@loaders.gl/geotiff 4.1.0-alpha.1 → 4.1.0-alpha.11

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (69) hide show
  1. package/dist/dist.dev.js +1257 -1073
  2. package/dist/geotiff-loader.d.ts +21 -0
  3. package/dist/geotiff-loader.d.ts.map +1 -0
  4. package/dist/geotiff-loader.js +59 -0
  5. package/dist/geotiff-loader.js.map +1 -0
  6. package/dist/index.cjs +46 -40
  7. package/dist/index.d.ts +2 -1
  8. package/dist/index.d.ts.map +1 -1
  9. package/dist/index.js +2 -1
  10. package/dist/index.js.map +1 -1
  11. package/dist/lib/load-geotiff.d.ts +1 -1
  12. package/dist/lib/load-geotiff.d.ts.map +1 -1
  13. package/dist/lib/load-geotiff.js +1 -5
  14. package/dist/lib/load-geotiff.js.map +1 -1
  15. package/dist/lib/ome/load-ome-tiff.d.ts +1 -1
  16. package/dist/lib/ome/load-ome-tiff.d.ts.map +1 -1
  17. package/dist/lib/ome/load-ome-tiff.js +1 -1
  18. package/dist/lib/ome/load-ome-tiff.js.map +1 -1
  19. package/dist/lib/ome/ome-indexers.d.ts +1 -0
  20. package/dist/lib/ome/ome-indexers.d.ts.map +1 -1
  21. package/dist/lib/ome/ome-indexers.js.map +1 -1
  22. package/dist/lib/ome/ome-utils.d.ts.map +1 -1
  23. package/dist/lib/ome/ome-utils.js.map +1 -1
  24. package/dist/lib/ome/omexml.d.ts.map +1 -1
  25. package/dist/lib/ome/omexml.js.map +1 -1
  26. package/dist/lib/ome/utils.d.ts.map +1 -1
  27. package/dist/lib/ome/utils.js.map +1 -1
  28. package/dist/lib/tiff-pixel-source.d.ts +1 -2
  29. package/dist/lib/tiff-pixel-source.d.ts.map +1 -1
  30. package/dist/lib/tiff-pixel-source.js +1 -2
  31. package/dist/lib/tiff-pixel-source.js.map +1 -1
  32. package/{src/lib/utils/Pool.ts → dist/lib/utils/Pool.ts.disabled} +3 -2
  33. package/{src/lib/utils/proxies.ts → dist/lib/utils/proxies.ts.disabled} +2 -1
  34. package/dist/lib/utils/tiff-utils.d.ts.map +1 -1
  35. package/dist/lib/utils/tiff-utils.js.map +1 -1
  36. package/dist/loaders.d.ts +13 -0
  37. package/dist/loaders.d.ts.map +1 -0
  38. package/dist/loaders.js +32 -0
  39. package/dist/loaders.js.map +1 -0
  40. package/dist/types.d.ts.map +1 -1
  41. package/dist/types.js.map +1 -1
  42. package/package.json +5 -5
  43. package/src/geotiff-loader.ts +115 -0
  44. package/src/index.ts +5 -2
  45. package/src/lib/load-geotiff.ts +10 -9
  46. package/src/lib/ome/load-ome-tiff.ts +3 -2
  47. package/src/lib/ome/ome-indexers.ts +7 -3
  48. package/src/lib/ome/ome-utils.ts +2 -1
  49. package/src/lib/ome/omexml.ts +2 -1
  50. package/src/lib/ome/utils.ts +2 -1
  51. package/src/lib/tiff-pixel-source.ts +7 -6
  52. package/src/lib/utils/Pool.ts.disabled +99 -0
  53. package/src/lib/utils/proxies.ts.disabled +96 -0
  54. package/src/lib/utils/tiff-utils.ts +2 -1
  55. package/src/loaders.ts +68 -0
  56. package/src/types.ts +2 -1
  57. package/dist/lib/utils/Pool.d.ts +0 -29
  58. package/dist/lib/utils/Pool.d.ts.map +0 -1
  59. package/dist/lib/utils/Pool.js +0 -60
  60. package/dist/lib/utils/Pool.js.map +0 -1
  61. package/dist/lib/utils/proxies.d.ts +0 -6
  62. package/dist/lib/utils/proxies.d.ts.map +0 -1
  63. package/dist/lib/utils/proxies.js +0 -54
  64. package/dist/lib/utils/proxies.js.map +0 -1
  65. package/dist/typings/geotiff.d.ts +0 -60
  66. package/dist/typings/geotiff.d.ts.map +0 -1
  67. package/dist/typings/geotiff.js +0 -2
  68. package/dist/typings/geotiff.js.map +0 -1
  69. package/src/typings/geotiff.ts +0 -75
@@ -0,0 +1,21 @@
1
+ import type { TypedArray } from '@loaders.gl/loader-utils';
2
+ import type { LoaderWithParser, LoaderOptions } from '@loaders.gl/loader-utils';
3
+ type GeoTIFFData = {
4
+ crs?: string;
5
+ bounds: number[];
6
+ metadata: Record<string, unknown>;
7
+ width: number;
8
+ height: number;
9
+ data: TypedArray;
10
+ };
11
+ /** GeoTIFF load options */
12
+ export type GeoTIFFLoaderOptions = LoaderOptions & {
13
+ geotiff?: {
14
+ enableAlpha: boolean;
15
+ };
16
+ };
17
+ /** GeoTIFF loader */
18
+ export declare const GeoTIFFLoader: LoaderWithParser<GeoTIFFData, never, GeoTIFFLoaderOptions>;
19
+ export declare function isTiff(arrayBuffer: ArrayBuffer): boolean;
20
+ export {};
21
+ //# sourceMappingURL=geotiff-loader.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"geotiff-loader.d.ts","sourceRoot":"","sources":["../src/geotiff-loader.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAC,UAAU,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,KAAK,EAAC,gBAAgB,EAAE,aAAa,EAAC,MAAM,0BAA0B,CAAC;AAQ9E,KAAK,WAAW,GAAG;IACjB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAElC,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,UAAU,CAAC;CAClB,CAAC;AAEF,2BAA2B;AAC3B,MAAM,MAAM,oBAAoB,GAAG,aAAa,GAAG;IACjD,OAAO,CAAC,EAAE;QACR,WAAW,EAAE,OAAO,CAAC;KACtB,CAAC;CACH,CAAC;AAEF,qBAAqB;AACrB,eAAO,MAAM,aAAa,EAAE,gBAAgB,CAAC,WAAW,EAAE,KAAK,EAAE,oBAAoB,CAWpF,CAAC;AAEF,wBAAgB,MAAM,CAAC,WAAW,EAAE,WAAW,GAAG,OAAO,CAuBxD"}
@@ -0,0 +1,59 @@
1
+ import { fromArrayBuffer } from 'geotiff';
2
+ const VERSION = typeof "4.1.0-alpha.11" !== 'undefined' ? "4.1.0-alpha.11" : 'latest';
3
+ export const GeoTIFFLoader = {
4
+ id: 'geotiff',
5
+ name: 'GeoTIFF',
6
+ module: 'geotiff',
7
+ version: VERSION,
8
+ options: {
9
+ enableAlpha: true
10
+ },
11
+ mimeTypes: ['image/tiff', 'image/geotiff'],
12
+ extensions: ['geotiff', 'tiff', 'geotif', 'tif'],
13
+ parse: parseGeoTIFF
14
+ };
15
+ export function isTiff(arrayBuffer) {
16
+ const dataView = new DataView(arrayBuffer);
17
+ const endianness = dataView.getUint16(0);
18
+ let littleEndian;
19
+ switch (endianness) {
20
+ case 0x4949:
21
+ littleEndian = true;
22
+ break;
23
+ case 0x4d4d:
24
+ littleEndian = false;
25
+ break;
26
+ default:
27
+ return false;
28
+ }
29
+ if (dataView.getUint16(2, littleEndian) !== 42) {
30
+ return false;
31
+ }
32
+ return true;
33
+ }
34
+ async function parseGeoTIFF(data, options) {
35
+ var _options$geotiff;
36
+ const tiff = await fromArrayBuffer(data);
37
+ const image = await tiff.getImage();
38
+ const rgbData = await image.readRGB({
39
+ enableAlpha: options === null || options === void 0 ? void 0 : (_options$geotiff = options.geotiff) === null || _options$geotiff === void 0 ? void 0 : _options$geotiff.enableAlpha
40
+ });
41
+ const width = image.getWidth();
42
+ const height = image.getHeight();
43
+ const imageData = new Uint8ClampedArray(rgbData);
44
+ const bounds = image.getBoundingBox();
45
+ const metadata = image.getGeoKeys();
46
+ let crs;
47
+ if (metadata !== null && metadata !== void 0 && metadata.ProjectedCSTypeGeoKey) {
48
+ crs = `EPSG:${metadata.ProjectedCSTypeGeoKey}`;
49
+ }
50
+ return {
51
+ crs,
52
+ bounds,
53
+ width,
54
+ height,
55
+ data: imageData,
56
+ metadata
57
+ };
58
+ }
59
+ //# sourceMappingURL=geotiff-loader.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"geotiff-loader.js","names":["fromArrayBuffer","VERSION","GeoTIFFLoader","id","name","module","version","options","enableAlpha","mimeTypes","extensions","parse","parseGeoTIFF","isTiff","arrayBuffer","dataView","DataView","endianness","getUint16","littleEndian","data","_options$geotiff","tiff","image","getImage","rgbData","readRGB","geotiff","width","getWidth","height","getHeight","imageData","Uint8ClampedArray","bounds","getBoundingBox","metadata","getGeoKeys","crs","ProjectedCSTypeGeoKey"],"sources":["../src/geotiff-loader.ts"],"sourcesContent":["// loaders.gl\n// SPDX-License-Identifier: MIT\n// Copyright (c) vis.gl contributors\n\nimport type {TypedArray} from '@loaders.gl/loader-utils';\nimport type {LoaderWithParser, LoaderOptions} from '@loaders.gl/loader-utils';\nimport {fromArrayBuffer} from 'geotiff';\n\n// __VERSION__ is injected by babel-plugin-version-inline\n// @ts-ignore TS2304: Cannot find name '__VERSION__'.\nconst VERSION = typeof __VERSION__ !== 'undefined' ? __VERSION__ : 'latest';\n\n// Return type definition for GeoTIFF loader\ntype GeoTIFFData = {\n crs?: string;\n bounds: number[];\n metadata: Record<string, unknown>;\n\n width: number;\n height: number;\n data: TypedArray;\n};\n\n/** GeoTIFF load options */\nexport type GeoTIFFLoaderOptions = LoaderOptions & {\n geotiff?: {\n enableAlpha: boolean;\n };\n};\n\n/** GeoTIFF loader */\nexport const GeoTIFFLoader: LoaderWithParser<GeoTIFFData, never, GeoTIFFLoaderOptions> = {\n id: 'geotiff',\n name: 'GeoTIFF',\n module: 'geotiff',\n version: VERSION,\n options: {\n enableAlpha: true\n },\n mimeTypes: ['image/tiff', 'image/geotiff'],\n extensions: ['geotiff', 'tiff', 'geotif', 'tif'],\n parse: parseGeoTIFF\n};\n\nexport function isTiff(arrayBuffer: ArrayBuffer): boolean {\n const dataView = new DataView(arrayBuffer);\n // Byte offset\n const endianness = dataView.getUint16(0);\n let littleEndian: boolean;\n switch (endianness) {\n case 0x4949:\n littleEndian = true;\n break;\n case 0x4d4d:\n littleEndian = false;\n break;\n default:\n return false;\n // throw new Error(`invalid byte order: 0x${endianness.toString(16)}`);\n }\n\n // Magic number\n if (dataView.getUint16(2, littleEndian) !== 42) {\n return false;\n }\n\n return true;\n}\n\n/**\n * Loads a GeoTIFF file containing a RGB image.\n */\nasync function parseGeoTIFF(\n data: ArrayBuffer,\n options?: GeoTIFFLoaderOptions\n): Promise<GeoTIFFData> {\n // Load using Geotiff.js\n const tiff = await fromArrayBuffer(data);\n\n // Assumes we only have one image inside TIFF\n const image = await tiff.getImage();\n\n // Read image and size\n // TODO: Add support for worker pools here.\n // TODO: Add support for more image formats.\n const rgbData = await image.readRGB({\n enableAlpha: options?.geotiff?.enableAlpha\n });\n\n const width = image.getWidth();\n const height = image.getHeight();\n\n // Create a new ImageData object\n const imageData = new Uint8ClampedArray(rgbData as unknown as Uint8Array);\n\n // Get geo data\n const bounds = image.getBoundingBox();\n const metadata = image.getGeoKeys();\n\n // ProjectedCSTypeGeoKey is the only key we support for now, we assume it is an EPSG code\n let crs: string | undefined;\n if (metadata?.ProjectedCSTypeGeoKey) {\n crs = `EPSG:${metadata.ProjectedCSTypeGeoKey}`;\n }\n\n // Return GeoReferenced image data\n return {\n crs,\n bounds,\n width,\n height,\n data: imageData,\n metadata\n };\n}\n"],"mappings":"AAMA,SAAQA,eAAe,QAAO,SAAS;AAIvC,MAAMC,OAAO,GAAG,uBAAkB,KAAK,WAAW,sBAAiB,QAAQ;AAqB3E,OAAO,MAAMC,aAAyE,GAAG;EACvFC,EAAE,EAAE,SAAS;EACbC,IAAI,EAAE,SAAS;EACfC,MAAM,EAAE,SAAS;EACjBC,OAAO,EAAEL,OAAO;EAChBM,OAAO,EAAE;IACPC,WAAW,EAAE;EACf,CAAC;EACDC,SAAS,EAAE,CAAC,YAAY,EAAE,eAAe,CAAC;EAC1CC,UAAU,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,CAAC;EAChDC,KAAK,EAAEC;AACT,CAAC;AAED,OAAO,SAASC,MAAMA,CAACC,WAAwB,EAAW;EACxD,MAAMC,QAAQ,GAAG,IAAIC,QAAQ,CAACF,WAAW,CAAC;EAE1C,MAAMG,UAAU,GAAGF,QAAQ,CAACG,SAAS,CAAC,CAAC,CAAC;EACxC,IAAIC,YAAqB;EACzB,QAAQF,UAAU;IAChB,KAAK,MAAM;MACTE,YAAY,GAAG,IAAI;MACnB;IACF,KAAK,MAAM;MACTA,YAAY,GAAG,KAAK;MACpB;IACF;MACE,OAAO,KAAK;EAEhB;EAGA,IAAIJ,QAAQ,CAACG,SAAS,CAAC,CAAC,EAAEC,YAAY,CAAC,KAAK,EAAE,EAAE;IAC9C,OAAO,KAAK;EACd;EAEA,OAAO,IAAI;AACb;AAKA,eAAeP,YAAYA,CACzBQ,IAAiB,EACjBb,OAA8B,EACR;EAAA,IAAAc,gBAAA;EAEtB,MAAMC,IAAI,GAAG,MAAMtB,eAAe,CAACoB,IAAI,CAAC;EAGxC,MAAMG,KAAK,GAAG,MAAMD,IAAI,CAACE,QAAQ,CAAC,CAAC;EAKnC,MAAMC,OAAO,GAAG,MAAMF,KAAK,CAACG,OAAO,CAAC;IAClClB,WAAW,EAAED,OAAO,aAAPA,OAAO,wBAAAc,gBAAA,GAAPd,OAAO,CAAEoB,OAAO,cAAAN,gBAAA,uBAAhBA,gBAAA,CAAkBb;EACjC,CAAC,CAAC;EAEF,MAAMoB,KAAK,GAAGL,KAAK,CAACM,QAAQ,CAAC,CAAC;EAC9B,MAAMC,MAAM,GAAGP,KAAK,CAACQ,SAAS,CAAC,CAAC;EAGhC,MAAMC,SAAS,GAAG,IAAIC,iBAAiB,CAACR,OAAgC,CAAC;EAGzE,MAAMS,MAAM,GAAGX,KAAK,CAACY,cAAc,CAAC,CAAC;EACrC,MAAMC,QAAQ,GAAGb,KAAK,CAACc,UAAU,CAAC,CAAC;EAGnC,IAAIC,GAAuB;EAC3B,IAAIF,QAAQ,aAARA,QAAQ,eAARA,QAAQ,CAAEG,qBAAqB,EAAE;IACnCD,GAAG,GAAI,QAAOF,QAAQ,CAACG,qBAAsB,EAAC;EAChD;EAGA,OAAO;IACLD,GAAG;IACHJ,MAAM;IACNN,KAAK;IACLE,MAAM;IACNV,IAAI,EAAEY,SAAS;IACfI;EACF,CAAC;AACH"}
package/dist/index.cjs CHANGED
@@ -20,48 +20,56 @@ var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: tru
20
20
  // src/index.ts
21
21
  var src_exports = {};
22
22
  __export(src_exports, {
23
- TiffPixelSource: () => tiff_pixel_source_default,
23
+ GeoTIFFLoader: () => GeoTIFFLoader,
24
+ TiffPixelSource: () => TiffPixelSource,
24
25
  loadGeoTiff: () => loadGeoTiff
25
26
  });
26
27
  module.exports = __toCommonJS(src_exports);
27
28
 
28
- // src/lib/load-geotiff.ts
29
+ // src/geotiff-loader.ts
29
30
  var import_geotiff = require("geotiff");
30
-
31
- // src/lib/utils/proxies.ts
32
- var VIV_PROXY_KEY = "__viv";
33
- var OFFSETS_PROXY_KEY = `${VIV_PROXY_KEY}-offsets`;
34
- var POOL_PROXY_KEY = `${VIV_PROXY_KEY}-decoder-pool`;
35
- function checkProxies(tiff) {
36
- if (!isProxy(tiff, OFFSETS_PROXY_KEY)) {
37
- console.warn("GeoTIFF source is missing offsets proxy.");
38
- }
39
- if (!isProxy(tiff, POOL_PROXY_KEY)) {
40
- console.warn("GeoTIFF source is missing decoder-pool proxy.");
31
+ var VERSION = typeof __VERSION__ !== "undefined" ? __VERSION__ : "latest";
32
+ var GeoTIFFLoader = {
33
+ id: "geotiff",
34
+ name: "GeoTIFF",
35
+ module: "geotiff",
36
+ version: VERSION,
37
+ options: {
38
+ enableAlpha: true
39
+ },
40
+ mimeTypes: ["image/tiff", "image/geotiff"],
41
+ extensions: ["geotiff", "tiff", "geotif", "tif"],
42
+ parse: parseGeoTIFF
43
+ };
44
+ async function parseGeoTIFF(data, options) {
45
+ var _a;
46
+ const tiff = await (0, import_geotiff.fromArrayBuffer)(data);
47
+ const image = await tiff.getImage();
48
+ const rgbData = await image.readRGB({
49
+ enableAlpha: (_a = options == null ? void 0 : options.geotiff) == null ? void 0 : _a.enableAlpha
50
+ });
51
+ const width = image.getWidth();
52
+ const height = image.getHeight();
53
+ const imageData = new Uint8ClampedArray(rgbData);
54
+ const bounds = image.getBoundingBox();
55
+ const metadata = image.getGeoKeys();
56
+ let crs;
57
+ if (metadata == null ? void 0 : metadata.ProjectedCSTypeGeoKey) {
58
+ crs = `EPSG:${metadata.ProjectedCSTypeGeoKey}`;
41
59
  }
42
- }
43
- function isProxy(tiff, proxyFlag) {
44
- return tiff[proxyFlag];
45
- }
46
- function createOffsetsProxy(tiff, offsets) {
47
- const get = (target, key) => {
48
- if (key === "getImage") {
49
- return (index) => {
50
- if (!(index in target.ifdRequests) && index in offsets) {
51
- const offset = offsets[index];
52
- target.ifdRequests[index] = target.parseFileDirectoryAt(offset);
53
- }
54
- return target.getImage(index);
55
- };
56
- }
57
- if (key === OFFSETS_PROXY_KEY) {
58
- return true;
59
- }
60
- return Reflect.get(target, key);
60
+ return {
61
+ crs,
62
+ bounds,
63
+ width,
64
+ height,
65
+ data: imageData,
66
+ metadata
61
67
  };
62
- return new Proxy(tiff, { get });
63
68
  }
64
69
 
70
+ // src/lib/load-geotiff.ts
71
+ var import_geotiff2 = require("geotiff");
72
+
65
73
  // src/lib/utils/tiff-utils.ts
66
74
  function ensureArray(x) {
67
75
  return Array.isArray(x) ? x : [x];
@@ -145,7 +153,6 @@ var TiffPixelSource = class {
145
153
  console.error(err);
146
154
  }
147
155
  };
148
- var tiff_pixel_source_default = TiffPixelSource;
149
156
 
150
157
  // src/lib/ome/ome-indexers.ts
151
158
  function getOmeLegacyIndexer(tiff, rootMeta) {
@@ -181,6 +188,7 @@ function getOmeSubIFDIndexer(tiff, rootMeta) {
181
188
  return new baseImage.constructor(
182
189
  ifd.fileDirectory,
183
190
  ifd.geoKeyDirectory,
191
+ // @ts-expect-error
184
192
  tiff.dataView,
185
193
  tiff.littleEndian,
186
194
  tiff.cache,
@@ -369,7 +377,7 @@ async function loadOmeTiff(tiff, firstImage) {
369
377
  const data = Array.from({ length: levels }).map((_, resolution) => {
370
378
  const shape = getShape(resolution);
371
379
  const indexer = (sel) => pyramidIndexer(sel, resolution);
372
- const source = new tiff_pixel_source_default(indexer, dtype, tileSize, shape, labels, meta);
380
+ const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);
373
381
  return source;
374
382
  });
375
383
  return { data, metadata: imgMeta };
@@ -379,17 +387,15 @@ async function loadOmeTiff(tiff, firstImage) {
379
387
  async function loadGeoTiff(source, opts = {}) {
380
388
  const { headers, offsets } = opts;
381
389
  let tiff;
382
- if (source instanceof import_geotiff.GeoTIFF) {
390
+ if (source instanceof import_geotiff2.GeoTIFF) {
383
391
  tiff = source;
384
392
  } else if (typeof source === "string") {
385
- tiff = await (0, import_geotiff.fromUrl)(source, headers);
393
+ tiff = await (0, import_geotiff2.fromUrl)(source, headers);
386
394
  } else {
387
- tiff = await (0, import_geotiff.fromBlob)(source);
395
+ tiff = await (0, import_geotiff2.fromBlob)(source);
388
396
  }
389
397
  if (offsets) {
390
- tiff = createOffsetsProxy(tiff, offsets);
391
398
  }
392
- checkProxies(tiff);
393
399
  const firstImage = await tiff.getImage(0);
394
400
  if (isOmeTiff(firstImage)) {
395
401
  return loadOmeTiff(tiff, firstImage);
package/dist/index.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ export { GeoTIFFLoader } from './geotiff-loader';
1
2
  export { loadGeoTiff } from './lib/load-geotiff';
2
- export { default as TiffPixelSource } from './lib/tiff-pixel-source';
3
+ export { TiffPixelSource } from './lib/tiff-pixel-source';
3
4
  //# sourceMappingURL=index.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,WAAW,EAAC,MAAM,oBAAoB,CAAC;AAC/C,OAAO,EAAC,OAAO,IAAI,eAAe,EAAC,MAAM,yBAAyB,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,aAAa,EAAC,MAAM,kBAAkB,CAAC;AAE/C,OAAO,EAAC,WAAW,EAAC,MAAM,oBAAoB,CAAC;AAC/C,OAAO,EAAC,eAAe,EAAC,MAAM,yBAAyB,CAAC"}
package/dist/index.js CHANGED
@@ -1,3 +1,4 @@
1
+ export { GeoTIFFLoader } from "./geotiff-loader.js";
1
2
  export { loadGeoTiff } from "./lib/load-geotiff.js";
2
- export { default as TiffPixelSource } from "./lib/tiff-pixel-source.js";
3
+ export { TiffPixelSource } from "./lib/tiff-pixel-source.js";
3
4
  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","names":["loadGeoTiff","default","TiffPixelSource"],"sources":["../src/index.ts"],"sourcesContent":["// loaders.gl, MIT license\n// Copyright (c) vis.gl contributors\n\nexport {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"mappings":"SAGQA,WAAW;AAAA,SACXC,OAAO,IAAIC,eAAe"}
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+ {"version":3,"file":"index.js","names":["GeoTIFFLoader","loadGeoTiff","TiffPixelSource"],"sources":["../src/index.ts"],"sourcesContent":["// loaders.gl\n// SPDX-License-Identifier: MIT\n// Copyright (c) vis.gl contributors\n\nexport {GeoTIFFLoader} from './geotiff-loader';\n\nexport {loadGeoTiff} from './lib/load-geotiff';\nexport {TiffPixelSource} from './lib/tiff-pixel-source';\n"],"mappings":"SAIQA,aAAa;AAAA,SAEbC,WAAW;AAAA,SACXC,eAAe"}
@@ -1,5 +1,5 @@
1
1
  import { GeoTIFF } from 'geotiff';
2
- import type TiffPixelSource from './tiff-pixel-source';
2
+ import type { TiffPixelSource } from './tiff-pixel-source';
3
3
  /** Options for initializing a tiff pixel source. */
4
4
  interface GeoTIFFOptions {
5
5
  /** Headers passed to each underlying request. */
@@ -1 +1 @@
1
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@@ -1,5 +1,4 @@
1
1
  import { fromUrl, fromBlob, GeoTIFF } from 'geotiff';
2
- import { createOffsetsProxy, checkProxies } from "./utils/proxies.js";
3
2
  import { loadOmeTiff, isOmeTiff } from "./ome/load-ome-tiff.js";
4
3
  export async function loadGeoTiff(source) {
5
4
  let opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
@@ -15,10 +14,7 @@ export async function loadGeoTiff(source) {
15
14
  } else {
16
15
  tiff = await fromBlob(source);
17
16
  }
18
- if (offsets) {
19
- tiff = createOffsetsProxy(tiff, offsets);
20
- }
21
- checkProxies(tiff);
17
+ if (offsets) {}
22
18
  const firstImage = await tiff.getImage(0);
23
19
  if (isOmeTiff(firstImage)) {
24
20
  return loadOmeTiff(tiff, firstImage);
@@ -1 +1 @@
1
- {"version":3,"file":"load-geotiff.js","names":["fromUrl","fromBlob","GeoTIFF","createOffsetsProxy","checkProxies","loadOmeTiff","isOmeTiff","loadGeoTiff","source","opts","arguments","length","undefined","headers","offsets","tiff","firstImage","getImage","Error"],"sources":["../../src/lib/load-geotiff.ts"],"sourcesContent":["// loaders.gl, MIT license\n// Copyright (c) vis.gl contributors\n\nimport {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":"AAGA,SAAQA,OAAO,EAAEC,QAAQ,EAAEC,OAAO,QAAO,SAAS;AAAC,SAIjDC,kBAAkB,EAClBC,YAAY;AAAA,SAINC,WAAW,EAAEC,SAAS;AA4B9B,OAAO,eAAeC,WAAWA,CAC/BC,MAA+B,EAET;EAAA,IADtBC,IAAoB,GAAAC,SAAA,CAAAC,MAAA,QAAAD,SAAA,QAAAE,SAAA,GAAAF,SAAA,MAAG,CAAC,CAAC;EAEzB,MAAM;IAACG,OAAO;IAAEC;EAAO,CAAC,GAAGL,IAAI;EAG/B,IAAIM,IAAa;EACjB,IAAIP,MAAM,YAAYN,OAAO,EAAE;IAC7Ba,IAAI,GAAGP,MAAM;EACf,CAAC,MAAM,IAAI,OAAOA,MAAM,KAAK,QAAQ,EAAE;IACrCO,IAAI,GAAG,MAAMf,OAAO,CAACQ,MAAM,EAAEK,OAAO,CAAC;EACvC,CAAC,MAAM;IACLE,IAAI,GAAG,MAAMd,QAAQ,CAACO,MAAM,CAAC;EAC/B;EAUA,IAAIM,OAAO,EAAE;IAMXC,IAAI,GAAGZ,kBAAkB,CAACY,IAAI,EAAED,OAAO,CAAC;EAC1C;EAMAV,YAAY,CAACW,IAAI,CAAC;EAElB,MAAMC,UAAU,GAAG,MAAMD,IAAI,CAACE,QAAQ,CAAC,CAAC,CAAC;EAEzC,IAAIX,SAAS,CAACU,UAAU,CAAC,EAAE;IACzB,OAAOX,WAAW,CAACU,IAAI,EAAEC,UAAU,CAAC;EACtC;EAEA,MAAM,IAAIE,KAAK,CAAC,yBAAyB,CAAC;AAC5C"}
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@@ -1,5 +1,5 @@
1
1
  import type { GeoTIFF, GeoTIFFImage } from 'geotiff';
2
- import TiffPixelSource from '../tiff-pixel-source';
2
+ import { TiffPixelSource } from '../tiff-pixel-source';
3
3
  export declare const isOmeTiff: (img: GeoTIFFImage) => any;
4
4
  export declare function loadOmeTiff(tiff: GeoTIFF, firstImage: GeoTIFFImage): Promise<{
5
5
  data: TiffPixelSource<["t", "c", "z"] | ["c", "t", "z"] | ["z", "t", "c"] | ["t", "z", "c"] | ["z", "c", "t"] | ["c", "z", "t"]>[];
@@ -1 +1 @@
1
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@@ -1,4 +1,4 @@
1
- import TiffPixelSource from "../tiff-pixel-source.js";
1
+ import { TiffPixelSource } from "../tiff-pixel-source.js";
2
2
  import { getOmeLegacyIndexer, getOmeSubIFDIndexer } from "./ome-indexers.js";
3
3
  import { getOmePixelSourceMeta } from "./ome-utils.js";
4
4
  import { fromString } from "./omexml.js";
@@ -1 +1 @@
1
- {"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":["// loaders.gl, MIT license\n// Copyright (c) vis.gl contributors\n\nimport 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":"OAKOA,eAAe;AAAA,SACdC,mBAAmB,EAAEC,mBAAmB;AAAA,SACxCC,qBAAqB;AAAA,SACrBC,UAAU;AAGlB,OAAO,MAAMC,SAAS,GAAIC,GAAiB,IAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAEnG,OAAO,eAAeC,WAAWA,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,CAAC,CAAC;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"}
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+ {"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":["// loaders.gl\n// SPDX-License-Identifier: MIT\n// Copyright (c) vis.gl contributors\n\nimport 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":"SAMQA,eAAe;AAAA,SACfC,mBAAmB,EAAEC,mBAAmB;AAAA,SACxCC,qBAAqB;AAAA,SACrBC,UAAU;AAGlB,OAAO,MAAMC,SAAS,GAAIC,GAAiB,IAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAEnG,OAAO,eAAeC,WAAWA,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,CAAC,CAAC;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"}
@@ -1,5 +1,6 @@
1
1
  import type { GeoTIFFImage, GeoTIFF } from 'geotiff';
2
2
  import type { OMEXML } from '../ome/omexml';
3
+ export type ImageFileDirectory = any;
3
4
  export type OmeTiffSelection = {
4
5
  t: number;
5
6
  c: number;
@@ -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 - 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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 - 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- {"version":3,"file":"omexml.js","names":["XMLParser","ensureArray","intToRgba","xmlParser","attributeNamePrefix","attributesGroupName","parseTagValue","parseAttributeValue","ignoreAttributes","parse","str","fromString","res","OME","Error","Image","map","img","Channels","Pixels","Channel","c","attr","Color","AquisitionDate","Description","image","format","sizes","name","size","unit","join","SizeX","SizeY","Type","SizeZ","SizeT","SizeC"],"sources":["../../../src/lib/ome/omexml.ts"],"sourcesContent":["// loaders.gl, MIT license\n// Copyright (c) vis.gl contributors\n\nimport {XMLParser} from 'fast-xml-parser';\nimport {ensureArray, intToRgba} from '../utils/tiff-utils';\n\n// WARNING: Changes to the parser options _will_ effect the types in types/omexml.d.ts.\nconst xmlParser = new XMLParser({\n // Nests attributes withtout prefix under 'attr' key for each node\n attributeNamePrefix: '',\n attributesGroupName: 'attr',\n\n // Parses numbers for both attributes and nodes\n parseTagValue: true,\n parseAttributeValue: true,\n\n // Forces attributes to be parsed\n ignoreAttributes: false\n});\n\nconst parse = (str: string): Root => xmlParser.parse(str);\n\nexport function fromString(str: string) {\n const res = parse(str);\n if (!res.OME) {\n throw Error('Failed to parse OME-XML metadata.');\n }\n return ensureArray(res.OME.Image).map((img) => {\n const Channels = ensureArray(img.Pixels.Channel).map((c) => {\n if ('Color' in c.attr) {\n return {...c.attr, Color: intToRgba(c.attr.Color)};\n }\n return {...c.attr};\n });\n const {AquisitionDate = '', Description = ''} = img;\n const image = {\n ...img.attr,\n AquisitionDate,\n Description,\n Pixels: {\n ...img.Pixels.attr,\n Channels\n }\n };\n return {\n ...image,\n format() {\n const {Pixels} = image;\n\n const sizes = (['X', 'Y', 'Z'] as const)\n .map((name) => {\n const size = Pixels[`PhysicalSize${name}` as const];\n const unit = Pixels[`PhysicalSize${name}Unit` as const];\n return size && unit ? 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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":"AAIA,SAAQA,SAAS,QAAO,iBAAiB;AAAC,SAClCC,WAAW,EAAEC,SAAS;AAG9B,MAAMC,SAAS,GAAG,IAAIH,SAAS,CAAC;EAE9BI,mBAAmB,EAAE,EAAE;EACvBC,mBAAmB,EAAE,MAAM;EAG3BC,aAAa,EAAE,IAAI;EACnBC,mBAAmB,EAAE,IAAI;EAGzBC,gBAAgB,EAAE;AACpB,CAAC,CAAC;AAEF,MAAMC,KAAK,GAAIC,GAAW,IAAWP,SAAS,CAACM,KAAK,CAACC,GAAG,CAAC;AAEzD,OAAO,SAASC,UAAUA,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,MAAMA,CAAA,EAAG;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,CAAE,eAAcU,IAAK,EAAC,CAAU;UACnD,MAAME,IAAI,GAAGZ,MAAM,CAAE,eAAcU,IAAK,MAAK,CAAU;UACvD,OAAOC,IAAI,IAAIC,IAAI,GAAI,GAAED,IAAK,IAAGC,IAAK,EAAC,GAAG,GAAG;QAC/C,CAAC,CAAC,CACDC,IAAI,CAAC,KAAK,CAAC;QAEd,OAAO;UACL,kBAAkB,EAAEN,KAAK,CAACF,cAAc;UACxC,iBAAiB,EAAG,GAAEL,MAAM,CAACc,KAAM,MAAKd,MAAM,CAACe,KAAM,EAAC;UACtD,aAAa,EAAEf,MAAM,CAACgB,IAAI;UAC1B,mBAAmB,EAAEP,KAAK;UAC1B,uBAAuB,EAAG,GAAET,MAAM,CAACiB,KAAM,MAAKjB,MAAM,CAACkB,KAAM,EAAC;UAC5DnB,QAAQ,EAAEC,MAAM,CAACmB;QACnB,CAAC;MACH;IACF,CAAC;EACH,CAAC,CAAC;AACJ"}
@@ -1 +1 @@
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@@ -1 +1 @@
1
- {"version":3,"file":"utils.js","names":["getLabels","dimOrder","toLowerCase","split","reverse","getDims","labels","lookup","Map","map","name","i","size","length","Error","index","get","undefined"],"sources":["../../../src/lib/ome/utils.ts"],"sourcesContent":["// loaders.gl, MIT license\n// Copyright (c) vis.gl contributors\n\nimport type {OMEXML} from '../ome/omexml';\nimport type {Labels} from '../../types';\n\n/*\n * Creates typed labels from DimensionOrder.\n * > imgMeta.Pixels.DimensionOrder === 'XYCZT'\n * > getLabels(imgMeta.Pixels) === ['t', 'z', 'c', 'y', 'x']\n */\n\n// eslint-disable-next-line @typescript-eslint/no-unused-vars\ntype Sel<Dim extends string> = Dim extends `${infer Z}${infer X}${infer A}${infer B}${infer C}`\n ? [C, B, A]\n : 'error';\nexport function getLabels(dimOrder: OMEXML[0]['Pixels']['DimensionOrder']) {\n return dimOrder.toLowerCase().split('').reverse() as Labels<Sel<Lowercase<typeof dimOrder>>>;\n}\n\n/*\n * Creates an ES6 map of 'label' -> index\n * > const labels = ['a', 'b', 'c', 'd'];\n * > const dims = getDims(labels);\n * > dims('a') === 0;\n * > dims('b') === 1;\n * > dims('c') === 2;\n * > dims('hi!'); // throws\n */\nexport function getDims<S extends string>(labels: S[]) {\n const lookup = new Map(labels.map((name, i) => [name, i]));\n if (lookup.size !== labels.length) {\n throw Error('Labels must be unique, found duplicated label.');\n }\n return (name: S) => {\n const index = lookup.get(name);\n if (index === undefined) {\n throw Error('Invalid dimension.');\n }\n return index;\n };\n}\n"],"mappings":"AAgBA,OAAO,SAASA,SAASA,CAACC,QAA+C,EAAE;EACzE,OAAOA,QAAQ,CAACC,WAAW,CAAC,CAAC,CAACC,KAAK,CAAC,EAAE,CAAC,CAACC,OAAO,CAAC,CAAC;AACnD;AAWA,OAAO,SAASC,OAAOA,CAAmBC,MAAW,EAAE;EACrD,MAAMC,MAAM,GAAG,IAAIC,GAAG,CAACF,MAAM,CAACG,GAAG,CAAC,CAACC,IAAI,EAAEC,CAAC,KAAK,CAACD,IAAI,EAAEC,CAAC,CAAC,CAAC,CAAC;EAC1D,IAAIJ,MAAM,CAACK,IAAI,KAAKN,MAAM,CAACO,MAAM,EAAE;IACjC,MAAMC,KAAK,CAAC,gDAAgD,CAAC;EAC/D;EACA,OAAQJ,IAAO,IAAK;IAClB,MAAMK,KAAK,GAAGR,MAAM,CAACS,GAAG,CAACN,IAAI,CAAC;IAC9B,IAAIK,KAAK,KAAKE,SAAS,EAAE;MACvB,MAAMH,KAAK,CAAC,oBAAoB,CAAC;IACnC;IACA,OAAOC,KAAK;EACd,CAAC;AACH"}
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@@ -1,6 +1,6 @@
1
1
  import type { GeoTIFFImage } from 'geotiff';
2
2
  import type { PixelSource, PixelSourceSelection, PixelSourceMeta, Dtype, Labels, RasterSelection, TileSelection, PixelData } from '../types';
3
- declare class TiffPixelSource<S extends string[]> implements PixelSource<S> {
3
+ export declare class TiffPixelSource<S extends string[]> implements PixelSource<S> {
4
4
  dtype: Dtype;
5
5
  tileSize: number;
6
6
  shape: number[];
@@ -14,5 +14,4 @@ declare class TiffPixelSource<S extends string[]> implements PixelSource<S> {
14
14
  private _getTileExtent;
15
15
  onTileError(err: Error): void;
16
16
  }
17
- export default TiffPixelSource;
18
17
  //# sourceMappingURL=tiff-pixel-source.d.ts.map
@@ -1 +1 @@
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@@ -1,5 +1,5 @@
1
1
  import { getImageSize, isInterleaved, SIGNAL_ABORTED } from "./utils/tiff-utils.js";
2
- class TiffPixelSource {
2
+ export class TiffPixelSource {
3
3
  constructor(indexer, dtype, tileSize, shape, labels, meta) {
4
4
  this.dtype = void 0;
5
5
  this.tileSize = void 0;
@@ -87,5 +87,4 @@ class TiffPixelSource {
87
87
  console.error(err);
88
88
  }
89
89
  }
90
- export default TiffPixelSource;
91
90
  //# sourceMappingURL=tiff-pixel-source.js.map
@@ -1 +1 @@
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