Use small dataset for tests

Author: keller-mark

tests/create_xenium_filtered_points.py

@@ -0,0 +1,48 @@
+import os
+from os.path import join, isfile, isdir
+from urllib.request import urlretrieve
+import zipfile
+import shutil
+
+# Used spatialdata==0.4.0 on October 30, 2025
+from spatialdata import read_zarr, SpatialData
+
+
+data_dir = "data"
+zip_filepath = join(data_dir, "xenium_rep1_io.spatialdata.zarr.zip")
+spatialdata_filepath = join(data_dir, "xenium_rep1_io.spatialdata.zarr")
+
+
+if not isdir(spatialdata_filepath):
+    if not isfile(zip_filepath):
+        os.makedirs(data_dir, exist_ok=True)
+        urlretrieve('https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip', zip_filepath)
+    with zipfile.ZipFile(zip_filepath,"r") as zip_ref:
+        zip_ref.extractall(data_dir)
+        os.rename(join(data_dir, "data.zarr"), spatialdata_filepath)
+        
+        # This Xenium dataset has an AnnData "raw" element.
+        # Reference: https://github.com/giovp/spatialdata-sandbox/issues/55
+        raw_dir = join(spatialdata_filepath, "tables", "table", "raw")
+        if isdir(raw_dir):
+            shutil.rmtree(raw_dir)
+
+sdata = read_zarr(spatialdata_filepath)
+
+ddf = sdata.points["transcripts"]
+
+# 2. Define a function to take every 100th row from a partition
+def select_every_200th(partition):
+    # Each 'partition' is a Pandas DataFrame
+    # .iloc[::100] is the efficient pandas way to get every 100th row
+    return partition.iloc[::200]
+
+# 3. Apply this function to every partition in the Dask DataFrame
+result = ddf.map_partitions(select_every_200th)
+
+# 4. Compute the result to see it
+filtered_ddf = result[["x", "y", "z", "feature_name", "cell_id"]]
+
+small_sdata = SpatialData(points={ "transcripts": filtered_ddf })
+
+small_sdata.write("xenium_rep1_io.points_only.spatialdata.zarr", overwrite=True)

tests/data/xenium_rep1_io.points_only.spatialdata.zarr/.zattrs

@@ -0,0 +1,6 @@
+{
+    "spatialdata_attrs": {
+        "spatialdata_software_version": "0.4.0",
+        "version": "0.1"
+    }
+}

tests/data/xenium_rep1_io.points_only.spatialdata.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/xenium_rep1_io.points_only.spatialdata.zarr/points/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/xenium_rep1_io.points_only.spatialdata.zarr/points/transcripts/.zattrs

@@ -0,0 +1,63 @@
+{
+    "axes": [
+        "x",
+        "y",
+        "z"
+    ],
+    "coordinateTransformations": [
+        {
+            "input": {
+                "axes": [
+                    {
+                        "name": "x",
+                        "type": "space",
+                        "unit": "unit"
+                    },
+                    {
+                        "name": "y",
+                        "type": "space",
+                        "unit": "unit"
+                    },
+                    {
+                        "name": "z",
+                        "type": "space",
+                        "unit": "unit"
+                    }
+                ],
+                "name": "xyz"
+            },
+            "output": {
+                "axes": [
+                    {
+                        "name": "x",
+                        "type": "space",
+                        "unit": "unit"
+                    },
+                    {
+                        "name": "y",
+                        "type": "space",
+                        "unit": "unit"
+                    },
+                    {
+                        "name": "z",
+                        "type": "space",
+                        "unit": "unit"
+                    }
+                ],
+                "name": "global"
+            },
+            "scale": [
+                4.705882352941177,
+                4.705882352941177,
+                1.0
+            ],
+            "type": "scale"
+        }
+    ],
+    "encoding-type": "ngff:points",
+    "spatialdata_attrs": {
+        "feature_key": "feature_name",
+        "instance_key": "cell_id",
+        "version": "0.1"
+    }
+}

tests/data/xenium_rep1_io.points_only.spatialdata.zarr/points/transcripts/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}