@cornerstonejs/adapters 0.1.5 → 0.2.1

package/src/adapters/Cornerstone3D/Probe.js

@@ -1,106 +0,0 @@
-import { utilities } from "dcmjs";
-import CORNERSTONE_3D_TAG from "./cornerstone3DTag";
-import MeasurementReport from "./MeasurementReport";
-
-const { Point: TID300Point } = utilities.TID300;
-
-const PROBE = "Probe";
-const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${PROBE}`;
-
-class Probe {
-    static getMeasurementData(
-        MeasurementGroup,
-        sopInstanceUIDToImageIdMap,
-        imageToWorldCoords,
-        metadata
-    ) {
-        const { defaultState, SCOORDGroup, ReferencedFrameNumber } =
-            MeasurementReport.getSetupMeasurementData(
-                MeasurementGroup,
-                sopInstanceUIDToImageIdMap,
-                metadata,
-                Probe.toolType
-            );
-
-        const referencedImageId =
-            defaultState.annotation.metadata.referencedImageId;
-
-        const { GraphicData } = SCOORDGroup;
-
-        const worldCoords = [];
-        for (let i = 0; i < GraphicData.length; i += 2) {
-            const point = imageToWorldCoords(referencedImageId, [
-                GraphicData[i],
-                GraphicData[i + 1]
-            ]);
-            worldCoords.push(point);
-        }
-
-        const state = defaultState;
-
-        state.annotation.data = {
-            handles: {
-                points: worldCoords,
-                activeHandleIndex: null,
-                textBox: {
-                    hasMoved: false
-                }
-            },
-            frameNumber: ReferencedFrameNumber
-        };
-
-        return state;
-    }
-
-    static getTID300RepresentationArguments(tool, worldToImageCoords) {
-        const { data, metadata } = tool;
-        let { finding, findingSites } = tool;
-        const { referencedImageId } = metadata;
-
-        if (!referencedImageId) {
-            throw new Error(
-                "Probe.getTID300RepresentationArguments: referencedImageId is not defined"
-            );
-        }
-
-        const { points } = data.handles;
-
-        const pointsImage = points.map(point => {
-            const pointImage = worldToImageCoords(referencedImageId, point);
-            return {
-                x: pointImage[0],
-                y: pointImage[1]
-            };
-        });
-
-        const TID300RepresentationArguments = {
-            points: pointsImage,
-            trackingIdentifierTextValue,
-            findingSites: findingSites || [],
-            finding
-        };
-
-        return TID300RepresentationArguments;
-    }
-}
-
-Probe.toolType = PROBE;
-Probe.utilityToolType = PROBE;
-Probe.TID300Representation = TID300Point;
-Probe.isValidCornerstoneTrackingIdentifier = TrackingIdentifier => {
-    if (!TrackingIdentifier.includes(":")) {
-        return false;
-    }
-
-    const [cornerstone3DTag, toolType] = TrackingIdentifier.split(":");
-
-    if (cornerstone3DTag !== CORNERSTONE_3D_TAG) {
-        return false;
-    }
-
-    return toolType === PROBE;
-};
-
-MeasurementReport.registerTool(Probe);
-
-export default Probe;

package/src/adapters/Cornerstone3D/cornerstone3DTag.js

@@ -1 +0,0 @@
-export default "Cornerstone3DTools@^0.1.0";

package/src/adapters/Cornerstone3D/index.js

@@ -1,24 +0,0 @@
-import MeasurementReport from "./MeasurementReport";
-import CodeScheme from "./CodingScheme";
-import CORNERSTONE_3D_TAG from "./cornerstone3DTag";
-
-import ArrowAnnotate from "./ArrowAnnotate";
-import Bidirectional from "./Bidirectional";
-import EllipticalROI from "./EllipticalROI";
-import Length from "./Length";
-import PlanarFreehandROI from "./PlanarFreehandROI";
-import Probe from "./Probe";
-
-const Cornerstone3D = {
-    Bidirectional,
-    Length,
-    EllipticalROI,
-    ArrowAnnotate,
-    Probe,
-    PlanarFreehandROI,
-    MeasurementReport,
-    CodeScheme,
-    CORNERSTONE_3D_TAG
-};
-
-export default Cornerstone3D;

package/src/adapters/VTKjs/Segmentation.js

@@ -1,223 +0,0 @@
-import {data} from 'dcmjs';
-
-const {Colors, BitArray} = data;
-
-// TODO: Is there a better name for this? RGBAInt?
-// Should we move it to Colors.js
-function dicomlab2RGBA(cielab) {
-    const rgba = Colors.dicomlab2RGB(cielab).map(x => Math.round(x * 255));
-    rgba.push(255);
-
-    return rgba;
-}
-
-// TODO: Copied these functions in from VTK Math so we don't need a dependency.
-// I guess we should put them somewhere
-// https://github.com/Kitware/vtk-js/blob/master/Sources/Common/Core/Math/index.js
-function cross(x, y, out) {
-    const Zx = x[1] * y[2] - x[2] * y[1];
-    const Zy = x[2] * y[0] - x[0] * y[2];
-    const Zz = x[0] * y[1] - x[1] * y[0];
-    out[0] = Zx;
-    out[1] = Zy;
-    out[2] = Zz;
-}
-
-function norm(x, n = 3) {
-    switch (n) {
-        case 1:
-            return Math.abs(x);
-        case 2:
-            return Math.sqrt(x[0] * x[0] + x[1] * x[1]);
-        case 3:
-            return Math.sqrt(x[0] * x[0] + x[1] * x[1] + x[2] * x[2]);
-        default: {
-            let sum = 0;
-            for (let i = 0; i < n; i++) {
-                sum += x[i] * x[i];
-            }
-            return Math.sqrt(sum);
-        }
-    }
-}
-
-function normalize(x) {
-    const den = norm(x);
-    if (den !== 0.0) {
-        x[0] /= den;
-        x[1] /= den;
-        x[2] /= den;
-    }
-    return den;
-}
-
-function subtract(a, b, out) {
-    out[0] = a[0] - b[0];
-    out[1] = a[1] - b[1];
-    out[2] = a[2] - b[2];
-}
-
-// TODO: This is a useful utility on its own. We should move it somewhere?
-// dcmjs.adapters.vtk.Multiframe? dcmjs.utils?
-function geometryFromFunctionalGroups(dataset, PerFrameFunctionalGroups) {
-    const geometry = {};
-    const pixelMeasures =
-        dataset.SharedFunctionalGroupsSequence.PixelMeasuresSequence;
-    const planeOrientation =
-        dataset.SharedFunctionalGroupsSequence.PlaneOrientationSequence;
-
-    // Find the origin of the volume from the PerFrameFunctionalGroups' ImagePositionPatient values
-    //
-    // TODO: assumes sorted frames. This should read the ImagePositionPatient from each frame and
-    // sort them to obtain the first and last position along the acquisition axis.
-    const firstFunctionalGroup = PerFrameFunctionalGroups[0];
-    const lastFunctionalGroup =
-        PerFrameFunctionalGroups[PerFrameFunctionalGroups.length - 1];
-    const firstPosition =
-        firstFunctionalGroup.PlanePositionSequence.ImagePositionPatient.map(
-            Number
-        );
-    const lastPosition =
-        lastFunctionalGroup.PlanePositionSequence.ImagePositionPatient.map(
-            Number
-        );
-
-    geometry.origin = firstPosition;
-
-    // NB: DICOM PixelSpacing is defined as Row then Column,
-    // unlike ImageOrientationPatient
-    geometry.spacing = [
-        pixelMeasures.PixelSpacing[1],
-        pixelMeasures.PixelSpacing[0],
-        pixelMeasures.SpacingBetweenSlices
-    ].map(Number);
-
-    geometry.dimensions = [
-        dataset.Columns,
-        dataset.Rows,
-        PerFrameFunctionalGroups.length
-    ].map(Number);
-
-    const orientation = planeOrientation.ImageOrientationPatient.map(Number);
-    const columnStepToPatient = orientation.slice(0, 3);
-    const rowStepToPatient = orientation.slice(3, 6);
-
-    geometry.planeNormal = [];
-
-    cross(columnStepToPatient, rowStepToPatient, geometry.planeNormal);
-
-    geometry.sliceStep = [];
-    subtract(lastPosition, firstPosition, geometry.sliceStep);
-    normalize(geometry.sliceStep);
-    geometry.direction = columnStepToPatient
-        .concat(rowStepToPatient)
-        .concat(geometry.sliceStep);
-
-    return geometry;
-}
-
-export default class Segmentation {
-    constructor() {}
-
-    /**
-     * Produces an array of Segments from an input DICOM Segmentation dataset
-     *
-     * Segments are returned with Geometry values that can be used to create
-     * VTK Image Data objects.
-     *
-     * @example Example usage to create VTK Volume actors from each segment:
-     *
-     * const actors = [];
-     * const segments = generateToolState(dataset);
-     * segments.forEach(segment => {
-     *   // now make actors using the segment information
-     *   const scalarArray = vtk.Common.Core.vtkDataArray.newInstance({
-     *        name: "Scalars",
-     *        numberOfComponents: 1,
-     *        values: segment.pixelData,
-     *    });
-     *
-     *    const imageData = vtk.Common.DataModel.vtkImageData.newInstance();
-     *    imageData.getPointData().setScalars(scalarArray);
-     *    imageData.setDimensions(geometry.dimensions);
-     *    imageData.setSpacing(geometry.spacing);
-     *    imageData.setOrigin(geometry.origin);
-     *    imageData.setDirection(geometry.direction);
-     *
-     *    const mapper = vtk.Rendering.Core.vtkVolumeMapper.newInstance();
-     *    mapper.setInputData(imageData);
-     *    mapper.setSampleDistance(2.);
-     *
-     *    const actor = vtk.Rendering.Core.vtkVolume.newInstance();
-     *    actor.setMapper(mapper);
-     *
-     *    actors.push(actor);
-     * });
-     *
-     * @param dataset
-     * @return {{}}
-     */
-    static generateSegments(dataset) {
-        if (dataset.SegmentSequence.constructor.name !== "Array") {
-            dataset.SegmentSequence = [dataset.SegmentSequence];
-        }
-
-        dataset.SegmentSequence.forEach(segment => {
-            // TODO: other interesting fields could be extracted from the segment
-            // TODO: Read SegmentsOverlay field
-            // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.20.2.html
-
-            // TODO: Looks like vtkColor only wants RGB in 0-1 values.
-            // Why was this example converting to RGBA with 0-255 values?
-            const color = dicomlab2RGBA(segment.RecommendedDisplayCIELabValue);
-
-            segments[segment.SegmentNumber] = {
-                color,
-                functionalGroups: [],
-                offset: null,
-                size: null,
-                pixelData: null
-            };
-        });
-
-        // make a list of functional groups per segment
-        dataset.PerFrameFunctionalGroupsSequence.forEach(functionalGroup => {
-            const segmentNumber =
-                functionalGroup.SegmentIdentificationSequence
-                    .ReferencedSegmentNumber;
-
-            segments[segmentNumber].functionalGroups.push(functionalGroup);
-        });
-
-        // determine per-segment index into the pixel data
-        // TODO: only handles one-bit-per pixel
-        const frameSize = Math.ceil((dataset.Rows * dataset.Columns) / 8);
-        let nextOffset = 0;
-
-        Object.keys(segments).forEach(segmentNumber => {
-            const segment = segments[segmentNumber];
-
-            segment.numberOfFrames = segment.functionalGroups.length;
-            segment.size = segment.numberOfFrames * frameSize;
-            segment.offset = nextOffset;
-
-            nextOffset = segment.offset + segment.size;
-
-            const packedSegment = dataset.PixelData.slice(
-                segment.offset,
-                nextOffset
-            );
-
-            segment.pixelData = BitArray.unpack(packedSegment);
-
-            const geometry = geometryFromFunctionalGroups(
-                dataset,
-                segment.functionalGroups
-            );
-
-            segment.geometry = geometry;
-        });
-
-        return segments;
-    }
-}

package/src/adapters/VTKjs/index.js

@@ -1,7 +0,0 @@
-import Segmentation from "./Segmentation.js";
-
-const VTKjs = {
-    Segmentation
-};
-
-export default VTKjs;

package/src/adapters/helpers.js

@@ -1,19 +0,0 @@
-const toArray = function (x) {
-    return Array.isArray(x) ? x : [x];
-};
-
-const codeMeaningEquals = codeMeaningName => {
-    return contentItem => {
-        return (
-            contentItem.ConceptNameCodeSequence.CodeMeaning === codeMeaningName
-        );
-    };
-};
-
-const graphicTypeEquals = graphicType => {
-    return contentItem => {
-        return contentItem && contentItem.GraphicType === graphicType;
-    };
-};
-
-export { toArray, codeMeaningEquals, graphicTypeEquals };

package/src/adapters/index.js

@@ -1,11 +0,0 @@
-import Cornerstone from "./Cornerstone";
-import Cornerstone3D from "./Cornerstone3D";
-import VTKjs from "./VTKjs";
-
-const adapters = {
-    Cornerstone,
-    Cornerstone3D,
-    VTKjs,
-};
-
-export default adapters;