feat(voi): add linear exact voi lut function

common/reviews/api/core.api.md

@@ -721,6 +721,7 @@ interface CPUFallbackViewport {
     voi?: {
         windowWidth: number;
         windowCenter: number;
+        voiLUTFunction: VOILUTFunctionType;
     };
     // (undocumented)
     voiLUT?: CPUFallbackLUT;
@@ -1722,7 +1723,7 @@ interface IImage {
     // (undocumented)
     voiLUT?: CPUFallbackLUT;
     // (undocumented)
-    voiLUTFunction: string;
+    voiLUTFunction: VOILUTFunctionType;
     // (undocumented)
     voxelManager?: IVoxelManager<number> | IVoxelManager<RGB>;
     // (undocumented)
@@ -3717,7 +3718,7 @@ class TargetEventListeners {
 function threePlaneIntersection(firstPlane: Plane, secondPlane: Plane, thirdPlane: Plane): Point3;
 
 // @public (undocumented)
-function toLowHighRange(windowWidth: number, windowCenter: number): {
+function toLowHighRange(windowWidth: number, windowCenter: number, voiLUTFunction?: VOILUTFunctionType): {
     lower: number;
     upper: number;
 };
@@ -4609,6 +4610,8 @@ enum VOILUTFunctionType {
     // (undocumented)
     LINEAR = "LINEAR",
     // (undocumented)
+    LINEAR_EXACT = "LINEAR_EXACT",
+    // (undocumented)
     SAMPLED_SIGMOID = "SIGMOID"
 }
 

common/reviews/api/dicom-image-loader.api.md

@@ -164,8 +164,6 @@ interface DICOMLoaderIImage extends Types_2.IImage {
     totalTimeInMS?: number;
     // (undocumented)
     transferSyntaxUID?: string;
-    // (undocumented)
-    voiLUTFunction: string | undefined;
 }
 
 // @public (undocumented)

packages/core/src/RenderingEngine/StackViewport.ts

@@ -1348,9 +1348,14 @@ class StackViewport extends Viewport {
       viewport.voi = {
         windowWidth: wwToUse,
         windowCenter: wcToUse,
+        voiLUTFunction: image.voiLUTFunction,
       };
 
-      const { lower, upper } = windowLevelUtil.toLowHighRange(wwToUse, wcToUse);
+      const { lower, upper } = windowLevelUtil.toLowHighRange(
+        wwToUse,
+        wcToUse,
+        image.voiLUTFunction
+      );
       voiRange = { lower, upper };
     } else {
       const { lower, upper } = voiRange;
@@ -1363,6 +1368,7 @@ class StackViewport extends Viewport {
         viewport.voi = {
           windowWidth: 0,
           windowCenter: 0,
+          voiLUTFunction: image.voiLUTFunction,
         };
       }
 
@@ -2288,8 +2294,12 @@ class StackViewport extends Viewport {
       this._cpuFallbackEnabledElement.viewport.colormap
     );
 
-    const { windowCenter, windowWidth } = viewport.voi;
-    this.voiRange = windowLevelUtil.toLowHighRange(windowWidth, windowCenter);
+    const { windowCenter, windowWidth, voiLUTFunction } = viewport.voi;
+    this.voiRange = windowLevelUtil.toLowHighRange(
+      windowWidth,
+      windowCenter,
+      voiLUTFunction
+    );
 
     this._cpuFallbackEnabledElement.image = image;
     this._cpuFallbackEnabledElement.metadata = {
@@ -2521,9 +2531,13 @@ class StackViewport extends Viewport {
     if (this.voiRange && this.voiUpdatedWithSetProperties) {
       return this.globalDefaultProperties.voiRange;
     }
-    const { windowCenter, windowWidth } = image;
+    const { windowCenter, windowWidth, voiLUTFunction } = image;
 
-    let voiRange = this._getVOIRangeFromWindowLevel(windowWidth, windowCenter);
+    let voiRange = this._getVOIRangeFromWindowLevel(
+      windowWidth,
+      windowCenter,
+      voiLUTFunction
+    );
 
     // Get the range for the PT since if it is prescaled
     // we set a default range of 0-5
@@ -2558,7 +2572,8 @@ class StackViewport extends Viewport {
 
   private _getVOIRangeFromWindowLevel(
     windowWidth: number | number[],
-    windowCenter: number | number[]
+    windowCenter: number | number[],
+    voiLUTFunction: VOILUTFunctionType = VOILUTFunctionType.LINEAR
   ): { lower: number; upper: number } | undefined {
     let center, width;
 
@@ -2572,7 +2587,7 @@ class StackViewport extends Viewport {
 
     // If center and width are defined, convert them to low-high range
     if (center !== undefined && width !== undefined) {
-      return windowLevelUtil.toLowHighRange(width, center);
+      return windowLevelUtil.toLowHighRange(width, center, voiLUTFunction);
     }
   }
 
@@ -2949,9 +2964,13 @@ class StackViewport extends Viewport {
   };
 
   private _getVOIRangeForCurrentImage() {
-    const { windowCenter, windowWidth } = this.csImage;
+    const { windowCenter, windowWidth, voiLUTFunction } = this.csImage;
 
-    return this._getVOIRangeFromWindowLevel(windowWidth, windowCenter);
+    return this._getVOIRangeFromWindowLevel(
+      windowWidth,
+      windowCenter,
+      voiLUTFunction
+    );
   }
 
   private _getValidVOILUTFunction(

packages/core/src/RenderingEngine/helpers/cpuFallback/rendering/computeAutoVoi.ts

@@ -23,6 +23,7 @@ export default function computeAutoVoi(
     viewport.voi = {
       windowWidth: ww,
       windowCenter: wc,
+      voiLUTFunction: image.voiLUTFunction,
     };
   } else {
     viewport.voi.windowWidth = ww;

packages/core/src/RenderingEngine/helpers/cpuFallback/rendering/createViewport.ts

@@ -3,6 +3,7 @@ import type {
   CPUFallbackViewportDisplayedArea,
   CPUFallbackViewport,
 } from '../../../../types';
+import { VOILUTFunctionType } from '../../../../enums';
 
 // eslint-disable-next-line valid-jsdoc
 /**
@@ -47,6 +48,7 @@ export default function createViewport(): CPUFallbackViewport {
     voi: {
       windowWidth: undefined,
       windowCenter: undefined,
+      voiLUTFunction: VOILUTFunctionType.LINEAR,
     },
     invert: false,
     pixelReplication: false,

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

@@ -81,11 +81,12 @@ function handlePreScaledVolume(imageVolume: IImageVolume, voi: VOIRange) {
 function getVOIFromMetadata(imageVolume: IImageVolume): VOIRange | undefined {
   const { imageIds, metadata } = imageVolume;
   let voi;
-  if (imageIds.length) {
+  if (imageIds?.length) {
     const imageIdIndex = Math.floor(imageIds.length / 2);
     const imageId = imageIds[imageIdIndex];
     const voiLutModule = metaData.get('voiLutModule', imageId);
-    if (voiLutModule?.windowWidth && voiLutModule.windowCenter) {
+    if (voiLutModule && voiLutModule.windowWidth && voiLutModule.windowCenter) {
+      voi.voiLUTFunction = voiLutModule.voiLUTFunction;
       const { windowWidth, windowCenter } = voiLutModule;
       const width = Array.isArray(windowWidth) ? windowWidth[0] : windowWidth;
       const center = Array.isArray(windowCenter)
@@ -104,7 +105,8 @@ function getVOIFromMetadata(imageVolume: IImageVolume): VOIRange | undefined {
   if (voi && (voi.windowWidth !== 0 || voi.windowCenter !== 0)) {
     const { lower, upper } = windowLevel.toLowHighRange(
       Number(voi.windowWidth),
-      Number(voi.windowCenter)
+      Number(voi.windowCenter),
+      voi.voiLUTFunction
     );
     return { lower, upper };
   }

packages/core/src/enums/VOILUTFunctionType.ts

@@ -4,7 +4,7 @@
 enum VOILUTFunctionType {
   LINEAR = 'LINEAR',
   SAMPLED_SIGMOID = 'SIGMOID', // SIGMOID is sampled in 1024 even steps so we call it SAMPLED_SIGMOID
-  // EXACT_LINEAR = 'EXACT_LINEAR', TODO: Add EXACT_LINEAR option from DICOM NEMA
+  LINEAR_EXACT = 'LINEAR_EXACT',
 }
 
 export default VOILUTFunctionType;

packages/core/src/types/CPUFallbackViewport.ts

@@ -1,6 +1,7 @@
 import type CPUFallbackViewportDisplayedArea from './CPUFallbackViewportDisplayedArea';
 import type CPUFallbackColormap from './CPUFallbackColormap';
 import type CPUFallbackLUT from './CPUFallbackLUT';
+import type VOILUTFunctionType from '../enums/VOILUTFunctionType';
 
 interface CPUFallbackViewport {
   scale?: number;
@@ -13,6 +14,7 @@ interface CPUFallbackViewport {
   voi?: {
     windowWidth: number;
     windowCenter: number;
+    voiLUTFunction: VOILUTFunctionType;
   };
   invert?: boolean;
   pixelReplication?: boolean;

packages/core/src/types/IImage.ts

@@ -3,7 +3,7 @@ import type {
   PixelDataTypedArray,
   PixelDataTypedArrayString,
 } from './PixelDataTypedArray';
-import type { ImageQualityStatus } from '../enums';
+import type { ImageQualityStatus, VOILUTFunctionType } from '../enums';
 import type IImageCalibration from './IImageCalibration';
 import type RGB from './RGB';
 import type IImageFrame from './IImageFrame';
@@ -59,7 +59,7 @@ interface IImage {
   /** windowWidth from metadata */
   windowWidth: number[] | number;
   /** voiLUTFunction from metadata */
-  voiLUTFunction: string;
+  voiLUTFunction: VOILUTFunctionType;
   /** function that returns the pixelData as an array */
   getPixelData: () => PixelDataTypedArray;
   getCanvas: () => HTMLCanvasElement;

packages/core/src/utilities/createSigmoidRGBTransferFunction.ts

@@ -2,6 +2,7 @@ import vtkColorTransferFunction from '@kitware/vtk.js/Rendering/Core/ColorTransf
 import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
 import type { VOIRange } from '../types/voi';
 import * as windowLevelUtil from './windowLevel';
+import { logit } from './logit';
 
 /**
  * A utility that can be used to generate an Sigmoid RgbTransferFunction.
@@ -24,29 +25,13 @@ import * as windowLevelUtil from './windowLevel';
  */
 export default function createSigmoidRGBTransferFunction(
   voiRange: VOIRange,
-  approximationNodes: number = 1024 // humans can precieve no more than 900 shades of gray doi: 10.1007/s10278-006-1052-3
+  approximationNodes: number = 1024 // humans can perceive no more than 900 shades of gray doi: 10.1007/s10278-006-1052-3
 ): vtkColorTransferFunction {
   const { windowWidth, windowCenter } = windowLevelUtil.toWindowLevel(
     voiRange.lower,
     voiRange.upper
   );
 
-  // Function is defined by dicom spec
-  // https://dicom.nema.org/medical/dicom/2018b/output/chtml/part03/sect_C.11.2.html
-  const sigmoid = (x: number, wc: number, ww: number): number => {
-    return 1 / (1 + Math.exp((-4 * (x - wc)) / ww));
-  };
-
-  // This function is the analytical inverse of the dicom spec sigmoid function
-  // for values y = [0, 1] exclusive. We use this to perform better sampling of
-  // points for the LUT as some images can have 2^16 unique values. This method
-  // can be deprecated if vtk supports LUTFunctions rather than look up tables
-  // or if vtk supports logistic scale. It currently only supports linear and
-  // log10 scaling which can be set on the vtkColorTransferFunction
-  const logit = (y: number, wc: number, ww: number): number => {
-    return wc - (ww / 4) * Math.log((1 - y) / y);
-  };
-
   // we slice out the first and last value to avoid 0 and 1 Infinity values
   const range: number[] = Array.from(
     { length: approximationNodes },

packages/core/src/utilities/logit.ts

@@ -0,0 +1,9 @@
+// This function is the analytical inverse of the dicom spec sigmoid function
+// for values y = [0, 1] exclusive. We use this to perform better sampling of
+// points for the LUT as some images can have 2^16 unique values. This method
+// can be deprecated if vtk supports LUTFunctions rather than look up tables
+// or if vtk supports logistic scale. It currently only supports linear and
+// log10 scaling which can be set on the vtkColorTransferFunction
+export const logit = (y: number, wc: number, ww: number): number => {
+  return wc - (ww / 4) * Math.log((1 - y) / y);
+};

packages/core/src/utilities/windowLevel.ts

@@ -1,3 +1,6 @@
+import VOILUTFunctionType from '../enums/VOILUTFunctionType';
+import { logit } from './logit';
+
 /**
  * Given a low and high window level, return the window width and window center
  * Formulas from note 4 in
@@ -20,31 +23,65 @@ function toWindowLevel(
 
   return { windowWidth, windowCenter };
 }
+
 /**
  * Given a window width and center, return the lower and upper bounds of the window.
- * The formulas for the calculation are specified in the DICOM standard:
- * {@link https://dicom.nema.org/medical/dicom/current/output/html/part03.html#sect_C.11.2.1.2.1}
+ * The calculation depends on the VOI LUT Function:
+ *
+ * LINEAR (default):
+ * - Uses the DICOM standard formula from C.11.2.1.2.1:
+ *   if x <= c - 0.5 - (w-1)/2 => lower bound
+ *   if x > c - 0.5 + (w-1)/2 => upper bound
  *
- * The window transformation is defined by:
- * - if `x <= c - 0.5 - (w-1)/2`, then `y = ymin`
- * - if `x > c - 0.5 + (w-1)/2`, then `y = ymax`
- * - else `y = ((x - (c - 0.5))/(w-1) + 0.5) * (ymax - ymin) + ymin`
+ * LINEAR_EXACT (C.11.2.1.3.2):
+ * - Uses:
+ *   lower = c - w/2
+ *   upper = c + w/2
  *
- * @param windowWidth - The width of the window in HU
+ * SIGMOID (C.11.2.1.3.1):
+ * - The sigmoid does not define linear "bounds" in the same way. It's asymptotic.
+ * - We define approximate bounds by choosing output thresholds (e.g., 1% and 99%)
+ *   and solving for input x:
+ *   y = 1/(1 + exp(-4*(x - c)/w))
+ *   For y=0.01 and y=0.99, solve for x.
+ *
+ * @param windowWidth - The width of the window
  * @param windowCenter - The center of the window
+ * @param voiLUTFunction - 'LINEAR' | 'LINEAR_EXACT' | 'SIGMOID'
  * @returns An object containing the lower and upper bounds of the window
  */
 function toLowHighRange(
   windowWidth: number,
-  windowCenter: number
+  windowCenter: number,
+  voiLUTFunction: VOILUTFunctionType = VOILUTFunctionType.LINEAR
 ): {
   lower: number;
   upper: number;
 } {
-  const lower = windowCenter - 0.5 - (windowWidth - 1) / 2;
-  const upper = windowCenter - 0.5 + (windowWidth - 1) / 2;
-
-  return { lower, upper };
+  if (voiLUTFunction === VOILUTFunctionType.LINEAR) {
+    // From C.11.2.1.2.1 (linear function)
+    return {
+      lower: windowCenter - 0.5 - (windowWidth - 1) / 2,
+      upper: windowCenter - 0.5 + (windowWidth - 1) / 2,
+    };
+  } else if (voiLUTFunction === VOILUTFunctionType.LINEAR_EXACT) {
+    // From C.11.2.1.3.2 (linear exact function)
+    return {
+      lower: windowCenter - windowWidth / 2,
+      upper: windowCenter + windowWidth / 2,
+    };
+  } else if (voiLUTFunction === VOILUTFunctionType.SAMPLED_SIGMOID) {
+    // From C.11.2.1.3.1 (sigmoid function)
+    // Sigmoid: y = 1 / (1 + exp(-4*(x - c)/w))
+    const xLower = logit(0.01, windowCenter, windowWidth);
+    const xUpper = logit(0.99, windowCenter, windowWidth);
+    return {
+      lower: xLower,
+      upper: xUpper,
+    };
+  } else {
+    throw new Error('Invalid VOI LUT function');
+  }
 }
 
 export { toWindowLevel, toLowHighRange };

packages/dicomImageLoader/src/imageLoader/wadors/metaData/metaDataProvider.ts

@@ -262,9 +262,10 @@ function metaDataProvider(type, imageId) {
 
   if (type === MetadataModules.VOI_LUT) {
     return {
-      // TODO VOT LUT Sequence
       windowCenter: getNumberValues(metaData['00281050'], 1),
       windowWidth: getNumberValues(metaData['00281051'], 1),
+      voiLUTFunction: getValue(metaData['00281056']),
+      // TODO VOT LUT Sequence
     };
   }
 

packages/dicomImageLoader/src/imageLoader/wadouri/metaData/metaDataProvider.ts

@@ -213,6 +213,7 @@ export function metadataForDataset(
         modalityLUTOutputPixelRepresentation,
         dataSet.elements.x00283010
       ),
+      voiLUTFunction: dataSet.string('x00281056'),
     };
   }
 

packages/dicomImageLoader/src/types/DICOMLoaderIImage.ts

@@ -7,6 +7,5 @@ export interface DICOMLoaderIImage extends Types.IImage {
   totalTimeInMS?: number;
   data?: DataSet;
   imageFrame?: Types.IImageFrame;
-  voiLUTFunction: string | undefined;
   transferSyntaxUID?: string;
 }