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Integrate TIFF access into vitessce-image-viewer and Improve Metadata…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| import loadZarr from './zarr-utils'; | ||
| import {loadZarr, getZarrConnections} from './zarr-utils'; | ||
| import {loadTiff, getTiffConnections} from './tiff-utils'; | ||
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| export {loadZarr} | ||
| export {loadZarr, loadTiff, getTiffConnections, getZarrConnections} |
46 changes: 46 additions & 0 deletions
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src/layers/microscopy-viewer-layer/data-utils/tiff-utils.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| import {fromUrl, Pool, getDecoder } from 'geotiff/dist/geotiff.bundle.min.js'; | ||
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| async function loadTile({image, channel, x, y, pool}) { | ||
| var tile = await image.getTileOrStrip(x,y, 0, pool) | ||
| var dataObj = {} | ||
| const is8Bits = image.fileDirectory.BitsPerSample[0]===8 | ||
| const is16Bits = image.fileDirectory.BitsPerSample[0]===16 | ||
| const is32Bits = image.fileDirectory.BitsPerSample[0]===32 | ||
| dataObj[channel] = (is8Bits && new Uint8Array(tile.data)) || | ||
| (is16Bits && new Uint16Array(tile.data)) || | ||
| (is32Bits && new Uint32Array(tile.data)) | ||
| return dataObj | ||
| } | ||
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| export function loadTiff({connections, x, y, z, pool}){ | ||
| const configListPromises = Object.keys(connections).map((channel) => { | ||
| var image = connections[channel][z] | ||
| return loadTile({image, channel, x, y, pool}) | ||
| }) | ||
| return Promise.all(configListPromises).then((dataList) => { | ||
| const orderedList = [] | ||
| const dataObj = Object.assign({}, ...dataList) | ||
| Object.keys(dataObj).sort().forEach((key) => { | ||
| orderedList.push(dataObj[key]); | ||
| }) | ||
| return orderedList; | ||
| }); | ||
| } | ||
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| export function getTiffConnections({sourceChannels, maxZoom}){ | ||
| const tiffConnections = Object.keys(sourceChannels).map(async (channel) => { | ||
| var tiff = await fromUrl(sourceChannels[channel]) | ||
| var imageObj = {} | ||
| for(var i = 0; i < -maxZoom; i++) { | ||
| var image = await tiff.getImage(i) | ||
| if(!imageObj[channel]) { | ||
| imageObj[channel] = [image] | ||
| } else { | ||
| imageObj[channel].push(image) | ||
| } | ||
|
|
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| } | ||
| return imageObj | ||
| }) | ||
| return Promise.all(tiffConnections) | ||
| } |
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97 changes: 97 additions & 0 deletions
97
src/layers/microscopy-viewer-layer/microscopy-viewer-layer-base.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| import {BaseTileLayer} from '@deck.gl/layers'; | ||
| import {Texture2D} from '@luma.gl/webgl' | ||
| import GL from '@luma.gl/constants'; | ||
| import { COORDINATE_SYSTEM } from 'deck.gl'; | ||
| import { XRLayer } from '../xr-layer'; | ||
| import {tileToBoundingBox} from './tiling-utils'; | ||
| import {getTileIndices} from './tiling-utils'; | ||
| import { loadZarr, loadTiff } from './data-utils'; | ||
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| const defaultProps = Object.assign({}, BaseTileLayer.defaultProps, { | ||
| id: `microscopy-tile-layer`, | ||
| pickable: false, | ||
| coordinateSystem: COORDINATE_SYSTEM.CARTESIAN, | ||
| maxZoom: 0, | ||
| onViewportLoad: false, | ||
| renderSubLayers: (props) => { | ||
| const { | ||
| bbox: { | ||
| west, south, east, north, | ||
| }, | ||
| } = props.tile; | ||
| const { sliderValues, data, colorValues } = props; | ||
| const xrl = new XRLayer(props, { | ||
| id: `XR-Layer-${west}-${south}-${east}-${north}`, | ||
| pickable: false, | ||
| coordinateSystem: COORDINATE_SYSTEM.CARTESIAN, | ||
| rgbData: data, | ||
| sliderValues, | ||
| colorValues, | ||
| bounds: [west, south, east, north], | ||
| visible: true, | ||
| }); | ||
| return xrl; | ||
| }, | ||
| }); | ||
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| export class MicroscopyViewerLayerBase extends BaseTileLayer { | ||
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| constructor(props) { | ||
| const minZoom = Math.floor(-1 * Math.log2(Math.max(props.imageHeight, props.imageWidth))); | ||
| const {sliderValues, colorValues} = props | ||
| var orderedSliderValues = [] | ||
| var orderedColorValues = [] | ||
| Object.keys(sliderValues).sort().forEach(function(key) { | ||
| orderedSliderValues.push(sliderValues[key]); | ||
| }) | ||
| Object.keys(colorValues).sort().forEach(function(key) { | ||
| orderedColorValues.push(colorValues[key]); | ||
| }) | ||
| var diff = 6 - orderedSliderValues.length | ||
| for (var i = 0; i < diff; i++) { | ||
| orderedSliderValues.push(65535); | ||
| } | ||
| var diff = 6 - orderedColorValues.length | ||
| for (var j = 0; j < diff; j++) { | ||
| orderedColorValues.push([0,0,0]); | ||
| } | ||
| orderedColorValues = orderedColorValues.map(color => color.map(ch => ch / 255)) | ||
| const getZarr = ({ x, y, z }) => { | ||
| return loadZarr({ | ||
| x, y, z: -1 * z, ...props, | ||
| }); | ||
| } | ||
| const getTiff = ({ x, y, z }) => { | ||
| return loadTiff({ | ||
| x, y, z: -1 * z, ...props, | ||
| }); | ||
| } | ||
| const getTileData = (props.useZarr && getZarr) || | ||
| (props.useTiff && getTiff) || | ||
| props.getTileData | ||
| const overrideValuesProps = Object.assign( | ||
| {}, props, { | ||
| sliderValues: orderedSliderValues, | ||
| colorValues: orderedColorValues, | ||
| minZoom, | ||
| getTileData, | ||
| getTileIndices: (viewport, maxZoom, minZoom) => { | ||
| return getTileIndices({ | ||
| viewport, maxZoom, minZoom, ...props, | ||
| }); | ||
| }, | ||
| tileToBoundingBox: (x, y, z) => { | ||
| return tileToBoundingBox({ | ||
| x, y, z, ...props, | ||
| }); | ||
| }, | ||
| } | ||
| ) | ||
| const layerProps = Object.assign({}, defaultProps, overrideValuesProps) | ||
| super(layerProps) | ||
| } | ||
|
|
||
| } | ||
|
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| MicroscopyViewerLayerBase.layerName = 'MicroscopyViewerLayerBase'; | ||
| MicroscopyViewerLayerBase.defaultProps = defaultProps; |
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