feature/parameterized-ome-tiff-writer-compression

bioio/tests/writers/test_ome_tiff_writer.py

@@ -476,3 +476,21 @@ def test_ome_tiff_writer_common_metadata(
                 scene = tiff.series[i]
                 assert scene.shape == read_shapes[i]
                 assert scene.pages.axes == read_dim_order[i]
+
+
+def test_ome_tiff_writer_custom_compression(tmp_path: pathlib.Path) -> None:
+    # Create array
+    arr = np.random.rand(5, 16, 16)
+
+    # Construct save end point
+    save_uri = tmp_path / "e.ome.tiff"
+
+    # Normal save
+    OmeTiffWriter.save(
+        arr,
+        save_uri,
+        tifffile_kwargs={
+            "compression": "zlib",
+            "compressionargs": {"level": 8},
+        },
+    )

bioio/writers/ome_tiff_writer.py

@@ -29,6 +29,9 @@
 # calculate it but for now this is a stopgap working value
 BIGTIFF_BYTE_LIMIT = 2**21
 
+# Default tifffile.write kwargs
+DEFAULT_TIFF_WRITE_KWARGS = {"compression": TIFF.COMPRESSION.ADOBE_DEFLATE}
+
 
 class OmeTiffWriter(Writer):
     @staticmethod
@@ -46,6 +49,7 @@ def save(
             Union[List[List[int]], List[Optional[List[List[int]]]]]
         ] = None,
         fs_kwargs: Dict[str, Any] = {},
+        tifffile_kwargs: Dict[str, Any] = DEFAULT_TIFF_WRITE_KWARGS,
         **kwargs: Any,
     ) -> None:
         """
@@ -102,6 +106,13 @@ def save(
             Any specific keyword arguments to pass down to the fsspec created
             filesystem.
             Default: {}
+        tifffile_kwargs: Dict[str, Any]
+            Any specific keyword arguments to pass down to tifffile write function.
+            Do not use these kwargs to provide the image `description`,
+            `photometric` configuration, or `planarconfig` parameters as those are all
+            determined via the image and metadata provided from caller.
+            Default: DEFAULT_TIFF_WRITE_KWARGS
+                Compression using ADOBE_DEFLATE (ZLIB)
 
         Raises
         ------
@@ -130,6 +141,18 @@ def save(
         ...     dim_order="CZYX",  # this single value will be repeated to each image
         ...     channel_names=[["C00","C01","C02"],["C10","C11","C12"]]
         ... )
+
+        Write data with custom compression scheme
+
+        >>> image = numpy.ndarray([1, 10, 3, 1024, 2048])
+        ... OmeTiffWriter.save(
+        ...     image,
+        ...     "file.ome.tif",
+        ...     tifffile_kwargs={
+        ...         "compression": "zlib",
+        ...         "compressionargs": {"level": 8},
+        ...     },
+        ... )
         """
         # Resolve final destination
         fs, path = biob.io.pathlike_to_fs(uri, fs_kwargs=fs_kwargs)
@@ -301,7 +324,7 @@ def save(
                     photometric=photometric,
                     metadata=None,
                     planarconfig=planarconfig,
-                    compression=TIFF.COMPRESSION.ADOBE_DEFLATE,
+                    **tifffile_kwargs,
                 )
 
             tif.close()