attempts to create a writer

environment.yml

@@ -1,4 +1,4 @@
-#name: z
+name: z
 channels:
   - defaults
   - ome

ome_zarr/writer.py

@@ -0,0 +1,76 @@
+"""Image writer utility
+
+"""
+import logging
+
+from typing import Any, Dict, Iterator, List, Optional, Type, Union, Tuple, cast
+import zarr
+
+import numpy as np
+
+from .io import parse_url
+from .reader import Node
+
+
+LOGGER = logging.getLogger("ome_zarr.writer")
+
+def write_image(
+        path: str,
+        image: np.ndarray,
+        name: str = "0",
+        group: str = None,
+        chunks: Union[Tuple[int], int] = None,
+        byte_order: Union[str, List[str]] = "tczyx",
+        **metadata):
+    """Writes an image to the zarr store according to ome-zarr specification
+
+    Parameters
+    ----------
+    path: str,
+      a path to the zarr store location
+    image: np.ndarray
+      the image to save
+    group: str, optional
+      the group within the zarr store to store the data in
+    chunks: int or tuple of ints,
+      size of the saved chunks to store the image
+    byte_order: str or list of str, default "tczyx"
+      combination of the letters defining the order
+      in which the dimensions are saved
+    """
+    zarr_location = parse_url(path)
+
+    ## I assume this should be dealt with in
+    ## the ZarrLocation classes
+    store = zarr.DirectoryStore(path)
+    image = np.asarray(image)
+
+    if image.ndim > 5:
+        # Maybe we can split the more than 5D images in subroups?
+        raise ValueError("Only images of 5D or less are supported")
+
+    shape_5d = (*(1,)*(5 - image.ndim), *image.shape)
+    image = image.reshape(shape_5d)
+    omero = metadata.get("omero", {})
+
+    # Update the size entry anyway
+    omero["size"]= {
+            "t": image.shape[0],
+            "c": image.shape[1],
+            "z": image.shape[2],
+            "height": image.shape[3],
+            "width": image.shape[4],
+            }
+
+    metadata["omero"] = omero
+
+    root = zarr.group(store)
+    if group is not None:
+        grp = root.create_group(group)
+    else:
+        grp = root
+
+    grp.create_dataset(name, data=image, chunks=chunks)
+
+    for entry, value in metadata.items():
+        grp.attrs[entry] = value

tests/test_writer.py

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+import pytest
+import numpy as np
+
+from ome_zarr.writer import write_image
+from ome_zarr.io import parse_url
+from ome_zarr.reader import Reader
+
+
+class TestWriter:
+    @pytest.fixture(autouse=True)
+    def initdir(self, tmpdir):
+        self.path = tmpdir.mkdir("data")
+
+    def create_data(self, shape, dtype, mean_val=10):
+        rng = np.random.default_rng(0)
+        return rng.poisson(mean_val, size=shape).astype(dtype)
+
+    def test_writer(self):
+
+        data = self.create_data((1, 2, 1, 256, 256), np.uint8)
+        write_image(self.path, data)
+        reader = Reader(self.path)
+        assert len(list(reader())) == 3