Add functions to interactive (#315)

* Add functions to interactive

In this commit two functions are added to the interactive class.
get_layer grabs the layer name and returns the layer if it matches the user input.
add_text_to_polygons adds annotations to the chosen polygons/shapes layer

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* Add tests for new functions in interactive

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* Loosen tests for interactive

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* Edit interactive polygon tests to use correct example dataset

* Fix interactive test

* Fix mixed line endings

* trigger ci

* Apply suggestions from code review

improve readability

Co-authored-by: Grzegorz Bokota <[email protected]>

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Luca Marconato <[email protected]>
Co-authored-by: Grzegorz Bokota <[email protected]>

CHANGELOG.md

@@ -8,6 +8,13 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## [0.5.5] - 2024-10-07
+
+### Added
+
+- New function to grab layer by name #315 @minhtien-trinh
+- New annotation function to add text to polygons #315 @minhtien-trinh
+
 ## [0.5.4] - 2024-xx-xx
 
 ### Fixed

src/napari_spatialdata/_interactive.py

@@ -3,6 +3,7 @@
 from typing import TYPE_CHECKING, Any
 
 import napari
+from napari.layers import Image, Labels, Points, Shapes
 from napari.utils.events import EventedList
 from spatialdata._types import ArrayLike
 
@@ -100,3 +101,27 @@ def run(self) -> None:
     def screenshot(self) -> ArrayLike | Any:
         """Take a screenshot of the viewer in its current state."""
         return self._viewer.screenshot(canvas_only=False)
+
+    def get_layer(self, layer_name: str) -> Image | Labels | Points | Shapes | None:
+        """Get a layer by name."""
+        try:
+            return self._viewer.layers[layer_name]
+        except KeyError:
+            return None
+
+    def add_text_to_polygons(self, layer_name: str, text_annotations: list[str]) -> None:
+        """Add text annotations to a polygon layer."""
+        polygon_layer = self.get_layer(layer_name)
+        if not polygon_layer:
+            raise ValueError(f"Polygon layer '{layer_name}' not found.")
+        if len(text_annotations) != len(polygon_layer.data):
+            raise ValueError(
+                f"The number of text annotations must match the number of polygons. "
+                f"Polygons: {len(polygon_layer.data)}, Text: {len(text_annotations)}."
+            )
+        polygon_layer.text = {
+            "string": text_annotations,
+            "size": 10,
+            "color": "red",
+            "anchor": "center",
+        }

tests/test_interactive.py

@@ -44,3 +44,32 @@ def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     assert i._sdata_widget.coordinate_system_widget._system == "global"
     assert i._viewer.layers[-1].visible
     i._viewer.close()
+
+
+class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
+    def test_get_layer_existing(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        i.add_element(element="blobs_image", element_coordinate_system="global")
+        layer = i.get_layer("blobs_image")
+        assert layer is not None, "Expected to retrieve the blobs_image layer, but got None"
+        assert layer.name == "blobs_image", f"Expected layer name 'blobs_image', got {layer.name}"
+        i._viewer.close()
+
+    def test_get_layer_non_existing(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        layer = i.get_layer("non_existing_layer")
+        assert layer is None, "Expected None for a non-existing layer, but got a layer"
+        i._viewer.close()
+
+    def test_add_text_to_polygons(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        i.add_element(element="blobs_polygons", element_coordinate_system="global")
+
+        # Mock polygon layer with some polygon data
+        text_annotations = ["Label 1", "Label 2", "Label 3", "Label 4", "Label 5"]
+        polygon_layer = i.get_layer("blobs_polygons")
+
+        # Verify that text is added
+        i.add_text_to_polygons(layer_name="blobs_polygons", text_annotations=text_annotations)
+        assert polygon_layer.text is not None, "Text annotations were not added to the polygon layer"
+        i._viewer.close()