exclude WCS-only layer subsets from plot options (#2699)

* exclude WCS-only layer subsets from plot options
* add to image rotation changelog entry

CHANGES.rst

@@ -32,7 +32,7 @@ Imviz
 ^^^^^
 
 - There is now option for image rotation in Orientation (was Links Control) plugin.
-  This feature requires WCS linking. [#2179, #2673]
+  This feature requires WCS linking. [#2179, #2673, #2699]
 
 Mosviz
 ^^^^^^

jdaviz/app.py

@@ -51,7 +51,7 @@
                                     data_parser_registry)
 from jdaviz.core.tools import ICON_DIR
 from jdaviz.utils import (SnackbarQueue, alpha_index, data_has_valid_wcs, layer_is_table_data,
-                          MultiMaskSubsetState)
+                          MultiMaskSubsetState, _wcs_only_label)
 
 __all__ = ['Application', 'ALL_JDAVIZ_CONFIGS']
 
@@ -306,7 +306,6 @@ def __init__(self, configuration=None, *args, **kwargs):
         self.auto_link = kwargs.pop('auto_link', True)
 
         # Imviz linking
-        self._wcs_only_label = "_WCS_ONLY"
         self._link_type = 'pixels'
         if self.config == "imviz":
             self._wcs_use_affine = None
@@ -470,7 +469,7 @@ def _color_to_level(color):
     def _on_layers_changed(self, msg):
         if hasattr(msg, 'data'):
             layer_name = msg.data.label
-            is_wcs_only = msg.data.meta.get(self._wcs_only_label, False)
+            is_wcs_only = msg.data.meta.get(_wcs_only_label, False)
         elif hasattr(msg, 'subset'):
             layer_name = msg.subset.label
             is_wcs_only = False
@@ -1947,7 +1946,7 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
 
         # set visibility state of all applicable layers
         for layer in viewer.layers:
-            layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(self._wcs_only_label, False)
+            layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(_wcs_only_label, False)
             if layer.layer.data.label == data_label:
                 if layer_is_wcs_only:
                     layer.visible = False
@@ -1976,7 +1975,7 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
 
         # remove WCS-only data from selected items, add to wcs_only_layers:
         for layer in viewer.layers:
-            layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(self._wcs_only_label, False)
+            layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(_wcs_only_label, False)
             if layer.layer.data.label == data_label and layer_is_wcs_only:
                 layer.visible = False
                 if data_label not in viewer.state.wcs_only_layers:
@@ -2100,7 +2099,7 @@ def _on_data_deleted(self, msg):
     def _create_data_item(self, data):
         ndims = len(data.shape)
         wcsaxes = data.meta.get('WCSAXES', None)
-        wcs_only = data.meta.get(self._wcs_only_label, False)
+        wcs_only = data.meta.get(_wcs_only_label, False)
         if wcsaxes is None:
             # then we'll need to determine type another way, we want to avoid
             # this when we can though since its not as cheap

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

@@ -28,6 +28,8 @@
 from jdaviz.core.user_api import PluginUserApi
 from jdaviz.core.tools import ICON_DIR
 from jdaviz.core.custom_traitlets import IntHandleEmpty
+from jdaviz.utils import is_not_wcs_only
+
 
 from scipy.interpolate import PchipInterpolator
 
@@ -388,10 +390,6 @@ def __init__(self, *args, **kwargs):
         self.layer = LayerSelect(self, 'layer_items', 'layer_selected',
                                  'viewer_selected', 'layer_multiselect')
 
-        def is_not_wcs_only(layer):
-            # exclude WCS-only layers from the layer choices:
-            return not getattr(layer.layer, 'meta', {}).get(self.app._wcs_only_label, False)
-
         self.layer.filters += [is_not_wcs_only]
 
         self.swatches_palette = [
@@ -427,7 +425,7 @@ def not_image_or_spatial_subset(state):
             return not is_image(state) and not is_spatial_subset(state)
 
         def is_spatial_subset(state):
-            return isinstance(state, ImageSubsetLayerState)
+            return isinstance(state, ImageSubsetLayerState) and is_not_wcs_only(state.layer)
 
         def is_not_subset(state):
             return not is_spatial_subset(state)

jdaviz/configs/default/plugins/viewers.py

@@ -11,7 +11,7 @@
 from jdaviz.core.astrowidgets_api import AstrowidgetsImageViewerMixin
 from jdaviz.core.registries import viewer_registry
 from jdaviz.core.user_api import ViewerUserApi
-from jdaviz.utils import ColorCycler, get_subset_type
+from jdaviz.utils import ColorCycler, get_subset_type, _wcs_only_label
 
 __all__ = ['JdavizViewerMixin']
 
@@ -215,7 +215,7 @@ def _get_layer_info(layer):
         for layer in self.state.layers[::-1]:
             layer_is_wcs_only = (
                     hasattr(layer.layer, 'meta') and
-                    layer.layer.meta.get(self.jdaviz_app._wcs_only_label, False)
+                    layer.layer.meta.get(_wcs_only_label, False)
             )
             if layer.visible and not layer_is_wcs_only:
                 prefix_icon, suffix = _get_layer_info(layer)

jdaviz/configs/imviz/helper.py

@@ -15,7 +15,7 @@
 from jdaviz.configs.imviz.wcs_utils import (
     _get_rotated_nddata_from_label, get_compass_info
 )
-from jdaviz.utils import data_has_valid_wcs
+from jdaviz.utils import data_has_valid_wcs, _wcs_only_label
 
 __all__ = ['Imviz']
 
@@ -191,7 +191,7 @@ def load_data(self, data, data_label=None, show_in_viewer=True, **kwargs):
             if label not in prev_data_labels:
                 applied_labels.append(label)
                 applied_visible.append(True)
-                layer_is_wcs_only.append(data.meta.get(self.app._wcs_only_label, False))
+                layer_is_wcs_only.append(data.meta.get(_wcs_only_label, False))
                 layer_has_wcs.append(data_has_valid_wcs(data))
 
         if show_in_viewer is True:
@@ -404,14 +404,12 @@ def layer_is_2d(layer):
     return isinstance(layer, BaseData) and layer.ndim == 2
 
 
-# NOTE: Sync with app._wcs_only_label as needed.
 def layer_is_image_data(layer):
-    return layer_is_2d(layer) and not layer.meta.get("_WCS_ONLY", False)
+    return layer_is_2d(layer) and not layer.meta.get(_wcs_only_label, False)
 
 
-# NOTE: Sync with app._wcs_only_label as needed.
 def layer_is_wcs_only(layer):
-    return layer_is_2d(layer) and layer.meta.get("_WCS_ONLY", False)
+    return layer_is_2d(layer) and layer.meta.get(_wcs_only_label, False)
 
 
 def get_wcs_only_layer_labels(app):
@@ -549,7 +547,7 @@ def link_image_data(app, link_type='pixels', wcs_fallback_scheme=None, wcs_use_a
     data_already_linked = []
     if link_type == app._link_type and wcs_use_affine == app._wcs_use_affine:
         for link in app.data_collection.external_links:
-            if link.data1.label != app._wcs_only_label:
+            if link.data1.label != _wcs_only_label:
                 data_already_linked.append(link.data2)
     else:
         for viewer in app._viewer_store.values():

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

@@ -22,6 +22,7 @@
     PluginTemplateMixin, SelectPluginComponent, LayerSelect, ViewerSelectMixin, AutoTextField
 )
 from jdaviz.core.user_api import PluginUserApi
+from jdaviz.utils import _wcs_only_label
 
 __all__ = ['Orientation']
 
@@ -230,7 +231,7 @@ def _update_link(self, msg={}):
         data_in_viewer = self.app.get_viewer(viewer_selected.reference).data()
 
         for data in self.app.data_collection:
-            is_wcs_only = data.meta.get(self.app._wcs_only_label, False)
+            is_wcs_only = data.meta.get(_wcs_only_label, False)
             has_wcs = hasattr(data.coords, 'pixel_to_world')
             if not is_wcs_only:
                 if data in data_in_viewer and wcs_linked and not has_wcs:
@@ -395,11 +396,11 @@ def _send_wcs_layers_to_all_viewers(self, *args, **kwargs):
 
     def _on_data_add_to_viewer(self, msg):
         all_wcs_only_layers = all(
-            layer.layer.meta.get(self.app._wcs_only_label)
+            layer.layer.meta.get(_wcs_only_label)
             for layer in self.viewer.selected_obj.layers
             if hasattr(layer.layer, "meta")
         )
-        if all_wcs_only_layers and msg.data.meta.get(self.app._wcs_only_label, False):
+        if all_wcs_only_layers and msg.data.meta.get(_wcs_only_label, False):
             # on adding first data layer, reset the limits:
             self.viewer.selected_obj.state.reset_limits()
 

jdaviz/configs/imviz/plugins/parsers.py

@@ -14,7 +14,7 @@
 
 from jdaviz.core.registries import data_parser_registry
 from jdaviz.core.events import SnackbarMessage
-from jdaviz.utils import standardize_metadata, PRIHDR_KEY
+from jdaviz.utils import standardize_metadata, PRIHDR_KEY, _wcs_only_label
 
 try:
     from roman_datamodels import datamodels as rdd
@@ -146,7 +146,7 @@ def get_image_data_iterator(app, file_obj, data_label, ext=None):
         data_iter = _hdu_to_glue_data(file_obj, data_label)
 
     elif isinstance(file_obj, NDData):
-        if file_obj.meta.get(app._wcs_only_label, False):
+        if file_obj.meta.get(_wcs_only_label, False):
             data_iter = _wcsonly_to_glue_data(file_obj, data_label)
         else:
             data_iter = _nddata_to_glue_data(file_obj, data_label)
@@ -184,7 +184,7 @@ def _parse_image(app, file_obj, data_label, ext=None):
             # for outside_*_bounding_box should also be updated.
             data.coords._orig_bounding_box = data.coords.bounding_box
             data.coords.bounding_box = None
-        if not data.meta.get(app._wcs_only_label, False):
+        if not data.meta.get(_wcs_only_label, False):
             data_label = app.return_data_label(data_label, alt_name="image_data")
         app.add_data(data, data_label)
 

jdaviz/configs/imviz/wcs_utils.py

@@ -21,6 +21,7 @@
 from gwcs.wcs import WCS as GWCS
 
 from matplotlib.patches import Polygon
+from jdaviz.utils import _wcs_only_label
 
 __all__ = ['get_compass_info', 'draw_compass_mpl']
 
@@ -530,7 +531,7 @@ def _get_rotated_nddata_from_label(
         data.coords,
         rotation_angle,
         refdata_shape,
-        wcs_only_key=app._wcs_only_label,
+        wcs_only_key=_wcs_only_label,
         data=data,
         cdelt_signs=cdelt_signs
     )

jdaviz/core/template_mixin.py

@@ -51,7 +51,7 @@
 from jdaviz.core.region_translators import regions2roi, _get_region_from_spatial_subset
 from jdaviz.core.user_api import UserApiWrapper, PluginUserApi
 from jdaviz.style_registry import PopoutStyleWrapper
-from jdaviz.utils import get_subset_type
+from jdaviz.utils import get_subset_type, is_wcs_only, is_not_wcs_only, _wcs_only_label
 
 
 __all__ = ['show_widget', 'TemplateMixin', 'PluginTemplateMixin',
@@ -1343,7 +1343,7 @@ def _layer_to_dict(self, layer_label):
         visibilities = []
         for viewer in self.viewer_objs:
             for layer in viewer.layers:
-                if layer.layer.label == layer_label:
+                if layer.layer.label == layer_label and is_not_wcs_only(layer.layer):
                     if is_subset is None:
                         is_subset = ((hasattr(layer, 'state') and hasattr(layer.state, 'subset_state')) or  # noqa
                                      (hasattr(layer, 'layer') and hasattr(layer.layer, 'subset_state')))  # noqa
@@ -1384,6 +1384,8 @@ def _on_viewer_selected_changed(self, msg=None):
                 # we call _update_layer_items in the PlotOptionsSyncState for color_mode
                 # old_viewer.state.remove_callback('color_mode', self._update_layer_items)
                 for layer in old_viewer.state.layers:
+                    if is_wcs_only(layer.layer):
+                        continue
                     layer.remove_callback('color', self._update_layer_items)
                     if hasattr(layer, 'cmap'):
                         layer.remove_callback('cmap', self._update_layer_items)
@@ -1400,6 +1402,8 @@ def _on_viewer_selected_changed(self, msg=None):
                 # we call _update_layer_items in the PlotOptionsSyncState for color_mode
                 # new_viewer.state.add_callback('color_mode', self._update_layer_items)
                 for layer in new_viewer.state.layers:
+                    if is_wcs_only(layer.layer):
+                        continue
                     layer.add_callback('color', self._update_layer_items)
                     if hasattr(layer, 'cmap'):
                         layer.add_callback('cmap', self._update_layer_items)
@@ -1413,11 +1417,9 @@ def _on_subset_created(self, msg=None):
         viewer = self.viewer if isinstance(self.viewer, list) else [self.viewer]
         for current_viewer in viewer:
             for layer in self._get_viewer(current_viewer).state.layers:
-                if layer.layer.label == new_subset_label:
-                    # Is it ok if only one subset layer has this callback?
+                if layer.layer.label == new_subset_label and is_not_wcs_only(layer.layer):
                     layer.add_callback('color', self._update_layer_items)
                     layer.add_callback('visible', self._update_layer_items)
-                    break
                     # TODO: Add ability to add new item to self.items instead of recompiling
         self._update_layer_items({'source': 'subset_added'})
 
@@ -1429,6 +1431,8 @@ def _on_data_added(self, msg=None):
         for current_viewer in viewer:
             for layer in self._get_viewer(current_viewer).state.layers:
                 if layer.layer.label == new_data_label and not hasattr(layer.layer, 'subset_state'):
+                    if is_wcs_only(layer.layer):
+                        continue
                     # Add a callback to the layer's color attribute to call
                     # _on_layers_changed whenever the color changes
                     # TODO: find out if this conflicts with another color change event
@@ -1454,7 +1458,7 @@ def _update_layer_items(self, msg={}):
         all_layers = [
             layer for viewer in self.viewer_objs
             for layer in getattr(viewer, 'layers', [])
-            if self._is_valid_item(layer)
+            if self._is_valid_item(layer.layer)
         ]
 
         # remove duplicates - we'll loop back through all selected viewers to get a list of colors
@@ -1491,8 +1495,6 @@ def update_wcs_only_filter(self, wcs_only):
             `True` will filter only the WCS-only layers, `False` will
             give the non-WCS-only layers.
         """
-        def is_wcs_only(layer):
-            return getattr(layer.layer, 'meta', {}).get(self.app._wcs_only_label, False)
 
         filter_names = [getattr(filt, '__name__', '') for filt in self.filters]
 
@@ -1520,7 +1522,7 @@ def selected_obj(self):
         viewers = [self._get_viewer(viewer_name) for viewer_name in viewer_names]
 
         layers = [[layer for layer in viewer.layers
-                   if layer.layer.label in selected]
+                   if layer.layer.label in selected and self._is_valid_item(layer.layer)]
                   for viewer in viewers]
 
         if not self.is_multiselect and len(layers) == 1:
@@ -2961,7 +2963,7 @@ def is_cube(data):
             return len(data.shape) == 3
 
         def is_not_wcs_only(data):
-            return not data.meta.get(self.app._wcs_only_label, False)
+            return not data.meta.get(_wcs_only_label, False)
 
         return super()._is_valid_item(data, locals())
 
@@ -3774,7 +3776,7 @@ def _on_glue_value_changed(self, value):
             value = value.name
         elif self._glue_name in GLUE_STATES_WITH_HELPERS:
             value = str(value)
-        elif isinstance(self.value, (int, float)) and self._glue_name != 'percentile':
+        elif self._glue_name != 'percentile' and isinstance(self.value, (int, float)):
             # glue might pass us ints for float or vice versa, but our traitlets care
             # so let's cast to the type expected by the traitlet to avoid having to
             # use Any traitlets for all of these.  We skip percentile as that needs

jdaviz/utils.py

@@ -229,6 +229,26 @@ def layer_is_table_data(layer):
     return isinstance(layer, BaseData) and layer.ndim == 1
 
 
+_wcs_only_label = "_WCS_ONLY"
+
+
+def is_wcs_only(layer):
+    # exclude WCS-only layers from the layer choices:
+    if hasattr(layer, 'layer'):
+        state = layer.layer
+    elif hasattr(layer, 'data'):
+        state = layer.data
+    elif hasattr(layer, 'meta'):
+        state = layer
+    else:
+        raise NotImplementedError
+    return getattr(state, 'meta', {}).get(_wcs_only_label, False)
+
+
+def is_not_wcs_only(layer):
+    return not is_wcs_only(layer)
+
+
 def standardize_metadata(metadata):
     """Standardize given metadata so it can be viewed in
     Metadata Viewer plugin. The input can be plain