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fix(nifti): fix ci test failed
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@yanqzsu
yanqzsu committed May 28, 2024
1 parent ec81d4b commit 3c1638b
Showing 1 changed file with 87 additions and 88 deletions.
175 changes: 87 additions & 88 deletions packages/core/src/RenderingEngine/helpers/setDefaultVolumeVOI.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -30,27 +30,27 @@ async function setDefaultVolumeVOI(
): Promise<void> {
let voi = getVOIFromMetadata(imageVolume);

if (!voi) {
if (!voi && imageVolume?.imageIds?.length) {
voi = await getVOIFromMinMax(imageVolume, useNativeDataType);
voi = handlePreScaledVolume(imageVolume, voi);
}

if (!voi || voi.lower === undefined || voi.upper === undefined) {
throw new Error(
'Could not get VOI from metadata, nor from the min max of the image middle slice'
);
}

voi = handlePreScaledVolume(imageVolume, voi);
const { lower, upper } = voi;

if (lower === 0 && upper === 0) {
// if (!voi || voi.lower === undefined || voi.upper === undefined) {
// throw new Error(
// 'Could not get VOI from metadata, nor from the min max of the image middle slice'
// );
// }
if (
(voi?.lower === 0 && voi?.upper === 0) ||
voi?.lower === undefined ||
voi?.upper === undefined
) {
return;
}

volumeActor
.getProperty()
.getRGBTransferFunction(0)
.setMappingRange(lower, upper);
.setMappingRange(voi.lower, voi.upper);
}

function handlePreScaledVolume(imageVolume: IImageVolume, voi: VOIRange) {
Expand Down Expand Up @@ -128,84 +128,83 @@ async function getVOIFromMinMax(
useNativeDataType: boolean
): Promise<VOIRange> {
const { imageIds } = imageVolume;
const numImages = imageIds?.length || imageVolume.dimensions[2];
let image;
if (imageIds?.length) {
// Get index of the middle image
const imageIdIndex = Math.floor(numImages / 2);
const imageId = imageVolume.imageIds[imageIdIndex];
const generalSeriesModule =
metaData.get('generalSeriesModule', imageId) || {};
const { modality } = generalSeriesModule;
const modalityLutModule = metaData.get('modalityLutModule', imageId) || {};
const scalingParameters: ScalingParameters = {
rescaleSlope: modalityLutModule.rescaleSlope,
rescaleIntercept: modalityLutModule.rescaleIntercept,
modality,
};
let scalingParametersToUse;
if (modality === 'PT') {
const suvFactor = metaData.get('scalingModule', imageId);
if (suvFactor) {
scalingParametersToUse = {
...scalingParameters,
suvbw: suvFactor.suvbw,
};
}
}
const options = {
targetBuffer: {
type: useNativeDataType ? undefined : 'Float32Array',
},
priority: PRIORITY,
requestType: REQUEST_TYPE,
useNativeDataType,
preScale: {
enabled: true,
scalingParameters: scalingParametersToUse,
},
};
// Loading the middle slice image for a volume has two scenarios, the first one is that
// uses the same volumeLoader which might not resolve to an image (since for performance
// reasons volumes' pixelData is set via offset and length on the volume arrayBuffer
// when each slice is loaded). The second scenario is that the image might not reach
// to the volumeLoader, and an already cached image (with Image object) is used
// instead. For the first scenario, we use the arrayBuffer of the volume to get the correct
// slice for the imageScalarData, and for the second scenario we use the getPixelData
// on the Cornerstone IImage object to get the pixel data.
// Note: we don't want to use the derived or generated images for setting the
// default VOI, because they are not the original. This is ugly but don't
// know how to do it better.
image = cache.getImage(imageId);
if (!imageVolume.referencedImageIds?.length) {
// we should ignore the cache here,
// since we want to load the image from with the most
// recent prescale settings
image = await loadAndCacheImage(imageId, {
...options,
ignoreCache: true,
});
const scalarData = imageVolume.getScalarData();

// Get the middle image from the list of imageIds
const imageIdIndex = Math.floor(imageIds.length / 2);
const imageId = imageVolume.imageIds[imageIdIndex];
const generalSeriesModule =
metaData.get('generalSeriesModule', imageId) || {};
const { modality } = generalSeriesModule;
const modalityLutModule = metaData.get('modalityLutModule', imageId) || {};

const numImages = imageIds.length;
const bytesPerImage = scalarData.byteLength / numImages;
const voxelsPerImage = scalarData.length / numImages;
const bytePerPixel = scalarData.BYTES_PER_ELEMENT;

const scalingParameters: ScalingParameters = {
rescaleSlope: modalityLutModule.rescaleSlope,
rescaleIntercept: modalityLutModule.rescaleIntercept,
modality,
};

let scalingParametersToUse;
if (modality === 'PT') {
const suvFactor = metaData.get('scalingModule', imageId);

if (suvFactor) {
scalingParametersToUse = {
...scalingParameters,
suvbw: suvFactor.suvbw,
};
}
}
let imageScalarData;
if (image) {
imageScalarData = image.getPixelData();
} else {
// If image data is missing such as .nifti and .nrrd image
// calculate offset of the middle slice
const scalarData = imageVolume.getScalarData();
const imageIdIndex = Math.floor(numImages / 2);
const bytesPerImage = scalarData.byteLength / numImages;
const voxelsPerImage = scalarData.length / numImages;
const bytePerPixel = scalarData.BYTES_PER_ELEMENT;
const byteOffset = imageIdIndex * bytesPerImage;
imageScalarData = _getImageScalarDataFromImageVolume(
imageVolume,
byteOffset,
bytePerPixel,
voxelsPerImage
);

const byteOffset = imageIdIndex * bytesPerImage;

const options = {
targetBuffer: {
type: useNativeDataType ? undefined : 'Float32Array',
},
priority: PRIORITY,
requestType: REQUEST_TYPE,
useNativeDataType,
preScale: {
enabled: true,
scalingParameters: scalingParametersToUse,
},
};

// Loading the middle slice image for a volume has two scenarios, the first one is that
// uses the same volumeLoader which might not resolve to an image (since for performance
// reasons volumes' pixelData is set via offset and length on the volume arrayBuffer
// when each slice is loaded). The second scenario is that the image might not reach
// to the volumeLoader, and an already cached image (with Image object) is used
// instead. For the first scenario, we use the arrayBuffer of the volume to get the correct
// slice for the imageScalarData, and for the second scenario we use the getPixelData
// on the Cornerstone IImage object to get the pixel data.
// Note: we don't want to use the derived or generated images for setting the
// default VOI, because they are not the original. This is ugly but don't
// know how to do it better.
let image = cache.getImage(imageId);

if (!imageVolume.referencedImageIds?.length) {
// we should ignore the cache here,
// since we want to load the image from with the most
// recent prescale settings
image = await loadAndCacheImage(imageId, { ...options, ignoreCache: true });
}

const imageScalarData = image
? image.getPixelData()
: _getImageScalarDataFromImageVolume(
imageVolume,
byteOffset,
bytePerPixel,
voxelsPerImage
);

// Get the min and max pixel values of the middle slice
const { min, max } = getMinMax(imageScalarData);

Expand Down

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