ome.ts

/**
 * @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;
}