add lasso reader

quentinblampey · Feb 7, 2024 · 56a9cb6 · 56a9cb6
1 parent d17b438
commit 56a9cb6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning][].
 
 -   (MCMICRO) support for TMAs (such as the data of exemplar-002)
 -   (Xenium) support for post-xenium aligned images (IF, HE)
+-   (Xenium) reader for the selection coordinates file from the Xenium Explorer
 
 ### Fixed
 

diff --git a/src/spatialdata_io/__init__.py b/src/spatialdata_io/__init__.py
@@ -1,5 +1,6 @@
 from importlib.metadata import version
 
+from spatialdata_io.readers._utils._utils import xenium_explorer_selection
 from spatialdata_io.readers.codex import codex
 from spatialdata_io.readers.cosmx import cosmx
 from spatialdata_io.readers.curio import curio
@@ -18,6 +19,7 @@
     "mcmicro",
     "steinbock",
     "merscope",
+    "xenium_explorer_selection",
 ]
 
 __version__ = version("spatialdata-io")
diff --git a/src/spatialdata_io/readers/_utils/_utils.py b/src/spatialdata_io/readers/_utils/_utils.py
@@ -5,8 +5,10 @@
 from typing import Any, Optional, Union
 
 import numpy as np
+import pandas as pd
 from anndata import AnnData, read_text
 from h5py import File
+from shapely.geometry import Polygon
 
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 
@@ -66,3 +68,24 @@ def _read_counts(
 
     adata.uns["spatial"] = {library_id: {"metadata": {}}}  # can overwrite
     return adata, library_id
+
+
+def xenium_explorer_selection(path: str | Path, pixelsize: float = 0.2125) -> Polygon:
+    """
+    Read the coordinates of a selection file exported from the Xenium Explorer.
+    This `.csv` file can be generated by the "Freehand Selection" as well
+    as the "Rectangular Selection".
+    The output `Polygon` can be used for a polygon query on the pixel coordinate
+    system (called `"global"` for Xenium data).
+    Parameters
+    ----------
+    path
+        Path to the `.csv` file containing the selection coordinates
+    pixelsize
+        Size of a pixel in microns. By default, the Xenium pixel size is used.
+    Returns
+    -------
+    :class:`shapely.geometry.Polygon`
+    """
+    df = pd.read_csv(path, skiprows=2)
+    return Polygon(df.values / pixelsize)