wip:quick and dirty viewer tooltip

brainrender_napari/brainrender_widget.py

@@ -20,6 +20,7 @@
 from brainrender_napari.napari_atlas_representation import (
     NapariAtlasRepresentation,
 )
+from brainrender_napari.utils.from_viewer import structure_from_viewer
 from brainrender_napari.widgets.atlas_table_view import AtlasTableView
 from brainrender_napari.widgets.structure_view import StructureView
 
@@ -97,6 +98,31 @@ def __init__(self, napari_viewer: Viewer):
             self._on_add_structure_requested
         )
 
+        @self._viewer.mouse_move_callbacks.append
+        def display_region_info(v, event):
+            """
+            Show brain region info on mouse over in status bar on the right
+            """
+            assert self._viewer == v
+            self.annotations_layer = self._viewer.layers[
+                -1
+            ]  # temporary hacks!!
+            self.atlas = BrainGlobeAtlas("allen_mouse_100um")
+            if v.dims.ndisplay == 2:
+                if len(v.layers) and self.annotations_layer and self.atlas:
+                    _, _, _, region_info = structure_from_viewer(
+                        self._viewer.cursor.position,
+                        self.annotations_layer,
+                        self.atlas,
+                    )
+                    self._viewer.tooltip.visible = True
+                    self._viewer.tooltip.text = region_info
+            else:
+                self._viewer.help = ""
+
+            print("annotations", self.annotations_layer)
+            print("help", self._viewer.help)
+
     def _on_download_atlas_confirmed(self, atlas_name):
         """Ensure structure view is displayed if new atlas downloaded."""
         show_structure_names = self.show_structure_names.isChecked()

brainrender_napari/utils/from_viewer.py

@@ -0,0 +1,63 @@
+def structure_from_viewer(coordinates, atlas_layer, atlas):
+    """
+    Get brain region info from mouse position in napari viewer.
+
+    Return brainglobe (BG) structure number, name, hemisphere, and a
+    "pretty" string that can be displayed for example in the status bar.
+
+    Parameter
+    ---------
+    coordinates   : tuple, nx3 coordinate of cursor position, from
+                    Viewer.cursor.position
+    atlas_layer   : Napari viewer layer
+                    Layer, which contains the annotation / region
+                    information for every structure in the (registered)
+                    atlas
+    atlas         : Brainglobe atlas (bg_atlasapi.bg_atlas.BrainGlobeAtlas)
+
+    Returns
+    -------
+
+    region_info   : str
+                    A string containing info about structure
+                    and hemisphere
+                    Returns empty string if not found
+    """
+
+    # Using a regex, extract list of coordinates from status string
+    assert hasattr(atlas_layer, "data"), "Atlas layer appears to be empty"
+    assert atlas_layer.data.ndim == 3, (
+        "Atlas layer data does not have the right dim "
+        f'("{atlas_layer.data.ndim}")'
+    )
+
+    coord_list = tuple(
+        [int(x / r) for x, r in zip(coordinates, atlas.resolution)]
+    )
+
+    # Extract structure number
+    try:
+        structure_no = atlas_layer.data[coord_list]
+    except IndexError:
+        return None, None, None, ""
+
+    if structure_no in [0]:  # 0 is "Null" region
+        return None, None, None, ""
+
+    # Extract structure information
+    try:
+        structure = atlas.structures[structure_no]["name"]
+    except KeyError:
+        return None, None, None, ""
+
+    # ... and make string pretty
+    region_info = []
+    for struct in structure.split(","):
+        region_info.append(struct.strip().capitalize())
+    hemisphere = atlas.hemisphere_from_coords(
+        coord_list, as_string=True
+    ).capitalize()
+    region_info.append(hemisphere)
+    region_info = " | ".join(region_info)
+
+    return structure_no, structure, hemisphere, region_info