Axes v0.4

setup.py

@@ -35,7 +35,7 @@ def get_long_description() -> str:
     author="The Open Microscopy Team",
     author_email="",
     python_requires=">=3",
-    install_requires=["omero-py>=5.6.0", "ome-zarr>=0.2.0"],
+    install_requires=["omero-py>=5.6.0", "ome-zarr>=0.3a1"],
     long_description=long_description,
     keywords=["OMERO.CLI", "plugin"],
     url="https://github.com/ome/omero-cli-zarr/",

src/omero_zarr/__init__.py

@@ -1,6 +1,8 @@
+from ome_zarr.format import CurrentFormat
+
 from ._version import version as __version__
 
-ngff_version = "0.3"
+ngff_version = CurrentFormat().version
 
 __all__ = [
     "__version__",

src/omero_zarr/masks.py

@@ -18,7 +18,8 @@
 from skimage.draw import polygon as sk_polygon
 from zarr.hierarchy import open_group
 
-from .util import open_store, print_status
+from . import ngff_version as VERSION
+from .util import marshal_axes, marshal_transformations, open_store, print_status
 
 # Mapping of dimension names to axes in the Zarr
 DIMENSION_ORDER: Dict[str, int] = {
@@ -215,6 +216,7 @@ def set_image(
         :param plate_path: The zarr path to the image
         :return: None
         """
+        self.image = image
         self.size_t = image.getSizeT()
         self.size_c = image.getSizeC()
         self.size_z = image.getSizeZ()
@@ -303,30 +305,31 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
             ignored_dimensions,
             check_overlaps=True,
         )
-        # For v0.3 ngff we want to reduce the number of dimensions to
+
+        axes = marshal_axes(self.image)
+        transformations = marshal_transformations(self.image, levels=1)
+
+        # For v0.3+ ngff we want to reduce the number of dimensions to
         # match the dims of the Image.
         dims_to_squeeze = []
-        axes = []
         for dim, size in enumerate(self.image_shape):
             if size == 1:
                 dims_to_squeeze.append(dim)
-            else:
-                axes.append("tczyx"[dim])
         labels = np.squeeze(labels, axis=tuple(dims_to_squeeze))
 
         scaler = Scaler(max_layer=input_pyramid_levels)
         label_pyramid = scaler.nearest(labels)
         pyramid_grp = out_labels.require_group(name)
 
         write_multiscale(
-            label_pyramid, pyramid_grp, axes=axes
+            label_pyramid, pyramid_grp, axes=axes, transformations=transformations
         )  # TODO: dtype, chunks, overwite
 
         # Specify and store metadata
         image_label_colors: List[JSONDict] = []
         label_properties: List[JSONDict] = []
         image_label = {
-            "version": "0.3",
+            "version": VERSION,
             "colors": image_label_colors,
             "properties": label_properties,
             "source": {"image": source_image_link},

src/omero_zarr/raw_pixels.py

@@ -7,13 +7,18 @@
 import numpy as np
 import omero.clients  # noqa
 import omero.gateway  # required to allow 'from omero_zarr import raw_pixels'
+from ome_zarr.writer import (
+    write_multiscales_metadata,
+    write_plate_metadata,
+    write_well_metadata,
+)
 from omero.rtypes import unwrap
 from skimage.transform import resize
 from zarr.hierarchy import Array, Group, open_group
 
 from . import __version__
 from . import ngff_version as VERSION
-from .util import open_store, print_status
+from .util import marshal_axes, marshal_transformations, open_store, print_status
 
 
 def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
@@ -24,16 +29,15 @@ def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -
     print(f"Exporting to {name} ({VERSION})")
     store = open_store(name)
     root = open_group(store)
-    n_levels, axes = add_image(image, root, cache_dir=cache_dir)
-    add_multiscales_metadata(root, axes, n_levels)
+    add_image(image, root, cache_dir=cache_dir)
     add_omero_metadata(root, image)
     add_toplevel_metadata(root)
     print("Finished.")
 
 
 def add_image(
     image: omero.gateway.ImageWrapper, parent: Group, cache_dir: Optional[str] = None
-) -> Tuple[int, List[str]]:
+) -> Tuple[int, List[Dict[str, Any]]]:
     """Adds an OMERO image pixel data as array to the given parent zarr group.
     Optionally caches the pixel data in the given cache_dir directory.
     Returns the number of resolution levels generated for the image.
@@ -79,7 +83,7 @@ def planeGen() -> np.ndarray:
         longest = longest // 2
         level_count += 1
 
-    return add_raw_image(
+    paths = add_raw_image(
         planes=planes,
         size_z=size_z,
         size_c=size_c,
@@ -91,6 +95,15 @@ def planeGen() -> np.ndarray:
         cache_file_name_func=get_cache_filename,
     )
 
+    axes = marshal_axes(image)
+    transformations = marshal_transformations(image, len(paths))
+
+    write_multiscales_metadata(
+        parent, paths, axes=axes, transformations=transformations
+    )
+
+    return (level_count, axes)
+
 
 def add_raw_image(
     *,
@@ -103,7 +116,7 @@ def add_raw_image(
     level_count: int,
     cache_dir: Optional[str] = None,
     cache_file_name_func: Callable[[int, int, int], str] = None,
-) -> Tuple[int, List[str]]:
+) -> List[str]:
     """Adds the raw image pixel data as array to the given parent zarr group.
     Optionally caches the pixel data in the given cache_dir directory.
     Returns the number of resolution levels generated for the image.
@@ -121,14 +134,8 @@ def add_raw_image(
         cache_dir = ""
 
     dims = [dim for dim in [size_t, size_c, size_z] if dim != 1]
-    axes = []
-    if size_t > 1:
-        axes.append("t")
-    if size_c > 1:
-        axes.append("c")
-    if size_z > 1:
-        axes.append("z")
 
+    paths: List[str] = []
     field_groups: List[Array] = []
     for t in range(size_t):
         for c in range(size_c):
@@ -151,9 +158,11 @@ def add_raw_image(
                     size_x = plane.shape[1]
                     # If on first plane, create a new group for this resolution level
                     if len(field_groups) <= level:
+                        path = str(level)
+                        paths.append(path)
                         field_groups.append(
                             parent.create(
-                                str(level),
+                                path,
                                 shape=tuple(dims + [size_y, size_x]),
                                 chunks=tuple([1] * len(dims) + [size_y, size_x]),
                                 dtype=d_type,
@@ -179,7 +188,8 @@ def add_raw_image(
                             preserve_range=True,
                             anti_aliasing=False,
                         ).astype(plane.dtype)
-    return (level_count, axes + ["y", "x"])
+
+    return paths
 
 
 def marshal_acquisition(acquisition: omero.gateway._PlateAcquisitionWrapper) -> Dict:
@@ -222,20 +232,14 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
 
     well_paths = set()
 
-    col_names = plate.getColumnLabels()
-    row_names = plate.getRowLabels()
+    col_names = [str(name) for name in plate.getColumnLabels()]
+    row_names = [str(name) for name in plate.getRowLabels()]
 
-    plate_metadata = {
-        "name": plate.name,
-        "rows": [{"name": str(name)} for name in row_names],
-        "columns": [{"name": str(name)} for name in col_names],
-        "version": VERSION,
-    }
     # Add acquisitions key if at least one plate acquisition exists
     acquisitions = list(plate.listPlateAcquisitions())
+    plate_acq = None
     if acquisitions:
-        plate_metadata["acquisitions"] = [marshal_acquisition(x) for x in acquisitions]
-    root.attrs["plate"] = plate_metadata
+        plate_acq = [marshal_acquisition(x) for x in acquisitions]
 
     for well in plate.listChildren():
         row = plate.getRowLabels()[well.row]
@@ -256,39 +260,28 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
                 row_group = root.require_group(row)
                 col_group = row_group.require_group(col)
                 field_group = col_group.require_group(field_name)
-                n_levels, axes = add_image(img, field_group, cache_dir=cache_dir)
-                add_multiscales_metadata(field_group, axes, n_levels)
+                add_image(img, field_group, cache_dir=cache_dir)
                 add_omero_metadata(field_group, img)
                 # Update Well metadata after each image
-                col_group.attrs["well"] = {"images": fields, "version": VERSION}
+                write_well_metadata(col_group, fields)
                 max_fields = max(max_fields, field + 1)
             print_status(int(t0), int(time.time()), count, total)
 
         # Update plate_metadata after each Well
-        plate_metadata["wells"] = [{"path": x} for x in well_paths]
-        plate_metadata["field_count"] = max_fields
-        root.attrs["plate"] = plate_metadata
+        write_plate_metadata(
+            root,
+            row_names,
+            col_names,
+            wells=list(well_paths),
+            field_count=max_fields,
+            acquisitions=plate_acq,
+            name=plate.name,
+        )
 
     add_toplevel_metadata(root)
     print("Finished.")
 
 
-def add_multiscales_metadata(
-    zarr_root: Group,
-    axes: List[str],
-    resolutions: int = 1,
-) -> None:
-
-    multiscales = [
-        {
-            "version": "0.3",
-            "datasets": [{"path": str(r)} for r in range(resolutions)],
-            "axes": axes,
-        }
-    ]
-    zarr_root.attrs["multiscales"] = multiscales
-
-
 def add_omero_metadata(zarr_root: Group, image: omero.gateway.ImageWrapper) -> None:
 
     image_data = {

src/omero_zarr/util.py

@@ -1,5 +1,7 @@
 import time
+from typing import Dict, List
 
+from omero.gateway import ImageWrapper
 from zarr.storage import FSStore
 
 
@@ -33,3 +35,83 @@ def open_store(name: str) -> FSStore:
         normalize_keys=False,
         mode="w",
     )
+
+
+def marshal_pixel_sizes(image: ImageWrapper) -> Dict[str, Dict]:
+
+    pixel_sizes: Dict[str, Dict] = {}
+    pix_size_x = image.getPixelSizeX(units=True)
+    pix_size_y = image.getPixelSizeY(units=True)
+    pix_size_z = image.getPixelSizeZ(units=True)
+    # All OMERO units.lower() are valid UDUNITS-2 and therefore NGFF spec
+    if pix_size_x is not None:
+        pixel_sizes["x"] = {
+            "units": str(pix_size_x.getUnit()).lower(),
+            "value": pix_size_x.getValue(),
+        }
+    if pix_size_y is not None:
+        pixel_sizes["y"] = {
+            "units": str(pix_size_y.getUnit()).lower(),
+            "value": pix_size_y.getValue(),
+        }
+    if pix_size_z is not None:
+        pixel_sizes["z"] = {
+            "units": str(pix_size_z.getUnit()).lower(),
+            "value": pix_size_z.getValue(),
+        }
+    return pixel_sizes
+
+
+def marshal_axes(image: ImageWrapper) -> List[Dict]:
+    # Prepare axes and transformations info...
+    size_c = image.getSizeC()
+    size_z = image.getSizeZ()
+    size_t = image.getSizeT()
+    pixel_sizes = marshal_pixel_sizes(image)
+
+    axes = []
+    if size_t > 1:
+        axes.append({"name": "t", "type": "time"})
+    if size_c > 1:
+        axes.append({"name": "c", "type": "channel"})
+    if size_z > 1:
+        axes.append({"name": "z", "type": "space"})
+        if pixel_sizes and "z" in pixel_sizes:
+            axes[-1]["units"] = pixel_sizes["z"]["units"]
+    # last 2 dimensions are always y and x
+    for dim in ("y", "x"):
+        axes.append({"name": dim, "type": "space"})
+        if pixel_sizes and dim in pixel_sizes:
+            axes[-1]["units"] = pixel_sizes[dim]["units"]
+
+    return axes
+
+
+def marshal_transformations(
+    image: ImageWrapper, levels: int = 1, multiscales_zoom: float = 2.0
+) -> List[List[Dict]]:
+
+    axes = marshal_axes(image)
+    pixel_sizes = marshal_pixel_sizes(image)
+
+    # Each path needs a transformations list...
+    transformations = []
+    zooms = {"x": 1.0, "y": 1.0, "z": 1.0}
+    for level in range(levels):
+        # {"type": "scale", "scale": [2.0, 2.0, 2.0], "axisIndices": [2, 3, 4]}
+        scales = []
+        axisIndices = []
+        for index, axis in enumerate(axes):
+            if axis["name"] in pixel_sizes:
+                scales.append(zooms[axis["name"]] * pixel_sizes[axis["name"]]["value"])
+                axisIndices.append(index)
+        # ...with a single 'scale' transformation each
+        if len(scales) > 0:
+            transformations.append(
+                [{"type": "scale", "scale": scales, "axisIndices": axisIndices}]
+            )
+        # NB we rescale X and Y for each level, but not Z
+        zooms["x"] = zooms["x"] * multiscales_zoom
+        zooms["y"] = zooms["y"] * multiscales_zoom
+
+    return transformations