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Merge pull request #107 from thewtex/validate-local
validate local
2 parents 3968030 + 7b35199 commit 81c9275

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‎.github/workflows/test.yml‎

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

‎ngff_zarr/__init__.py‎

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from .to_multiscales import to_multiscales
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from .to_ngff_image import to_ngff_image
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from .to_ngff_zarr import to_ngff_zarr
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from .validate import validate
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from .zarr_metadata import (
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AxesType,
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SpatialDims,
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"detect_cli_io_backend",
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"ConversionBackend",
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"cli_input_to_ngff_image",
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"validate",
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"Metadata",
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"AxesType",
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"SpatialDims",

‎ngff_zarr/from_ngff_zarr.py‎

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

‎ngff_zarr/spec/0.4/copyright.include‎

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

‎ngff_zarr/spec/0.4/schemas/bf2raw.schema‎

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

‎ngff_zarr/spec/0.4/schemas/image.schema‎

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

‎ngff_zarr/spec/0.4/schemas/label.schema‎

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

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