Clean up tutorial

docs/tutorial.py

@@ -1,5 +1,7 @@
 # # Tutorial
 
+import matplotlib.pyplot as plt
+import pydantic
 import zarr
 import zarr.storage
 from rich.pretty import pprint
@@ -15,14 +17,13 @@
 # We can create an Image model from a zarr group, that points to an
 # OME-zarr dataset:
 
-print(tutorial_data_path.absolute())
 group = zarr.open(tutorial_data_path)
 ome_zarr_image = Image(group)
 pprint(ome_zarr_image)
 
 # This image contains both the zarr group, and a model of the multiscales metadata
 
-multiscales_meta = ome_zarr_image.attributes.multiscales
+multiscales_meta = ome_zarr_image.multiscales
 pprint(multiscales_meta)
 
 # ## Updating models
@@ -40,9 +41,12 @@
 # scale, or a scale then translation (strictly in that order). So if we try and make a
 # transformation just a translation, it will raise an error.
 
-multiscales_meta[0].datasets[0].coordinateTransformations = VectorTranslation(
-    type="translation", translation=[1, 2, 3]
-)
+try:
+    multiscales_meta[0].datasets[0].coordinateTransformations = (
+        VectorTranslation(type="translation", translation=[1, 2, 3]),
+    )
+except pydantic.ValidationError as e:
+    print(str(e))
 
 
 # This means validation happens early, allowing you to catch errors
@@ -53,8 +57,12 @@
 # Although these models do not handle reading or writing data, they do expose the zarr
 # arrays.
 
-zarr_arr = ome_zarr_image.group[multiscales_meta[0].datasets[0].path]
-pprint(zarr_arr)
+print(ome_zarr_image.arrays)
+full_res_path = ome_zarr_image.multiscales[0].datasets[0].path
+zarr_arr = ome_zarr_image.arrays[full_res_path]
+
+fig, ax = plt.subplots()
+ax.imshow(zarr_arr)
 
 # ## Not using validation
 #

mkdocs.yml

@@ -6,7 +6,7 @@ theme:
 plugins:
   - mkdocs-jupyter:
       execute: true
-      allow_errors: true
+      allow_errors: false
   - mkdocstrings:
       handlers:
         python:

pyproject.toml

@@ -15,6 +15,7 @@ docs = [
     "gcsfs",
     "rich",
     "griffe-pydantic",
+    "matplotlib",
     "zarr<3",
 ]
 pydantic = ["pydantic"]
@@ -36,6 +37,7 @@ docs = [
     "rich",
     "griffe-pydantic",
     "zarr<3",
+    "matplotlib",
 ]
 dev = [
     "jupyter[notebook]>=1.1.1",

src/ome_zarr_models/v04/image.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Annotated, Self
+from typing import Annotated
 
 import zarr.errors
 from pydantic import Field, model_validator
@@ -79,15 +79,20 @@ class ImageAttrs(Base):
     #  series MUST have the same number of entries."
 
 
-class Image(GroupSpec[ImageAttrs, ArraySpec | GroupSpec]):
+class ImageSpec(GroupSpec[ImageAttrs, ArraySpec | GroupSpec]):
+    _check_arrays_compatible = model_validator(mode="after")(_check_arrays_compatible)
+
+
+class Image:
     """
     An OME-zarr multiscale dataset.
     """
 
-    _check_arrays_compatible = model_validator(mode="after")(_check_arrays_compatible)
+    def __init__(self, group: zarr.Group) -> None:
+        self._spec = self._get_spec(group)
+        self._group = group
 
-    @classmethod
-    def from_zarr(cls, node: zarr.Group) -> Self:
+    def _get_spec(self, node: zarr.Group) -> ImageSpec:
         """
         Create an instance of an OME-zarr image from a `zarr.Group`.
 
@@ -136,18 +141,25 @@ def from_zarr(cls, node: zarr.Group) -> Self:
         guess_inferred_members = guess.model_copy(
             update={"members": members_normalized.members}
         )
-        return cls(**guess_inferred_members.model_dump())
+        return ImageSpec(**guess_inferred_members.model_dump())
+
+    @property
+    def arrays(self) -> zarr.Group:
+        """
+        Multiscale array group in this image.
+        """
+        return self._group
 
     @property
     def multiscales(self) -> Multiscales:
         """
         Multiscales metadata model.
         """
-        return self.attributes.multiscales
+        return self._spec.attributes.multiscales
 
     @property
     def omero(self) -> Omero | None:
         """
         omero metadata model (if present).
         """
-        return self.attributes.omero
+        return self._spec.attributes.omero