@cornerstonejs/adapters 2.0.0-beta.8 → 2.0.1

package/dist/esm/adapters/Cornerstone/Segmentation_4X.js

@@ -0,0 +1,1152 @@
+import { asyncToGenerator as _asyncToGenerator, regeneratorRuntime as _regeneratorRuntime, toConsumableArray as _toConsumableArray, createForOfIteratorHelper as _createForOfIteratorHelper, slicedToArray as _slicedToArray } from '../../_virtual/_rollupPluginBabelHelpers.js';
+import { utilities, data, normalizers, derivations, log } from 'dcmjs';
+import ndarray from 'ndarray';
+import getDatasetsFromImages from '../helpers/getDatasetsFromImages.js';
+import checkOrientation from '../helpers/checkOrientation.js';
+import compareArrays from '../helpers/compareArrays.js';
+import Events from '../enums/Events.js';
+
+var _utilities$orientatio = utilities.orientation,
+  rotateDirectionCosinesInPlane = _utilities$orientatio.rotateDirectionCosinesInPlane,
+  flipIOP = _utilities$orientatio.flipImageOrientationPatient,
+  flipMatrix2D = _utilities$orientatio.flipMatrix2D,
+  rotateMatrix902D = _utilities$orientatio.rotateMatrix902D;
+var BitArray = data.BitArray,
+  DicomMessage = data.DicomMessage,
+  DicomMetaDictionary = data.DicomMetaDictionary;
+var Normalizer = normalizers.Normalizer;
+var SegmentationDerivation = derivations.Segmentation;
+var _utilities$compressio = utilities.compression,
+  encode = _utilities$compressio.encode,
+  decode = _utilities$compressio.decode;
+
+/**
+ *
+ * @typedef {Object} BrushData
+ * @property {Object} toolState - The cornerstoneTools global toolState.
+ * @property {Object[]} segments - The cornerstoneTools segment metadata that corresponds to the
+ *                                 seriesInstanceUid.
+ */
+var generateSegmentationDefaultOptions = {
+  includeSliceSpacing: true,
+  rleEncode: false
+};
+
+/**
+ * generateSegmentation - Generates cornerstoneTools brush data, given a stack of
+ * imageIds, images and the cornerstoneTools brushData.
+ *
+ * @param  {object[]} images An array of cornerstone images that contain the source
+ *                           data under `image.data.byteArray.buffer`.
+ * @param  {Object|Object[]} inputLabelmaps3D The cornerstone `Labelmap3D` object, or an array of objects.
+ * @param  {Object} userOptions Options to pass to the segmentation derivation and `fillSegmentation`.
+ * @returns {Blob}
+ */
+function generateSegmentation(images, inputLabelmaps3D) {
+  var userOptions = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
+  var isMultiframe = images[0].imageId.includes("?frame");
+  var segmentation = _createSegFromImages(images, isMultiframe, userOptions);
+  return fillSegmentation(segmentation, inputLabelmaps3D, userOptions);
+}
+
+/**
+ * Fills a given segmentation object with data from the input labelmaps3D
+ *
+ * @param segmentation - The segmentation object to be filled.
+ * @param inputLabelmaps3D - An array of 3D labelmaps, or a single 3D labelmap.
+ * @param userOptions - Optional configuration settings. Will override the default options.
+ *
+ * @returns {object} The filled segmentation object.
+ */
+function fillSegmentation(segmentation, inputLabelmaps3D) {
+  var userOptions = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
+  var options = Object.assign({}, generateSegmentationDefaultOptions, userOptions);
+
+  // Use another variable so we don't redefine labelmaps3D.
+  var labelmaps3D = Array.isArray(inputLabelmaps3D) ? inputLabelmaps3D : [inputLabelmaps3D];
+  var numberOfFrames = 0;
+  var referencedFramesPerLabelmap = [];
+  var _loop = function _loop() {
+    var labelmap3D = labelmaps3D[labelmapIndex];
+    var labelmaps2D = labelmap3D.labelmaps2D,
+      metadata = labelmap3D.metadata;
+    var referencedFramesPerSegment = [];
+    for (var i = 1; i < metadata.length; i++) {
+      if (metadata[i]) {
+        referencedFramesPerSegment[i] = [];
+      }
+    }
+    var _loop2 = function _loop2(_i) {
+      var labelmap2D = labelmaps2D[_i];
+      if (labelmaps2D[_i]) {
+        var segmentsOnLabelmap = labelmap2D.segmentsOnLabelmap;
+        segmentsOnLabelmap.forEach(function (segmentIndex) {
+          if (segmentIndex !== 0) {
+            referencedFramesPerSegment[segmentIndex].push(_i);
+            numberOfFrames++;
+          }
+        });
+      }
+    };
+    for (var _i = 0; _i < labelmaps2D.length; _i++) {
+      _loop2(_i);
+    }
+    referencedFramesPerLabelmap[labelmapIndex] = referencedFramesPerSegment;
+  };
+  for (var labelmapIndex = 0; labelmapIndex < labelmaps3D.length; labelmapIndex++) {
+    _loop();
+  }
+  segmentation.setNumberOfFrames(numberOfFrames);
+  for (var _labelmapIndex = 0; _labelmapIndex < labelmaps3D.length; _labelmapIndex++) {
+    var referencedFramesPerSegment = referencedFramesPerLabelmap[_labelmapIndex];
+    var labelmap3D = labelmaps3D[_labelmapIndex];
+    var metadata = labelmap3D.metadata;
+    for (var segmentIndex = 1; segmentIndex < referencedFramesPerSegment.length; segmentIndex++) {
+      var referencedFrameIndicies = referencedFramesPerSegment[segmentIndex];
+      if (referencedFrameIndicies) {
+        // Frame numbers start from 1.
+        var referencedFrameNumbers = referencedFrameIndicies.map(function (element) {
+          return element + 1;
+        });
+        var segmentMetadata = metadata[segmentIndex];
+        var labelmaps = _getLabelmapsFromReferencedFrameIndicies(labelmap3D, referencedFrameIndicies);
+        segmentation.addSegmentFromLabelmap(segmentMetadata, labelmaps, segmentIndex, referencedFrameNumbers);
+      }
+    }
+  }
+  if (options.rleEncode) {
+    var rleEncodedFrames = encode(segmentation.dataset.PixelData, numberOfFrames, segmentation.dataset.Rows, segmentation.dataset.Columns);
+
+    // Must use fractional now to RLE encode, as the DICOM standard only allows BitStored && BitsAllocated
+    // to be 1 for BINARY. This is not ideal and there should be a better format for compression in this manner
+    // added to the standard.
+    segmentation.assignToDataset({
+      BitsAllocated: "8",
+      BitsStored: "8",
+      HighBit: "7",
+      SegmentationType: "FRACTIONAL",
+      SegmentationFractionalType: "PROBABILITY",
+      MaximumFractionalValue: "255"
+    });
+    segmentation.dataset._meta.TransferSyntaxUID = {
+      Value: ["1.2.840.10008.1.2.5"],
+      vr: "UI"
+    };
+    segmentation.dataset.SpecificCharacterSet = "ISO_IR 192";
+    segmentation.dataset._vrMap.PixelData = "OB";
+    segmentation.dataset.PixelData = rleEncodedFrames;
+  } else {
+    // If no rleEncoding, at least bitpack the data.
+    segmentation.bitPackPixelData();
+  }
+  return segmentation;
+}
+function _getLabelmapsFromReferencedFrameIndicies(labelmap3D, referencedFrameIndicies) {
+  var labelmaps2D = labelmap3D.labelmaps2D;
+  var labelmaps = [];
+  for (var i = 0; i < referencedFrameIndicies.length; i++) {
+    var frame = referencedFrameIndicies[i];
+    labelmaps.push(labelmaps2D[frame].pixelData);
+  }
+  return labelmaps;
+}
+
+/**
+ * _createSegFromImages - description
+ *
+ * @param  {Object[]} images    An array of the cornerstone image objects.
+ * @param  {Boolean} isMultiframe Whether the images are multiframe.
+ * @returns {Object}              The Seg derived dataSet.
+ */
+function _createSegFromImages(images, isMultiframe, options) {
+  var multiframe = getDatasetsFromImages(images, isMultiframe);
+  return new SegmentationDerivation([multiframe], options);
+}
+
+/**
+ * generateToolState - Given a set of cornerstoneTools imageIds and a Segmentation buffer,
+ * derive cornerstoneTools toolState and brush metadata.
+ *
+ * @param  {string[]} imageIds - An array of the imageIds.
+ * @param  {ArrayBuffer} arrayBuffer - The SEG arrayBuffer.
+ * @param  {*} metadataProvider.
+ * @param  {obj} options - Options object.
+ *
+ * @return {[]ArrayBuffer}a list of array buffer for each labelMap
+ * @return {Object} an object from which the segment metadata can be derived
+ * @return {[][][]} 2D list containing the track of segments per frame
+ * @return {[][][]} 3D list containing the track of segments per frame for each labelMap
+ *                  (available only for the overlapping case).
+ */
+function generateToolState(_x, _x2, _x3, _x4) {
+  return _generateToolState.apply(this, arguments);
+} // function insertPixelDataPerpendicular(
+//     segmentsOnFrame,
+//     labelmapBuffer,
+//     pixelData,
+//     multiframe,
+//     imageIds,
+//     validOrientations,
+//     metadataProvider
+// ) {
+//     const {
+//         SharedFunctionalGroupsSequence,
+//         PerFrameFunctionalGroupsSequence,
+//         Rows,
+//         Columns
+//     } = multiframe;
+//     const firstImagePlaneModule = metadataProvider.get(
+//         "imagePlaneModule",
+//         imageIds[0]
+//     );
+//     const lastImagePlaneModule = metadataProvider.get(
+//         "imagePlaneModule",
+//         imageIds[imageIds.length - 1]
+//     );
+//     console.log(firstImagePlaneModule);
+//     console.log(lastImagePlaneModule);
+//     const corners = [
+//         ...getCorners(firstImagePlaneModule),
+//         ...getCorners(lastImagePlaneModule)
+//     ];
+//     console.log(`corners:`);
+//     console.log(corners);
+//     const indexToWorld = mat4.create();
+//     const ippFirstFrame = firstImagePlaneModule.imagePositionPatient;
+//     const rowCosines = Array.isArray(firstImagePlaneModule.rowCosines)
+//         ? [...firstImagePlaneModule.rowCosines]
+//         : [
+//               firstImagePlaneModule.rowCosines.x,
+//               firstImagePlaneModule.rowCosines.y,
+//               firstImagePlaneModule.rowCosines.z
+//           ];
+//     const columnCosines = Array.isArray(firstImagePlaneModule.columnCosines)
+//         ? [...firstImagePlaneModule.columnCosines]
+//         : [
+//               firstImagePlaneModule.columnCosines.x,
+//               firstImagePlaneModule.columnCosines.y,
+//               firstImagePlaneModule.columnCosines.z
+//           ];
+//     const { pixelSpacing } = firstImagePlaneModule;
+//     mat4.set(
+//         indexToWorld,
+//         // Column 1
+//         0,
+//         0,
+//         0,
+//         ippFirstFrame[0],
+//         // Column 2
+//         0,
+//         0,
+//         0,
+//         ippFirstFrame[1],
+//         // Column 3
+//         0,
+//         0,
+//         0,
+//         ippFirstFrame[2],
+//         // Column 4
+//         0,
+//         0,
+//         0,
+//         1
+//     );
+//     // TODO -> Get origin and (x,y,z) increments to build a translation matrix:
+//     // TODO -> Equation C.7.6.2.1-1
+//     // | cx*di rx* Xx 0 |  |x|
+//     // | cy*di ry Xy 0 |  |y|
+//     // | cz*di rz Xz 0 |  |z|
+//     // | tx ty tz 1 |  |1|
+//     // const [
+//     //     0, 0 , 0 , 0,
+//     //     0, 0 , 0 , 0,
+//     //     0, 0 , 0 , 0,
+//     //     ipp[0], ipp[1] , ipp[2] , 1,
+//     // ]
+//     // Each frame:
+//     // Find which corner the first voxel lines up with (one of 8 corners.)
+//     // Find how i,j,k orient with respect to source volume.
+//     // Go through each frame, find location in source to start, and whether to increment +/ix,+/-y,+/-z
+//     //   through each voxel.
+//     // [1,0,0,0,1,0]
+//     // const [
+//     // ]
+//     // Invert transformation matrix to get worldToIndex
+//     // Apply world to index on each point to fill up the matrix.
+//     // const sharedImageOrientationPatient = SharedFunctionalGroupsSequence.PlaneOrientationSequence
+//     //     ? SharedFunctionalGroupsSequence.PlaneOrientationSequence
+//     //           .ImageOrientationPatient
+//     //     : undefined;
+//     // const sliceLength = Columns * Rows;
+// }
+// function getCorners(imagePlaneModule) {
+//     // console.log(imagePlaneModule);
+//     const {
+//         rows,
+//         columns,
+//         rowCosines,
+//         columnCosines,
+//         imagePositionPatient: ipp,
+//         rowPixelSpacing,
+//         columnPixelSpacing
+//     } = imagePlaneModule;
+//     const rowLength = columns * columnPixelSpacing;
+//     const columnLength = rows * rowPixelSpacing;
+//     const entireRowVector = [
+//         rowLength * columnCosines[0],
+//         rowLength * columnCosines[1],
+//         rowLength * columnCosines[2]
+//     ];
+//     const entireColumnVector = [
+//         columnLength * rowCosines[0],
+//         columnLength * rowCosines[1],
+//         columnLength * rowCosines[2]
+//     ];
+//     const topLeft = [ipp[0], ipp[1], ipp[2]];
+//     const topRight = [
+//         topLeft[0] + entireRowVector[0],
+//         topLeft[1] + entireRowVector[1],
+//         topLeft[2] + entireRowVector[2]
+//     ];
+//     const bottomLeft = [
+//         topLeft[0] + entireColumnVector[0],
+//         topLeft[1] + entireColumnVector[1],
+//         topLeft[2] + entireColumnVector[2]
+//     ];
+//     const bottomRight = [
+//         bottomLeft[0] + entireRowVector[0],
+//         bottomLeft[1] + entireRowVector[1],
+//         bottomLeft[2] + entireRowVector[2]
+//     ];
+//     return [topLeft, topRight, bottomLeft, bottomRight];
+// }
+/**
+ * Find the reference frame of the segmentation frame in the source data.
+ *
+ * @param  {Object}      multiframe        dicom metadata
+ * @param  {Int}         frameSegment      frame dicom index
+ * @param  {String[]}    imageIds          A list of imageIds.
+ * @param  {Object}      sopUIDImageIdIndexMap  A map of SOPInstanceUID to imageId
+ * @param  {Float}       tolerance         The tolerance parameter
+ *
+ * @returns {String}     Returns the imageId
+ */
+function _generateToolState() {
+  _generateToolState = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(imageIds, arrayBuffer, metadataProvider, options) {
+    var _options$skipOverlapp, skipOverlapping, _options$tolerance, tolerance, _options$TypedArrayCo, TypedArrayConstructor, _options$maxBytesPerC, maxBytesPerChunk, eventTarget, triggerEvent, dicomData, dataset, multiframe, imagePlaneModule, generalSeriesModule, SeriesInstanceUID, ImageOrientationPatient, validOrientations, sliceLength, segMetadata, TransferSyntaxUID, pixelData, pixelDataChunks, rleEncodedFrames, orientation, sopUIDImageIdIndexMap, overlapping, insertFunction, segmentsOnFrameArray, segmentsOnFrame, arrayBufferLength, labelmapBufferArray, imageIdMaps, segmentsPixelIndices, overlappingSegments, centroidXYZ;
+    return _regeneratorRuntime().wrap(function _callee$(_context) {
+      while (1) switch (_context.prev = _context.next) {
+        case 0:
+          _options$skipOverlapp = options.skipOverlapping, skipOverlapping = _options$skipOverlapp === void 0 ? false : _options$skipOverlapp, _options$tolerance = options.tolerance, tolerance = _options$tolerance === void 0 ? 1e-3 : _options$tolerance, _options$TypedArrayCo = options.TypedArrayConstructor, TypedArrayConstructor = _options$TypedArrayCo === void 0 ? Uint8Array : _options$TypedArrayCo, _options$maxBytesPerC = options.maxBytesPerChunk, maxBytesPerChunk = _options$maxBytesPerC === void 0 ? 199000000 : _options$maxBytesPerC, eventTarget = options.eventTarget, triggerEvent = options.triggerEvent;
+          dicomData = DicomMessage.readFile(arrayBuffer);
+          dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
+          dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+          multiframe = Normalizer.normalizeToDataset([dataset]);
+          imagePlaneModule = metadataProvider.get("imagePlaneModule", imageIds[0]);
+          generalSeriesModule = metadataProvider.get("generalSeriesModule", imageIds[0]);
+          SeriesInstanceUID = generalSeriesModule.seriesInstanceUID;
+          if (!imagePlaneModule) {
+            console.warn("Insufficient metadata, imagePlaneModule missing.");
+          }
+          ImageOrientationPatient = Array.isArray(imagePlaneModule.rowCosines) ? [].concat(_toConsumableArray(imagePlaneModule.rowCosines), _toConsumableArray(imagePlaneModule.columnCosines)) : [imagePlaneModule.rowCosines.x, imagePlaneModule.rowCosines.y, imagePlaneModule.rowCosines.z, imagePlaneModule.columnCosines.x, imagePlaneModule.columnCosines.y, imagePlaneModule.columnCosines.z]; // Get IOP from ref series, compute supported orientations:
+          validOrientations = getValidOrientations(ImageOrientationPatient);
+          sliceLength = multiframe.Columns * multiframe.Rows;
+          segMetadata = getSegmentMetadata(multiframe, SeriesInstanceUID);
+          TransferSyntaxUID = multiframe._meta.TransferSyntaxUID.Value[0];
+          if (!(TransferSyntaxUID === "1.2.840.10008.1.2.5")) {
+            _context.next = 23;
+            break;
+          }
+          rleEncodedFrames = Array.isArray(multiframe.PixelData) ? multiframe.PixelData : [multiframe.PixelData];
+          pixelData = decode(rleEncodedFrames, multiframe.Rows, multiframe.Columns);
+          if (!(multiframe.BitsStored === 1)) {
+            _context.next = 20;
+            break;
+          }
+          console.warn("No implementation for rle + bitbacking.");
+          return _context.abrupt("return");
+        case 20:
+          // Todo: need to test this with rle data
+          pixelDataChunks = [pixelData];
+          _context.next = 26;
+          break;
+        case 23:
+          pixelDataChunks = unpackPixelData(multiframe, {
+            maxBytesPerChunk: maxBytesPerChunk
+          });
+          if (pixelDataChunks) {
+            _context.next = 26;
+            break;
+          }
+          throw new Error("Fractional segmentations are not yet supported");
+        case 26:
+          orientation = checkOrientation(multiframe, validOrientations, [imagePlaneModule.rows, imagePlaneModule.columns, imageIds.length], tolerance); // Pre-compute the sop UID to imageId index map so that in the for loop
+          // we don't have to call metadataProvider.get() for each imageId over
+          // and over again.
+          sopUIDImageIdIndexMap = imageIds.reduce(function (acc, imageId) {
+            var _metadataProvider$get = metadataProvider.get("generalImageModule", imageId),
+              sopInstanceUID = _metadataProvider$get.sopInstanceUID;
+            acc[sopInstanceUID] = imageId;
+            return acc;
+          }, {});
+          overlapping = false;
+          if (!skipOverlapping) {
+            overlapping = checkSEGsOverlapping(pixelDataChunks, multiframe, imageIds, validOrientations, metadataProvider, tolerance, TypedArrayConstructor, sopUIDImageIdIndexMap);
+          }
+          _context.t0 = orientation;
+          _context.next = _context.t0 === "Planar" ? 33 : _context.t0 === "Perpendicular" ? 35 : _context.t0 === "Oblique" ? 36 : 37;
+          break;
+        case 33:
+          if (overlapping) {
+            insertFunction = insertOverlappingPixelDataPlanar;
+          } else {
+            insertFunction = insertPixelDataPlanar;
+          }
+          return _context.abrupt("break", 37);
+        case 35:
+          throw new Error("Segmentations orthogonal to the acquisition plane of the source data are not yet supported.");
+        case 36:
+          throw new Error("Segmentations oblique to the acquisition plane of the source data are not yet supported.");
+        case 37:
+          /* if SEGs are overlapping:
+          1) the labelmapBuffer will contain M volumes which have non-overlapping segments;
+          2) segmentsOnFrame will have M * numberOfFrames values to track in which labelMap are the segments;
+          3) insertFunction will return the number of LabelMaps
+          4) generateToolState return is an array*/
+          segmentsOnFrameArray = [];
+          segmentsOnFrameArray[0] = [];
+          segmentsOnFrame = [];
+          arrayBufferLength = sliceLength * imageIds.length * TypedArrayConstructor.BYTES_PER_ELEMENT;
+          labelmapBufferArray = [];
+          labelmapBufferArray[0] = new ArrayBuffer(arrayBufferLength);
+
+          // Pre-compute the indices and metadata so that we don't have to call
+          // a function for each imageId in the for loop.
+          imageIdMaps = imageIds.reduce(function (acc, curr, index) {
+            acc.indices[curr] = index;
+            acc.metadata[curr] = metadataProvider.get("instance", curr);
+            return acc;
+          }, {
+            indices: {},
+            metadata: {}
+          }); // This is the centroid calculation for each segment Index, the data structure
+          // is a Map with key = segmentIndex and value = {imageIdIndex: centroid, ...}
+          // later on we will use this data structure to calculate the centroid of the
+          // segment in the labelmapBuffer
+          segmentsPixelIndices = new Map();
+          _context.next = 47;
+          return insertFunction(segmentsOnFrame, segmentsOnFrameArray, labelmapBufferArray, pixelDataChunks, multiframe, imageIds, validOrientations, metadataProvider, tolerance, TypedArrayConstructor, segmentsPixelIndices, sopUIDImageIdIndexMap, imageIdMaps, eventTarget, triggerEvent);
+        case 47:
+          overlappingSegments = _context.sent;
+          // calculate the centroid of each segment
+          centroidXYZ = new Map();
+          segmentsPixelIndices.forEach(function (imageIdIndexBufferIndex, segmentIndex) {
+            var centroids = calculateCentroid(imageIdIndexBufferIndex, multiframe, metadataProvider, imageIds);
+            centroidXYZ.set(segmentIndex, centroids);
+          });
+          return _context.abrupt("return", {
+            labelmapBufferArray: labelmapBufferArray,
+            segMetadata: segMetadata,
+            segmentsOnFrame: segmentsOnFrame,
+            segmentsOnFrameArray: segmentsOnFrameArray,
+            centroids: centroidXYZ,
+            overlappingSegments: overlappingSegments
+          });
+        case 51:
+        case "end":
+          return _context.stop();
+      }
+    }, _callee);
+  }));
+  return _generateToolState.apply(this, arguments);
+}
+function findReferenceSourceImageId(multiframe, frameSegment, imageIds, metadataProvider, tolerance, sopUIDImageIdIndexMap) {
+  var imageId = undefined;
+  if (!multiframe) {
+    return imageId;
+  }
+  var FrameOfReferenceUID = multiframe.FrameOfReferenceUID,
+    PerFrameFunctionalGroupsSequence = multiframe.PerFrameFunctionalGroupsSequence,
+    SourceImageSequence = multiframe.SourceImageSequence,
+    ReferencedSeriesSequence = multiframe.ReferencedSeriesSequence;
+  if (!PerFrameFunctionalGroupsSequence || PerFrameFunctionalGroupsSequence.length === 0) {
+    return imageId;
+  }
+  var PerFrameFunctionalGroup = PerFrameFunctionalGroupsSequence[frameSegment];
+  if (!PerFrameFunctionalGroup) {
+    return imageId;
+  }
+  var frameSourceImageSequence = undefined;
+  if (PerFrameFunctionalGroup.DerivationImageSequence) {
+    var DerivationImageSequence = PerFrameFunctionalGroup.DerivationImageSequence;
+    if (Array.isArray(DerivationImageSequence)) {
+      if (DerivationImageSequence.length !== 0) {
+        DerivationImageSequence = DerivationImageSequence[0];
+      } else {
+        DerivationImageSequence = undefined;
+      }
+    }
+    if (DerivationImageSequence) {
+      frameSourceImageSequence = DerivationImageSequence.SourceImageSequence;
+      if (Array.isArray(frameSourceImageSequence)) {
+        if (frameSourceImageSequence.length !== 0) {
+          frameSourceImageSequence = frameSourceImageSequence[0];
+        } else {
+          frameSourceImageSequence = undefined;
+        }
+      }
+    }
+  } else if (SourceImageSequence && SourceImageSequence.length !== 0) {
+    console.warn("DerivationImageSequence not present, using SourceImageSequence assuming SEG has the same geometry as the source image.");
+    frameSourceImageSequence = SourceImageSequence[frameSegment];
+  }
+  if (frameSourceImageSequence) {
+    imageId = getImageIdOfSourceImageBySourceImageSequence(frameSourceImageSequence, sopUIDImageIdIndexMap);
+  }
+  if (imageId === undefined && ReferencedSeriesSequence) {
+    var referencedSeriesSequence = Array.isArray(ReferencedSeriesSequence) ? ReferencedSeriesSequence[0] : ReferencedSeriesSequence;
+    var ReferencedSeriesInstanceUID = referencedSeriesSequence.SeriesInstanceUID;
+    imageId = getImageIdOfSourceImagebyGeometry(ReferencedSeriesInstanceUID, FrameOfReferenceUID, PerFrameFunctionalGroup, imageIds, metadataProvider, tolerance);
+  }
+  return imageId;
+}
+
+/**
+ * Checks if there is any overlapping segmentations.
+ *  @returns {boolean} Returns a flag if segmentations overlapping
+ */
+
+function checkSEGsOverlapping(pixelData, multiframe, imageIds, validOrientations, metadataProvider, tolerance, TypedArrayConstructor, sopUIDImageIdIndexMap) {
+  var SharedFunctionalGroupsSequence = multiframe.SharedFunctionalGroupsSequence,
+    PerFrameFunctionalGroupsSequence = multiframe.PerFrameFunctionalGroupsSequence,
+    SegmentSequence = multiframe.SegmentSequence,
+    Rows = multiframe.Rows,
+    Columns = multiframe.Columns;
+  var numberOfSegs = SegmentSequence.length;
+  if (numberOfSegs < 2) {
+    return false;
+  }
+  var sharedImageOrientationPatient = SharedFunctionalGroupsSequence.PlaneOrientationSequence ? SharedFunctionalGroupsSequence.PlaneOrientationSequence.ImageOrientationPatient : undefined;
+  var sliceLength = Columns * Rows;
+  var groupsLen = PerFrameFunctionalGroupsSequence.length;
+
+  /** sort groupsLen to have all the segments for each frame in an array
+   * frame 2 : 1, 2
+   * frame 4 : 1, 3
+   * frame 5 : 4
+   */
+
+  var frameSegmentsMapping = new Map();
+  var _loop3 = function _loop3() {
+      var segmentIndex = getSegmentIndex(multiframe, frameSegment);
+      if (segmentIndex === undefined) {
+        console.warn("Could not retrieve the segment index for frame segment " + frameSegment + ", skipping this frame.");
+        return 0; // continue
+      }
+      var imageId = findReferenceSourceImageId(multiframe, frameSegment, imageIds, metadataProvider, tolerance, sopUIDImageIdIndexMap);
+      if (!imageId) {
+        console.warn("Image not present in stack, can't import frame : " + frameSegment + ".");
+        return 0; // continue
+      }
+      var imageIdIndex = imageIds.findIndex(function (element) {
+        return element === imageId;
+      });
+      if (frameSegmentsMapping.has(imageIdIndex)) {
+        var segmentArray = frameSegmentsMapping.get(imageIdIndex);
+        if (!segmentArray.includes(frameSegment)) {
+          segmentArray.push(frameSegment);
+          frameSegmentsMapping.set(imageIdIndex, segmentArray);
+        }
+      } else {
+        frameSegmentsMapping.set(imageIdIndex, [frameSegment]);
+      }
+    },
+    _ret;
+  for (var frameSegment = 0; frameSegment < groupsLen; ++frameSegment) {
+    _ret = _loop3();
+    if (_ret === 0) continue;
+  }
+  var _iterator = _createForOfIteratorHelper(frameSegmentsMapping.entries()),
+    _step;
+  try {
+    for (_iterator.s(); !(_step = _iterator.n()).done;) {
+      var _step$value = _slicedToArray(_step.value, 2),
+        role = _step$value[1];
+      var temp2DArray = new TypedArrayConstructor(sliceLength).fill(0);
+      for (var i = 0; i < role.length; ++i) {
+        var _frameSegment = role[i];
+        var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[_frameSegment];
+        var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+        var view = readFromUnpackedChunks(pixelData, _frameSegment * sliceLength, sliceLength);
+        var pixelDataI2D = ndarray(view, [Rows, Columns]);
+        var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+        if (!alignedPixelDataI) {
+          console.warn("Individual SEG frames are out of plane with respect to the first SEG frame, this is not yet supported, skipping this frame.");
+          continue;
+        }
+        var data = alignedPixelDataI.data;
+        for (var j = 0, len = data.length; j < len; ++j) {
+          if (data[j] !== 0) {
+            temp2DArray[j]++;
+            if (temp2DArray[j] > 1) {
+              return true;
+            }
+          }
+        }
+      }
+    }
+  } catch (err) {
+    _iterator.e(err);
+  } finally {
+    _iterator.f();
+  }
+  return false;
+}
+function insertOverlappingPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray, labelmapBufferArray, pixelData, multiframe, imageIds, validOrientations, metadataProvider, tolerance, TypedArrayConstructor, segmentsPixelIndices, sopUIDImageIdIndexMap) {
+  var SharedFunctionalGroupsSequence = multiframe.SharedFunctionalGroupsSequence,
+    PerFrameFunctionalGroupsSequence = multiframe.PerFrameFunctionalGroupsSequence,
+    Rows = multiframe.Rows,
+    Columns = multiframe.Columns;
+  var sharedImageOrientationPatient = SharedFunctionalGroupsSequence.PlaneOrientationSequence ? SharedFunctionalGroupsSequence.PlaneOrientationSequence.ImageOrientationPatient : undefined;
+  var sliceLength = Columns * Rows;
+  var arrayBufferLength = sliceLength * imageIds.length * TypedArrayConstructor.BYTES_PER_ELEMENT;
+  // indicate the number of labelMaps
+  var M = 1;
+
+  // indicate the current labelMap array index;
+  var m = 0;
+
+  // temp array for checking overlaps
+  var tempBuffer = labelmapBufferArray[m].slice(0);
+
+  // temp list for checking overlaps
+  var tempSegmentsOnFrame = structuredClone(segmentsOnFrameArray[m]);
+
+  /** split overlapping SEGs algorithm for each segment:
+   *  A) copy the labelmapBuffer in the array with index 0
+   *  B) add the segment pixel per pixel on the copied buffer from (A)
+   *  C) if no overlap, copy the results back on the orignal array from (A)
+   *  D) if overlap, repeat increasing the index m up to M (if out of memory, add new buffer in the array and M++);
+   */
+
+  var numberOfSegs = multiframe.SegmentSequence.length;
+  for (var segmentIndexToProcess = 1; segmentIndexToProcess <= numberOfSegs; ++segmentIndexToProcess) {
+    var _loop4 = function _loop4(_i2) {
+        var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[_i2];
+        var segmentIndex = getSegmentIndex(multiframe, _i2);
+        if (segmentIndex === undefined) {
+          throw new Error("Could not retrieve the segment index. Aborting segmentation loading.");
+        }
+        if (segmentIndex !== segmentIndexToProcess) {
+          i = _i2;
+          return 0; // continue
+        }
+        var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+
+        // Since we moved to the chunks approach, we need to read the data
+        // and handle scenarios where the portion of data is in one chunk
+        // and the other portion is in another chunk
+        var view = readFromUnpackedChunks(pixelData, _i2 * sliceLength, sliceLength);
+        var pixelDataI2D = ndarray(view, [Rows, Columns]);
+        var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+        if (!alignedPixelDataI) {
+          throw new Error("Individual SEG frames are out of plane with respect to the first SEG frame. " + "This is not yet supported. Aborting segmentation loading.");
+        }
+        var imageId = findReferenceSourceImageId(multiframe, _i2, imageIds, metadataProvider, tolerance, sopUIDImageIdIndexMap);
+        if (!imageId) {
+          console.warn("Image not present in stack, can't import frame : " + _i2 + ".");
+          i = _i2;
+          return 0; // continue
+        }
+        var sourceImageMetadata = metadataProvider.get("instance", imageId);
+        if (Rows !== sourceImageMetadata.Rows || Columns !== sourceImageMetadata.Columns) {
+          throw new Error("Individual SEG frames have different geometry dimensions (Rows and Columns) " + "respect to the source image reference frame. This is not yet supported. " + "Aborting segmentation loading. ");
+        }
+        var imageIdIndex = imageIds.findIndex(function (element) {
+          return element === imageId;
+        });
+        var byteOffset = sliceLength * imageIdIndex * TypedArrayConstructor.BYTES_PER_ELEMENT;
+        var labelmap2DView = new TypedArrayConstructor(tempBuffer, byteOffset, sliceLength);
+        var data = alignedPixelDataI.data;
+        var segmentOnFrame = false;
+        for (var j = 0, len = alignedPixelDataI.data.length; j < len; ++j) {
+          if (data[j]) {
+            if (labelmap2DView[j] !== 0) {
+              m++;
+              if (m >= M) {
+                labelmapBufferArray[m] = new ArrayBuffer(arrayBufferLength);
+                segmentsOnFrameArray[m] = [];
+                M++;
+              }
+              tempBuffer = labelmapBufferArray[m].slice(0);
+              tempSegmentsOnFrame = structuredClone(segmentsOnFrameArray[m]);
+              _i2 = 0;
+              break;
+            } else {
+              labelmap2DView[j] = segmentIndex;
+              segmentOnFrame = true;
+            }
+          }
+        }
+        if (segmentOnFrame) {
+          if (!tempSegmentsOnFrame[imageIdIndex]) {
+            tempSegmentsOnFrame[imageIdIndex] = [];
+          }
+          tempSegmentsOnFrame[imageIdIndex].push(segmentIndex);
+          if (!segmentsOnFrame[imageIdIndex]) {
+            segmentsOnFrame[imageIdIndex] = [];
+          }
+          segmentsOnFrame[imageIdIndex].push(segmentIndex);
+        }
+        i = _i2;
+      },
+      _ret2;
+    for (var i = 0, groupsLen = PerFrameFunctionalGroupsSequence.length; i < groupsLen; ++i) {
+      _ret2 = _loop4(i);
+      if (_ret2 === 0) continue;
+    }
+    labelmapBufferArray[m] = tempBuffer.slice(0);
+    segmentsOnFrameArray[m] = structuredClone(tempSegmentsOnFrame);
+
+    // reset temp variables/buffers for new segment
+    m = 0;
+    tempBuffer = labelmapBufferArray[m].slice(0);
+    tempSegmentsOnFrame = structuredClone(segmentsOnFrameArray[m]);
+  }
+}
+var getSegmentIndex = function getSegmentIndex(multiframe, frame) {
+  var PerFrameFunctionalGroupsSequence = multiframe.PerFrameFunctionalGroupsSequence,
+    SharedFunctionalGroupsSequence = multiframe.SharedFunctionalGroupsSequence;
+  var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[frame];
+  return PerFrameFunctionalGroups && PerFrameFunctionalGroups.SegmentIdentificationSequence ? PerFrameFunctionalGroups.SegmentIdentificationSequence.ReferencedSegmentNumber : SharedFunctionalGroupsSequence.SegmentIdentificationSequence ? SharedFunctionalGroupsSequence.SegmentIdentificationSequence.ReferencedSegmentNumber : undefined;
+};
+function insertPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray, labelmapBufferArray, pixelData, multiframe, imageIds, validOrientations, metadataProvider, tolerance, TypedArrayConstructor, segmentsPixelIndices, sopUIDImageIdIndexMap, imageIdMaps, eventTarget, triggerEvent) {
+  var SharedFunctionalGroupsSequence = multiframe.SharedFunctionalGroupsSequence,
+    PerFrameFunctionalGroupsSequence = multiframe.PerFrameFunctionalGroupsSequence,
+    Rows = multiframe.Rows,
+    Columns = multiframe.Columns;
+  var sharedImageOrientationPatient = SharedFunctionalGroupsSequence.PlaneOrientationSequence ? SharedFunctionalGroupsSequence.PlaneOrientationSequence.ImageOrientationPatient : undefined;
+  var sliceLength = Columns * Rows;
+  var i = 0;
+  var groupsLen = PerFrameFunctionalGroupsSequence.length;
+  var chunkSize = Math.ceil(groupsLen / 10); // 10% of total length
+
+  var shouldTriggerEvent = triggerEvent && eventTarget;
+  var overlapping = false;
+  // Below, we chunk the processing of the frames to avoid blocking the main thread
+  // if the segmentation is large. We also use a promise to allow the caller to
+  // wait for the processing to finish.
+  return new Promise(function (resolve) {
+    function processInChunks() {
+      // process one chunk
+      for (var end = Math.min(i + chunkSize, groupsLen); i < end; ++i) {
+        var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[i];
+        var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+        var view = readFromUnpackedChunks(pixelData, i * sliceLength, sliceLength);
+        var pixelDataI2D = ndarray(view, [Rows, Columns]);
+        var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+        if (!alignedPixelDataI) {
+          throw new Error("Individual SEG frames are out of plane with respect to the first SEG frame. " + "This is not yet supported. Aborting segmentation loading.");
+        }
+        var segmentIndex = getSegmentIndex(multiframe, i);
+        if (segmentIndex === undefined) {
+          throw new Error("Could not retrieve the segment index. Aborting segmentation loading.");
+        }
+        if (!segmentsPixelIndices.has(segmentIndex)) {
+          segmentsPixelIndices.set(segmentIndex, {});
+        }
+        var imageId = findReferenceSourceImageId(multiframe, i, imageIds, metadataProvider, tolerance, sopUIDImageIdIndexMap);
+        if (!imageId) {
+          console.warn("Image not present in stack, can't import frame : " + i + ".");
+          continue;
+        }
+        var sourceImageMetadata = imageIdMaps.metadata[imageId];
+        if (Rows !== sourceImageMetadata.Rows || Columns !== sourceImageMetadata.Columns) {
+          throw new Error("Individual SEG frames have different geometry dimensions (Rows and Columns) " + "respect to the source image reference frame. This is not yet supported. " + "Aborting segmentation loading. ");
+        }
+        var imageIdIndex = imageIdMaps.indices[imageId];
+        var byteOffset = sliceLength * imageIdIndex * TypedArrayConstructor.BYTES_PER_ELEMENT;
+        var labelmap2DView = new TypedArrayConstructor(labelmapBufferArray[0], byteOffset, sliceLength);
+        var data = alignedPixelDataI.data;
+        var indexCache = [];
+        for (var j = 0, len = alignedPixelDataI.data.length; j < len; ++j) {
+          if (data[j]) {
+            for (var x = j; x < len; ++x) {
+              if (data[x]) {
+                if (!overlapping && labelmap2DView[x] !== 0) {
+                  overlapping = true;
+                }
+                labelmap2DView[x] = segmentIndex;
+                indexCache.push(x);
+              }
+            }
+            if (!segmentsOnFrame[imageIdIndex]) {
+              segmentsOnFrame[imageIdIndex] = [];
+            }
+            segmentsOnFrame[imageIdIndex].push(segmentIndex);
+            break;
+          }
+        }
+        var segmentIndexObject = segmentsPixelIndices.get(segmentIndex);
+        segmentIndexObject[imageIdIndex] = indexCache;
+        segmentsPixelIndices.set(segmentIndex, segmentIndexObject);
+      }
+
+      // trigger an event after each chunk
+      if (shouldTriggerEvent) {
+        var percentComplete = Math.round(i / groupsLen * 100);
+        triggerEvent(eventTarget, Events.SEGMENTATION_LOAD_PROGRESS, {
+          percentComplete: percentComplete
+        });
+      }
+
+      // schedule next chunk
+      if (i < groupsLen) {
+        setTimeout(processInChunks, 0);
+      } else {
+        // resolve the Promise when all chunks have been processed
+        resolve(overlapping);
+      }
+    }
+    processInChunks();
+  });
+}
+
+/**
+ * unpackPixelData - Unpacks bit packed pixelData if the Segmentation is BINARY.
+ *
+ * @param  {Object} multiframe The multiframe dataset.
+ * @param  {Object} options    Options for the unpacking.
+ * @return {Uint8Array}      The unpacked pixelData.
+ */
+function unpackPixelData(multiframe, options) {
+  var segType = multiframe.SegmentationType;
+  var data;
+  if (Array.isArray(multiframe.PixelData)) {
+    data = multiframe.PixelData[0];
+  } else {
+    data = multiframe.PixelData;
+  }
+  if (data === undefined) {
+    log.error("This segmentation pixelData is undefined.");
+  }
+  if (segType === "BINARY") {
+    // For extreme big data, we can't unpack the data at once and we need to
+    // chunk it and unpack each chunk separately.
+    // MAX 2GB is the limit right now to allocate a buffer
+    return getUnpackedChunks(data, options.maxBytesPerChunk);
+  }
+  var pixelData = new Uint8Array(data);
+  var max = multiframe.MaximumFractionalValue;
+  var onlyMaxAndZero = pixelData.find(function (element) {
+    return element !== 0 && element !== max;
+  }) === undefined;
+  if (!onlyMaxAndZero) {
+    // This is a fractional segmentation, which is not currently supported.
+    return;
+  }
+  log.warn("This segmentation object is actually binary... processing as such.");
+  return pixelData;
+}
+function getUnpackedChunks(data, maxBytesPerChunk) {
+  var bitArray = new Uint8Array(data);
+  var chunks = [];
+  var maxBitsPerChunk = maxBytesPerChunk * 8;
+  var numberOfChunks = Math.ceil(bitArray.length * 8 / maxBitsPerChunk);
+  for (var i = 0; i < numberOfChunks; i++) {
+    var startBit = i * maxBitsPerChunk;
+    var endBit = Math.min(startBit + maxBitsPerChunk, bitArray.length * 8);
+    var startByte = Math.floor(startBit / 8);
+    var endByte = Math.ceil(endBit / 8);
+    var chunk = bitArray.slice(startByte, endByte);
+    var unpackedChunk = BitArray.unpack(chunk);
+    chunks.push(unpackedChunk);
+  }
+  return chunks;
+}
+
+/**
+ * getImageIdOfSourceImageBySourceImageSequence - Returns the Cornerstone imageId of the source image.
+ *
+ * @param  {Object}   SourceImageSequence  Sequence describing the source image.
+ * @param  {String[]} imageIds             A list of imageIds.
+ * @param  {Object}   sopUIDImageIdIndexMap A map of SOPInstanceUIDs to imageIds.
+ * @return {String}                        The corresponding imageId.
+ */
+function getImageIdOfSourceImageBySourceImageSequence(SourceImageSequence, sopUIDImageIdIndexMap) {
+  var ReferencedSOPInstanceUID = SourceImageSequence.ReferencedSOPInstanceUID,
+    ReferencedFrameNumber = SourceImageSequence.ReferencedFrameNumber;
+  return ReferencedFrameNumber ? getImageIdOfReferencedFrame(ReferencedSOPInstanceUID, ReferencedFrameNumber, sopUIDImageIdIndexMap) : sopUIDImageIdIndexMap[ReferencedSOPInstanceUID];
+}
+
+/**
+ * getImageIdOfSourceImagebyGeometry - Returns the Cornerstone imageId of the source image.
+ *
+ * @param  {String}    ReferencedSeriesInstanceUID    Referenced series of the source image.
+ * @param  {String}    FrameOfReferenceUID            Frame of reference.
+ * @param  {Object}    PerFrameFunctionalGroup        Sequence describing segmentation reference attributes per frame.
+ * @param  {String[]}  imageIds                       A list of imageIds.
+ * @param  {Object}    sopUIDImageIdIndexMap          A map of SOPInstanceUIDs to imageIds.
+ * @param  {Float}     tolerance                      The tolerance parameter
+ *
+ * @return {String}                                   The corresponding imageId.
+ */
+function getImageIdOfSourceImagebyGeometry(ReferencedSeriesInstanceUID, FrameOfReferenceUID, PerFrameFunctionalGroup, imageIds, metadataProvider, tolerance) {
+  if (ReferencedSeriesInstanceUID === undefined || PerFrameFunctionalGroup.PlanePositionSequence === undefined || PerFrameFunctionalGroup.PlanePositionSequence[0] === undefined || PerFrameFunctionalGroup.PlanePositionSequence[0].ImagePositionPatient === undefined) {
+    return undefined;
+  }
+  for (var imageIdsIndexc = 0; imageIdsIndexc < imageIds.length; ++imageIdsIndexc) {
+    var sourceImageMetadata = metadataProvider.get("instance", imageIds[imageIdsIndexc]);
+    if (sourceImageMetadata === undefined || sourceImageMetadata.ImagePositionPatient === undefined || sourceImageMetadata.FrameOfReferenceUID !== FrameOfReferenceUID || sourceImageMetadata.SeriesInstanceUID !== ReferencedSeriesInstanceUID) {
+      continue;
+    }
+    if (compareArrays(PerFrameFunctionalGroup.PlanePositionSequence[0].ImagePositionPatient, sourceImageMetadata.ImagePositionPatient, tolerance)) {
+      return imageIds[imageIdsIndexc];
+    }
+  }
+}
+
+/**
+ * getImageIdOfReferencedFrame - Returns the imageId corresponding to the
+ * specified sopInstanceUid and frameNumber for multi-frame images.
+ *
+ * @param  {String} sopInstanceUid   The sopInstanceUid of the desired image.
+ * @param  {Number} frameNumber      The frame number.
+ * @param  {String} imageIds         The list of imageIds.
+ * @param  {Object} sopUIDImageIdIndexMap A map of SOPInstanceUIDs to imageIds.
+ * @return {String}                  The imageId that corresponds to the sopInstanceUid.
+ */
+function getImageIdOfReferencedFrame(sopInstanceUid, frameNumber, sopUIDImageIdIndexMap) {
+  var imageId = sopUIDImageIdIndexMap[sopInstanceUid];
+  if (!imageId) {
+    return;
+  }
+  var imageIdFrameNumber = Number(imageId.split("frame=")[1]);
+  return imageIdFrameNumber === frameNumber - 1 ? imageId : undefined;
+}
+
+/**
+ * getValidOrientations - returns an array of valid orientations.
+ *
+ * @param  {Number[6]} iop The row (0..2) an column (3..5) direction cosines.
+ * @return {Number[8][6]} An array of valid orientations.
+ */
+function getValidOrientations(iop) {
+  var orientations = [];
+
+  // [0,  1,  2]: 0,   0hf,   0vf
+  // [3,  4,  5]: 90,  90hf,  90vf
+  // [6, 7]:      180, 270
+
+  orientations[0] = iop;
+  orientations[1] = flipIOP.h(iop);
+  orientations[2] = flipIOP.v(iop);
+  var iop90 = rotateDirectionCosinesInPlane(iop, Math.PI / 2);
+  orientations[3] = iop90;
+  orientations[4] = flipIOP.h(iop90);
+  orientations[5] = flipIOP.v(iop90);
+  orientations[6] = rotateDirectionCosinesInPlane(iop, Math.PI);
+  orientations[7] = rotateDirectionCosinesInPlane(iop, 1.5 * Math.PI);
+  return orientations;
+}
+
+/**
+ * alignPixelDataWithSourceData -
+ *
+ * @param {Ndarray} pixelData2D - The data to align.
+ * @param {Number[6]} iop - The orientation of the image slice.
+ * @param {Number[8][6]} orientations - An array of valid imageOrientationPatient values.
+ * @param {Number} tolerance.
+ * @return {Ndarray} The aligned pixelData.
+ */
+function alignPixelDataWithSourceData(pixelData2D, iop, orientations, tolerance) {
+  if (compareArrays(iop, orientations[0], tolerance)) {
+    return pixelData2D;
+  } else if (compareArrays(iop, orientations[1], tolerance)) {
+    // Flipped vertically.
+
+    // Undo Flip
+    return flipMatrix2D.v(pixelData2D);
+  } else if (compareArrays(iop, orientations[2], tolerance)) {
+    // Flipped horizontally.
+
+    // Unfo flip
+    return flipMatrix2D.h(pixelData2D);
+  } else if (compareArrays(iop, orientations[3], tolerance)) {
+    //Rotated 90 degrees
+
+    // Rotate back
+    return rotateMatrix902D(pixelData2D);
+  } else if (compareArrays(iop, orientations[4], tolerance)) {
+    //Rotated 90 degrees and fliped horizontally.
+
+    // Undo flip and rotate back.
+    return rotateMatrix902D(flipMatrix2D.h(pixelData2D));
+  } else if (compareArrays(iop, orientations[5], tolerance)) {
+    // Rotated 90 degrees and fliped vertically
+
+    // Unfo flip and rotate back.
+    return rotateMatrix902D(flipMatrix2D.v(pixelData2D));
+  } else if (compareArrays(iop, orientations[6], tolerance)) {
+    // Rotated 180 degrees. // TODO -> Do this more effeciently, there is a 1:1 mapping like 90 degree rotation.
+
+    return rotateMatrix902D(rotateMatrix902D(pixelData2D));
+  } else if (compareArrays(iop, orientations[7], tolerance)) {
+    // Rotated 270 degrees
+
+    // Rotate back.
+    return rotateMatrix902D(rotateMatrix902D(rotateMatrix902D(pixelData2D)));
+  }
+}
+function getSegmentMetadata(multiframe, seriesInstanceUid) {
+  var segmentSequence = multiframe.SegmentSequence;
+  var data = [];
+  if (Array.isArray(segmentSequence)) {
+    data = [undefined].concat(_toConsumableArray(segmentSequence));
+  } else {
+    // Only one segment, will be stored as an object.
+    data = [undefined, segmentSequence];
+  }
+  return {
+    seriesInstanceUid: seriesInstanceUid,
+    data: data
+  };
+}
+
+/**
+ * Reads a range of bytes from an array of ArrayBuffer chunks and
+ * aggregate them into a new Uint8Array.
+ *
+ * @param {ArrayBuffer[]} chunks - An array of ArrayBuffer chunks.
+ * @param {number} offset - The offset of the first byte to read.
+ * @param {number} length - The number of bytes to read.
+ * @returns {Uint8Array} A new Uint8Array containing the requested bytes.
+ */
+function readFromUnpackedChunks(chunks, offset, length) {
+  var mapping = getUnpackedOffsetAndLength(chunks, offset, length);
+
+  // If all the data is in one chunk, we can just slice that chunk
+  if (mapping.start.chunkIndex === mapping.end.chunkIndex) {
+    return new Uint8Array(chunks[mapping.start.chunkIndex].buffer, mapping.start.offset, length);
+  } else {
+    // If the data spans multiple chunks, we need to create a new Uint8Array and copy the data from each chunk
+    var result = new Uint8Array(length);
+    var resultOffset = 0;
+    for (var i = mapping.start.chunkIndex; i <= mapping.end.chunkIndex; i++) {
+      var start = i === mapping.start.chunkIndex ? mapping.start.offset : 0;
+      var end = i === mapping.end.chunkIndex ? mapping.end.offset : chunks[i].length;
+      result.set(new Uint8Array(chunks[i].buffer, start, end - start), resultOffset);
+      resultOffset += end - start;
+    }
+    return result;
+  }
+}
+function getUnpackedOffsetAndLength(chunks, offset, length) {
+  var totalBytes = chunks.reduce(function (total, chunk) {
+    return total + chunk.length;
+  }, 0);
+  if (offset < 0 || offset + length > totalBytes) {
+    throw new Error("Offset and length out of bounds");
+  }
+  var startChunkIndex = 0;
+  var startOffsetInChunk = offset;
+  while (startOffsetInChunk >= chunks[startChunkIndex].length) {
+    startOffsetInChunk -= chunks[startChunkIndex].length;
+    startChunkIndex++;
+  }
+  var endChunkIndex = startChunkIndex;
+  var endOffsetInChunk = startOffsetInChunk + length;
+  while (endOffsetInChunk > chunks[endChunkIndex].length) {
+    endOffsetInChunk -= chunks[endChunkIndex].length;
+    endChunkIndex++;
+  }
+  return {
+    start: {
+      chunkIndex: startChunkIndex,
+      offset: startOffsetInChunk
+    },
+    end: {
+      chunkIndex: endChunkIndex,
+      offset: endOffsetInChunk
+    }
+  };
+}
+function calculateCentroid(imageIdIndexBufferIndex, multiframe, metadataProvider, imageIds) {
+  var xAcc = 0;
+  var yAcc = 0;
+  var zAcc = 0;
+  var worldXAcc = 0;
+  var worldYAcc = 0;
+  var worldZAcc = 0;
+  var count = 0;
+  for (var _i3 = 0, _Object$entries = Object.entries(imageIdIndexBufferIndex); _i3 < _Object$entries.length; _i3++) {
+    var _Object$entries$_i = _slicedToArray(_Object$entries[_i3], 2),
+      imageIdIndex = _Object$entries$_i[0],
+      bufferIndices = _Object$entries$_i[1];
+    var z = Number(imageIdIndex);
+    if (!bufferIndices || bufferIndices.length === 0) {
+      continue;
+    }
+
+    // Get metadata for this slice
+    var imageId = imageIds[z];
+    var imagePlaneModule = metadataProvider.get("imagePlaneModule", imageId);
+    if (!imagePlaneModule) {
+      console.debug("Missing imagePlaneModule metadata for centroid calculation");
+      continue;
+    }
+    var imagePositionPatient = imagePlaneModule.imagePositionPatient,
+      rowCosines = imagePlaneModule.rowCosines,
+      columnCosines = imagePlaneModule.columnCosines,
+      rowPixelSpacing = imagePlaneModule.rowPixelSpacing,
+      columnPixelSpacing = imagePlaneModule.columnPixelSpacing;
+    var _iterator2 = _createForOfIteratorHelper(bufferIndices),
+      _step2;
+    try {
+      for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+        var bufferIndex = _step2.value;
+        var y = Math.floor(bufferIndex / multiframe.Rows);
+        var x = bufferIndex % multiframe.Rows;
+
+        // Image coordinates
+        xAcc += x;
+        yAcc += y;
+        zAcc += z;
+
+        // Calculate world coordinates
+        // P(world) = P(image) * IOP * spacing + IPP
+        var worldX = imagePositionPatient[0] + x * rowCosines[0] * columnPixelSpacing + y * columnCosines[0] * rowPixelSpacing;
+        var worldY = imagePositionPatient[1] + x * rowCosines[1] * columnPixelSpacing + y * columnCosines[1] * rowPixelSpacing;
+        var worldZ = imagePositionPatient[2] + x * rowCosines[2] * columnPixelSpacing + y * columnCosines[2] * rowPixelSpacing;
+        worldXAcc += worldX;
+        worldYAcc += worldY;
+        worldZAcc += worldZ;
+        count++;
+      }
+    } catch (err) {
+      _iterator2.e(err);
+    } finally {
+      _iterator2.f();
+    }
+  }
+  return {
+    image: {
+      x: Math.floor(xAcc / count),
+      y: Math.floor(yAcc / count),
+      z: Math.floor(zAcc / count)
+    },
+    world: {
+      x: worldXAcc / count,
+      y: worldYAcc / count,
+      z: worldZAcc / count
+    },
+    count: count
+  };
+}
+var Segmentation = {
+  generateSegmentation: generateSegmentation,
+  generateToolState: generateToolState,
+  fillSegmentation: fillSegmentation
+};
+
+export { Segmentation as default, fillSegmentation, generateSegmentation, generateToolState };