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

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Merged
merged 2 commits into from
Nov 1, 2019
Merged

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

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2ee88e6
fix: 🐛 Switch to orienting the volume actor differently
JamesAPetts Nov 1, 2019
b9e77cb
Address Steve's comments on the PR.
JamesAPetts Nov 1, 2019
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2 changes: 2 additions & 0 deletions src/VTKViewport/View2D.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
19 changes: 3 additions & 16 deletions src/VTKViewport/vtkInteractorStyleMPRSlice.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand All @@ -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
Expand Down
161 changes: 1 addition & 160 deletions src/lib/data/insertSlice.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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;

Expand All @@ -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);

Expand Down
49 changes: 3 additions & 46 deletions src/lib/getImageData.js
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Expand Up @@ -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);
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Ahhh, sooo much nicer!


imageData.setOrigin(...origin);
imageData.getPointData().setScalars(scalarArray);
Expand All @@ -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];
}
10 changes: 0 additions & 10 deletions src/lib/loadImageData.js
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Expand Up @@ -15,7 +15,6 @@ export default function loadImageDataProgressively(imageDataObject) {
vtkImageData,
metaDataMap,
sortedDatasets,
acquistionDirection,
} = imageDataObject;
const loadImagePromises = imageIds.map(cornerstone.loadAndCacheImage);
const imageId0 = imageIds[0];
Expand Down Expand Up @@ -69,7 +68,6 @@ export default function loadImageDataProgressively(imageDataObject) {
const { max, min } = insertSlice(
vtkImageData,
sliceIndex,
acquistionDirection,
image,
modality,
modalitySpecificScalingParameters
Expand Down Expand Up @@ -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.
}