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import bilinear from './shared/scaling/bilinear';
import replicate from './shared/scaling/replicate';
import { expose } from 'comlink';
import decodeLittleEndian from './shared/decoders/decodeLittleEndian';
import decodeBigEndian from './shared/decoders/decodeBigEndian';
import decodeRLE from './shared/decoders/decodeRLE';
import decodeJPEGBaseline8Bit from './shared/decoders/decodeJPEGBaseline8Bit';
// import decodeJPEGBaseline12Bit from './shared/decoders/decodeJPEGBaseline12Bit';
import decodeJPEGBaseline12Bit from './shared/decoders/decodeJPEGBaseline12Bit-js';
import decodeJPEGLossless from './shared/decoders/decodeJPEGLossless';
import decodeJPEGLS from './shared/decoders/decodeJPEGLS';
import decodeJPEG2000 from './shared/decoders/decodeJPEG2000';
import decodeHTJ2K from './shared/decoders/decodeHTJ2K';
// Note that the scaling is pixel value scaling, which is applying a modality LUT
import applyModalityLUT from './shared/scaling/scaleArray';
import getMinMax from './shared/getMinMax';
import getPixelDataTypeFromMinMax, {
validatePixelDataType,
} from './shared/getPixelDataTypeFromMinMax';
import isColorImage from './shared/isColorImage';
const imageUtils = {
bilinear,
replicate,
};
const typedArrayConstructors = {
Uint8Array,
Uint16Array,
Int16Array,
Float32Array,
Uint32Array,
};
function postProcessDecodedPixels(imageFrame, options, start, decodeConfig) {
const shouldShift =
imageFrame.pixelRepresentation !== undefined &&
imageFrame.pixelRepresentation === 1;
const shift =
shouldShift && imageFrame.bitsStored !== undefined
? 32 - imageFrame.bitsStored
: undefined;
if (shouldShift && shift !== undefined) {
for (let i = 0; i < imageFrame.pixelData.length; i++) {
imageFrame.pixelData[i] = (imageFrame.pixelData[i] << shift) >> shift;
}
}
// Cache the pixelData reference quickly incase we want to set a targetBuffer _and_ scale.
let pixelDataArray = imageFrame.pixelData;
imageFrame.pixelDataLength = imageFrame.pixelData.length;
const { min: minBeforeScale, max: maxBeforeScale } = getMinMax(
imageFrame.pixelData
);
const canRenderFloat =
typeof options.allowFloatRendering !== 'undefined'
? options.allowFloatRendering
: true;
// Sometimes the type is specified before the DICOM header data has been
// read. This is fine except for color data, where the wrong type gets
// specified. Don't use the target buffer in that case.
let invalidType =
isColorImage(imageFrame.photometricInterpretation) &&
options.targetBuffer?.offset === undefined;
const willScale = options.preScale?.enabled;
const hasFloatRescale =
willScale &&
Object.values(options.preScale.scalingParameters).some(
(v) => typeof v === 'number' && !Number.isInteger(v)
);
const disableScale =
!options.preScale.enabled || (!canRenderFloat && hasFloatRescale);
const type = options.targetBuffer?.type;
// if there is a type, we need to check whether the min and max AFTER scale
// are actually within the range of the type. If not, we need to convert the
// pixel data to the correct type.
if (type && options.preScale.enabled && !disableScale) {
const scalingParameters = options.preScale.scalingParameters;
const scaledValues = _calculateScaledMinMax(
minBeforeScale,
maxBeforeScale,
scalingParameters
);
invalidType = !validatePixelDataType(
scaledValues.min,
scaledValues.max,
typedArrayConstructors[type]
);
}
if (type && !invalidType) {
pixelDataArray = _handleTargetBuffer(
options,
imageFrame,
typedArrayConstructors,
pixelDataArray
);
} else if (options.preScale.enabled && !disableScale) {
pixelDataArray = _handlePreScaleSetup(
options,
minBeforeScale,
maxBeforeScale,
imageFrame
);
} else {
pixelDataArray = _getDefaultPixelDataArray(
minBeforeScale,
maxBeforeScale,
imageFrame
);
}
let minAfterScale = minBeforeScale;
let maxAfterScale = maxBeforeScale;
if (options.preScale.enabled && !disableScale) {
const scalingParameters = options.preScale.scalingParameters;
_validateScalingParameters(scalingParameters);
const isRequiredScaling = _isRequiredScaling(scalingParameters);
if (isRequiredScaling) {
applyModalityLUT(pixelDataArray, scalingParameters);
imageFrame.preScale = {
...options.preScale,
scaled: true,
};
const scaledValues = _calculateScaledMinMax(
minBeforeScale,
maxBeforeScale,
scalingParameters
);
minAfterScale = scaledValues.min;
maxAfterScale = scaledValues.max;
}
} else if (disableScale) {
imageFrame.preScale = {
enabled: true,
scaled: false,
};
minAfterScale = minBeforeScale;
maxAfterScale = maxBeforeScale;
}
imageFrame.pixelData = pixelDataArray;
imageFrame.smallestPixelValue = minAfterScale;
imageFrame.largestPixelValue = maxAfterScale;
const end = new Date().getTime();
imageFrame.decodeTimeInMS = end - start;
return imageFrame;
}
function _isRequiredScaling(scalingParameters) {
const { rescaleSlope, rescaleIntercept, modality, doseGridScaling, suvbw } =
scalingParameters;
const hasRescaleValues =
typeof rescaleSlope === 'number' && typeof rescaleIntercept === 'number';
const isRTDOSEWithScaling =
modality === 'RTDOSE' && typeof doseGridScaling === 'number';
const isPTWithSUV = modality === 'PT' && typeof suvbw === 'number';
return hasRescaleValues || isRTDOSEWithScaling || isPTWithSUV;
}
function _handleTargetBuffer(
options,
imageFrame,
typedArrayConstructors,
pixelDataArray
) {
const {
arrayBuffer,
type,
offset: rawOffset = 0,
length: rawLength,
rows,
} = options.targetBuffer;
const TypedArrayConstructor = typedArrayConstructors[type];
if (!TypedArrayConstructor) {
throw new Error(`target array ${type} is not supported, or doesn't exist.`);
}
if (rows && rows != imageFrame.rows) {
scaleImageFrame(imageFrame, options.targetBuffer, TypedArrayConstructor);
}
const imageFrameLength = imageFrame.pixelDataLength;
const offset = rawOffset;
const length =
rawLength !== null && rawLength !== undefined
? rawLength
: imageFrameLength - offset;
const imageFramePixelData = imageFrame.pixelData;
if (length !== imageFramePixelData.length) {
throw new Error(
`target array for image does not have the same length (${length}) as the decoded image length (${imageFramePixelData.length}).`
);
}
// TypedArray.Set is api level and ~50x faster than copying elements even for
// Arrays of different types, which aren't simply memcpy ops.
const typedArray = arrayBuffer
? new TypedArrayConstructor(arrayBuffer, offset, length)
: new TypedArrayConstructor(length);
typedArray.set(imageFramePixelData, 0);
// If need to scale, need to scale correct array.
pixelDataArray = typedArray;
return pixelDataArray;
}
function _handlePreScaleSetup(
options,
minBeforeScale,
maxBeforeScale,
imageFrame
) {
const scalingParameters = options.preScale.scalingParameters;
_validateScalingParameters(scalingParameters);
const scaledValues = _calculateScaledMinMax(
minBeforeScale,
maxBeforeScale,
scalingParameters
);
return _getDefaultPixelDataArray(
scaledValues.min,
scaledValues.max,
imageFrame
);
}
function _getDefaultPixelDataArray(min, max, imageFrame) {
const TypedArrayConstructor = getPixelDataTypeFromMinMax(min, max);
// @ts-ignore
const typedArray = new TypedArrayConstructor(imageFrame.pixelData.length);
typedArray.set(imageFrame.pixelData, 0);
return typedArray;
}
function _calculateScaledMinMax(minValue, maxValue, scalingParameters) {
const { rescaleSlope, rescaleIntercept, modality, doseGridScaling, suvbw } =
scalingParameters;
if (modality === 'PT' && typeof suvbw === 'number' && !isNaN(suvbw)) {
return {
min: suvbw * (minValue * rescaleSlope + rescaleIntercept),
max: suvbw * (maxValue * rescaleSlope + rescaleIntercept),
};
} else if (
modality === 'RTDOSE' &&
typeof doseGridScaling === 'number' &&
!isNaN(doseGridScaling)
) {
return {
min: minValue * doseGridScaling,
max: maxValue * doseGridScaling,
};
} else if (
typeof rescaleSlope === 'number' &&
typeof rescaleIntercept === 'number'
) {
return {
min: rescaleSlope * minValue + rescaleIntercept,
max: rescaleSlope * maxValue + rescaleIntercept,
};
} else {
return {
min: minValue,
max: maxValue,
};
}
}
function _validateScalingParameters(scalingParameters) {
if (!scalingParameters) {
throw new Error(
'options.preScale.scalingParameters must be defined if preScale.enabled is true, and scalingParameters cannot be derived from the metadata providers.'
);
}
}
function createDestinationImage(
imageFrame,
targetBuffer,
TypedArrayConstructor
) {
const { samplesPerPixel } = imageFrame;
const { rows, columns } = targetBuffer;
const typedLength = rows * columns * samplesPerPixel;
const pixelData = new TypedArrayConstructor(typedLength);
const bytesPerPixel = pixelData.byteLength / typedLength;
return {
pixelData,
rows,
columns,
frameInfo: {
...imageFrame.frameInfo,
rows,
columns,
},
imageInfo: {
...imageFrame.imageInfo,
rows,
columns,
bytesPerPixel,
},
};
}
/** Scales the image frame, updating the frame in place with a new scaled
* version of it (in place modification)
*/
function scaleImageFrame(imageFrame, targetBuffer, TypedArrayConstructor) {
const dest = createDestinationImage(
imageFrame,
targetBuffer,
TypedArrayConstructor
);
const { scalingType = 'replicate' } = targetBuffer;
imageUtils[scalingType](imageFrame, dest);
Object.assign(imageFrame, dest);
imageFrame.pixelDataLength = imageFrame.pixelData.length;
return imageFrame;
}
/**
* Decodes the provided image frame.
* This is an async function return the result, or you can provide an optional
* callbackFn that is called with the results.
*/
export async function decodeImageFrame(
imageFrame,
transferSyntax,
pixelData,
decodeConfig,
options,
callbackFn
) {
const start = new Date().getTime();
let decodePromise = null;
let opts;
switch (transferSyntax) {
case '1.2.840.10008.1.2':
case '1.2.840.10008.1.2.1':
// Implicit or Explicit VR Little Endian
decodePromise = decodeLittleEndian(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.2':
// Explicit VR Big Endian (retired)
decodePromise = decodeBigEndian(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.1.99':
// Deflate transfer syntax (deflated by dicomParser)
decodePromise = decodeLittleEndian(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.5':
// RLE Lossless
decodePromise = decodeRLE(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.4.50':
// JPEG Baseline lossy process 1 (8 bit)
opts = {
...imageFrame,
};
decodePromise = decodeJPEGBaseline8Bit(pixelData, opts);
break;
case '1.2.840.10008.1.2.4.51':
// JPEG Baseline lossy process 2 & 4 (12 bit)
// opts = {
// ...imageFrame,
// };
// decodePromise = decodeJPEGBaseline12Bit(pixelData, opts);
//throw new Error('Currently unsupported: 1.2.840.10008.1.2.4.51');
decodePromise = decodeJPEGBaseline12Bit(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.4.57':
// JPEG Lossless, Nonhierarchical (Processes 14)
decodePromise = decodeJPEGLossless(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.4.70':
// JPEG Lossless, Nonhierarchical (Processes 14 [Selection 1])
decodePromise = decodeJPEGLossless(imageFrame, pixelData);
break;
case '1.2.840.10008.1.2.4.80':
// JPEG-LS Lossless Image Compression
opts = {
signed: imageFrame.pixelRepresentation === 1, // imageFrame.signed,
// shouldn't need...
bytesPerPixel: imageFrame.bitsAllocated <= 8 ? 1 : 2,
...imageFrame,
};
decodePromise = decodeJPEGLS(pixelData, opts);
break;
case '1.2.840.10008.1.2.4.81':
// JPEG-LS Lossy (Near-Lossless) Image Compression
opts = {
signed: imageFrame.pixelRepresentation === 1, // imageFrame.signed,
// shouldn't need...
bytesPerPixel: imageFrame.bitsAllocated <= 8 ? 1 : 2,
...imageFrame,
};
decodePromise = decodeJPEGLS(pixelData, opts);
break;
case '1.2.840.10008.1.2.4.90':
opts = {
...imageFrame,
};
// JPEG 2000 Lossless
// imageFrame, pixelData, decodeConfig, options
decodePromise = decodeJPEG2000(pixelData, opts);
break;
case '1.2.840.10008.1.2.4.91':
// JPEG 2000 Lossy
opts = {
...imageFrame,
};
// JPEG 2000 Lossy
// imageFrame, pixelData, decodeConfig, options
decodePromise = decodeJPEG2000(pixelData, opts);
break;
case '3.2.840.10008.1.2.4.96':
case '1.2.840.10008.1.2.4.201':
case '1.2.840.10008.1.2.4.202':
case '1.2.840.10008.1.2.4.203':
// HTJ2K
opts = {
...imageFrame,
};
decodePromise = decodeHTJ2K(pixelData, opts);
break;
default:
throw new Error(`no decoder for transfer syntax ${transferSyntax}`);
}
/* Don't know if these work...
// JPEG 2000 Part 2 Multicomponent Image Compression (Lossless Only)
else if(transferSyntax === "1.2.840.10008.1.2.4.92")
{
return decodeJPEG2000(dataSet, frame);
}
// JPEG 2000 Part 2 Multicomponent Image Compression
else if(transferSyntax === "1.2.840.10008.1.2.4.93")
{
return decodeJPEG2000(dataSet, frame);
}
*/
if (!decodePromise) {
throw new Error('decodePromise not defined');
}
const decodedFrame = await decodePromise;
const postProcessed = postProcessDecodedPixels(
decodedFrame,
options,
start,
decodeConfig
);
// Call the callbackFn to agree with older arguments
callbackFn?.(postProcessed);
return postProcessed;
}
const obj = {
decodeTask({
imageFrame,
transferSyntax,
decodeConfig,
options,
pixelData,
callbackFn,
}) {
return decodeImageFrame(
imageFrame,
transferSyntax,
pixelData,
decodeConfig,
options,
callbackFn
);
},
};
expose(obj);
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