@loaders.gl/geotiff 3.3.0-alpha.5 → 3.3.0-alpha.6

package/dist/es5/lib/utils/tiff-utils.js

@@ -1,18 +1,15 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.SIGNAL_ABORTED = void 0;
 exports.ensureArray = ensureArray;
+exports.getImageSize = getImageSize;
 exports.intToRgba = intToRgba;
 exports.isInterleaved = isInterleaved;
-exports.getImageSize = getImageSize;
-exports.SIGNAL_ABORTED = void 0;
-
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
 function ensureArray(x) {
   return Array.isArray(x) ? x : [x];
 }
@@ -25,6 +22,7 @@ function intToRgba(int) {
   var buffer = new ArrayBuffer(4);
   var view = new DataView(buffer);
   view.setInt32(0, int, false);
+
   var bytes = new Uint8Array(buffer);
   return Array.from(bytes);
 }
@@ -33,21 +31,17 @@ function isInterleaved(shape) {
   var lastDimSize = shape[shape.length - 1];
   return lastDimSize === 3 || lastDimSize === 4;
 }
-
 function getImageSize(source) {
   var interleaved = isInterleaved(source.shape);
-
   var _source$shape$slice = source.shape.slice(interleaved ? -3 : -2),
-      _source$shape$slice2 = (0, _slicedToArray2.default)(_source$shape$slice, 2),
-      height = _source$shape$slice2[0],
-      width = _source$shape$slice2[1];
-
+    _source$shape$slice2 = (0, _slicedToArray2.default)(_source$shape$slice, 2),
+    height = _source$shape$slice2[0],
+    width = _source$shape$slice2[1];
   return {
     height: height,
     width: width
   };
 }
-
 var SIGNAL_ABORTED = '__vivSignalAborted';
 exports.SIGNAL_ABORTED = SIGNAL_ABORTED;
 //# sourceMappingURL=tiff-utils.js.map

package/dist/es5/lib/utils/tiff-utils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tiff-utils.js","names":["ensureArray","x","Array","isArray","intToRgba","int","Number","isInteger","Error","buffer","ArrayBuffer","view","DataView","setInt32","bytes","Uint8Array","from","isInterleaved","shape","lastDimSize","length","getImageSize","source","interleaved","slice","height","width","SIGNAL_ABORTED"],"sources":["../../../../src/lib/utils/tiff-utils.ts"],"sourcesContent":["import type {PixelSource} from '../../types';\n\nexport function ensureArray<T>(x: T | T[]) {\n  return Array.isArray(x) ? x : [x];\n}\n\n/*\n * Converts 32-bit integer color representation to RGBA tuple.\n * Used to serialize colors from OME-XML metadata.\n *\n * > console.log(intToRgba(100100));\n * > // [0, 1, 135, 4]\n */\nexport function intToRgba(int: number) {\n  if (!Number.isInteger(int)) {\n    throw Error('Not an integer.');\n  }\n\n  // Write number to int32 representation (4 bytes).\n  const buffer = new ArrayBuffer(4);\n  const view = new DataView(buffer);\n  view.setInt32(0, int, false); // offset === 0, littleEndian === false\n\n  // Take u8 view and extract number for each byte (1 byte for R/G/B/A).\n  const bytes = new Uint8Array(buffer);\n  return Array.from(bytes) as [number, number, number, number];\n}\n\n/*\n * Helper method to determine whether pixel data is interleaved or not.\n * > isInterleaved([1, 24, 24]) === false;\n * > isInterleaved([1, 24, 24, 3]) === true;\n */\nexport function isInterleaved(shape: number[]) {\n  const lastDimSize = shape[shape.length - 1];\n  return lastDimSize === 3 || lastDimSize === 4;\n}\n\nexport function getImageSize<T extends string[]>(source: PixelSource<T>) {\n  const interleaved = isInterleaved(source.shape);\n  const [height, width] = source.shape.slice(interleaved ? -3 : -2);\n  return {height, width};\n}\n\nexport const SIGNAL_ABORTED = '__vivSignalAborted';\n"],"mappings":";;;;;;;;;;;;AAEO,SAASA,WAAW,CAAIC,CAAU,EAAE;EACzC,OAAOC,KAAK,CAACC,OAAO,CAACF,CAAC,CAAC,GAAGA,CAAC,GAAG,CAACA,CAAC,CAAC;AACnC;;AASO,SAASG,SAAS,CAACC,GAAW,EAAE;EACrC,IAAI,CAACC,MAAM,CAACC,SAAS,CAACF,GAAG,CAAC,EAAE;IAC1B,MAAMG,KAAK,CAAC,iBAAiB,CAAC;EAChC;;EAGA,IAAMC,MAAM,GAAG,IAAIC,WAAW,CAAC,CAAC,CAAC;EACjC,IAAMC,IAAI,GAAG,IAAIC,QAAQ,CAACH,MAAM,CAAC;EACjCE,IAAI,CAACE,QAAQ,CAAC,CAAC,EAAER,GAAG,EAAE,KAAK,CAAC;;EAG5B,IAAMS,KAAK,GAAG,IAAIC,UAAU,CAACN,MAAM,CAAC;EACpC,OAAOP,KAAK,CAACc,IAAI,CAACF,KAAK,CAAC;AAC1B;;AAOO,SAASG,aAAa,CAACC,KAAe,EAAE;EAC7C,IAAMC,WAAW,GAAGD,KAAK,CAACA,KAAK,CAACE,MAAM,GAAG,CAAC,CAAC;EAC3C,OAAOD,WAAW,KAAK,CAAC,IAAIA,WAAW,KAAK,CAAC;AAC/C;AAEO,SAASE,YAAY,CAAqBC,MAAsB,EAAE;EACvE,IAAMC,WAAW,GAAGN,aAAa,CAACK,MAAM,CAACJ,KAAK,CAAC;EAC/C,0BAAwBI,MAAM,CAACJ,KAAK,CAACM,KAAK,CAACD,WAAW,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IAAA;IAA1DE,MAAM;IAAEC,KAAK;EACpB,OAAO;IAACD,MAAM,EAANA,MAAM;IAAEC,KAAK,EAALA;EAAK,CAAC;AACxB;AAEO,IAAMC,cAAc,GAAG,oBAAoB;AAAC"}

package/dist/es5/types.js.map

@@ -1 +1 @@
-{"version":3,"sources":[],"names":[],"mappings":"","sourcesContent":[],"file":"types.js"}
+{"version":3,"file":"types.js","names":[],"sources":["../../src/types.ts"],"sourcesContent":["import {DTYPE_LOOKUP} from './lib/ome/ome-utils';\n\nexport type Dtype = typeof DTYPE_LOOKUP[keyof typeof DTYPE_LOOKUP];\nexport type TypedArray = InstanceType<typeof globalThis[`${Dtype}Array`]>;\n\nexport interface PixelData {\n  data: TypedArray;\n  width: number;\n  height: number;\n}\n\nexport type PixelSourceSelection<S extends string[]> = {\n  [K in S[number]]: number;\n};\n\nexport interface RasterSelection<S extends string[]> {\n  selection: PixelSourceSelection<S>;\n  signal?: AbortSignal;\n}\n\nexport interface TileSelection<S extends string[]> {\n  x: number;\n  y: number;\n  selection: PixelSourceSelection<S>;\n  signal?: AbortSignal;\n}\n\ninterface PhysicalSize {\n  size: number;\n  unit: string;\n}\n\nexport interface PixelSourceMeta {\n  physicalSizes?: Record<string, PhysicalSize>;\n  photometricInterpretation?: number;\n}\n\nexport type Labels<S extends string[]> = [...S, 'y', 'x'] | [...S, 'y', 'x', '_c'];\n\n/**\n * Interface to load tiles from a data source\n */\nexport interface PixelSource<S extends string[]> {\n  /** Loads a 2D plane */\n  getRaster(sel: RasterSelection<S>): Promise<PixelData>;\n  /** Loads a tile */\n  getTile(sel: TileSelection<S>): Promise<PixelData>;\n  onTileError(err: Error): void;\n  shape: number[];\n  dtype: Dtype;\n  labels: Labels<S>;\n  tileSize: number;\n  meta?: PixelSourceMeta;\n}\n"],"mappings":""}

package/dist/es5/typings/geotiff.js.map

@@ -1 +1 @@
-{"version":3,"sources":[],"names":[],"mappings":"","sourcesContent":[],"file":"geotiff.js"}
+{"version":3,"file":"geotiff.js","names":[],"sources":["../../../src/typings/geotiff.ts"],"sourcesContent":["declare type TypedArray = import('../types').TypedArray;\n\ndeclare module 'geotiff' {\n  function fromUrl(url: string, headers?: Record<string, unknown>): Promise<GeoTIFF>;\n  function fromBlob(blob: Blob): Promise<GeoTIFF>;\n  function fromFile(path: string): Promise<GeoTIFF>;\n\n  class GeoTIFF {\n    readRasters(options?: RasterOptions): Promise<TypedArray>;\n    getImage(index: number): Promise<GeoTIFFImage>;\n    parseFileDirectoryAt(offset: number): Promise<ImageFileDirectory>;\n    ifdRequests: {[key: number]: Promise<ImageFileDirectory>};\n    dataView: DataView;\n    littleEndian: boolean;\n    cache: any;\n    source: any;\n  }\n\n  interface Pool {\n    decode(fileDirectory: FileDirectory, buffer: ArrayBuffer): Promise<ArrayBuffer>;\n  }\n\n  interface RasterOptions {\n    window?: number[];\n    bbox?: number[];\n    samples?: number[];\n    interleave?: boolean;\n    pool?: Pool;\n    width?: number;\n    height?: number;\n    resampleMethod?: string;\n    enableAlpha?: boolean;\n    signal?: AbortSignal;\n  }\n\n  type RasterData = (TypedArray | TypedArray[]) & {\n    width: number;\n    height: number;\n  };\n  class GeoTIFFImage {\n    constructor(\n      fileDirectory: FileDirectory,\n      geoKeyDirectory: any,\n      dataView: DataView,\n      littleEndian: boolean,\n      cache: any,\n      source: any\n    );\n    fileDirectory: FileDirectory;\n    getBoundingBox(): number[];\n    getFileDirectory(): FileDirectory;\n    getBytesPerPixel(): number;\n    getHeight(): number;\n    getSamplesPerPixel(): number;\n    getTileHeight(): number;\n    getTileWidth(): number;\n    getWidth(): number;\n    readRasters(options?: RasterOptions): Promise<RasterData>;\n  }\n\n  interface FileDirectory {\n    ImageDescription: string;\n    SubIFDs?: number[];\n    PhotometricInterpretation?: number;\n  }\n\n  interface ImageFileDirectory {\n    fileDirectory: FileDirectory;\n    geoKeyDirectory: any;\n  }\n}\n"],"mappings":""}

package/dist/esm/bundle.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/bundle.ts"],"names":["moduleExports","globalThis","loaders","module","exports","Object","assign"],"mappings":"AAAA,OAAO,KAAKA,aAAZ,MAA+B,SAA/B;AAEAC,UAAU,CAACC,OAAX,GAAqBD,UAAU,CAACC,OAAX,IAAsB,EAA3C;AAEAC,MAAM,CAACC,OAAP,GAAiBC,MAAM,CAACC,MAAP,CAAcL,UAAU,CAACC,OAAzB,EAAkCF,aAAlC,CAAjB","sourcesContent":["import * as moduleExports from './index';\n// @ts-ignore\nglobalThis.loaders = globalThis.loaders || {};\n// @ts-ignore\nmodule.exports = Object.assign(globalThis.loaders, moduleExports);\n"],"file":"bundle.js"}
+{"version":3,"file":"bundle.js","names":["moduleExports","globalThis","loaders","module","exports","Object","assign"],"sources":["../../src/bundle.ts"],"sourcesContent":["import * as moduleExports from './index';\n// @ts-ignore\nglobalThis.loaders = globalThis.loaders || {};\n// @ts-ignore\nmodule.exports = Object.assign(globalThis.loaders, moduleExports);\n"],"mappings":"AAAA,OAAO,KAAKA,aAAa,MAAM,SAAS;AAExCC,UAAU,CAACC,OAAO,GAAGD,UAAU,CAACC,OAAO,IAAI,CAAC,CAAC;AAE7CC,MAAM,CAACC,OAAO,GAAGC,MAAM,CAACC,MAAM,CAACL,UAAU,CAACC,OAAO,EAAEF,aAAa,CAAC"}

package/dist/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/index.ts"],"names":["loadGeoTiff","default","TiffPixelSource"],"mappings":"AAAA,SAAQA,WAAR,QAA0B,oBAA1B;AACA,SAAQC,OAAO,IAAIC,eAAnB,QAAyC,yBAAzC","sourcesContent":["export {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"file":"index.js"}
+{"version":3,"file":"index.js","names":["loadGeoTiff","default","TiffPixelSource"],"sources":["../../src/index.ts"],"sourcesContent":["export {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"mappings":"AAAA,SAAQA,WAAW,QAAO,oBAAoB;AAC9C,SAAQC,OAAO,IAAIC,eAAe,QAAO,yBAAyB"}

package/dist/esm/lib/load-geotiff.js

@@ -1,13 +1,16 @@
 import { fromUrl, fromBlob, GeoTIFF } from 'geotiff';
-import { createOffsetsProxy, checkProxies } from './utils/proxies';
+import {
+createOffsetsProxy, checkProxies } from './utils/proxies';
+
 import { loadOmeTiff, isOmeTiff } from './ome/load-ome-tiff';
-export async function loadGeoTiff(source, opts = {}) {
+export async function loadGeoTiff(source) {
+  let opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
   const {
     headers,
     offsets
   } = opts;
-  let tiff;
 
+  let tiff;
   if (source instanceof GeoTIFF) {
     tiff = source;
   } else if (typeof source === 'string') {
@@ -22,11 +25,9 @@ export async function loadGeoTiff(source, opts = {}) {
 
   checkProxies(tiff);
   const firstImage = await tiff.getImage(0);
-
   if (isOmeTiff(firstImage)) {
     return loadOmeTiff(tiff, firstImage);
   }
-
   throw new Error('GeoTIFF not recognized.');
 }
 //# sourceMappingURL=load-geotiff.js.map

package/dist/esm/lib/load-geotiff.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../src/lib/load-geotiff.ts"],"names":["fromUrl","fromBlob","GeoTIFF","createOffsetsProxy","checkProxies","loadOmeTiff","isOmeTiff","loadGeoTiff","source","opts","headers","offsets","tiff","firstImage","getImage","Error"],"mappings":"AAAA,SAAQA,OAAR,EAAiBC,QAAjB,EAA2BC,OAA3B,QAAyC,SAAzC;AAEA,SAEEC,kBAFF,EAGEC,YAHF,QAIO,iBAJP;AAOA,SAAQC,WAAR,EAAqBC,SAArB,QAAqC,qBAArC;AA4BA,OAAO,eAAeC,WAAf,CACLC,MADK,EAELC,IAAoB,GAAG,EAFlB,EAGiB;AACtB,QAAM;AAACC,IAAAA,OAAD;AAAUC,IAAAA;AAAV,MAAqBF,IAA3B;AAGA,MAAIG,IAAJ;;AACA,MAAIJ,MAAM,YAAYN,OAAtB,EAA+B;AAC7BU,IAAAA,IAAI,GAAGJ,MAAP;AACD,GAFD,MAEO,IAAI,OAAOA,MAAP,KAAkB,QAAtB,EAAgC;AACrCI,IAAAA,IAAI,GAAG,MAAMZ,OAAO,CAACQ,MAAD,EAASE,OAAT,CAApB;AACD,GAFM,MAEA;AACLE,IAAAA,IAAI,GAAG,MAAMX,QAAQ,CAACO,MAAD,CAArB;AACD;;AAUD,MAAIG,OAAJ,EAAa;AAMXC,IAAAA,IAAI,GAAGT,kBAAkB,CAACS,IAAD,EAAOD,OAAP,CAAzB;AACD;;AAMDP,EAAAA,YAAY,CAACQ,IAAD,CAAZ;AAEA,QAAMC,UAAU,GAAG,MAAMD,IAAI,CAACE,QAAL,CAAc,CAAd,CAAzB;;AAEA,MAAIR,SAAS,CAACO,UAAD,CAAb,EAA2B;AACzB,WAAOR,WAAW,CAACO,IAAD,EAAOC,UAAP,CAAlB;AACD;;AAED,QAAM,IAAIE,KAAJ,CAAU,yBAAV,CAAN;AACD","sourcesContent":["import {fromUrl, fromBlob, GeoTIFF} from 'geotiff';\n\nimport {\n  // createPoolProxy,\n  createOffsetsProxy,\n  checkProxies\n} from './utils/proxies';\n// import Pool from './lib/Pool';\n\nimport {loadOmeTiff, isOmeTiff} from './ome/load-ome-tiff';\nimport type TiffPixelSource from './tiff-pixel-source';\n\n/** Options for initializing a tiff pixel source. */\ninterface GeoTIFFOptions {\n  /** Headers passed to each underlying request. */\n  headers?: Record<string, unknown>;\n  /** Performance enhancment to index the remote tiff source using pre-computed byte-offsets. Generated via https://github.com/ilan-gold/generate-tiff-offsets */\n  offsets?: number[];\n  /** Indicates whether a multi-threaded pool of image decoders should be used to decode tiles. */\n  pool?: boolean;\n}\n\ninterface GeoTIFFData {\n  data: TiffPixelSource<string[]>[];\n  metadata: Record<string, unknown>;\n}\n\n/**\n * Opens an OME-TIFF via URL and returns data source and associated metadata for first image.\n *\n * @param source url string, File/Blob object, or GeoTIFF object\n * @param opts options for initializing a tiff pixel source.\n *  - `opts.headers` are passed to each underlying fetch request.\n *  - `opts.offsets` are a performance enhancment to index the remote tiff source using pre-computed byte-offsets.\n *  - `opts.pool` indicates whether a multi-threaded pool of image decoders should be used to decode tiles (default = true).\n * @return data source and associated OME-Zarr metadata.\n */\nexport async function loadGeoTiff(\n  source: string | Blob | GeoTIFF,\n  opts: GeoTIFFOptions = {}\n): Promise<GeoTIFFData> {\n  const {headers, offsets} = opts;\n\n  // Create tiff source\n  let tiff: GeoTIFF;\n  if (source instanceof GeoTIFF) {\n    tiff = source;\n  } else if (typeof source === 'string') {\n    tiff = await fromUrl(source, headers);\n  } else {\n    tiff = await fromBlob(source);\n  }\n\n  // if (pool) {\n  /*\n   * Creates a worker pool to decode tiff tiles. Wraps tiff\n   * in a Proxy that injects 'pool' into `tiff.readRasters`.\n   */\n  // tiff = createPoolProxy(tiff, new Pool());\n  // }\n\n  if (offsets) {\n    /*\n     * Performance enhancement. If offsets are provided, we\n     * create a proxy that intercepts calls to `tiff.getImage`\n     * and injects the pre-computed offsets.\n     */\n    tiff = createOffsetsProxy(tiff, offsets);\n  }\n\n  /*\n   * Inspect tiff source for our performance enhancing proxies.\n   * Prints warnings to console if `offsets` or `pool` are missing.\n   */\n  checkProxies(tiff);\n\n  const firstImage = await tiff.getImage(0);\n\n  if (isOmeTiff(firstImage)) {\n    return loadOmeTiff(tiff, firstImage);\n  }\n\n  throw new Error('GeoTIFF not recognized.');\n}\n"],"file":"load-geotiff.js"}
+{"version":3,"file":"load-geotiff.js","names":["fromUrl","fromBlob","GeoTIFF","createOffsetsProxy","checkProxies","loadOmeTiff","isOmeTiff","loadGeoTiff","source","opts","headers","offsets","tiff","firstImage","getImage","Error"],"sources":["../../../src/lib/load-geotiff.ts"],"sourcesContent":["import {fromUrl, fromBlob, GeoTIFF} from 'geotiff';\n\nimport {\n  // createPoolProxy,\n  createOffsetsProxy,\n  checkProxies\n} from './utils/proxies';\n// import Pool from './lib/Pool';\n\nimport {loadOmeTiff, isOmeTiff} from './ome/load-ome-tiff';\nimport type TiffPixelSource from './tiff-pixel-source';\n\n/** Options for initializing a tiff pixel source. */\ninterface GeoTIFFOptions {\n  /** Headers passed to each underlying request. */\n  headers?: Record<string, unknown>;\n  /** Performance enhancment to index the remote tiff source using pre-computed byte-offsets. Generated via https://github.com/ilan-gold/generate-tiff-offsets */\n  offsets?: number[];\n  /** Indicates whether a multi-threaded pool of image decoders should be used to decode tiles. */\n  pool?: boolean;\n}\n\ninterface GeoTIFFData {\n  data: TiffPixelSource<string[]>[];\n  metadata: Record<string, unknown>;\n}\n\n/**\n * Opens an OME-TIFF via URL and returns data source and associated metadata for first image.\n *\n * @param source url string, File/Blob object, or GeoTIFF object\n * @param opts options for initializing a tiff pixel source.\n *  - `opts.headers` are passed to each underlying fetch request.\n *  - `opts.offsets` are a performance enhancment to index the remote tiff source using pre-computed byte-offsets.\n *  - `opts.pool` indicates whether a multi-threaded pool of image decoders should be used to decode tiles (default = true).\n * @return data source and associated OME-Zarr metadata.\n */\nexport async function loadGeoTiff(\n  source: string | Blob | GeoTIFF,\n  opts: GeoTIFFOptions = {}\n): Promise<GeoTIFFData> {\n  const {headers, offsets} = opts;\n\n  // Create tiff source\n  let tiff: GeoTIFF;\n  if (source instanceof GeoTIFF) {\n    tiff = source;\n  } else if (typeof source === 'string') {\n    tiff = await fromUrl(source, headers);\n  } else {\n    tiff = await fromBlob(source);\n  }\n\n  // if (pool) {\n  /*\n   * Creates a worker pool to decode tiff tiles. Wraps tiff\n   * in a Proxy that injects 'pool' into `tiff.readRasters`.\n   */\n  // tiff = createPoolProxy(tiff, new Pool());\n  // }\n\n  if (offsets) {\n    /*\n     * Performance enhancement. If offsets are provided, we\n     * create a proxy that intercepts calls to `tiff.getImage`\n     * and injects the pre-computed offsets.\n     */\n    tiff = createOffsetsProxy(tiff, offsets);\n  }\n\n  /*\n   * Inspect tiff source for our performance enhancing proxies.\n   * Prints warnings to console if `offsets` or `pool` are missing.\n   */\n  checkProxies(tiff);\n\n  const firstImage = await tiff.getImage(0);\n\n  if (isOmeTiff(firstImage)) {\n    return loadOmeTiff(tiff, firstImage);\n  }\n\n  throw new Error('GeoTIFF not recognized.');\n}\n"],"mappings":"AAAA,SAAQA,OAAO,EAAEC,QAAQ,EAAEC,OAAO,QAAO,SAAS;AAElD;AAEEC,kBAAkB,EAClBC,YAAY,QACP,iBAAiB;;AAGxB,SAAQC,WAAW,EAAEC,SAAS,QAAO,qBAAqB;AA4B1D,OAAO,eAAeC,WAAW,CAC/BC,MAA+B,EAET;EAAA,IADtBC,IAAoB,uEAAG,CAAC,CAAC;EAEzB,MAAM;IAACC,OAAO;IAAEC;EAAO,CAAC,GAAGF,IAAI;;EAG/B,IAAIG,IAAa;EACjB,IAAIJ,MAAM,YAAYN,OAAO,EAAE;IAC7BU,IAAI,GAAGJ,MAAM;EACf,CAAC,MAAM,IAAI,OAAOA,MAAM,KAAK,QAAQ,EAAE;IACrCI,IAAI,GAAG,MAAMZ,OAAO,CAACQ,MAAM,EAAEE,OAAO,CAAC;EACvC,CAAC,MAAM;IACLE,IAAI,GAAG,MAAMX,QAAQ,CAACO,MAAM,CAAC;EAC/B;;EAUA,IAAIG,OAAO,EAAE;IAMXC,IAAI,GAAGT,kBAAkB,CAACS,IAAI,EAAED,OAAO,CAAC;EAC1C;;EAMAP,YAAY,CAACQ,IAAI,CAAC;EAElB,MAAMC,UAAU,GAAG,MAAMD,IAAI,CAACE,QAAQ,CAAC,CAAC,CAAC;EAEzC,IAAIR,SAAS,CAACO,UAAU,CAAC,EAAE;IACzB,OAAOR,WAAW,CAACO,IAAI,EAAEC,UAAU,CAAC;EACtC;EAEA,MAAM,IAAIE,KAAK,CAAC,yBAAyB,CAAC;AAC5C"}

package/dist/esm/lib/ome/load-ome-tiff.js

@@ -10,9 +10,9 @@ export async function loadOmeTiff(tiff, firstImage) {
     PhotometricInterpretation: photometricInterpretation
   } = firstImage.fileDirectory;
   const omexml = fromString(ImageDescription);
+
   let levels;
   let pyramidIndexer;
-
   if (SubIFDs) {
     levels = SubIFDs.length + 1;
     pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);
@@ -37,9 +37,7 @@ export async function loadOmeTiff(tiff, firstImage) {
     length: levels
   }).map((_, resolution) => {
     const shape = getShape(resolution);
-
     const indexer = sel => pyramidIndexer(sel, resolution);
-
     const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);
     return source;
   });

package/dist/esm/lib/ome/load-ome-tiff.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"names":["TiffPixelSource","getOmeLegacyIndexer","getOmeSubIFDIndexer","getOmePixelSourceMeta","fromString","isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","PhotometricInterpretation","photometricInterpretation","omexml","levels","pyramidIndexer","length","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","metadata"],"mappings":"AAEA,OAAOA,eAAP,MAA4B,sBAA5B;AACA,SAAQC,mBAAR,EAA6BC,mBAA7B,QAAuE,gBAAvE;AACA,SAAQC,qBAAR,QAAoC,aAApC;AACA,SAAQC,UAAR,QAAyB,UAAzB;AAGA,OAAO,MAAMC,SAAS,GAAIC,GAAD,IAAuBA,GAAG,CAACC,aAAJ,CAAkBC,gBAAlB,CAAmCC,QAAnC,CAA4C,MAA5C,CAAzC;AAEP,OAAO,eAAeC,WAAf,CAA2BC,IAA3B,EAA0CC,UAA1C,EAAoE;AAEzE,QAAM;AACJJ,IAAAA,gBADI;AAEJK,IAAAA,OAFI;AAGJC,IAAAA,yBAAyB,EAAEC;AAHvB,MAIFH,UAAU,CAACL,aAJf;AAKA,QAAMS,MAAM,GAAGZ,UAAU,CAACI,gBAAD,CAAzB;AAMA,MAAIS,MAAJ;AACA,MAAIC,cAAJ;;AAEA,MAAIL,OAAJ,EAAa;AAEXI,IAAAA,MAAM,GAAGJ,OAAO,CAACM,MAAR,GAAiB,CAA1B;AACAD,IAAAA,cAAc,GAAGhB,mBAAmB,CAACS,IAAD,EAAOK,MAAP,CAApC;AACD,GAJD,MAIO;AAELC,IAAAA,MAAM,GAAGD,MAAM,CAACG,MAAhB;AACAD,IAAAA,cAAc,GAAGjB,mBAAmB,CAACU,IAAD,EAAOK,MAAP,CAApC;AACD;;AAGD,QAAMI,OAAO,GAAGJ,MAAM,CAAC,CAAD,CAAtB;AACA,QAAM;AAACK,IAAAA,MAAD;AAASC,IAAAA,QAAT;AAAmBC,IAAAA,aAAnB;AAAkCC,IAAAA;AAAlC,MAA2CrB,qBAAqB,CAACiB,OAAD,CAAtE;AACA,QAAMK,QAAQ,GAAGb,UAAU,CAACc,YAAX,EAAjB;AACA,QAAMC,IAAI,GAAG;AAACZ,IAAAA,yBAAD;AAA4BQ,IAAAA;AAA5B,GAAb;AAEA,QAAMK,IAAI,GAAGC,KAAK,CAACC,IAAN,CAAW;AAACX,IAAAA,MAAM,EAAEF;AAAT,GAAX,EAA6Bc,GAA7B,CAAiC,CAACC,CAAD,EAAIC,UAAJ,KAAmB;AAC/D,UAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAD,CAAtB;;AACA,UAAME,OAAO,GAAIC,GAAD,IAA2BlB,cAAc,CAACkB,GAAD,EAAMH,UAAN,CAAzD;;AACA,UAAMI,MAAM,GAAG,IAAIrC,eAAJ,CAAoBmC,OAApB,EAA6BX,KAA7B,EAAoCC,QAApC,EAA8CS,KAA9C,EAAqDb,MAArD,EAA6DM,IAA7D,CAAf;AACA,WAAOU,MAAP;AACD,GALY,CAAb;AAOA,SAAO;AAACT,IAAAA,IAAD;AAAOU,IAAAA,QAAQ,EAAElB;AAAjB,GAAP;AACD","sourcesContent":["import type {GeoTIFF, GeoTIFFImage} from 'geotiff';\n\nimport TiffPixelSource from '../tiff-pixel-source';\nimport {getOmeLegacyIndexer, getOmeSubIFDIndexer, OmeTiffIndexer} from './ome-indexers';\nimport {getOmePixelSourceMeta} from './ome-utils';\nimport {fromString} from './omexml';\nimport type {OmeTiffSelection} from './ome-indexers';\n\nexport const isOmeTiff = (img: GeoTIFFImage) => img.fileDirectory.ImageDescription.includes('<OME');\n\nexport async function loadOmeTiff(tiff: GeoTIFF, firstImage: GeoTIFFImage) {\n  // Get first image from tiff and inspect OME-XML metadata\n  const {\n    ImageDescription,\n    SubIFDs,\n    PhotometricInterpretation: photometricInterpretation\n  } = firstImage.fileDirectory;\n  const omexml = fromString(ImageDescription);\n\n  /*\n   * Image pyramids are stored differently between versions of Bioformats.\n   * Thus we need a different indexer depending on which format we have.\n   */\n  let levels: number;\n  let pyramidIndexer: OmeTiffIndexer;\n\n  if (SubIFDs) {\n    // Image is >= Bioformats 6.0 and resolutions are stored using SubIFDs.\n    levels = SubIFDs.length + 1;\n    pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);\n  } else {\n    // Image is legacy format; resolutions are stored as separate images.\n    levels = omexml.length;\n    pyramidIndexer = getOmeLegacyIndexer(tiff, omexml);\n  }\n\n  // TODO: The OmeTIFF loader only works for the _first_ image in the metadata.\n  const imgMeta = omexml[0];\n  const {labels, getShape, physicalSizes, dtype} = getOmePixelSourceMeta(imgMeta);\n  const tileSize = firstImage.getTileWidth();\n  const meta = {photometricInterpretation, physicalSizes};\n\n  const data = Array.from({length: levels}).map((_, resolution) => {\n    const shape = getShape(resolution);\n    const indexer = (sel: OmeTiffSelection) => pyramidIndexer(sel, resolution);\n    const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);\n    return source;\n  });\n\n  return {data, metadata: imgMeta};\n}\n"],"file":"load-ome-tiff.js"}
+{"version":3,"file":"load-ome-tiff.js","names":["TiffPixelSource","getOmeLegacyIndexer","getOmeSubIFDIndexer","getOmePixelSourceMeta","fromString","isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","PhotometricInterpretation","photometricInterpretation","omexml","levels","pyramidIndexer","length","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","metadata"],"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"sourcesContent":["import type {GeoTIFF, GeoTIFFImage} from 'geotiff';\n\nimport TiffPixelSource from '../tiff-pixel-source';\nimport {getOmeLegacyIndexer, getOmeSubIFDIndexer, OmeTiffIndexer} from './ome-indexers';\nimport {getOmePixelSourceMeta} from './ome-utils';\nimport {fromString} from './omexml';\nimport type {OmeTiffSelection} from './ome-indexers';\n\nexport const isOmeTiff = (img: GeoTIFFImage) => img.fileDirectory.ImageDescription.includes('<OME');\n\nexport async function loadOmeTiff(tiff: GeoTIFF, firstImage: GeoTIFFImage) {\n  // Get first image from tiff and inspect OME-XML metadata\n  const {\n    ImageDescription,\n    SubIFDs,\n    PhotometricInterpretation: photometricInterpretation\n  } = firstImage.fileDirectory;\n  const omexml = fromString(ImageDescription);\n\n  /*\n   * Image pyramids are stored differently between versions of Bioformats.\n   * Thus we need a different indexer depending on which format we have.\n   */\n  let levels: number;\n  let pyramidIndexer: OmeTiffIndexer;\n\n  if (SubIFDs) {\n    // Image is >= Bioformats 6.0 and resolutions are stored using SubIFDs.\n    levels = SubIFDs.length + 1;\n    pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);\n  } else {\n    // Image is legacy format; resolutions are stored as separate images.\n    levels = omexml.length;\n    pyramidIndexer = getOmeLegacyIndexer(tiff, omexml);\n  }\n\n  // TODO: The OmeTIFF loader only works for the _first_ image in the metadata.\n  const imgMeta = omexml[0];\n  const {labels, getShape, physicalSizes, dtype} = getOmePixelSourceMeta(imgMeta);\n  const tileSize = firstImage.getTileWidth();\n  const meta = {photometricInterpretation, physicalSizes};\n\n  const data = Array.from({length: levels}).map((_, resolution) => {\n    const shape = getShape(resolution);\n    const indexer = (sel: OmeTiffSelection) => pyramidIndexer(sel, resolution);\n    const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);\n    return source;\n  });\n\n  return {data, metadata: imgMeta};\n}\n"],"mappings":"AAEA,OAAOA,eAAe,MAAM,sBAAsB;AAClD,SAAQC,mBAAmB,EAAEC,mBAAmB,QAAuB,gBAAgB;AACvF,SAAQC,qBAAqB,QAAO,aAAa;AACjD,SAAQC,UAAU,QAAO,UAAU;AAGnC,OAAO,MAAMC,SAAS,GAAIC,GAAiB,IAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAEnG,OAAO,eAAeC,WAAW,CAACC,IAAa,EAAEC,UAAwB,EAAE;EAEzE,MAAM;IACJJ,gBAAgB;IAChBK,OAAO;IACPC,yBAAyB,EAAEC;EAC7B,CAAC,GAAGH,UAAU,CAACL,aAAa;EAC5B,MAAMS,MAAM,GAAGZ,UAAU,CAACI,gBAAgB,CAAC;;EAM3C,IAAIS,MAAc;EAClB,IAAIC,cAA8B;EAElC,IAAIL,OAAO,EAAE;IAEXI,MAAM,GAAGJ,OAAO,CAACM,MAAM,GAAG,CAAC;IAC3BD,cAAc,GAAGhB,mBAAmB,CAACS,IAAI,EAAEK,MAAM,CAAC;EACpD,CAAC,MAAM;IAELC,MAAM,GAAGD,MAAM,CAACG,MAAM;IACtBD,cAAc,GAAGjB,mBAAmB,CAACU,IAAI,EAAEK,MAAM,CAAC;EACpD;;EAGA,MAAMI,OAAO,GAAGJ,MAAM,CAAC,CAAC,CAAC;EACzB,MAAM;IAACK,MAAM;IAAEC,QAAQ;IAAEC,aAAa;IAAEC;EAAK,CAAC,GAAGrB,qBAAqB,CAACiB,OAAO,CAAC;EAC/E,MAAMK,QAAQ,GAAGb,UAAU,CAACc,YAAY,EAAE;EAC1C,MAAMC,IAAI,GAAG;IAACZ,yBAAyB;IAAEQ;EAAa,CAAC;EAEvD,MAAMK,IAAI,GAAGC,KAAK,CAACC,IAAI,CAAC;IAACX,MAAM,EAAEF;EAAM,CAAC,CAAC,CAACc,GAAG,CAAC,CAACC,CAAC,EAAEC,UAAU,KAAK;IAC/D,MAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAU,CAAC;IAClC,MAAME,OAAO,GAAIC,GAAqB,IAAKlB,cAAc,CAACkB,GAAG,EAAEH,UAAU,CAAC;IAC1E,MAAMI,MAAM,GAAG,IAAIrC,eAAe,CAACmC,OAAO,EAAEX,KAAK,EAAEC,QAAQ,EAAES,KAAK,EAAEb,MAAM,EAAEM,IAAI,CAAC;IACjF,OAAOU,MAAM;EACf,CAAC,CAAC;EAEF,OAAO;IAACT,IAAI;IAAEU,QAAQ,EAAElB;EAAO,CAAC;AAClC"}

package/dist/esm/lib/ome/ome-indexers.js

@@ -1,3 +1,5 @@
+
+
 export function getOmeLegacyIndexer(tiff, rootMeta) {
   const imgMeta = rootMeta[0];
   const {
@@ -12,6 +14,7 @@ export function getOmeLegacyIndexer(tiff, rootMeta) {
     return tiff.getImage(index + pyramidIndex);
   };
 }
+
 export function getOmeSubIFDIndexer(tiff, rootMeta) {
   const imgMeta = rootMeta[0];
   const ifdIndexer = getOmeIFDIndexer(imgMeta);
@@ -23,23 +26,20 @@ export function getOmeSubIFDIndexer(tiff, rootMeta) {
     if (pyramidLevel === 0) {
       return baseImage;
     }
-
     const {
       SubIFDs
     } = baseImage.fileDirectory;
-
     if (!SubIFDs) {
       throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
     }
 
     const key = "".concat(sel.t, "-").concat(sel.c, "-").concat(sel.z, "-").concat(pyramidLevel);
-
     if (!ifdCache.has(key)) {
       const subIfdOffset = SubIFDs[pyramidLevel - 1];
       ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
     }
-
     const ifd = await ifdCache.get(key);
+
     return new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source);
   };
 }
@@ -51,62 +51,73 @@ function getOmeIFDIndexer(imgMeta) {
     SizeT,
     DimensionOrder
   } = imgMeta.Pixels;
-
   switch (DimensionOrder) {
     case 'XYZCT':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => t * SizeZ * SizeC + c * SizeZ + z;
+        return _ref => {
+          let {
+            t,
+            c,
+            z
+          } = _ref;
+          return t * SizeZ * SizeC + c * SizeZ + z;
+        };
       }
-
     case 'XYZTC':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => c * SizeZ * SizeT + t * SizeZ + z;
+        return _ref2 => {
+          let {
+            t,
+            c,
+            z
+          } = _ref2;
+          return c * SizeZ * SizeT + t * SizeZ + z;
+        };
       }
-
     case 'XYCTZ':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => z * SizeC * SizeT + t * SizeC + c;
+        return _ref3 => {
+          let {
+            t,
+            c,
+            z
+          } = _ref3;
+          return z * SizeC * SizeT + t * SizeC + c;
+        };
       }
-
     case 'XYCZT':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => t * SizeC * SizeZ + z * SizeC + c;
+        return _ref4 => {
+          let {
+            t,
+            c,
+            z
+          } = _ref4;
+          return t * SizeC * SizeZ + z * SizeC + c;
+        };
       }
-
     case 'XYTCZ':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => z * SizeT * SizeC + c * SizeT + t;
+        return _ref5 => {
+          let {
+            t,
+            c,
+            z
+          } = _ref5;
+          return z * SizeT * SizeC + c * SizeT + t;
+        };
       }
-
     case 'XYTZC':
       {
-        return ({
-          t,
-          c,
-          z
-        }) => c * SizeT * SizeZ + z * SizeT + t;
+        return _ref6 => {
+          let {
+            t,
+            c,
+            z
+          } = _ref6;
+          return c * SizeT * SizeZ + z * SizeT + t;
+        };
       }
-
     default:
       {
         throw new Error("Invalid OME-XML DimensionOrder, got ".concat(DimensionOrder, "."));

package/dist/esm/lib/ome/ome-indexers.js.map

@@ -1 +1 @@
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However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n  return (sel: OmeTiffSelection, pyramidLevel: number) => {\n    // Get IFD index at base pyramid level\n    const index = ifdIndexer(sel);\n    // Get index of first image at pyramidal level\n    const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n    // Return image at IFD index for pyramidal level\n    return tiff.getImage(index + pyramidIndex);\n  };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n  const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n  return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n    const index = ifdIndexer(sel);\n    const baseImage = await tiff.getImage(index);\n\n    // It's the highest resolution, no need to look up SubIFDs.\n    if (pyramidLevel === 0) {\n      return baseImage;\n    }\n\n    const {SubIFDs} = baseImage.fileDirectory;\n    if (!SubIFDs) {\n      throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n    }\n\n    // Get IFD for the selection at the pyramidal level\n    const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n    if (!ifdCache.has(key)) {\n      // Only create a new request if we don't have the key.\n      const subIfdOffset = SubIFDs[pyramidLevel - 1];\n      ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n    }\n    const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n    // Create a new image object manually from IFD\n    // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n    return new (baseImage.constructor as any)(\n      ifd.fileDirectory,\n      ifd.geoKeyDirectory,\n      tiff.dataView,\n      tiff.littleEndian,\n      tiff.cache,\n      tiff.source\n    ) as GeoTIFFImage;\n  };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n  const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n  switch (DimensionOrder) {\n    case 'XYZCT': {\n      return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n    }\n    case 'XYZTC': {\n      return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n    }\n    case 'XYCTZ': {\n      return ({t, c, z}) => z * SizeC * SizeT + t * SizeC + c;\n    }\n    case 'XYCZT': {\n      return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n    }\n    case 'XYTCZ': {\n      return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n    }\n    case 'XYTZC': {\n      return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n    }\n    default: {\n      throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n    }\n  }\n}\n"],"file":"ome-indexers.js"}
+{"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","SizeT","SizeC","SizeZ","Pixels","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","ifd","get","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","DimensionOrder"],"sources":["../../../../src/lib/ome/ome-indexers.ts"],"sourcesContent":["import type {GeoTIFFImage, GeoTIFF, ImageFileDirectory} from 'geotiff';\nimport type {OMEXML} from '../ome/omexml';\n\nexport type OmeTiffSelection = {t: number; c: number; z: number};\nexport type OmeTiffIndexer = (sel: OmeTiffSelection, z: number) => Promise<GeoTIFFImage>;\n\n/*\n * An \"indexer\" for a GeoTIFF-based source is a function that takes a\n * \"selection\" (e.g. { z, t, c }) and returns a Promise for the GeoTIFFImage\n * object corresponding to that selection.\n *\n * For OME-TIFF images, the \"selection\" object is the same regardless of\n * the format version. However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n  return (sel: OmeTiffSelection, pyramidLevel: number) => {\n    // Get IFD index at base pyramid level\n    const index = ifdIndexer(sel);\n    // Get index of first image at pyramidal level\n    const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n    // Return image at IFD index for pyramidal level\n    return tiff.getImage(index + pyramidIndex);\n  };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n  const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n  return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n    const index = ifdIndexer(sel);\n    const baseImage = await tiff.getImage(index);\n\n    // It's the highest resolution, no need to look up SubIFDs.\n    if (pyramidLevel === 0) {\n      return baseImage;\n    }\n\n    const {SubIFDs} = baseImage.fileDirectory;\n    if (!SubIFDs) {\n      throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n    }\n\n    // Get IFD for the selection at the pyramidal level\n    const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n    if (!ifdCache.has(key)) {\n      // Only create a new request if we don't have the key.\n      const subIfdOffset = SubIFDs[pyramidLevel - 1];\n      ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n    }\n    const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n    // Create a new image object manually from IFD\n    // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n    return new (baseImage.constructor as any)(\n      ifd.fileDirectory,\n      ifd.geoKeyDirectory,\n      tiff.dataView,\n      tiff.littleEndian,\n      tiff.cache,\n      tiff.source\n    ) as GeoTIFFImage;\n  };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n  const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n  switch (DimensionOrder) {\n    case 'XYZCT': {\n      return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n    }\n    case 'XYZTC': {\n      return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n    }\n    case 'XYCTZ': {\n      return ({t, c, z}) => z * SizeC * SizeT + t * SizeC + c;\n    }\n    case 'XYCZT': {\n      return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n    }\n    case 'XYTCZ': {\n      return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n    }\n    case 'XYTZC': {\n      return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n    }\n    default: {\n      throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n    }\n  }\n}\n"],"mappings":";;AAyBA,OAAO,SAASA,mBAAmB,CAACC,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEC;EAAK,CAAC,GAAGH,OAAO,CAACI,MAAM;EAC5C,MAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAE5C,OAAO,CAACO,GAAqB,EAAEC,YAAoB,KAAK;IAEtD,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAE7B,MAAMG,YAAY,GAAGF,YAAY,GAAGL,KAAK,GAAGF,KAAK,GAAGC,KAAK;IAEzD,OAAOJ,IAAI,CAACa,QAAQ,CAACF,KAAK,GAAGC,YAAY,CAAC;EAC5C,CAAC;AACH;;AAgBA,OAAO,SAASE,mBAAmB,CAACd,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAC5C,MAAMa,QAAkD,GAAG,IAAIC,GAAG,EAAE;EAEpE,OAAO,OAAOP,GAAqB,EAAEC,YAAoB,KAAK;IAC5D,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAC7B,MAAMQ,SAAS,GAAG,MAAMjB,IAAI,CAACa,QAAQ,CAACF,KAAK,CAAC;;IAG5C,IAAID,YAAY,KAAK,CAAC,EAAE;MACtB,OAAOO,SAAS;IAClB;IAEA,MAAM;MAACC;IAAO,CAAC,GAAGD,SAAS,CAACE,aAAa;IACzC,IAAI,CAACD,OAAO,EAAE;MACZ,MAAME,KAAK,CAAC,8CAA8C,CAAC;IAC7D;;IAGA,MAAMC,GAAG,aAAMZ,GAAG,CAACa,CAAC,cAAIb,GAAG,CAACc,CAAC,cAAId,GAAG,CAACe,CAAC,cAAId,YAAY,CAAE;IACxD,IAAI,CAACK,QAAQ,CAACU,GAAG,CAACJ,GAAG,CAAC,EAAE;MAEtB,MAAMK,YAAY,GAAGR,OAAO,CAACR,YAAY,GAAG,CAAC,CAAC;MAC9CK,QAAQ,CAACY,GAAG,CAACN,GAAG,EAAErB,IAAI,CAAC4B,oBAAoB,CAACF,YAAY,CAAC,CAAC;IAC5D;IACA,MAAMG,GAAG,GAAI,MAAMd,QAAQ,CAACe,GAAG,CAACT,GAAG,CAAwB;;IAI3D,OAAO,IAAKJ,SAAS,CAACc,WAAW,CAC/BF,GAAG,CAACV,aAAa,EACjBU,GAAG,CAACG,eAAe,EACnBhC,IAAI,CAACiC,QAAQ,EACbjC,IAAI,CAACkC,YAAY,EACjBlC,IAAI,CAACmC,KAAK,EACVnC,IAAI,CAACoC,MAAM,CACZ;EACH,CAAC;AACH;;AAMA,SAAS5B,gBAAgB,CAACN,OAAkB,EAAqC;EAC/E,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEF,KAAK;IAAEkC;EAAc,CAAC,GAAGnC,OAAO,CAACI,MAAM;EAC5D,QAAQ+B,cAAc;IACpB,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACf,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKF,CAAC,GAAGjB,KAAK,GAAGD,KAAK,GAAGmB,CAAC,GAAGlB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACF,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKD,CAAC,GAAGlB,KAAK,GAAGF,KAAK,GAAGmB,CAAC,GAAGjB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACF,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKA,CAAC,GAAGpB,KAAK,GAAGD,KAAK,GAAGmB,CAAC,GAAGlB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACD,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKF,CAAC,GAAGlB,KAAK,GAAGC,KAAK,GAAGmB,CAAC,GAAGpB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACD,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKA,CAAC,GAAGrB,KAAK,GAAGC,KAAK,GAAGmB,CAAC,GAAGpB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAC;YAACA,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC;UAAA,OAAKD,CAAC,GAAGpB,KAAK,GAAGE,KAAK,GAAGmB,CAAC,GAAGrB,KAAK,GAAGmB,CAAC;QAAA;MACzD;IACA;MAAS;QACP,MAAM,IAAIF,KAAK,+CAAwCiB,cAAc,OAAI;MAC3E;EAAC;AAEL"}

package/dist/esm/lib/ome/ome-utils.js

@@ -9,10 +9,12 @@ export const DTYPE_LOOKUP = {
   int16: 'Int16',
   int32: 'Int32'
 };
-export function getOmePixelSourceMeta({
-  Pixels
-}) {
+export function getOmePixelSourceMeta(_ref) {
+  let {
+    Pixels
+  } = _ref;
   const labels = getLabels(Pixels.DimensionOrder);
+
   const dims = getDims(labels);
   const shape = Array(labels.length).fill(0);
   shape[dims('t')] = Pixels.SizeT;
@@ -30,13 +32,10 @@ export function getOmePixelSourceMeta({
     s[dims('y')] = Pixels.SizeY >> level;
     return s;
   };
-
   if (!(Pixels.Type in DTYPE_LOOKUP)) {
     throw Error("Pixel type ".concat(Pixels.Type, " not supported."));
   }
-
   const dtype = DTYPE_LOOKUP[Pixels.Type];
-
   if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
     const physicalSizes = {
       x: {
@@ -48,14 +47,12 @@ export function getOmePixelSourceMeta({
         unit: Pixels.PhysicalSizeYUnit
       }
     };
-
     if (Pixels.PhysicalSizeZ) {
       physicalSizes.z = {
         size: Pixels.PhysicalSizeZ,
         unit: Pixels.PhysicalSizeZUnit
       };
     }
-
     return {
       labels,
       getShape,
@@ -63,7 +60,6 @@ export function getOmePixelSourceMeta({
       dtype
     };
   }
-
   return {
     labels,
     getShape,

package/dist/esm/lib/ome/ome-utils.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/ome-utils.ts"],"names":["getDims","getLabels","DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","SizeX","SizeY","Type","Error","dtype","PhysicalSizeX","PhysicalSizeY","physicalSizes","x","size","unit","PhysicalSizeXUnit","y","PhysicalSizeYUnit","PhysicalSizeZ","z","PhysicalSizeZUnit"],"mappings":"AAAA,SAAQA,OAAR,EAAiBC,SAAjB,QAAiC,SAAjC;AAGA,OAAO,MAAMC,YAAY,GAAG;AAC1BC,EAAAA,KAAK,EAAE,OADmB;AAE1BC,EAAAA,MAAM,EAAE,QAFkB;AAG1BC,EAAAA,MAAM,EAAE,QAHkB;AAI1BC,EAAAA,KAAK,EAAE,SAJmB;AAK1BC,EAAAA,MAAM,EAAE,SALkB;AAM1BC,EAAAA,IAAI,EAAE,MANoB;AAO1BC,EAAAA,KAAK,EAAE,OAPmB;AAQ1BC,EAAAA,KAAK,EAAE;AARmB,CAArB;AAWP,OAAO,SAASC,qBAAT,CAA+B;AAACC,EAAAA;AAAD,CAA/B,EAAoD;AAEzD,QAAMC,MAAM,GAAGZ,SAAS,CAACW,MAAM,CAACE,cAAR,CAAxB;AAGA,QAAMC,IAAI,GAAGf,OAAO,CAACa,MAAD,CAApB;AACA,QAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAR,CAAL,CAAqBC,IAArB,CAA0B,CAA1B,CAAxB;AACAH,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACQ,KAA1B;AACAJ,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACS,KAA1B;AACAL,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACU,KAA1B;;AAGA,MAAIV,MAAM,CAACW,WAAX,EAAwB;AAEtBV,IAAAA,MAAM,CAACW,IAAP,CAAY,IAAZ;AACAR,IAAAA,KAAK,CAACQ,IAAN,CAAW,CAAX;AACD;;AAID,QAAMC,QAAQ,GAAIC,KAAD,IAAmB;AAClC,UAAMC,CAAC,GAAG,CAAC,GAAGX,KAAJ,CAAV;AACAW,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACgB,KAAP,IAAgBF,KAA/B;AACAC,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACiB,KAAP,IAAgBH,KAA/B;AACA,WAAOC,CAAP;AACD,GALD;;AAOA,MAAI,EAAEf,MAAM,CAACkB,IAAP,IAAe5B,YAAjB,CAAJ,EAAoC;AAClC,UAAM6B,KAAK,sBAAenB,MAAM,CAACkB,IAAtB,qBAAX;AACD;;AAED,QAAME,KAAK,GAAG9B,YAAY,CAACU,MAAM,CAACkB,IAAR,CAA1B;;AACA,MAAIlB,MAAM,CAACqB,aAAP,IAAwBrB,MAAM,CAACsB,aAAnC,EAAkD;AAChD,UAAMC,aAEL,GAAG;AACFC,MAAAA,CAAC,EAAE;AACDC,QAAAA,IAAI,EAAEzB,MAAM,CAACqB,aADZ;AAEDK,QAAAA,IAAI,EAAE1B,MAAM,CAAC2B;AAFZ,OADD;AAKFC,MAAAA,CAAC,EAAE;AACDH,QAAAA,IAAI,EAAEzB,MAAM,CAACsB,aADZ;AAEDI,QAAAA,IAAI,EAAE1B,MAAM,CAAC6B;AAFZ;AALD,KAFJ;;AAYA,QAAI7B,MAAM,CAAC8B,aAAX,EAA0B;AACxBP,MAAAA,aAAa,CAACQ,CAAd,GAAkB;AAChBN,QAAAA,IAAI,EAAEzB,MAAM,CAAC8B,aADG;AAEhBJ,QAAAA,IAAI,EAAE1B,MAAM,CAACgC;AAFG,OAAlB;AAID;;AACD,WAAO;AAAC/B,MAAAA,MAAD;AAASY,MAAAA,QAAT;AAAmBU,MAAAA,aAAnB;AAAkCH,MAAAA;AAAlC,KAAP;AACD;;AAED,SAAO;AAACnB,IAAAA,MAAD;AAASY,IAAAA,QAAT;AAAmBO,IAAAA;AAAnB,GAAP;AACD","sourcesContent":["import {getDims, getLabels} from './utils';\nimport type {OMEXML, UnitsLength} from './omexml';\n\nexport const DTYPE_LOOKUP = {\n  uint8: 'Uint8',\n  uint16: 'Uint16',\n  uint32: 'Uint32',\n  float: 'Float32',\n  double: 'Float64',\n  int8: 'Int8',\n  int16: 'Int16',\n  int32: 'Int32'\n} as const;\n\nexport function getOmePixelSourceMeta({Pixels}: OMEXML[0]) {\n  // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']\n  const labels = getLabels(Pixels.DimensionOrder);\n\n  // Compute \"shape\" of image\n  const dims = getDims(labels);\n  const shape: number[] = Array(labels.length).fill(0);\n  shape[dims('t')] = Pixels.SizeT;\n  shape[dims('c')] = Pixels.SizeC;\n  shape[dims('z')] = Pixels.SizeZ;\n\n  // Push extra dimension if data are interleaved.\n  if (Pixels.Interleaved) {\n    // @ts-ignore\n    labels.push('_c');\n    shape.push(3);\n  }\n\n  // Creates a new shape for different level of pyramid.\n  // Assumes factor-of-two downsampling.\n  const getShape = (level: number) => {\n    const s = [...shape];\n    s[dims('x')] = Pixels.SizeX >> level;\n    s[dims('y')] = Pixels.SizeY >> level;\n    return s;\n  };\n\n  if (!(Pixels.Type in DTYPE_LOOKUP)) {\n    throw Error(`Pixel type ${Pixels.Type} not supported.`);\n  }\n\n  const dtype = DTYPE_LOOKUP[Pixels.Type as keyof typeof DTYPE_LOOKUP];\n  if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {\n    const physicalSizes: {\n      [k: string]: {size: number; unit: UnitsLength};\n    } = {\n      x: {\n        size: Pixels.PhysicalSizeX,\n        unit: Pixels.PhysicalSizeXUnit\n      },\n      y: {\n        size: Pixels.PhysicalSizeY,\n        unit: Pixels.PhysicalSizeYUnit\n      }\n    };\n    if (Pixels.PhysicalSizeZ) {\n      physicalSizes.z = {\n        size: Pixels.PhysicalSizeZ,\n        unit: Pixels.PhysicalSizeZUnit\n      };\n    }\n    return {labels, getShape, physicalSizes, dtype};\n  }\n\n  return {labels, getShape, dtype};\n}\n"],"file":"ome-utils.js"}
+{"version":3,"file":"ome-utils.js","names":["getDims","getLabels","DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","SizeX","SizeY","Type","Error","dtype","PhysicalSizeX","PhysicalSizeY","physicalSizes","x","size","unit","PhysicalSizeXUnit","y","PhysicalSizeYUnit","PhysicalSizeZ","z","PhysicalSizeZUnit"],"sources":["../../../../src/lib/ome/ome-utils.ts"],"sourcesContent":["import {getDims, getLabels} from './utils';\nimport type {OMEXML, UnitsLength} from './omexml';\n\nexport const DTYPE_LOOKUP = {\n  uint8: 'Uint8',\n  uint16: 'Uint16',\n  uint32: 'Uint32',\n  float: 'Float32',\n  double: 'Float64',\n  int8: 'Int8',\n  int16: 'Int16',\n  int32: 'Int32'\n} as const;\n\nexport function getOmePixelSourceMeta({Pixels}: OMEXML[0]) {\n  // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']\n  const labels = getLabels(Pixels.DimensionOrder);\n\n  // Compute \"shape\" of image\n  const dims = getDims(labels);\n  const shape: number[] = Array(labels.length).fill(0);\n  shape[dims('t')] = Pixels.SizeT;\n  shape[dims('c')] = Pixels.SizeC;\n  shape[dims('z')] = Pixels.SizeZ;\n\n  // Push extra dimension if data are interleaved.\n  if (Pixels.Interleaved) {\n    // @ts-ignore\n    labels.push('_c');\n    shape.push(3);\n  }\n\n  // Creates a new shape for different level of pyramid.\n  // Assumes factor-of-two downsampling.\n  const getShape = (level: number) => {\n    const s = [...shape];\n    s[dims('x')] = Pixels.SizeX >> level;\n    s[dims('y')] = Pixels.SizeY >> level;\n    return s;\n  };\n\n  if (!(Pixels.Type in DTYPE_LOOKUP)) {\n    throw Error(`Pixel type ${Pixels.Type} not supported.`);\n  }\n\n  const dtype = DTYPE_LOOKUP[Pixels.Type as keyof typeof DTYPE_LOOKUP];\n  if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {\n    const physicalSizes: {\n      [k: string]: {size: number; unit: UnitsLength};\n    } = {\n      x: {\n        size: Pixels.PhysicalSizeX,\n        unit: Pixels.PhysicalSizeXUnit\n      },\n      y: {\n        size: Pixels.PhysicalSizeY,\n        unit: Pixels.PhysicalSizeYUnit\n      }\n    };\n    if (Pixels.PhysicalSizeZ) {\n      physicalSizes.z = {\n        size: Pixels.PhysicalSizeZ,\n        unit: Pixels.PhysicalSizeZUnit\n      };\n    }\n    return {labels, getShape, physicalSizes, dtype};\n  }\n\n  return {labels, getShape, dtype};\n}\n"],"mappings":"AAAA,SAAQA,OAAO,EAAEC,SAAS,QAAO,SAAS;AAG1C,OAAO,MAAMC,YAAY,GAAG;EAC1BC,KAAK,EAAE,OAAO;EACdC,MAAM,EAAE,QAAQ;EAChBC,MAAM,EAAE,QAAQ;EAChBC,KAAK,EAAE,SAAS;EAChBC,MAAM,EAAE,SAAS;EACjBC,IAAI,EAAE,MAAM;EACZC,KAAK,EAAE,OAAO;EACdC,KAAK,EAAE;AACT,CAAU;AAEV,OAAO,SAASC,qBAAqB,OAAsB;EAAA,IAArB;IAACC;EAAiB,CAAC;EAEvD,MAAMC,MAAM,GAAGZ,SAAS,CAACW,MAAM,CAACE,cAAc,CAAC;;EAG/C,MAAMC,IAAI,GAAGf,OAAO,CAACa,MAAM,CAAC;EAC5B,MAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAM,CAAC,CAACC,IAAI,CAAC,CAAC,CAAC;EACpDH,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACQ,KAAK;EAC/BJ,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACS,KAAK;EAC/BL,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACU,KAAK;;EAG/B,IAAIV,MAAM,CAACW,WAAW,EAAE;IAEtBV,MAAM,CAACW,IAAI,CAAC,IAAI,CAAC;IACjBR,KAAK,CAACQ,IAAI,CAAC,CAAC,CAAC;EACf;;EAIA,MAAMC,QAAQ,GAAIC,KAAa,IAAK;IAClC,MAAMC,CAAC,GAAG,CAAC,GAAGX,KAAK,CAAC;IACpBW,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACgB,KAAK,IAAIF,KAAK;IACpCC,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACiB,KAAK,IAAIH,KAAK;IACpC,OAAOC,CAAC;EACV,CAAC;EAED,IAAI,EAAEf,MAAM,CAACkB,IAAI,IAAI5B,YAAY,CAAC,EAAE;IAClC,MAAM6B,KAAK,sBAAenB,MAAM,CAACkB,IAAI,qBAAkB;EACzD;EAEA,MAAME,KAAK,GAAG9B,YAAY,CAACU,MAAM,CAACkB,IAAI,CAA8B;EACpE,IAAIlB,MAAM,CAACqB,aAAa,IAAIrB,MAAM,CAACsB,aAAa,EAAE;IAChD,MAAMC,aAEL,GAAG;MACFC,CAAC,EAAE;QACDC,IAAI,EAAEzB,MAAM,CAACqB,aAAa;QAC1BK,IAAI,EAAE1B,MAAM,CAAC2B;MACf,CAAC;MACDC,CAAC,EAAE;QACDH,IAAI,EAAEzB,MAAM,CAACsB,aAAa;QAC1BI,IAAI,EAAE1B,MAAM,CAAC6B;MACf;IACF,CAAC;IACD,IAAI7B,MAAM,CAAC8B,aAAa,EAAE;MACxBP,aAAa,CAACQ,CAAC,GAAG;QAChBN,IAAI,EAAEzB,MAAM,CAAC8B,aAAa;QAC1BJ,IAAI,EAAE1B,MAAM,CAACgC;MACf,CAAC;IACH;IACA,OAAO;MAAC/B,MAAM;MAAEY,QAAQ;MAAEU,aAAa;MAAEH;IAAK,CAAC;EACjD;EAEA,OAAO;IAACnB,MAAM;IAAEY,QAAQ;IAAEO;EAAK,CAAC;AAClC"}

package/dist/esm/lib/ome/omexml.js

@@ -1,5 +1,6 @@
 import parser from 'fast-xml-parser';
 import { ensureArray, intToRgba } from '../utils/tiff-utils';
+
 const PARSER_OPTIONS = {
   attributeNamePrefix: '',
   attrNodeName: 'attr',
@@ -7,40 +8,39 @@ const PARSER_OPTIONS = {
   parseAttributeValue: true,
   ignoreAttributes: false
 };
-
 const parse = str => parser.parse(str, PARSER_OPTIONS);
-
 export function fromString(str) {
   const res = parse(str);
-
   if (!res.OME) {
     throw Error('Failed to parse OME-XML metadata.');
   }
-
   return ensureArray(res.OME.Image).map(img => {
     const Channels = ensureArray(img.Pixels.Channel).map(c => {
       if ('Color' in c.attr) {
-        return { ...c.attr,
+        return {
+          ...c.attr,
           Color: intToRgba(c.attr.Color)
         };
       }
-
-      return { ...c.attr
+      return {
+        ...c.attr
       };
     });
     const {
       AquisitionDate = '',
       Description = ''
     } = img;
-    const image = { ...img.attr,
+    const image = {
+      ...img.attr,
       AquisitionDate,
       Description,
-      Pixels: { ...img.Pixels.attr,
+      Pixels: {
+        ...img.Pixels.attr,
         Channels
       }
     };
-    return { ...image,
-
+    return {
+      ...image,
       format() {
         const {
           Pixels
@@ -59,7 +59,6 @@ export function fromString(str) {
           Channels: Pixels.SizeC
         };
       }
-
     };
   });
 }

package/dist/esm/lib/ome/omexml.js.map

@@ -1 +1 @@
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`${size} ${unit}` : '-';\n          })\n          .join(' x ');\n\n        return {\n          'Acquisition Date': image.AquisitionDate,\n          'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,\n          'Pixels Type': Pixels.Type,\n          'Pixels Size (XYZ)': sizes,\n          'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,\n          Channels: Pixels.SizeC\n        };\n      }\n    };\n  });\n}\n\nexport type OMEXML = ReturnType<typeof fromString>;\nexport type DimensionOrder = 'XYZCT' | 'XYZTC' | 'XYCTZ' | 'XYCZT' | 'XYTCZ' | 'XYTZC';\n\n// Structure of node is determined by the PARSER_OPTIONS.\ntype Node<T, A> = T & {attr: A};\ntype Attrs<Fields extends string, T = string> = {[K in Fields]: T};\n\ntype OMEAttrs = Attrs<'xmlns' | 'xmlns:xsi' | 'xsi:schemaLocation'>;\ntype OME = Node<{Insturment: Insturment; Image: Image | Image[]}, OMEAttrs>;\n\ntype Insturment = Node<\n  {Objective: Node<{}, Attrs<'ID' | 'Model' | 'NominalMagnification'>>},\n  Attrs<'ID'>\n>;\n\ninterface ImageNodes {\n  AquisitionDate?: string;\n  Description?: string;\n  Pixels: Pixels;\n  InstrumentRef: Node<{}, {ID: string}>;\n  ObjectiveSettings: Node<{}, {ID: string}>;\n}\ntype Image = Node<ImageNodes, Attrs<'ID' | 'Name'>>;\n\ntype PixelType =\n  | 'int8'\n  | 'int16'\n  | 'int32'\n  | 'uint8'\n  | 'uint16'\n  | 'uint32'\n  | 'float'\n  | 'bit'\n  | 'double'\n  | 'complex'\n  | 'double-complex';\n\nexport type UnitsLength =\n  | 'Ym'\n  | 'Zm'\n  | 'Em'\n  | 'Pm'\n  | 'Tm'\n  | 'Gm'\n  | 'Mm'\n  | 'km'\n  | 'hm'\n  | 'dam'\n  | 'm'\n  | 'dm'\n  | 'cm'\n  | 'mm'\n  | 'µm'\n  | 'nm'\n  | 'pm'\n  | 'fm'\n  | 'am'\n  | 'zm'\n  | 'ym'\n  | 'Å'\n  | 'thou'\n  | 'li'\n  | 'in'\n  | 'ft'\n  | 'yd'\n  | 'mi'\n  | 'ua'\n  | 'ly'\n  | 'pc'\n  | 'pt'\n  | 'pixel'\n  | 'reference frame';\n\ntype PhysicalSize<Name extends string> = `PhysicalSize${Name}`;\ntype PhysicalSizeUnit<Name extends string> = `PhysicalSize${Name}Unit`;\ntype Size<Names extends string> = `Size${Names}`;\n\ntype PixelAttrs = Attrs<\n  PhysicalSize<'X' | 'Y' | 'Z'> | 'SignificantBits' | Size<'T' | 'C' | 'Z' | 'Y' | 'X'>,\n  number\n> &\n  Attrs<PhysicalSizeUnit<'X' | 'Y' | 'Z'>, UnitsLength> &\n  Attrs<'BigEndian' | 'Interleaved', boolean> & {\n    ID: string;\n    DimensionOrder: DimensionOrder;\n    Type: PixelType;\n  };\n\ntype Pixels = Node<\n  {\n    Channel: Channel | Channel[];\n    TiffData: Node<{}, Attrs<'IFD' | 'PlaneCount'>>;\n  },\n  PixelAttrs\n>;\n\ntype ChannelAttrs =\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n    }\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n      Color: number;\n    };\n\ntype Channel = Node<{}, ChannelAttrs>;\n\ntype Root = {OME: OME};\n"],"file":"omexml.js"}
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`${size} ${unit}` : '-';\n          })\n          .join(' x ');\n\n        return {\n          'Acquisition Date': image.AquisitionDate,\n          'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,\n          'Pixels Type': Pixels.Type,\n          'Pixels Size (XYZ)': sizes,\n          'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,\n          Channels: Pixels.SizeC\n        };\n      }\n    };\n  });\n}\n\nexport type OMEXML = ReturnType<typeof fromString>;\nexport type DimensionOrder = 'XYZCT' | 'XYZTC' | 'XYCTZ' | 'XYCZT' | 'XYTCZ' | 'XYTZC';\n\n// Structure of node is determined by the PARSER_OPTIONS.\ntype Node<T, A> = T & {attr: A};\ntype Attrs<Fields extends string, T = string> = {[K in Fields]: T};\n\ntype OMEAttrs = Attrs<'xmlns' | 'xmlns:xsi' | 'xsi:schemaLocation'>;\ntype OME = Node<{Insturment: Insturment; Image: Image | Image[]}, OMEAttrs>;\n\ntype Insturment = Node<\n  {Objective: Node<{}, Attrs<'ID' | 'Model' | 'NominalMagnification'>>},\n  Attrs<'ID'>\n>;\n\ninterface ImageNodes {\n  AquisitionDate?: string;\n  Description?: string;\n  Pixels: Pixels;\n  InstrumentRef: Node<{}, {ID: string}>;\n  ObjectiveSettings: Node<{}, {ID: string}>;\n}\ntype Image = Node<ImageNodes, Attrs<'ID' | 'Name'>>;\n\ntype PixelType =\n  | 'int8'\n  | 'int16'\n  | 'int32'\n  | 'uint8'\n  | 'uint16'\n  | 'uint32'\n  | 'float'\n  | 'bit'\n  | 'double'\n  | 'complex'\n  | 'double-complex';\n\nexport type UnitsLength =\n  | 'Ym'\n  | 'Zm'\n  | 'Em'\n  | 'Pm'\n  | 'Tm'\n  | 'Gm'\n  | 'Mm'\n  | 'km'\n  | 'hm'\n  | 'dam'\n  | 'm'\n  | 'dm'\n  | 'cm'\n  | 'mm'\n  | 'µm'\n  | 'nm'\n  | 'pm'\n  | 'fm'\n  | 'am'\n  | 'zm'\n  | 'ym'\n  | 'Å'\n  | 'thou'\n  | 'li'\n  | 'in'\n  | 'ft'\n  | 'yd'\n  | 'mi'\n  | 'ua'\n  | 'ly'\n  | 'pc'\n  | 'pt'\n  | 'pixel'\n  | 'reference frame';\n\ntype PhysicalSize<Name extends string> = `PhysicalSize${Name}`;\ntype PhysicalSizeUnit<Name extends string> = `PhysicalSize${Name}Unit`;\ntype Size<Names extends string> = `Size${Names}`;\n\ntype PixelAttrs = Attrs<\n  PhysicalSize<'X' | 'Y' | 'Z'> | 'SignificantBits' | Size<'T' | 'C' | 'Z' | 'Y' | 'X'>,\n  number\n> &\n  Attrs<PhysicalSizeUnit<'X' | 'Y' | 'Z'>, UnitsLength> &\n  Attrs<'BigEndian' | 'Interleaved', boolean> & {\n    ID: string;\n    DimensionOrder: DimensionOrder;\n    Type: PixelType;\n  };\n\ntype Pixels = Node<\n  {\n    Channel: Channel | Channel[];\n    TiffData: Node<{}, Attrs<'IFD' | 'PlaneCount'>>;\n  },\n  PixelAttrs\n>;\n\ntype ChannelAttrs =\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n    }\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n      Color: number;\n    };\n\ntype Channel = Node<{}, ChannelAttrs>;\n\ntype Root = {OME: OME};\n"],"mappings":"AAAA,OAAOA,MAAM,MAAM,iBAAiB;AACpC,SAAQC,WAAW,EAAEC,SAAS,QAAO,qBAAqB;;AAG1D,MAAMC,cAAc,GAAG;EAErBC,mBAAmB,EAAE,EAAE;EACvBC,YAAY,EAAE,MAAM;EAGpBC,cAAc,EAAE,IAAI;EACpBC,mBAAmB,EAAE,IAAI;EAGzBC,gBAAgB,EAAE;AACpB,CAAC;AAED,MAAMC,KAAK,GAAIC,GAAW,IAAWV,MAAM,CAACS,KAAK,CAACC,GAAG,EAAEP,cAAc,CAAC;AAEtE,OAAO,SAASQ,UAAU,CAACD,GAAW,EAAE;EACtC,MAAME,GAAG,GAAGH,KAAK,CAACC,GAAG,CAAC;EACtB,IAAI,CAACE,GAAG,CAACC,GAAG,EAAE;IACZ,MAAMC,KAAK,CAAC,mCAAmC,CAAC;EAClD;EACA,OAAOb,WAAW,CAACW,GAAG,CAACC,GAAG,CAACE,KAAK,CAAC,CAACC,GAAG,CAAEC,GAAG,IAAK;IAC7C,MAAMC,QAAQ,GAAGjB,WAAW,CAACgB,GAAG,CAACE,MAAM,CAACC,OAAO,CAAC,CAACJ,GAAG,CAAEK,CAAC,IAAK;MAC1D,IAAI,OAAO,IAAIA,CAAC,CAACC,IAAI,EAAE;QACrB,OAAO;UAAC,GAAGD,CAAC,CAACC,IAAI;UAAEC,KAAK,EAAErB,SAAS,CAACmB,CAAC,CAACC,IAAI,CAACC,KAAK;QAAC,CAAC;MACpD;MACA,OAAO;QAAC,GAAGF,CAAC,CAACC;MAAI,CAAC;IACpB,CAAC,CAAC;IACF,MAAM;MAACE,cAAc,GAAG,EAAE;MAAEC,WAAW,GAAG;IAAE,CAAC,GAAGR,GAAG;IACnD,MAAMS,KAAK,GAAG;MACZ,GAAGT,GAAG,CAACK,IAAI;MACXE,cAAc;MACdC,WAAW;MACXN,MAAM,EAAE;QACN,GAAGF,GAAG,CAACE,MAAM,CAACG,IAAI;QAClBJ;MACF;IACF,CAAC;IACD,OAAO;MACL,GAAGQ,KAAK;MACRC,MAAM,GAAG;QACP,MAAM;UAACR;QAAM,CAAC,GAAGO,KAAK;QAEtB,MAAME,KAAK,GAAI,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAC3BZ,GAAG,CAAEa,IAAI,IAAK;UACb,MAAMC,IAAI,GAAGX,MAAM,uBAAgBU,IAAI,EAAY;UACnD,MAAME,IAAI,GAAGZ,MAAM,uBAAgBU,IAAI,UAAgB;UACvD,OAAOC,IAAI,IAAIC,IAAI,aAAMD,IAAI,cAAIC,IAAI,IAAK,GAAG;QAC/C,CAAC,CAAC,CACDC,IAAI,CAAC,KAAK,CAAC;QAEd,OAAO;UACL,kBAAkB,EAAEN,KAAK,CAACF,cAAc;UACxC,iBAAiB,YAAKL,MAAM,CAACc,KAAK,gBAAMd,MAAM,CAACe,KAAK,CAAE;UACtD,aAAa,EAAEf,MAAM,CAACgB,IAAI;UAC1B,mBAAmB,EAAEP,KAAK;UAC1B,uBAAuB,YAAKT,MAAM,CAACiB,KAAK,gBAAMjB,MAAM,CAACkB,KAAK,CAAE;UAC5DnB,QAAQ,EAAEC,MAAM,CAACmB;QACnB,CAAC;MACH;IACF,CAAC;EACH,CAAC,CAAC;AACJ"}

package/dist/esm/lib/ome/utils.js

@@ -1,20 +1,19 @@
+
+
 export function getLabels(dimOrder) {
   return dimOrder.toLowerCase().split('').reverse();
 }
+
 export function getDims(labels) {
   const lookup = new Map(labels.map((name, i) => [name, i]));
-
   if (lookup.size !== labels.length) {
     throw Error('Labels must be unique, found duplicated label.');
   }
-
   return name => {
     const index = lookup.get(name);
-
     if (index === undefined) {
       throw Error('Invalid dimension.');
     }
-
     return index;
   };
 }

package/dist/esm/lib/ome/utils.js.map

@@ -1 +1 @@
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