@loaders.gl/geotiff 4.2.0-alpha.3 → 4.2.0-alpha.5

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

@@ -1,120 +1,108 @@
+// loaders.gl
+// SPDX-License-Identifier: MIT
+// Copyright (c) vis.gl contributors
+/*
+ * An "indexer" for a GeoTIFF-based source is a function that takes a
+ * "selection" (e.g. { z, t, c }) and returns a Promise for the GeoTIFFImage
+ * object corresponding to that selection.
+ *
+ * For OME-TIFF images, the "selection" object is the same regardless of
+ * the format version. However, modern version of Bioformats have a different
+ * memory layout for pyramidal resolutions. Thus, we have two different "indexers"
+ * depending on which format version is detected.
+ *
+ * TODO: We currently only support indexing the first image in the OME-TIFF with
+ * our indexers. There can be multiple images in an OME-TIFF, so supporting these
+ * images will require extending these indexers or creating new methods.
+ */
+/*
+ * Returns an indexer for legacy Bioformats images. This assumes that
+ * downsampled resolutions are stored sequentially in the OME-TIFF.
+ */
 export function getOmeLegacyIndexer(tiff, rootMeta) {
-  const imgMeta = rootMeta[0];
-  const {
-    SizeT,
-    SizeC,
-    SizeZ
-  } = imgMeta.Pixels;
-  const ifdIndexer = getOmeIFDIndexer(imgMeta);
-  return (sel, pyramidLevel) => {
-    const index = ifdIndexer(sel);
-    const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;
-    return tiff.getImage(index + pyramidIndex);
-  };
+    const imgMeta = rootMeta[0];
+    const { SizeT, SizeC, SizeZ } = imgMeta.Pixels;
+    const ifdIndexer = getOmeIFDIndexer(imgMeta);
+    return (sel, pyramidLevel) => {
+        // Get IFD index at base pyramid level
+        const index = ifdIndexer(sel);
+        // Get index of first image at pyramidal level
+        const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;
+        // Return image at IFD index for pyramidal level
+        return tiff.getImage(index + pyramidIndex);
+    };
 }
+/*
+ * Returns an indexer for modern Bioforamts images that store multiscale
+ * resolutions using SubIFDs.
+ *
+ * The ifdIndexer returns the 'index' to the base resolution for a
+ * particular 'selection'. The SubIFDs to the downsampled resolutions
+ * of the 'selection' are stored within the `baseImage.fileDirectory`.
+ * We use the SubIFDs to get the IFD for the corresponding sub-resolution.
+ *
+ * NOTE: This function create a custom IFD cache rather than mutating
+ * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in
+ * an ES6 Map that maps a string key that identifies the selection uniquely
+ * to the corresponding IFD.
+ */
 export function getOmeSubIFDIndexer(tiff, rootMeta) {
-  const imgMeta = rootMeta[0];
-  const ifdIndexer = getOmeIFDIndexer(imgMeta);
-  const ifdCache = new Map();
-  return async (sel, pyramidLevel) => {
-    const index = ifdIndexer(sel);
-    const baseImage = await tiff.getImage(index);
-    if (pyramidLevel === 0) {
-      return baseImage;
-    }
-    const {
-      SubIFDs
-    } = baseImage.fileDirectory;
-    if (!SubIFDs) {
-      throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
-    }
-    const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;
-    if (!ifdCache.has(key)) {
-      const subIfdOffset = SubIFDs[pyramidLevel - 1];
-      ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
-    }
-    const ifd = await ifdCache.get(key);
-    return new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source);
-  };
+    const imgMeta = rootMeta[0];
+    const ifdIndexer = getOmeIFDIndexer(imgMeta);
+    const ifdCache = new Map();
+    return async (sel, pyramidLevel) => {
+        const index = ifdIndexer(sel);
+        const baseImage = await tiff.getImage(index);
+        // It's the highest resolution, no need to look up SubIFDs.
+        if (pyramidLevel === 0) {
+            return baseImage;
+        }
+        const { SubIFDs } = baseImage.fileDirectory;
+        if (!SubIFDs) {
+            throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');
+        }
+        // Get IFD for the selection at the pyramidal level
+        const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;
+        if (!ifdCache.has(key)) {
+            // Only create a new request if we don't have the key.
+            const subIfdOffset = SubIFDs[pyramidLevel - 1];
+            ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));
+        }
+        const ifd = await ifdCache.get(key);
+        // Create a new image object manually from IFD
+        // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453
+        return new baseImage.constructor(ifd.fileDirectory, ifd.geoKeyDirectory, 
+        // @ts-expect-error
+        tiff.dataView, tiff.littleEndian, tiff.cache, tiff.source);
+    };
 }
+/*
+ * Returns a function that computes the image index based on the dimension
+ * order and dimension sizes.
+ */
 function getOmeIFDIndexer(imgMeta) {
-  const {
-    SizeC,
-    SizeZ,
-    SizeT,
-    DimensionOrder
-  } = imgMeta.Pixels;
-  switch (DimensionOrder) {
-    case 'XYZCT':
-      {
-        return _ref => {
-          let {
-            t,
-            c,
-            z
-          } = _ref;
-          return t * SizeZ * SizeC + c * SizeZ + z;
-        };
-      }
-    case 'XYZTC':
-      {
-        return _ref2 => {
-          let {
-            t,
-            c,
-            z
-          } = _ref2;
-          return c * SizeZ * SizeT + t * SizeZ + z;
-        };
-      }
-    case 'XYCTZ':
-      {
-        return _ref3 => {
-          let {
-            t,
-            c,
-            z
-          } = _ref3;
-          return z * SizeC * SizeT + t * SizeC + c;
-        };
-      }
-    case 'XYCZT':
-      {
-        return _ref4 => {
-          let {
-            t,
-            c,
-            z
-          } = _ref4;
-          return t * SizeC * SizeZ + z * SizeC + c;
-        };
-      }
-    case 'XYTCZ':
-      {
-        return _ref5 => {
-          let {
-            t,
-            c,
-            z
-          } = _ref5;
-          return z * SizeT * SizeC + c * SizeT + t;
-        };
-      }
-    case 'XYTZC':
-      {
-        return _ref6 => {
-          let {
-            t,
-            c,
-            z
-          } = _ref6;
-          return c * SizeT * SizeZ + z * SizeT + t;
-        };
-      }
-    default:
-      {
-        throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);
-      }
-  }
+    const { SizeC, SizeZ, SizeT, DimensionOrder } = imgMeta.Pixels;
+    switch (DimensionOrder) {
+        case 'XYZCT': {
+            return ({ t, c, z }) => t * SizeZ * SizeC + c * SizeZ + z;
+        }
+        case 'XYZTC': {
+            return ({ t, c, z }) => c * SizeZ * SizeT + t * SizeZ + z;
+        }
+        case 'XYCTZ': {
+            return ({ t, c, z }) => z * SizeC * SizeT + t * SizeC + c;
+        }
+        case 'XYCZT': {
+            return ({ t, c, z }) => t * SizeC * SizeZ + z * SizeC + c;
+        }
+        case 'XYTCZ': {
+            return ({ t, c, z }) => z * SizeT * SizeC + c * SizeT + t;
+        }
+        case 'XYTZC': {
+            return ({ t, c, z }) => c * SizeT * SizeZ + z * SizeT + t;
+        }
+        default: {
+            throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);
+        }
+    }
 }
-//# sourceMappingURL=ome-indexers.js.map

package/dist/lib/ome/ome-utils.d.ts

@@ -1,4 +1,4 @@
-import type { OMEXML, UnitsLength } from './omexml';
+import type { OMEXML, UnitsLength } from "./omexml.js";
 export declare const DTYPE_LOOKUP: {
     readonly uint8: "Uint8";
     readonly uint16: "Uint16";

package/dist/lib/ome/ome-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ome-utils.d.ts","sourceRoot":"","sources":["../../../src/lib/ome/ome-utils.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAC,MAAM,EAAE,WAAW,EAAC,oBAAiB;AAElD,eAAO,MAAM,YAAY;;;;;;;;;CASf,CAAC;AAEX,wBAAgB,qBAAqB,CAAC,EAAC,MAAM,EAAC,EAAE,MAAM,CAAC,CAAC,CAAC;;sBAoB9B,MAAM;;;kBAcP,MAAM;kBAAQ,WAAW;;;;;;sBAdxB,MAAM;;;EAmChC"}

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

@@ -1,66 +1,62 @@
+// loaders.gl
+// SPDX-License-Identifier: MIT
+// Copyright (c) vis.gl contributors
 import { getDims, getLabels } from "./utils.js";
 export const DTYPE_LOOKUP = {
-  uint8: 'Uint8',
-  uint16: 'Uint16',
-  uint32: 'Uint32',
-  float: 'Float32',
-  double: 'Float64',
-  int8: 'Int8',
-  int16: 'Int16',
-  int32: 'Int32'
+    uint8: 'Uint8',
+    uint16: 'Uint16',
+    uint32: 'Uint32',
+    float: 'Float32',
+    double: 'Float64',
+    int8: 'Int8',
+    int16: 'Int16',
+    int32: 'Int32'
 };
-export function getOmePixelSourceMeta(_ref) {
-  let {
-    Pixels
-  } = _ref;
-  const labels = getLabels(Pixels.DimensionOrder);
-  const dims = getDims(labels);
-  const shape = Array(labels.length).fill(0);
-  shape[dims('t')] = Pixels.SizeT;
-  shape[dims('c')] = Pixels.SizeC;
-  shape[dims('z')] = Pixels.SizeZ;
-  if (Pixels.Interleaved) {
-    labels.push('_c');
-    shape.push(3);
-  }
-  const getShape = level => {
-    const s = [...shape];
-    s[dims('x')] = Pixels.SizeX >> level;
-    s[dims('y')] = Pixels.SizeY >> level;
-    return s;
-  };
-  if (!(Pixels.Type in DTYPE_LOOKUP)) {
-    throw Error(`Pixel type ${Pixels.Type} not supported.`);
-  }
-  const dtype = DTYPE_LOOKUP[Pixels.Type];
-  if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
-    const physicalSizes = {
-      x: {
-        size: Pixels.PhysicalSizeX,
-        unit: Pixels.PhysicalSizeXUnit
-      },
-      y: {
-        size: Pixels.PhysicalSizeY,
-        unit: Pixels.PhysicalSizeYUnit
-      }
-    };
-    if (Pixels.PhysicalSizeZ) {
-      physicalSizes.z = {
-        size: Pixels.PhysicalSizeZ,
-        unit: Pixels.PhysicalSizeZUnit
-      };
+export function getOmePixelSourceMeta({ Pixels }) {
+    // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']
+    const labels = getLabels(Pixels.DimensionOrder);
+    // Compute "shape" of image
+    const dims = getDims(labels);
+    const shape = Array(labels.length).fill(0);
+    shape[dims('t')] = Pixels.SizeT;
+    shape[dims('c')] = Pixels.SizeC;
+    shape[dims('z')] = Pixels.SizeZ;
+    // Push extra dimension if data are interleaved.
+    if (Pixels.Interleaved) {
+        // @ts-ignore
+        labels.push('_c');
+        shape.push(3);
     }
-    return {
-      labels,
-      getShape,
-      physicalSizes,
-      dtype
+    // Creates a new shape for different level of pyramid.
+    // Assumes factor-of-two downsampling.
+    const getShape = (level) => {
+        const s = [...shape];
+        s[dims('x')] = Pixels.SizeX >> level;
+        s[dims('y')] = Pixels.SizeY >> level;
+        return s;
     };
-  }
-  return {
-    labels,
-    getShape,
-    dtype
-  };
+    if (!(Pixels.Type in DTYPE_LOOKUP)) {
+        throw Error(`Pixel type ${Pixels.Type} not supported.`);
+    }
+    const dtype = DTYPE_LOOKUP[Pixels.Type];
+    if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
+        const physicalSizes = {
+            x: {
+                size: Pixels.PhysicalSizeX,
+                unit: Pixels.PhysicalSizeXUnit
+            },
+            y: {
+                size: Pixels.PhysicalSizeY,
+                unit: Pixels.PhysicalSizeYUnit
+            }
+        };
+        if (Pixels.PhysicalSizeZ) {
+            physicalSizes.z = {
+                size: Pixels.PhysicalSizeZ,
+                unit: Pixels.PhysicalSizeZUnit
+            };
+        }
+        return { labels, getShape, physicalSizes, dtype };
+    }
+    return { labels, getShape, dtype };
 }
-//# sourceMappingURL=ome-utils.js.map

package/dist/lib/ome/omexml.js

@@ -1,64 +1,62 @@
+// loaders.gl
+// SPDX-License-Identifier: MIT
+// Copyright (c) vis.gl contributors
 import { XMLParser } from 'fast-xml-parser';
 import { ensureArray, intToRgba } from "../utils/tiff-utils.js";
+// WARNING: Changes to the parser options _will_ effect the types in types/omexml.d.ts.
 const xmlParser = new XMLParser({
-  attributeNamePrefix: '',
-  attributesGroupName: 'attr',
-  parseTagValue: true,
-  parseAttributeValue: true,
-  ignoreAttributes: false
+    // Nests attributes withtout prefix under 'attr' key for each node
+    attributeNamePrefix: '',
+    attributesGroupName: 'attr',
+    // Parses numbers for both attributes and nodes
+    parseTagValue: true,
+    parseAttributeValue: true,
+    // Forces attributes to be parsed
+    ignoreAttributes: false
 });
-const parse = str => xmlParser.parse(str);
+const parse = (str) => xmlParser.parse(str);
 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)
+    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 {
-        ...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${name}`];
-          const unit = Pixels[`PhysicalSize${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 ${Pixels.SizeT}`,
-          Channels: Pixels.SizeC
+            ...image,
+            format() {
+                const { Pixels } = image;
+                const sizes = ['X', 'Y', 'Z']
+                    .map((name) => {
+                    const size = Pixels[`PhysicalSize${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
+                };
+            }
         };
-      }
-    };
-  });
+    });
 }
-//# sourceMappingURL=omexml.js.map

package/dist/lib/ome/utils.d.ts

@@ -1,5 +1,5 @@
-import type { OMEXML } from '../ome/omexml';
-import type { Labels } from '../../types';
+import type { OMEXML } from "../ome/omexml.js";
+import type { Labels } from "../../types.js";
 export declare function getLabels(dimOrder: OMEXML[0]['Pixels']['DimensionOrder']): Labels<["t", "c", "z"] | ["c", "t", "z"] | ["z", "t", "c"] | ["t", "z", "c"] | ["z", "c", "t"] | ["c", "z", "t"]>;
 export declare function getDims<S extends string>(labels: S[]): (name: S) => number;
 //# sourceMappingURL=utils.d.ts.map

package/dist/lib/ome/utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../../../src/lib/ome/utils.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAC,MAAM,EAAC,MAAM,eAAe,CAAC;AAC1C,OAAO,KAAK,EAAC,MAAM,EAAC,MAAM,aAAa,CAAC;AAYxC,wBAAgB,SAAS,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,gBAAgB,CAAC,qHAExE;AAWD,wBAAgB,OAAO,CAAC,CAAC,SAAS,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,UAKrC,CAAC,YAOhB"}
+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../../../src/lib/ome/utils.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAC,MAAM,EAAC,yBAAsB;AAC1C,OAAO,KAAK,EAAC,MAAM,EAAC,uBAAoB;AAYxC,wBAAgB,SAAS,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,gBAAgB,CAAC,qHAExE;AAWD,wBAAgB,OAAO,CAAC,CAAC,SAAS,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,UAKrC,CAAC,YAOhB"}

package/dist/lib/ome/utils.js

@@ -1,17 +1,28 @@
+// loaders.gl
+// SPDX-License-Identifier: MIT
+// Copyright (c) vis.gl contributors
 export function getLabels(dimOrder) {
-  return dimOrder.toLowerCase().split('').reverse();
+    return dimOrder.toLowerCase().split('').reverse();
 }
+/*
+ * 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
+ */
 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.');
+    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 index;
-  };
+    return (name) => {
+        const index = lookup.get(name);
+        if (index === undefined) {
+            throw Error('Invalid dimension.');
+        }
+        return index;
+    };
 }
-//# sourceMappingURL=utils.js.map

package/dist/lib/tiff-pixel-source.d.ts

@@ -1,5 +1,5 @@
 import type { GeoTIFFImage } from 'geotiff';
-import type { PixelSource, PixelSourceSelection, PixelSourceMeta, Dtype, Labels, RasterSelection, TileSelection, PixelData } from '../types';
+import type { PixelSource, PixelSourceSelection, PixelSourceMeta, Dtype, Labels, RasterSelection, TileSelection, PixelData } from "../types.js";
 export declare class TiffPixelSource<S extends string[]> implements PixelSource<S> {
     dtype: Dtype;
     tileSize: number;

package/dist/lib/tiff-pixel-source.d.ts.map

@@ -1 +1 @@
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