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Merged
JamesAPetts merged 2 commits into from
Oct 8, 2019
Merged

refactor: 💡 Combine rescale computation with slice insertion #47

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0db3ca2
refactor: 💡 Combine rescale computation with slice insertion
JamesAPetts Oct 8, 2019
6624909
Removed unused typed array.
JamesAPetts Oct 8, 2019
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113 changes: 111 additions & 2 deletions src/lib/data/insertSlice.js
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Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
import computeImageDataIncrements from './computeImageDataIncrements.js';
import computeIndex from './computeIndex.js';
import cornerstone from 'cornerstone-core';

// insert the slice at the z index location.
export default function insertSlice(imageData, pixels, index) {
export default function insertSlice(imageData, index, image) {
const pixels = image.getPixelData();
const scalingParameters = _calculateScalingParametersForModality(image);

const datasetDefinition = imageData.get('extent', 'spacing', 'origin');
const scalars = imageData.getPointData().getScalars();
const increments = computeImageDataIncrements(imageData, 1); // TODO number of components.
Expand All @@ -20,8 +24,113 @@ export default function insertSlice(imageData, pixels, index) {
increments,
indexXYZ
);
scalarData[destIdx] = pixels[pixelIndex++];
const pixel = pixels[pixelIndex];

scalarData[destIdx] = _getModalityPixelsOrSUV(pixel, scalingParameters);

pixelIndex++;
}
}
imageData.modified();
}

function _calculateScalingParametersForModality(image) {
const patientStudyModule = cornerstone.metaData.get(
'patientStudyModule',
image.imageId
);
const seriesModule = cornerstone.metaData.get(
'generalSeriesModule',
image.imageId
);

if (!patientStudyModule) {
throw new Error('patientStudyModule metadata is required');
}

if (!seriesModule) {
throw new Error('seriesModule metadata is required');
}

const modality = seriesModule.modality;

const scalingParameters = {
slope: image.slope,
intercept: image.intercept,
modality,
};

if (modality === 'PT') {
const patientWeight = patientStudyModule.patientWeight; // In kg

if (!patientWeight) {
throw new Error(
'patientWeight must be present in patientStudyModule for modality PT'
);
}

const petSequenceModule = cornerstone.metaData.get(
'petIsotopeModule',
image.imageId
);

if (!petSequenceModule) {
throw new Error('petSequenceModule metadata is required');
}

// TODO:
// - Update this to match the SUV logic provided here:
// https://github.com/salimkanoun/fijiPlugins/blob/master/Pet_Ct_Viewer/src/SUVDialog.java
// - Test with PET datasets from various providers to ensure SUV is correct
const radiopharmaceuticalInfo = petSequenceModule.radiopharmaceuticalInfo;
const startTime = radiopharmaceuticalInfo.radiopharmaceuticalStartTime;
const totalDose = radiopharmaceuticalInfo.radionuclideTotalDose;
const halfLife = radiopharmaceuticalInfo.radionuclideHalfLife;
const seriesAcquisitionTime = seriesModule.seriesTime;

if (!startTime || !totalDose || !halfLife || !seriesAcquisitionTime) {
throw new Error(
'The required radiopharmaceutical information was not present.'
);
}

const acquisitionTimeInSeconds =
fracToDec(seriesAcquisitionTime.fractionalSeconds || 0) +
seriesAcquisitionTime.seconds +
seriesAcquisitionTime.minutes * 60 +
seriesAcquisitionTime.hours * 60 * 60;
const injectionStartTimeInSeconds =
fracToDec(startTime.fractionalSeconds) +
startTime.seconds +
startTime.minutes * 60 +
startTime.hours * 60 * 60;
const durationInSeconds =
acquisitionTimeInSeconds - injectionStartTimeInSeconds;
const correctedDose =
totalDose * Math.exp((-durationInSeconds * Math.log(2)) / halfLife);

scalingParameters.patientWeight = patientWeight;
scalingParameters.correctedDose = correctedDose;
}

return scalingParameters;
}

function _getModalityPixelsOrSUV(pixel, scalingParameters) {
if (scalingParameters.modality === 'PT') {
const {
slope,
intercept,
patientWeight,
correctedDose,
} = scalingParameters;

const modalityPixelValue = pixel * slope + intercept;
const suv = (1000 * modalityPixelValue * patientWeight) / correctedDose;
return suv;
}

const { slope, intercept } = scalingParameters;

return pixel * slope + intercept;
}
90 changes: 1 addition & 89 deletions src/lib/loadImageData.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,96 +8,8 @@ function loadImageDataProgressively(imageIds, imageData, metaDataMap, zAxis) {
const insertPixelData = image => {
const { imagePositionPatient } = metaDataMap.get(image.imageId);
const sliceIndex = getSliceIndex(zAxis, imagePositionPatient);
const pixels = image.getPixelData();
const { slope, intercept } = image;
const numPixels = pixels.length;

// TODO: Sometimes after scaling from stored pixel value to modality
// pixel value, the result is negative. In this case, we need to use a
// signed array. I've hardcoded Int16 for now but I guess we can try to
// figure out if Int8 is also an option.
const modalityPixelsOrSUV = new Int16Array(numPixels);

const patientStudyModule = cornerstone.metaData.get(
'patientStudyModule',
image.imageId
);
const seriesModule = cornerstone.metaData.get(
'generalSeriesModule',
image.imageId
);

if (!patientStudyModule) {
throw new Error('patientStudyModule metadata is required');
}

if (!seriesModule) {
throw new Error('seriesModule metadata is required');
}

const modality = seriesModule.modality;

if (modality === 'PT') {
const patientWeight = patientStudyModule.patientWeight; // In kg

if (!patientWeight) {
throw new Error(
'patientWeight must be present in patientStudyModule for modality PT'
);
}

const petSequenceModule = cornerstone.metaData.get(
'petIsotopeModule',
image.imageId
);

if (!petSequenceModule) {
throw new Error('petSequenceModule metadata is required');
}

// TODO:
// - Update this to match the SUV logic provided here:
// https://github.com/salimkanoun/fijiPlugins/blob/master/Pet_Ct_Viewer/src/SUVDialog.java
// - Test with PET datasets from various providers to ensure SUV is correct
const radiopharmaceuticalInfo = petSequenceModule.radiopharmaceuticalInfo;
const startTime = radiopharmaceuticalInfo.radiopharmaceuticalStartTime;
const totalDose = radiopharmaceuticalInfo.radionuclideTotalDose;
const halfLife = radiopharmaceuticalInfo.radionuclideHalfLife;
const seriesAcquisitionTime = seriesModule.seriesTime;

if (!startTime || !totalDose || !halfLife || !seriesAcquisitionTime) {
throw new Error(
'The required radiopharmaceutical information was not present.'
);
}

const acquisitionTimeInSeconds =
fracToDec(seriesAcquisitionTime.fractionalSeconds || 0) +
seriesAcquisitionTime.seconds +
seriesAcquisitionTime.minutes * 60 +
seriesAcquisitionTime.hours * 60 * 60;
const injectionStartTimeInSeconds =
fracToDec(startTime.fractionalSeconds) +
startTime.seconds +
startTime.minutes * 60 +
startTime.hours * 60 * 60;
const durationInSeconds =
acquisitionTimeInSeconds - injectionStartTimeInSeconds;
const correctedDose =
totalDose * Math.exp((-durationInSeconds * Math.log(2)) / halfLife);

for (let i = 0; i < numPixels; i++) {
const modalityPixelValue = pixels[i] * slope + intercept;
const suv = (1000 * modalityPixelValue * patientWeight) / correctedDose;
modalityPixelsOrSUV[i] = suv;
}
} else {
for (let i = 0; i < numPixels; i++) {
modalityPixelsOrSUV[i] = pixels[i] * slope + intercept;
}
}

insertSlice(imageData, modalityPixelsOrSUV, sliceIndex);
insertSlice(imageData, sliceIndex, image);
};

loadImagePromises.forEach(promise => {
Expand Down