larvitar 0.18.2 → 1.2.0

package/imaging/image_parsing.js

@@ -1,307 +0,0 @@
-/** @module imaging/parsing
- *  @desc  This file provides functionalities for parsing DICOM image files
- */
-
-// external libraries
-import { parseDicom } from "dicom-parser";
-import { forEach, each, has, pick } from "lodash";
-
-// internal libraries
-import { getPixelRepresentation, randomId, parseTag } from "./image_utils.js";
-import { updateLoadedStack } from "./image_loading.js";
-import { checkMemoryAllocation } from "./monitors/memory.js";
-
-// global module variables
-var parsingQueueFlag = null; // flag to handle the queue
-var t0 = null; // t0 variable for timing debugging purpose
-
-/*
- * This module provides the following functions to be exported:
- * readFiles(fileList, callback)
- * readFile(file, callback)
- * dumpDataSet(dataSet, metadata, customFilter)
- * clearImageParsing(seriesStack)
- */
-
-/**
- * Reset series stack object and its internal data
- * @instance
- * @function clearImageParsing
- * @param {Object} seriesStack - Parsed series stack object
- */
-export const clearImageParsing = function (seriesStack) {
-  each(seriesStack, function (stack) {
-    each(stack.instances, function (instance) {
-      if (instance.dataSet) {
-        instance.dataSet.byteArray = null;
-      }
-      instance.dataSet = null;
-      instance.file = null;
-      instance.metadata = null;
-    });
-  });
-  seriesStack = null;
-};
-
-/**
- * Read dicom files and return allSeriesStack object
- * @instance
- * @function readFiles
- * @param {Array} entries - List of file objects
- * @param {Function} callback - Will receive (imageObject, errorString) as args
- */
-export const readFiles = function (entries, callback) {
-  let allSeriesStack = {};
-  let parsingQueue = [];
-  dumpFiles(entries, parsingQueue, allSeriesStack, callback);
-};
-
-/**
- * Read a single dicom file and return parsed object
- * @instance
- * @function readFile
- * @param {File} entry - File object
- * @param {Function} callback - Will receive (imageObject, errorString) as args
- */
-export const readFile = function (entry, callback) {
-  dumpFile(entry, callback);
-};
-
-/* Internal module functions */
-
-/**
- * Dump metadata from dicom parser dataSet object
- * @instance
- * @function dumpDataSet
- * @param {Object} dataSet - dicom parser dataSet object
- * @param {Array} metadata - Initialized metadata object
- * @param {Array} customFilter - Optional filter: {tags:[], frameId: 0}
- */
-// This function iterates through dataSet recursively and adds new HTML strings
-// to the output array passed into it
-export const dumpDataSet = function (dataSet, metadata, customFilter) {
-  // customFilter= {tags:[], frameId:xxx}
-  // the dataSet.elements object contains properties for each element parsed.  The name of the property
-  // is based on the elements tag and looks like 'xGGGGEEEE' where GGGG is the group number and EEEE is the
-  // element number both with lowercase hexadecimal letters.  For example, the Series Description DICOM element 0008,103E would
-  // be named 'x0008103e'.  Here we iterate over each property (element) so we can build a string describing its
-  // contents to add to the output array
-  try {
-    let elements =
-      customFilter && has(customFilter, "tags")
-        ? pick(dataSet.elements, customFilter.tags)
-        : dataSet.elements;
-    for (let propertyName in elements) {
-      let element = elements[propertyName];
-      // Here we check for Sequence items and iterate over them if present.  items will not be set in the
-      // element object for elements that don't have SQ VR type.  Note that implicit little endian
-      // sequences will are currently not parsed.
-      if (element.items) {
-        // each item contains its own data set so we iterate over the items
-        // and recursively call this function
-        if (customFilter && has(customFilter, "frameId")) {
-          let item = element.items[customFilter.frameId];
-          dumpDataSet(item.dataSet, metadata);
-        } else {
-          element.items.forEach(function (item) {
-            dumpDataSet(item.dataSet, metadata);
-          });
-        }
-      } else {
-        let tagValue = parseTag(dataSet, propertyName, element);
-        metadata[propertyName] = tagValue;
-      }
-    }
-  } catch (err) {
-    console.log(err);
-  }
-};
-
-/**
- * Manage the parsing process waiting for the parsed object before proceeding with the next parse request
- * @inner
- * @function parseNextFile
- * @param {Array} parsingQueue - Array of queued files to be parsed
- * @param {Object} allSeriesStack - Series stack object to be populated
- * @param {Function} callback - Passed through
- */
-let parseNextFile = function (parsingQueue, allSeriesStack, callback) {
-  // initialize t0 on first file of the queue
-  if (
-    Object.keys(allSeriesStack).length === 0 &&
-    allSeriesStack.constructor === Object
-  ) {
-    t0 = performance.now();
-  }
-
-  if (!parsingQueueFlag || parsingQueue.length === 0) {
-    if (parsingQueue.length === 0) {
-      let t1 = performance.now();
-      console.log(`Call to readFiles took ${t1 - t0} milliseconds.`);
-      parsingQueueFlag = null;
-      callback(allSeriesStack);
-    }
-    return;
-  }
-
-  parsingQueueFlag = false;
-
-  // remove and return first item from queue
-  let file = parsingQueue.shift();
-
-  // Check if there is enough memory to dump the file
-  if (checkMemoryAllocation(file.size) === false) {
-    // do not parse the file and stop parsing
-    clearImageParsing(allSeriesStack);
-    let t1 = performance.now();
-    console.log(`Call to readFiles took ${t1 - t0} milliseconds.`);
-    parsingQueueFlag = null;
-    file = null;
-    callback(allSeriesStack, "Available memory is not enough");
-  } else {
-    // parse the file and wait for results
-    dumpFile(file, function (seriesData, err) {
-      if (parsingQueueFlag === null) {
-        console.log("parsingQueueFlag is null");
-        // parsing process has been stopped, but there could be a
-        // dumpFile callback still working: prevent actions
-        return;
-      }
-      if (err) {
-        console.warn(err);
-        parsingQueueFlag = true;
-        parseNextFile(parsingQueue, allSeriesStack, callback);
-      } else {
-        // add file to cornerstoneWADOImageLoader file manager
-        updateLoadedStack(seriesData, allSeriesStack);
-        // proceed with the next file to parse
-        parsingQueueFlag = true;
-        parseNextFile(parsingQueue, allSeriesStack, callback);
-      }
-      file = null;
-      seriesData = null;
-    });
-  }
-};
-
-/**
- * Push files in queue and start parsing next file
- * @inner
- * @function dumpFiles
- * @param {Array} fileList - Array of file objects
- * @param {Array} parsingQueue - Array of queued files to be parsed
- * @param {Object} allSeriesStack - Series stack object to be populated
- * @param {Function} callback - Passed through
- */
-let dumpFiles = function (fileList, parsingQueue, allSeriesStack, callback) {
-  forEach(fileList, function (file) {
-    if (!file.name.startsWith(".") && !file.name.startsWith("DICOMDIR")) {
-      parsingQueue.push(file);
-      // enable parsing on first available path
-      if (parsingQueueFlag === null) {
-        parsingQueueFlag = true;
-      }
-    }
-  });
-  parseNextFile(parsingQueue, allSeriesStack, callback);
-};
-
-/**
- * Dump a single DICOM File (metaData and pixelData)
- * @inner
- * @function dumpFile
- * @param {File} file - File object to be dumped
- * @param {Function} callback - called with (imageObject, errorString)
- */
-let dumpFile = function (file, callback) {
-  let reader = new FileReader();
-  reader.onload = function () {
-    let arrayBuffer = reader.result;
-    // Here we have the file data as an ArrayBuffer.
-    // dicomParser requires as input a Uint8Array so we create that here.
-    let byteArray = new Uint8Array(arrayBuffer);
-
-    let dataSet;
-    try {
-      dataSet = parseDicom(byteArray);
-      byteArray = null;
-      let metadata = {};
-      dumpDataSet(dataSet, metadata);
-
-      let numberOfFrames = metadata["x00280008"];
-      let isMultiframe = numberOfFrames > 1 ? true : false;
-      // Overwrite SOPInstanceUID to manage multiframes.
-      // Usually different SeriesInstanceUID means different series and that value
-      // is used into the application to group different instances into the same series,
-      // but if a DICOM file contains a multiframe series, then the SeriesInstanceUID
-      // can be shared by other files of the same study.
-      // In multiframe cases, the SOPInstanceUID (unique) is used as SeriesInstanceUID.
-      let seriesInstanceUID = isMultiframe
-        ? metadata["x00080018"]
-        : metadata["x0020000e"];
-      let pixelSpacing = metadata["x00280030"];
-      let imageOrientation = metadata["x00200037"];
-      let imagePosition = metadata["x00200032"];
-      let sliceThickness = metadata["x00180050"];
-
-      if (dataSet.warnings.length > 0) {
-        // warnings
-        callback(null, dataSet.warnings);
-      } else {
-        let pixelDataElement = dataSet.elements.x7fe00010;
-
-        if (pixelDataElement) {
-          // done, pixelDataElement found
-          let instanceUID = metadata["x00080018"] || randomId();
-          let imageObject = {
-            // data needed for rendering
-            file: file,
-            dataSet: dataSet
-          };
-          imageObject.metadata = metadata;
-          imageObject.metadata.seriesUID = seriesInstanceUID;
-          imageObject.metadata.instanceUID = instanceUID;
-          imageObject.metadata.studyUID = metadata["x0020000d"];
-          imageObject.metadata.accessionNumber = metadata["x00080050"];
-          imageObject.metadata.studyDescription = metadata["x00081030"];
-          imageObject.metadata.patientName = metadata["x00100010"];
-          imageObject.metadata.patientBirthdate = metadata["x00100030"];
-          imageObject.metadata.seriesDescription = metadata["x0008103e"];
-          imageObject.metadata.seriesDate = metadata["x00080021"];
-          imageObject.metadata.seriesModality =
-            metadata["x00080060"].toLowerCase();
-          imageObject.metadata.intercept = metadata["x00281052"];
-          imageObject.metadata.slope = metadata["x00281053"];
-          imageObject.metadata.pixelSpacing = pixelSpacing;
-          imageObject.metadata.sliceThickness = sliceThickness;
-          imageObject.metadata.imageOrientation = imageOrientation;
-          imageObject.metadata.imagePosition = imagePosition;
-          imageObject.metadata.rows = metadata["x00280010"];
-          imageObject.metadata.cols = metadata["x00280011"];
-          imageObject.metadata.numberOfSlices = metadata["x00540081"]
-            ? metadata["x00540081"] // number of slices
-            : metadata["x00201002"]; // number of instances
-          imageObject.metadata.numberOfFrames = numberOfFrames;
-          if (isMultiframe) {
-            imageObject.metadata.frameTime = metadata["x00181063"];
-            imageObject.metadata.frameDelay = metadata["x00181066"];
-          }
-          imageObject.metadata.windowCenter = metadata["x00281050"];
-          imageObject.metadata.windowWidth = metadata["x00281051"];
-          imageObject.metadata.minPixelValue = metadata["x00280106"];
-          imageObject.metadata.maxPixelValue = metadata["x00280107"];
-          imageObject.metadata.length = pixelDataElement.length;
-          imageObject.metadata.repr = getPixelRepresentation(dataSet);
-          callback(imageObject);
-        } else {
-          // done, no pixelData
-          callback(null, "no pixelData.");
-        }
-      }
-    } catch (err) {
-      console.log(err);
-      callback(null, "can not read this file.");
-    }
-  };
-  reader.readAsArrayBuffer(file);
-};

package/imaging/image_reslice.js

@@ -1,80 +0,0 @@
-/** @module imaging/reslice
- *  @desc  This file provides functionalities for
- *         image reslice in orthogonal directions
- */
-
-// external libraries
-import { v4 as uuidv4 } from "uuid";
-import { each } from "lodash";
-
-// internal libraries
-import { getReslicedMetadata, getReslicedPixeldata } from "./image_utils";
-import {
-  getLarvitarImageTracker,
-  getLarvitarManager
-} from "./loaders/commonLoader";
-import { larvitar_store } from "./image_store";
-
-/*
- * This module provides the following functions to be exported:
- * resliceSeries(seriesId, seriesData, orientation, callback)
- */
-
-/**
- * Reslice a serie from native orientation to coronal or sagittal orientation
- * @instance
- * @function resliceSeries
- * @param {Object} seriesData the original series data
- * @param {String} orientation the reslice orientation [coronal or sagittal]
- * @param {String} seriesId the series id
- * @return {Object} cornerstone data
- */
-export function resliceSeries(seriesData, orientation, callback) {
-  let reslicedSeries = {};
-  let reslicedSeriesId = uuidv4();
-  let reslicedMetaData = getReslicedMetadata(
-    reslicedSeriesId,
-    "axial",
-    orientation,
-    seriesData,
-    "resliceLoader"
-  );
-
-  reslicedSeries.imageIds = reslicedMetaData.imageIds;
-  reslicedSeries.instances = reslicedMetaData.instances;
-
-  reslicedSeries.currentImageIdIndex = Math.floor(
-    reslicedSeries.imageIds.length / 2
-  );
-
-  function computeReslice(
-    seriesData,
-    reslicedSeriesId,
-    reslicedSeries,
-    callback
-  ) {
-    let t0 = performance.now();
-    let imageTracker = getLarvitarImageTracker();
-    let manager = getLarvitarManager();
-    each(reslicedSeries.imageIds, function (imageId) {
-      reslicedSeries.instances[imageId].pixelData = getReslicedPixeldata(
-        imageId,
-        seriesData,
-        reslicedSeries
-      );
-      imageTracker[imageId] = reslicedSeriesId;
-    });
-    larvitar_store.addSeriesIds(reslicedSeriesId, reslicedSeries.imageIds);
-    reslicedSeries.numberOfImages = reslicedSeries.imageIds.length;
-    reslicedSeries.seriesUID = reslicedSeriesId;
-    reslicedSeries.seriesDescription = seriesData.seriesDescription;
-    reslicedSeries.orientation = orientation;
-    manager[reslicedSeriesId] = reslicedSeries;
-    manager[seriesData.seriesUID][orientation] = reslicedSeriesId;
-    let t1 = performance.now();
-    console.log(`Call to resliceSeries took ${t1 - t0} milliseconds.`);
-    callback(reslicedSeries);
-  }
-  // reslice the data
-  computeReslice(seriesData, reslicedSeriesId, reslicedSeries, callback);
-}