napari-spatialdata 0.2.2__tar.gz → 0.2.3__tar.gz

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.2.2
+Version: 0.2.3
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla

napari-spatialdata-0.2.3/examples/spatialdata_visium.py

@@ -0,0 +1,12 @@
+# In this script, we are reading the Visium dataset into a SpatialData object and visualising
+# it with the Interactive class from napari_spatialdata.
+
+# The dataset can be downloaded from https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html
+
+from napari_spatialdata import Interactive
+from spatialdata import SpatialData
+
+if __name__ == "__main__":
+    sdata = SpatialData.read("../data/visium/data.zarr")  # Change this path!
+    i = Interactive(sdata)
+    i.run()

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/src/napari_spatialdata/_interactive.py

@@ -2,6 +2,7 @@ from typing import Any, Iterable, Union
 
 import napari
 import numpy as np
+import shapely
 from anndata import AnnData
 from loguru import logger
 from multiscale_spatial_image import MultiscaleSpatialImage
@@ -9,7 +10,7 @@ from napari.viewer import Viewer
 from qtpy.QtWidgets import QLabel, QListWidget, QListWidgetItem, QVBoxLayout, QWidget
 from spatialdata import SpatialData
 
-from napari_spatialdata._utils import NDArrayA, _get_transform
+from napari_spatialdata._utils import NDArrayA, _get_transform, _swap_coordinates
 
 
 class ElementWidget(QListWidget):
@@ -71,9 +72,66 @@ class SdataWidget(QWidget):
             self._add_image(text)
         elif self.elements_widget._elements[text] == "points":
             self._add_points(text)
+        elif self.elements_widget._elements[text] == "shapes":
+            self._add_shapes(text)
+
+    def _add_circles(self, key: str) -> None:
+        circles = []
+        df = self._sdata.shapes[key]
+        affine = _get_transform(self._sdata.shapes[key], self.coordinate_system_widget._system)
+
+        for i in range(0, len(df)):
+            circles.append([df.geometry[i].coords[0], [df.radius[i], df.radius[i]]])
+
+        circles = _swap_coordinates(circles)
+
+        self._viewer.add_shapes(
+            circles,
+            name=key,
+            affine=affine,
+            shape_type="ellipse",
+            metadata={
+                "adata": self._sdata.table[
+                    self._sdata.table.obs[self._sdata.table.uns["spatialdata_attrs"]["region_key"]] == key
+                ],
+                "shapes_key": self._sdata.table.uns["spatialdata_attrs"]["region_key"],
+            },
+        )
+
+    def _add_polygons(self, key: str) -> None:
+        polygons = []
+        df = self._sdata.shapes[key]
+        affine = _get_transform(self._sdata.shapes[key], self.coordinate_system_widget._system)
+
+        for i in range(0, len(df)):
+            polygons.append(list(df.geometry[i].exterior.coords))
+
+        polygons = _swap_coordinates(polygons)
+
+        self._viewer.add_shapes(
+            polygons,
+            name=key,
+            affine=affine,
+            shape_type="polygon",
+            metadata={
+                "adata": self._sdata.table[
+                    self._sdata.table.obs[self._sdata.table.uns["spatialdata_attrs"]["region_key"]] == key
+                ],
+                "shapes_key": self._sdata.table.uns["spatialdata_attrs"]["region_key"],
+            },
+        )
+
+    def _add_shapes(self, key: str) -> None:
+        if type(self._sdata.shapes[key].iloc[0][0]) == shapely.geometry.point.Point:
+            self._add_circles(key)
+        elif type(self._sdata.shapes[key].iloc[0][0]) == shapely.geometry.polygon.Polygon:
+            self._add_polygons(key)
+        else:
+            raise TypeError("Incorrect data type passed for shapes (should be Shapely Point or Polygon).")
 
     def _add_label(self, key: str) -> None:
         affine = _get_transform(self._sdata.labels[key], self.coordinate_system_widget._system)
+
         self._viewer.add_labels(
             self._sdata.labels[key],
             name=key,
@@ -89,6 +147,7 @@ class SdataWidget(QWidget):
     def _add_image(self, key: str) -> None:
         img = self._sdata.images[key]
         affine = _get_transform(self._sdata.images[key], self.coordinate_system_widget._system)
+
         if isinstance(img, MultiscaleSpatialImage):
             img = img["scale0"][key]
         # TODO: type check

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/src/napari_spatialdata/_utils.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from functools import wraps
-from typing import TYPE_CHECKING, Any, Callable, Optional, Sequence, Tuple, Union
+from typing import TYPE_CHECKING, Any, Callable, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 import pandas as pd
@@ -170,6 +170,10 @@ def _min_max_norm(vec: Union[spmatrix, NDArrayA]) -> NDArrayA:
     )
 
 
+def _swap_coordinates(data: List[Any]) -> List[Any]:
+    return [[(y, x) for x, y in sublist] for sublist in data]
+
+
 def _get_transform(element: SpatialElement, coordinate_system_name: Optional[str] = None) -> NDArrayA:
     affine: NDArrayA
     transformations = get_transformation(element, get_all=True)

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/src/napari_spatialdata/_version.py

@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.2.2'
-__version_tuple__ = version_tuple = (0, 2, 2)
+__version__ = version = '0.2.3'
+__version_tuple__ = version_tuple = (0, 2, 3)

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/src/napari_spatialdata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.2.2
+Version: 0.2.3
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla

{napari-spatialdata-0.2.2 → napari-spatialdata-0.2.3}/src/napari_spatialdata.egg-info/SOURCES.txt

@@ -31,6 +31,7 @@ docs/notebooks/spatialdata.ipynb
 examples/README.md
 examples/spatialdata_mibitof.py
 examples/spatialdata_nanostring.py
+examples/spatialdata_visium.py
 src/napari_spatialdata/__init__.py
 src/napari_spatialdata/_categoricals_utils.py
 src/napari_spatialdata/_interactive.py