cornerstone-tools-cacalc
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Medical imaging tools for the Cornerstone library with added functionality for computing Agatston calcium scores
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<h2><a href="index.html">Home</a></h2><h3>Global</h3><ul><li><a href="global.html#applyWWWCRegion">applyWWWCRegion</a></li><li><a href="global.html#calculateMinMaxMean">calculateMinMaxMean</a></li><li><a href="global.html#createMagnificationCanvas">createMagnificationCanvas</a></li><li><a href="global.html#dragCallback">dragCallback</a></li><li><a href="global.html#drawMagnificationTool">drawMagnificationTool</a></li><li><a href="global.html#getPlayClipTimeouts">getPlayClipTimeouts</a></li><li><a href="global.html#mouseDownCallback">mouseDownCallback</a></li><li><a href="global.html#mouseUpCallback">mouseUpCallback</a></li><li><a href="global.html#onImageRendered">onImageRendered</a></li><li><a href="global.html#performThresholding">performThresholding</a></li><li><a href="global.html#playClip">playClip</a></li><li><a href="global.html#recordStartPoint">recordStartPoint</a></li><li><a href="global.html#removeMagnificationCanvas">removeMagnificationCanvas</a></li><li><a href="global.html#stopClip">stopClip</a></li><li><a href="global.html#stopClipWithData">stopClipWithData</a></li><li><a href="global.html#triggerStopEvent">triggerStopEvent</a></li></ul>
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<h1 class="page-title">regions/thresholding.js</h1>
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<pre class="prettyprint source linenums"><code>import * as cornerstone from 'cornerstone-core';
import { addToolState, getToolState } from '../stateManagement/toolState';
// UNUSED const toolType = 'thresholding';
let LASTELEMENT = null;
export function getLastElement () {
return LASTELEMENT;
}
const LABEL_SIZE_BYTES = 1;
let configuration = {
historySize: 4,
historyPosition: 0,
toolRegionValue: 2,
calciumThresholdHu: 130,
layersAbove: 0,
layersBelow: 0,
drawAlpha: 1,
regionColorsRGB: [
[255, 0, 255],
[246, 193, 91],
[237, 148, 69],
[230, 103, 49],
[184, 74, 41],
[106, 58, 45]
],
kvpToMultiplier: {
140: 1.04,
130: 1.02,
120: 1,
110: 0.98,
100: 0.96,
90: 0.93,
80: 0.89,
// add dummy for 70
70: 0.86,
},
growIterationsPerChunk: 2
};
/**
* Perform the thresholding on a stack
*/
function performThresholding (stack, afterwards) {
let width, height;
const imageIds = stack.imageIds;
const slices = imageIds.length;
// Get slope and intercept
return cornerstone.loadImage(imageIds[0]).then(function (image) {
width = image.width;
height = image.height;
const length = width * height * slices * LABEL_SIZE_BYTES;
const buffer = new ArrayBuffer(length);
const view = new Uint8Array(buffer);
// Thresholding promises
const promises = imageIds.map(function (imageId, imageIdx) {
return cornerstone.loadImage(imageId).then(function (image) {
const slope = image.slope;
const intercept = image.intercept;
const pixelData = image.getPixelData();
const n = width * height;
for (let i = 0; i < n; i++) {
const pixel = pixelData[i];
const hu = (pixel * slope) + intercept;
const label = (hu >= configuration.calciumThresholdHu) ? 1 : 0;
const viewIdx = (imageIdx) * n + i;
view[viewIdx] = label;
}
});
});
// Callback with buffer
return Promise.all(promises).then(function () {
const result = {
buffer,
width,
height
};
if (afterwards) {
afterwards(result);
}
return result;
});
});
}
let imgdata = null;
/**
* Draw regions on image
*/
function onImageRendered (e, eventData) {
const element = eventData.element;
const stackData = getToolState(element, 'stack');
const thresholdingData = getToolState(element, 'regions');
if (!thresholdingData || !thresholdingData.data || !thresholdingData.data.length) {
return;
}
const slice = stackData.data[0].currentImageIdIndex;
const buffer = thresholdingData.data[0].buffer;
const context = eventData.canvasContext;
const enabledElement = eventData.enabledElement;
const image = eventData.image;
const width = image.width;
const height = image.height;
const doubleBuffer = document.createElement('canvas');
const doubleBufferContext = doubleBuffer.getContext('2d');
doubleBuffer.width = width;
doubleBuffer.height = height;
imgdata = imgdata || doubleBufferContext.createImageData(width, height);
const pixels = imgdata.data;
const sliceSize = width * height;
const sliceOffset = slice * sliceSize;
const view = new Uint8Array(buffer, sliceOffset, sliceSize);
for (let i = 0; i < view.length; i += 1) {
const label = view[i];
const pi = i * 4;
if (label) {
const color = configuration.regionColorsRGB[label - 1];
pixels[pi + 0] = color[0];
pixels[pi + 1] = color[1];
pixels[pi + 2] = color[2];
pixels[pi + 3] = configuration.drawAlpha * 255;
} else {
pixels[pi + 3] = 0;
}
}
doubleBufferContext.putImageData(imgdata, 0, 0);
cornerstone.setToPixelCoordinateSystem(enabledElement, context);
context.drawImage(doubleBuffer, 0, 0);
}
function enable (element) {
LASTELEMENT = element;
// First check that there is stack data available
const stackData = getToolState(element, 'stack');
if (!stackData || !stackData.data || !stackData.data.length) {
return;
}
const initialThresholdingData = {
enabled: 1,
buffer: null,
width: null,
height: null,
history: []
};
addToolState(element, 'regions', initialThresholdingData);
const stack = stackData.data[0];
performThresholding(stack, function (regions) {
// Add threshold data to tool state
const thresholdingData = getToolState(element, 'regions');
thresholdingData.data[0].buffer = regions.buffer;
thresholdingData.data[0].width = regions.width;
thresholdingData.data[0].height = regions.height;
// Draw regions on image
$(element).on('CornerstoneImageRendered', onImageRendered);
// Update the element to apply the viewport and tool changes
cornerstone.updateImage(element);
});
}
function disable (element) {
const thresholdingData = getToolState(element, 'regions');
// If there is actually something to disable, disable it
if (thresholdingData && thresholdingData.data.length) {
thresholdingData.data[0].enabled = false;
}
}
export function createUndoStep (element) {
const thresholdingData = getToolState(element, 'regions');
const state = thresholdingData.data[0];
// Make a copy using .slice()
const current = state.buffer.slice();
// Put at end of history
state.history.push(current);
// Remove oldest if too much history
if (state.history.length > configuration.historySize) {
state.history.shift();
}
}
export function getConfiguration () {
return configuration;
}
export function setConfiguration (config) {
configuration = config;
}
// Module/private exports
export default {
activate: enable,
deactivate: disable,
enable,
disable,
getConfiguration,
setConfiguration
};
</code></pre>
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