@loaders.gl/geotiff 4.0.0-alpha.1 → 4.0.0-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 (117) hide show
  1. package/dist/bundle.d.ts +2 -0
  2. package/dist/bundle.d.ts.map +1 -0
  3. package/dist/bundle.js +28 -2
  4. package/dist/es5/bundle.js +9 -0
  5. package/dist/es5/bundle.js.map +1 -0
  6. package/dist/es5/index.js +21 -0
  7. package/dist/es5/index.js.map +1 -0
  8. package/dist/es5/lib/load-geotiff.js +76 -0
  9. package/dist/es5/lib/load-geotiff.js.map +1 -0
  10. package/dist/es5/lib/ome/load-ome-tiff.js +66 -0
  11. package/dist/es5/lib/ome/load-ome-tiff.js.map +1 -0
  12. package/dist/es5/lib/ome/ome-indexers.js +140 -0
  13. package/dist/es5/lib/ome/ome-indexers.js.map +1 -0
  14. package/dist/es5/lib/ome/ome-utils.js +74 -0
  15. package/dist/es5/lib/ome/ome-utils.js.map +1 -0
  16. package/dist/es5/lib/ome/omexml.js +68 -0
  17. package/dist/es5/lib/ome/omexml.js.map +1 -0
  18. package/dist/es5/lib/ome/utils.js +26 -0
  19. package/dist/es5/lib/ome/utils.js.map +1 -0
  20. package/dist/es5/lib/tiff-pixel-source.js +163 -0
  21. package/dist/es5/lib/tiff-pixel-source.js.map +1 -0
  22. package/dist/es5/lib/utils/Pool.js +136 -0
  23. package/dist/es5/lib/utils/Pool.js.map +1 -0
  24. package/dist/es5/lib/utils/proxies.js +65 -0
  25. package/dist/es5/lib/utils/proxies.js.map +1 -0
  26. package/dist/es5/lib/utils/tiff-utils.js +43 -0
  27. package/dist/es5/lib/utils/tiff-utils.js.map +1 -0
  28. package/dist/es5/types.js +2 -0
  29. package/dist/es5/types.js.map +1 -0
  30. package/dist/es5/typings/geotiff.js +2 -0
  31. package/dist/es5/typings/geotiff.js.map +1 -0
  32. package/dist/esm/bundle.js +4 -0
  33. package/dist/esm/bundle.js.map +1 -0
  34. package/dist/esm/index.js +3 -0
  35. package/dist/esm/index.js.map +1 -0
  36. package/dist/esm/lib/load-geotiff.js +28 -0
  37. package/dist/esm/lib/load-geotiff.js.map +1 -0
  38. package/dist/esm/lib/ome/load-ome-tiff.js +47 -0
  39. package/dist/esm/lib/ome/load-ome-tiff.js.map +1 -0
  40. package/dist/esm/lib/ome/ome-indexers.js +120 -0
  41. package/dist/esm/lib/ome/ome-indexers.js.map +1 -0
  42. package/dist/esm/lib/ome/ome-utils.js +66 -0
  43. package/dist/esm/lib/ome/ome-utils.js.map +1 -0
  44. package/dist/esm/lib/ome/omexml.js +64 -0
  45. package/dist/esm/lib/ome/omexml.js.map +1 -0
  46. package/dist/esm/lib/ome/utils.js +17 -0
  47. package/dist/esm/lib/ome/utils.js.map +1 -0
  48. package/dist/esm/lib/tiff-pixel-source.js +92 -0
  49. package/dist/esm/lib/tiff-pixel-source.js.map +1 -0
  50. package/dist/esm/lib/utils/Pool.js +61 -0
  51. package/dist/esm/lib/utils/Pool.js.map +1 -0
  52. package/dist/esm/lib/utils/decoder.worker.ts.disabled +21 -0
  53. package/dist/esm/lib/utils/proxies.js +54 -0
  54. package/dist/esm/lib/utils/proxies.js.map +1 -0
  55. package/dist/esm/lib/utils/tiff-utils.js +27 -0
  56. package/dist/esm/lib/utils/tiff-utils.js.map +1 -0
  57. package/dist/esm/types.js +2 -0
  58. package/dist/esm/types.js.map +1 -0
  59. package/dist/esm/typings/geotiff.js +2 -0
  60. package/dist/esm/typings/geotiff.js.map +1 -0
  61. package/dist/index.d.ts +3 -0
  62. package/dist/index.d.ts.map +1 -0
  63. package/dist/index.js +10 -3
  64. package/dist/lib/load-geotiff.d.ts +28 -0
  65. package/dist/lib/load-geotiff.d.ts.map +1 -0
  66. package/dist/lib/load-geotiff.js +56 -31
  67. package/dist/lib/ome/load-ome-tiff.d.ts +50 -0
  68. package/dist/lib/ome/load-ome-tiff.d.ts.map +1 -0
  69. package/dist/lib/ome/load-ome-tiff.js +45 -50
  70. package/dist/lib/ome/ome-indexers.d.ts +11 -0
  71. package/dist/lib/ome/ome-indexers.d.ts.map +1 -0
  72. package/dist/lib/ome/ome-indexers.js +104 -112
  73. package/dist/lib/ome/ome-utils.d.ts +28 -0
  74. package/dist/lib/ome/ome-utils.d.ts.map +1 -0
  75. package/dist/lib/ome/ome-utils.js +59 -69
  76. package/dist/lib/ome/omexml.d.ts +49 -0
  77. package/dist/lib/ome/omexml.d.ts.map +1 -0
  78. package/dist/lib/ome/omexml.js +60 -60
  79. package/dist/lib/ome/utils.d.ts +5 -0
  80. package/dist/lib/ome/utils.d.ts.map +1 -0
  81. package/dist/lib/ome/utils.js +27 -18
  82. package/dist/lib/tiff-pixel-source.d.ts +18 -0
  83. package/dist/lib/tiff-pixel-source.d.ts.map +1 -0
  84. package/dist/lib/tiff-pixel-source.js +59 -106
  85. package/dist/lib/utils/Pool.d.ts +29 -0
  86. package/dist/lib/utils/Pool.d.ts.map +1 -0
  87. package/dist/lib/utils/Pool.js +78 -72
  88. package/dist/lib/utils/proxies.d.ts +6 -0
  89. package/dist/lib/utils/proxies.d.ts.map +1 -0
  90. package/dist/lib/utils/proxies.js +79 -56
  91. package/dist/lib/utils/tiff-utils.d.ts +10 -0
  92. package/dist/lib/utils/tiff-utils.d.ts.map +1 -0
  93. package/dist/lib/utils/tiff-utils.js +40 -24
  94. package/dist/types.d.ts +47 -0
  95. package/dist/types.d.ts.map +1 -0
  96. package/dist/types.js +2 -2
  97. package/dist/typings/geotiff.d.ts +60 -0
  98. package/dist/typings/geotiff.d.ts.map +1 -0
  99. package/dist/typings/geotiff.js +1 -2
  100. package/package.json +7 -7
  101. package/dist/bundle.js.map +0 -1
  102. package/dist/dist.min.js +0 -13
  103. package/dist/dist.min.js.map +0 -1
  104. package/dist/index.js.map +0 -1
  105. package/dist/lib/load-geotiff.js.map +0 -1
  106. package/dist/lib/ome/load-ome-tiff.js.map +0 -1
  107. package/dist/lib/ome/ome-indexers.js.map +0 -1
  108. package/dist/lib/ome/ome-utils.js.map +0 -1
  109. package/dist/lib/ome/omexml.js.map +0 -1
  110. package/dist/lib/ome/utils.js.map +0 -1
  111. package/dist/lib/tiff-pixel-source.js.map +0 -1
  112. package/dist/lib/utils/Pool.js.map +0 -1
  113. package/dist/lib/utils/proxies.js.map +0 -1
  114. package/dist/lib/utils/tiff-utils.js.map +0 -1
  115. package/dist/types.js.map +0 -1
  116. package/dist/typings/geotiff.js.map +0 -1
  117. /package/dist/{lib → es5/lib}/utils/decoder.worker.ts.disabled +0 -0
@@ -0,0 +1,2 @@
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+ export {};
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+ //# sourceMappingURL=bundle.d.ts.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"bundle.d.ts","sourceRoot":"","sources":["../src/bundle.ts"],"names":[],"mappings":""}
package/dist/bundle.js CHANGED
@@ -1,4 +1,30 @@
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- import * as moduleExports from './index';
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+ "use strict";
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+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ var desc = Object.getOwnPropertyDescriptor(m, k);
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+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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+ desc = { enumerable: true, get: function() { return m[k]; } };
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+ }
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+ Object.defineProperty(o, k2, desc);
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+ }) : (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ o[k2] = m[k];
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+ }));
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+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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+ Object.defineProperty(o, "default", { enumerable: true, value: v });
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+ }) : function(o, v) {
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+ o["default"] = v;
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+ });
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+ var __importStar = (this && this.__importStar) || function (mod) {
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+ if (mod && mod.__esModule) return mod;
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+ var result = {};
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+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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+ __setModuleDefault(result, mod);
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+ return result;
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ const moduleExports = __importStar(require("./index"));
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+ // @ts-ignore
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  globalThis.loaders = globalThis.loaders || {};
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+ // @ts-ignore
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  module.exports = Object.assign(globalThis.loaders, moduleExports);
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- //# sourceMappingURL=bundle.js.map
@@ -0,0 +1,9 @@
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+ "use strict";
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+
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+ var _typeof = require("@babel/runtime/helpers/typeof");
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+ var moduleExports = _interopRequireWildcard(require("./index"));
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+ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
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+ function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
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+ globalThis.loaders = globalThis.loaders || {};
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+ module.exports = Object.assign(globalThis.loaders, moduleExports);
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+ //# sourceMappingURL=bundle.js.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"bundle.js","names":["moduleExports","_interopRequireWildcard","require","_getRequireWildcardCache","nodeInterop","WeakMap","cacheBabelInterop","cacheNodeInterop","obj","__esModule","_typeof","default","cache","has","get","newObj","hasPropertyDescriptor","Object","defineProperty","getOwnPropertyDescriptor","key","prototype","hasOwnProperty","call","desc","set","globalThis","loaders","module","exports","assign"],"sources":["../../src/bundle.ts"],"sourcesContent":["import * as moduleExports from './index';\n// @ts-ignore\nglobalThis.loaders = globalThis.loaders || {};\n// @ts-ignore\nmodule.exports = Object.assign(globalThis.loaders, moduleExports);\n"],"mappings":";;;AAAA,IAAAA,aAAA,GAAAC,uBAAA,CAAAC,OAAA;AAAyC,SAAAC,yBAAAC,WAAA,eAAAC,OAAA,kCAAAC,iBAAA,OAAAD,OAAA,QAAAE,gBAAA,OAAAF,OAAA,YAAAF,wBAAA,YAAAA,yBAAAC,WAAA,WAAAA,WAAA,GAAAG,gBAAA,GAAAD,iBAAA,KAAAF,WAAA;AAAA,SAAAH,wBAAAO,GAAA,EAAAJ,WAAA,SAAAA,WAAA,IAAAI,GAAA,IAAAA,GAAA,CAAAC,UAAA,WAAAD,GAAA,QAAAA,GAAA,aAAAE,OAAA,CAAAF,GAAA,yBAAAA,GAAA,4BAAAG,OAAA,EAAAH,GAAA,UAAAI,KAAA,GAAAT,wBAAA,CAAAC,WAAA,OAAAQ,KAAA,IAAAA,KAAA,CAAAC,GAAA,CAAAL,GAAA,YAAAI,KAAA,CAAAE,GAAA,CAAAN,GAAA,SAAAO,MAAA,WAAAC,qBAAA,GAAAC,MAAA,CAAAC,cAAA,IAAAD,MAAA,CAAAE,wBAAA,WAAAC,GAAA,IAAAZ,GAAA,QAAAY,GAAA,kBAAAH,MAAA,CAAAI,SAAA,CAAAC,cAAA,CAAAC,IAAA,CAAAf,GAAA,EAAAY,GAAA,SAAAI,IAAA,GAAAR,qBAAA,GAAAC,MAAA,CAAAE,wBAAA,CAAAX,GAAA,EAAAY,GAAA,cAAAI,IAAA,KAAAA,IAAA,CAAAV,GAAA,IAAAU,IAAA,CAAAC,GAAA,KAAAR,MAAA,CAAAC,cAAA,CAAAH,MAAA,EAAAK,GAAA,EAAAI,IAAA,YAAAT,MAAA,CAAAK,GAAA,IAAAZ,GAAA,CAAAY,GAAA,SAAAL,MAAA,CAAAJ,OAAA,GAAAH,GAAA,MAAAI,KAAA,IAAAA,KAAA,CAAAa,GAAA,CAAAjB,GAAA,EAAAO,MAAA,YAAAA,MAAA;AAEzCW,UAAU,CAACC,OAAO,GAAGD,UAAU,CAACC,OAAO,IAAI,CAAC,CAAC;AAE7CC,MAAM,CAACC,OAAO,GAAGZ,MAAM,CAACa,MAAM,CAACJ,UAAU,CAACC,OAAO,EAAE3B,aAAa,CAAC"}
@@ -0,0 +1,21 @@
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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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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ });
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+ Object.defineProperty(exports, "TiffPixelSource", {
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+ enumerable: true,
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+ get: function get() {
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+ return _tiffPixelSource.default;
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+ }
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+ });
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+ Object.defineProperty(exports, "loadGeoTiff", {
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+ enumerable: true,
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+ get: function get() {
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+ return _loadGeotiff.loadGeoTiff;
17
+ }
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+ });
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+ var _loadGeotiff = require("./lib/load-geotiff");
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+ var _tiffPixelSource = _interopRequireDefault(require("./lib/tiff-pixel-source"));
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+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"index.js","names":["_loadGeotiff","require","_tiffPixelSource","_interopRequireDefault"],"sources":["../../src/index.ts"],"sourcesContent":["export {loadGeoTiff} from './lib/load-geotiff';\nexport {default as TiffPixelSource} from './lib/tiff-pixel-source';\n"],"mappings":";;;;;;;;;;;;;;;;;;AAAA,IAAAA,YAAA,GAAAC,OAAA;AACA,IAAAC,gBAAA,GAAAC,sBAAA,CAAAF,OAAA"}
@@ -0,0 +1,76 @@
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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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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ });
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+ exports.loadGeoTiff = loadGeoTiff;
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+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
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+ var _geotiff = require("geotiff");
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+ var _proxies = require("./utils/proxies");
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+ var _loadOmeTiff = require("./ome/load-ome-tiff");
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+ function loadGeoTiff(_x) {
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+ return _loadGeoTiff.apply(this, arguments);
15
+ }
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+ function _loadGeoTiff() {
17
+ _loadGeoTiff = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(source) {
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+ var opts,
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+ headers,
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+ offsets,
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+ tiff,
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+ firstImage,
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+ _args = arguments;
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+ return _regenerator.default.wrap(function _callee$(_context) {
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+ while (1) switch (_context.prev = _context.next) {
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+ case 0:
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+ opts = _args.length > 1 && _args[1] !== undefined ? _args[1] : {};
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+ headers = opts.headers, offsets = opts.offsets;
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+ if (!(source instanceof _geotiff.GeoTIFF)) {
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+ _context.next = 6;
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+ break;
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+ }
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+ tiff = source;
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+ _context.next = 15;
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+ break;
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+ case 6:
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+ if (!(typeof source === 'string')) {
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+ _context.next = 12;
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+ break;
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+ }
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+ _context.next = 9;
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+ return (0, _geotiff.fromUrl)(source, headers);
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+ case 9:
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+ tiff = _context.sent;
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+ _context.next = 15;
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+ break;
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+ case 12:
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+ _context.next = 14;
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+ return (0, _geotiff.fromBlob)(source);
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+ case 14:
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+ tiff = _context.sent;
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+ case 15:
53
+ if (offsets) {
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+ tiff = (0, _proxies.createOffsetsProxy)(tiff, offsets);
55
+ }
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+ (0, _proxies.checkProxies)(tiff);
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+ _context.next = 19;
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+ return tiff.getImage(0);
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+ case 19:
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+ firstImage = _context.sent;
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+ if (!(0, _loadOmeTiff.isOmeTiff)(firstImage)) {
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+ _context.next = 22;
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+ break;
64
+ }
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+ return _context.abrupt("return", (0, _loadOmeTiff.loadOmeTiff)(tiff, firstImage));
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+ case 22:
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+ throw new Error('GeoTIFF not recognized.');
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+ case 23:
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+ case "end":
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+ return _context.stop();
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+ }
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+ }, _callee);
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+ }));
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+ return _loadGeoTiff.apply(this, arguments);
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+ }
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+ //# sourceMappingURL=load-geotiff.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"load-geotiff.js","names":["_geotiff","require","_proxies","_loadOmeTiff","loadGeoTiff","_x","_loadGeoTiff","apply","arguments","_asyncToGenerator2","default","_regenerator","mark","_callee","source","opts","headers","offsets","tiff","firstImage","_args","wrap","_callee$","_context","prev","next","length","undefined","GeoTIFF","fromUrl","sent","fromBlob","createOffsetsProxy","checkProxies","getImage","isOmeTiff","abrupt","loadOmeTiff","Error","stop"],"sources":["../../../src/lib/load-geotiff.ts"],"sourcesContent":["import {fromUrl, fromBlob, GeoTIFF} from 'geotiff';\n\nimport {\n // createPoolProxy,\n createOffsetsProxy,\n checkProxies\n} from './utils/proxies';\n// import Pool from './lib/Pool';\n\nimport {loadOmeTiff, isOmeTiff} from './ome/load-ome-tiff';\nimport type TiffPixelSource from './tiff-pixel-source';\n\n/** Options for initializing a tiff pixel source. */\ninterface GeoTIFFOptions {\n /** Headers passed to each underlying request. */\n headers?: Record<string, unknown>;\n /** Performance enhancment to index the remote tiff source using pre-computed byte-offsets. Generated via https://github.com/ilan-gold/generate-tiff-offsets */\n offsets?: number[];\n /** Indicates whether a multi-threaded pool of image decoders should be used to decode tiles. */\n pool?: boolean;\n}\n\ninterface GeoTIFFData {\n data: TiffPixelSource<string[]>[];\n metadata: Record<string, unknown>;\n}\n\n/**\n * Opens an OME-TIFF via URL and returns data source and associated metadata for first image.\n *\n * @param source url string, File/Blob object, or GeoTIFF object\n * @param opts options for initializing a tiff pixel source.\n * - `opts.headers` are passed to each underlying fetch request.\n * - `opts.offsets` are a performance enhancment to index the remote tiff source using pre-computed byte-offsets.\n * - `opts.pool` indicates whether a multi-threaded pool of image decoders should be used to decode tiles (default = true).\n * @return data source and associated OME-Zarr metadata.\n */\nexport async function loadGeoTiff(\n source: string | Blob | GeoTIFF,\n opts: GeoTIFFOptions = {}\n): Promise<GeoTIFFData> {\n const {headers, offsets} = opts;\n\n // Create tiff source\n let tiff: GeoTIFF;\n if (source instanceof GeoTIFF) {\n tiff = source;\n } else if (typeof source === 'string') {\n tiff = await fromUrl(source, headers);\n } else {\n tiff = await fromBlob(source);\n }\n\n // if (pool) {\n /*\n * Creates a worker pool to decode tiff tiles. Wraps tiff\n * in a Proxy that injects 'pool' into `tiff.readRasters`.\n */\n // tiff = createPoolProxy(tiff, new Pool());\n // }\n\n if (offsets) {\n /*\n * Performance enhancement. If offsets are provided, we\n * create a proxy that intercepts calls to `tiff.getImage`\n * and injects the pre-computed offsets.\n */\n tiff = createOffsetsProxy(tiff, offsets);\n }\n\n /*\n * Inspect tiff source for our performance enhancing proxies.\n * Prints warnings to console if `offsets` or `pool` are missing.\n */\n checkProxies(tiff);\n\n const firstImage = await tiff.getImage(0);\n\n if (isOmeTiff(firstImage)) {\n return loadOmeTiff(tiff, firstImage);\n }\n\n throw new Error('GeoTIFF not recognized.');\n}\n"],"mappings":";;;;;;;;;AAAA,IAAAA,QAAA,GAAAC,OAAA;AAEA,IAAAC,QAAA,GAAAD,OAAA;AAOA,IAAAE,YAAA,GAAAF,OAAA;AAA2D,SA4BrCG,WAAWA,CAAAC,EAAA;EAAA,OAAAC,YAAA,CAAAC,KAAA,OAAAC,SAAA;AAAA;AAAA,SAAAF,aAAA;EAAAA,YAAA,OAAAG,kBAAA,CAAAC,OAAA,EAAAC,YAAA,CAAAD,OAAA,CAAAE,IAAA,CAA1B,SAAAC,QACLC,MAA+B;IAAA,IAAAC,IAAA;MAAAC,OAAA;MAAAC,OAAA;MAAAC,IAAA;MAAAC,UAAA;MAAAC,KAAA,GAAAZ,SAAA;IAAA,OAAAG,YAAA,CAAAD,OAAA,CAAAW,IAAA,UAAAC,SAAAC,QAAA;MAAA,kBAAAA,QAAA,CAAAC,IAAA,GAAAD,QAAA,CAAAE,IAAA;QAAA;UAC/BV,IAAoB,GAAAK,KAAA,CAAAM,MAAA,QAAAN,KAAA,QAAAO,SAAA,GAAAP,KAAA,MAAG,CAAC,CAAC;UAElBJ,OAAO,GAAaD,IAAI,CAAxBC,OAAO,EAAEC,OAAO,GAAIF,IAAI,CAAfE,OAAO;UAAA,MAInBH,MAAM,YAAYc,gBAAO;YAAAL,QAAA,CAAAE,IAAA;YAAA;UAAA;UAC3BP,IAAI,GAAGJ,MAAM;UAACS,QAAA,CAAAE,IAAA;UAAA;QAAA;UAAA,MACL,OAAOX,MAAM,KAAK,QAAQ;YAAAS,QAAA,CAAAE,IAAA;YAAA;UAAA;UAAAF,QAAA,CAAAE,IAAA;UAAA,OACtB,IAAAI,gBAAO,EAACf,MAAM,EAAEE,OAAO,CAAC;QAAA;UAArCE,IAAI,GAAAK,QAAA,CAAAO,IAAA;UAAAP,QAAA,CAAAE,IAAA;UAAA;QAAA;UAAAF,QAAA,CAAAE,IAAA;UAAA,OAES,IAAAM,iBAAQ,EAACjB,MAAM,CAAC;QAAA;UAA7BI,IAAI,GAAAK,QAAA,CAAAO,IAAA;QAAA;UAWN,IAAIb,OAAO,EAAE;YAMXC,IAAI,GAAG,IAAAc,2BAAkB,EAACd,IAAI,EAAED,OAAO,CAAC;UAC1C;UAMA,IAAAgB,qBAAY,EAACf,IAAI,CAAC;UAACK,QAAA,CAAAE,IAAA;UAAA,OAEMP,IAAI,CAACgB,QAAQ,CAAC,CAAC,CAAC;QAAA;UAAnCf,UAAU,GAAAI,QAAA,CAAAO,IAAA;UAAA,KAEZ,IAAAK,sBAAS,EAAChB,UAAU,CAAC;YAAAI,QAAA,CAAAE,IAAA;YAAA;UAAA;UAAA,OAAAF,QAAA,CAAAa,MAAA,WAChB,IAAAC,wBAAW,EAACnB,IAAI,EAAEC,UAAU,CAAC;QAAA;UAAA,MAGhC,IAAImB,KAAK,CAAC,yBAAyB,CAAC;QAAA;QAAA;UAAA,OAAAf,QAAA,CAAAgB,IAAA;MAAA;IAAA,GAAA1B,OAAA;EAAA,CAC3C;EAAA,OAAAP,YAAA,CAAAC,KAAA,OAAAC,SAAA;AAAA"}
@@ -0,0 +1,66 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+ Object.defineProperty(exports, "__esModule", {
5
+ value: true
6
+ });
7
+ exports.isOmeTiff = void 0;
8
+ exports.loadOmeTiff = loadOmeTiff;
9
+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
10
+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
11
+ var _tiffPixelSource = _interopRequireDefault(require("../tiff-pixel-source"));
12
+ var _omeIndexers = require("./ome-indexers");
13
+ var _omeUtils = require("./ome-utils");
14
+ var _omexml = require("./omexml");
15
+ var isOmeTiff = function isOmeTiff(img) {
16
+ return img.fileDirectory.ImageDescription.includes('<OME');
17
+ };
18
+ exports.isOmeTiff = isOmeTiff;
19
+ function loadOmeTiff(_x, _x2) {
20
+ return _loadOmeTiff.apply(this, arguments);
21
+ }
22
+ function _loadOmeTiff() {
23
+ _loadOmeTiff = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(tiff, firstImage) {
24
+ var _firstImage$fileDirec, ImageDescription, SubIFDs, photometricInterpretation, omexml, levels, pyramidIndexer, imgMeta, _getOmePixelSourceMet, labels, getShape, physicalSizes, dtype, tileSize, meta, data;
25
+ return _regenerator.default.wrap(function _callee$(_context) {
26
+ while (1) switch (_context.prev = _context.next) {
27
+ case 0:
28
+ _firstImage$fileDirec = firstImage.fileDirectory, ImageDescription = _firstImage$fileDirec.ImageDescription, SubIFDs = _firstImage$fileDirec.SubIFDs, photometricInterpretation = _firstImage$fileDirec.PhotometricInterpretation;
29
+ omexml = (0, _omexml.fromString)(ImageDescription);
30
+ if (SubIFDs) {
31
+ levels = SubIFDs.length + 1;
32
+ pyramidIndexer = (0, _omeIndexers.getOmeSubIFDIndexer)(tiff, omexml);
33
+ } else {
34
+ levels = omexml.length;
35
+ pyramidIndexer = (0, _omeIndexers.getOmeLegacyIndexer)(tiff, omexml);
36
+ }
37
+ imgMeta = omexml[0];
38
+ _getOmePixelSourceMet = (0, _omeUtils.getOmePixelSourceMeta)(imgMeta), labels = _getOmePixelSourceMet.labels, getShape = _getOmePixelSourceMet.getShape, physicalSizes = _getOmePixelSourceMet.physicalSizes, dtype = _getOmePixelSourceMet.dtype;
39
+ tileSize = firstImage.getTileWidth();
40
+ meta = {
41
+ photometricInterpretation: photometricInterpretation,
42
+ physicalSizes: physicalSizes
43
+ };
44
+ data = Array.from({
45
+ length: levels
46
+ }).map(function (_, resolution) {
47
+ var shape = getShape(resolution);
48
+ var indexer = function indexer(sel) {
49
+ return pyramidIndexer(sel, resolution);
50
+ };
51
+ var source = new _tiffPixelSource.default(indexer, dtype, tileSize, shape, labels, meta);
52
+ return source;
53
+ });
54
+ return _context.abrupt("return", {
55
+ data: data,
56
+ metadata: imgMeta
57
+ });
58
+ case 9:
59
+ case "end":
60
+ return _context.stop();
61
+ }
62
+ }, _callee);
63
+ }));
64
+ return _loadOmeTiff.apply(this, arguments);
65
+ }
66
+ //# sourceMappingURL=load-ome-tiff.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"load-ome-tiff.js","names":["_tiffPixelSource","_interopRequireDefault","require","_omeIndexers","_omeUtils","_omexml","isOmeTiff","img","fileDirectory","ImageDescription","includes","exports","loadOmeTiff","_x","_x2","_loadOmeTiff","apply","arguments","_asyncToGenerator2","default","_regenerator","mark","_callee","tiff","firstImage","_firstImage$fileDirec","SubIFDs","photometricInterpretation","omexml","levels","pyramidIndexer","imgMeta","_getOmePixelSourceMet","labels","getShape","physicalSizes","dtype","tileSize","meta","data","wrap","_callee$","_context","prev","next","PhotometricInterpretation","fromString","length","getOmeSubIFDIndexer","getOmeLegacyIndexer","getOmePixelSourceMeta","getTileWidth","Array","from","map","_","resolution","shape","indexer","sel","source","TiffPixelSource","abrupt","metadata","stop"],"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"sourcesContent":["import type {GeoTIFF, GeoTIFFImage} from 'geotiff';\n\nimport TiffPixelSource from '../tiff-pixel-source';\nimport {getOmeLegacyIndexer, getOmeSubIFDIndexer, OmeTiffIndexer} from './ome-indexers';\nimport {getOmePixelSourceMeta} from './ome-utils';\nimport {fromString} from './omexml';\nimport type {OmeTiffSelection} from './ome-indexers';\n\nexport const isOmeTiff = (img: GeoTIFFImage) => img.fileDirectory.ImageDescription.includes('<OME');\n\nexport async function loadOmeTiff(tiff: GeoTIFF, firstImage: GeoTIFFImage) {\n // Get first image from tiff and inspect OME-XML metadata\n const {\n ImageDescription,\n SubIFDs,\n PhotometricInterpretation: photometricInterpretation\n } = firstImage.fileDirectory;\n const omexml = fromString(ImageDescription);\n\n /*\n * Image pyramids are stored differently between versions of Bioformats.\n * Thus we need a different indexer depending on which format we have.\n */\n let levels: number;\n let pyramidIndexer: OmeTiffIndexer;\n\n if (SubIFDs) {\n // Image is >= Bioformats 6.0 and resolutions are stored using SubIFDs.\n levels = SubIFDs.length + 1;\n pyramidIndexer = getOmeSubIFDIndexer(tiff, omexml);\n } else {\n // Image is legacy format; resolutions are stored as separate images.\n levels = omexml.length;\n pyramidIndexer = getOmeLegacyIndexer(tiff, omexml);\n }\n\n // TODO: The OmeTIFF loader only works for the _first_ image in the metadata.\n const imgMeta = omexml[0];\n const {labels, getShape, physicalSizes, dtype} = getOmePixelSourceMeta(imgMeta);\n const tileSize = firstImage.getTileWidth();\n const meta = {photometricInterpretation, physicalSizes};\n\n const data = Array.from({length: levels}).map((_, resolution) => {\n const shape = getShape(resolution);\n const indexer = (sel: OmeTiffSelection) => pyramidIndexer(sel, resolution);\n const source = new TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta);\n return source;\n });\n\n return {data, metadata: imgMeta};\n}\n"],"mappings":";;;;;;;;;;AAEA,IAAAA,gBAAA,GAAAC,sBAAA,CAAAC,OAAA;AACA,IAAAC,YAAA,GAAAD,OAAA;AACA,IAAAE,SAAA,GAAAF,OAAA;AACA,IAAAG,OAAA,GAAAH,OAAA;AAGO,IAAMI,SAAS,GAAG,SAAZA,SAASA,CAAIC,GAAiB;EAAA,OAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAAA;AAACC,OAAA,CAAAL,SAAA,GAAAA,SAAA;AAAA,SAE9EM,WAAWA,CAAAC,EAAA,EAAAC,GAAA;EAAA,OAAAC,YAAA,CAAAC,KAAA,OAAAC,SAAA;AAAA;AAAA,SAAAF,aAAA;EAAAA,YAAA,OAAAG,kBAAA,CAAAC,OAAA,EAAAC,YAAA,CAAAD,OAAA,CAAAE,IAAA,CAA1B,SAAAC,QAA2BC,IAAa,EAAEC,UAAwB;IAAA,IAAAC,qBAAA,EAAAhB,gBAAA,EAAAiB,OAAA,EAAAC,yBAAA,EAAAC,MAAA,EAAAC,MAAA,EAAAC,cAAA,EAAAC,OAAA,EAAAC,qBAAA,EAAAC,MAAA,EAAAC,QAAA,EAAAC,aAAA,EAAAC,KAAA,EAAAC,QAAA,EAAAC,IAAA,EAAAC,IAAA;IAAA,OAAAnB,YAAA,CAAAD,OAAA,CAAAqB,IAAA,UAAAC,SAAAC,QAAA;MAAA,kBAAAA,QAAA,CAAAC,IAAA,GAAAD,QAAA,CAAAE,IAAA;QAAA;UAAAnB,qBAAA,GAMnED,UAAU,CAAChB,aAAa,EAH1BC,gBAAgB,GAAAgB,qBAAA,CAAhBhB,gBAAgB,EAChBiB,OAAO,GAAAD,qBAAA,CAAPC,OAAO,EACoBC,yBAAyB,GAAAF,qBAAA,CAApDoB,yBAAyB;UAErBjB,MAAM,GAAG,IAAAkB,kBAAU,EAACrC,gBAAgB,CAAC;UAS3C,IAAIiB,OAAO,EAAE;YAEXG,MAAM,GAAGH,OAAO,CAACqB,MAAM,GAAG,CAAC;YAC3BjB,cAAc,GAAG,IAAAkB,gCAAmB,EAACzB,IAAI,EAAEK,MAAM,CAAC;UACpD,CAAC,MAAM;YAELC,MAAM,GAAGD,MAAM,CAACmB,MAAM;YACtBjB,cAAc,GAAG,IAAAmB,gCAAmB,EAAC1B,IAAI,EAAEK,MAAM,CAAC;UACpD;UAGMG,OAAO,GAAGH,MAAM,CAAC,CAAC,CAAC;UAAAI,qBAAA,GACwB,IAAAkB,+BAAqB,EAACnB,OAAO,CAAC,EAAxEE,MAAM,GAAAD,qBAAA,CAANC,MAAM,EAAEC,QAAQ,GAAAF,qBAAA,CAARE,QAAQ,EAAEC,aAAa,GAAAH,qBAAA,CAAbG,aAAa,EAAEC,KAAK,GAAAJ,qBAAA,CAALI,KAAK;UACvCC,QAAQ,GAAGb,UAAU,CAAC2B,YAAY,CAAC,CAAC;UACpCb,IAAI,GAAG;YAACX,yBAAyB,EAAzBA,yBAAyB;YAAEQ,aAAa,EAAbA;UAAa,CAAC;UAEjDI,IAAI,GAAGa,KAAK,CAACC,IAAI,CAAC;YAACN,MAAM,EAAElB;UAAM,CAAC,CAAC,CAACyB,GAAG,CAAC,UAACC,CAAC,EAAEC,UAAU,EAAK;YAC/D,IAAMC,KAAK,GAAGvB,QAAQ,CAACsB,UAAU,CAAC;YAClC,IAAME,OAAO,GAAG,SAAVA,OAAOA,CAAIC,GAAqB;cAAA,OAAK7B,cAAc,CAAC6B,GAAG,EAAEH,UAAU,CAAC;YAAA;YAC1E,IAAMI,MAAM,GAAG,IAAIC,wBAAe,CAACH,OAAO,EAAEtB,KAAK,EAAEC,QAAQ,EAAEoB,KAAK,EAAExB,MAAM,EAAEK,IAAI,CAAC;YACjF,OAAOsB,MAAM;UACf,CAAC,CAAC;UAAA,OAAAlB,QAAA,CAAAoB,MAAA,WAEK;YAACvB,IAAI,EAAJA,IAAI;YAAEwB,QAAQ,EAAEhC;UAAO,CAAC;QAAA;QAAA;UAAA,OAAAW,QAAA,CAAAsB,IAAA;MAAA;IAAA,GAAA1C,OAAA;EAAA,CACjC;EAAA,OAAAP,YAAA,CAAAC,KAAA,OAAAC,SAAA;AAAA"}
@@ -0,0 +1,140 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+ Object.defineProperty(exports, "__esModule", {
5
+ value: true
6
+ });
7
+ exports.getOmeLegacyIndexer = getOmeLegacyIndexer;
8
+ exports.getOmeSubIFDIndexer = getOmeSubIFDIndexer;
9
+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
10
+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
11
+ function getOmeLegacyIndexer(tiff, rootMeta) {
12
+ var imgMeta = rootMeta[0];
13
+ var _imgMeta$Pixels = imgMeta.Pixels,
14
+ SizeT = _imgMeta$Pixels.SizeT,
15
+ SizeC = _imgMeta$Pixels.SizeC,
16
+ SizeZ = _imgMeta$Pixels.SizeZ;
17
+ var ifdIndexer = getOmeIFDIndexer(imgMeta);
18
+ return function (sel, pyramidLevel) {
19
+ var index = ifdIndexer(sel);
20
+ var pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;
21
+ return tiff.getImage(index + pyramidIndex);
22
+ };
23
+ }
24
+ function getOmeSubIFDIndexer(tiff, rootMeta) {
25
+ var imgMeta = rootMeta[0];
26
+ var ifdIndexer = getOmeIFDIndexer(imgMeta);
27
+ var ifdCache = new Map();
28
+ return function () {
29
+ var _ref = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(sel, pyramidLevel) {
30
+ var index, baseImage, SubIFDs, key, subIfdOffset, ifd;
31
+ return _regenerator.default.wrap(function _callee$(_context) {
32
+ while (1) switch (_context.prev = _context.next) {
33
+ case 0:
34
+ index = ifdIndexer(sel);
35
+ _context.next = 3;
36
+ return tiff.getImage(index);
37
+ case 3:
38
+ baseImage = _context.sent;
39
+ if (!(pyramidLevel === 0)) {
40
+ _context.next = 6;
41
+ break;
42
+ }
43
+ return _context.abrupt("return", baseImage);
44
+ case 6:
45
+ SubIFDs = baseImage.fileDirectory.SubIFDs;
46
+ if (SubIFDs) {
47
+ _context.next = 9;
48
+ break;
49
+ }
50
+ throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
51
+ case 9:
52
+ key = "".concat(sel.t, "-").concat(sel.c, "-").concat(sel.z, "-").concat(pyramidLevel);
53
+ if (!ifdCache.has(key)) {
54
+ subIfdOffset = SubIFDs[pyramidLevel - 1];
55
+ ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
56
+ }
57
+ _context.next = 13;
58
+ return ifdCache.get(key);
59
+ case 13:
60
+ ifd = _context.sent;
61
+ return _context.abrupt("return", new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source));
62
+ case 15:
63
+ case "end":
64
+ return _context.stop();
65
+ }
66
+ }, _callee);
67
+ }));
68
+ return function (_x, _x2) {
69
+ return _ref.apply(this, arguments);
70
+ };
71
+ }();
72
+ }
73
+ function getOmeIFDIndexer(imgMeta) {
74
+ var _imgMeta$Pixels2 = imgMeta.Pixels,
75
+ SizeC = _imgMeta$Pixels2.SizeC,
76
+ SizeZ = _imgMeta$Pixels2.SizeZ,
77
+ SizeT = _imgMeta$Pixels2.SizeT,
78
+ DimensionOrder = _imgMeta$Pixels2.DimensionOrder;
79
+ switch (DimensionOrder) {
80
+ case 'XYZCT':
81
+ {
82
+ return function (_ref2) {
83
+ var t = _ref2.t,
84
+ c = _ref2.c,
85
+ z = _ref2.z;
86
+ return t * SizeZ * SizeC + c * SizeZ + z;
87
+ };
88
+ }
89
+ case 'XYZTC':
90
+ {
91
+ return function (_ref3) {
92
+ var t = _ref3.t,
93
+ c = _ref3.c,
94
+ z = _ref3.z;
95
+ return c * SizeZ * SizeT + t * SizeZ + z;
96
+ };
97
+ }
98
+ case 'XYCTZ':
99
+ {
100
+ return function (_ref4) {
101
+ var t = _ref4.t,
102
+ c = _ref4.c,
103
+ z = _ref4.z;
104
+ return z * SizeC * SizeT + t * SizeC + c;
105
+ };
106
+ }
107
+ case 'XYCZT':
108
+ {
109
+ return function (_ref5) {
110
+ var t = _ref5.t,
111
+ c = _ref5.c,
112
+ z = _ref5.z;
113
+ return t * SizeC * SizeZ + z * SizeC + c;
114
+ };
115
+ }
116
+ case 'XYTCZ':
117
+ {
118
+ return function (_ref6) {
119
+ var t = _ref6.t,
120
+ c = _ref6.c,
121
+ z = _ref6.z;
122
+ return z * SizeT * SizeC + c * SizeT + t;
123
+ };
124
+ }
125
+ case 'XYTZC':
126
+ {
127
+ return function (_ref7) {
128
+ var t = _ref7.t,
129
+ c = _ref7.c,
130
+ z = _ref7.z;
131
+ return c * SizeT * SizeZ + z * SizeT + t;
132
+ };
133
+ }
134
+ default:
135
+ {
136
+ throw new Error("Invalid OME-XML DimensionOrder, got ".concat(DimensionOrder, "."));
137
+ }
138
+ }
139
+ }
140
+ //# sourceMappingURL=ome-indexers.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","_imgMeta$Pixels","Pixels","SizeT","SizeC","SizeZ","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","_ref","_asyncToGenerator2","default","_regenerator","mark","_callee","baseImage","SubIFDs","key","subIfdOffset","ifd","wrap","_callee$","_context","prev","next","sent","abrupt","fileDirectory","Error","concat","t","c","z","has","set","parseFileDirectoryAt","get","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","stop","_x","_x2","apply","arguments","_imgMeta$Pixels2","DimensionOrder","_ref2","_ref3","_ref4","_ref5","_ref6","_ref7"],"sources":["../../../../src/lib/ome/ome-indexers.ts"],"sourcesContent":["import type {GeoTIFFImage, GeoTIFF, ImageFileDirectory} from 'geotiff';\nimport type {OMEXML} from '../ome/omexml';\n\nexport type OmeTiffSelection = {t: number; c: number; z: number};\nexport type OmeTiffIndexer = (sel: OmeTiffSelection, z: number) => Promise<GeoTIFFImage>;\n\n/*\n * An \"indexer\" for a GeoTIFF-based source is a function that takes a\n * \"selection\" (e.g. { z, t, c }) and returns a Promise for the GeoTIFFImage\n * object corresponding to that selection.\n *\n * For OME-TIFF images, the \"selection\" object is the same regardless of\n * the format version. However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n const imgMeta = rootMeta[0];\n const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n return (sel: OmeTiffSelection, pyramidLevel: number) => {\n // Get IFD index at base pyramid level\n const index = ifdIndexer(sel);\n // Get index of first image at pyramidal level\n const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n // Return image at IFD index for pyramidal level\n return tiff.getImage(index + pyramidIndex);\n };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n const imgMeta = rootMeta[0];\n const ifdIndexer = getOmeIFDIndexer(imgMeta);\n const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n const index = ifdIndexer(sel);\n const baseImage = await tiff.getImage(index);\n\n // It's the highest resolution, no need to look up SubIFDs.\n if (pyramidLevel === 0) {\n return baseImage;\n }\n\n const {SubIFDs} = baseImage.fileDirectory;\n if (!SubIFDs) {\n throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n }\n\n // Get IFD for the selection at the pyramidal level\n const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n if (!ifdCache.has(key)) {\n // Only create a new request if we don't have the key.\n const subIfdOffset = SubIFDs[pyramidLevel - 1];\n ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n }\n const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n // Create a new image object manually from IFD\n // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n return new (baseImage.constructor as any)(\n ifd.fileDirectory,\n ifd.geoKeyDirectory,\n tiff.dataView,\n tiff.littleEndian,\n tiff.cache,\n tiff.source\n ) as GeoTIFFImage;\n };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n switch (DimensionOrder) {\n case 'XYZCT': {\n return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n }\n case 'XYZTC': {\n return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n }\n case 'XYCTZ': {\n return ({t, c, 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@@ -0,0 +1,74 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+ Object.defineProperty(exports, "__esModule", {
5
+ value: true
6
+ });
7
+ exports.DTYPE_LOOKUP = void 0;
8
+ exports.getOmePixelSourceMeta = getOmePixelSourceMeta;
9
+ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
10
+ var _utils = require("./utils");
11
+ var DTYPE_LOOKUP = {
12
+ uint8: 'Uint8',
13
+ uint16: 'Uint16',
14
+ uint32: 'Uint32',
15
+ float: 'Float32',
16
+ double: 'Float64',
17
+ int8: 'Int8',
18
+ int16: 'Int16',
19
+ int32: 'Int32'
20
+ };
21
+ exports.DTYPE_LOOKUP = DTYPE_LOOKUP;
22
+ function getOmePixelSourceMeta(_ref) {
23
+ var Pixels = _ref.Pixels;
24
+ var labels = (0, _utils.getLabels)(Pixels.DimensionOrder);
25
+ var dims = (0, _utils.getDims)(labels);
26
+ var shape = Array(labels.length).fill(0);
27
+ shape[dims('t')] = Pixels.SizeT;
28
+ shape[dims('c')] = Pixels.SizeC;
29
+ shape[dims('z')] = Pixels.SizeZ;
30
+ if (Pixels.Interleaved) {
31
+ labels.push('_c');
32
+ shape.push(3);
33
+ }
34
+ var getShape = function getShape(level) {
35
+ var s = (0, _toConsumableArray2.default)(shape);
36
+ s[dims('x')] = Pixels.SizeX >> level;
37
+ s[dims('y')] = Pixels.SizeY >> level;
38
+ return s;
39
+ };
40
+ if (!(Pixels.Type in DTYPE_LOOKUP)) {
41
+ throw Error("Pixel type ".concat(Pixels.Type, " not supported."));
42
+ }
43
+ var dtype = DTYPE_LOOKUP[Pixels.Type];
44
+ if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
45
+ var physicalSizes = {
46
+ x: {
47
+ size: Pixels.PhysicalSizeX,
48
+ unit: Pixels.PhysicalSizeXUnit
49
+ },
50
+ y: {
51
+ size: Pixels.PhysicalSizeY,
52
+ unit: Pixels.PhysicalSizeYUnit
53
+ }
54
+ };
55
+ if (Pixels.PhysicalSizeZ) {
56
+ physicalSizes.z = {
57
+ size: Pixels.PhysicalSizeZ,
58
+ unit: Pixels.PhysicalSizeZUnit
59
+ };
60
+ }
61
+ return {
62
+ labels: labels,
63
+ getShape: getShape,
64
+ physicalSizes: physicalSizes,
65
+ dtype: dtype
66
+ };
67
+ }
68
+ return {
69
+ labels: labels,
70
+ getShape: getShape,
71
+ dtype: dtype
72
+ };
73
+ }
74
+ //# sourceMappingURL=ome-utils.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"ome-utils.js","names":["_utils","require","DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","exports","getOmePixelSourceMeta","_ref","Pixels","labels","getLabels","DimensionOrder","dims","getDims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","_toConsumableArray2","default","SizeX","SizeY","Type","Error","concat","dtype","PhysicalSizeX","PhysicalSizeY","physicalSizes","x","size","unit","PhysicalSizeXUnit","y","PhysicalSizeYUnit","PhysicalSizeZ","z","PhysicalSizeZUnit"],"sources":["../../../../src/lib/ome/ome-utils.ts"],"sourcesContent":["import {getDims, getLabels} from './utils';\nimport type {OMEXML, UnitsLength} from './omexml';\n\nexport const DTYPE_LOOKUP = {\n uint8: 'Uint8',\n uint16: 'Uint16',\n uint32: 'Uint32',\n float: 'Float32',\n double: 'Float64',\n int8: 'Int8',\n int16: 'Int16',\n int32: 'Int32'\n} as const;\n\nexport function getOmePixelSourceMeta({Pixels}: OMEXML[0]) {\n // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']\n const labels = getLabels(Pixels.DimensionOrder);\n\n // Compute \"shape\" of image\n const dims = getDims(labels);\n const shape: number[] = Array(labels.length).fill(0);\n shape[dims('t')] = Pixels.SizeT;\n shape[dims('c')] = Pixels.SizeC;\n shape[dims('z')] = Pixels.SizeZ;\n\n // Push extra dimension if data are interleaved.\n if (Pixels.Interleaved) {\n // @ts-ignore\n labels.push('_c');\n shape.push(3);\n }\n\n // Creates a new shape for different level of pyramid.\n // Assumes factor-of-two downsampling.\n const getShape = (level: number) => {\n const s = [...shape];\n s[dims('x')] = Pixels.SizeX >> level;\n s[dims('y')] = Pixels.SizeY >> level;\n return s;\n };\n\n if (!(Pixels.Type in DTYPE_LOOKUP)) {\n throw Error(`Pixel type ${Pixels.Type} not supported.`);\n }\n\n const dtype = DTYPE_LOOKUP[Pixels.Type as keyof typeof DTYPE_LOOKUP];\n if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {\n const physicalSizes: {\n [k: string]: {size: number; unit: UnitsLength};\n } = {\n x: {\n size: Pixels.PhysicalSizeX,\n unit: Pixels.PhysicalSizeXUnit\n },\n y: {\n size: Pixels.PhysicalSizeY,\n unit: Pixels.PhysicalSizeYUnit\n }\n };\n if (Pixels.PhysicalSizeZ) {\n physicalSizes.z = {\n size: Pixels.PhysicalSizeZ,\n unit: Pixels.PhysicalSizeZUnit\n };\n }\n return {labels, getShape, physicalSizes, dtype};\n }\n\n return {labels, getShape, dtype};\n}\n"],"mappings":";;;;;;;;;AAAA,IAAAA,MAAA,GAAAC,OAAA;AAGO,IAAMC,YAAY,GAAG;EAC1BC,KAAK,EAAE,OAAO;EACdC,MAAM,EAAE,QAAQ;EAChBC,MAAM,EAAE,QAAQ;EAChBC,KAAK,EAAE,SAAS;EAChBC,MAAM,EAAE,SAAS;EACjBC,IAAI,EAAE,MAAM;EACZC,KAAK,EAAE,OAAO;EACdC,KAAK,EAAE;AACT,CAAU;AAACC,OAAA,CAAAT,YAAA,GAAAA,YAAA;AAEJ,SAASU,qBAAqBA,CAAAC,IAAA,EAAsB;EAAA,IAApBC,MAAM,GAAAD,IAAA,CAANC,MAAM;EAE3C,IAAMC,MAAM,GAAG,IAAAC,gBAAS,EAACF,MAAM,CAACG,cAAc,CAAC;EAG/C,IAAMC,IAAI,GAAG,IAAAC,cAAO,EAACJ,MAAM,CAAC;EAC5B,IAAMK,KAAe,GAAGC,KAAK,CAACN,MAAM,CAACO,MAAM,CAAC,CAACC,IAAI,CAAC,CAAC,CAAC;EACpDH,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACU,KAAK;EAC/BJ,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACW,KAAK;EAC/BL,KAAK,CAACF,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACY,KAAK;EAG/B,IAAIZ,MAAM,CAACa,WAAW,EAAE;IAEtBZ,MAAM,CAACa,IAAI,CAAC,IAAI,CAAC;IACjBR,KAAK,CAACQ,IAAI,CAAC,CAAC,CAAC;EACf;EAIA,IAAMC,QAAQ,GAAG,SAAXA,QAAQA,CAAIC,KAAa,EAAK;IAClC,IAAMC,CAAC,OAAAC,mBAAA,CAAAC,OAAA,EAAOb,KAAK,CAAC;IACpBW,CAAC,CAACb,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACoB,KAAK,IAAIJ,KAAK;IACpCC,CAAC,CAACb,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGJ,MAAM,CAACqB,KAAK,IAAIL,KAAK;IACpC,OAAOC,CAAC;EACV,CAAC;EAED,IAAI,EAAEjB,MAAM,CAACsB,IAAI,IAAIlC,YAAY,CAAC,EAAE;IAClC,MAAMmC,KAAK,eAAAC,MAAA,CAAexB,MAAM,CAACsB,IAAI,oBAAiB,CAAC;EACzD;EAEA,IAAMG,KAAK,GAAGrC,YAAY,CAACY,MAAM,CAACsB,IAAI,CAA8B;EACpE,IAAItB,MAAM,CAAC0B,aAAa,IAAI1B,MAAM,CAAC2B,aAAa,EAAE;IAChD,IAAMC,aAEL,GAAG;MACFC,CAAC,EAAE;QACDC,IAAI,EAAE9B,MAAM,CAAC0B,aAAa;QAC1BK,IAAI,EAAE/B,MAAM,CAACgC;MACf,CAAC;MACDC,CAAC,EAAE;QACDH,IAAI,EAAE9B,MAAM,CAAC2B,aAAa;QAC1BI,IAAI,EAAE/B,MAAM,CAACkC;MACf;IACF,CAAC;IACD,IAAIlC,MAAM,CAACmC,aAAa,EAAE;MACxBP,aAAa,CAACQ,CAAC,GAAG;QAChBN,IAAI,EAAE9B,MAAM,CAACmC,aAAa;QAC1BJ,IAAI,EAAE/B,MAAM,CAACqC;MACf,CAAC;IACH;IACA,OAAO;MAACpC,MAAM,EAANA,MAAM;MAAEc,QAAQ,EAARA,QAAQ;MAAEa,aAAa,EAAbA,aAAa;MAAEH,KAAK,EAALA;IAAK,CAAC;EACjD;EAEA,OAAO;IAACxB,MAAM,EAANA,MAAM;IAAEc,QAAQ,EAARA,QAAQ;IAAEU,KAAK,EAALA;EAAK,CAAC;AAClC"}
@@ -0,0 +1,68 @@
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+ "use strict";
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+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ });
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+ exports.fromString = fromString;
8
+ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
9
+ var _fastXmlParser = _interopRequireDefault(require("fast-xml-parser"));
10
+ var _tiffUtils = require("../utils/tiff-utils");
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+ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
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+ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
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+ var PARSER_OPTIONS = {
14
+ attributeNamePrefix: '',
15
+ attrNodeName: 'attr',
16
+ parseNodeValue: true,
17
+ parseAttributeValue: true,
18
+ ignoreAttributes: false
19
+ };
20
+ var parse = function parse(str) {
21
+ return _fastXmlParser.default.parse(str, PARSER_OPTIONS);
22
+ };
23
+ function fromString(str) {
24
+ var res = parse(str);
25
+ if (!res.OME) {
26
+ throw Error('Failed to parse OME-XML metadata.');
27
+ }
28
+ return (0, _tiffUtils.ensureArray)(res.OME.Image).map(function (img) {
29
+ var Channels = (0, _tiffUtils.ensureArray)(img.Pixels.Channel).map(function (c) {
30
+ if ('Color' in c.attr) {
31
+ return _objectSpread(_objectSpread({}, c.attr), {}, {
32
+ Color: (0, _tiffUtils.intToRgba)(c.attr.Color)
33
+ });
34
+ }
35
+ return _objectSpread({}, c.attr);
36
+ });
37
+ var _img$AquisitionDate = img.AquisitionDate,
38
+ AquisitionDate = _img$AquisitionDate === void 0 ? '' : _img$AquisitionDate,
39
+ _img$Description = img.Description,
40
+ Description = _img$Description === void 0 ? '' : _img$Description;
41
+ var image = _objectSpread(_objectSpread({}, img.attr), {}, {
42
+ AquisitionDate: AquisitionDate,
43
+ Description: Description,
44
+ Pixels: _objectSpread(_objectSpread({}, img.Pixels.attr), {}, {
45
+ Channels: Channels
46
+ })
47
+ });
48
+ return _objectSpread(_objectSpread({}, image), {}, {
49
+ format: function format() {
50
+ var Pixels = image.Pixels;
51
+ var sizes = ['X', 'Y', 'Z'].map(function (name) {
52
+ var size = Pixels["PhysicalSize".concat(name)];
53
+ var unit = Pixels["PhysicalSize".concat(name, "Unit")];
54
+ return size && unit ? "".concat(size, " ").concat(unit) : '-';
55
+ }).join(' x ');
56
+ return {
57
+ 'Acquisition Date': image.AquisitionDate,
58
+ 'Dimensions (XY)': "".concat(Pixels.SizeX, " x ").concat(Pixels.SizeY),
59
+ 'Pixels Type': Pixels.Type,
60
+ 'Pixels Size (XYZ)': sizes,
61
+ 'Z-sections/Timepoints': "".concat(Pixels.SizeZ, " x ").concat(Pixels.SizeT),
62
+ Channels: Pixels.SizeC
63
+ };
64
+ }
65
+ });
66
+ });
67
+ }
68
+ //# sourceMappingURL=omexml.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"omexml.js","names":["_fastXmlParser","_interopRequireDefault","require","_tiffUtils","ownKeys","object","enumerableOnly","keys","Object","getOwnPropertySymbols","symbols","filter","sym","getOwnPropertyDescriptor","enumerable","push","apply","_objectSpread","target","i","arguments","length","source","forEach","key","_defineProperty2","default","getOwnPropertyDescriptors","defineProperties","defineProperty","PARSER_OPTIONS","attributeNamePrefix","attrNodeName","parseNodeValue","parseAttributeValue","ignoreAttributes","parse","str","parser","fromString","res","OME","Error","ensureArray","Image","map","img","Channels","Pixels","Channel","c","attr","Color","intToRgba","_img$AquisitionDate","AquisitionDate","_img$Description","Description","image","format","sizes","name","size","concat","unit","join","SizeX","SizeY","Type","SizeZ","SizeT","SizeC"],"sources":["../../../../src/lib/ome/omexml.ts"],"sourcesContent":["import parser from 'fast-xml-parser';\nimport {ensureArray, intToRgba} from '../utils/tiff-utils';\n\n// WARNING: Changes to the parser options _will_ effect the types in types/omexml.d.ts.\nconst PARSER_OPTIONS = {\n // Nests attributes withtout prefix under 'attr' key for each node\n attributeNamePrefix: '',\n attrNodeName: 'attr',\n\n // Parses numbers for both attributes and nodes\n parseNodeValue: true,\n parseAttributeValue: true,\n\n // Forces attributes to be parsed\n ignoreAttributes: false\n};\n\nconst parse = (str: string): Root => parser.parse(str, PARSER_OPTIONS);\n\nexport function fromString(str: string) {\n const res = parse(str);\n if (!res.OME) {\n throw Error('Failed to parse OME-XML metadata.');\n }\n return ensureArray(res.OME.Image).map((img) => {\n const Channels = ensureArray(img.Pixels.Channel).map((c) => {\n if ('Color' in c.attr) {\n return {...c.attr, Color: intToRgba(c.attr.Color)};\n }\n return {...c.attr};\n });\n const {AquisitionDate = '', Description = ''} = img;\n const image = {\n ...img.attr,\n AquisitionDate,\n Description,\n Pixels: {\n ...img.Pixels.attr,\n Channels\n }\n };\n return {\n ...image,\n format() {\n const {Pixels} = image;\n\n const sizes = (['X', 'Y', 'Z'] as const)\n .map((name) => {\n const size = Pixels[`PhysicalSize${name}` as const];\n const unit = Pixels[`PhysicalSize${name}Unit` as const];\n return size && unit ? `${size} ${unit}` : '-';\n })\n .join(' x ');\n\n return {\n 'Acquisition Date': image.AquisitionDate,\n 'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,\n 'Pixels Type': Pixels.Type,\n 'Pixels Size (XYZ)': sizes,\n 'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,\n Channels: Pixels.SizeC\n };\n }\n };\n });\n}\n\nexport type OMEXML = ReturnType<typeof fromString>;\nexport type DimensionOrder = 'XYZCT' | 'XYZTC' | 'XYCTZ' | 'XYCZT' | 'XYTCZ' | 'XYTZC';\n\n// Structure of node is determined by the PARSER_OPTIONS.\ntype Node<T, A> = T & {attr: A};\ntype Attrs<Fields extends string, T = string> = {[K in Fields]: T};\n\ntype OMEAttrs = Attrs<'xmlns' | 'xmlns:xsi' | 'xsi:schemaLocation'>;\ntype OME = Node<{Insturment: Insturment; Image: Image | Image[]}, OMEAttrs>;\n\ntype Insturment = Node<\n {Objective: Node<{}, Attrs<'ID' | 'Model' | 'NominalMagnification'>>},\n Attrs<'ID'>\n>;\n\ninterface ImageNodes {\n AquisitionDate?: string;\n Description?: string;\n Pixels: Pixels;\n InstrumentRef: Node<{}, {ID: string}>;\n ObjectiveSettings: Node<{}, {ID: string}>;\n}\ntype Image = Node<ImageNodes, Attrs<'ID' | 'Name'>>;\n\ntype PixelType =\n | 'int8'\n | 'int16'\n | 'int32'\n | 'uint8'\n | 'uint16'\n | 'uint32'\n | 'float'\n | 'bit'\n | 'double'\n | 'complex'\n | 'double-complex';\n\nexport type UnitsLength =\n | 'Ym'\n | 'Zm'\n | 'Em'\n | 'Pm'\n | 'Tm'\n | 'Gm'\n | 'Mm'\n | 'km'\n | 'hm'\n | 'dam'\n | 'm'\n | 'dm'\n | 'cm'\n | 'mm'\n | 'µm'\n | 'nm'\n | 'pm'\n | 'fm'\n | 'am'\n | 'zm'\n | 'ym'\n | 'Å'\n | 'thou'\n | 'li'\n | 'in'\n | 'ft'\n | 'yd'\n | 'mi'\n | 'ua'\n | 'ly'\n | 'pc'\n | 'pt'\n | 'pixel'\n | 'reference frame';\n\ntype PhysicalSize<Name extends string> = `PhysicalSize${Name}`;\ntype PhysicalSizeUnit<Name extends string> = `PhysicalSize${Name}Unit`;\ntype Size<Names extends string> = `Size${Names}`;\n\ntype PixelAttrs = Attrs<\n PhysicalSize<'X' | 'Y' | 'Z'> | 'SignificantBits' | Size<'T' | 'C' | 'Z' | 'Y' | 'X'>,\n number\n> &\n Attrs<PhysicalSizeUnit<'X' | 'Y' | 'Z'>, UnitsLength> &\n Attrs<'BigEndian' | 'Interleaved', boolean> & {\n ID: string;\n DimensionOrder: DimensionOrder;\n Type: PixelType;\n };\n\ntype Pixels = Node<\n {\n Channel: Channel | Channel[];\n TiffData: Node<{}, Attrs<'IFD' | 'PlaneCount'>>;\n },\n PixelAttrs\n>;\n\ntype ChannelAttrs =\n | {\n ID: string;\n SamplesPerPixel: number;\n Name?: string;\n }\n | {\n ID: string;\n SamplesPerPixel: number;\n Name?: string;\n Color: number;\n };\n\ntype Channel = Node<{}, ChannelAttrs>;\n\ntype Root = {OME: OME};\n"],"mappings":";;;;;;;;AAAA,IAAAA,cAAA,GAAAC,sBAAA,CAAAC,OAAA;AACA,IAAAC,UAAA,GAAAD,OAAA;AAA2D,SAAAE,QAAAC,MAAA,EAAAC,cAAA,QAAAC,IAAA,GAAAC,MAAA,CAAAD,IAAA,CAAAF,MAAA,OAAAG,MAAA,CAAAC,qBAAA,QAAAC,OAAA,GAAAF,MAAA,CAAAC,qBAAA,CAAAJ,MAAA,GAAAC,cAAA,KAAAI,OAAA,GAAAA,OAAA,CAAAC,MAAA,WAAAC,GAAA,WAAAJ,MAAA,CAAAK,wBAAA,CAAAR,MAAA,EAAAO,GAAA,EAAAE,UAAA,OAAAP,IAAA,CAAAQ,IAAA,CAAAC,KAAA,CAAAT,IAAA,EAAAG,OAAA,YAAAH,IAAA;AAAA,SAAAU,cAAAC,MAAA,aAAAC,CAAA,MAAAA,CAAA,GAAAC,SAAA,CAAAC,MAAA,EAAAF,CAAA,UAAAG,MAAA,WAAAF,SAAA,CAAAD,CAAA,IAAAC,SAAA,CAAAD,CAAA,QAAAA,CAAA,OAAAf,OAAA,CAAAI,MAAA,CAAAc,MAAA,OAAAC,OAAA,WAAAC,GAAA,QAAAC,gBAAA,CAAAC,OAAA,EAAAR,MAAA,EAAAM,GAAA,EAAAF,MAAA,CAAAE,GAAA,SAAAhB,MAAA,CAAAmB,yBAAA,GAAAnB,MAAA,CAAAoB,gBAAA,CAAAV,MAAA,EAAAV,MAAA,CAAAmB,yBAAA,CAAAL,MAAA,KAAAlB,OAAA,CAAAI,MAAA,CAAAc,MAAA,GAAAC,OAAA,WAAAC,GAAA,IAAAhB,MAAA,CAAAqB,cAAA,CAAAX,MAAA,EAAAM,GAAA,EAAAhB,MAAA,CAAAK,wBAAA,CAAAS,MAAA,EAAAE,GAAA,iBAAAN,MAAA;AAG3D,IAAMY,cAAc,GAAG;EAErBC,mBAAmB,EAAE,EAAE;EACvBC,YAAY,EAAE,MAAM;EAGpBC,cAAc,EAAE,IAAI;EACpBC,mBAAmB,EAAE,IAAI;EAGzBC,gBAAgB,EAAE;AACpB,CAAC;AAED,IAAMC,KAAK,GAAG,SAARA,KAAKA,CAAIC,GAAW;EAAA,OAAWC,sBAAM,CAACF,KAAK,CAACC,GAAG,EAAEP,cAAc,CAAC;AAAA;AAE/D,SAASS,UAAUA,CAACF,GAAW,EAAE;EACtC,IAAMG,GAAG,GAAGJ,KAAK,CAACC,GAAG,CAAC;EACtB,IAAI,CAACG,GAAG,CAACC,GAAG,EAAE;IACZ,MAAMC,KAAK,CAAC,mCAAmC,CAAC;EAClD;EACA,OAAO,IAAAC,sBAAW,EAACH,GAAG,CAACC,GAAG,CAACG,KAAK,CAAC,CAACC,GAAG,CAAC,UAACC,GAAG,EAAK;IAC7C,IAAMC,QAAQ,GAAG,IAAAJ,sBAAW,EAACG,GAAG,CAACE,MAAM,CAACC,OAAO,CAAC,CAACJ,GAAG,CAAC,UAACK,CAAC,EAAK;MAC1D,IAAI,OAAO,IAAIA,CAAC,CAACC,IAAI,EAAE;QACrB,OAAAlC,aAAA,CAAAA,aAAA,KAAWiC,CAAC,CAACC,IAAI;UAAEC,KAAK,EAAE,IAAAC,oBAAS,EAACH,CAAC,CAACC,IAAI,CAACC,KAAK;QAAC;MACnD;MACA,OAAAnC,aAAA,KAAWiC,CAAC,CAACC,IAAI;IACnB,CAAC,CAAC;IACF,IAAAG,mBAAA,GAAgDR,GAAG,CAA5CS,cAAc;MAAdA,cAAc,GAAAD,mBAAA,cAAG,EAAE,GAAAA,mBAAA;MAAAE,gBAAA,GAAsBV,GAAG,CAAvBW,WAAW;MAAXA,WAAW,GAAAD,gBAAA,cAAG,EAAE,GAAAA,gBAAA;IAC5C,IAAME,KAAK,GAAAzC,aAAA,CAAAA,aAAA,KACN6B,GAAG,CAACK,IAAI;MACXI,cAAc,EAAdA,cAAc;MACdE,WAAW,EAAXA,WAAW;MACXT,MAAM,EAAA/B,aAAA,CAAAA,aAAA,KACD6B,GAAG,CAACE,MAAM,CAACG,IAAI;QAClBJ,QAAQ,EAARA;MAAQ;IACT,EACF;IACD,OAAA9B,aAAA,CAAAA,aAAA,KACKyC,KAAK;MACRC,MAAM,WAAAA,OAAA,EAAG;QACP,IAAOX,MAAM,GAAIU,KAAK,CAAfV,MAAM;QAEb,IAAMY,KAAK,GAAI,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAC3Bf,GAAG,CAAC,UAACgB,IAAI,EAAK;UACb,IAAMC,IAAI,GAAGd,MAAM,gBAAAe,MAAA,CAAgBF,IAAI,EAAY;UACnD,IAAMG,IAAI,GAAGhB,MAAM,gBAAAe,MAAA,CAAgBF,IAAI,UAAgB;UACvD,OAAOC,IAAI,IAAIE,IAAI,MAAAD,MAAA,CAAMD,IAAI,OAAAC,MAAA,CAAIC,IAAI,IAAK,GAAG;QAC/C,CAAC,CAAC,CACDC,IAAI,CAAC,KAAK,CAAC;QAEd,OAAO;UACL,kBAAkB,EAAEP,KAAK,CAACH,cAAc;UACxC,iBAAiB,KAAAQ,MAAA,CAAKf,MAAM,CAACkB,KAAK,SAAAH,MAAA,CAAMf,MAAM,CAACmB,KAAK,CAAE;UACtD,aAAa,EAAEnB,MAAM,CAACoB,IAAI;UAC1B,mBAAmB,EAAER,KAAK;UAC1B,uBAAuB,KAAAG,MAAA,CAAKf,MAAM,CAACqB,KAAK,SAAAN,MAAA,CAAMf,MAAM,CAACsB,KAAK,CAAE;UAC5DvB,QAAQ,EAAEC,MAAM,CAACuB;QACnB,CAAC;MACH;IAAC;EAEL,CAAC,CAAC;AACJ"}
@@ -0,0 +1,26 @@
1
+ "use strict";
2
+
3
+ Object.defineProperty(exports, "__esModule", {
4
+ value: true
5
+ });
6
+ exports.getDims = getDims;
7
+ exports.getLabels = getLabels;
8
+ function getLabels(dimOrder) {
9
+ return dimOrder.toLowerCase().split('').reverse();
10
+ }
11
+ function getDims(labels) {
12
+ var lookup = new Map(labels.map(function (name, i) {
13
+ return [name, i];
14
+ }));
15
+ if (lookup.size !== labels.length) {
16
+ throw Error('Labels must be unique, found duplicated label.');
17
+ }
18
+ return function (name) {
19
+ var index = lookup.get(name);
20
+ if (index === undefined) {
21
+ throw Error('Invalid dimension.');
22
+ }
23
+ return index;
24
+ };
25
+ }
26
+ //# sourceMappingURL=utils.js.map
@@ -0,0 +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":["import 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":";;;;;;;AAaO,SAASA,SAASA,CAACC,QAA+C,EAAE;EACzE,OAAOA,QAAQ,CAACC,WAAW,CAAC,CAAC,CAACC,KAAK,CAAC,EAAE,CAAC,CAACC,OAAO,CAAC,CAAC;AACnD;AAWO,SAASC,OAAOA,CAAmBC,MAAW,EAAE;EACrD,IAAMC,MAAM,GAAG,IAAIC,GAAG,CAACF,MAAM,CAACG,GAAG,CAAC,UAACC,IAAI,EAAEC,CAAC;IAAA,OAAK,CAACD,IAAI,EAAEC,CAAC,CAAC;EAAA,EAAC,CAAC;EAC1D,IAAIJ,MAAM,CAACK,IAAI,KAAKN,MAAM,CAACO,MAAM,EAAE;IACjC,MAAMC,KAAK,CAAC,gDAAgD,CAAC;EAC/D;EACA,OAAO,UAACJ,IAAO,EAAK;IAClB,IAAMK,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"}