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ome.ts
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ome.ts
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/**
* @license
* Copyright 2022 Google Inc.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import type { CoordinateSpace } from "#src/coordinate_transform.js";
import { makeCoordinateSpace } from "#src/coordinate_transform.js";
import {
parseArray,
parseFixedLengthArray,
verifyFiniteFloat,
verifyFinitePositiveFloat,
verifyObject,
verifyObjectProperty,
verifyOptionalObjectProperty,
verifyString,
} from "#src/util/json.js";
import * as matrix from "#src/util/matrix.js";
import { allSiPrefixes } from "#src/util/si_units.js";
export interface OmeMultiscaleScale {
url: string;
transform: Float64Array;
}
export interface OmeMultiscaleMetadata {
scales: OmeMultiscaleScale[];
coordinateSpace: CoordinateSpace;
}
const SUPPORTED_OME_MULTISCALE_VERSIONS = new Set(["0.4", "0.5-dev"]);
const OME_UNITS = new Map<string, { unit: string; scale: number }>([
["angstrom", { unit: "m", scale: 1e-10 }],
["foot", { unit: "m", scale: 0.3048 }],
["inch", { unit: "m", scale: 0.0254 }],
["mile", { unit: "m", scale: 1609.34 }],
// eslint-disable-next-line @typescript-eslint/no-loss-of-precision
["parsec", { unit: "m", scale: 3.0856775814913673e16 }],
["yard", { unit: "m", scale: 0.9144 }],
["minute", { unit: "s", scale: 60 }],
["hour", { unit: "s", scale: 60 * 60 }],
["day", { unit: "s", scale: 60 * 60 * 24 }],
]);
for (const unit of ["meter", "second"]) {
for (const siPrefix of allSiPrefixes) {
const { longPrefix } = siPrefix;
if (longPrefix === undefined) continue;
OME_UNITS.set(`${longPrefix}${unit}`, {
unit: unit[0],
scale: 10 ** siPrefix.exponent,
});
}
}
interface Axis {
name: string;
unit: string;
scale: number;
type: string | undefined;
}
function parseOmeAxis(axis: unknown): Axis {
verifyObject(axis);
const name = verifyObjectProperty(axis, "name", verifyString);
const type = verifyOptionalObjectProperty(axis, "type", verifyString);
const parsedUnit = verifyOptionalObjectProperty(
axis,
"unit",
(unit) => {
const x = OME_UNITS.get(unit);
if (x === undefined) {
throw new Error(`Unsupported unit: ${JSON.stringify(unit)}`);
}
return x;
},
{ unit: "", scale: 1 },
);
return { name, unit: parsedUnit.unit, scale: parsedUnit.scale, type };
}
function parseOmeAxes(axes: unknown): CoordinateSpace {
const parsedAxes = parseArray(axes, parseOmeAxis);
return makeCoordinateSpace({
names: parsedAxes.map((axis) => {
const { name, type } = axis;
if (type === "channel") {
return `${name}'`;
}
return name;
}),
scales: Float64Array.from(parsedAxes, (axis) => axis.scale),
units: parsedAxes.map((axis) => axis.unit),
});
}
function parseScaleTransform(rank: number, obj: unknown) {
const scales = verifyObjectProperty(obj, "scale", (values) =>
parseFixedLengthArray(
new Float64Array(rank),
values,
verifyFinitePositiveFloat,
),
);
return matrix.createHomogeneousScaleMatrix(Float64Array, scales);
}
function parseIdentityTransform(rank: number, obj: unknown) {
obj;
return matrix.createIdentity(Float64Array, rank + 1);
}
function parseTranslationTransform(rank: number, obj: unknown) {
const translation = verifyObjectProperty(obj, "translation", (values) =>
parseFixedLengthArray(new Float64Array(rank), values, verifyFiniteFloat),
);
return matrix.createHomogeneousTranslationMatrix(Float64Array, translation);
}
const coordinateTransformParsers = new Map([
["scale", parseScaleTransform],
["identity", parseIdentityTransform],
["translation", parseTranslationTransform],
]);
function parseOmeCoordinateTransform(
rank: number,
transformJson: unknown,
): Float64Array {
verifyObject(transformJson);
const transformType = verifyObjectProperty(
transformJson,
"type",
verifyString,
);
const parser = coordinateTransformParsers.get(transformType);
if (parser === undefined) {
throw new Error(
`Unsupported coordinate transform type: ${JSON.stringify(transformType)}`,
);
}
return parser(rank, transformJson);
}
function parseOmeCoordinateTransforms(
rank: number,
transforms: unknown,
): Float64Array {
let transform = matrix.createIdentity(Float64Array, rank + 1);
if (transforms === undefined) return transform;
parseArray(transforms, (transformJson) => {
const newTransform = parseOmeCoordinateTransform(rank, transformJson);
transform = matrix.multiply(
new Float64Array(transform.length),
rank + 1,
newTransform,
rank + 1,
transform,
rank + 1,
rank + 1,
rank + 1,
rank + 1,
);
});
return transform;
}
function parseMultiscaleScale(
rank: number,
url: string,
obj: unknown,
): OmeMultiscaleScale {
const path = verifyObjectProperty(obj, "path", verifyString);
const transform = verifyObjectProperty(
obj,
"coordinateTransformations",
(x) => parseOmeCoordinateTransforms(rank, x),
);
const scaleUrl = `${url}/${path}`;
return { url: scaleUrl, transform };
}
function parseOmeMultiscale(
url: string,
multiscale: unknown,
): OmeMultiscaleMetadata {
const coordinateSpace = verifyObjectProperty(
multiscale,
"axes",
parseOmeAxes,
);
const rank = coordinateSpace.rank;
const transform = verifyObjectProperty(
multiscale,
"coordinateTransformations",
(x) => parseOmeCoordinateTransforms(rank, x),
);
const scales = verifyObjectProperty(multiscale, "datasets", (obj) =>
parseArray(obj, (x) => {
const scale = parseMultiscaleScale(rank, url, x);
scale.transform = matrix.multiply(
new Float64Array((rank + 1) ** 2),
rank + 1,
transform,
rank + 1,
scale.transform,
rank + 1,
rank + 1,
rank + 1,
rank + 1,
);
return scale;
}),
);
if (scales.length === 0) {
throw new Error("At least one scale must be specified");
}
const baseTransform = scales[0].transform;
// Extract the scale factor from `baseTransform`.
//
// TODO(jbms): If coordinate transformations other than `scale` and `translation` are supported,
// this will need to be modified.
const baseScales = new Float64Array(rank);
for (let i = 0; i < rank; ++i) {
const scale = (baseScales[i] = baseTransform[i * (rank + 1) + i]);
coordinateSpace.scales[i] *= scale;
}
for (const scale of scales) {
const t = scale.transform;
// In OME's coordinate space, the origin of a voxel is its center, while in Neuroglancer it is
// the "lower" (in coordinates) corner. Translate by the physical size of half a voxel in the
// current scale.
for (let i = 0; i < rank; ++i) {
let offset = 0;
for (let j = 0; j < rank; ++j) {
offset += t[j * (rank + 1) + i] * 0.5;
}
t[rank * (rank + 1) + i] -= offset;
}
// Make the scale relative to the base scale.
for (let i = 0; i < rank; ++i) {
for (let j = 0; j <= rank; ++j) {
t[j * (rank + 1) + i] /= baseScales[i];
}
}
}
return { coordinateSpace, scales };
}
export function parseOmeMetadata(
url: string,
attrs: any,
): OmeMultiscaleMetadata | undefined {
const multiscales = attrs.multiscales;
if (!Array.isArray(multiscales)) return undefined;
const errors: string[] = [];
for (const multiscale of multiscales) {
if (
typeof multiscale !== "object" ||
multiscale == null ||
Array.isArray(multiscale)
) {
// Not valid OME multiscale spec.
return undefined;
}
const version = multiscale.version;
if (version === undefined) return undefined;
if (!SUPPORTED_OME_MULTISCALE_VERSIONS.has(version)) {
errors.push(
`OME multiscale metadata version ${JSON.stringify(
version,
)} is not supported`,
);
continue;
}
return parseOmeMultiscale(url, multiscale);
}
if (errors.length !== 0) {
throw new Error(errors[0]);
}
return undefined;
}