npm - @loaders.gl/geotiff - Versions diffs - 3.4.0-alpha.3 → 3.4.0-alpha.5 - Mend

@loaders.gl/geotiff 3.4.0-alpha.3 → 3.4.0-alpha.5

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package/dist/es5/lib/ome/load-ome-tiff.js.map +1 -1
package/dist/es5/lib/ome/ome-indexers.js.map +1 -1
package/dist/es5/lib/ome/ome-utils.js.map +1 -1
package/dist/es5/lib/ome/utils.js.map +1 -1
package/dist/es5/lib/tiff-pixel-source.js.map +1 -1
package/dist/es5/lib/utils/Pool.js.map +1 -1
package/dist/es5/lib/utils/proxies.js.map +1 -1
package/dist/esm/lib/ome/load-ome-tiff.js.map +1 -1
package/dist/esm/lib/ome/ome-indexers.js.map +1 -1
package/dist/esm/lib/ome/ome-utils.js.map +1 -1
package/dist/esm/lib/ome/utils.js.map +1 -1
package/dist/esm/lib/utils/Pool.js.map +1 -1
package/package.json +2 -2

package/dist/es5/lib/ome/load-ome-tiff.js.map CHANGED Viewed

	@@ -1 +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; 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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"}

package/dist/es5/lib/ome/ome-indexers.js.map CHANGED Viewed

	@@ -1 +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}-${pyramidLevel}`;\n if (!ifdCache.has(key)) {\n // Only create a new request if we don't have the key.\n const subIfdOffset = SubIFDs[pyramidLevel - 1];\n ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n }\n const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n // Create a new image object manually from IFD\n // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n return new (baseImage.constructor as any)(\n ifd.fileDirectory,\n ifd.geoKeyDirectory,\n tiff.dataView,\n tiff.littleEndian,\n tiff.cache,\n tiff.source\n ) as GeoTIFFImage;\n };\n}\n\n/\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n /\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n switch (DimensionOrder) {\n case 'XYZCT': {\n return ({t, c, z}) => t SizeZ * SizeC + c * SizeZ + z;\n }\n case 'XYZTC': {\n return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n }\n case 'XYCTZ': {\n return ({t, c, z}) => 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1	+ {"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","_imgMeta$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, z}) => 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package/dist/es5/lib/ome/ome-utils.js.map CHANGED Viewed

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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,~~qBAAkB~~;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"}
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package/dist/es5/lib/ome/utils.js.map CHANGED Viewed

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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,~~EAAE~~,CAACC,KAAK,CAAC,EAAE,CAAC,CAACC,OAAO,~~EAAE~~;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"}
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"}

package/dist/es5/lib/tiff-pixel-source.js.map CHANGED Viewed

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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 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package/dist/es5/lib/utils/Pool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/es5/lib/utils/proxies.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"proxies.js","names":["VIV_PROXY_KEY","OFFSETS_PROXY_KEY","concat","POOL_PROXY_KEY","checkProxies","tiff","isProxy","console","warn","proxyFlag","createOffsetsProxy","offsets","get","target","key","index","ifdRequests","offset","parseFileDirectoryAt","getImage","Reflect","Proxy","createPoolProxy","pool","options","readRasters","_objectSpread"],"sources":["../../../../src/lib/utils/proxies.ts"],"sourcesContent":["import type {GeoTIFF} from 'geotiff';\nimport type Pool from './Pool';\n\nconst VIV_PROXY_KEY = '__viv';\nconst OFFSETS_PROXY_KEY = `${VIV_PROXY_KEY}-offsets` as const;\nconst POOL_PROXY_KEY = `${VIV_PROXY_KEY}-decoder-pool` as const;\n\n/\n Inspect if the GeoTIFF source is wrapped in our proxies,\n * and warn if missing.\n /\nexport function checkProxies(tiff: GeoTIFF) {\n if (!isProxy(tiff, OFFSETS_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing offsets proxy.'); // eslint-disable-line no-console\n }\n\n if (!isProxy(tiff, POOL_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing decoder-pool proxy.'); // eslint-disable-line no-console\n }\n}\n\n/\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // false\n * > tiff = createPoolProxy(tiff, new Pool());\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // true\n /\nfunction isProxy(tiff: GeoTIFF, proxyFlag: string) {\n return (tiff as any)[proxyFlag] as boolean;\n}\n\n/\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.getImage` and uses our custom\n * pre-computed offsets to pre-fetch the correct file directory.\n \n This is a bit of a hack. Internally GeoTIFF inspects `this.ifdRequests`\n * to see which fileDirectories need to be traversed. By adding the\n * ifdRequest for an 'index' manually, GeoTIFF will await that request\n * rather than traversing the file system remotely.\n /\nexport function createOffsetsProxy(tiff: GeoTIFF, offsets: number[]) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept `tiff.getImage`\n if (key === 'getImage') {\n return (index: number) => {\n // Manually add ifdRequest to tiff if missing and we have an offset.\n if (!(index in target.ifdRequests) && index in offsets) {\n const offset = offsets[index];\n target.ifdRequests[index] = target.parseFileDirectoryAt(offset);\n }\n return target.getImage(index);\n };\n }\n\n // tiff['__viv-offsets'] === true\n if (key === OFFSETS_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n\n/\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.readRasters` and injects\n * a pool argument to every call. This means our TiffPixelSource\n * doesn't need to be aware of whether a decoder pool is in use.\n \n > tiff.readRasters({ window }) -> tiff.readRasters({ window, pool });\n */\nexport function createPoolProxy(tiff: GeoTIFF, pool: Pool) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept calls to `image.readRasters`\n if (key === 'readRasters') {\n return (options: Parameters<typeof target.readRasters>) => {\n // Inject `pool` argument with other raster options.\n // @ts-ignore\n return target.readRasters({...options, pool});\n };\n }\n\n // tiff['__viv-decoder-pool'] === true\n if (key === POOL_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n"],"mappings":";;;;;;;;;;;;AAGA,IAAMA,aAAa,GAAG,OAAO;AAC7B,IAAMC,iBAAiB,MAAAC,MAAA,CAAMF,aAAa,aAAmB;AAC7D,IAAMG,cAAc,MAAAD,MAAA,CAAMF,aAAa,kBAAwB;AAMxD,SAASI,YAAYA,CAACC,IAAa,EAAE;EAC1C,IAAI,CAACC,OAAO,CAACD,IAAI,EAAEJ,iBAAiB,CAAC,EAAE;IACrCM,OAAO,CAACC,IAAI,CAAC,0CAA0C,CAAC;EAC1D;EAEA,IAAI,CAACF,OAAO,CAACD,IAAI,EAAEF,cAAc,CAAC,EAAE;IAClCI,OAAO,CAACC,IAAI,CAAC,+CAA+C,CAAC;EAC/D;AACF;AAOA,SAASF,OAAOA,CAACD,IAAa,EAAEI,SAAiB,EAAE;EACjD,OAAQJ,IAAI,CAASI,SAAS,CAAC;AACjC;AAYO,SAASC,kBAAkBA,CAACL,IAAa,EAAEM,OAAiB,EAAE;EACnE,IAAMC,GAAG,GAAG,SAANA,GAAGA,CAAIC,MAAe,EAAEC,GAAQ,EAAK;IAEzC,IAAIA,GAAG,KAAK,UAAU,EAAE;MACtB,OAAO,UAACC,KAAa,EAAK;QAExB,IAAI,EAAEA,KAAK,IAAIF,MAAM,CAACG,WAAW,CAAC,IAAID,KAAK,IAAIJ,OAAO,EAAE;UACtD,IAAMM,MAAM,GAAGN,OAAO,CAACI,KAAK,CAAC;UAC7BF,MAAM,CAACG,WAAW,CAACD,KAAK,CAAC,GAAGF,MAAM,CAACK,oBAAoB,CAACD,MAAM,CAAC;QACjE;QACA,OAAOJ,MAAM,CAACM,QAAQ,CAACJ,KAAK,CAAC;MAC/B,CAAC;IACH;IAGA,IAAID,GAAG,KAAKb,iBAAiB,EAAE;MAC7B,OAAO,IAAI;IACb;IAEA,OAAOmB,OAAO,CAACR,GAAG,CAACC,MAAM,EAAEC,GAAG,CAAC;EACjC,CAAC;EACD,OAAO,IAAIO,KAAK,CAAChB,IAAI,EAAE;IAACO,GAAG,EAAHA;EAAG,CAAC,CAAC;AAC/B;AAUO,SAASU,eAAeA,CAACjB,IAAa,EAAEkB,IAAU,EAAE;EACzD,IAAMX,GAAG,GAAG,SAANA,GAAGA,CAAIC,MAAe,EAAEC,GAAQ,EAAK;IAEzC,IAAIA,GAAG,KAAK,aAAa,EAAE;MACzB,OAAO,UAACU,OAA8C,EAAK;QAGzD,OAAOX,MAAM,CAACY,WAAW,CAAAC,aAAA,CAAAA,aAAA,KAAKF,OAAO;UAAED,IAAI,EAAJA;QAAI,~~GAAE~~;MAC/C,CAAC;IACH;IAGA,IAAIT,GAAG,KAAKX,cAAc,EAAE;MAC1B,OAAO,IAAI;IACb;IAEA,OAAOiB,OAAO,CAACR,GAAG,CAACC,MAAM,EAAEC,GAAG,CAAC;EACjC,CAAC;EACD,OAAO,IAAIO,KAAK,CAAChB,IAAI,EAAE;IAACO,GAAG,EAAHA;EAAG,CAAC,CAAC;AAC/B"}
1	+ {"version":3,"file":"proxies.js","names":["VIV_PROXY_KEY","OFFSETS_PROXY_KEY","concat","POOL_PROXY_KEY","checkProxies","tiff","isProxy","console","warn","proxyFlag","createOffsetsProxy","offsets","get","target","key","index","ifdRequests","offset","parseFileDirectoryAt","getImage","Reflect","Proxy","createPoolProxy","pool","options","readRasters","_objectSpread"],"sources":["../../../../src/lib/utils/proxies.ts"],"sourcesContent":["import type {GeoTIFF} from 'geotiff';\nimport type Pool from './Pool';\n\nconst VIV_PROXY_KEY = '__viv';\nconst OFFSETS_PROXY_KEY = `${VIV_PROXY_KEY}-offsets` as const;\nconst POOL_PROXY_KEY = `${VIV_PROXY_KEY}-decoder-pool` as const;\n\n/\n Inspect if the GeoTIFF source is wrapped in our proxies,\n * and warn if missing.\n /\nexport function checkProxies(tiff: GeoTIFF) {\n if (!isProxy(tiff, OFFSETS_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing offsets proxy.'); // eslint-disable-line no-console\n }\n\n if (!isProxy(tiff, POOL_PROXY_KEY)) {\n console.warn('GeoTIFF source is missing decoder-pool proxy.'); // eslint-disable-line no-console\n }\n}\n\n/\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // false\n * > tiff = createPoolProxy(tiff, new Pool());\n * > isProxy(tiff, POOL_PROXY_KEY) === true; // true\n /\nfunction isProxy(tiff: GeoTIFF, proxyFlag: string) {\n return (tiff as any)[proxyFlag] as boolean;\n}\n\n/\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.getImage` and uses our custom\n * pre-computed offsets to pre-fetch the correct file directory.\n \n This is a bit of a hack. Internally GeoTIFF inspects `this.ifdRequests`\n * to see which fileDirectories need to be traversed. By adding the\n * ifdRequest for an 'index' manually, GeoTIFF will await that request\n * rather than traversing the file system remotely.\n /\nexport function createOffsetsProxy(tiff: GeoTIFF, offsets: number[]) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept `tiff.getImage`\n if (key === 'getImage') {\n return (index: number) => {\n // Manually add ifdRequest to tiff if missing and we have an offset.\n if (!(index in target.ifdRequests) && index in offsets) {\n const offset = offsets[index];\n target.ifdRequests[index] = target.parseFileDirectoryAt(offset);\n }\n return target.getImage(index);\n };\n }\n\n // tiff['__viv-offsets'] === true\n if (key === OFFSETS_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n\n/\n * Creates an ES6 Proxy that wraps a GeoTIFF object. The proxy\n * handler intercepts calls to `tiff.readRasters` and injects\n * a pool argument to every call. This means our TiffPixelSource\n * doesn't need to be aware of whether a decoder pool is in use.\n \n > tiff.readRasters({ window }) -> tiff.readRasters({ window, pool });\n */\nexport function createPoolProxy(tiff: GeoTIFF, pool: Pool) {\n const get = (target: GeoTIFF, key: any) => {\n // Intercept calls to `image.readRasters`\n if (key === 'readRasters') {\n return (options: Parameters<typeof target.readRasters>) => {\n // Inject `pool` argument with other raster options.\n // @ts-ignore\n return target.readRasters({...options, pool});\n };\n }\n\n // tiff['__viv-decoder-pool'] === true\n if (key === POOL_PROXY_KEY) {\n return true;\n }\n\n return Reflect.get(target, key);\n };\n return new Proxy(tiff, {get});\n}\n"],"mappings":";;;;;;;;;;;;AAGA,IAAMA,aAAa,GAAG,OAAO;AAC7B,IAAMC,iBAAiB,MAAAC,MAAA,CAAMF,aAAa,aAAmB;AAC7D,IAAMG,cAAc,MAAAD,MAAA,CAAMF,aAAa,kBAAwB;AAMxD,SAASI,YAAYA,CAACC,IAAa,EAAE;EAC1C,IAAI,CAACC,OAAO,CAACD,IAAI,EAAEJ,iBAAiB,CAAC,EAAE;IACrCM,OAAO,CAACC,IAAI,CAAC,0CAA0C,CAAC;EAC1D;EAEA,IAAI,CAACF,OAAO,CAACD,IAAI,EAAEF,cAAc,CAAC,EAAE;IAClCI,OAAO,CAACC,IAAI,CAAC,+CAA+C,CAAC;EAC/D;AACF;AAOA,SAASF,OAAOA,CAACD,IAAa,EAAEI,SAAiB,EAAE;EACjD,OAAQJ,IAAI,CAASI,SAAS,CAAC;AACjC;AAYO,SAASC,kBAAkBA,CAACL,IAAa,EAAEM,OAAiB,EAAE;EACnE,IAAMC,GAAG,GAAG,SAANA,GAAGA,CAAIC,MAAe,EAAEC,GAAQ,EAAK;IAEzC,IAAIA,GAAG,KAAK,UAAU,EAAE;MACtB,OAAO,UAACC,KAAa,EAAK;QAExB,IAAI,EAAEA,KAAK,IAAIF,MAAM,CAACG,WAAW,CAAC,IAAID,KAAK,IAAIJ,OAAO,EAAE;UACtD,IAAMM,MAAM,GAAGN,OAAO,CAACI,KAAK,CAAC;UAC7BF,MAAM,CAACG,WAAW,CAACD,KAAK,CAAC,GAAGF,MAAM,CAACK,oBAAoB,CAACD,MAAM,CAAC;QACjE;QACA,OAAOJ,MAAM,CAACM,QAAQ,CAACJ,KAAK,CAAC;MAC/B,CAAC;IACH;IAGA,IAAID,GAAG,KAAKb,iBAAiB,EAAE;MAC7B,OAAO,IAAI;IACb;IAEA,OAAOmB,OAAO,CAACR,GAAG,CAACC,MAAM,EAAEC,GAAG,CAAC;EACjC,CAAC;EACD,OAAO,IAAIO,KAAK,CAAChB,IAAI,EAAE;IAACO,GAAG,EAAHA;EAAG,CAAC,CAAC;AAC/B;AAUO,SAASU,eAAeA,CAACjB,IAAa,EAAEkB,IAAU,EAAE;EACzD,IAAMX,GAAG,GAAG,SAANA,GAAGA,CAAIC,MAAe,EAAEC,GAAQ,EAAK;IAEzC,IAAIA,GAAG,KAAK,aAAa,EAAE;MACzB,OAAO,UAACU,OAA8C,EAAK;QAGzD,OAAOX,MAAM,CAACY,WAAW,CAAAC,aAAA,CAAAA,aAAA,KAAKF,OAAO;UAAED,IAAI,EAAJA;QAAI,EAAC,CAAC;MAC/C,CAAC;IACH;IAGA,IAAIT,GAAG,KAAKX,cAAc,EAAE;MAC1B,OAAO,IAAI;IACb;IAEA,OAAOiB,OAAO,CAACR,GAAG,CAACC,MAAM,EAAEC,GAAG,CAAC;EACjC,CAAC;EACD,OAAO,IAAIO,KAAK,CAAChB,IAAI,EAAE;IAACO,GAAG,EAAHA;EAAG,CAAC,CAAC;AAC/B"}

package/dist/esm/lib/ome/load-ome-tiff.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"load-ome-tiff.js","names":["TiffPixelSource","getOmeLegacyIndexer","getOmeSubIFDIndexer","getOmePixelSourceMeta","fromString","isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","PhotometricInterpretation","photometricInterpretation","omexml","levels","pyramidIndexer","length","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","metadata"],"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"sourcesContent":["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,OAAOA,eAAe,MAAM,sBAAsB;AAClD,SAAQC,mBAAmB,EAAEC,mBAAmB,QAAuB,gBAAgB;AACvF,SAAQC,qBAAqB,QAAO,aAAa;AACjD,SAAQC,UAAU,QAAO,UAAU;AAGnC,OAAO,MAAMC,SAAS,GAAIC,GAAiB,IAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAEnG,OAAO,eAAeC,WAAWA,CAACC,IAAa,EAAEC,UAAwB,EAAE;EAEzE,MAAM;IACJJ,gBAAgB;IAChBK,OAAO;IACPC,yBAAyB,EAAEC;EAC7B,CAAC,GAAGH,UAAU,CAACL,aAAa;EAC5B,MAAMS,MAAM,GAAGZ,UAAU,CAACI,gBAAgB,CAAC;EAM3C,IAAIS,MAAc;EAClB,IAAIC,cAA8B;EAElC,IAAIL,OAAO,EAAE;IAEXI,MAAM,GAAGJ,OAAO,CAACM,MAAM,GAAG,CAAC;IAC3BD,cAAc,GAAGhB,mBAAmB,CAACS,IAAI,EAAEK,MAAM,CAAC;EACpD,CAAC,MAAM;IAELC,MAAM,GAAGD,MAAM,CAACG,MAAM;IACtBD,cAAc,GAAGjB,mBAAmB,CAACU,IAAI,EAAEK,MAAM,CAAC;EACpD;EAGA,MAAMI,OAAO,GAAGJ,MAAM,CAAC,CAAC,CAAC;EACzB,MAAM;IAACK,MAAM;IAAEC,QAAQ;IAAEC,aAAa;IAAEC;EAAK,CAAC,GAAGrB,qBAAqB,CAACiB,OAAO,CAAC;EAC/E,MAAMK,QAAQ,GAAGb,UAAU,CAACc,YAAY,~~EAAE~~;EAC1C,MAAMC,IAAI,GAAG;IAACZ,yBAAyB;IAAEQ;EAAa,CAAC;EAEvD,MAAMK,IAAI,GAAGC,KAAK,CAACC,IAAI,CAAC;IAACX,MAAM,EAAEF;EAAM,CAAC,CAAC,CAACc,GAAG,CAAC,CAACC,CAAC,EAAEC,UAAU,KAAK;IAC/D,MAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAU,CAAC;IAClC,MAAME,OAAO,GAAIC,GAAqB,IAAKlB,cAAc,CAACkB,GAAG,EAAEH,UAAU,CAAC;IAC1E,MAAMI,MAAM,GAAG,IAAIrC,eAAe,CAACmC,OAAO,EAAEX,KAAK,EAAEC,QAAQ,EAAES,KAAK,EAAEb,MAAM,EAAEM,IAAI,CAAC;IACjF,OAAOU,MAAM;EACf,CAAC,CAAC;EAEF,OAAO;IAACT,IAAI;IAAEU,QAAQ,EAAElB;EAAO,CAAC;AAClC"}
1	+ {"version":3,"file":"load-ome-tiff.js","names":["TiffPixelSource","getOmeLegacyIndexer","getOmeSubIFDIndexer","getOmePixelSourceMeta","fromString","isOmeTiff","img","fileDirectory","ImageDescription","includes","loadOmeTiff","tiff","firstImage","SubIFDs","PhotometricInterpretation","photometricInterpretation","omexml","levels","pyramidIndexer","length","imgMeta","labels","getShape","physicalSizes","dtype","tileSize","getTileWidth","meta","data","Array","from","map","_","resolution","shape","indexer","sel","source","metadata"],"sources":["../../../../src/lib/ome/load-ome-tiff.ts"],"sourcesContent":["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,OAAOA,eAAe,MAAM,sBAAsB;AAClD,SAAQC,mBAAmB,EAAEC,mBAAmB,QAAuB,gBAAgB;AACvF,SAAQC,qBAAqB,QAAO,aAAa;AACjD,SAAQC,UAAU,QAAO,UAAU;AAGnC,OAAO,MAAMC,SAAS,GAAIC,GAAiB,IAAKA,GAAG,CAACC,aAAa,CAACC,gBAAgB,CAACC,QAAQ,CAAC,MAAM,CAAC;AAEnG,OAAO,eAAeC,WAAWA,CAACC,IAAa,EAAEC,UAAwB,EAAE;EAEzE,MAAM;IACJJ,gBAAgB;IAChBK,OAAO;IACPC,yBAAyB,EAAEC;EAC7B,CAAC,GAAGH,UAAU,CAACL,aAAa;EAC5B,MAAMS,MAAM,GAAGZ,UAAU,CAACI,gBAAgB,CAAC;EAM3C,IAAIS,MAAc;EAClB,IAAIC,cAA8B;EAElC,IAAIL,OAAO,EAAE;IAEXI,MAAM,GAAGJ,OAAO,CAACM,MAAM,GAAG,CAAC;IAC3BD,cAAc,GAAGhB,mBAAmB,CAACS,IAAI,EAAEK,MAAM,CAAC;EACpD,CAAC,MAAM;IAELC,MAAM,GAAGD,MAAM,CAACG,MAAM;IACtBD,cAAc,GAAGjB,mBAAmB,CAACU,IAAI,EAAEK,MAAM,CAAC;EACpD;EAGA,MAAMI,OAAO,GAAGJ,MAAM,CAAC,CAAC,CAAC;EACzB,MAAM;IAACK,MAAM;IAAEC,QAAQ;IAAEC,aAAa;IAAEC;EAAK,CAAC,GAAGrB,qBAAqB,CAACiB,OAAO,CAAC;EAC/E,MAAMK,QAAQ,GAAGb,UAAU,CAACc,YAAY,CAAC,CAAC;EAC1C,MAAMC,IAAI,GAAG;IAACZ,yBAAyB;IAAEQ;EAAa,CAAC;EAEvD,MAAMK,IAAI,GAAGC,KAAK,CAACC,IAAI,CAAC;IAACX,MAAM,EAAEF;EAAM,CAAC,CAAC,CAACc,GAAG,CAAC,CAACC,CAAC,EAAEC,UAAU,KAAK;IAC/D,MAAMC,KAAK,GAAGZ,QAAQ,CAACW,UAAU,CAAC;IAClC,MAAME,OAAO,GAAIC,GAAqB,IAAKlB,cAAc,CAACkB,GAAG,EAAEH,UAAU,CAAC;IAC1E,MAAMI,MAAM,GAAG,IAAIrC,eAAe,CAACmC,OAAO,EAAEX,KAAK,EAAEC,QAAQ,EAAES,KAAK,EAAEb,MAAM,EAAEM,IAAI,CAAC;IACjF,OAAOU,MAAM;EACf,CAAC,CAAC;EAEF,OAAO;IAACT,IAAI;IAAEU,QAAQ,EAAElB;EAAO,CAAC;AAClC"}

package/dist/esm/lib/ome/ome-indexers.js.map CHANGED Viewed

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1	- {"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","SizeT","SizeC","SizeZ","Pixels","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","concat","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","ifd","get","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","DimensionOrder","_ref","_ref2","_ref3","_ref4","_ref5","_ref6"],"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, z}) => z * SizeC * SizeT + t * SizeC + c;\n }\n case 'XYCZT': {\n return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n }\n case 'XYTCZ': {\n return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n }\n case 'XYTZC': {\n return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n }\n default: {\n throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n }\n }\n}\n"],"mappings":"AAyBA,OAAO,SAASA,mBAAmBA,CAACC,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEC;EAAK,CAAC,GAAGH,OAAO,CAACI,MAAM;EAC5C,MAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAE5C,OAAO,CAACO,GAAqB,EAAEC,YAAoB,KAAK;IAEtD,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAE7B,MAAMG,YAAY,GAAGF,YAAY,GAAGL,KAAK,GAAGF,KAAK,GAAGC,KAAK;IAEzD,OAAOJ,IAAI,CAACa,QAAQ,CAACF,KAAK,GAAGC,YAAY,CAAC;EAC5C,CAAC;AACH;AAgBA,OAAO,SAASE,mBAAmBA,CAACd,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAC5C,MAAMa,QAAkD,GAAG,IAAIC,GAAG,~~EAAE~~;EAEpE,OAAO,OAAOP,GAAqB,EAAEC,YAAoB,KAAK;IAC5D,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAC7B,MAAMQ,SAAS,GAAG,MAAMjB,IAAI,CAACa,QAAQ,CAACF,KAAK,CAAC;IAG5C,IAAID,YAAY,KAAK,CAAC,EAAE;MACtB,OAAOO,SAAS;IAClB;IAEA,MAAM;MAACC;IAAO,CAAC,GAAGD,SAAS,CAACE,aAAa;IACzC,IAAI,CAACD,OAAO,EAAE;MACZ,MAAME,KAAK,CAAC,8CAA8C,CAAC;IAC7D;IAGA,MAAMC,GAAG,MAAAC,MAAA,CAAMb,GAAG,CAACc,CAAC,OAAAD,MAAA,CAAIb,GAAG,CAACe,CAAC,OAAAF,MAAA,CAAIb,GAAG,CAACgB,CAAC,OAAAH,MAAA,CAAIZ,YAAY,CAAE;IACxD,IAAI,CAACK,QAAQ,CAACW,GAAG,CAACL,GAAG,CAAC,EAAE;MAEtB,MAAMM,YAAY,GAAGT,OAAO,CAACR,YAAY,GAAG,CAAC,CAAC;MAC9CK,QAAQ,CAACa,GAAG,CAACP,GAAG,EAAErB,IAAI,CAAC6B,oBAAoB,CAACF,YAAY,CAAC,CAAC;IAC5D;IACA,MAAMG,GAAG,GAAI,MAAMf,QAAQ,CAACgB,GAAG,CAACV,GAAG,CAAwB;IAI3D,OAAO,IAAKJ,SAAS,CAACe,WAAW,CAC/BF,GAAG,CAACX,aAAa,EACjBW,GAAG,CAACG,eAAe,EACnBjC,IAAI,CAACkC,QAAQ,EACblC,IAAI,CAACmC,YAAY,EACjBnC,IAAI,CAACoC,KAAK,EACVpC,IAAI,CAACqC,~~MAAM~~,~~CACZ~~;EACH,CAAC;AACH;AAMA,SAAS7B,gBAAgBA,CAACN,OAAkB,EAAqC;EAC/E,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEF,KAAK;IAAEmC;EAAc,CAAC,GAAGpC,OAAO,CAACI,MAAM;EAC5D,QAAQgC,cAAc;IACpB,KAAK,OAAO;MAAE;QACZ,OAAOC,IAAA;UAAA,IAAC;YAAChB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAc,IAAA;UAAA,OAAKhB,CAAC,GAAGlB,KAAK,GAAGD,KAAK,GAAGoB,CAAC,GAAGnB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOe,KAAA;UAAA,IAAC;YAACjB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAe,KAAA;UAAA,OAAKhB,CAAC,GAAGnB,KAAK,GAAGF,KAAK,GAAGoB,CAAC,GAAGlB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOgB,KAAA;UAAA,IAAC;YAAClB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAgB,KAAA;UAAA,OAAKhB,CAAC,GAAGrB,KAAK,GAAGD,KAAK,GAAGoB,CAAC,GAAGnB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOkB,KAAA;UAAA,IAAC;YAACnB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAiB,KAAA;UAAA,OAAKnB,CAAC,GAAGnB,KAAK,GAAGC,KAAK,GAAGoB,CAAC,GAAGrB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOmB,KAAA;UAAA,IAAC;YAACpB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAkB,KAAA;UAAA,OAAKlB,CAAC,GAAGtB,KAAK,GAAGC,KAAK,GAAGoB,CAAC,GAAGrB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOqB,KAAA;UAAA,IAAC;YAACrB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAmB,KAAA;UAAA,OAAKpB,CAAC,GAAGrB,KAAK,GAAGE,KAAK,GAAGoB,CAAC,GAAGtB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA;MAAS;QACP,MAAM,IAAIH,KAAK,wCAAAE,MAAA,CAAwCgB,cAAc,~~OAAI~~;MAC3E;~~EAAC~~;~~AAEL~~"}
1	+ {"version":3,"file":"ome-indexers.js","names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","SizeT","SizeC","SizeZ","Pixels","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","concat","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","ifd","get","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","DimensionOrder","_ref","_ref2","_ref3","_ref4","_ref5","_ref6"],"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, z}) => z * SizeC * SizeT + t * SizeC + c;\n }\n case 'XYCZT': {\n return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n }\n case 'XYTCZ': {\n return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n }\n case 'XYTZC': {\n return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n }\n default: {\n throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n }\n }\n}\n"],"mappings":"AAyBA,OAAO,SAASA,mBAAmBA,CAACC,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEC;EAAK,CAAC,GAAGH,OAAO,CAACI,MAAM;EAC5C,MAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAE5C,OAAO,CAACO,GAAqB,EAAEC,YAAoB,KAAK;IAEtD,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAE7B,MAAMG,YAAY,GAAGF,YAAY,GAAGL,KAAK,GAAGF,KAAK,GAAGC,KAAK;IAEzD,OAAOJ,IAAI,CAACa,QAAQ,CAACF,KAAK,GAAGC,YAAY,CAAC;EAC5C,CAAC;AACH;AAgBA,OAAO,SAASE,mBAAmBA,CAACd,IAAa,EAAEC,QAAgB,EAAkB;EACnF,MAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAC,CAAC;EAC3B,MAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAO,CAAC;EAC5C,MAAMa,QAAkD,GAAG,IAAIC,GAAG,CAAC,CAAC;EAEpE,OAAO,OAAOP,GAAqB,EAAEC,YAAoB,KAAK;IAC5D,MAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAG,CAAC;IAC7B,MAAMQ,SAAS,GAAG,MAAMjB,IAAI,CAACa,QAAQ,CAACF,KAAK,CAAC;IAG5C,IAAID,YAAY,KAAK,CAAC,EAAE;MACtB,OAAOO,SAAS;IAClB;IAEA,MAAM;MAACC;IAAO,CAAC,GAAGD,SAAS,CAACE,aAAa;IACzC,IAAI,CAACD,OAAO,EAAE;MACZ,MAAME,KAAK,CAAC,8CAA8C,CAAC;IAC7D;IAGA,MAAMC,GAAG,MAAAC,MAAA,CAAMb,GAAG,CAACc,CAAC,OAAAD,MAAA,CAAIb,GAAG,CAACe,CAAC,OAAAF,MAAA,CAAIb,GAAG,CAACgB,CAAC,OAAAH,MAAA,CAAIZ,YAAY,CAAE;IACxD,IAAI,CAACK,QAAQ,CAACW,GAAG,CAACL,GAAG,CAAC,EAAE;MAEtB,MAAMM,YAAY,GAAGT,OAAO,CAACR,YAAY,GAAG,CAAC,CAAC;MAC9CK,QAAQ,CAACa,GAAG,CAACP,GAAG,EAAErB,IAAI,CAAC6B,oBAAoB,CAACF,YAAY,CAAC,CAAC;IAC5D;IACA,MAAMG,GAAG,GAAI,MAAMf,QAAQ,CAACgB,GAAG,CAACV,GAAG,CAAwB;IAI3D,OAAO,IAAKJ,SAAS,CAACe,WAAW,CAC/BF,GAAG,CAACX,aAAa,EACjBW,GAAG,CAACG,eAAe,EACnBjC,IAAI,CAACkC,QAAQ,EACblC,IAAI,CAACmC,YAAY,EACjBnC,IAAI,CAACoC,KAAK,EACVpC,IAAI,CAACqC,MACP,CAAC;EACH,CAAC;AACH;AAMA,SAAS7B,gBAAgBA,CAACN,OAAkB,EAAqC;EAC/E,MAAM;IAACE,KAAK;IAAEC,KAAK;IAAEF,KAAK;IAAEmC;EAAc,CAAC,GAAGpC,OAAO,CAACI,MAAM;EAC5D,QAAQgC,cAAc;IACpB,KAAK,OAAO;MAAE;QACZ,OAAOC,IAAA;UAAA,IAAC;YAAChB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAc,IAAA;UAAA,OAAKhB,CAAC,GAAGlB,KAAK,GAAGD,KAAK,GAAGoB,CAAC,GAAGnB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOe,KAAA;UAAA,IAAC;YAACjB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAe,KAAA;UAAA,OAAKhB,CAAC,GAAGnB,KAAK,GAAGF,KAAK,GAAGoB,CAAC,GAAGlB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOgB,KAAA;UAAA,IAAC;YAAClB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAgB,KAAA;UAAA,OAAKhB,CAAC,GAAGrB,KAAK,GAAGD,KAAK,GAAGoB,CAAC,GAAGnB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOkB,KAAA;UAAA,IAAC;YAACnB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAiB,KAAA;UAAA,OAAKnB,CAAC,GAAGnB,KAAK,GAAGC,KAAK,GAAGoB,CAAC,GAAGrB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOmB,KAAA;UAAA,IAAC;YAACpB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAkB,KAAA;UAAA,OAAKlB,CAAC,GAAGtB,KAAK,GAAGC,KAAK,GAAGoB,CAAC,GAAGrB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA,KAAK,OAAO;MAAE;QACZ,OAAOqB,KAAA;UAAA,IAAC;YAACrB,CAAC;YAAEC,CAAC;YAAEC;UAAC,CAAC,GAAAmB,KAAA;UAAA,OAAKpB,CAAC,GAAGrB,KAAK,GAAGE,KAAK,GAAGoB,CAAC,GAAGtB,KAAK,GAAGoB,CAAC;QAAA;MACzD;IACA;MAAS;QACP,MAAM,IAAIH,KAAK,wCAAAE,MAAA,CAAwCgB,cAAc,MAAG,CAAC;MAC3E;EACF;AACF"}

package/dist/esm/lib/ome/ome-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ome-utils.js","names":["getDims","getLabels","DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","_ref","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","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,SAAQA,OAAO,EAAEC,SAAS,QAAO,SAAS;AAG1C,OAAO,MAAMC,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;AAEV,OAAO,SAASC,qBAAqBA,CAAAC,IAAA,EAAsB;EAAA,IAArB;IAACC;EAAiB,CAAC,GAAAD,IAAA;EAEvD,MAAME,MAAM,GAAGb,SAAS,CAACY,MAAM,CAACE,cAAc,CAAC;EAG/C,MAAMC,IAAI,GAAGhB,OAAO,CAACc,MAAM,CAAC;EAC5B,MAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAM,CAAC,CAACC,IAAI,CAAC,CAAC,CAAC;EACpDH,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACQ,KAAK;EAC/BJ,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACS,KAAK;EAC/BL,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACU,KAAK;EAG/B,IAAIV,MAAM,CAACW,WAAW,EAAE;IAEtBV,MAAM,CAACW,IAAI,CAAC,IAAI,CAAC;IACjBR,KAAK,CAACQ,IAAI,CAAC,CAAC,CAAC;EACf;EAIA,MAAMC,QAAQ,GAAIC,KAAa,IAAK;IAClC,MAAMC,CAAC,GAAG,CAAC,GAAGX,KAAK,CAAC;IACpBW,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACgB,KAAK,IAAIF,KAAK;IACpCC,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACiB,KAAK,IAAIH,KAAK;IACpC,OAAOC,CAAC;EACV,CAAC;EAED,IAAI,EAAEf,MAAM,CAACkB,IAAI,IAAI7B,YAAY,CAAC,EAAE;IAClC,MAAM8B,KAAK,eAAAC,MAAA,CAAepB,MAAM,CAACkB,IAAI,~~qBAAkB~~;EACzD;EAEA,MAAMG,KAAK,GAAGhC,YAAY,CAACW,MAAM,CAACkB,IAAI,CAA8B;EACpE,IAAIlB,MAAM,CAACsB,aAAa,IAAItB,MAAM,CAACuB,aAAa,EAAE;IAChD,MAAMC,aAEL,GAAG;MACFC,CAAC,EAAE;QACDC,IAAI,EAAE1B,MAAM,CAACsB,aAAa;QAC1BK,IAAI,EAAE3B,MAAM,CAAC4B;MACf,CAAC;MACDC,CAAC,EAAE;QACDH,IAAI,EAAE1B,MAAM,CAACuB,aAAa;QAC1BI,IAAI,EAAE3B,MAAM,CAAC8B;MACf;IACF,CAAC;IACD,IAAI9B,MAAM,CAAC+B,aAAa,EAAE;MACxBP,aAAa,CAACQ,CAAC,GAAG;QAChBN,IAAI,EAAE1B,MAAM,CAAC+B,aAAa;QAC1BJ,IAAI,EAAE3B,MAAM,CAACiC;MACf,CAAC;IACH;IACA,OAAO;MAAChC,MAAM;MAAEY,QAAQ;MAAEW,aAAa;MAAEH;IAAK,CAAC;EACjD;EAEA,OAAO;IAACpB,MAAM;IAAEY,QAAQ;IAAEQ;EAAK,CAAC;AAClC"}
1	+ {"version":3,"file":"ome-utils.js","names":["getDims","getLabels","DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","_ref","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","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,SAAQA,OAAO,EAAEC,SAAS,QAAO,SAAS;AAG1C,OAAO,MAAMC,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;AAEV,OAAO,SAASC,qBAAqBA,CAAAC,IAAA,EAAsB;EAAA,IAArB;IAACC;EAAiB,CAAC,GAAAD,IAAA;EAEvD,MAAME,MAAM,GAAGb,SAAS,CAACY,MAAM,CAACE,cAAc,CAAC;EAG/C,MAAMC,IAAI,GAAGhB,OAAO,CAACc,MAAM,CAAC;EAC5B,MAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAM,CAAC,CAACC,IAAI,CAAC,CAAC,CAAC;EACpDH,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACQ,KAAK;EAC/BJ,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACS,KAAK;EAC/BL,KAAK,CAACD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACU,KAAK;EAG/B,IAAIV,MAAM,CAACW,WAAW,EAAE;IAEtBV,MAAM,CAACW,IAAI,CAAC,IAAI,CAAC;IACjBR,KAAK,CAACQ,IAAI,CAAC,CAAC,CAAC;EACf;EAIA,MAAMC,QAAQ,GAAIC,KAAa,IAAK;IAClC,MAAMC,CAAC,GAAG,CAAC,GAAGX,KAAK,CAAC;IACpBW,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACgB,KAAK,IAAIF,KAAK;IACpCC,CAAC,CAACZ,IAAI,CAAC,GAAG,CAAC,CAAC,GAAGH,MAAM,CAACiB,KAAK,IAAIH,KAAK;IACpC,OAAOC,CAAC;EACV,CAAC;EAED,IAAI,EAAEf,MAAM,CAACkB,IAAI,IAAI7B,YAAY,CAAC,EAAE;IAClC,MAAM8B,KAAK,eAAAC,MAAA,CAAepB,MAAM,CAACkB,IAAI,oBAAiB,CAAC;EACzD;EAEA,MAAMG,KAAK,GAAGhC,YAAY,CAACW,MAAM,CAACkB,IAAI,CAA8B;EACpE,IAAIlB,MAAM,CAACsB,aAAa,IAAItB,MAAM,CAACuB,aAAa,EAAE;IAChD,MAAMC,aAEL,GAAG;MACFC,CAAC,EAAE;QACDC,IAAI,EAAE1B,MAAM,CAACsB,aAAa;QAC1BK,IAAI,EAAE3B,MAAM,CAAC4B;MACf,CAAC;MACDC,CAAC,EAAE;QACDH,IAAI,EAAE1B,MAAM,CAACuB,aAAa;QAC1BI,IAAI,EAAE3B,MAAM,CAAC8B;MACf;IACF,CAAC;IACD,IAAI9B,MAAM,CAAC+B,aAAa,EAAE;MACxBP,aAAa,CAACQ,CAAC,GAAG;QAChBN,IAAI,EAAE1B,MAAM,CAAC+B,aAAa;QAC1BJ,IAAI,EAAE3B,MAAM,CAACiC;MACf,CAAC;IACH;IACA,OAAO;MAAChC,MAAM;MAAEY,QAAQ;MAAEW,aAAa;MAAEH;IAAK,CAAC;EACjD;EAEA,OAAO;IAACpB,MAAM;IAAEY,QAAQ;IAAEQ;EAAK,CAAC;AAClC"}

package/dist/esm/lib/ome/utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"utils.js","names":["getLabels","dimOrder","toLowerCase","split","reverse","getDims","labels","lookup","Map","map","name","i","size","length","Error","index","get","undefined"],"sources":["../../../../src/lib/ome/utils.ts"],"sourcesContent":["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":"AAaA,OAAO,SAASA,SAASA,CAACC,QAA+C,EAAE;EACzE,OAAOA,QAAQ,CAACC,WAAW,~~EAAE~~,CAACC,KAAK,CAAC,EAAE,CAAC,CAACC,OAAO,~~EAAE~~;AACnD;AAWA,OAAO,SAASC,OAAOA,CAAmBC,MAAW,EAAE;EACrD,MAAMC,MAAM,GAAG,IAAIC,GAAG,CAACF,MAAM,CAACG,GAAG,CAAC,CAACC,IAAI,EAAEC,CAAC,KAAK,CAACD,IAAI,EAAEC,CAAC,CAAC,CAAC,CAAC;EAC1D,IAAIJ,MAAM,CAACK,IAAI,KAAKN,MAAM,CAACO,MAAM,EAAE;IACjC,MAAMC,KAAK,CAAC,gDAAgD,CAAC;EAC/D;EACA,OAAQJ,IAAO,IAAK;IAClB,MAAMK,KAAK,GAAGR,MAAM,CAACS,GAAG,CAACN,IAAI,CAAC;IAC9B,IAAIK,KAAK,KAAKE,SAAS,EAAE;MACvB,MAAMH,KAAK,CAAC,oBAAoB,CAAC;IACnC;IACA,OAAOC,KAAK;EACd,CAAC;AACH"}
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":"AAaA,OAAO,SAASA,SAASA,CAACC,QAA+C,EAAE;EACzE,OAAOA,QAAQ,CAACC,WAAW,CAAC,CAAC,CAACC,KAAK,CAAC,EAAE,CAAC,CAACC,OAAO,CAAC,CAAC;AACnD;AAWA,OAAO,SAASC,OAAOA,CAAmBC,MAAW,EAAE;EACrD,MAAMC,MAAM,GAAG,IAAIC,GAAG,CAACF,MAAM,CAACG,GAAG,CAAC,CAACC,IAAI,EAAEC,CAAC,KAAK,CAACD,IAAI,EAAEC,CAAC,CAAC,CAAC,CAAC;EAC1D,IAAIJ,MAAM,CAACK,IAAI,KAAKN,MAAM,CAACO,MAAM,EAAE;IACjC,MAAMC,KAAK,CAAC,gDAAgD,CAAC;EAC/D;EACA,OAAQJ,IAAO,IAAK;IAClB,MAAMK,KAAK,GAAGR,MAAM,CAACS,GAAG,CAACN,IAAI,CAAC;IAC9B,IAAIK,KAAK,KAAKE,SAAS,EAAE;MACvB,MAAMH,KAAK,CAAC,oBAAoB,CAAC;IACnC;IACA,OAAOC,KAAK;EACd,CAAC;AACH"}

package/dist/esm/lib/utils/Pool.js.map CHANGED Viewed

	@@ -1 +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"],"mappings":";;AASA,MAAMA,eAAe,IAAAC,qBAAA,GAAGC,UAAU,aAAVA,UAAU,wBAAAC,sBAAA,GAAVD,UAAU,CAAEE,SAAS,cAAAD,sBAAA,uBAArBA,sBAAA,CAAuBE,mBAAmB,cAAAJ,qBAAA,cAAAA,qBAAA,GAAI,CAAC;AAMvE,eAAe,MAAMK,IAAI,CAAC;EAYxBC,WAAWA,CAAA,EAAyB;IAAA,IAAxBC,IAAI,GAAAC,SAAA,CAAAC,MAAA,QAAAD,SAAA,QAAAE,SAAA,GAAAF,SAAA,MAAGT,eAAe;IAAAY,eAAA;IAAAA,eAAA;IAAAA,eAAA;IAAAA,eAAA;IAChC,IAAI,CAACC,OAAO,GAAG,EAAE;IACjB,IAAI,CAACC,WAAW,GAAG,EAAE;IACrB,IAAI,CAACC,SAAS,GAAG,EAAE;IACnB,IAAI,CAACC,OAAO,GAAG,IAAI;IAGnB,KAAK,IAAIC,CAAC,GAAG,CAAC,EAAEA,CAAC,GAAGT,IAAI,EAAE,EAAES,CAAC,EAAE;MAC7B,MAAMC,CAAC,GAAG,IAAIC,MAAM,CAAC,kBAAkB,CAAC;MACxC,IAAI,CAACN,OAAO,CAACO,IAAI,CAACF,CAAC,CAAC;MACpB,IAAI,CAACJ,WAAW,CAACM,IAAI,CAACF,CAAC,CAAC;IAC1B;EACF;EAOA,MAAMG,MAAMA,CAACC,aAA4B,EAAEC,MAAmB,EAAE;IAC9D,MAAMC,aAAa,GAAG,MAAM,IAAI,CAACC,aAAa,~~EAAE~~;IAChD,OAAO,IAAIC,OAAO,CAAC,CAACC,OAAO,EAAEC,MAAM,KAAK;MACtCJ,aAAa,CAACK,SAAS,GAAIC,KAAK,IAAK;QAGnC,IAAI,CAACC,UAAU,CAACP,aAAa,CAAC;QAC9BG,OAAO,CAACG,KAAK,CAACE,IAAI,CAAC,CAAC,CAAC,CAAC;MACxB,CAAC;MACDR,aAAa,CAACS,OAAO,GAAIC,KAAK,IAAK;QAGjC,IAAI,CAACH,UAAU,CAACP,aAAa,CAAC;QAC9BI,MAAM,CAACM,KAAK,CAAC;MACf,CAAC;MACDV,aAAa,CAACW,WAAW,CAAC,CAAC,QAAQ,EAAEb,aAAa,EAAEC,MAAM,CAAC,EAAE,CAACA,MAAM,CAAC,CAAC;IACxE,CAAC,CAAC;EACJ;EAEA,MAAME,aAAaA,CAAA,EAAG;IACpB,MAAMW,UAAU,GAAG,IAAI,CAACtB,WAAW,CAACuB,GAAG,~~EAAE~~;IACzC,IAAID,UAAU,EAAE;MACd,OAAOA,UAAU;IACnB;IACA,MAAME,MAAW,GAAG,CAAC,CAAC;IACtB,MAAMC,OAAO,GAAG,IAAIb,OAAO,CAAEC,OAAO,IAAK;MACvCW,MAAM,CAACX,OAAO,GAAGA,OAAO;IAC1B,CAAC,CAAC;IAEF,IAAI,CAACZ,SAAS,CAACK,IAAI,CAACkB,MAAM,CAAC;IAC3B,OAAOC,OAAO;EAChB;EAEA,MAAMR,UAAUA,CAACP,aAAqB,EAAE;IACtC,MAAMc,MAAM,GAAG,IAAI,CAACvB,SAAS,CAACsB,GAAG,~~EAAE~~;IACnC,IAAIC,MAAM,EAAE;MACVA,MAAM,CAACX,OAAO,CAACH,aAAa,CAAC;IAC/B,CAAC,MAAM;MACL,IAAI,CAACV,WAAW,CAACM,IAAI,CAACI,aAAa,CAAC;IACtC;EACF;EAEAgB,OAAOA,CAAA,EAAG;IAER,KAAK,IAAIvB,CAAC,GAAG,CAAC,EAAEA,CAAC,GAAG,IAAI,CAACJ,OAAO,CAACH,MAAM,EAAE,EAAEO,CAAC,EAAE;MAC5C,IAAI,CAACJ,OAAO,CAACI,CAAC,CAAC,CAACwB,SAAS,~~EAAE~~;IAC7B;EACF;AACF"}
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@loaders.gl/geotiff",
-  "version": "3.4.0-alpha.3",
+  "version": "3.4.0-alpha.5",
   "description": "Framework-independent loaders for tiff and geotiff",
   "license": "MIT",
   "publishConfig": {
@@ -39,5 +39,5 @@
     "fast-xml-parser": "^3.16.0",
     "geotiff": "^1.0.4"
   },
-  "gitHead": "a954528dd1d78a1f128d8f6b07e4baeb7a296924"
+  "gitHead": "686929f85b3420c15df051eab769942b260dd242"
 }