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

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

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

package/dist/lib/ome/omexml.js

@@ -1,66 +1,66 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fromString = void 0;
-const fast_xml_parser_1 = __importDefault(require("fast-xml-parser"));
-const tiff_utils_1 = require("../utils/tiff-utils");
-// WARNING: Changes to the parser options _will_ effect the types in types/omexml.d.ts.
+import parser from 'fast-xml-parser';
+import { ensureArray, intToRgba } from '../utils/tiff-utils';
 const PARSER_OPTIONS = {
-    // Nests attributes withtout prefix under 'attr' key for each node
-    attributeNamePrefix: '',
-    attrNodeName: 'attr',
-    // Parses numbers for both attributes and nodes
-    parseNodeValue: true,
-    parseAttributeValue: true,
-    // Forces attributes to be parsed
-    ignoreAttributes: false
+  attributeNamePrefix: '',
+  attrNodeName: 'attr',
+  parseNodeValue: true,
+  parseAttributeValue: true,
+  ignoreAttributes: false
 };
-const parse = (str) => fast_xml_parser_1.default.parse(str, PARSER_OPTIONS);
-function fromString(str) {
-    const res = parse(str);
-    if (!res.OME) {
-        throw Error('Failed to parse OME-XML metadata.');
-    }
-    return (0, tiff_utils_1.ensureArray)(res.OME.Image).map((img) => {
-        const Channels = (0, tiff_utils_1.ensureArray)(img.Pixels.Channel).map((c) => {
-            if ('Color' in c.attr) {
-                return { ...c.attr, Color: (0, tiff_utils_1.intToRgba)(c.attr.Color) };
-            }
-            return { ...c.attr };
-        });
-        const { AquisitionDate = '', Description = '' } = img;
-        const image = {
-            ...img.attr,
-            AquisitionDate,
-            Description,
-            Pixels: {
-                ...img.Pixels.attr,
-                Channels
-            }
+
+const parse = str => parser.parse(str, PARSER_OPTIONS);
+
+export function fromString(str) {
+  const res = parse(str);
+
+  if (!res.OME) {
+    throw Error('Failed to parse OME-XML metadata.');
+  }
+
+  return ensureArray(res.OME.Image).map(img => {
+    const Channels = ensureArray(img.Pixels.Channel).map(c => {
+      if ('Color' in c.attr) {
+        return { ...c.attr,
+          Color: intToRgba(c.attr.Color)
         };
+      }
+
+      return { ...c.attr
+      };
+    });
+    const {
+      AquisitionDate = '',
+      Description = ''
+    } = img;
+    const image = { ...img.attr,
+      AquisitionDate,
+      Description,
+      Pixels: { ...img.Pixels.attr,
+        Channels
+      }
+    };
+    return { ...image,
+
+      format() {
+        const {
+          Pixels
+        } = image;
+        const sizes = ['X', 'Y', 'Z'].map(name => {
+          const size = Pixels["PhysicalSize".concat(name)];
+          const unit = Pixels["PhysicalSize".concat(name, "Unit")];
+          return size && unit ? "".concat(size, " ").concat(unit) : '-';
+        }).join(' x ');
         return {
-            ...image,
-            format() {
-                const { Pixels } = image;
-                const sizes = ['X', 'Y', 'Z']
-                    .map((name) => {
-                    const size = Pixels[`PhysicalSize${name}`];
-                    const unit = Pixels[`PhysicalSize${name}Unit`];
-                    return size && unit ? `${size} ${unit}` : '-';
-                })
-                    .join(' x ');
-                return {
-                    'Acquisition Date': image.AquisitionDate,
-                    'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,
-                    'Pixels Type': Pixels.Type,
-                    'Pixels Size (XYZ)': sizes,
-                    'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,
-                    Channels: Pixels.SizeC
-                };
-            }
+          'Acquisition Date': image.AquisitionDate,
+          'Dimensions (XY)': "".concat(Pixels.SizeX, " x ").concat(Pixels.SizeY),
+          'Pixels Type': Pixels.Type,
+          'Pixels Size (XYZ)': sizes,
+          'Z-sections/Timepoints': "".concat(Pixels.SizeZ, " x ").concat(Pixels.SizeT),
+          Channels: Pixels.SizeC
         };
-    });
+      }
+
+    };
+  });
 }
-exports.fromString = fromString;
+//# sourceMappingURL=omexml.js.map

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

@@ -0,0 +1 @@
+{"version":3,"sources":["../../../src/lib/ome/omexml.ts"],"names":["parser","ensureArray","intToRgba","PARSER_OPTIONS","attributeNamePrefix","attrNodeName","parseNodeValue","parseAttributeValue","ignoreAttributes","parse","str","fromString","res","OME","Error","Image","map","img","Channels","Pixels","Channel","c","attr","Color","AquisitionDate","Description","image","format","sizes","name","size","unit","join","SizeX","SizeY","Type","SizeZ","SizeT","SizeC"],"mappings":"AAAA,OAAOA,MAAP,MAAmB,iBAAnB;AACA,SAAQC,WAAR,EAAqBC,SAArB,QAAqC,qBAArC;AAGA,MAAMC,cAAc,GAAG;AAErBC,EAAAA,mBAAmB,EAAE,EAFA;AAGrBC,EAAAA,YAAY,EAAE,MAHO;AAMrBC,EAAAA,cAAc,EAAE,IANK;AAOrBC,EAAAA,mBAAmB,EAAE,IAPA;AAUrBC,EAAAA,gBAAgB,EAAE;AAVG,CAAvB;;AAaA,MAAMC,KAAK,GAAIC,GAAD,IAAuBV,MAAM,CAACS,KAAP,CAAaC,GAAb,EAAkBP,cAAlB,CAArC;;AAEA,OAAO,SAASQ,UAAT,CAAoBD,GAApB,EAAiC;AACtC,QAAME,GAAG,GAAGH,KAAK,CAACC,GAAD,CAAjB;;AACA,MAAI,CAACE,GAAG,CAACC,GAAT,EAAc;AACZ,UAAMC,KAAK,CAAC,mCAAD,CAAX;AACD;;AACD,SAAOb,WAAW,CAACW,GAAG,CAACC,GAAJ,CAAQE,KAAT,CAAX,CAA2BC,GAA3B,CAAgCC,GAAD,IAAS;AAC7C,UAAMC,QAAQ,GAAGjB,WAAW,CAACgB,GAAG,CAACE,MAAJ,CAAWC,OAAZ,CAAX,CAAgCJ,GAAhC,CAAqCK,CAAD,IAAO;AAC1D,UAAI,WAAWA,CAAC,CAACC,IAAjB,EAAuB;AACrB,eAAO,EAAC,GAAGD,CAAC,CAACC,IAAN;AAAYC,UAAAA,KAAK,EAAErB,SAAS,CAACmB,CAAC,CAACC,IAAF,CAAOC,KAAR;AAA5B,SAAP;AACD;;AACD,aAAO,EAAC,GAAGF,CAAC,CAACC;AAAN,OAAP;AACD,KALgB,CAAjB;AAMA,UAAM;AAACE,MAAAA,cAAc,GAAG,EAAlB;AAAsBC,MAAAA,WAAW,GAAG;AAApC,QAA0CR,GAAhD;AACA,UAAMS,KAAK,GAAG,EACZ,GAAGT,GAAG,CAACK,IADK;AAEZE,MAAAA,cAFY;AAGZC,MAAAA,WAHY;AAIZN,MAAAA,MAAM,EAAE,EACN,GAAGF,GAAG,CAACE,MAAJ,CAAWG,IADR;AAENJ,QAAAA;AAFM;AAJI,KAAd;AASA,WAAO,EACL,GAAGQ,KADE;;AAELC,MAAAA,MAAM,GAAG;AACP,cAAM;AAACR,UAAAA;AAAD,YAAWO,KAAjB;AAEA,cAAME,KAAK,GAAI,CAAC,GAAD,EAAM,GAAN,EAAW,GAAX,CAAD,CACXZ,GADW,CACNa,IAAD,IAAU;AACb,gBAAMC,IAAI,GAAGX,MAAM,uBAAgBU,IAAhB,EAAnB;AACA,gBAAME,IAAI,GAAGZ,MAAM,uBAAgBU,IAAhB,UAAnB;AACA,iBAAOC,IAAI,IAAIC,IAAR,aAAkBD,IAAlB,cAA0BC,IAA1B,IAAmC,GAA1C;AACD,SALW,EAMXC,IANW,CAMN,KANM,CAAd;AAQA,eAAO;AACL,8BAAoBN,KAAK,CAACF,cADrB;AAEL,uCAAsBL,MAAM,CAACc,KAA7B,gBAAwCd,MAAM,CAACe,KAA/C,CAFK;AAGL,yBAAef,MAAM,CAACgB,IAHjB;AAIL,+BAAqBP,KAJhB;AAKL,6CAA4BT,MAAM,CAACiB,KAAnC,gBAA8CjB,MAAM,CAACkB,KAArD,CALK;AAMLnB,UAAAA,QAAQ,EAAEC,MAAM,CAACmB;AANZ,SAAP;AAQD;;AArBI,KAAP;AAuBD,GAxCM,CAAP;AAyCD","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"],"file":"omexml.js"}

package/dist/lib/ome/utils.js

@@ -1,30 +1,21 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getDims = exports.getLabels = void 0;
-function getLabels(dimOrder) {
-    return dimOrder.toLowerCase().split('').reverse();
+export function getLabels(dimOrder) {
+  return dimOrder.toLowerCase().split('').reverse();
 }
-exports.getLabels = getLabels;
-/*
- * Creates an ES6 map of 'label' -> index
- * > const labels = ['a', 'b', 'c', 'd'];
- * > const dims = getDims(labels);
- * > dims('a') === 0;
- * > dims('b') === 1;
- * > dims('c') === 2;
- * > dims('hi!'); // throws
- */
-function getDims(labels) {
-    const lookup = new Map(labels.map((name, i) => [name, i]));
-    if (lookup.size !== labels.length) {
-        throw Error('Labels must be unique, found duplicated label.');
+export function getDims(labels) {
+  const lookup = new Map(labels.map((name, i) => [name, i]));
+
+  if (lookup.size !== labels.length) {
+    throw Error('Labels must be unique, found duplicated label.');
+  }
+
+  return name => {
+    const index = lookup.get(name);
+
+    if (index === undefined) {
+      throw Error('Invalid dimension.');
     }
-    return (name) => {
-        const index = lookup.get(name);
-        if (index === undefined) {
-            throw Error('Invalid dimension.');
-        }
-        return index;
-    };
+
+    return index;
+  };
 }
-exports.getDims = getDims;
+//# sourceMappingURL=utils.js.map

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

@@ -0,0 +1 @@
+{"version":3,"sources":["../../../src/lib/ome/utils.ts"],"names":["getLabels","dimOrder","toLowerCase","split","reverse","getDims","labels","lookup","Map","map","name","i","size","length","Error","index","get","undefined"],"mappings":"AAaA,OAAO,SAASA,SAAT,CAAmBC,QAAnB,EAAoE;AACzE,SAAOA,QAAQ,CAACC,WAAT,GAAuBC,KAAvB,CAA6B,EAA7B,EAAiCC,OAAjC,EAAP;AACD;AAWD,OAAO,SAASC,OAAT,CAAmCC,MAAnC,EAAgD;AACrD,QAAMC,MAAM,GAAG,IAAIC,GAAJ,CAAQF,MAAM,CAACG,GAAP,CAAW,CAACC,IAAD,EAAOC,CAAP,KAAa,CAACD,IAAD,EAAOC,CAAP,CAAxB,CAAR,CAAf;;AACA,MAAIJ,MAAM,CAACK,IAAP,KAAgBN,MAAM,CAACO,MAA3B,EAAmC;AACjC,UAAMC,KAAK,CAAC,gDAAD,CAAX;AACD;;AACD,SAAQJ,IAAD,IAAa;AAClB,UAAMK,KAAK,GAAGR,MAAM,CAACS,GAAP,CAAWN,IAAX,CAAd;;AACA,QAAIK,KAAK,KAAKE,SAAd,EAAyB;AACvB,YAAMH,KAAK,CAAC,oBAAD,CAAX;AACD;;AACD,WAAOC,KAAP;AACD,GAND;AAOD","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"],"file":"utils.js"}

package/dist/lib/tiff-pixel-source.js

@@ -1,64 +1,111 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const tiff_utils_1 = require("./utils/tiff-utils");
+import _defineProperty from "@babel/runtime/helpers/esm/defineProperty";
+import { getImageSize, isInterleaved, SIGNAL_ABORTED } from './utils/tiff-utils';
+
 class TiffPixelSource {
-    // eslint-disable-next-line max-params
-    constructor(indexer, dtype, tileSize, shape, labels, meta) {
-        this._indexer = indexer;
-        this.dtype = dtype;
-        this.tileSize = tileSize;
-        this.shape = shape;
-        this.labels = labels;
-        this.meta = meta;
+  constructor(indexer, dtype, tileSize, shape, labels, meta) {
+    _defineProperty(this, "dtype", void 0);
+
+    _defineProperty(this, "tileSize", void 0);
+
+    _defineProperty(this, "shape", void 0);
+
+    _defineProperty(this, "labels", void 0);
+
+    _defineProperty(this, "meta", void 0);
+
+    _defineProperty(this, "_indexer", void 0);
+
+    this._indexer = indexer;
+    this.dtype = dtype;
+    this.tileSize = tileSize;
+    this.shape = shape;
+    this.labels = labels;
+    this.meta = meta;
+  }
+
+  async getRaster({
+    selection,
+    signal
+  }) {
+    const image = await this._indexer(selection);
+    return this._readRasters(image, {
+      signal
+    });
+  }
+
+  async getTile({
+    x,
+    y,
+    selection,
+    signal
+  }) {
+    const {
+      height,
+      width
+    } = this._getTileExtent(x, y);
+
+    const x0 = x * this.tileSize;
+    const y0 = y * this.tileSize;
+    const window = [x0, y0, x0 + width, y0 + height];
+    const image = await this._indexer(selection);
+    return this._readRasters(image, {
+      window,
+      width,
+      height,
+      signal
+    });
+  }
+
+  async _readRasters(image, props) {
+    var _props$signal;
+
+    const interleave = isInterleaved(this.shape);
+    const raster = await image.readRasters({
+      interleave,
+      ...props
+    });
+
+    if (props !== null && props !== void 0 && (_props$signal = props.signal) !== null && _props$signal !== void 0 && _props$signal.aborted) {
+      throw SIGNAL_ABORTED;
     }
-    async getRaster({ selection, signal }) {
-        const image = await this._indexer(selection);
-        return this._readRasters(image, { signal });
+
+    const data = interleave ? raster : raster[0];
+    return {
+      data,
+      width: raster.width,
+      height: raster.height
+    };
+  }
+
+  _getTileExtent(x, y) {
+    const {
+      height: zoomLevelHeight,
+      width: zoomLevelWidth
+    } = getImageSize(this);
+    let height = this.tileSize;
+    let width = this.tileSize;
+    const maxXTileCoord = Math.floor(zoomLevelWidth / this.tileSize);
+    const maxYTileCoord = Math.floor(zoomLevelHeight / this.tileSize);
+
+    if (x === maxXTileCoord) {
+      width = zoomLevelWidth % this.tileSize;
     }
-    async getTile({ x, y, selection, signal }) {
-        const { height, width } = this._getTileExtent(x, y);
-        const x0 = x * this.tileSize;
-        const y0 = y * this.tileSize;
-        const window = [x0, y0, x0 + width, y0 + height];
-        const image = await this._indexer(selection);
-        return this._readRasters(image, { window, width, height, signal });
-    }
-    async _readRasters(image, props) {
-        const interleave = (0, tiff_utils_1.isInterleaved)(this.shape);
-        const raster = await image.readRasters({ interleave, ...props });
-        if (props?.signal?.aborted) {
-            throw tiff_utils_1.SIGNAL_ABORTED;
-        }
-        /*
-         * geotiff.js returns objects with different structure
-         * depending on `interleave`. It's weird, but this seems to work.
-         */
-        const data = (interleave ? raster : raster[0]);
-        return {
-            data,
-            width: raster.width,
-            height: raster.height
-        };
-    }
-    /*
-     * Computes tile size given x, y coord.
-     */
-    _getTileExtent(x, y) {
-        const { height: zoomLevelHeight, width: zoomLevelWidth } = (0, tiff_utils_1.getImageSize)(this);
-        let height = this.tileSize;
-        let width = this.tileSize;
-        const maxXTileCoord = Math.floor(zoomLevelWidth / this.tileSize);
-        const maxYTileCoord = Math.floor(zoomLevelHeight / this.tileSize);
-        if (x === maxXTileCoord) {
-            width = zoomLevelWidth % this.tileSize;
-        }
-        if (y === maxYTileCoord) {
-            height = zoomLevelHeight % this.tileSize;
-        }
-        return { height, width };
-    }
-    onTileError(err) {
-        console.error(err); // eslint-disable-line no-console
+
+    if (y === maxYTileCoord) {
+      height = zoomLevelHeight % this.tileSize;
     }
+
+    return {
+      height,
+      width
+    };
+  }
+
+  onTileError(err) {
+    console.error(err);
+  }
+
 }
-exports.default = TiffPixelSource;
+
+export default TiffPixelSource;
+//# sourceMappingURL=tiff-pixel-source.js.map

package/dist/lib/tiff-pixel-source.js.map

@@ -0,0 +1 @@
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It's weird, but this seems to work.\n     */\n    const data = (interleave ? raster : raster[0]) as TypedArray;\n    return {\n      data,\n      width: raster.width,\n      height: raster.height\n    } as PixelData;\n  }\n\n  /*\n   * Computes tile size given x, y coord.\n   */\n  private _getTileExtent(x: number, y: number) {\n    const {height: zoomLevelHeight, width: zoomLevelWidth} = getImageSize(this);\n    let height = this.tileSize;\n    let width = this.tileSize;\n    const maxXTileCoord = Math.floor(zoomLevelWidth / this.tileSize);\n    const maxYTileCoord = Math.floor(zoomLevelHeight / this.tileSize);\n    if (x === maxXTileCoord) {\n      width = zoomLevelWidth % this.tileSize;\n    }\n    if (y === maxYTileCoord) {\n      height = zoomLevelHeight % this.tileSize;\n    }\n    return {height, width};\n  }\n\n  onTileError(err: Error) {\n    console.error(err); // eslint-disable-line no-console\n  }\n}\n\nexport default TiffPixelSource;\n"],"file":"tiff-pixel-source.js"}

package/dist/lib/utils/Pool.js

@@ -1,83 +1,77 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-// import Worker from 'web-worker:./decoder.worker.ts';
-// https://developer.mozilla.org/en-US/docs/Web/API/NavigatorConcurrentHardware/hardwareConcurrency
-// We need to give a different way of getting this for safari, so 4 is probably a safe bet
-// for parallel processing in the meantime.  More can't really hurt since they'll just block
-// each other and not the UI thread, which is the real benefit.
-const defaultPoolSize = globalThis?.navigator?.hardwareConcurrency ?? 4;
-/**
- * Pool for workers to decode chunks of the images.
- * 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
- */
-class Pool {
-    /**
-     * @constructor
-     * @param {Number} size The size of the pool. Defaults to the number of CPUs
-     *                      available. When this parameter is `null` or 0, then the
-     *                      decoding will be done in the main thread.
-     */
-    constructor(size = defaultPoolSize) {
-        this.workers = [];
-        this.idleWorkers = [];
-        this.waitQueue = [];
-        this.decoder = null;
-        // eslint-disable-next-line no-plusplus
-        for (let i = 0; i < size; ++i) {
-            const w = new Worker('./decoder.worker');
-            this.workers.push(w);
-            this.idleWorkers.push(w);
-        }
+import _defineProperty from "@babel/runtime/helpers/esm/defineProperty";
+
+var _globalThis$navigator, _globalThis$navigator2;
+
+const 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;
+export default class Pool {
+  constructor(size = defaultPoolSize) {
+    _defineProperty(this, "workers", void 0);
+
+    _defineProperty(this, "idleWorkers", void 0);
+
+    _defineProperty(this, "waitQueue", void 0);
+
+    _defineProperty(this, "decoder", void 0);
+
+    this.workers = [];
+    this.idleWorkers = [];
+    this.waitQueue = [];
+    this.decoder = null;
+
+    for (let i = 0; i < size; ++i) {
+      const w = new Worker('./decoder.worker');
+      this.workers.push(w);
+      this.idleWorkers.push(w);
     }
-    /**
-     * Decode the given block of bytes with the set compression method.
-     * @param {ArrayBuffer} buffer the array buffer of bytes to decode.
-     * @returns {Promise.<ArrayBuffer>} the decoded result as a `Promise`
-     */
-    async decode(fileDirectory, buffer) {
-        const currentWorker = await this.waitForWorker();
-        return new Promise((resolve, reject) => {
-            currentWorker.onmessage = (event) => {
-                // this.workers.push(currentWorker);
-                // eslint-disable-next-line
-                this.finishTask(currentWorker);
-                resolve(event.data[0]);
-            };
-            currentWorker.onerror = (error) => {
-                // this.workers.push(currentWorker);
-                // eslint-disable-next-line
-                this.finishTask(currentWorker);
-                reject(error);
-            };
-            currentWorker.postMessage(['decode', fileDirectory, buffer], [buffer]);
-        });
+  }
+
+  async decode(fileDirectory, buffer) {
+    const currentWorker = await this.waitForWorker();
+    return new Promise((resolve, reject) => {
+      currentWorker.onmessage = event => {
+        this.finishTask(currentWorker);
+        resolve(event.data[0]);
+      };
+
+      currentWorker.onerror = error => {
+        this.finishTask(currentWorker);
+        reject(error);
+      };
+
+      currentWorker.postMessage(['decode', fileDirectory, buffer], [buffer]);
+    });
+  }
+
+  async waitForWorker() {
+    const idleWorker = this.idleWorkers.pop();
+
+    if (idleWorker) {
+      return idleWorker;
     }
-    async waitForWorker() {
-        const idleWorker = this.idleWorkers.pop();
-        if (idleWorker) {
-            return idleWorker;
-        }
-        const waiter = {};
-        const promise = new Promise((resolve) => {
-            waiter.resolve = resolve;
-        });
-        this.waitQueue.push(waiter);
-        return promise;
+
+    const waiter = {};
+    const promise = new Promise(resolve => {
+      waiter.resolve = resolve;
+    });
+    this.waitQueue.push(waiter);
+    return promise;
+  }
+
+  async finishTask(currentWorker) {
+    const waiter = this.waitQueue.pop();
+
+    if (waiter) {
+      waiter.resolve(currentWorker);
+    } else {
+      this.idleWorkers.push(currentWorker);
     }
-    async finishTask(currentWorker) {
-        const waiter = this.waitQueue.pop();
-        if (waiter) {
-            waiter.resolve(currentWorker);
-        }
-        else {
-            this.idleWorkers.push(currentWorker);
-        }
-    }
-    destroy() {
-        // eslint-disable-next-line no-plusplus
-        for (let i = 0; i < this.workers.length; ++i) {
-            this.workers[i].terminate();
-        }
+  }
+
+  destroy() {
+    for (let i = 0; i < this.workers.length; ++i) {
+      this.workers[i].terminate();
     }
+  }
+
 }
-exports.default = Pool;
+//# sourceMappingURL=Pool.js.map

package/dist/lib/utils/Pool.js.map

@@ -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"}