@loaders.gl/geotiff 3.1.3 → 4.0.0-alpha.5

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 (85) hide show
  1. package/dist/bundle.js +2 -24
  2. package/dist/bundle.js.map +1 -0
  3. package/dist/index.js +3 -10
  4. package/dist/index.js.map +1 -0
  5. package/dist/lib/load-geotiff.js +31 -56
  6. package/dist/lib/load-geotiff.js.map +1 -0
  7. package/dist/lib/ome/load-ome-tiff.js +50 -45
  8. package/dist/lib/ome/load-ome-tiff.js.map +1 -0
  9. package/dist/lib/ome/ome-indexers.js +112 -104
  10. package/dist/lib/ome/ome-indexers.js.map +1 -0
  11. package/dist/lib/ome/ome-utils.js +69 -59
  12. package/dist/lib/ome/ome-utils.js.map +1 -0
  13. package/dist/lib/ome/omexml.js +60 -60
  14. package/dist/lib/ome/omexml.js.map +1 -0
  15. package/dist/lib/ome/utils.js +18 -27
  16. package/dist/lib/ome/utils.js.map +1 -0
  17. package/dist/lib/tiff-pixel-source.js +106 -59
  18. package/dist/lib/tiff-pixel-source.js.map +1 -0
  19. package/dist/lib/utils/Pool.js +72 -78
  20. package/dist/lib/utils/Pool.js.map +1 -0
  21. package/dist/{es5/lib → lib}/utils/decoder.worker.ts.disabled +0 -0
  22. package/dist/lib/utils/proxies.js +56 -79
  23. package/dist/lib/utils/proxies.js.map +1 -0
  24. package/dist/lib/utils/tiff-utils.js +24 -40
  25. package/dist/lib/utils/tiff-utils.js.map +1 -0
  26. package/dist/types.js +2 -2
  27. package/dist/{es5/types.js.map → types.js.map} +0 -0
  28. package/dist/typings/geotiff.js +2 -1
  29. package/dist/{es5/typings → typings}/geotiff.js.map +0 -0
  30. package/package.json +4 -4
  31. package/dist/es5/bundle.js +0 -13
  32. package/dist/es5/bundle.js.map +0 -1
  33. package/dist/es5/index.js +0 -24
  34. package/dist/es5/index.js.map +0 -1
  35. package/dist/es5/lib/load-geotiff.js +0 -100
  36. package/dist/es5/lib/load-geotiff.js.map +0 -1
  37. package/dist/es5/lib/ome/load-ome-tiff.js +0 -85
  38. package/dist/es5/lib/ome/load-ome-tiff.js.map +0 -1
  39. package/dist/es5/lib/ome/ome-indexers.js +0 -167
  40. package/dist/es5/lib/ome/ome-indexers.js.map +0 -1
  41. package/dist/es5/lib/ome/ome-utils.js +0 -87
  42. package/dist/es5/lib/ome/ome-utils.js.map +0 -1
  43. package/dist/es5/lib/ome/omexml.js +0 -82
  44. package/dist/es5/lib/ome/omexml.js.map +0 -1
  45. package/dist/es5/lib/ome/utils.js +0 -32
  46. package/dist/es5/lib/ome/utils.js.map +0 -1
  47. package/dist/es5/lib/tiff-pixel-source.js +0 -202
  48. package/dist/es5/lib/tiff-pixel-source.js.map +0 -1
  49. package/dist/es5/lib/utils/Pool.js +0 -173
  50. package/dist/es5/lib/utils/Pool.js.map +0 -1
  51. package/dist/es5/lib/utils/proxies.js +0 -82
  52. package/dist/es5/lib/utils/proxies.js.map +0 -1
  53. package/dist/es5/lib/utils/tiff-utils.js +0 -53
  54. package/dist/es5/lib/utils/tiff-utils.js.map +0 -1
  55. package/dist/es5/types.js +0 -2
  56. package/dist/es5/typings/geotiff.js +0 -2
  57. package/dist/esm/bundle.js +0 -4
  58. package/dist/esm/bundle.js.map +0 -1
  59. package/dist/esm/index.js +0 -3
  60. package/dist/esm/index.js.map +0 -1
  61. package/dist/esm/lib/load-geotiff.js +0 -32
  62. package/dist/esm/lib/load-geotiff.js.map +0 -1
  63. package/dist/esm/lib/ome/load-ome-tiff.js +0 -51
  64. package/dist/esm/lib/ome/load-ome-tiff.js.map +0 -1
  65. package/dist/esm/lib/ome/ome-indexers.js +0 -116
  66. package/dist/esm/lib/ome/ome-indexers.js.map +0 -1
  67. package/dist/esm/lib/ome/ome-utils.js +0 -73
  68. package/dist/esm/lib/ome/ome-utils.js.map +0 -1
  69. package/dist/esm/lib/ome/omexml.js +0 -66
  70. package/dist/esm/lib/ome/omexml.js.map +0 -1
  71. package/dist/esm/lib/ome/utils.js +0 -21
  72. package/dist/esm/lib/ome/utils.js.map +0 -1
  73. package/dist/esm/lib/tiff-pixel-source.js +0 -111
  74. package/dist/esm/lib/tiff-pixel-source.js.map +0 -1
  75. package/dist/esm/lib/utils/Pool.js +0 -77
  76. package/dist/esm/lib/utils/Pool.js.map +0 -1
  77. package/dist/esm/lib/utils/decoder.worker.ts.disabled +0 -21
  78. package/dist/esm/lib/utils/proxies.js +0 -63
  79. package/dist/esm/lib/utils/proxies.js.map +0 -1
  80. package/dist/esm/lib/utils/tiff-utils.js +0 -28
  81. package/dist/esm/lib/utils/tiff-utils.js.map +0 -1
  82. package/dist/esm/types.js +0 -2
  83. package/dist/esm/types.js.map +0 -1
  84. package/dist/esm/typings/geotiff.js +0 -2
  85. package/dist/esm/typings/geotiff.js.map +0 -1
@@ -1,173 +0,0 @@
1
- "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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- exports.default = void 0;
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-
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- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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-
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- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
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-
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- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
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-
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- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
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-
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- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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-
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- var _globalThis$navigator, _globalThis$navigator2;
21
-
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- var defaultPoolSize = (_globalThis$navigator = globalThis === null || globalThis === void 0 ? void 0 : (_globalThis$navigator2 = globalThis.navigator) === null || _globalThis$navigator2 === void 0 ? void 0 : _globalThis$navigator2.hardwareConcurrency) !== null && _globalThis$navigator !== void 0 ? _globalThis$navigator : 4;
23
-
24
- var Pool = function () {
25
- function Pool() {
26
- var size = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : defaultPoolSize;
27
- (0, _classCallCheck2.default)(this, Pool);
28
- (0, _defineProperty2.default)(this, "workers", void 0);
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- (0, _defineProperty2.default)(this, "idleWorkers", void 0);
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- (0, _defineProperty2.default)(this, "waitQueue", void 0);
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- (0, _defineProperty2.default)(this, "decoder", void 0);
32
- this.workers = [];
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- this.idleWorkers = [];
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- this.waitQueue = [];
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- this.decoder = null;
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-
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- for (var i = 0; i < size; ++i) {
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- var w = new Worker('./decoder.worker');
39
- this.workers.push(w);
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- this.idleWorkers.push(w);
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- }
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- }
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-
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- (0, _createClass2.default)(Pool, [{
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- key: "decode",
46
- value: function () {
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- var _decode = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(fileDirectory, buffer) {
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- var _this = this;
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-
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- var currentWorker;
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- return _regenerator.default.wrap(function _callee$(_context) {
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- while (1) {
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- switch (_context.prev = _context.next) {
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- case 0:
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- _context.next = 2;
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- return this.waitForWorker();
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-
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- case 2:
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- currentWorker = _context.sent;
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- return _context.abrupt("return", new Promise(function (resolve, reject) {
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- currentWorker.onmessage = function (event) {
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- _this.finishTask(currentWorker);
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-
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- resolve(event.data[0]);
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- };
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-
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- currentWorker.onerror = function (error) {
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- _this.finishTask(currentWorker);
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-
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- reject(error);
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- };
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-
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- currentWorker.postMessage(['decode', fileDirectory, buffer], [buffer]);
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- }));
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-
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- case 4:
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- case "end":
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- return _context.stop();
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- }
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- }
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- }, _callee, this);
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- }));
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-
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- function decode(_x, _x2) {
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- return _decode.apply(this, arguments);
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- }
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-
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- return decode;
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- }()
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- }, {
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- key: "waitForWorker",
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- value: function () {
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- var _waitForWorker = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee2() {
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- var idleWorker, waiter, promise;
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- return _regenerator.default.wrap(function _callee2$(_context2) {
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- while (1) {
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- switch (_context2.prev = _context2.next) {
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- case 0:
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- idleWorker = this.idleWorkers.pop();
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-
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- if (!idleWorker) {
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- _context2.next = 3;
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- break;
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- }
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-
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- return _context2.abrupt("return", idleWorker);
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-
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- case 3:
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- waiter = {};
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- promise = new Promise(function (resolve) {
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- waiter.resolve = resolve;
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- });
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- this.waitQueue.push(waiter);
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- return _context2.abrupt("return", promise);
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-
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- case 7:
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- case "end":
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- return _context2.stop();
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- }
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- }
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- }, _callee2, this);
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- }));
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-
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- function waitForWorker() {
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- return _waitForWorker.apply(this, arguments);
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- }
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-
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- return waitForWorker;
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- }()
130
- }, {
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- key: "finishTask",
132
- value: function () {
133
- var _finishTask = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee3(currentWorker) {
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- var waiter;
135
- return _regenerator.default.wrap(function _callee3$(_context3) {
136
- while (1) {
137
- switch (_context3.prev = _context3.next) {
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- case 0:
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- waiter = this.waitQueue.pop();
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-
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- if (waiter) {
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- waiter.resolve(currentWorker);
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- } else {
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- this.idleWorkers.push(currentWorker);
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- }
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-
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- case 2:
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- case "end":
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- return _context3.stop();
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- }
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- }
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- }, _callee3, this);
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- }));
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-
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- function finishTask(_x3) {
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- return _finishTask.apply(this, arguments);
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- }
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-
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- return finishTask;
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- }()
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- }, {
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- key: "destroy",
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- value: function destroy() {
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- for (var i = 0; i < this.workers.length; ++i) {
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- this.workers[i].terminate();
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- }
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- }
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- }]);
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- return Pool;
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- }();
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-
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- exports.default = Pool;
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- //# sourceMappingURL=Pool.js.map
@@ -1 +0,0 @@
1
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More can't really hurt since they'll just block\n// each other and not the UI thread, which is the real benefit.\nconst defaultPoolSize = globalThis?.navigator?.hardwareConcurrency ?? 4;\n\n/**\n * Pool for workers to decode chunks of the images.\n * This is a line-for-line copy of GeoTIFFs old implementation: https://github.com/geotiffjs/geotiff.js/blob/v1.0.0-beta.6/src/pool.js\n */\nexport default class Pool {\n workers: Worker[];\n idleWorkers: Worker[];\n waitQueue: any[];\n decoder: null;\n\n /**\n * @constructor\n * @param {Number} size The size of the pool. Defaults to the number of CPUs\n * available. When this parameter is `null` or 0, then the\n * decoding will be done in the main thread.\n */\n constructor(size = defaultPoolSize) {\n this.workers = [];\n this.idleWorkers = [];\n this.waitQueue = [];\n this.decoder = null;\n\n // eslint-disable-next-line no-plusplus\n for (let i = 0; i < size; ++i) {\n const w = new Worker('./decoder.worker');\n this.workers.push(w);\n this.idleWorkers.push(w);\n }\n }\n\n /**\n * Decode the given block of bytes with the set compression method.\n * @param {ArrayBuffer} buffer the array buffer of bytes to decode.\n * @returns {Promise.<ArrayBuffer>} the decoded result as a `Promise`\n */\n async decode(fileDirectory: FileDirectory, buffer: ArrayBuffer) {\n const currentWorker = await this.waitForWorker();\n return new Promise((resolve, reject) => {\n currentWorker.onmessage = (event) => {\n // this.workers.push(currentWorker);\n // eslint-disable-next-line\n this.finishTask(currentWorker);\n resolve(event.data[0]);\n };\n currentWorker.onerror = (error) => {\n // this.workers.push(currentWorker);\n // eslint-disable-next-line\n this.finishTask(currentWorker);\n reject(error);\n };\n currentWorker.postMessage(['decode', fileDirectory, buffer], [buffer]);\n });\n }\n\n async waitForWorker() {\n const idleWorker = this.idleWorkers.pop();\n if (idleWorker) {\n return idleWorker;\n }\n const waiter: any = {};\n const promise = new Promise((resolve) => {\n waiter.resolve = resolve;\n });\n\n this.waitQueue.push(waiter);\n return promise as Promise<Worker>;\n }\n\n async finishTask(currentWorker: Worker) {\n const waiter = this.waitQueue.pop();\n if (waiter) {\n waiter.resolve(currentWorker);\n } else {\n this.idleWorkers.push(currentWorker);\n }\n }\n\n destroy() {\n // eslint-disable-next-line no-plusplus\n for (let i = 0; i < this.workers.length; ++i) {\n this.workers[i].terminate();\n }\n }\n}\n"],"file":"Pool.js"}
@@ -1,82 +0,0 @@
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- "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
7
- });
8
- exports.checkProxies = checkProxies;
9
- exports.createOffsetsProxy = createOffsetsProxy;
10
- exports.createPoolProxy = createPoolProxy;
11
-
12
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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-
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- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
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-
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- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
17
-
18
- var VIV_PROXY_KEY = '__viv';
19
- var OFFSETS_PROXY_KEY = "".concat(VIV_PROXY_KEY, "-offsets");
20
- var POOL_PROXY_KEY = "".concat(VIV_PROXY_KEY, "-decoder-pool");
21
-
22
- function checkProxies(tiff) {
23
- if (!isProxy(tiff, OFFSETS_PROXY_KEY)) {
24
- console.warn('GeoTIFF source is missing offsets proxy.');
25
- }
26
-
27
- if (!isProxy(tiff, POOL_PROXY_KEY)) {
28
- console.warn('GeoTIFF source is missing decoder-pool proxy.');
29
- }
30
- }
31
-
32
- function isProxy(tiff, proxyFlag) {
33
- return tiff[proxyFlag];
34
- }
35
-
36
- function createOffsetsProxy(tiff, offsets) {
37
- var get = function get(target, key) {
38
- if (key === 'getImage') {
39
- return function (index) {
40
- if (!(index in target.ifdRequests) && index in offsets) {
41
- var offset = offsets[index];
42
- target.ifdRequests[index] = target.parseFileDirectoryAt(offset);
43
- }
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-
45
- return target.getImage(index);
46
- };
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- }
48
-
49
- if (key === OFFSETS_PROXY_KEY) {
50
- return true;
51
- }
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-
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- return Reflect.get(target, key);
54
- };
55
-
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- return new Proxy(tiff, {
57
- get: get
58
- });
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- }
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-
61
- function createPoolProxy(tiff, pool) {
62
- var get = function get(target, key) {
63
- if (key === 'readRasters') {
64
- return function (options) {
65
- return target.readRasters(_objectSpread(_objectSpread({}, options), {}, {
66
- pool: pool
67
- }));
68
- };
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- }
70
-
71
- if (key === POOL_PROXY_KEY) {
72
- return true;
73
- }
74
-
75
- return Reflect.get(target, key);
76
- };
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-
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- return new Proxy(tiff, {
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- get: get
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- });
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- }
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- //# sourceMappingURL=proxies.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../../../src/lib/utils/proxies.ts"],"names":["VIV_PROXY_KEY","OFFSETS_PROXY_KEY","POOL_PROXY_KEY","checkProxies","tiff","isProxy","console","warn","proxyFlag","createOffsetsProxy","offsets","get","target","key","index","ifdRequests","offset","parseFileDirectoryAt","getImage","Reflect","Proxy","createPoolProxy","pool","options","readRasters"],"mappings":";;;;;;;;;;;;;;;;;AAGA,IAAMA,aAAa,GAAG,OAAtB;AACA,IAAMC,iBAAiB,aAAMD,aAAN,aAAvB;AACA,IAAME,cAAc,aAAMF,aAAN,kBAApB;;AAMO,SAASG,YAAT,CAAsBC,IAAtB,EAAqC;AAC1C,MAAI,CAACC,OAAO,CAACD,IAAD,EAAOH,iBAAP,CAAZ,EAAuC;AACrCK,IAAAA,OAAO,CAACC,IAAR,CAAa,0CAAb;AACD;;AAED,MAAI,CAACF,OAAO,CAACD,IAAD,EAAOF,cAAP,CAAZ,EAAoC;AAClCI,IAAAA,OAAO,CAACC,IAAR,CAAa,+CAAb;AACD;AACF;;AAOD,SAASF,OAAT,CAAiBD,IAAjB,EAAgCI,SAAhC,EAAmD;AACjD,SAAQJ,IAAD,CAAcI,SAAd,CAAP;AACD;;AAYM,SAASC,kBAAT,CAA4BL,IAA5B,EAA2CM,OAA3C,EAA8D;AACnE,MAAMC,GAAG,GAAG,SAANA,GAAM,CAACC,MAAD,EAAkBC,GAAlB,EAA+B;AAEzC,QAAIA,GAAG,KAAK,UAAZ,EAAwB;AACtB,aAAO,UAACC,KAAD,EAAmB;AAExB,YAAI,EAAEA,KAAK,IAAIF,MAAM,CAACG,WAAlB,KAAkCD,KAAK,IAAIJ,OAA/C,EAAwD;AACtD,cAAMM,MAAM,GAAGN,OAAO,CAACI,KAAD,CAAtB;AACAF,UAAAA,MAAM,CAACG,WAAP,CAAmBD,KAAnB,IAA4BF,MAAM,CAACK,oBAAP,CAA4BD,MAA5B,CAA5B;AACD;;AACD,eAAOJ,MAAM,CAACM,QAAP,CAAgBJ,KAAhB,CAAP;AACD,OAPD;AAQD;;AAGD,QAAID,GAAG,KAAKZ,iBAAZ,EAA+B;AAC7B,aAAO,IAAP;AACD;;AAED,WAAOkB,OAAO,CAACR,GAAR,CAAYC,MAAZ,EAAoBC,GAApB,CAAP;AACD,GAnBD;;AAoBA,SAAO,IAAIO,KAAJ,CAAUhB,IAAV,EAAgB;AAACO,IAAAA,GAAG,EAAHA;AAAD,GAAhB,CAAP;AACD;;AAUM,SAASU,eAAT,CAAyBjB,IAAzB,EAAwCkB,IAAxC,EAAoD;AACzD,MAAMX,GAAG,GAAG,SAANA,GAAM,CAACC,MAAD,EAAkBC,GAAlB,EAA+B;AAEzC,QAAIA,GAAG,KAAK,aAAZ,EAA2B;AACzB,aAAO,UAACU,OAAD,EAAoD;AAGzD,eAAOX,MAAM,CAACY,WAAP,iCAAuBD,OAAvB;AAAgCD,UAAAA,IAAI,EAAJA;AAAhC,WAAP;AACD,OAJD;AAKD;;AAGD,QAAIT,GAAG,KAAKX,cAAZ,EAA4B;AAC1B,aAAO,IAAP;AACD;;AAED,WAAOiB,OAAO,CAACR,GAAR,CAAYC,MAAZ,EAAoBC,GAApB,CAAP;AACD,GAhBD;;AAiBA,SAAO,IAAIO,KAAJ,CAAUhB,IAAV,EAAgB;AAACO,IAAAA,GAAG,EAAHA;AAAD,GAAhB,CAAP;AACD","sourcesContent":["import type {GeoTIFF} from 'geotiff';\nimport type Pool from './Pool';\n\nconst VIV_PROXY_KEY = '__viv';\nconst OFFSETS_PROXY_KEY = `${VIV_PROXY_KEY}-offsets` as const;\nconst POOL_PROXY_KEY = `${VIV_PROXY_KEY}-decoder-pool` as const;\n\n/*\n * Inspect if the GeoTIFF source is wrapped in our proxies,\n * and warn if missing.\n */\nexport function checkProxies(tiff: GeoTIFF) {\n if (!isProxy(tiff, OFFSETS_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing offsets proxy.'); // eslint-disable-line no-console\n }\n\n if (!isProxy(tiff, POOL_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing decoder-pool proxy.'); // eslint-disable-line no-console\n }\n}\n\n/*\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // false\n * > tiff = createPoolProxy(tiff, new Pool());\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // true\n */\nfunction isProxy(tiff: GeoTIFF, proxyFlag: string) {\n return (tiff as any)[proxyFlag] as boolean;\n}\n\n/*\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.getImage` and uses our custom\n * pre-computed offsets to pre-fetch the correct file directory.\n *\n * This is a bit of a hack. Internally GeoTIFF inspects `this.ifdRequests`\n * to see which fileDirectories need to be traversed. By adding the\n * ifdRequest for an 'index' manually, GeoTIFF will await that request\n * rather than traversing the file system remotely.\n */\nexport function createOffsetsProxy(tiff: GeoTIFF, offsets: number[]) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept `tiff.getImage`\n if (key === 'getImage') {\n return (index: number) => {\n // Manually add ifdRequest to tiff if missing and we have an offset.\n if (!(index in target.ifdRequests) && index in offsets) {\n const offset = offsets[index];\n target.ifdRequests[index] = target.parseFileDirectoryAt(offset);\n }\n return target.getImage(index);\n };\n }\n\n // tiff['__viv-offsets'] === true\n if (key === OFFSETS_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n\n/*\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.readRasters` and injects\n * a pool argument to every call. This means our TiffPixelSource\n * doesn't need to be aware of whether a decoder pool is in use.\n *\n * > tiff.readRasters({ window }) -> tiff.readRasters({ window, pool });\n */\nexport function createPoolProxy(tiff: GeoTIFF, pool: Pool) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept calls to `image.readRasters`\n if (key === 'readRasters') {\n return (options: Parameters<typeof target.readRasters>) => {\n // Inject `pool` argument with other raster options.\n // @ts-ignore\n return target.readRasters({...options, pool});\n };\n }\n\n // tiff['__viv-decoder-pool'] === true\n if (key === POOL_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n"],"file":"proxies.js"}
@@ -1,53 +0,0 @@
1
- "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
7
- });
8
- exports.ensureArray = ensureArray;
9
- exports.intToRgba = intToRgba;
10
- exports.isInterleaved = isInterleaved;
11
- exports.getImageSize = getImageSize;
12
- exports.SIGNAL_ABORTED = void 0;
13
-
14
- var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
15
-
16
- function ensureArray(x) {
17
- return Array.isArray(x) ? x : [x];
18
- }
19
-
20
- function intToRgba(int) {
21
- if (!Number.isInteger(int)) {
22
- throw Error('Not an integer.');
23
- }
24
-
25
- var buffer = new ArrayBuffer(4);
26
- var view = new DataView(buffer);
27
- view.setInt32(0, int, false);
28
- var bytes = new Uint8Array(buffer);
29
- return Array.from(bytes);
30
- }
31
-
32
- function isInterleaved(shape) {
33
- var lastDimSize = shape[shape.length - 1];
34
- return lastDimSize === 3 || lastDimSize === 4;
35
- }
36
-
37
- function getImageSize(source) {
38
- var interleaved = isInterleaved(source.shape);
39
-
40
- var _source$shape$slice = source.shape.slice(interleaved ? -3 : -2),
41
- _source$shape$slice2 = (0, _slicedToArray2.default)(_source$shape$slice, 2),
42
- height = _source$shape$slice2[0],
43
- width = _source$shape$slice2[1];
44
-
45
- return {
46
- height: height,
47
- width: width
48
- };
49
- }
50
-
51
- var SIGNAL_ABORTED = '__vivSignalAborted';
52
- exports.SIGNAL_ABORTED = SIGNAL_ABORTED;
53
- //# sourceMappingURL=tiff-utils.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../../../src/lib/utils/tiff-utils.ts"],"names":["ensureArray","x","Array","isArray","intToRgba","int","Number","isInteger","Error","buffer","ArrayBuffer","view","DataView","setInt32","bytes","Uint8Array","from","isInterleaved","shape","lastDimSize","length","getImageSize","source","interleaved","slice","height","width","SIGNAL_ABORTED"],"mappings":";;;;;;;;;;;;;;;AAEO,SAASA,WAAT,CAAwBC,CAAxB,EAAoC;AACzC,SAAOC,KAAK,CAACC,OAAN,CAAcF,CAAd,IAAmBA,CAAnB,GAAuB,CAACA,CAAD,CAA9B;AACD;;AASM,SAASG,SAAT,CAAmBC,GAAnB,EAAgC;AACrC,MAAI,CAACC,MAAM,CAACC,SAAP,CAAiBF,GAAjB,CAAL,EAA4B;AAC1B,UAAMG,KAAK,CAAC,iBAAD,CAAX;AACD;;AAGD,MAAMC,MAAM,GAAG,IAAIC,WAAJ,CAAgB,CAAhB,CAAf;AACA,MAAMC,IAAI,GAAG,IAAIC,QAAJ,CAAaH,MAAb,CAAb;AACAE,EAAAA,IAAI,CAACE,QAAL,CAAc,CAAd,EAAiBR,GAAjB,EAAsB,KAAtB;AAGA,MAAMS,KAAK,GAAG,IAAIC,UAAJ,CAAeN,MAAf,CAAd;AACA,SAAOP,KAAK,CAACc,IAAN,CAAWF,KAAX,CAAP;AACD;;AAOM,SAASG,aAAT,CAAuBC,KAAvB,EAAwC;AAC7C,MAAMC,WAAW,GAAGD,KAAK,CAACA,KAAK,CAACE,MAAN,GAAe,CAAhB,CAAzB;AACA,SAAOD,WAAW,KAAK,CAAhB,IAAqBA,WAAW,KAAK,CAA5C;AACD;;AAEM,SAASE,YAAT,CAA0CC,MAA1C,EAAkE;AACvE,MAAMC,WAAW,GAAGN,aAAa,CAACK,MAAM,CAACJ,KAAR,CAAjC;;AACA,4BAAwBI,MAAM,CAACJ,KAAP,CAAaM,KAAb,CAAmBD,WAAW,GAAG,CAAC,CAAJ,GAAQ,CAAC,CAAvC,CAAxB;AAAA;AAAA,MAAOE,MAAP;AAAA,MAAeC,KAAf;;AACA,SAAO;AAACD,IAAAA,MAAM,EAANA,MAAD;AAASC,IAAAA,KAAK,EAALA;AAAT,GAAP;AACD;;AAEM,IAAMC,cAAc,GAAG,oBAAvB","sourcesContent":["import type {PixelSource} from '../../types';\n\nexport function ensureArray<T>(x: T | T[]) {\n return Array.isArray(x) ? x : [x];\n}\n\n/*\n * Converts 32-bit integer color representation to RGBA tuple.\n * Used to serialize colors from OME-XML metadata.\n *\n * > console.log(intToRgba(100100));\n * > // [0, 1, 135, 4]\n */\nexport function intToRgba(int: number) {\n if (!Number.isInteger(int)) {\n throw Error('Not an integer.');\n }\n\n // Write number to int32 representation (4 bytes).\n const buffer = new ArrayBuffer(4);\n const view = new DataView(buffer);\n view.setInt32(0, int, false); // offset === 0, littleEndian === false\n\n // Take u8 view and extract number for each byte (1 byte for R/G/B/A).\n const bytes = new Uint8Array(buffer);\n return Array.from(bytes) as [number, number, number, number];\n}\n\n/*\n * Helper method to determine whether pixel data is interleaved or not.\n * > isInterleaved([1, 24, 24]) === false;\n * > isInterleaved([1, 24, 24, 3]) === true;\n */\nexport function isInterleaved(shape: number[]) {\n const lastDimSize = shape[shape.length - 1];\n return lastDimSize === 3 || lastDimSize === 4;\n}\n\nexport function getImageSize<T extends string[]>(source: PixelSource<T>) {\n const interleaved = isInterleaved(source.shape);\n const [height, width] = source.shape.slice(interleaved ? -3 : -2);\n return {height, width};\n}\n\nexport const SIGNAL_ABORTED = '__vivSignalAborted';\n"],"file":"tiff-utils.js"}
package/dist/es5/types.js DELETED
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=types.js.map
@@ -1,2 +0,0 @@
1
- "use strict";
2
- //# sourceMappingURL=geotiff.js.map
@@ -1,4 +0,0 @@
1
- import * as moduleExports from './index';
2
- globalThis.loaders = globalThis.loaders || {};
3
- module.exports = Object.assign(globalThis.loaders, moduleExports);
4
- //# sourceMappingURL=bundle.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../src/bundle.ts"],"names":["moduleExports","globalThis","loaders","module","exports","Object","assign"],"mappings":"AAAA,OAAO,KAAKA,aAAZ,MAA+B,SAA/B;AAEAC,UAAU,CAACC,OAAX,GAAqBD,UAAU,CAACC,OAAX,IAAsB,EAA3C;AAEAC,MAAM,CAACC,OAAP,GAAiBC,MAAM,CAACC,MAAP,CAAcL,UAAU,CAACC,OAAzB,EAAkCF,aAAlC,CAAjB","sourcesContent":["import * as moduleExports from './index';\n// @ts-ignore\nglobalThis.loaders = globalThis.loaders || {};\n// @ts-ignore\nmodule.exports = Object.assign(globalThis.loaders, moduleExports);\n"],"file":"bundle.js"}
package/dist/esm/index.js DELETED
@@ -1,3 +0,0 @@
1
- export { loadGeoTiff } from './lib/load-geotiff';
2
- export { default as TiffPixelSource } from './lib/tiff-pixel-source';
3
- //# sourceMappingURL=index.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../src/index.ts"],"names":["loadGeoTiff","default","TiffPixelSource"],"mappings":"AAAA,SAAQA,WAAR,QAA0B,oBAA1B;AACA,SAAQC,OAAO,IAAIC,eAAnB,QAAyC,yBAAzC","sourcesContent":["export {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"file":"index.js"}
@@ -1,32 +0,0 @@
1
- import { fromUrl, fromBlob, GeoTIFF } from 'geotiff';
2
- import { createOffsetsProxy, checkProxies } from './utils/proxies';
3
- import { loadOmeTiff, isOmeTiff } from './ome/load-ome-tiff';
4
- export async function loadGeoTiff(source, opts = {}) {
5
- const {
6
- headers,
7
- offsets
8
- } = opts;
9
- let tiff;
10
-
11
- if (source instanceof GeoTIFF) {
12
- tiff = source;
13
- } else if (typeof source === 'string') {
14
- tiff = await fromUrl(source, headers);
15
- } else {
16
- tiff = await fromBlob(source);
17
- }
18
-
19
- if (offsets) {
20
- tiff = createOffsetsProxy(tiff, offsets);
21
- }
22
-
23
- checkProxies(tiff);
24
- const firstImage = await tiff.getImage(0);
25
-
26
- if (isOmeTiff(firstImage)) {
27
- return loadOmeTiff(tiff, firstImage);
28
- }
29
-
30
- throw new Error('GeoTIFF not recognized.');
31
- }
32
- //# sourceMappingURL=load-geotiff.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../../src/lib/load-geotiff.ts"],"names":["fromUrl","fromBlob","GeoTIFF","createOffsetsProxy","checkProxies","loadOmeTiff","isOmeTiff","loadGeoTiff","source","opts","headers","offsets","tiff","firstImage","getImage","Error"],"mappings":"AAAA,SAAQA,OAAR,EAAiBC,QAAjB,EAA2BC,OAA3B,QAAyC,SAAzC;AAEA,SAEEC,kBAFF,EAGEC,YAHF,QAIO,iBAJP;AAOA,SAAQC,WAAR,EAAqBC,SAArB,QAAqC,qBAArC;AA4BA,OAAO,eAAeC,WAAf,CACLC,MADK,EAELC,IAAoB,GAAG,EAFlB,EAGiB;AACtB,QAAM;AAACC,IAAAA,OAAD;AAAUC,IAAAA;AAAV,MAAqBF,IAA3B;AAGA,MAAIG,IAAJ;;AACA,MAAIJ,MAAM,YAAYN,OAAtB,EAA+B;AAC7BU,IAAAA,IAAI,GAAGJ,MAAP;AACD,GAFD,MAEO,IAAI,OAAOA,MAAP,KAAkB,QAAtB,EAAgC;AACrCI,IAAAA,IAAI,GAAG,MAAMZ,OAAO,CAACQ,MAAD,EAASE,OAAT,CAApB;AACD,GAFM,MAEA;AACLE,IAAAA,IAAI,GAAG,MAAMX,QAAQ,CAACO,MAAD,CAArB;AACD;;AAUD,MAAIG,OAAJ,EAAa;AAMXC,IAAAA,IAAI,GAAGT,kBAAkB,CAACS,IAAD,EAAOD,OAAP,CAAzB;AACD;;AAMDP,EAAAA,YAAY,CAACQ,IAAD,CAAZ;AAEA,QAAMC,UAAU,GAAG,MAAMD,IAAI,CAACE,QAAL,CAAc,CAAd,CAAzB;;AAEA,MAAIR,SAAS,CAACO,UAAD,CAAb,EAA2B;AACzB,WAAOR,WAAW,CAACO,IAAD,EAAOC,UAAP,CAAlB;AACD;;AAED,QAAM,IAAIE,KAAJ,CAAU,yBAAV,CAAN;AACD","sourcesContent":["import {fromUrl, fromBlob, GeoTIFF} from 'geotiff';\n\nimport {\n // createPoolProxy,\n createOffsetsProxy,\n checkProxies\n} from './utils/proxies';\n// import Pool from './lib/Pool';\n\nimport {loadOmeTiff, isOmeTiff} from './ome/load-ome-tiff';\nimport type TiffPixelSource from './tiff-pixel-source';\n\n/** Options for initializing a tiff pixel source. */\ninterface GeoTIFFOptions {\n /** Headers passed to each underlying request. */\n headers?: Record<string, unknown>;\n /** Performance enhancment to index the remote tiff source using pre-computed byte-offsets. Generated via https://github.com/ilan-gold/generate-tiff-offsets */\n offsets?: number[];\n /** Indicates whether a multi-threaded pool of image decoders should be used to decode tiles. */\n pool?: boolean;\n}\n\ninterface GeoTIFFData {\n data: TiffPixelSource<string[]>[];\n metadata: Record<string, unknown>;\n}\n\n/**\n * Opens an OME-TIFF via URL and returns data source and associated metadata for first image.\n *\n * @param source url string, File/Blob object, or GeoTIFF object\n * @param opts options for initializing a tiff pixel source.\n * - `opts.headers` are passed to each underlying fetch request.\n * - `opts.offsets` are a performance enhancment to index the remote tiff source using pre-computed byte-offsets.\n * - `opts.pool` indicates whether a multi-threaded pool of image decoders should be used to decode tiles (default = true).\n * @return data source and associated OME-Zarr metadata.\n */\nexport async function loadGeoTiff(\n source: string | Blob | GeoTIFF,\n opts: GeoTIFFOptions = {}\n): Promise<GeoTIFFData> {\n const {headers, offsets} = opts;\n\n // Create tiff source\n let tiff: GeoTIFF;\n if (source instanceof GeoTIFF) {\n tiff = source;\n } else if (typeof source === 'string') {\n tiff = await fromUrl(source, headers);\n } else {\n tiff = await fromBlob(source);\n }\n\n // if (pool) {\n /*\n * Creates a worker pool to decode tiff tiles. Wraps tiff\n * in a Proxy that injects 'pool' into `tiff.readRasters`.\n */\n // tiff = createPoolProxy(tiff, new Pool());\n // }\n\n if (offsets) {\n /*\n * Performance enhancement. If offsets are provided, we\n * create a proxy that intercepts calls to `tiff.getImage`\n * and injects the pre-computed offsets.\n */\n tiff = createOffsetsProxy(tiff, offsets);\n }\n\n /*\n * Inspect tiff source for our performance enhancing proxies.\n * Prints warnings to console if `offsets` or `pool` are missing.\n */\n checkProxies(tiff);\n\n const firstImage = await tiff.getImage(0);\n\n if (isOmeTiff(firstImage)) {\n return loadOmeTiff(tiff, firstImage);\n }\n\n throw new Error('GeoTIFF not recognized.');\n}\n"],"file":"load-geotiff.js"}
@@ -1,51 +0,0 @@
1
- import TiffPixelSource from '../tiff-pixel-source';
2
- import { getOmeLegacyIndexer, getOmeSubIFDIndexer } from './ome-indexers';
3
- import { getOmePixelSourceMeta } from './ome-utils';
4
- import { fromString } from './omexml';
5
- export const isOmeTiff = img => img.fileDirectory.ImageDescription.includes('<OME');
6
- export async function loadOmeTiff(tiff, firstImage) {
7
- const {
8
- ImageDescription,
9
- SubIFDs,
10
- PhotometricInterpretation: photometricInterpretation
11
- } = firstImage.fileDirectory;
12
- const omexml = fromString(ImageDescription);
13
- let levels;
14
- let pyramidIndexer;
15
-
16
- if (SubIFDs) {
17
- levels = SubIFDs.length + 1;
18
- pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);
19
- } else {
20
- levels = omexml.length;
21
- pyramidIndexer = getOmeLegacyIndexer(tiff, omexml);
22
- }
23
-
24
- const imgMeta = omexml[0];
25
- const {
26
- labels,
27
- getShape,
28
- physicalSizes,
29
- dtype
30
- } = getOmePixelSourceMeta(imgMeta);
31
- const tileSize = firstImage.getTileWidth();
32
- const meta = {
33
- photometricInterpretation,
34
- physicalSizes
35
- };
36
- const data = Array.from({
37
- length: levels
38
- }).map((_, resolution) => {
39
- const shape = getShape(resolution);
40
-
41
- const indexer = sel => pyramidIndexer(sel, resolution);
42
-
43
- const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);
44
- return source;
45
- });
46
- return {
47
- data,
48
- metadata: imgMeta
49
- };
50
- }
51
- //# sourceMappingURL=load-ome-tiff.js.map
@@ -1 +0,0 @@
1
- {"version":3,"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"names":["TiffPixelSource","getOmeLegacyIndexer","getOmeSubIFDIndexer","getOmePixelSourceMeta","fromString","isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","PhotometricInterpretation","photometricInterpretation","omexml","levels","pyramidIndexer","length","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","metadata"],"mappings":"AAEA,OAAOA,eAAP,MAA4B,sBAA5B;AACA,SAAQC,mBAAR,EAA6BC,mBAA7B,QAAuE,gBAAvE;AACA,SAAQC,qBAAR,QAAoC,aAApC;AACA,SAAQC,UAAR,QAAyB,UAAzB;AAGA,OAAO,MAAMC,SAAS,GAAIC,GAAD,IAAuBA,GAAG,CAACC,aAAJ,CAAkBC,gBAAlB,CAAmCC,QAAnC,CAA4C,MAA5C,CAAzC;AAEP,OAAO,eAAeC,WAAf,CAA2BC,IAA3B,EAA0CC,UAA1C,EAAoE;AAEzE,QAAM;AACJJ,IAAAA,gBADI;AAEJK,IAAAA,OAFI;AAGJC,IAAAA,yBAAyB,EAAEC;AAHvB,MAIFH,UAAU,CAACL,aAJf;AAKA,QAAMS,MAAM,GAAGZ,UAAU,CAACI,gBAAD,CAAzB;AAMA,MAAIS,MAAJ;AACA,MAAIC,cAAJ;;AAEA,MAAIL,OAAJ,EAAa;AAEXI,IAAAA,MAAM,GAAGJ,OAAO,CAACM,MAAR,GAAiB,CAA1B;AACAD,IAAAA,cAAc,GAAGhB,mBAAmB,CAACS,IAAD,EAAOK,MAAP,CAApC;AACD,GAJD,MAIO;AAELC,IAAAA,MAAM,GAAGD,MAAM,CAACG,MAAhB;AACAD,IAAAA,cAAc,GAAGjB,mBAAmB,CAACU,IAAD,EAAOK,MAAP,CAApC;AACD;;AAGD,QAAMI,OAAO,GAAGJ,MAAM,CAAC,CAAD,CAAtB;AACA,QAAM;AAACK,IAAAA,MAAD;AAASC,IAAAA,QAAT;AAAmBC,IAAAA,aAAnB;AAAkCC,IAAAA;AAAlC,MAA2CrB,qBAAqB,CAACiB,OAAD,CAAtE;AACA,QAAMK,QAAQ,GAAGb,UAAU,CAACc,YAAX,EAAjB;AACA,QAAMC,IAAI,GAAG;AAACZ,IAAAA,yBAAD;AAA4BQ,IAAAA;AAA5B,GAAb;AAEA,QAAMK,IAAI,GAAGC,KAAK,CAACC,IAAN,CAAW;AAACX,IAAAA,MAAM,EAAEF;AAAT,GAAX,EAA6Bc,GAA7B,CAAiC,CAACC,CAAD,EAAIC,UAAJ,KAAmB;AAC/D,UAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAD,CAAtB;;AACA,UAAME,OAAO,GAAIC,GAAD,IAA2BlB,cAAc,CAACkB,GAAD,EAAMH,UAAN,CAAzD;;AACA,UAAMI,MAAM,GAAG,IAAIrC,eAAJ,CAAoBmC,OAApB,EAA6BX,KAA7B,EAAoCC,QAApC,EAA8CS,KAA9C,EAAqDb,MAArD,EAA6DM,IAA7D,CAAf;AACA,WAAOU,MAAP;AACD,GALY,CAAb;AAOA,SAAO;AAACT,IAAAA,IAAD;AAAOU,IAAAA,QAAQ,EAAElB;AAAjB,GAAP;AACD","sourcesContent":["import type {GeoTIFF, GeoTIFFImage} from 'geotiff';\n\nimport TiffPixelSource from '../tiff-pixel-source';\nimport {getOmeLegacyIndexer, getOmeSubIFDIndexer, OmeTiffIndexer} from './ome-indexers';\nimport {getOmePixelSourceMeta} from './ome-utils';\nimport {fromString} from './omexml';\nimport type {OmeTiffSelection} from './ome-indexers';\n\nexport const isOmeTiff = (img: GeoTIFFImage) => img.fileDirectory.ImageDescription.includes('<OME');\n\nexport async function loadOmeTiff(tiff: GeoTIFF, firstImage: GeoTIFFImage) {\n // Get first image from tiff and inspect OME-XML metadata\n const {\n ImageDescription,\n SubIFDs,\n PhotometricInterpretation: photometricInterpretation\n } = firstImage.fileDirectory;\n const omexml = fromString(ImageDescription);\n\n /*\n * Image pyramids are stored differently between versions of Bioformats.\n * Thus we need a different indexer depending on which format we have.\n */\n let levels: number;\n let pyramidIndexer: OmeTiffIndexer;\n\n if (SubIFDs) {\n // Image is >= Bioformats 6.0 and resolutions are stored using SubIFDs.\n levels = SubIFDs.length + 1;\n pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);\n } else {\n // Image is legacy format; resolutions are stored as separate images.\n levels = omexml.length;\n pyramidIndexer = getOmeLegacyIndexer(tiff, omexml);\n }\n\n // TODO: The OmeTIFF loader only works for the _first_ image in the metadata.\n const imgMeta = omexml[0];\n const {labels, getShape, physicalSizes, dtype} = getOmePixelSourceMeta(imgMeta);\n const tileSize = firstImage.getTileWidth();\n const meta = {photometricInterpretation, physicalSizes};\n\n const data = Array.from({length: levels}).map((_, resolution) => {\n const shape = getShape(resolution);\n const indexer = (sel: OmeTiffSelection) => pyramidIndexer(sel, resolution);\n const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);\n return source;\n });\n\n return {data, metadata: imgMeta};\n}\n"],"file":"load-ome-tiff.js"}
@@ -1,116 +0,0 @@
1
- export function getOmeLegacyIndexer(tiff, rootMeta) {
2
- const imgMeta = rootMeta[0];
3
- const {
4
- SizeT,
5
- SizeC,
6
- SizeZ
7
- } = imgMeta.Pixels;
8
- const ifdIndexer = getOmeIFDIndexer(imgMeta);
9
- return (sel, pyramidLevel) => {
10
- const index = ifdIndexer(sel);
11
- const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;
12
- return tiff.getImage(index + pyramidIndex);
13
- };
14
- }
15
- export function getOmeSubIFDIndexer(tiff, rootMeta) {
16
- const imgMeta = rootMeta[0];
17
- const ifdIndexer = getOmeIFDIndexer(imgMeta);
18
- const ifdCache = new Map();
19
- return async (sel, pyramidLevel) => {
20
- const index = ifdIndexer(sel);
21
- const baseImage = await tiff.getImage(index);
22
-
23
- if (pyramidLevel === 0) {
24
- return baseImage;
25
- }
26
-
27
- const {
28
- SubIFDs
29
- } = baseImage.fileDirectory;
30
-
31
- if (!SubIFDs) {
32
- throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
33
- }
34
-
35
- const key = "".concat(sel.t, "-").concat(sel.c, "-").concat(sel.z, "-").concat(pyramidLevel);
36
-
37
- if (!ifdCache.has(key)) {
38
- const subIfdOffset = SubIFDs[pyramidLevel - 1];
39
- ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
40
- }
41
-
42
- const ifd = await ifdCache.get(key);
43
- return new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source);
44
- };
45
- }
46
-
47
- function getOmeIFDIndexer(imgMeta) {
48
- const {
49
- SizeC,
50
- SizeZ,
51
- SizeT,
52
- DimensionOrder
53
- } = imgMeta.Pixels;
54
-
55
- switch (DimensionOrder) {
56
- case 'XYZCT':
57
- {
58
- return ({
59
- t,
60
- c,
61
- z
62
- }) => t * SizeZ * SizeC + c * SizeZ + z;
63
- }
64
-
65
- case 'XYZTC':
66
- {
67
- return ({
68
- t,
69
- c,
70
- z
71
- }) => c * SizeZ * SizeT + t * SizeZ + z;
72
- }
73
-
74
- case 'XYCTZ':
75
- {
76
- return ({
77
- t,
78
- c,
79
- z
80
- }) => z * SizeC * SizeT + t * SizeC + c;
81
- }
82
-
83
- case 'XYCZT':
84
- {
85
- return ({
86
- t,
87
- c,
88
- z
89
- }) => t * SizeC * SizeZ + z * SizeC + c;
90
- }
91
-
92
- case 'XYTCZ':
93
- {
94
- return ({
95
- t,
96
- c,
97
- z
98
- }) => z * SizeT * SizeC + c * SizeT + t;
99
- }
100
-
101
- case 'XYTZC':
102
- {
103
- return ({
104
- t,
105
- c,
106
- z
107
- }) => c * SizeT * SizeZ + z * SizeT + t;
108
- }
109
-
110
- default:
111
- {
112
- throw new Error("Invalid OME-XML DimensionOrder, got ".concat(DimensionOrder, "."));
113
- }
114
- }
115
- }
116
- //# sourceMappingURL=ome-indexers.js.map
@@ -1 +0,0 @@
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However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n const imgMeta = rootMeta[0];\n const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n return (sel: OmeTiffSelection, pyramidLevel: number) => {\n // Get IFD index at base pyramid level\n const index = ifdIndexer(sel);\n // Get index of first image at pyramidal level\n const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n // Return image at IFD index for pyramidal level\n return tiff.getImage(index + pyramidIndex);\n };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n const imgMeta = rootMeta[0];\n const ifdIndexer = getOmeIFDIndexer(imgMeta);\n const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n const index = ifdIndexer(sel);\n const baseImage = await tiff.getImage(index);\n\n // It's the highest resolution, no need to look up SubIFDs.\n if (pyramidLevel === 0) {\n return baseImage;\n }\n\n const {SubIFDs} = baseImage.fileDirectory;\n if (!SubIFDs) {\n throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n }\n\n // Get IFD for the selection at the pyramidal level\n const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n if (!ifdCache.has(key)) {\n // Only create a new request if we don't have the key.\n const subIfdOffset = SubIFDs[pyramidLevel - 1];\n ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n }\n const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n // Create a new image object manually from IFD\n // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n return new (baseImage.constructor as any)(\n ifd.fileDirectory,\n ifd.geoKeyDirectory,\n tiff.dataView,\n tiff.littleEndian,\n tiff.cache,\n tiff.source\n ) as GeoTIFFImage;\n };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n switch (DimensionOrder) {\n case 'XYZCT': {\n return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n }\n case 'XYZTC': {\n return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n }\n case 'XYCTZ': {\n return ({t, c, z}) => z * SizeC * SizeT + t * SizeC + c;\n }\n case 'XYCZT': {\n return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n }\n case 'XYTCZ': {\n return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n }\n case 'XYTZC': {\n return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n }\n default: {\n throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n }\n }\n}\n"],"file":"ome-indexers.js"}