support reading multi-polygon selection files from the Xenium Explorer

quentinblampey · Apr 11, 2024 · 94fb593 · 94fb593
1 parent 4bd5636
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.1.3] - xxxx-xx-xx
 
+### Added
+
+-   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
 
 ## [0.1.2] - 2024-03-30
 

diff --git a/src/spatialdata_io/_constants/_constants.py b/src/spatialdata_io/_constants/_constants.py
@@ -121,6 +121,10 @@ class XeniumKeys(ModeEnum):
     NUCLEUS_COUNT = "nucleus_count"
     Z_LEVEL = "z_level"
 
+    EXPLORER_SELECTION_X = "X"
+    EXPLORER_SELECTION_Y = "Y"
+    EXPLORER_SELECTION_KEY = "Selection"
+
 
 @unique
 class VisiumKeys(ModeEnum):

diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
@@ -615,7 +615,14 @@ def xenium_aligned_image(
     )
 
 
-def xenium_explorer_selection(path: str | Path, pixel_size: float = 0.2125) -> Polygon:
+def _selection_to_polygon(df: pd.DataFrame, pixel_size: float) -> Polygon:
+    xy_keys = [XeniumKeys.EXPLORER_SELECTION_X, XeniumKeys.EXPLORER_SELECTION_Y]
+    return Polygon(df[xy_keys].values / pixel_size)
+
+
+def xenium_explorer_selection(
+    path: str | Path, pixel_size: float = 0.2125, return_list: bool = False
+) -> Polygon | list[Polygon]:
     """Read the coordinates of a selection `.csv` file exported from the `Xenium Explorer  <https://www.10xgenomics.com/support/software/xenium-explorer/latest>`_.
 
     This file can be generated by the "Freehand Selection" or the "Rectangular Selection".
@@ -624,19 +631,28 @@ def xenium_explorer_selection(path: str | Path, pixel_size: float = 0.2125) -> P
     If `spatialdata_xenium_explorer  <https://github.com/quentinblampey/spatialdata_xenium_explorer>`_ was used,
     the `pixel_size` argument must be set to the one used during conversion with `spatialdata_xenium_explorer`.
 
+    In case multiple polygons were selected on the Explorer and exported into a single file, it will return a list of polygons.
+
     Parameters
     ----------
     path
         Path to the `.csv` file containing the selection coordinates
     pixel_size
         Size of a pixel in microns. By default, the Xenium pixel size is used.
+    return_list
+        If `True`, returns a list of Polygon even if only one polygon was selected
 
     Returns
     -------
     :class:`shapely.geometry.polygon.Polygon`
     """
     df = pd.read_csv(path, skiprows=2)
-    return Polygon(df.values / pixel_size)
+
+    if XeniumKeys.EXPLORER_SELECTION_KEY not in df:
+        polygon = _selection_to_polygon(df, pixel_size)
+        return [polygon] if return_list else polygon
+
+    return [_selection_to_polygon(sub_df, pixel_size) for _, sub_df in df.groupby(XeniumKeys.EXPLORER_SELECTION_KEY)]
 
 
 def _parse_version_of_xenium_analyzer(