validate local

.github/workflows/test.yml

@@ -22,18 +22,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e ".[test,dask-image,itk,cli]"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e ".[test,dask-image,itk]"
-          python -m pip install itkwasm-image-io
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e ".[test,dask-image,itk,cli]"
+          python -m pip install -e ".[test,dask-image,itk,cli,validate]"
 
       - name: Test with pytest
         if: ${{ matrix.os != 'ubuntu-22.04' && matrix.os != 'macos-14' }}

ngff_zarr/__init__.py

@@ -17,6 +17,7 @@
 from .to_multiscales import to_multiscales
 from .to_ngff_image import to_ngff_image
 from .to_ngff_zarr import to_ngff_zarr
+from .validate import validate
 from .zarr_metadata import (
     AxesType,
     SpatialDims,
@@ -51,6 +52,7 @@
     "detect_cli_io_backend",
     "ConversionBackend",
     "cli_input_to_ngff_image",
+    "validate",
     "Metadata",
     "AxesType",
     "SpatialDims",

ngff_zarr/from_ngff_zarr.py

@@ -9,17 +9,21 @@
 from .ngff_image import NgffImage
 from .to_multiscales import Multiscales
 from .zarr_metadata import Axis, Dataset, Metadata, Scale, Translation
+from .validate import validate as validate_ngff
 
 
 def from_ngff_zarr(
     store: Union[MutableMapping, str, Path, BaseStore],
+    validate: bool = False,
 ) -> Multiscales:
     """
     Read an OME-Zarr NGFF Multiscales data structure from a Zarr store.
 
     store : MutableMapping, str or Path, zarr.storage.BaseStore
         Store or path to directory in file system.
 
+    validate : bool
+        If True, validate the NGFF metadata against the schema.
 
     Returns
     -------
@@ -29,6 +33,8 @@ def from_ngff_zarr(
     """
 
     root = zarr.open_group(store, mode="r")
+    if validate:
+        validate_ngff(root.attrs.asdict())
     metadata = root.attrs["multiscales"][0]
 
     dims = [a["name"] for a in metadata["axes"]]

ngff_zarr/spec/0.4/copyright.include

@@ -0,0 +1,4 @@
+Copyright © 2020-[YEAR]
+<a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup>
+(<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+OME trademark rules apply.

ngff_zarr/spec/0.4/schemas/bf2raw.schema

@@ -0,0 +1,14 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/latest/schemas/bf2raw.schema",
+  "title": "NGFF container produced by bioformats2raw",
+  "description": "JSON from OME-NGFF .zattrs",
+  "type": "object",
+  "properties": {
+    "bioformats2raw.layout": {
+      "description": "The top-level identifier metadata added by bioformats2raw",
+      "type": "number",
+      "enum": [3]
+    }
+  }
+}

ngff_zarr/spec/0.4/schemas/image.schema

@@ -0,0 +1,233 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.4/schemas/image.schema",
+  "title": "NGFF Image",
+  "description": "JSON from OME-NGFF .zattrs",
+  "type": "object",
+  "properties": {
+    "multiscales": {
+      "description": "The multiscale datasets for this image",
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
+          },
+          "datasets": {
+            "type": "array",
+            "minItems": 1,
+            "items": {
+              "type": "object",
+              "properties": {
+                "path": {
+                  "type": "string"
+                },
+                "coordinateTransformations": {
+                  "$ref": "#/$defs/coordinateTransformations"
+                }
+              },
+              "required": ["path", "coordinateTransformations"]
+            }
+          },
+          "version": {
+            "type": "string",
+            "enum": [
+              "0.4"
+            ]
+          },
+          "axes": {
+            "$ref": "#/$defs/axes"
+          },
+          "coordinateTransformations": {
+            "$ref": "#/$defs/coordinateTransformations"
+                }
+        },
+        "required": [
+          "datasets", "axes"
+        ]
+      },
+      "minItems": 1,
+      "uniqueItems": true
+    },
+    "omero": {
+      "type": "object",
+      "properties": {
+        "channels": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "window": {
+                "type": "object",
+                "properties": {
+                  "end": {
+                    "type": "number"
+                  },
+                  "max": {
+                    "type": "number"
+                  },
+                  "min": {
+                    "type": "number"
+                  },
+                  "start": {
+                    "type": "number"
+                  }
+                },
+                "required": [
+                  "start",
+                  "min",
+                  "end",
+                  "max"
+                ]
+              },
+              "label": {
+                "type": "string"
+              },
+              "family": {
+                "type": "string"
+              },
+              "color": {
+                "type": "string"
+              },
+              "active": {
+                "type": "boolean"
+              }
+            },
+            "required": [
+              "window",
+              "color"
+            ]
+          }
+        }
+      },
+      "required": [
+        "channels"
+      ]
+    }
+  },
+  "required": [ "multiscales" ],
+
+  "$defs": {
+    "axes": {
+      "type": "array",
+      "uniqueItems": true,
+      "minItems": 2,
+      "maxItems": 5,
+      "contains": {
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
+          },
+          "type": {
+            "type": "string",
+            "enum": ["space"]
+          },
+          "unit": {
+            "type": "string"
+          }
+        }
+      },
+      "minContains": 2,
+      "maxContains": 3,
+      "items": {
+        "oneOf": [
+          {
+            "type": "object",
+            "properties": {
+              "name": {
+                "type": "string"
+              },
+              "type": {
+                "type": "string",
+                "enum": ["channel", "time", "space"]
+              }
+            },
+            "required": ["name", "type"]
+          },
+          {
+            "type": "object",
+            "properties": {
+              "name": {
+                "type": "string"
+              },
+              "type": {
+                "type": "string",
+                "not": {
+                  "enum": ["space", "time", "channel"]
+                }
+              }
+            },
+            "required": ["name"]
+          }
+        ]
+      }
+    },
+    "coordinateTransformations": {
+      "type": "array",
+      "minItems": 1,
+      "contains": {
+        "type": "object",
+        "properties": {
+          "type": {
+            "type": "string",
+            "enum": [
+              "scale"
+            ]
+          },
+          "scale": {
+            "type": "array",
+            "minItems": 2,
+            "items": {
+              "type": "number"
+            }
+          }
+        }
+      },
+      "maxContains": 1,
+      "items": {
+        "oneOf": [
+          {
+            "type": "object",
+            "properties": {
+              "type": {
+                "type": "string",
+                "enum": [
+                  "scale"
+                ]
+              },
+              "scale": {
+                "type": "array",
+                "minItems": 2,
+                "items": {
+                  "type": "number"
+                }
+              }
+            },
+            "required": ["type", "scale"]
+          },
+          {
+            "type": "object",
+            "properties": {
+              "type": {
+                "type": "string",
+                "enum": [
+                  "translation"
+                ]
+              },
+              "translation": {
+                "type": "array",
+                "minItems": 2,
+                "items": {
+                  "type": "number"
+                }
+              }
+            },
+            "required": ["type", "translation"]
+          }
+        ]
+      }
+    }
+  }
+}

ngff_zarr/spec/0.4/schemas/label.schema

@@ -0,0 +1,77 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.4/schemas/label.schema",
+  "title": "OME-NGFF labelled image schema",
+  "description": "JSON from OME-NGFF .zattrs",
+  "type": "object",
+  "properties": {
+    "image-label": {
+      "type": "object",
+      "properties": {
+        "colors": {
+          "description": "The colors for this label image",
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "label-value": {
+                "description": "The value of the label",
+                "type": "number"
+              },
+              "rgba": {
+                "description": "The RGBA color stored as an array of four integers between 0 and 255",
+                "type": "array",
+                "items": {
+                  "type": "integer",
+                  "minimum": 0,
+                  "maximum": 255
+                },
+                "minItems": 4,
+                "maxItems": 4
+              }
+            },
+            "required": [
+              "label-value"
+            ]
+          },
+          "minItems": 1,
+          "uniqueItems": true
+        },
+        "properties": {
+          "description": "The properties for this label image",
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "label-value": {
+                "description": "The pixel value for this label",
+                "type": "integer"
+              }
+            },
+            "required": [
+              "label-value"
+            ]
+          },
+          "minItems": 1,
+          "uniqueItems": true
+        },
+        "source": {
+          "description": "The source of this label image",
+          "type": "object",
+          "properties": {
+            "image": {
+              "type": "string"
+            }
+          }
+        },
+        "version": {
+          "description": "The version of the specification",
+          "type": "string",
+          "enum": [
+            "0.4"
+          ]
+        }
+      }
+    }
+  }
+}