cornerstone-wado-image-loader

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>imageLoader/createImage.js - Documentation</title> <script src="scripts/prettify/prettify.js"></script> <script src="scripts/prettify/lang-css.js"></script>  <link type="text/css" rel="stylesheet" href="styles/prettify.css"> <link type="text/css" rel="stylesheet" href="styles/jsdoc.css"> <script src="scripts/nav.js" defer></script> <meta name="viewport" content="width=device-width, initial-scale=1.0"> </head> <body> <input type="checkbox" id="nav-trigger" class="nav-trigger" /> <label for="nav-trigger" class="navicon-button x"> <div class="navicon"></div> </label> <label for="nav-trigger" class="overlay"></label> <nav > <h2><a href="index.html">Home</a></h2><h3>Global</h3><ul><li><a href="global.html#addTask">addTask</a></li><li><a href="global.html#arrayBufferToString">arrayBufferToString</a></li><li><a href="global.html#cacheSizeInBytes">cacheSizeInBytes</a></li><li><a href="global.html#cancelTask">cancelTask</a></li><li><a href="global.html#decodeAsync">decodeAsync</a></li><li><a href="global.html#decodeImageFrame">decodeImageFrame</a></li><li><a href="global.html#extractOrientationFromDataset">extractOrientationFromDataset</a></li><li><a href="global.html#extractOrientationFromMetadata">extractOrientationFromMetadata</a></li><li><a href="global.html#extractOrientationFromNMMultiframeDataset">extractOrientationFromNMMultiframeDataset</a></li><li><a href="global.html#extractOrientationFromNMMultiframeMetadata">extractOrientationFromNMMultiframeMetadata</a></li><li><a href="global.html#extractPositionFromDataset">extractPositionFromDataset</a></li><li><a href="global.html#extractPositionFromMetadata">extractPositionFromMetadata</a></li><li><a href="global.html#extractPositionFromNMMultiframeDataset">extractPositionFromNMMultiframeDataset</a></li><li><a href="global.html#extractPositionFromNMMultiframeMetadata">extractPositionFromNMMultiframeMetadata</a></li><li><a href="global.html#extractSliceThicknessFromDataset">extractSliceThicknessFromDataset</a></li><li><a href="global.html#extractSpacingFromDataset">extractSpacingFromDataset</a></li><li><a href="global.html#framesAreFragmented">framesAreFragmented</a></li><li><a href="global.html#getImageTypeSubItemFromDataset">getImageTypeSubItemFromDataset</a></li><li><a href="global.html#getImageTypeSubItemFromMetadata">getImageTypeSubItemFromMetadata</a></li><li><a href="global.html#getMinMax">getMinMax</a></li><li><a href="global.html#getNumberString">getNumberString</a></li><li><a href="global.html#getNumberValues">getNumberValues</a></li><li><a href="global.html#getStatistics">getStatistics</a></li><li><a href="global.html#getTransferSyntaxForContentType">getTransferSyntaxForContentType</a></li><li><a href="global.html#getUncompressedImageFrame">getUncompressedImageFrame</a></li><li><a href="global.html#getValue">getValue</a></li><li><a href="global.html#handleMessageFromWorker">handleMessageFromWorker</a></li><li><a href="global.html#handler">handler</a></li><li><a href="global.html#initialize">initialize</a></li><li><a href="global.html#loadCodecs">loadCodecs</a></li><li><a href="global.html#loadWebWorkerTask">loadWebWorkerTask</a></li><li><a href="global.html#registerLoaders">registerLoaders</a></li><li><a href="global.html#registerTaskHandler">registerTaskHandler</a></li><li><a href="global.html#removeAFromRGBA">removeAFromRGBA</a></li><li><a href="global.html#setPixelDataType">setPixelDataType</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#terminate">terminate</a></li><li><a href="global.html#unpackBinaryFrame">unpackBinaryFrame</a></li></ul> </nav> <div id="main"> <h1 class="page-title">imageLoader/createImage.js</h1> <section> <article> <pre class="prettyprint source linenums"><code>import external from '../externalModules.js'; import getImageFrame from './getImageFrame.js'; import decodeImageFrame from './decodeImageFrame.js'; import isColorImageFn from './isColorImage.js'; import convertColorSpace from './convertColorSpace.js'; import getMinMax from '../shared/getMinMax.js'; import isJPEGBaseline8BitColor from './isJPEGBaseline8BitColor.js'; import { getOptions } from './internal/options.js'; import getScalingParameters from './getScalingParameters.js'; let lastImageIdDrawn = ''; function isModalityLUTForDisplay(sopClassUid) { // special case for XA and XRF // https://groups.google.com/forum/#!searchin/comp.protocols.dicom/Modality$20LUT$20XA/comp.protocols.dicom/UBxhOZ2anJ0/D0R_QP8V2wIJ return ( sopClassUid !== '1.2.840.10008.5.1.4.1.1.12.1' && // XA sopClassUid !== '1.2.840.10008.5.1.4.1.1.12.2.1' ); // XRF } function convertToIntPixelData(floatPixelData) { const floatMinMax = getMinMax(floatPixelData); const floatRange = Math.abs(floatMinMax.max - floatMinMax.min); const intRange = 65535; const slope = floatRange / intRange; const intercept = floatMinMax.min; const numPixels = floatPixelData.length; const intPixelData = new Uint16Array(numPixels); let min = 65535; let max = 0; for (let i = 0; i < numPixels; i++) { const rescaledPixel = Math.floor((floatPixelData[i] - intercept) / slope); intPixelData[i] = rescaledPixel; min = Math.min(min, rescaledPixel); max = Math.max(max, rescaledPixel); } return { min, max, intPixelData, slope, intercept, }; } /** * Helper function to set pixel data to the right typed array. This is needed because web workers * can transfer array buffers but not typed arrays * @param imageFrame */ function setPixelDataType(imageFrame, preScale) { const isScaled = preScale?.scaled; const scalingParmeters = preScale?.scalingParameters; let isNegative = false; if (isScaled && scalingParmeters) { const rescaleSlope = scalingParmeters?.rescaleSlope || 1; const rescaleIntercept = scalingParmeters?.rescaleIntercep || 0; const suvbw = scalingParmeters?.suvbw || 1; isNegative = suvbw * (imageFrame.smallestPixelValue * rescaleSlope + rescaleIntercept) < 0; } if (imageFrame.bitsAllocated === 32) { imageFrame.pixelData = new Float32Array(imageFrame.pixelData); } else if (imageFrame.bitsAllocated === 16) { if (imageFrame.pixelRepresentation === 0 && !isNegative) { imageFrame.pixelData = new Uint16Array(imageFrame.pixelData); } else { imageFrame.pixelData = new Int16Array(imageFrame.pixelData); } } else { imageFrame.pixelData = new Uint8Array(imageFrame.pixelData); } } /** * Removes the A from RGBA to return RGB buffer, this is used when the * decoding happens with browser API which results in RGBA, but if useRGBA flag * is set to false, we want to return RGB * * @param imageFrame - decoded image in RGBA * @param targetBuffer - target buffer to write to */ function removeAFromRGBA(imageFrame, targetBuffer) { const numPixels = imageFrame.length / 4; let rgbIndex = 0; let bufferIndex = 0; for (let i = 0; i < numPixels; i++) { targetBuffer[bufferIndex++] = imageFrame[rgbIndex++]; // red targetBuffer[bufferIndex++] = imageFrame[rgbIndex++]; // green targetBuffer[bufferIndex++] = imageFrame[rgbIndex++]; // blue rgbIndex++; // skip alpha } return targetBuffer; } function createImage(imageId, pixelData, transferSyntax, options = {}) { // whether to use RGBA for color images, default true as cs-legacy uses RGBA // but we don't need RGBA in cs3d, and it's faster, and memory-efficient // in cs3d let useRGBA = true; if (options.useRGBA !== undefined) { useRGBA = options.useRGBA; } // always preScale the pixel array unless it is asked not to options.preScale = { enabled: options.preScale && options.preScale.enabled !== undefined ? options.preScale.enabled : false, }; if (!pixelData || !pixelData.length) { return Promise.reject(new Error('The file does not contain image data.')); } const { cornerstone } = external; const canvas = document.createElement('canvas'); const imageFrame = getImageFrame(imageId); // Get the scaling parameters from the metadata if (options.preScale.enabled) { const scalingParameters = getScalingParameters( cornerstone.metaData, imageId ); if (scalingParameters) { options.preScale = { ...options.preScale, scalingParameters, }; } } const { decodeConfig } = getOptions(); const decodePromise = decodeImageFrame( imageFrame, transferSyntax, pixelData, canvas, options, decodeConfig ); const { convertFloatPixelDataToInt, use16BitDataType } = decodeConfig; return new Promise((resolve, reject) => { // eslint-disable-next-line complexity decodePromise.then(function (imageFrame) { // if it is desired to skip creating image, return the imageFrame // after the decode. This might be useful for some applications // that only need the decoded pixel data and not the image object if (options.skipCreateImage) { return resolve(imageFrame); } // If we have a target buffer that was written to in the // Decode task, point the image to it here. // We can't have done it within the thread incase it was a SharedArrayBuffer. let alreadyTyped = false; if (options.targetBuffer) { let offset, length; // If we have a target buffer, write to that instead. This helps reduce memory duplication. ({ offset, length } = options.targetBuffer); const { arrayBuffer, type } = options.targetBuffer; let TypedArrayConstructor; if (length === null || length === undefined) { length = imageFrame.pixelDataLength; } if (offset === null || offset === undefined) { offset = 0; } switch (type) { case 'Uint8Array': TypedArrayConstructor = Uint8Array; break; case use16BitDataType && 'Uint16Array': TypedArrayConstructor = Uint16Array; break; case use16BitDataType && 'Int16Array': TypedArrayConstructor = Int16Array; break; case 'Float32Array': TypedArrayConstructor = Float32Array; break; default: throw new Error( 'target array for image does not have a valid type.' ); } if (length !== imageFrame.pixelDataLength) { throw new Error( 'target array for image does not have the same length as the decoded image length.' ); } // TypedArray.Set is api level and ~50x faster than copying elements even for // Arrays of different types, which aren't simply memcpy ops. let typedArray; if (arrayBuffer) { typedArray = new TypedArrayConstructor(arrayBuffer, offset, length); } else { typedArray = new TypedArrayConstructor(imageFrame.pixelData); } // If need to scale, need to scale correct array. imageFrame.pixelData = typedArray; alreadyTyped = true; } if (!alreadyTyped) { setPixelDataType(imageFrame, imageFrame.preScale); } const imagePlaneModule = cornerstone.metaData.get('imagePlaneModule', imageId) || {}; const voiLutModule = cornerstone.metaData.get('voiLutModule', imageId) || {}; const modalityLutModule = cornerstone.metaData.get('modalityLutModule', imageId) || {}; const sopCommonModule = cornerstone.metaData.get('sopCommonModule', imageId) || {}; const isColorImage = isColorImageFn(imageFrame.photometricInterpretation); if (isColorImage) { if (useRGBA) { // JPEGBaseline (8 bits) is already returning the pixel data in the right format (rgba) // because it's using a canvas to load and decode images. if (!isJPEGBaseline8BitColor(imageFrame, transferSyntax)) { canvas.height = imageFrame.rows; canvas.width = imageFrame.columns; const context = canvas.getContext('2d'); const imageData = context.createImageData( imageFrame.columns, imageFrame.rows ); convertColorSpace(imageFrame, imageData.data, useRGBA); imageFrame.imageData = imageData; imageFrame.pixelData = imageData.data; } } else if (isJPEGBaseline8BitColor(imageFrame, transferSyntax)) { // If we don't need the RGBA but the decoding is done with RGBA (the case // for JPEG Baseline 8 bit color), AND the option specifies to use RGB (no RGBA) // we need to remove the A channel from pixel data const colorBuffer = new Uint8ClampedArray( (imageFrame.pixelData.length / 4) * 3 ); // remove the A from the RGBA of the imageFrame imageFrame.pixelData = removeAFromRGBA( imageFrame.pixelData, colorBuffer ); } else if (imageFrame.photometricInterpretation === 'PALETTE COLOR') { canvas.height = imageFrame.rows; canvas.width = imageFrame.columns; const context = canvas.getContext('2d'); const imageData = context.createImageData( imageFrame.columns, imageFrame.rows ); convertColorSpace(imageFrame, imageData.data, true); const colorBuffer = new imageData.data.constructor( (imageData.data.length / 4) * 3 ); // remove the A from the RGBA of the imageFrame imageFrame.pixelData = removeAFromRGBA(imageData.data, colorBuffer); } // calculate smallest and largest PixelValue of the converted pixelData const minMax = getMinMax(imageFrame.pixelData); imageFrame.smallestPixelValue = minMax.min; imageFrame.largestPixelValue = minMax.max; } const image = { imageId, color: isColorImage, columnPixelSpacing: imagePlaneModule.columnPixelSpacing, columns: imageFrame.columns, height: imageFrame.rows, preScale: imageFrame.preScale, intercept: modalityLutModule.rescaleIntercept ? modalityLutModule.rescaleIntercept : 0, slope: modalityLutModule.rescaleSlope ? modalityLutModule.rescaleSlope : 1, invert: imageFrame.photometricInterpretation === 'MONOCHROME1', minPixelValue: imageFrame.smallestPixelValue, maxPixelValue: imageFrame.largestPixelValue, rowPixelSpacing: imagePlaneModule.rowPixelSpacing, rows: imageFrame.rows, sizeInBytes: imageFrame.pixelData.byteLength, width: imageFrame.columns, windowCenter: voiLutModule.windowCenter ? voiLutModule.windowCenter[0] : undefined, windowWidth: voiLutModule.windowWidth ? voiLutModule.windowWidth[0] : undefined, voiLUTFunction: voiLutModule.voiLUTFunction ? voiLutModule.voiLUTFunction : undefined, decodeTimeInMS: imageFrame.decodeTimeInMS, floatPixelData: undefined, imageFrame, rgba: isColorImage && useRGBA, }; // If pixel data is intrinsically floating 32 array, we convert it to int for // display in cornerstone. For other cases when pixel data is typed as // Float32Array for scaling; this conversion is not needed. if ( imageFrame.pixelData instanceof Float32Array && convertFloatPixelDataToInt ) { const floatPixelData = imageFrame.pixelData; const results = convertToIntPixelData(floatPixelData); image.minPixelValue = results.min; image.maxPixelValue = results.max; image.slope = results.slope; image.intercept = results.intercept; image.floatPixelData = floatPixelData; image.getPixelData = () => results.intPixelData; } else { image.getPixelData = () => imageFrame.pixelData; } if (image.color) { image.getCanvas = function () { if (lastImageIdDrawn === imageId) { return canvas; } canvas.height = image.rows; canvas.width = image.columns; const context = canvas.getContext('2d'); context.putImageData(imageFrame.imageData, 0, 0); lastImageIdDrawn = imageId; return canvas; }; } // Modality LUT if ( modalityLutModule.modalityLUTSequence && modalityLutModule.modalityLUTSequence.length > 0 && isModalityLUTForDisplay(sopCommonModule.sopClassUID) ) { image.modalityLUT = modalityLutModule.modalityLUTSequence[0]; } // VOI LUT if ( voiLutModule.voiLUTSequence && voiLutModule.voiLUTSequence.length > 0 ) { image.voiLUT = voiLutModule.voiLUTSequence[0]; } if (image.color) { image.windowWidth = 255; image.windowCenter = 127; } // set the ww/wc to cover the dynamic range of the image if no values are supplied if (image.windowCenter === undefined || image.windowWidth === undefined) { const maxVoi = image.maxPixelValue * image.slope + image.intercept; const minVoi = image.minPixelValue * image.slope + image.intercept; image.windowWidth = maxVoi - minVoi; image.windowCenter = (maxVoi + minVoi) / 2; } resolve(image); }, reject); }); } export default createImage; </code></pre> </article> </section> </div> <br class="clear"> <footer> Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.6.7</a> using the <a href="https://github.com/clenemt/docdash">docdash</a> theme. </footer> <script>prettyPrint();</script> <script src="scripts/polyfill.js"></script> <script src="scripts/linenumber.js"></script> </body> </html>