@loaders.gl/geotiff 3.3.0-alpha.4 → 3.3.0-alpha.6

package/dist/bundle.js

@@ -1,7 +1,11 @@
 "use strict";
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
 }) : (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     o[k2] = m[k];

package/dist/es5/bundle.js

@@ -1,13 +1,9 @@
 "use strict";
 
 var _typeof = require("@babel/runtime/helpers/typeof");
-
 var moduleExports = _interopRequireWildcard(require("./index"));
-
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
 globalThis.loaders = globalThis.loaders || {};
 module.exports = Object.assign(globalThis.loaders, moduleExports);
 //# sourceMappingURL=bundle.js.map

package/dist/es5/bundle.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/bundle.ts"],"names":["globalThis","loaders","module","exports","Object","assign","moduleExports"],"mappings":";;;;AAAA;;;;;;AAEAA,UAAU,CAACC,OAAX,GAAqBD,UAAU,CAACC,OAAX,IAAsB,EAA3C;AAEAC,MAAM,CAACC,OAAP,GAAiBC,MAAM,CAACC,MAAP,CAAcL,UAAU,CAACC,OAAzB,EAAkCK,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":["globalThis","loaders","module","exports","Object","assign","moduleExports"],"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;AAAyC;AAAA;AAEzCA,UAAU,CAACC,OAAO,GAAGD,UAAU,CAACC,OAAO,IAAI,CAAC,CAAC;AAE7CC,MAAM,CAACC,OAAO,GAAGC,MAAM,CAACC,MAAM,CAACL,UAAU,CAACC,OAAO,EAAEK,aAAa,CAAC"}

package/dist/es5/index.js

@@ -1,24 +1,21 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "loadGeoTiff", {
+Object.defineProperty(exports, "TiffPixelSource", {
   enumerable: true,
   get: function get() {
-    return _loadGeotiff.loadGeoTiff;
+    return _tiffPixelSource.default;
   }
 });
-Object.defineProperty(exports, "TiffPixelSource", {
+Object.defineProperty(exports, "loadGeoTiff", {
   enumerable: true,
   get: function get() {
-    return _tiffPixelSource.default;
+    return _loadGeotiff.loadGeoTiff;
   }
 });
-
 var _loadGeotiff = require("./lib/load-geotiff");
-
 var _tiffPixelSource = _interopRequireDefault(require("./lib/tiff-pixel-source"));
 //# sourceMappingURL=index.js.map

package/dist/es5/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA;;AACA","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":[],"sources":["../../src/index.ts"],"sourcesContent":["export {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"mappings":";;;;;;;;;;;;;;;;;;AAAA;AACA"}

package/dist/es5/lib/load-geotiff.js

@@ -1,72 +1,57 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.loadGeoTiff = loadGeoTiff;
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
 var _geotiff = require("geotiff");
-
 var _proxies = require("./utils/proxies");
-
 var _loadOmeTiff = require("./ome/load-ome-tiff");
-
 function loadGeoTiff(_x) {
   return _loadGeoTiff.apply(this, arguments);
 }
-
 function _loadGeoTiff() {
   _loadGeoTiff = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(source) {
     var opts,
-        headers,
-        offsets,
-        tiff,
-        firstImage,
-        _args = arguments;
+      headers,
+      offsets,
+      tiff,
+      firstImage,
+      _args = arguments;
     return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
             opts = _args.length > 1 && _args[1] !== undefined ? _args[1] : {};
             headers = opts.headers, offsets = opts.offsets;
-
             if (!(source instanceof _geotiff.GeoTIFF)) {
               _context.next = 6;
               break;
             }
-
             tiff = source;
             _context.next = 15;
             break;
-
           case 6:
             if (!(typeof source === 'string')) {
               _context.next = 12;
               break;
             }
-
             _context.next = 9;
             return (0, _geotiff.fromUrl)(source, headers);
-
           case 9:
             tiff = _context.sent;
             _context.next = 15;
             break;
-
           case 12:
             _context.next = 14;
             return (0, _geotiff.fromBlob)(source);
-
           case 14:
             tiff = _context.sent;
-
           case 15:
+
             if (offsets) {
               tiff = (0, _proxies.createOffsetsProxy)(tiff, offsets);
             }
@@ -74,20 +59,15 @@ function _loadGeoTiff() {
             (0, _proxies.checkProxies)(tiff);
             _context.next = 19;
             return tiff.getImage(0);
-
           case 19:
             firstImage = _context.sent;
-
             if (!(0, _loadOmeTiff.isOmeTiff)(firstImage)) {
               _context.next = 22;
               break;
             }
-
             return _context.abrupt("return", (0, _loadOmeTiff.loadOmeTiff)(tiff, firstImage));
-
           case 22:
             throw new Error('GeoTIFF not recognized.');
-
           case 23:
           case "end":
             return _context.stop();

package/dist/es5/lib/load-geotiff.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../src/lib/load-geotiff.ts"],"names":["loadGeoTiff","source","opts","headers","offsets","GeoTIFF","tiff","getImage","firstImage","Error"],"mappings":";;;;;;;;;;;;;AAAA;;AAEA;;AAOA;;SA4BsBA,W;;;;;2EAAf,iBACLC,MADK;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAELC,YAAAA,IAFK,2DAEkB,EAFlB;AAIEC,YAAAA,OAJF,GAIsBD,IAJtB,CAIEC,OAJF,EAIWC,OAJX,GAIsBF,IAJtB,CAIWE,OAJX;;AAAA,kBAQDH,MAAM,YAAYI,gBARjB;AAAA;AAAA;AAAA;;AASHC,YAAAA,IAAI,GAAGL,MAAP;AATG;AAAA;;AAAA;AAAA,kBAUM,OAAOA,MAAP,KAAkB,QAVxB;AAAA;AAAA;AAAA;;AAAA;AAAA,mBAWU,sBAAQA,MAAR,EAAgBE,OAAhB,CAXV;;AAAA;AAWHG,YAAAA,IAXG;AAAA;AAAA;;AAAA;AAAA;AAAA,mBAaU,uBAASL,MAAT,CAbV;;AAAA;AAaHK,YAAAA,IAbG;;AAAA;AAwBL,gBAAIF,OAAJ,EAAa;AAMXE,cAAAA,IAAI,GAAG,iCAAmBA,IAAnB,EAAyBF,OAAzB,CAAP;AACD;;AAMD,uCAAaE,IAAb;AArCK;AAAA,mBAuCoBA,IAAI,CAACC,QAAL,CAAc,CAAd,CAvCpB;;AAAA;AAuCCC,YAAAA,UAvCD;;AAAA,iBAyCD,4BAAUA,UAAV,CAzCC;AAAA;AAAA;AAAA;;AAAA,6CA0CI,8BAAYF,IAAZ,EAAkBE,UAAlB,CA1CJ;;AAAA;AAAA,kBA6CC,IAAIC,KAAJ,CAAU,yBAAV,CA7CD;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,G","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":["loadGeoTiff","source","opts","headers","offsets","GeoTIFF","tiff","fromUrl","fromBlob","createOffsetsProxy","checkProxies","getImage","firstImage","isOmeTiff","loadOmeTiff","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;AAEA;AAOA;AAA2D,SA4BrCA,WAAW;EAAA;AAAA;AAAA;EAAA,yEAA1B,iBACLC,MAA+B;IAAA;MAAA;MAAA;MAAA;MAAA;MAAA;IAAA;MAAA;QAAA;UAAA;YAC/BC,IAAoB,2DAAG,CAAC,CAAC;YAElBC,OAAO,GAAaD,IAAI,CAAxBC,OAAO,EAAEC,OAAO,GAAIF,IAAI,CAAfE,OAAO;YAAA,MAInBH,MAAM,YAAYI,gBAAO;cAAA;cAAA;YAAA;YAC3BC,IAAI,GAAGL,MAAM;YAAC;YAAA;UAAA;YAAA,MACL,OAAOA,MAAM,KAAK,QAAQ;cAAA;cAAA;YAAA;YAAA;YAAA,OACtB,IAAAM,gBAAO,EAACN,MAAM,EAAEE,OAAO,CAAC;UAAA;YAArCG,IAAI;YAAA;YAAA;UAAA;YAAA;YAAA,OAES,IAAAE,iBAAQ,EAACP,MAAM,CAAC;UAAA;YAA7BK,IAAI;UAAA;;YAWN,IAAIF,OAAO,EAAE;cAMXE,IAAI,GAAG,IAAAG,2BAAkB,EAACH,IAAI,EAAEF,OAAO,CAAC;YAC1C;;YAMA,IAAAM,qBAAY,EAACJ,IAAI,CAAC;YAAC;YAAA,OAEMA,IAAI,CAACK,QAAQ,CAAC,CAAC,CAAC;UAAA;YAAnCC,UAAU;YAAA,KAEZ,IAAAC,sBAAS,EAACD,UAAU,CAAC;cAAA;cAAA;YAAA;YAAA,iCAChB,IAAAE,wBAAW,EAACR,IAAI,EAAEM,UAAU,CAAC;UAAA;YAAA,MAGhC,IAAIG,KAAK,CAAC,yBAAyB,CAAC;UAAA;UAAA;YAAA;QAAA;MAAA;IAAA;EAAA,CAC3C;EAAA;AAAA"}

package/dist/es5/lib/ome/load-ome-tiff.js

@@ -1,46 +1,33 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.loadOmeTiff = loadOmeTiff;
 exports.isOmeTiff = void 0;
-
+exports.loadOmeTiff = loadOmeTiff;
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
 var _tiffPixelSource = _interopRequireDefault(require("../tiff-pixel-source"));
-
 var _omeIndexers = require("./ome-indexers");
-
 var _omeUtils = require("./ome-utils");
-
 var _omexml = require("./omexml");
-
 var isOmeTiff = function isOmeTiff(img) {
   return img.fileDirectory.ImageDescription.includes('<OME');
 };
-
 exports.isOmeTiff = isOmeTiff;
-
 function loadOmeTiff(_x, _x2) {
   return _loadOmeTiff.apply(this, arguments);
 }
-
 function _loadOmeTiff() {
   _loadOmeTiff = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(tiff, firstImage) {
     var _firstImage$fileDirec, ImageDescription, SubIFDs, photometricInterpretation, omexml, levels, pyramidIndexer, imgMeta, _getOmePixelSourceMet, labels, getShape, physicalSizes, dtype, tileSize, meta, data;
-
     return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
             _firstImage$fileDirec = firstImage.fileDirectory, ImageDescription = _firstImage$fileDirec.ImageDescription, SubIFDs = _firstImage$fileDirec.SubIFDs, photometricInterpretation = _firstImage$fileDirec.PhotometricInterpretation;
             omexml = (0, _omexml.fromString)(ImageDescription);
-
             if (SubIFDs) {
               levels = SubIFDs.length + 1;
               pyramidIndexer = (0, _omeIndexers.getOmeSubIFDIndexer)(tiff, omexml);
@@ -60,11 +47,9 @@ function _loadOmeTiff() {
               length: levels
             }).map(function (_, resolution) {
               var shape = getShape(resolution);
-
               var indexer = function indexer(sel) {
                 return pyramidIndexer(sel, resolution);
               };
-
               var source = new _tiffPixelSource.default(indexer, dtype, tileSize, shape, labels, meta);
               return source;
             });
@@ -72,7 +57,6 @@ function _loadOmeTiff() {
               data: data,
               metadata: imgMeta
             });
-
           case 9:
           case "end":
             return _context.stop();

package/dist/es5/lib/ome/load-ome-tiff.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"names":["isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","photometricInterpretation","PhotometricInterpretation","omexml","levels","length","pyramidIndexer","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","TiffPixelSource","metadata"],"mappings":";;;;;;;;;;;;;;AAEA;;AACA;;AACA;;AACA;;AAGO,IAAMA,SAAS,GAAG,SAAZA,SAAY,CAACC,GAAD;AAAA,SAAuBA,GAAG,CAACC,aAAJ,CAAkBC,gBAAlB,CAAmCC,QAAnC,CAA4C,MAA5C,CAAvB;AAAA,CAAlB;;;;SAEeC,W;;;;;2EAAf,iBAA2BC,IAA3B,EAA0CC,UAA1C;AAAA;;AAAA;AAAA;AAAA;AAAA;AAAA,oCAMDA,UAAU,CAACL,aANV,EAGHC,gBAHG,yBAGHA,gBAHG,EAIHK,OAJG,yBAIHA,OAJG,EAKwBC,yBALxB,yBAKHC,yBALG;AAOCC,YAAAA,MAPD,GAOU,wBAAWR,gBAAX,CAPV;;AAgBL,gBAAIK,OAAJ,EAAa;AAEXI,cAAAA,MAAM,GAAGJ,OAAO,CAACK,MAAR,GAAiB,CAA1B;AACAC,cAAAA,cAAc,GAAG,sCAAoBR,IAApB,EAA0BK,MAA1B,CAAjB;AACD,aAJD,MAIO;AAELC,cAAAA,MAAM,GAAGD,MAAM,CAACE,MAAhB;AACAC,cAAAA,cAAc,GAAG,sCAAoBR,IAApB,EAA0BK,MAA1B,CAAjB;AACD;;AAGKI,YAAAA,OA3BD,GA2BWJ,MAAM,CAAC,CAAD,CA3BjB;AAAA,oCA4B4C,qCAAsBI,OAAtB,CA5B5C,EA4BEC,MA5BF,yBA4BEA,MA5BF,EA4BUC,QA5BV,yBA4BUA,QA5BV,EA4BoBC,aA5BpB,yBA4BoBA,aA5BpB,EA4BmCC,KA5BnC,yBA4BmCA,KA5BnC;AA6BCC,YAAAA,QA7BD,GA6BYb,UAAU,CAACc,YAAX,EA7BZ;AA8BCC,YAAAA,IA9BD,GA8BQ;AAACb,cAAAA,yBAAyB,EAAzBA,yBAAD;AAA4BS,cAAAA,aAAa,EAAbA;AAA5B,aA9BR;AAgCCK,YAAAA,IAhCD,GAgCQC,KAAK,CAACC,IAAN,CAAW;AAACZ,cAAAA,MAAM,EAAED;AAAT,aAAX,EAA6Bc,GAA7B,CAAiC,UAACC,CAAD,EAAIC,UAAJ,EAAmB;AAC/D,kBAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAD,CAAtB;;AACA,kBAAME,OAAO,GAAG,SAAVA,OAAU,CAACC,GAAD;AAAA,uBAA2BjB,cAAc,CAACiB,GAAD,EAAMH,UAAN,CAAzC;AAAA,eAAhB;;AACA,kBAAMI,MAAM,GAAG,IAAIC,wBAAJ,CAAoBH,OAApB,EAA6BX,KAA7B,EAAoCC,QAApC,EAA8CS,KAA9C,EAAqDb,MAArD,EAA6DM,IAA7D,CAAf;AACA,qBAAOU,MAAP;AACD,aALY,CAhCR;AAAA,6CAuCE;AAACT,cAAAA,IAAI,EAAJA,IAAD;AAAOW,cAAAA,QAAQ,EAAEnB;AAAjB,aAvCF;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,G","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":["isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","photometricInterpretation","PhotometricInterpretation","omexml","fromString","levels","length","pyramidIndexer","getOmeSubIFDIndexer","getOmeLegacyIndexer","imgMeta","getOmePixelSourceMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","TiffPixelSource","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;AACA;AACA;AACA;AAGO,IAAMA,SAAS,GAAG,SAAZA,SAAS,CAAIC,GAAiB;EAAA,OAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAAA;AAAC;AAAA,SAE9EC,WAAW;EAAA;AAAA;AAAA;EAAA,yEAA1B,iBAA2BC,IAAa,EAAEC,UAAwB;IAAA;IAAA;MAAA;QAAA;UAAA;YAAA,wBAMnEA,UAAU,CAACL,aAAa,EAH1BC,gBAAgB,yBAAhBA,gBAAgB,EAChBK,OAAO,yBAAPA,OAAO,EACoBC,yBAAyB,yBAApDC,yBAAyB;YAErBC,MAAM,GAAG,IAAAC,kBAAU,EAACT,gBAAgB,CAAC;YAS3C,IAAIK,OAAO,EAAE;cAEXK,MAAM,GAAGL,OAAO,CAACM,MAAM,GAAG,CAAC;cAC3BC,cAAc,GAAG,IAAAC,gCAAmB,EAACV,IAAI,EAAEK,MAAM,CAAC;YACpD,CAAC,MAAM;cAELE,MAAM,GAAGF,MAAM,CAACG,MAAM;cACtBC,cAAc,GAAG,IAAAE,gCAAmB,EAACX,IAAI,EAAEK,MAAM,CAAC;YACpD;;YAGMO,OAAO,GAAGP,MAAM,CAAC,CAAC,CAAC;YAAA,wBACwB,IAAAQ,+BAAqB,EAACD,OAAO,CAAC,EAAxEE,MAAM,yBAANA,MAAM,EAAEC,QAAQ,yBAARA,QAAQ,EAAEC,aAAa,yBAAbA,aAAa,EAAEC,KAAK,yBAALA,KAAK;YACvCC,QAAQ,GAAGjB,UAAU,CAACkB,YAAY,EAAE;YACpCC,IAAI,GAAG;cAACjB,yBAAyB,EAAzBA,yBAAyB;cAAEa,aAAa,EAAbA;YAAa,CAAC;YAEjDK,IAAI,GAAGC,KAAK,CAACC,IAAI,CAAC;cAACf,MAAM,EAAED;YAAM,CAAC,CAAC,CAACiB,GAAG,CAAC,UAACC,CAAC,EAAEC,UAAU,EAAK;cAC/D,IAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAU,CAAC;cAClC,IAAME,OAAO,GAAG,SAAVA,OAAO,CAAIC,GAAqB;gBAAA,OAAKpB,cAAc,CAACoB,GAAG,EAAEH,UAAU,CAAC;cAAA;cAC1E,IAAMI,MAAM,GAAG,IAAIC,wBAAe,CAACH,OAAO,EAAEX,KAAK,EAAEC,QAAQ,EAAES,KAAK,EAAEb,MAAM,EAAEM,IAAI,CAAC;cACjF,OAAOU,MAAM;YACf,CAAC,CAAC;YAAA,iCAEK;cAACT,IAAI,EAAJA,IAAI;cAAEW,QAAQ,EAAEpB;YAAO,CAAC;UAAA;UAAA;YAAA;QAAA;MAAA;IAAA;EAAA,CACjC;EAAA;AAAA"}

package/dist/es5/lib/ome/ome-indexers.js

@@ -1,23 +1,20 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.getOmeLegacyIndexer = getOmeLegacyIndexer;
 exports.getOmeSubIFDIndexer = getOmeSubIFDIndexer;
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 function getOmeLegacyIndexer(tiff, rootMeta) {
   var imgMeta = rootMeta[0];
   var _imgMeta$Pixels = imgMeta.Pixels,
-      SizeT = _imgMeta$Pixels.SizeT,
-      SizeC = _imgMeta$Pixels.SizeC,
-      SizeZ = _imgMeta$Pixels.SizeZ;
+    SizeT = _imgMeta$Pixels.SizeT,
+    SizeC = _imgMeta$Pixels.SizeC,
+    SizeZ = _imgMeta$Pixels.SizeZ;
   var ifdIndexer = getOmeIFDIndexer(imgMeta);
   return function (sel, pyramidLevel) {
     var index = ifdIndexer(sel);
@@ -40,42 +37,31 @@ function getOmeSubIFDIndexer(tiff, rootMeta) {
               index = ifdIndexer(sel);
               _context.next = 3;
               return tiff.getImage(index);
-
             case 3:
               baseImage = _context.sent;
-
               if (!(pyramidLevel === 0)) {
                 _context.next = 6;
                 break;
               }
-
               return _context.abrupt("return", baseImage);
-
             case 6:
               SubIFDs = baseImage.fileDirectory.SubIFDs;
-
               if (SubIFDs) {
                 _context.next = 9;
                 break;
               }
-
               throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
-
             case 9:
               key = "".concat(sel.t, "-").concat(sel.c, "-").concat(sel.z, "-").concat(pyramidLevel);
-
               if (!ifdCache.has(key)) {
                 subIfdOffset = SubIFDs[pyramidLevel - 1];
                 ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
               }
-
               _context.next = 13;
               return ifdCache.get(key);
-
             case 13:
               ifd = _context.sent;
               return _context.abrupt("return", new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source));
-
             case 15:
             case "end":
               return _context.stop();
@@ -83,7 +69,6 @@ function getOmeSubIFDIndexer(tiff, rootMeta) {
         }
       }, _callee);
     }));
-
     return function (_x, _x2) {
       return _ref.apply(this, arguments);
     };
@@ -92,72 +77,65 @@ function getOmeSubIFDIndexer(tiff, rootMeta) {
 
 function getOmeIFDIndexer(imgMeta) {
   var _imgMeta$Pixels2 = imgMeta.Pixels,
-      SizeC = _imgMeta$Pixels2.SizeC,
-      SizeZ = _imgMeta$Pixels2.SizeZ,
-      SizeT = _imgMeta$Pixels2.SizeT,
-      DimensionOrder = _imgMeta$Pixels2.DimensionOrder;
-
+    SizeC = _imgMeta$Pixels2.SizeC,
+    SizeZ = _imgMeta$Pixels2.SizeZ,
+    SizeT = _imgMeta$Pixels2.SizeT,
+    DimensionOrder = _imgMeta$Pixels2.DimensionOrder;
   switch (DimensionOrder) {
     case 'XYZCT':
       {
         return function (_ref2) {
           var t = _ref2.t,
-              c = _ref2.c,
-              z = _ref2.z;
+            c = _ref2.c,
+            z = _ref2.z;
           return t * SizeZ * SizeC + c * SizeZ + z;
         };
       }
-
     case 'XYZTC':
       {
         return function (_ref3) {
           var t = _ref3.t,
-              c = _ref3.c,
-              z = _ref3.z;
+            c = _ref3.c,
+            z = _ref3.z;
           return c * SizeZ * SizeT + t * SizeZ + z;
         };
       }
-
     case 'XYCTZ':
       {
         return function (_ref4) {
           var t = _ref4.t,
-              c = _ref4.c,
-              z = _ref4.z;
+            c = _ref4.c,
+            z = _ref4.z;
           return z * SizeC * SizeT + t * SizeC + c;
         };
       }
-
     case 'XYCZT':
       {
         return function (_ref5) {
           var t = _ref5.t,
-              c = _ref5.c,
-              z = _ref5.z;
+            c = _ref5.c,
+            z = _ref5.z;
           return t * SizeC * SizeZ + z * SizeC + c;
         };
       }
-
     case 'XYTCZ':
       {
         return function (_ref6) {
           var t = _ref6.t,
-              c = _ref6.c,
-              z = _ref6.z;
+            c = _ref6.c,
+            z = _ref6.z;
           return z * SizeT * SizeC + c * SizeT + t;
         };
       }
-
     case 'XYTZC':
       {
         return function (_ref7) {
           var t = _ref7.t,
-              c = _ref7.c,
-              z = _ref7.z;
+            c = _ref7.c,
+            z = _ref7.z;
           return c * SizeT * SizeZ + z * SizeT + t;
         };
       }
-
     default:
       {
         throw new Error("Invalid OME-XML DimensionOrder, got ".concat(DimensionOrder, "."));

package/dist/es5/lib/ome/ome-indexers.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/ome-indexers.ts"],"names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","Pixels","SizeT","SizeC","SizeZ","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","get","ifd","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","DimensionOrder"],"mappings":";;;;;;;;;;;;;;AAyBO,SAASA,mBAAT,CAA6BC,IAA7B,EAA4CC,QAA5C,EAA8E;AACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAD,CAAxB;AACA,wBAA8BC,OAAO,CAACC,MAAtC;AAAA,MAAOC,KAAP,mBAAOA,KAAP;AAAA,MAAcC,KAAd,mBAAcA,KAAd;AAAA,MAAqBC,KAArB,mBAAqBA,KAArB;AACA,MAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAD,CAAnC;AAEA,SAAO,UAACO,GAAD,EAAwBC,YAAxB,EAAiD;AAEtD,QAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAD,CAAxB;AAEA,QAAMG,YAAY,GAAGF,YAAY,GAAGJ,KAAf,GAAuBF,KAAvB,GAA+BC,KAApD;AAEA,WAAOL,IAAI,CAACa,QAAL,CAAcF,KAAK,GAAGC,YAAtB,CAAP;AACD,GAPD;AAQD;;AAgBM,SAASE,mBAAT,CAA6Bd,IAA7B,EAA4CC,QAA5C,EAA8E;AACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAD,CAAxB;AACA,MAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAD,CAAnC;AACA,MAAMa,QAAkD,GAAG,IAAIC,GAAJ,EAA3D;AAEA;AAAA,yEAAO,iBAAOP,GAAP,EAA8BC,YAA9B;AAAA;AAAA;AAAA;AAAA;AAAA;AACCC,cAAAA,KADD,GACSJ,UAAU,CAACE,GAAD,CADnB;AAAA;AAAA,qBAEmBT,IAAI,CAACa,QAAL,CAAcF,KAAd,CAFnB;;AAAA;AAECM,cAAAA,SAFD;;AAAA,oBAKDP,YAAY,KAAK,CALhB;AAAA;AAAA;AAAA;;AAAA,+CAMIO,SANJ;;AAAA;AASEC,cAAAA,OATF,GASaD,SAAS,CAACE,aATvB,CASED,OATF;;AAAA,kBAUAA,OAVA;AAAA;AAAA;AAAA;;AAAA,oBAWGE,KAAK,CAAC,8CAAD,CAXR;;AAAA;AAeCC,cAAAA,GAfD,aAeUZ,GAAG,CAACa,CAfd,cAemBb,GAAG,CAACc,CAfvB,cAe4Bd,GAAG,CAACe,CAfhC,cAeqCd,YAfrC;;AAgBL,kBAAI,CAACK,QAAQ,CAACU,GAAT,CAAaJ,GAAb,CAAL,EAAwB;AAEhBK,gBAAAA,YAFgB,GAEDR,OAAO,CAACR,YAAY,GAAG,CAAhB,CAFN;AAGtBK,gBAAAA,QAAQ,CAACY,GAAT,CAAaN,GAAb,EAAkBrB,IAAI,CAAC4B,oBAAL,CAA0BF,YAA1B,CAAlB;AACD;;AApBI;AAAA,qBAqBcX,QAAQ,CAACc,GAAT,CAAaR,GAAb,CArBd;;AAAA;AAqBCS,cAAAA,GArBD;AAAA,+CAyBE,IAAKb,SAAS,CAACc,WAAf,CACLD,GAAG,CAACX,aADC,EAELW,GAAG,CAACE,eAFC,EAGLhC,IAAI,CAACiC,QAHA,EAILjC,IAAI,CAACkC,YAJA,EAKLlC,IAAI,CAACmC,KALA,EAMLnC,IAAI,CAACoC,MANA,CAzBF;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,KAAP;;AAAA;AAAA;AAAA;AAAA;AAkCD;;AAMD,SAAS5B,gBAAT,CAA0BN,OAA1B,EAAiF;AAC/E,yBAA8CA,OAAO,CAACC,MAAtD;AAAA,MAAOE,KAAP,oBAAOA,KAAP;AAAA,MAAcC,KAAd,oBAAcA,KAAd;AAAA,MAAqBF,KAArB,oBAAqBA,KAArB;AAAA,MAA4BiC,cAA5B,oBAA4BA,cAA5B;;AACA,UAAQA,cAAR;AACE,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAEf,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeF,CAAC,GAAGhB,KAAJ,GAAYD,KAAZ,GAAoBkB,CAAC,GAAGjB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAEF,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeD,CAAC,GAAGjB,KAAJ,GAAYF,KAAZ,GAAoBkB,CAAC,GAAGhB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAEF,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeA,CAAC,GAAGnB,KAAJ,GAAYD,KAAZ,GAAoBkB,CAAC,GAAGjB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAED,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeF,CAAC,GAAGjB,KAAJ,GAAYC,KAAZ,GAAoBkB,CAAC,GAAGnB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAED,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeA,CAAC,GAAGpB,KAAJ,GAAYC,KAAZ,GAAoBkB,CAAC,GAAGnB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO;AAAA,cAAEA,CAAF,SAAEA,CAAF;AAAA,cAAKC,CAAL,SAAKA,CAAL;AAAA,cAAQC,CAAR,SAAQA,CAAR;AAAA,iBAAeD,CAAC,GAAGnB,KAAJ,GAAYE,KAAZ,GAAoBkB,CAAC,GAAGpB,KAAxB,GAAgCkB,CAA/C;AAAA,SAAP;AACD;;AACD;AAAS;AACP,cAAM,IAAIF,KAAJ,+CAAiDiB,cAAjD,OAAN;AACD;AArBH;AAuBD","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"],"file":"ome-indexers.js"}
+{"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","Pixels","SizeT","SizeC","SizeZ","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","get","ifd","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":";;;;;;;;;;;AAyBO,SAASA,mBAAmB,CAACC,IAAa,EAAEC,QAAgB,EAAkB;EACnF,IAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,sBAA8BC,OAAO,CAACC,MAAM;IAArCC,KAAK,mBAALA,KAAK;IAAEC,KAAK,mBAALA,KAAK;IAAEC,KAAK,mBAALA,KAAK;EAC1B,IAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAE5C,OAAO,UAACO,GAAqB,EAAEC,YAAoB,EAAK;IAEtD,IAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAE7B,IAAMG,YAAY,GAAGF,YAAY,GAAGJ,KAAK,GAAGF,KAAK,GAAGC,KAAK;IAEzD,OAAOL,IAAI,CAACa,QAAQ,CAACF,KAAK,GAAGC,YAAY,CAAC;EAC5C,CAAC;AACH;;AAgBO,SAASE,mBAAmB,CAACd,IAAa,EAAEC,QAAgB,EAAkB;EACnF,IAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,IAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAC5C,IAAMa,QAAkD,GAAG,IAAIC,GAAG,EAAE;EAEpE;IAAA,qEAAO,iBAAOP,GAAqB,EAAEC,YAAoB;MAAA;MAAA;QAAA;UAAA;YAAA;cACjDC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;cAAA;cAAA,OACLT,IAAI,CAACa,QAAQ,CAACF,KAAK,CAAC;YAAA;cAAtCM,SAAS;cAAA,MAGXP,YAAY,KAAK,CAAC;gBAAA;gBAAA;cAAA;cAAA,iCACbO,SAAS;YAAA;cAGXC,OAAO,GAAID,SAAS,CAACE,aAAa,CAAlCD,OAAO;cAAA,IACTA,OAAO;gBAAA;gBAAA;cAAA;cAAA,MACJE,KAAK,CAAC,8CAA8C,CAAC;YAAA;cAIvDC,GAAG,aAAMZ,GAAG,CAACa,CAAC,cAAIb,GAAG,CAACc,CAAC,cAAId,GAAG,CAACe,CAAC,cAAId,YAAY;cACtD,IAAI,CAACK,QAAQ,CAACU,GAAG,CAACJ,GAAG,CAAC,EAAE;gBAEhBK,YAAY,GAAGR,OAAO,CAACR,YAAY,GAAG,CAAC,CAAC;gBAC9CK,QAAQ,CAACY,GAAG,CAACN,GAAG,EAAErB,IAAI,CAAC4B,oBAAoB,CAACF,YAAY,CAAC,CAAC;cAC5D;cAAC;cAAA,OACkBX,QAAQ,CAACc,GAAG,CAACR,GAAG,CAAC;YAAA;cAA9BS,GAAG;cAAA,iCAIF,IAAKb,SAAS,CAACc,WAAW,CAC/BD,GAAG,CAACX,aAAa,EACjBW,GAAG,CAACE,eAAe,EACnBhC,IAAI,CAACiC,QAAQ,EACbjC,IAAI,CAACkC,YAAY,EACjBlC,IAAI,CAACmC,KAAK,EACVnC,IAAI,CAACoC,MAAM,CACZ;YAAA;YAAA;cAAA;UAAA;QAAA;MAAA;IAAA,CACF;IAAA;MAAA;IAAA;EAAA;AACH;;AAMA,SAAS5B,gBAAgB,CAACN,OAAkB,EAAqC;EAC/E,uBAA8CA,OAAO,CAACC,MAAM;IAArDE,KAAK,oBAALA,KAAK;IAAEC,KAAK,oBAALA,KAAK;IAAEF,KAAK,oBAALA,KAAK;IAAEiC,cAAc,oBAAdA,cAAc;EAC1C,QAAQA,cAAc;IACpB,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAEf,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMF,CAAC,GAAGhB,KAAK,GAAGD,KAAK,GAAGkB,CAAC,GAAGjB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAEF,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMD,CAAC,GAAGjB,KAAK,GAAGF,KAAK,GAAGkB,CAAC,GAAGhB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAEF,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMA,CAAC,GAAGnB,KAAK,GAAGD,KAAK,GAAGkB,CAAC,GAAGjB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAED,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMF,CAAC,GAAGjB,KAAK,GAAGC,KAAK,GAAGkB,CAAC,GAAGnB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAED,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMA,CAAC,GAAGpB,KAAK,GAAGC,KAAK,GAAGkB,CAAC,GAAGnB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAO;UAAA,IAAEA,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;YAAEC,CAAC,SAADA,CAAC;UAAA,OAAMD,CAAC,GAAGnB,KAAK,GAAGE,KAAK,GAAGkB,CAAC,GAAGpB,KAAK,GAAGkB,CAAC;QAAA;MACzD;IACA;MAAS;QACP,MAAM,IAAIF,KAAK,+CAAwCiB,cAAc,OAAI;MAC3E;EAAC;AAEL"}

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

@@ -1,17 +1,13 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getOmePixelSourceMeta = getOmePixelSourceMeta;
 exports.DTYPE_LOOKUP = void 0;
-
+exports.getOmePixelSourceMeta = getOmePixelSourceMeta;
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _utils = require("./utils");
-
 var DTYPE_LOOKUP = {
   uint8: 'Uint8',
   uint16: 'Uint16',
@@ -23,10 +19,10 @@ var DTYPE_LOOKUP = {
   int32: 'Int32'
 };
 exports.DTYPE_LOOKUP = DTYPE_LOOKUP;
-
 function getOmePixelSourceMeta(_ref) {
   var Pixels = _ref.Pixels;
   var labels = (0, _utils.getLabels)(Pixels.DimensionOrder);
+
   var dims = (0, _utils.getDims)(labels);
   var shape = Array(labels.length).fill(0);
   shape[dims('t')] = Pixels.SizeT;
@@ -44,13 +40,10 @@ function getOmePixelSourceMeta(_ref) {
     s[dims('y')] = Pixels.SizeY >> level;
     return s;
   };
-
   if (!(Pixels.Type in DTYPE_LOOKUP)) {
     throw Error("Pixel type ".concat(Pixels.Type, " not supported."));
   }
-
   var dtype = DTYPE_LOOKUP[Pixels.Type];
-
   if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
     var physicalSizes = {
       x: {
@@ -62,14 +55,12 @@ function getOmePixelSourceMeta(_ref) {
         unit: Pixels.PhysicalSizeYUnit
       }
     };
-
     if (Pixels.PhysicalSizeZ) {
       physicalSizes.z = {
         size: Pixels.PhysicalSizeZ,
         unit: Pixels.PhysicalSizeZUnit
       };
     }
-
     return {
       labels: labels,
       getShape: getShape,
@@ -77,7 +68,6 @@ function getOmePixelSourceMeta(_ref) {
       dtype: dtype
     };
   }
-
   return {
     labels: labels,
     getShape: getShape,

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

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/ome-utils.ts"],"names":["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;;AAGO,IAAMA,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;;;AAWA,SAASC,qBAAT,OAAoD;AAAA,MAApBC,MAAoB,QAApBA,MAAoB;AAEzD,MAAMC,MAAM,GAAG,sBAAUD,MAAM,CAACE,cAAjB,CAAf;AAGA,MAAMC,IAAI,GAAG,oBAAQF,MAAR,CAAb;AACA,MAAMG,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,MAAMC,QAAQ,GAAG,SAAXA,QAAW,CAACC,KAAD,EAAmB;AAClC,QAAMC,CAAC,oCAAOX,KAAP,CAAP;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,MAAME,KAAK,GAAG9B,YAAY,CAACU,MAAM,CAACkB,IAAR,CAA1B;;AACA,MAAIlB,MAAM,CAACqB,aAAP,IAAwBrB,MAAM,CAACsB,aAAnC,EAAkD;AAChD,QAAMC,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,MAAM,EAANA,MAAD;AAASY,MAAAA,QAAQ,EAARA,QAAT;AAAmBU,MAAAA,aAAa,EAAbA,aAAnB;AAAkCH,MAAAA,KAAK,EAALA;AAAlC,KAAP;AACD;;AAED,SAAO;AAACnB,IAAAA,MAAM,EAANA,MAAD;AAASY,IAAAA,QAAQ,EAARA,QAAT;AAAmBO,IAAAA,KAAK,EAALA;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":["DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","Pixels","labels","getLabels","DimensionOrder","dims","getDims","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;AAGO,IAAMA,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;AAAC;AAEJ,SAASC,qBAAqB,OAAsB;EAAA,IAApBC,MAAM,QAANA,MAAM;EAE3C,IAAMC,MAAM,GAAG,IAAAC,gBAAS,EAACF,MAAM,CAACG,cAAc,CAAC;;EAG/C,IAAMC,IAAI,GAAG,IAAAC,cAAO,EAACJ,MAAM,CAAC;EAC5B,IAAMK,KAAe,GAAGC,KAAK,CAACN,MAAM,CAACO,MAAM,CAAC,CAACC,IAAI,CAAC,CAAC,CAAC;EACpDH,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACU,KAAK;EAC/BJ,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACW,KAAK;EAC/BL,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACY,KAAK;;EAG/B,IAAIZ,MAAM,CAACa,WAAW,EAAE;IAEtBZ,MAAM,CAACa,IAAI,CAAC,IAAI,CAAC;IACjBR,KAAK,CAACQ,IAAI,CAAC,CAAC,CAAC;EACf;;EAIA,IAAMC,QAAQ,GAAG,SAAXA,QAAQ,CAAIC,KAAa,EAAK;IAClC,IAAMC,CAAC,oCAAOX,KAAK,CAAC;IACpBW,CAAC,CAACb,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACkB,KAAK,IAAIF,KAAK;IACpCC,CAAC,CAACb,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACmB,KAAK,IAAIH,KAAK;IACpC,OAAOC,CAAC;EACV,CAAC;EAED,IAAI,EAAEjB,MAAM,CAACoB,IAAI,IAAI9B,YAAY,CAAC,EAAE;IAClC,MAAM+B,KAAK,sBAAerB,MAAM,CAACoB,IAAI,qBAAkB;EACzD;EAEA,IAAME,KAAK,GAAGhC,YAAY,CAACU,MAAM,CAACoB,IAAI,CAA8B;EACpE,IAAIpB,MAAM,CAACuB,aAAa,IAAIvB,MAAM,CAACwB,aAAa,EAAE;IAChD,IAAMC,aAEL,GAAG;MACFC,CAAC,EAAE;QACDC,IAAI,EAAE3B,MAAM,CAACuB,aAAa;QAC1BK,IAAI,EAAE5B,MAAM,CAAC6B;MACf,CAAC;MACDC,CAAC,EAAE;QACDH,IAAI,EAAE3B,MAAM,CAACwB,aAAa;QAC1BI,IAAI,EAAE5B,MAAM,CAAC+B;MACf;IACF,CAAC;IACD,IAAI/B,MAAM,CAACgC,aAAa,EAAE;MACxBP,aAAa,CAACQ,CAAC,GAAG;QAChBN,IAAI,EAAE3B,MAAM,CAACgC,aAAa;QAC1BJ,IAAI,EAAE5B,MAAM,CAACkC;MACf,CAAC;IACH;IACA,OAAO;MAACjC,MAAM,EAANA,MAAM;MAAEc,QAAQ,EAARA,QAAQ;MAAEU,aAAa,EAAbA,aAAa;MAAEH,KAAK,EAALA;IAAK,CAAC;EACjD;EAEA,OAAO;IAACrB,MAAM,EAANA,MAAM;IAAEc,QAAQ,EAARA,QAAQ;IAAEO,KAAK,EAALA;EAAK,CAAC;AAClC"}