fix: 🐛 Switch to orienting the volume actor differently (OHIF#70)

JamesAPetts · web-flow · commit 3f0eaec33c37 · 2019-11-01T14:36:42.000Z
* fix: 🐛 Switch to orienting the volume actor differently

Switch to orienting the volume actor differently depending on its
acquisition direction, rather than filling up the volume differently.

* Address Steve's comments on the PR.
diff --git a/src/VTKViewport/View2D.js b/src/VTKViewport/View2D.js
@@ -315,6 +315,8 @@ export default class View2D extends Component {
       istyle.setViewport(currentViewport);
     }
 
+    istyle.getVolumeMapper();
+
     if (istyle.getVolumeMapper() !== volumes[0]) {
       if (slabThickness && istyle.setSlabThickness) {
         istyle.setSlabThickness(slabThickness);
diff --git a/src/VTKViewport/vtkInteractorStyleMPRSlice.js b/src/VTKViewport/vtkInteractorStyleMPRSlice.js
@@ -116,14 +116,7 @@ function vtkInteractorStyleMPRSlice(publicAPI, model) {
     const _viewUp = [...viewUp];
 
     if (model.volumeMapper) {
-      let mapper = model.volumeMapper;
-      // get the mapper if the model is actually the actor, not the mapper
-      if (!model.volumeMapper.getInputData && model.volumeMapper.getMapper) {
-        mapper = model.volumeMapper.getMapper();
-      }
-      let volumeCoordinateSpace = vec9toMat3(
-        mapper.getInputData().getDirection()
-      );
+      let volumeCoordinateSpace = vec9toMat3([1, 0, 0, 0, 1, 0, 0, 0, 1]);
       // Transpose the volume's coordinate space to create a transformation matrix
       vtkMath.transpose3x3(volumeCoordinateSpace, volumeCoordinateSpace);
 
@@ -142,14 +135,8 @@ function vtkInteractorStyleMPRSlice(publicAPI, model) {
 
     if (model.volumeMapper) {
       vtkMath.normalize(_normal);
-      let mapper = model.volumeMapper;
-      // get the mapper if the model is actually the actor, not the mapper
-      if (!model.volumeMapper.getInputData && model.volumeMapper.getMapper) {
-        mapper = model.volumeMapper.getMapper();
-      }
-      let volumeCoordinateSpace = vec9toMat3(
-        mapper.getInputData().getDirection()
-      );
+
+      let volumeCoordinateSpace = vec9toMat3([1, 0, 0, 0, 1, 0, 0, 0, 1]);
       // Transpose the volume's coordinate space to create a transformation matrix
       vtkMath.transpose3x3(volumeCoordinateSpace, volumeCoordinateSpace);
       // Convert the provided normal into the volume's space
diff --git a/src/lib/data/insertSlice.js b/src/lib/data/insertSlice.js
@@ -2,15 +2,13 @@
  *
  * @param {Object} imageData - The vtkImageData
  * @param {*} sliceIndex - The index of the slice you are inserting.
- * @param {*} acquistionDirection - The acquistion direction of the slice.
  * @param {*} image The cornerstone image to pull pixel data data from.
  * @param {*} modality The modality of the image.
  * @param {*} modalitySpecificScalingParameters Specific scaling paramaters for this modality. E.g. Patient weight.
  */
 export default function insertSlice(
   imageData,
   sliceIndex,
-  acquistionDirection,
   image,
   modality,
   modalitySpecificScalingParameters
@@ -24,163 +22,6 @@ export default function insertSlice(
     modalitySpecificScalingParameters
   );
 
-  const vtkImageDimensions = imageData.getDimensions();
-
-  let minAndMax;
-
-  switch (acquistionDirection) {
-    case 'coronal':
-      minAndMax = insertCoronalSlice(
-        image,
-        sliceIndex,
-        vtkImageDimensions,
-        scalarData,
-        scalingFunction
-      );
-      break;
-    case 'sagittal':
-      minAndMax = insertSagittalSlice(
-        image,
-        sliceIndex,
-        vtkImageDimensions,
-        scalarData,
-        scalingFunction
-      );
-      break;
-    case 'axial':
-      minAndMax = insertAxialSlice(
-        image,
-        sliceIndex,
-        scalarData,
-        scalingFunction
-      );
-      break;
-  }
-
-  return minAndMax;
-}
-
-/**
- *
- * @param {object} image The cornerstone image to pull pixel data data from.
- * @param {number} xIndex The x index of axially oriented vtk volume to put the sagital slice.
- * @param {number[]} vtkImageDimensions The dimensions of the axially oriented vtk volume.
- * @param {number[]} scalarData The data array for the axially oriented vtk volume.
- * @param {function} scalingFunction The modality specific scaling function.
- *
- * @returns {object} The min and max pixel values in the inserted slice.
- */
-function insertSagittalSlice(
-  image,
-  xIndex,
-  vtkImageDimensions,
-  scalarData,
-  scalingFunction
-) {
-  const pixels = image.getPixelData();
-  const { rows, columns } = image;
-
-  let pixelIndex = 0;
-  let max = scalingFunction(pixels[pixelIndex]);
-  let min = max;
-
-  const vtkImageDimensionsX = vtkImageDimensions[0];
-  const vtkImageDimensionsY = vtkImageDimensions[1];
-  const vtkImageDimensionsZ = vtkImageDimensions[2];
-
-  const axialSliceLength = vtkImageDimensionsX * vtkImageDimensionsY;
-
-  for (let row = 0; row < rows; row++) {
-    for (let col = 0; col < columns; col++) {
-      const yPos = vtkImageDimensionsY - col;
-      const zPos = vtkImageDimensionsZ - row;
-
-      const destIdx =
-        zPos * axialSliceLength + yPos * vtkImageDimensionsX + xIndex;
-
-      const pixel = pixels[pixelIndex];
-      const pixelValue = scalingFunction(pixel);
-
-      if (pixelValue > max) {
-        max = pixelValue;
-      } else if (pixelValue < min) {
-        min = pixelValue;
-      }
-
-      scalarData[destIdx] = pixelValue;
-      pixelIndex++;
-    }
-  }
-
-  return { min, max };
-}
-
-/**
- *
- * @param {object} image The cornerstone image to pull pixel data data from.
- * @param {number} yIndex The y index of axially oriented vtk volume to put the coronal slice.
- * @param {number[]} vtkImageDimensions The dimensions of the axially oriented vtk volume.
- * @param {number[]} scalarData The data array for the axially oriented vtk volume.
- * @param {function} scalingFunction The modality specific scaling function.
- *
- * @returns {object} The min and max pixel values in the inserted slice.
- */
-function insertCoronalSlice(
-  image,
-  yIndex,
-  vtkImageDimensions,
-  scalarData,
-  scalingFunction
-) {
-  const pixels = image.getPixelData();
-  const { rows, columns } = image;
-
-  let pixelIndex = 0;
-  let max = scalingFunction(pixels[pixelIndex]);
-  let min = max;
-
-  const vtkImageDimensionsX = vtkImageDimensions[0];
-  const vtkImageDimensionsY = vtkImageDimensions[1];
-  const vtkImageDimensionsZ = vtkImageDimensions[2];
-
-  const axialSliceLength = vtkImageDimensionsX * vtkImageDimensionsY;
-
-  for (let row = 0; row < rows; row++) {
-    for (let col = 0; col < columns; col++) {
-      const xPos = col;
-      const yPos = yIndex;
-      const zPos = vtkImageDimensionsZ - row;
-
-      const destIdx =
-        zPos * axialSliceLength + yPos * vtkImageDimensionsX + xPos;
-
-      const pixel = pixels[pixelIndex];
-      const pixelValue = scalingFunction(pixel);
-
-      if (pixelValue > max) {
-        max = pixelValue;
-      } else if (pixelValue < min) {
-        min = pixelValue;
-      }
-
-      scalarData[destIdx] = pixelValue;
-      pixelIndex++;
-    }
-  }
-
-  return { min, max };
-}
-
-/**
- *
- * @param {object} image The cornerstone image to pull pixel data data from.
- * @param {number} zIndex The z index of axially oriented vtk volume to put the axial slice.
- * @param {number[]} scalarData The data array for the axially oriented vtk volume.
- * @param {function} scalingFunction The modality specific scaling function.
- *
- * @returns {object} The min and max pixel values in the inserted slice.
- */
-function insertAxialSlice(image, zIndex, scalarData, scalingFunction) {
   const pixels = image.getPixelData();
   const sliceLength = pixels.length;
 
@@ -189,7 +30,7 @@ function insertAxialSlice(image, zIndex, scalarData, scalingFunction) {
   let min = max;
 
   for (let pixelIndex = 0; pixelIndex < pixels.length; pixelIndex++) {
-    const destIdx = pixelIndex + zIndex * sliceLength;
+    const destIdx = pixelIndex + sliceIndex * sliceLength;
     const pixel = pixels[pixelIndex];
     const pixelValue = scalingFunction(pixel);
 
diff --git a/src/lib/getImageData.js b/src/lib/getImageData.js
@@ -87,27 +87,10 @@ export default function getImageData(imageIds, displaySetInstanceUid) {
     scanAxisNormal.z,
   ];
 
-  const acquistionDirection = _getAcquisitionDirection(scanAxisNormal);
+  imageData.setDimensions(xVoxels, yVoxels, zVoxels);
+  imageData.setSpacing(xSpacing, ySpacing, zSpacing);
 
-  console.log(rowCosineVec);
-  console.log(colCosineVec);
-  console.log(scanAxisNormal);
-  console.log(acquistionDirection);
-
-  switch (acquistionDirection) {
-    case 'sagittal':
-      imageData.setDimensions(zVoxels, xVoxels, yVoxels);
-      imageData.setSpacing(zSpacing, xSpacing, ySpacing);
-      break;
-    case 'coronal':
-      imageData.setDimensions(xVoxels, zVoxels, yVoxels);
-      imageData.setSpacing(xSpacing, zSpacing, ySpacing);
-      break;
-    case 'axial':
-      imageData.setDimensions(xVoxels, yVoxels, zVoxels);
-      imageData.setSpacing(xSpacing, ySpacing, zSpacing);
-      break;
-  }
+  imageData.setDirection(direction);
 
   imageData.setOrigin(...origin);
   imageData.getPointData().setScalars(scalarArray);
@@ -123,36 +106,10 @@ export default function getImageData(imageIds, displaySetInstanceUid) {
     vtkImageData: imageData,
     metaDataMap,
     sortedDatasets,
-    acquistionDirection,
     loaded: false,
   };
 
   imageDataCache.set(displaySetInstanceUid, imageDataObject);
 
   return imageDataObject;
 }
-
-const sagittal = new Vector3(1, 0, 0);
-const coronal = new Vector3(0, 1, 0);
-const axial = new Vector3(0, 0, 1);
-
-function _getAcquisitionDirection(zDirection) {
-  const zAbs = new Vector3(
-    Math.abs(zDirection.x),
-    Math.abs(zDirection.y),
-    Math.abs(zDirection.z)
-  );
-
-  // Get the direction of the acquisition.
-  const dotProducts = [
-    zAbs.dot(sagittal), // z . Sagittal
-    zAbs.dot(coronal), // z . Coronal
-    zAbs.dot(axial), // z . Axial
-  ];
-
-  const directionIndex = dotProducts.indexOf(Math.max(...dotProducts));
-
-  const acquisitionDirections = ['sagittal', 'coronal', 'axial'];
-
-  return acquisitionDirections[directionIndex];
-}
diff --git a/src/lib/loadImageData.js b/src/lib/loadImageData.js
@@ -15,7 +15,6 @@ export default function loadImageDataProgressively(imageDataObject) {
     vtkImageData,
     metaDataMap,
     sortedDatasets,
-    acquistionDirection,
   } = imageDataObject;
   const loadImagePromises = imageIds.map(cornerstone.loadAndCacheImage);
   const imageId0 = imageIds[0];
@@ -69,7 +68,6 @@ export default function loadImageDataProgressively(imageDataObject) {
       const { max, min } = insertSlice(
         vtkImageData,
         sliceIndex,
-        acquistionDirection,
         image,
         modality,
         modalitySpecificScalingParameters
@@ -114,12 +112,4 @@ export default function loadImageDataProgressively(imageDataObject) {
   });
 
   imageDataObject.insertPixelDataPromises = insertPixelDataPromises;
-
-  // TODO: Investigate progressive loading. Right now the UI gets super slow because
-  // we are rendering and decoding simultaneously. We might want to use fewer web workers
-  // for the decoding tasks.
-  //
-  // Update: Had some success with this locally. But it completely freezes up when stuck
-  // In an app like OHIF. There seems to be many small calls made to various vtk functions.
-  // Putting it aside for now, but a progressive loader still shows promise.
 }

Original file line number	Diff line number	Diff line change
`@@ -315,6 +315,8 @@ export default class View2D extends Component {`
`315`	`315`	`istyle.setViewport(currentViewport);`
`316`	`316`	`}`
`317`	`317`
	`318`	`+ istyle.getVolumeMapper();`
	`319`	`+`
`318`	`320`	`if (istyle.getVolumeMapper() !== volumes[0]) {`
`319`	`321`	`if (slabThickness && istyle.setSlabThickness) {`
`320`	`322`	`istyle.setSlabThickness(slabThickness);`