labels fixture

tests/conftest.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
-from typing import TYPE_CHECKING
+
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import numpy as np
 from iohub import open_ome_zarr
@@ -17,6 +18,7 @@ def _build_hcs(
     channel_names: list[str],
     zyx_shape: tuple[int, int, int],
     dtype: DTypeLike,
+    max_value: int | float,
 ):
     dataset = open_ome_zarr(
         path,
@@ -30,15 +32,17 @@ def _build_hcs(
                 pos = dataset.create_position(row, col, fov)
                 pos.create_image(
                     "0",
-                    np.random.rand(2, len(channel_names), *zyx_shape).astype(dtype),
+                    (
+                        np.random.rand(2, len(channel_names), *zyx_shape) * max_value
+                    ).astype(dtype),
                 )
 
 
 @fixture(scope="session")
 def preprocessed_hcs_dataset(tmp_path_factory: TempPathFactory) -> Path:
     """Provides a preprocessed HCS OME-Zarr dataset."""
     dataset_path = tmp_path_factory.mktemp("preprocessed.zarr")
-    _build_hcs(dataset_path, channel_names, (12, 256, 256), np.float32)
+    _build_hcs(dataset_path, channel_names, (12, 256, 256), np.float32, 1.0)
     # U[0, 1)
     expected = {"mean": 0.5, "std": 1 / np.sqrt(12), "median": 0.5, "iqr": 0.5}
     norm_meta = {channel: {"dataset_statistics": expected} for channel in channel_names}
@@ -53,5 +57,13 @@ def preprocessed_hcs_dataset(tmp_path_factory: TempPathFactory) -> Path:
 def small_hcs_dataset(tmp_path_factory: TempPathFactory) -> Path:
     """Provides a small, not preprocessed HCS OME-Zarr dataset."""
     dataset_path = tmp_path_factory.mktemp("small.zarr")
-    _build_hcs(dataset_path, channel_names, (12, 64, 64), np.uint16)
+    _build_hcs(dataset_path, channel_names, (12, 64, 64), np.uint16, 1)
+    return dataset_path
+
+
+@fixture(scope="function")
+def labels_hcs_dataset(tmp_path_factory: TempPathFactory) -> Path:
+    """Provides a small, not preprocessed HCS OME-Zarr dataset."""
+    dataset_path = tmp_path_factory.mktemp("labels.zarr")
+    _build_hcs(dataset_path, ["DAPI"], (2, 16, 16), np.uint16, 3)
     return dataset_path