Test spatialelement table join (#208)

* fixed all the non-cytassist images * refactor get_init_table_list * fix permutation * use join * use join for view * change hardcoded sample threshold * bunch of updates * adjust test * change into left join * change into left join * random hex colors * get actual index * change indices and adata * match rows left * fix joins * rename to vars * fix color by * fix radii * pass cs * fix _calc_default_radii() * fix tests * improve speed test * removed comments * added code to show circles as ellipses * correct point layer size after scaling * fix labels color by * fix mibitof example * last bug fixes * initial step points columns * add dask import back * fix points columns --------- Co-authored-by: wmv_hpomen <[email protected]> Co-authored-by: Wouter-Michiel Vierdag <[email protected]>
scverse · Mar 19, 2024 · 8f9ac6a · 8f9ac6a
1 parent cb1f6c4
commit 8f9ac6a
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Showing 15 changed files with 514 additions and 196 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -135,7 +135,7 @@
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.insertAction"),
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.scroll"),
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.setTabOrder"),
-    # ("py:class", "napari_spatialdata._model.ImageModel"),
+    # ("py:class", "napari_spatialdata._model.DataModel"),
     # ("py:obj", "napari_spatialdata.QtAdataScatterWidget.scroll"),
     # ("py:obj", "napari_spatialdata.QtAdataScatterWidget.insertAction"),
     # If building the documentation fails because of a missing link that is outside your control,

diff --git a/src/napari_spatialdata/_constants/config.py b/src/napari_spatialdata/_constants/config.py
@@ -0,0 +1,2 @@
+POLYGON_THRESHOLD = 100
+POINT_THRESHOLD = 100000
diff --git a/src/napari_spatialdata/_model.py b/src/napari_spatialdata/_model.py
@@ -10,15 +10,16 @@
 from napari_spatialdata._constants._constants import Symbol
 from napari_spatialdata.utils._utils import NDArrayA, _ensure_dense_vector
 
-__all__ = ["ImageModel"]
+__all__ = ["DataModel"]
 
 
 @dataclass
-class ImageModel:
+class DataModel:
     """Model which holds the data for interactive visualization."""
 
     events: EmitterGroup = field(init=False, default=None, repr=True)
     _table_names: Sequence[Optional[str]] = field(default_factory=list, init=False)
+    _active_table_name: Optional[str] = field(default=None, init=False, repr=True)
     _layer: Layer = field(init=False, default=None, repr=True)
     _adata: Optional[AnnData] = field(init=False, default=None, repr=True)
     _adata_layer: Optional[str] = field(init=False, default=None, repr=False)
@@ -58,6 +59,8 @@ def get_items(self, attr: str) -> Tuple[str, ...]:
         """
         if attr in ("obs", "obsm"):
             return tuple(map(str, getattr(self.adata, attr).keys()))
+        if attr == "points" and self.layer is not None and (point_cols := self.layer.metadata.get("points_columns")):
+            return tuple(map(str, point_cols.columns))
         return tuple(map(str, getattr(self.adata, attr).index))
 
     @_ensure_dense_vector
@@ -78,7 +81,18 @@ def get_obs(
         """
         if name not in self.adata.obs.columns:
             raise KeyError(f"Key `{name}` not found in `adata.obs`.")
-        return self.adata.obs[name], self._format_key(name)
+        if name != self.instance_key:
+            adata_obs = self.adata.obs[[self.instance_key, name]]
+            adata_obs.set_index(self.instance_key, inplace=True)
+        else:
+            adata_obs = self.adata.obs
+        return adata_obs[name], self._format_key(name)
+
+    @_ensure_dense_vector
+    def get_points(self, name: Union[str, int], **_: Any) -> Tuple[Optional[NDArrayA], str]:
+        if self.layer is None:
+            raise ValueError("Layer must be present")
+        return self.layer.metadata["points_columns"][name], self._format_key(name)
 
     @_ensure_dense_vector
     def get_var(self, name: Union[str, int], **_: Any) -> Tuple[Optional[NDArrayA], str]:  # TODO(giovp): fix docstring
@@ -179,6 +193,14 @@ def layer(self, layer: Optional[Layer]) -> None:
         self._layer = layer
         self.events.layer()
 
+    @property
+    def active_table_name(self) -> Optional[str]:
+        return self._active_table_name
+
+    @active_table_name.setter
+    def active_table_name(self, active_table_name: Optional[str]) -> None:
+        self._active_table_name = active_table_name
+
     @property
     def adata(self) -> AnnData:  # noqa: D102
         return self._adata

diff --git a/src/napari_spatialdata/_scatterwidgets.py b/src/napari_spatialdata/_scatterwidgets.py
@@ -18,7 +18,7 @@
 from qtpy import QtWidgets
 from qtpy.QtCore import Signal
 
-from napari_spatialdata._model import ImageModel
+from napari_spatialdata._model import DataModel
 from napari_spatialdata._widgets import AListWidget, ComponentWidget
 from napari_spatialdata.utils._categoricals_utils import _add_categorical_legend
 from napari_spatialdata.utils._utils import NDArrayA, _get_categorical, _set_palette
@@ -57,7 +57,7 @@ class SelectFromCollection:
 
     def __init__(
         self,
-        model: ImageModel,
+        model: DataModel,
         ax: Axes,
         collection: Collection,
         data: list[NDArrayA],
@@ -113,7 +113,7 @@ class ScatterListWidget(AListWidget):
     _text = None
     _chosen = None
 
-    def __init__(self, model: ImageModel, attr: str, color: bool, **kwargs: Any):
+    def __init__(self, model: DataModel, attr: str, color: bool, **kwargs: Any):
         AListWidget.__init__(self, None, model, attr, **kwargs)
         self.attrChanged.connect(self._onChange)
         self._color = color
@@ -209,7 +209,7 @@ def data(self, data: NDArrayA | dict[str, Any]) -> None:
 
 
 class MatplotlibWidget(NapariMPLWidget):
-    def __init__(self, viewer: Viewer | None, model: ImageModel):
+    def __init__(self, viewer: Viewer | None, model: DataModel):
         self.is_widget = False
         if viewer is None:
             viewer = Viewer()
@@ -291,7 +291,7 @@ def clear(self) -> None:
 
 
 class AxisWidgets(QtWidgets.QWidget):
-    def __init__(self, model: ImageModel, name: str, color: bool = False):
+    def __init__(self, model: DataModel, name: str, color: bool = False):
         super().__init__()
 
         self._model = model
@@ -346,6 +346,6 @@ def clear(self) -> None:
         self.component_widget.clear()
 
     @property
-    def model(self) -> ImageModel:
+    def model(self) -> DataModel:
         """:mod:`napari` viewer."""
         return self._model
diff --git a/src/napari_spatialdata/_view.py b/src/napari_spatialdata/_view.py
@@ -5,7 +5,7 @@
 from loguru import logger
 from napari._qt.qt_resources import get_stylesheet
 from napari._qt.utils import QImg2array
-from napari.layers import Labels
+from napari.layers import Labels, Points
 from napari.viewer import Viewer
 from qtpy.QtCore import QSize, Qt
 from qtpy.QtWidgets import (
@@ -16,8 +16,9 @@
     QVBoxLayout,
     QWidget,
 )
+from spatialdata import join_sdata_spatialelement_table
 
-from napari_spatialdata._model import ImageModel
+from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import AxisWidgets, MatplotlibWidget
 from napari_spatialdata._widgets import (
     AListWidget,
@@ -28,14 +29,16 @@
 
 __all__ = ["QtAdataViewWidget", "QtAdataScatterWidget"]
 
+from napari_spatialdata.utils._utils import _get_init_table_list
+
 
 class QtAdataScatterWidget(QWidget):
     """Adata viewer widget."""
 
     def __init__(self, input: Viewer):
         super().__init__()
 
-        self._model = ImageModel()
+        self._model = DataModel()
 
         self.setLayout(QGridLayout())
 
@@ -109,14 +112,13 @@ def export(self) -> None:
     def _update_adata(self) -> None:
         if (table_name := self.table_name_widget.currentText()) == "":
             return
+        self.model.active_table_name = table_name
         layer = self._viewer.layers.selection.active
-        adata = None
 
         if sdata := layer.metadata.get("sdata"):
             element_name = layer.metadata.get("name")
-            table = sdata[table_name]
-            adata = table[table.obs[table.uns["spatialdata_attrs"]["region_key"]] == element_name]
-            layer.metadata["adata"] = adata
+            _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left")
+            layer.metadata["adata"] = table
 
         if layer is not None and "adata" in layer.metadata:
             with self.model.events.adata.blocker():
@@ -126,10 +128,10 @@ def _update_adata(self) -> None:
             return
 
         self.model.instance_key = layer.metadata["instance_key"] = (
-            adata.uns["spatialdata_attrs"]["instance_key"] if adata is not None else None
+            table.uns["spatialdata_attrs"]["instance_key"] if table is not None else None
         )
         self.model.region_key = layer.metadata["region_key"] = (
-            adata.uns["spatialdata_attrs"]["region_key"] if adata is not None else None
+            table.uns["spatialdata_attrs"]["region_key"] if table is not None else None
         )
         self.model.system_name = layer.metadata["name"] if "name" in layer.metadata else None
 
@@ -148,7 +150,7 @@ def _on_selection(self, event: Any) -> None:
         self.table_name_widget.clear()
         self.table_name_widget.clear()
         if event.source == self.model or event.source.active:
-            table_list = self._get_init_table_list()
+            table_list = _get_init_table_list(self.viewer.layers.selection.active)
             if table_list:
                 self.model.table_names = table_list
                 self.table_name_widget.addItems(table_list)
@@ -161,14 +163,6 @@ def _on_selection(self, event: Any) -> None:
         self.color_widget.widget._onChange()
         self.color_widget.component_widget._onChange()
 
-    def _get_init_table_list(self) -> Optional[Sequence[Optional[str]]]:
-        layer = self.viewer.layers.selection.active
-
-        table_names: Optional[Sequence[Optional[str]]]
-        if table_names := layer.metadata.get("table_names"):
-            return table_names  # type: ignore[no-any-return]
-        return None
-
     def _select_layer(self) -> None:
         """Napari layers."""
         layer = self._viewer.layers.selection.active
@@ -193,7 +187,7 @@ def viewer(self) -> napari.Viewer:
         return self._viewer
 
     @property
-    def model(self) -> ImageModel:
+    def model(self) -> DataModel:
         """:mod:`napari` viewer."""
         return self._model
 
@@ -205,7 +199,7 @@ def __init__(self, viewer: Viewer):
         super().__init__()
 
         self._viewer = viewer
-        self._model = ImageModel()
+        self._model = DataModel()
 
         self._select_layer()
         self._viewer.layers.selection.events.changed.connect(self._select_layer)
@@ -229,9 +223,9 @@ def __init__(self, viewer: Viewer):
         self.layout().addWidget(obs_label)
         self.layout().addWidget(self.obs_widget)
 
-        # gene
-        var_label = QLabel("Genes:")
-        var_label.setToolTip("Gene names from `adata.var_names` or `adata.raw.var_names`.")
+        # Vars
+        var_label = QLabel("Vars:")
+        var_label.setToolTip("Names from `adata.var_names` or `adata.raw.var_names`.")
         self.var_widget = AListWidget(self.viewer, self.model, attr="var")
         self.var_widget.setAdataLayer("X")
 
@@ -245,6 +239,7 @@ def __init__(self, viewer: Viewer):
 
         self.adata_layer_widget.currentTextChanged.connect(self.var_widget.setAdataLayer)
 
+        self.layout().addWidget(adata_layer_label)
         self.layout().addWidget(self.adata_layer_widget)
         self.layout().addWidget(var_label)
         self.layout().addWidget(self.var_widget)
@@ -262,6 +257,13 @@ def __init__(self, viewer: Viewer):
         self.layout().addWidget(self.obsm_widget)
         self.layout().addWidget(self.obsm_index_widget)
 
+        # Points columns
+        points_label = QLabel("Points columns:")
+        points_label.setToolTip("Columns in points element excluding dimension columns.")
+        self.points_widget = AListWidget(self.viewer, self.model, attr="points", multiselect=False)
+        self.layout().addWidget(points_label)
+        self.layout().addWidget(self.points_widget)
+
         # color by
         self.color_by = QLabel("Colored by:")
         self.layout().addWidget(self.color_by)
@@ -282,7 +284,7 @@ def _on_layer_update(self, event: Optional[Any] = None) -> None:
 
         self.table_name_widget.clear()
 
-        table_list = self._get_init_table_list()
+        table_list = _get_init_table_list(self.viewer.layers.selection.active)
         if table_list:
             self.model.table_names = table_list
             self.table_name_widget.addItems(table_list)
@@ -291,6 +293,7 @@ def _on_layer_update(self, event: Optional[Any] = None) -> None:
         self.adata_layer_widget.clear()
         self.adata_layer_widget.addItem("X", None)
         self.adata_layer_widget.addItems(self._get_adata_layer())
+        self.points_widget.clear()
         self.obs_widget._onChange()
         self.var_widget._onChange()
         self.obsm_widget._onChange()
@@ -303,10 +306,16 @@ def _select_layer(self) -> None:
             if hasattr(self, "obs_widget"):
                 self.table_name_widget.clear()
                 self.adata_layer_widget.clear()
+                self.points_widget.clear()
                 self.obs_widget.clear()
                 self.var_widget.clear()
                 self.obsm_widget.clear()
                 self.color_by.clear()
+                if (
+                    isinstance(layer, Points)
+                    and len(cols := layer.metadata["sdata"][layer.metadata["name"]].columns.drop(["x", "y"])) != 0
+                ):
+                    self.points_widget.addItems(map(str, cols))
             return
 
         if layer is not None and "adata" in layer.metadata:
@@ -329,14 +338,15 @@ def _select_layer(self) -> None:
     def _update_adata(self) -> None:
         if (table_name := self.table_name_widget.currentText()) == "":
             return
+        self.model.active_table_name = table_name
+
         layer = self._viewer.layers.selection.active
-        adata = None
 
         if sdata := layer.metadata.get("sdata"):
             element_name = layer.metadata.get("name")
-            table = sdata[table_name]
-            adata = table[table.obs[table.uns["spatialdata_attrs"]["region_key"]] == element_name]
-            layer.metadata["adata"] = adata
+            how = "left" if isinstance(layer, Labels) else "inner"
+            _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, how)
+            layer.metadata["adata"] = table
 
         if layer is not None and "adata" in layer.metadata:
             with self.model.events.adata.blocker():
@@ -346,10 +356,10 @@ def _update_adata(self) -> None:
             return
 
         self.model.instance_key = layer.metadata["instance_key"] = (
-            adata.uns["spatialdata_attrs"]["instance_key"] if adata is not None else None
+            table.uns["spatialdata_attrs"]["instance_key"] if table is not None else None
         )
         self.model.region_key = layer.metadata["region_key"] = (
-            adata.uns["spatialdata_attrs"]["region_key"] if adata is not None else None
+            table.uns["spatialdata_attrs"]["region_key"] if table is not None else None
         )
         self.model.system_name = layer.metadata["name"] if "name" in layer.metadata else None
 
@@ -371,15 +381,6 @@ def _get_adata_layer(self) -> Sequence[Optional[str]]:
             return adata_layers
         return [None]
 
-    def _get_init_table_list(self) -> Optional[Sequence[Optional[str]]]:
-        layer = self.viewer.layers.selection.active
-
-        table_names: Optional[Sequence[Optional[str]]]
-        if table_names := layer.metadata.get("table_names"):
-            return table_names  # type: ignore[no-any-return]
-
-        return None
-
     def _change_color_by(self) -> None:
         self.color_by.setText(f"Color by: {self.model.color_by}")
 
@@ -389,7 +390,7 @@ def viewer(self) -> napari.Viewer:
         return self._viewer
 
     @property
-    def model(self) -> ImageModel:
+    def model(self) -> DataModel:
         """:mod:`napari` viewer."""
         return self._model
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		POLYGON_THRESHOLD = 100
		POINT_THRESHOLD = 100000