pixel normalization

packages/core/src/RenderingEngine/StackViewport.ts

@@ -157,6 +157,7 @@ class StackViewport extends Viewport implements IStackViewport, IImagesLoader {
   private voiUpdatedWithSetProperties = false;
   private VOILUTFunction: VOILUTFunctionType;
   //
+  private outOfRange = false;
   private invert = false;
   // The initial invert of the image loaded as opposed to the invert status of the viewport itself (see above).
   private initialInvert = false;
@@ -1386,7 +1387,8 @@ class StackViewport extends Viewport implements IStackViewport, IImagesLoader {
 
     let voiRangeToUse = voiRange;
 
-    if (typeof voiRangeToUse === 'undefined') {
+    if (typeof voiRangeToUse === 'undefined' || this.outOfRange) {
+      this.outOfRange = false;
       const imageData = imageActor.getMapper().getInputData();
       const range = imageData.getPointData().getScalars().getRange();
       const maxVoiRange = { lower: range[0], upper: range[1] };
@@ -1782,7 +1784,10 @@ class StackViewport extends Viewport implements IStackViewport, IImagesLoader {
 
     // Update the pixel data in the vtkImageData object with the pixelData
     // from the loaded Cornerstone image
-    updateVTKImageDataWithCornerstoneImage(this._imageData, image);
+    this.outOfRange = updateVTKImageDataWithCornerstoneImage(
+      this._imageData,
+      image
+    );
   }
 
   /**
@@ -3047,7 +3052,6 @@ class StackViewport extends Viewport implements IStackViewport, IImagesLoader {
     };
 
     triggerEvent(this.element, Events.COLORMAP_MODIFIED, eventDetail);
-
   }
 
   private unsetColormapGPU() {

packages/core/src/RenderingEngine/helpers/normalizePixels.ts

@@ -0,0 +1,51 @@
+import { IImage } from '../../types';
+import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
+import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
+import generateLut from './cpuFallback/rendering/generateLut';
+
+export function normalizePixels(vtkImage: vtkImageData, image: IImage): any {
+  const { windowCenter, windowWidth } = image;
+  const width = Array.isArray(windowWidth) ? windowWidth[0] : windowWidth;
+  const center = Array.isArray(windowCenter) ? windowCenter[0] : windowCenter;
+
+  const lut = generateLut(image, width, center, false, undefined, undefined);
+  const pixelData = image.getPixelData();
+
+  const numPixels = pixelData.length;
+  const minPixelValue = image.minPixelValue;
+  let storedPixelDataIndex = 0;
+
+  const numComp = vtkImage.getPointData().getNumberOfComponents();
+  const textureData = new Float32Array(numPixels);
+  for (let i = 0; i < numPixels; i++) {
+    textureData[i * numComp] = 255; // Red
+    textureData[i * numComp + 1] = 255; // Green
+    textureData[i * numComp + 2] = 255; // Blue
+    textureData[i * numComp + 3] = 255; // Alpha
+  }
+
+  if (pixelData instanceof Float32Array) {
+    while (storedPixelDataIndex < numPixels) {
+      if (minPixelValue < 0) {
+        textureData[storedPixelDataIndex * numComp + 3] =
+          lut[pixelData[storedPixelDataIndex++] + -minPixelValue]; // Alpha
+      } else {
+        textureData[storedPixelDataIndex * numComp + 3] =
+          lut[pixelData[storedPixelDataIndex++]]; // Alpha
+      }
+    }
+  } else {
+    while (storedPixelDataIndex < numPixels) {
+      textureData[storedPixelDataIndex * numComp + 3] =
+        lut[pixelData[storedPixelDataIndex++]]; // Alpha
+    }
+  }
+
+  const dataArray = vtkDataArray.newInstance({
+    name: 'Pixels',
+    numberOfComponents: numComp,
+    values: textureData,
+  });
+
+  return dataArray;
+}

packages/core/src/utilities/updateVTKImageDataWithCornerstoneImage.ts

@@ -1,10 +1,12 @@
 import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
 import { IImage, PixelDataTypedArray } from '../types';
+import { normalizePixels } from '../RenderingEngine/helpers/normalizePixels';
 
 function updateVTKImageDataWithCornerstoneImage(
   sourceImageData: vtkImageData,
   image: IImage
 ) {
+  let outOfRange = false;
   const pixelData = image.getPixelData();
   if (!sourceImageData.getPointData) {
     // This happens for a CanvasActor, that doesn't have the getPointData
@@ -31,12 +33,22 @@ function updateVTKImageDataWithCornerstoneImage(
     image.getPixelData = () => newPixelData;
     scalarData.set(newPixelData);
   } else {
-    scalarData.set(pixelData);
+    const maxPixelValue = image.maxPixelValue;
+    const minPixelValue = image.minPixelValue;
+
+    if (maxPixelValue < 0 && minPixelValue < 0) {
+      outOfRange = true;
+      const newPixelData = normalizePixels(sourceImageData, image);
+      sourceImageData.getPointData().setScalars(newPixelData);
+    } else {
+      scalarData.set(pixelData);
+    }
   }
 
   // Trigger modified on the VTK Object so the texture is updated
   // TODO: evaluate directly changing things with texSubImage3D later
   sourceImageData.modified();
+  return outOfRange;
 }
 
 export { updateVTKImageDataWithCornerstoneImage };