Expose chunk encoding and compression options for TIFF and OME-Zarr ingestion

src/ome_arrow/ingest.py

@@ -1213,6 +1213,9 @@ def from_tiff(
     channel_names: Optional[Sequence[str]] = None,
     acquisition_datetime: Optional[datetime] = None,
     clamp_to_uint16: bool = True,
+    chunk_encoding: Literal["list", "bytes"] = "list",
+    chunk_compression: str | None = None,
+    chunk_compression_level: int | None = None,
 ) -> pa.StructScalar:
     """
     Read a TIFF and return a typed OME-Arrow StructScalar.
@@ -1228,6 +1231,11 @@ def from_tiff(
         channel_names: Optional channel names; defaults to C0..C{n-1}.
         acquisition_datetime: Optional acquisition time (UTC now if None).
         clamp_to_uint16: If True, clamp/cast planes to uint16.
+        chunk_encoding: ``"list"`` stores historical numeric pixel lists.
+            ``"bytes"`` stores compact typed chunk byte buffers.
+        chunk_compression: Optional leaf-level compression for byte chunks,
+            such as ``"zstd"`` or ``"lz4"``.
+        chunk_compression_level: Optional codec compression level.
 
     Returns:
         pa.StructScalar validated against `struct`.
@@ -1307,6 +1315,9 @@ def from_tiff(
         physical_size_unit=psize_unit,
         channels=channels,
         planes=planes,
+        chunk_encoding=chunk_encoding,
+        chunk_compression=chunk_compression,
+        chunk_compression_level=chunk_compression_level,
         masks=None,
     )
 
@@ -1631,6 +1642,9 @@ def from_ome_zarr(
     channel_names: Optional[Sequence[str]] = None,
     acquisition_datetime: Optional[datetime] = None,
     clamp_to_uint16: bool = True,
+    chunk_encoding: Literal["list", "bytes"] = "list",
+    chunk_compression: str | None = None,
+    chunk_compression_level: int | None = None,
 ) -> pa.StructScalar:
     """
     Read an OME-Zarr directory and return a typed OME-Arrow StructScalar.
@@ -1654,6 +1668,14 @@ def from_ome_zarr(
             Optional datetime (defaults to UTC now).
         clamp_to_uint16:
             If True, cast pixels to uint16.
+        chunk_encoding:
+            ``"list"`` stores historical numeric pixel lists. ``"bytes"``
+            stores compact typed chunk byte buffers.
+        chunk_compression:
+            Optional leaf-level compression for byte chunks, such as
+            ``"zstd"`` or ``"lz4"``.
+        chunk_compression_level:
+            Optional codec compression level.
 
     Returns:
         pa.StructScalar: Validated OME-Arrow struct for this image.
@@ -1742,6 +1764,9 @@ def from_ome_zarr(
         physical_size_unit=psize_unit,
         channels=channels,
         planes=planes,
+        chunk_encoding=chunk_encoding,
+        chunk_compression=chunk_compression,
+        chunk_compression_level=chunk_compression_level,
         masks=None,
     )
 

tests/test_ingest.py

@@ -0,0 +1,64 @@
+"""Tests for image-file ingestion helpers."""
+
+from pathlib import Path
+from types import SimpleNamespace
+from typing import Callable
+
+import numpy as np
+import pytest
+
+import ome_arrow.ingest as ingest_mod
+from ome_arrow import OME_ARROW_BYTE_STRUCT
+from ome_arrow.export import to_numpy
+
+
+@pytest.mark.parametrize(
+    ("converter", "path"),
+    [
+        (ingest_mod.from_tiff, Path("image.tiff")),
+        (ingest_mod.from_ome_zarr, Path("image.ome.zarr")),
+    ],
+)
+def test_file_ingest_forwards_byte_chunk_options(
+    monkeypatch: pytest.MonkeyPatch,
+    converter: Callable[..., object],
+    path: Path,
+) -> None:
+    """Encode and compress chunks requested through file ingest helpers."""
+    arr = np.zeros((1, 1, 1, 32, 32), dtype=np.uint16)
+    image = SimpleNamespace(
+        data=arr,
+        dims=SimpleNamespace(T=1, C=1, Z=1, Y=32, X=32),
+        physical_pixel_sizes=SimpleNamespace(X=1.0, Y=1.0, Z=1.0, unit="µm"),
+        channel_names=["C0"],
+    )
+    monkeypatch.setattr(ingest_mod, "BioImage", lambda **_kwargs: image)
+
+    scalar = converter(
+        path,
+        chunk_encoding="bytes",
+        chunk_compression="zstd",
+        chunk_compression_level=1,
+    )
+
+    assert scalar.type == OME_ARROW_BYTE_STRUCT
+    assert scalar.as_py()["chunks"][0]["compression"] == "zstd"
+    np.testing.assert_array_equal(to_numpy(scalar), arr)
+
+
+def test_file_ingest_keeps_list_chunks_by_default(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """Preserve the historical list encoding for existing callers."""
+    arr = np.arange(12, dtype=np.uint16).reshape(1, 1, 1, 3, 4)
+    image = SimpleNamespace(
+        data=arr,
+        dims=SimpleNamespace(T=1, C=1, Z=1, Y=3, X=4),
+        physical_pixel_sizes=SimpleNamespace(X=1.0, Y=1.0, Z=1.0, unit="µm"),
+    )
+    monkeypatch.setattr(ingest_mod, "BioImage", lambda **_kwargs: image)
+
+    scalar = ingest_mod.from_tiff("image.tiff")
+
+    assert "pixels" in scalar.as_py()["chunks"][0]
+    np.testing.assert_array_equal(to_numpy(scalar), arr)