_ONLY', False))
         if hasattr(self, 'viewer'):
             ref_data = self.ref_data
             viewer = self.app.get_viewer(self.viewer.selected)
@@ -406,10 +427,15 @@ def _on_refdata_change(self, msg={}):
             elif not len(viewer.data()):
                 self.link_type_selected = link_type_msg_to_trait['pixels']
 
+            if msg._data.label not in self.orientation.choices:
+                return
+
+            self.orientation.selected = msg._data.label
+
             # we never want to highlight subsets of pixels within WCS-only layers,
             # so if this layer is an ImageSubsetLayerState on a WCS-only layer,
             # ensure that it is never visible:
-            for layer in viewer.state.layers:
+            for layer in self.viewer.selected_obj.state.layers:
                 if (
                     hasattr(layer.layer, 'label') and
                     layer.layer.label.startswith("Subset") and
@@ -426,16 +452,15 @@ def ref_data(self):
     @property
     def _refdata_change_available(self):
         viewer = self.app.get_viewer(self.viewer.selected)
-        ref_data = self.ref_data
         selected_layer = [lyr.layer for lyr in viewer.layers
                           if lyr.layer.label == self.orientation.selected]
         if len(selected_layer):
             is_subset = isinstance(selected_layer[0], (Subset, GroupedSubset))
         else:
             is_subset = False
         return (
-            ref_data is not None and
-            len(self.orientation.selected) and len(self.viewer.selected) and
+            len(self.orientation.selected) and
+            len(self.viewer.selected) and
             not is_subset
         )
 

jdaviz/configs/imviz/plugins/tools.py

@@ -51,7 +51,10 @@ def on_click(self, data):
         if x is None or y is None:  # Out of bounds
             return
         x, y, _, _ = self.viewer._get_real_xy(image, x, y)
-        self.viewer.center_on((x, y))
+        if image.coords is not None:
+            self.viewer.center_on(image.coords.pixel_to_world(x, y))
+        else:
+            self.viewer.center_on((x, y))
 
 
 @viewer_tool

jdaviz/configs/imviz/tests/test_tools.py

@@ -53,15 +53,15 @@ def test_panzoom_tools(self):
         t_normpan.activate()
         t_normpan.on_click({'event': 'click', 'domain': {'x': 1, 'y': 1}})
         # make sure only first viewer re-centered since this mode is not linked mode
-        assert_allclose((v.state.x_min, v.state.x_max, v.state.y_min, v.state.y_max), (-2.5, 4.5, -2.5, 4.5))  # noqa
+        assert_allclose((v.state.x_min, v.state.x_max, v.state.y_min, v.state.y_max), (-1.5, 5.5, -2.5, 4.5))  # noqa
         assert_allclose((v2.state.x_min, v2.state.x_max, v2.state.y_min, v2.state.y_max), (-3.5, 3.5, -3.5, 3.5))  # noqa
         t_normpan.deactivate()
 
         t_linkedpan.activate()
         t_linkedpan.on_click({'event': 'click', 'domain': {'x': 2, 'y': 2}})
         # make sure both viewers moved to the new center
-        assert_allclose((v.state.x_min, v.state.x_max, v.state.y_min, v.state.y_max), (-1.5, 5.5, -1.5, 5.5))  # noqa
-        assert_allclose((v2.state.x_min, v2.state.x_max, v2.state.y_min, v2.state.y_max), (-1.5, 5.5, -1.5, 5.5))  # noqa
+        assert_allclose((v.state.x_min, v.state.x_max, v.state.y_min, v.state.y_max), (-0.5, 6.5, -1.5, 5.5))  # noqa
+        assert_allclose((v2.state.x_min, v2.state.x_max, v2.state.y_min, v2.state.y_max), (-0.5, 6.5, -1.5, 5.5))  # noqa
         t_linkedpan.deactivate()
 
 

jdaviz/configs/imviz/wcs_utils.py

@@ -438,6 +438,16 @@ def _prepare_rotated_nddata(real_image_shape, wcs, rotation_angle, refdata_shape
         image_shape=real_image_shape
     )
 
+    # # create a fake NDData (we use arange so data boundaries show up in Imviz
+    # # if it ever is accidentally exposed) with the rotated GWCS:
+    # placeholder_data = np.nan * np.ones(refdata_shape)
+    #
+    # ndd = NDData(
+    #     data=placeholder_data,
+    #     wcs=new_rotated_gwcs,
+    #     meta={wcs_only_key: True, '_pixel_scales': pixel_scales}
+    # )
+
     # create a fake NDData (we use arange so data boundaries show up in Imviz
     # if it ever is accidentally exposed) with the rotated GWCS:
     sequential_data = np.arange(

jdaviz/core/astrowidgets_api.py

@@ -9,7 +9,7 @@
 from glue.config import colormaps
 from glue.core import Data
 
-from jdaviz.configs.imviz.helper import get_top_layer_index
+from jdaviz.configs.imviz.helper import get_top_layer_index, get_reference_image_data
 from jdaviz.core.events import SnackbarMessage, AstrowidgetMarkersChangedMessage
 from jdaviz.core.helpers import data_has_valid_wcs
 
@@ -178,8 +178,11 @@ def zoom_level(self):
             raise ValueError('Viewer is still loading, try again later')
 
         if hasattr(self, '_get_real_xy'):
-            i_top = get_top_layer_index(self)
-            image = self.layers[i_top].layer
+            if self.state.reference_data is not None:
+                image, i_ref = get_reference_image_data(self.jdaviz_app, self.reference)
+            else:
+                i_top = get_top_layer_index(self)
+                image = self.layers[i_top].layer
             real_min = self._get_real_xy(image, self.state.x_min, self.state.y_min)
             real_max = self._get_real_xy(image, self.state.x_max, self.state.y_max)
         else:
@@ -210,8 +213,11 @@ def zoom_level(self, val):
 
         new_dx = self.shape[1] * 0.5 / val
         if hasattr(self, '_get_real_xy'):
-            i_top = get_top_layer_index(self)
-            image = self.layers[i_top].layer
+            if self.state.reference_data is not None:
+                image, i_ref = get_reference_image_data(self.jdaviz_app, self.reference)
+            else:
+                i_top = get_top_layer_index(self)
+                image = self.layers[i_top].layer
             real_min = self._get_real_xy(image, self.state.x_min, self.state.y_min)
             real_max = self._get_real_xy(image, self.state.x_max, self.state.y_max)
             cur_xcen = (real_min[0] + real_max[0]) * 0.5

jdaviz/core/template_mixin.py

@@ -1226,7 +1226,7 @@ class LayerSelect(SelectPluginComponent):
     * register with all the automatic logic in the plugin's init by passing the string names
       of the respective traitlets.
     * use component in plugin template (see below)
-    * refer to properties above based on the interally stored reference to the
+    * refer to properties above based on the internally stored reference to the
       instantiated object of this component
     * observe the traitlets created and defined in the plugin, as necessary
 
@@ -1265,7 +1265,6 @@ def __init__(self, plugin, items, selected, viewer,
             ``default`` text is provided but not in ``manual_options`` it will still be included as
             the first item in the list.
         """
-
         super().__init__(plugin,
                          items=items,
                          selected=selected,
@@ -1275,8 +1274,6 @@ def __init__(self, plugin, items, selected, viewer,
                          manual_options=manual_options,
                          default_mode=default_mode)
 
-        self.only_wcs_layers = only_wcs_layers
-
         self.hub.subscribe(self, AddDataMessage,
                            handler=self._on_data_added)
         self.hub.subscribe(self, RemoveDataMessage,
@@ -1295,6 +1292,7 @@ def __init__(self, plugin, items, selected, viewer,
         self.add_observe(viewer, self._on_viewer_selected_changed)
         self.add_observe(selected, self._update_layer_items)
         self._update_layer_items()
+        self.set_wcs_only_filter(only_wcs_layers)
 
     def _get_viewer(self, viewer):
         # newer will likely be the viewer name in most cases, but viewer id in the case
@@ -1424,6 +1422,7 @@ def _update_layer_items(self, msg={}):
         manual_items = [{'label': label} for label in self.manual_options]
         # use getattr so the super() call above doesn't try to access the attr before
         # it is initialized:
+
         if not getattr(self, 'only_wcs_layers', False):
             all_layers = [
                 layer for viewer in self.viewer_objs
@@ -1448,7 +1447,7 @@ def _update_layer_items(self, msg={}):
         layer_labels = [
             layer.layer.label for layer in all_layers
             if self.app.state.layer_icons.get(layer.layer.label) or
-            getattr(self, 'only_wcs_layers', False)
+            self.only_wcs_layers
         ]
         unique_layer_labels = list(set(layer_labels))
         layer_items = [self._layer_to_dict(layer_label) for layer_label in unique_layer_labels]
@@ -1463,6 +1462,22 @@ def _sort_by_icon(items_dict):
 
         self._apply_default_selection()
 
+    def set_wcs_only_filter(self, wcs_only):
+        def is_wcs_only(data):
+            return data.meta.get(self.app._wcs_only_label, False)
+
+        filter_names = [getattr(filt, '__name__', '') for filt in self.filters]
+
+        if not wcs_only and 'is_wcs_only' in filter_names:
+            self.filters.remove(*[filt for filt in self.filters
+                                  if getattr(filt, '__name__', '') == 'is_wcs_only'])
+        elif wcs_only and 'is_wcs_only' not in filter_names:
+            self.add_filter(is_wcs_only)
+
+    @property
+    def only_wcs_layers(self):
+        return 'is_wcs_only' in [getattr(filt, '__name__', '') for filt in self.filters]
+
     @cached_property
     def selected_obj(self):
         viewer_names = self.viewer