dicom-microscopy-viewer
Version:
Interactive web-based viewer for DICOM Microscopy Images
635 lines (581 loc) • 21.8 kB
HTML
<html lang="en">
<head>
<meta charset="utf-8">
<title>JSDoc: Source: metadata.js</title>
<script src="scripts/prettify/prettify.js"> </script>
<script src="scripts/prettify/lang-css.js"> </script>
<!--[if lt IE 9]>
<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<link type="text/css" rel="stylesheet" href="styles/prettify-tomorrow.css">
<link type="text/css" rel="stylesheet" href="styles/jsdoc-default.css">
</head>
<body>
<div id="main">
<h1 class="page-title">Source: metadata.js</h1>
<section>
<article>
<pre class="prettyprint source linenums"><code>import { tagToKeyword } from './dictionary'
import { SOPClassUIDs } from './enums'
import { _groupFramesPerMapping } from './mapping'
const _metadata = Symbol('metadata')
const _bulkdataReferences = Symbol('bulkdataReferences')
function _base64ToUint8Array (value) {
const blob = window.atob(value)
const array = new Uint8Array(blob.length)
for (let i = 0; i < blob.length; i++) {
array[i] = blob.charCodeAt(i)
}
return array
}
function _base64ToUint16Array (value) {
const blob = window.atob(value)
const n = Uint16Array.BYTES_PER_ELEMENT
const length = blob.length / n
const buffer = new ArrayBuffer(n)
const view = new DataView(buffer)
const array = new Uint16Array(length)
let p = 0
for (let i = 0; i < length; i++) {
p = i * n
for (let j = 0; j < n; j++) {
view.setUint8(j, blob.charCodeAt(p + j))
}
array[i] = view.getUint16(0, true)
}
return array
}
function _base64ToUint32Array (value) {
const blob = window.atob(value)
const n = Uint32Array.BYTES_PER_ELEMENT
const length = blob.length / n
const buffer = new ArrayBuffer(n)
const view = new DataView(buffer)
const array = new Uint32Array(length)
let p = 0
for (let i = 0; i < length; i++) {
p = i * n
for (let j = 0; j < n; j++) {
view.setUint8(j, blob.charCodeAt(p + j))
}
array[i] = view.getUint32(0, true)
}
return array
}
function _base64ToFloat32Array (value) {
const blob = window.atob(value)
const n = Float32Array.BYTES_PER_ELEMENT
const length = blob.length / n
const buffer = new ArrayBuffer(n)
const view = new DataView(buffer)
const array = new Float32Array(length)
let p = 0
for (let i = 0; i < length; i++) {
p = i * n
for (let j = 0; j < n; j++) {
view.setUint8(j, blob.charCodeAt(p + j))
}
array[i] = view.getFloat32(0, true)
}
return array
}
function _base64ToFloat64Array (value) {
const blob = window.atob(value)
const n = Float64Array.BYTES_PER_ELEMENT
const length = blob.length / n
const buffer = new ArrayBuffer(n)
const view = new DataView(buffer)
const array = new Float64Array(length)
let p = 0
for (let i = 0; i < length; i++) {
p = i * n
for (let j = 0; j < n; j++) {
view.setUint8(j, blob.charCodeAt(p + j))
}
array[i] = view.getFloat64(0, true)
}
return array
}
/** Determine the mapping of pyramid tile positions to frame numbers.
*
* @param {Object} Formatted metadata of a VL Whole Slide Microscopy Image instance
* @returns {Object} Mapping of pyramid tile position (Row-Column) to frame URI
* @private
*/
function getFrameMapping (metadata) {
const rows = metadata.Rows
const columns = metadata.Columns
const totalPixelMatrixColumns = metadata.TotalPixelMatrixColumns
const totalPixelMatrixRows = metadata.TotalPixelMatrixRows
const sopInstanceUID = metadata.SOPInstanceUID
const numberOfFrames = Number(metadata.NumberOfFrames || 1)
/**
* Handle images that may contain multiple "planes"
* - z-planes (VL Whole Slide Microscopy Image)
* - optical paths (VL Whole Slide Microscopy Image)
* - segments (Segmentation)
* - mappings (Parametric Map)
*/
const numberOfFocalPlanes = Number(metadata.NumberOfFocalPlanes || 1)
if (numberOfFocalPlanes > 1) {
throw new Error('Images with multiple focal planes are not yet supported.')
}
const {
mappingNumberToFrameNumbers,
frameNumberToMappingNumber
} = _groupFramesPerMapping(metadata)
let numberOfChannels = 0
let numberOfOpticalPaths = 0
let numberOfSegments = 0
let numberOfMappings = 0
if (metadata.OpticalPathSequence != null) {
numberOfOpticalPaths = Number(metadata.NumberOfOpticalPaths || 1)
numberOfChannels = numberOfOpticalPaths
} else if (metadata.SegmentSequence != null) {
numberOfSegments = Number(metadata.SegmentSequence.length)
numberOfChannels = numberOfSegments
} else if (Object.keys(mappingNumberToFrameNumbers).length > 0) {
numberOfMappings = Number(Object.keys(mappingNumberToFrameNumbers).length)
numberOfChannels = numberOfMappings
} else {
throw new Error('Could not determine the number of image channels.')
}
const tileColumns = Math.ceil(totalPixelMatrixColumns / columns)
const tileRows = Math.ceil(totalPixelMatrixRows / rows)
const frameMapping = {}
/**
* The values "TILED_SPARSE" and "TILED_FULL" were introduced in the 2018
* edition of the standard. Older datasets are equivalent to "TILED_SPARSE".
*/
const dimensionOrganizationType = (
metadata.DimensionOrganizationType || 'TILED_SPARSE'
)
if (dimensionOrganizationType === 'TILED_FULL') {
let number = 1
// Forth, along "channels"
for (let i = 0; i < numberOfChannels; i++) {
// Third, along the depth direction from glass slide -> coverslip
for (let p = 0; p < numberOfFocalPlanes; p++) {
// Second, along the column direction from top -> bottom
for (let r = 0; r < tileRows; r++) {
// First, along the row direction from left -> right
for (let c = 0; c < tileColumns; c++) {
/*
* The standard currently only defines TILED_FULL for optical paths
* and not any other types of "channels" such as segments or
* parameter mappings.
*/
let channelIdentifier
if (numberOfOpticalPaths > 0) {
const opticalPath = metadata.OpticalPathSequence[i]
channelIdentifier = String(opticalPath.OpticalPathIdentifier)
} else if (numberOfSegments > 0) {
const segment = metadata.SegmentSequence[i]
channelIdentifier = String(segment.SegmentNumber)
} else if (numberOfMappings > 0) {
// TODO: ensure that frames are mapped accordingly
channelIdentifier = String(frameNumberToMappingNumber[number])
} else {
throw new Error(
`Could not determine channel of frame #${number}.`
)
}
const key = `${r + 1}-${c + 1}-${channelIdentifier}`
frameMapping[key] = `${sopInstanceUID}/frames/${number}`
number += 1
}
}
}
}
} else {
const sharedFuncGroups = metadata.SharedFunctionalGroupsSequence
const perframeFuncGroups = metadata.PerFrameFunctionalGroupsSequence
for (let j = 0; j < numberOfFrames; j++) {
const planePositions = perframeFuncGroups[j].PlanePositionSlideSequence[0]
const rowPosition = planePositions.RowPositionInTotalImagePixelMatrix
const columnPosition = planePositions.ColumnPositionInTotalImagePixelMatrix
const rowIndex = Math.ceil(rowPosition / rows)
const colIndex = Math.ceil(columnPosition / columns)
const number = j + 1
let channelIdentifier
if (numberOfOpticalPaths === 1) {
try {
channelIdentifier = String(
sharedFuncGroups[0]
.OpticalPathIdentificationSequence[0]
.OpticalPathIdentifier
)
} catch {
channelIdentifier = String(
perframeFuncGroups[j]
.OpticalPathIdentificationSequence[0]
.OpticalPathIdentifier
)
}
} else if (numberOfOpticalPaths > 1) {
channelIdentifier = String(
perframeFuncGroups[j]
.OpticalPathIdentificationSequence[0]
.OpticalPathIdentifier
)
} else if (numberOfSegments === 1) {
try {
channelIdentifier = String(
sharedFuncGroups[0]
.SegmentIdentificationSequence[0]
.ReferencedSegmentNumber
)
} catch {
channelIdentifier = String(
perframeFuncGroups[j]
.SegmentIdentificationSequence[0]
.ReferencedSegmentNumber
)
}
} else if (numberOfSegments > 1) {
channelIdentifier = String(
perframeFuncGroups[j]
.SegmentIdentificationSequence[0]
.ReferencedSegmentNumber
)
} else if (numberOfMappings > 0) {
channelIdentifier = String(frameNumberToMappingNumber[number])
} else {
throw new Error(`Could not determine channel of frame ${number}.`)
}
const key = `${rowIndex}-${colIndex}-${channelIdentifier}`
const frameNumber = j + 1
frameMapping[key] = `${sopInstanceUID}/frames/${frameNumber}`
}
}
return {
frameMapping,
numberOfChannels
}
}
/**
* Format DICOM metadata structured according to the DICOM JSON model.
*
* Transforms the DICOM JSON representation into a more human friendly
* representation, where values of data elements can be directly accessed via
* their keyword (e.g., "SOPInstanceUID").
* Bulkdata elements will be extracted and returned as a separate mapping.
*
* @param {Object} metadata - Metadata structured according to the DICOM JSON model
*
* @returns {Object} Formatted dataset and remaining bulkdata
*
* @memberof metadata
*/
function formatMetadata (metadata) {
const loadJSONDataset = (elements) => {
const dataset = {}
const bulkdataReferences = {}
Object.keys(elements).forEach(tag => {
const keyword = tagToKeyword[tag]
const vr = elements[tag].vr
if ('BulkDataURI' in elements[tag]) {
bulkdataReferences[keyword] = elements[tag]
} else if ('Value' in elements[tag]) {
const value = elements[tag].Value
if (vr === 'SQ') {
dataset[keyword] = []
const mappings = []
value.forEach(item => {
const loaded = loadJSONDataset(item)
dataset[keyword].push(loaded.dataset)
mappings.push(loaded.bulkdataReferences)
})
if (mappings.some(item => Object.keys(item).length > 0)) {
bulkdataReferences[keyword] = mappings
}
} else {
// Handle value multiplicity.
if (value.length === 1) {
if (vr === 'DS' || vr === 'IS') {
dataset[keyword] = Number(value[0])
} else {
dataset[keyword] = value[0]
}
} else {
if (vr === 'DS' || vr === 'IS') {
dataset[keyword] = value.map(v => Number(v))
} else {
dataset[keyword] = value
}
}
}
} else if ('InlineBinary' in elements[tag]) {
const value = elements[tag].InlineBinary
if (vr === 'OB') {
dataset[keyword] = _base64ToUint8Array(value)
} else if (vr === 'OW') {
dataset[keyword] = _base64ToUint16Array(value)
} else if (vr === 'OL') {
dataset[keyword] = _base64ToUint32Array(value)
} else if (vr === 'OF') {
dataset[keyword] = _base64ToFloat32Array(value)
} else if (vr === 'OD') {
dataset[keyword] = _base64ToFloat64Array(value)
}
} else {
if (vr === 'SQ') {
dataset[keyword] = []
} else {
dataset[keyword] = null
}
}
})
return { dataset, bulkdataReferences }
}
const { dataset, bulkdataReferences } = loadJSONDataset(metadata)
// The top level (lowest resolution) image may be a single frame image in
// which case the "NumberOfFrames" attribute is optional. We include it for
// consistency.
if (dataset === undefined) {
throw new Error('Could not format metadata: ', metadata)
}
if (!('NumberOfFrames' in dataset) && (dataset.Modality === 'SM')) {
dataset.NumberOfFrames = 1
}
return { dataset, bulkdataReferences }
}
/**
* Group DICOM metadata of monochrome slides by Optical Path Identifier.
*
* @param {metadata.VLWholeSlideMicroscopyImage[]} images - DICOM VL Whole
* Slide Microscopy Image instances.
*
* @returns {Object} Groups of DICOM VL Whole Slide Microscopy Image instances
* @memberof metadata
*/
function groupMonochromeInstances (images) {
const channels = {}
images.forEach(img => {
if (
img.SamplesPerPixel === 1 &&
img.PhotometricInterpretation === 'MONOCHROME2' &&
(img.ImageType[2] === 'VOLUME' || img.ImageType[2] === 'THUMBNAIL')
) {
img.OpticalPathSequence.forEach((opticalPathItem, opticalPathIndex) => {
const id = opticalPathItem.OpticalPathIdentifier
if (id in channels) {
channels[id].push(img)
} else {
channels[id] = [img]
}
})
}
})
return channels
}
/**
* Group DICOM metadata of color images slides by Optical Path Identifier.
*
* @param {metadata.VLWholeSlideMicroscopyImage[]} images - DICOM VL Whole
* Slide Microscopy Image instances.
*
* @returns {Object} Groups of DICOM VL Whole Slide Microscopy Image instances
* @memberof metadata
*/
function groupColorInstances (images) {
const channels = {}
images.forEach(img => {
if (
img.SamplesPerPixel !== 1 &&
(img.ImageType[2] === 'THUMBNAIL' || img.ImageType[2] === 'VOLUME') &&
(
img.PhotometricInterpretation === 'RGB' ||
img.PhotometricInterpretation.includes('YBR')
)
) {
const id = img.OpticalPathSequence[0].OpticalPathIdentifier
if (id in channels) {
channels[id].push(img)
} else {
channels[id] = [img]
}
}
})
return channels
}
/**
* DICOM Service Object Pair (SOP) Class.
*
* @class
* @abstract
* @memberof metadata
*/
class SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of a DICOM SOP instance in DICOM JSON format
*/
constructor ({ metadata }) {
if (metadata == null) {
throw new Error(
'Cannot construct SOP Instance because no metadata was provided.'
)
}
const { dataset, bulkdataReferences } = formatMetadata(metadata)
Object.assign(this, dataset)
this[_metadata] = metadata
this[_bulkdataReferences] = bulkdataReferences
Object.freeze(this)
}
/**
* Get metadata of instance in DICOM JSON format.
*
* The metadata may include bulkdata references via "BulkDataURI".
*
* @returns {Object} metadata in DICOM JSON format
*/
get json () {
return this[_metadata]
}
/**
* Get references to bulkdata of instance in DICOM JSON format.
*
* @returns {Object} bulkdata references in DICOM JSON format
*/
get bulkdataReferences () {
return this[_bulkdataReferences]
}
}
/**
* DICOM VL Whole Slide Microscopy Image instance.
*
* @class
* @extends metadata.SOPClass
* @memberof metadata
*/
class VLWholeSlideMicroscopyImage extends SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of a VL Whole Slide Microscopy Image in DICOM JSON format
*/
constructor ({ metadata }) {
super({ metadata })
if (this.SOPClassUID !== SOPClassUIDs.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE) {
throw new Error(
'Cannot construct VL Whole Slide Microscopy Image instance ' +
`given dataset with SOP Class UID "${this.SOPClassUID}"`
)
}
}
}
/**
* DICOM Comprehensive 3D SR instance.
*
* @class
* @extends metadata.SOPClass
* @memberof metadata
*/
class Comprehensive3DSR extends SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of DICOM Structured Report instance in DICOM JSON format
*/
constructor ({ metadata }) {
super({ metadata })
if (this.SOPClassUID !== SOPClassUIDs.COMPREHENSIVE_3D_SR) {
throw new Error(
'Cannot construct Comprehensive 3D SR instance ' +
`given dataset with SOP Class UID "${this.SOPClassUID}"`
)
}
}
}
/**
* DICOM Microscopy Bulk Simple Annotations instance.
*
* @class
* @extends metadata.SOPClass
* @memberof metadata
*/
class MicroscopyBulkSimpleAnnotations extends SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of a DICOM Microscopy Bulk Simple Annotations instance in DICOM JSON format
*/
constructor ({ metadata }) {
super({ metadata })
if (this.SOPClassUID !== SOPClassUIDs.MICROSCOPY_BULK_SIMPLE_ANNOTATIONS) {
throw new Error(
'Cannot construct Microscopy Bulk Simple Annotations instance ' +
`given dataset with SOP Class UID "${this.SOPClassUID}"`
)
}
}
}
/**
* DICOM Parametric Map instance.
*
* @class
* @extends metadata.SOPClass
* @memberof metadata
*/
class ParametricMap extends SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of a DICOM Parametric Map instance in DICOM JSON format
*/
constructor ({ metadata }) {
super({ metadata })
if (this.SOPClassUID !== SOPClassUIDs.PARAMETRIC_MAP) {
throw new Error(
'Cannot construct Parametric Map instance ' +
`given dataset with SOP Class UID "${this.SOPClassUID}"`
)
}
}
}
/**
* DICOM Segmentation instance.
*
* @class
* @extends metadata.SOPClass
* @memberof metadata
*/
class Segmentation extends SOPClass {
/**
* @param {Object} options
* @param {Object} options.metadata - Metadata of a DICOM Segmentation instance in DICOM JSON format
*/
constructor ({ metadata }) {
super({ metadata })
if (this.SOPClassUID !== SOPClassUIDs.SEGMENTATION) {
throw new Error(
'Cannot construct Segmentation instance ' +
`given dataset with SOP Class UID "${this.SOPClassUID}"`
)
}
}
}
export {
Comprehensive3DSR,
formatMetadata,
groupMonochromeInstances,
groupColorInstances,
getFrameMapping,
MicroscopyBulkSimpleAnnotations,
ParametricMap,
Segmentation,
VLWholeSlideMicroscopyImage
}
</code></pre>
</article>
</section>
</div>
<nav>
<h2><a href="index.html">Home</a></h2><h3>Namespaces</h3><ul><li><a href="annotation.html">annotation</a></li><li><a href="api.html">api</a></li><li><a href="color.html">color</a></li><li><a href="events.html">events</a></li><li><a href="mapping.html">mapping</a></li><li><a href="metadata.html">metadata</a></li><li><a href="opticalPath.html">opticalPath</a></li><li><a href="roi.html">roi</a></li><li><a href="scoord3d.html">scoord3d</a></li><li><a href="segment.html">segment</a></li><li><a href="utils.html">utils</a></li><li><a href="viewer.html">viewer</a></li></ul><h3>Classes</h3><ul><li><a href="annotation.AnnotationGroup.html">AnnotationGroup</a></li><li><a href="color.PaletteColorLookupTable.html">PaletteColorLookupTable</a></li><li><a href="mapping.ParameterMapping.html">ParameterMapping</a></li><li><a href="mapping.Transformation.html">Transformation</a></li><li><a href="metadata.Comprehensive3DSR.html">Comprehensive3DSR</a></li><li><a href="metadata.MicroscopyBulkSimpleAnnotations.html">MicroscopyBulkSimpleAnnotations</a></li><li><a href="metadata.ParametricMap.html">ParametricMap</a></li><li><a href="metadata.Segmentation.html">Segmentation</a></li><li><a href="metadata.SOPClass.html">SOPClass</a></li><li><a href="metadata.VLWholeSlideMicroscopyImage.html">VLWholeSlideMicroscopyImage</a></li><li><a href="module.exports_module.exports.html">exports</a></li><li><a href="opticalPath.OpticalPath.html">OpticalPath</a></li><li><a href="roi.ROI.html">ROI</a></li><li><a href="scoord3d.Ellipse.html">Ellipse</a></li><li><a href="scoord3d.Ellipsoid.html">Ellipsoid</a></li><li><a href="scoord3d.Multipoint.html">Multipoint</a></li><li><a href="scoord3d.Point.html">Point</a></li><li><a href="scoord3d.Polygon.html">Polygon</a></li><li><a href="scoord3d.Polyline.html">Polyline</a></li><li><a href="scoord3d.Scoord3D.html">Scoord3D</a></li><li><a href="segment.Segment.html">Segment</a></li><li><a href="viewer.LabelImageViewer.html">LabelImageViewer</a></li><li><a href="viewer.OverviewImageViewer.html">OverviewImageViewer</a></li><li><a href="viewer.VolumeImageViewer.html">VolumeImageViewer</a></li></ul><h3>Global</h3><ul><li><a href="global.html#addTask">addTask</a></li><li><a href="global.html#cancelTask">cancelTask</a></li><li><a href="global.html#decode">decode</a></li><li><a href="global.html#getStatistics">getStatistics</a></li><li><a href="global.html#handleMessageFromWorker">handleMessageFromWorker</a></li><li><a href="global.html#initialize">initialize</a></li><li><a href="global.html#loadWebWorkerTask">loadWebWorkerTask</a></li><li><a href="global.html#setTaskPriority">setTaskPriority</a></li><li><a href="global.html#spawnWebWorker">spawnWebWorker</a></li><li><a href="global.html#startTaskOnWebWorker">startTaskOnWebWorker</a></li><li><a href="global.html#terminateAllWebWorkers">terminateAllWebWorkers</a></li><li><a href="global.html#transform">transform</a></li></ul>
</nav>
<br class="clear">
<footer>
Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.10</a> on Thu Sep 29 2022 16:54:54 GMT-0400 (Eastern Daylight Time)
</footer>
<script> prettyPrint(); </script>
<script src="scripts/linenumber.js"> </script>
</body>
</html>