larvitar 2.0.4 → 2.0.6

package/imaging/parsers/nrrd.js

@@ -1,485 +0,0 @@
-import pako from "pako";
-
-/**
- * This is the mapping from the NRRD datatype as written in the NRRD header
- * to the JS typed array equivalent.
- */
-const NRRD_TYPES_TO_TYPEDARRAY = {
-  "signed char": Int8Array,
-  int8: Int8Array,
-  int8_t: Int8Array,
-  uchar: Uint8Array,
-  "unsigned char": Uint8Array,
-  uint8: Uint8Array,
-  uint8_t: Uint8Array,
-  short: Int16Array,
-  "short int": Int16Array,
-  "signed short": Int16Array,
-  "signed short int": Int16Array,
-  int16: Int16Array,
-  int16_t: Int16Array,
-  ushort: Uint16Array,
-  "unsigned short": Uint16Array,
-  "unsigned short int": Uint16Array,
-  uint16: Uint16Array,
-  uint16_t: Uint16Array,
-  int: Int32Array,
-  "signed int": Int32Array,
-  int32: Int32Array,
-  int32_t: Int32Array,
-  uint: Uint32Array,
-  "unsigned int": Uint32Array,
-  uint32: Uint32Array,
-  uint32_t: Uint32Array,
-  // OK for Node/V8/Chrome but not Firefox
-  // longlong: BigInt64Array,
-  // "long long": BigInt64Array,
-  // "long long int": BigInt64Array,
-  // "signed long long": BigInt64Array,
-  // "signed long long int": BigInt64Array,
-  // int64: BigInt64Array,
-  // int64_t: BigInt64Array,
-  // ulonglong: BigUint64Array,
-  // "unsigned long long": BigUint64Array,
-  // "unsigned long long int": BigUint64Array,
-  // uint64: BigUint64Array,
-  // uint64_t: BigUint64Array,
-  float: Float32Array,
-  double: Float64Array
-};
-
-const NRRD_TYPES_TO_VIEW_GET = {
-  "signed char": "getInt8",
-  int8: "getInt8",
-  int8_t: "getInt8",
-  uchar: "getUint8",
-  "unsigned char": "getUint8",
-  uint8: "getUint8",
-  uint8_t: "getUint8",
-  short: "getInt16",
-  "short int": "getInt16",
-  "signed short": "getInt16",
-  "signed short int": "getInt16",
-  int16: "getInt16",
-  int16_t: "getInt16",
-  ushort: "getUint16",
-  "unsigned short": "getUint16",
-  "unsigned short int": "getUint16",
-  uint16: "getUint16",
-  uint16_t: "getUint16",
-  int: "getInt32",
-  "signed int": "getInt32",
-  int32: "getInt32",
-  int32_t: "getInt32",
-  uint: "getUint32",
-  "unsigned int": "getUint32",
-  uint32: "getUint32",
-  uint32_t: "getUint32",
-  // OK for Node/V8/Chrome but not Firefox
-  // longlong: null,
-  // "long long": null,
-  // "long long int": null,
-  // "signed long long": null,
-  // "signed long long int": null,
-  // int64: null,
-  // int64_t: null,
-  // ulonglong: null,
-  // "unsigned long long": null,
-  // "unsigned long long int": null,
-  // uint64: null,
-  // uint64_t: null,
-  float: "getFloat32",
-  double: "getFloat64"
-};
-
-const SPACE_TO_SPACEDIMENSIONS = {
-  "right-anterior-superior": 3,
-  ras: 3,
-  "left-anterior-superior": 3,
-  las: 3,
-  "left-posterior-superior": 3,
-  lps: 3,
-  "right-anterior-superior-time": 4,
-  rast: 4,
-  "left-anterior-superior-time": 4,
-  last: 4,
-  "left-posterior-superior-time": 4,
-  lpst: 4,
-  "scanner-xyz": 3,
-  "scanner-xyz-time": 4,
-  "3d-right-handed": 3,
-  "3d-left-handed": 3,
-  "3d-right-handed-time": 4,
-  "3d-left-handed-time": 4
-};
-
-// in NRRD, some "kinds" have to respect a certain size. For example, the kind
-// "quaternion" has to be of size 4 (xyzw).
-// When the value is 'null', then no enforcement is made.
-// Note: the fields have been turned to lowercase here
-const KIND_TO_SIZE = {
-  domain: null,
-  space: null,
-  time: null,
-  list: null,
-  point: null,
-  vector: null,
-  "covariant-vector": null,
-  normal: null,
-  stub: 1,
-  scalar: 1,
-  complex: 2,
-  "2-vector": 2,
-  "3-color": 3,
-  "rgb-color": 3,
-  "hsv-color": 3,
-  "xyz-color": 3,
-  "4-color": 4,
-  "rgba-color": 4,
-  "3-vector": 3,
-  "3-gradient": 3,
-  "3-normal": 3,
-  "4-vector": 4,
-  quaternion: 4,
-  "2d-symmetric-matrix": 3,
-  "2d-masked-symmetric-matrix": 4,
-  "2d-matrix": 4,
-  "2d-masked-matrix": 4,
-  "3d-symmetric-matrix": 6,
-  "3d-masked-symmetric-matrix": 7,
-  "3d-matrix": 9,
-  "3d-masked-matrix": 10,
-  "???": null
-};
-
-/**
- * Parse a buffer of a NRRD file.
- * Throws an exception if the file is not a proper NRRD file.
- * @instance
- * @function parse
- * @param {ArrayBuffer} nrrdBuffer - the NRRD file buffer
- * @param {Object} options - the option object
- * @param {boolean} options.headerOnly - Parses only the header if true, parses header and data if false (default: false)
- * @return {Object} NRRD header and data such as {header: Object, data: TypedArray }
- */
-export const parse = function (nrrdBuffer, options) {
-  let magicControl = "NRRD000";
-  let magicTest = String.fromCharCode.apply(
-    null,
-    new Uint8Array(nrrdBuffer, 0, magicControl.length)
-  );
-
-  if (magicControl !== magicTest) {
-    throw new Error("This file is not a NRRD file");
-  }
-
-  let { header, dataByteOffset } = parseHeader(nrrdBuffer);
-
-  if ("headerOnly" in options && options.headerOnly) {
-    return { header: header, data: null };
-  }
-
-  let data = parseData(nrrdBuffer, header, dataByteOffset);
-  return { header: header, data: data };
-};
-
-/**
- * @private
- * Parses the header
- */
-function parseHeader(nrrdBuffer) {
-  let byteArrayHeader = [];
-  let dataStartPosition = null;
-  let view = new DataView(nrrdBuffer);
-
-  for (let i = 0; i < nrrdBuffer.byteLength; i++) {
-    byteArrayHeader.push(String.fromCharCode(view.getUint8(i)));
-
-    if (
-      i > 0 &&
-      byteArrayHeader[i - 1] === "\n" &&
-      byteArrayHeader[i] === "\n"
-    ) {
-      dataStartPosition = i + 1;
-      break;
-    }
-  }
-
-  if (dataStartPosition === null) {
-    throw new Error("The NRRD header is corrupted.");
-  }
-
-  let comments = [];
-
-  let headerLines = byteArrayHeader
-    .join("")
-    .trim()
-    .split(/\r\n|\n/)
-    .map(l => l.trim());
-
-  let preMap = headerLines
-    .slice(1)
-    .filter(s => {
-      // removing empty lines
-      return s.length > 0;
-    })
-    .filter(s => {
-      // removing comments
-      if (s[0] === "#") {
-        comments.push(s.slice(1).trim());
-      }
-      return s[0] !== "#";
-    })
-    .map(s => {
-      let keyVal = s.split(":");
-      return {
-        key: keyVal[0].trim(),
-        val: keyVal[1].trim()
-      };
-    });
-
-  let nrrdHeader = {};
-
-  preMap.forEach(field => {
-    nrrdHeader[field.key] = field.val;
-  });
-
-  // parsing each fields of the header
-  if (nrrdHeader["sizes"]) {
-    nrrdHeader["sizes"] = nrrdHeader.sizes.split(/\s+/).map(n => parseInt(n));
-  }
-
-  if (nrrdHeader["space dimension"]) {
-    nrrdHeader["space dimension"] = parseInt(nrrdHeader["space dimension"]);
-  }
-
-  if (nrrdHeader["space"]) {
-    nrrdHeader["space dimension"] =
-      SPACE_TO_SPACEDIMENSIONS[nrrdHeader["space"].toLowerCase()];
-  }
-
-  if (nrrdHeader["dimension"]) {
-    nrrdHeader["dimension"] = parseInt(nrrdHeader["dimension"]);
-  }
-
-  if (nrrdHeader["space directions"]) {
-    nrrdHeader["space directions"] = nrrdHeader["space directions"]
-      .split(/\s+/)
-      .map(triple => {
-        if (triple.trim() === "none") {
-          return null;
-        }
-        return triple
-          .slice(1, triple.length - 1)
-          .split(",")
-          .map(n => parseFloat(n));
-      });
-
-    if (nrrdHeader["space directions"].length !== nrrdHeader["dimension"]) {
-      throw new Error(
-        '"space direction" property has to contain as many elements as dimensions. Non-spatial dimesnsions must be refered as "none". See http://teem.sourceforge.net/nrrd/format.html#spacedirections for more info.'
-      );
-    }
-  }
-
-  if (nrrdHeader["space units"]) {
-    nrrdHeader["space units"] = nrrdHeader["space units"].split(/\s+/);
-  }
-
-  if (nrrdHeader["space origin"]) {
-    nrrdHeader["space origin"] = nrrdHeader["space origin"]
-      .slice(1, nrrdHeader["space origin"].length - 1)
-      .split(",")
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["measurement frame"]) {
-    nrrdHeader["measurement frame"] = nrrdHeader["measurement frame"]
-      .split(/\s+/)
-      .map(triple => {
-        if (triple.trim() === "none") {
-          return null;
-        }
-        return triple
-          .slice(1, triple.length - 1)
-          .split(",")
-          .map(n => parseFloat(n));
-      });
-  }
-
-  if (nrrdHeader["kinds"]) {
-    nrrdHeader["kinds"] = nrrdHeader["kinds"].split(/\s+/);
-
-    if (nrrdHeader["kinds"].length !== nrrdHeader["sizes"].length) {
-      throw new Error(
-        `The "kinds" property is expected to have has many elements as the "size" property.`
-      );
-    }
-
-    nrrdHeader["kinds"].forEach((k, i) => {
-      let expectedLength = KIND_TO_SIZE[k.toLowerCase()];
-      let foundLength = nrrdHeader["sizes"][i];
-      if (expectedLength !== null && expectedLength !== foundLength) {
-        throw new Error(
-          `The kind "${k}" expect a size of ${expectedLength} but ${foundLength} found`
-        );
-      }
-    });
-  }
-
-  if (nrrdHeader["min"]) {
-    nrrdHeader["min"] = parseFloat(nrrdHeader["min"]);
-  }
-
-  if (nrrdHeader["max"]) {
-    nrrdHeader["max"] = parseFloat(nrrdHeader["max"]);
-  }
-
-  if (nrrdHeader["old min"]) {
-    nrrdHeader["old min"] = parseFloat(nrrdHeader["old min"]);
-  }
-
-  if (nrrdHeader["old max"]) {
-    nrrdHeader["old max"] = parseFloat(nrrdHeader["old max"]);
-  }
-
-  if (nrrdHeader["spacings"]) {
-    nrrdHeader["spacings"] = nrrdHeader["spacings"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["thicknesses"]) {
-    nrrdHeader["thicknesses"] = nrrdHeader["thicknesses"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["axis mins"]) {
-    nrrdHeader["axis mins"] = nrrdHeader["axis mins"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["axismins"]) {
-    nrrdHeader["axismins"] = nrrdHeader["axismins"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["axis maxs"]) {
-    nrrdHeader["axis maxs"] = nrrdHeader["axis maxs"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["axismaxs"]) {
-    nrrdHeader["axismaxs"] = nrrdHeader["axismaxs"]
-      .split(/\s+/)
-      .map(n => parseFloat(n));
-  }
-
-  if (nrrdHeader["centers"]) {
-    nrrdHeader["centers"] = nrrdHeader["centers"].split(/\s+/).map(mode => {
-      if (mode === "cell" || mode === "node") {
-        return mode;
-      } else {
-        return null;
-      }
-    });
-  }
-
-  if (nrrdHeader["labels"]) {
-    nrrdHeader["labels"] = nrrdHeader["labels"].split(/\s+/);
-  }
-
-  // some additional metadata that are not part of the header will be added here
-  nrrdHeader.extra = {};
-
-  // adding the comments from lines starting with #
-  nrrdHeader.extra.comments = comments;
-
-  // having the stride can be handy.
-  nrrdHeader.extra.stride = [1];
-  for (let i = 1; i < nrrdHeader.sizes.length; i++) {
-    nrrdHeader.extra.stride.push(
-      nrrdHeader.extra.stride[i - 1] * nrrdHeader.sizes[i - 1]
-    );
-  }
-
-  return {
-    header: nrrdHeader,
-    dataByteOffset: dataStartPosition
-  };
-}
-
-/**
- * @private
- * Parses the data
- */
-function parseData(nrrdBuffer, header, dataByteOffset) {
-  let dataBuffer = null;
-  let arrayType = NRRD_TYPES_TO_TYPEDARRAY[header.type];
-  let nbElementsFromHeader = header.sizes.reduce((prev, curr) => prev * curr);
-  let min = +Infinity;
-  let max = -Infinity;
-  let data = null;
-
-  let isTextEncoded =
-    header.encoding === "ascii" ||
-    header.encoding === "txt" ||
-    header.encoding === "text";
-
-  if (header.encoding === "raw") {
-    dataBuffer = new Uint8Array(nrrdBuffer).slice(dataByteOffset).buffer;
-  } else if (isTextEncoded) {
-    let numbers = String.fromCharCode
-      .apply(null, new Uint8Array(nrrdBuffer, dataByteOffset))
-      .split(/\r\n|\n|\s/)
-      .map(s => s.trim())
-      .filter(s => s !== "")
-      .map(s => {
-        let numValue = parseFloat(s);
-        min = Math.min(min, numValue);
-        max = Math.max(max, numValue);
-        return numValue;
-      });
-    data = new arrayType(numbers);
-  } else if (header.encoding === "gzip" || header.encoding === "gz") {
-    dataBuffer = pako.inflate(new Uint8Array(nrrdBuffer).slice(dataByteOffset))
-      .buffer;
-  } else {
-    throw new Error('Only "raw", "ascii" and "gzip" encoding are supported.');
-  }
-
-  if (isTextEncoded) {
-    if (nbElementsFromHeader !== data.length) {
-      throw new Error("Unconsistency in data buffer length");
-    }
-  } else {
-    let nbElementsFromBufferAndType =
-      dataBuffer.byteLength / arrayType.BYTES_PER_ELEMENT;
-
-    if (nbElementsFromHeader !== nbElementsFromBufferAndType) {
-      throw new Error("Unconsistency in data buffer length");
-    }
-
-    data = new arrayType(nbElementsFromHeader);
-    let dataView = new DataView(dataBuffer);
-    let viewMethod = NRRD_TYPES_TO_VIEW_GET[header.type];
-    let littleEndian = header.endian === "little" ? true : false;
-
-    for (let i = 0; i < nbElementsFromHeader; i++) {
-      data[i] = dataView[viewMethod](
-        i * arrayType.BYTES_PER_ELEMENT,
-        littleEndian
-      );
-      min = Math.min(min, data[i]);
-      max = Math.max(max, data[i]);
-    }
-  }
-
-  header.extra.min = min;
-  header.extra.max = max;
-  return data;
-}

package/imaging/tools/README.md

@@ -1,27 +0,0 @@
-# Tools Management
-
-## Default tools
-
-In `default.ts` the list of Larvitar default tools is exported as `DEFAULT_TOOLS`, along with their default configuration, that extendes the cornerstoneTools configuration with these properties:
-
-```
-{
-    name : toolName (string),
-    viewports : "all" or [array of target viewports],
-    configuration : configuration {object},
-    options : options {object},
-    class : cornerstone tool library class name (ie "LengthTool" for Length tool),
-    sync : cornerstone synchronizer name (ie "wwwcSynchronizer" for Wwwc sync tool),
-    cleanable : if true, this tool will be removed when calling "no tools",
-    defaultActive : if true, this tool will be activated when calling "addDefaultTools",
-    shortcut : keyboard shortcut [not implemented],
-    type : tool category inside Larvitar (one of: "utils", "annotation", "segmentation", "overlay"),
-    description: a string that describes the tool (eg to be shown in a tooltip)
-}
-```
-
-These are the tools that will be added calling `addDefaultTools`. User can override defaults calling `setDefaultToolsProps`.
-
-## External Tools
-
-User can add custom tools calling `registerExternalTool`. The tool will be registered in the dvTools object and in DEFAULT*TOOLS array. If done \_before* adding the tools with `addDefaultTools`, the tool will be added automatically along with the default ones. Otherwise, the user can simply add its tool using `addTool`.

package/imaging/tools/custom/4dSliceScrollTool.js

@@ -1,146 +0,0 @@
-/** @module imaging/tools/custom/4dSliceScrollTool
- *  @desc  This file provides functionalities for an alternative scroll tool
- *  to handle 4d exam and navigate to the correct slice
- *
- *
- */
-
-// external libraries
-import cornerstoneTools from "cornerstone-tools";
-const external = cornerstoneTools.external;
-
-const BaseTool = cornerstoneTools.importInternal("base/BaseTool");
-const scroll = cornerstoneTools.importInternal("util/scroll");
-const scrollToIndex = cornerstoneTools.importInternal("util/scrollToIndex");
-const getToolState = cornerstoneTools.getToolState;
-const clip = cornerstoneTools.importInternal("util/clip");
-
-/**
- * @public
- * @class 4DScrollMouseWheelTool
- * @memberof Tools
- *
- * @classdesc Tool for scrolling through a series using the mouse wheel.
- * @extends Tools.Base.BaseTool
- */
-export default class Slice4DScrollMouseWheelTool extends BaseTool {
-  constructor(props = {}) {
-    const defaultProps = {
-      name: "Slice4DScrollMouseWheel",
-      supportedInteractionTypes: ["MouseWheel"],
-      configuration: {
-        loop: false,
-        allowSkipping: true,
-        invert: false
-      }
-    };
-    super(props, defaultProps);
-  }
-
-  mouseWheelCallback(evt) {
-    const { direction: images, element } = evt.detail;
-    const { loop, allowSkipping, invert, framesNumber } = this.configuration;
-    const direction = invert
-      ? images * framesNumber * -1
-      : images * framesNumber;
-    scroll(element, direction, loop, allowSkipping);
-    // scroll4DSlices(element, direction, loop, allowSkipping);
-  }
-}
-/**
- * Scrolls through the slice of a 4D stack.
- * @export @public @method
- * @name scroll4DSlices
- *
- * @param  {HTMLElement} element          The element to scroll.
- * @param  {number} images                The number of images to scroll through.
- * @param  {type} [loop = false]          Whether to loop the scrolling.
- * @param  {type} [allowSkipping = true]  Whether frames can be skipped.
- * @returns {void}
- */
-const scroll4DSlices = function (
-  element,
-  images,
-  loop,
-  allowSkipping,
-  framesNumber
-) {
-  const toolData = getToolState(element, "stack");
-
-  if (!toolData || !toolData.data || !toolData.data.length) {
-    return;
-  }
-
-  const stackData = toolData.data[0];
-
-  if (!stackData.pending) {
-    stackData.pending = [];
-  }
-
-  let newImageIdIndex = stackData.currentImageIdIndex + images; //+ 1 + framesNumber;
-  if (loop) {
-    const nbImages = stackData.imageIds.length;
-    newImageIdIndex %= nbImages;
-  } else {
-    newImageIdIndex = clip(newImageIdIndex, 0, stackData.imageIds.length - 1);
-  }
-
-  if (allowSkipping) {
-    scrollToIndex(element, newImageIdIndex);
-  } else {
-    const pendingEvent = {
-      index: newImageIdIndex
-    };
-
-    stackData.pending.push(pendingEvent);
-    scrollWithoutSkipping(stackData, pendingEvent, element);
-  }
-};
-
-/**
- * Recursively scrolls the stack until the desired image is reached.
- * @private
- * @method
- * @name scrollWithoutSkipping
- *
- * @param  {type} stackData    Data object containing information about the stack.
- * @param  {Object} pendingEvent The event to process next.
- * @param  {HTMLElement} element      The element being scrolled through.
- * @returns {void}
- */
-function scrollWithoutSkipping(stackData, pendingEvent, element) {
-  if (stackData.pending[0] === pendingEvent) {
-    if (stackData.currentImageIdIndex === pendingEvent.index) {
-      stackData.pending.splice(stackData.pending.indexOf(pendingEvent), 1);
-
-      if (stackData.pending.length > 0) {
-        scrollWithoutSkipping(stackData, stackData.pending[0], element);
-      }
-
-      return;
-    }
-
-    const newImageHandler = function (event) {
-      const index = stackData.imageIds.indexOf(event.detail.image.imageId);
-
-      if (index === pendingEvent.index) {
-        stackData.pending.splice(stackData.pending.indexOf(pendingEvent), 1);
-        element.removeEventListener(
-          external.cornerstone.EVENTS.NEW_IMAGE,
-          newImageHandler
-        );
-
-        if (stackData.pending.length > 0) {
-          scrollWithoutSkipping(stackData, stackData.pending[0], element);
-        }
-      }
-    };
-
-    element.addEventListener(
-      external.cornerstone.EVENTS.NEW_IMAGE,
-      newImageHandler
-    );
-
-    scrollToIndex(element, pendingEvent.index);
-  }
-}