larvitar 0.20.0 → 1.2.2

package/index.js

@@ -5,6 +5,7 @@ console.log(`LARVITAR v${VERSION}`);
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
 import cornerstoneWADOImageLoader from "cornerstone-wado-image-loader";
+const segModule = cornerstoneTools.getModule("segmentation");
 
 import larvitarModule from "./modules/vuex/larvitar";
 
@@ -14,15 +15,15 @@ import {
   getAvailableMemory
 } from "./imaging/monitors/memory";
 
-import { initLarvitarStore, larvitar_store } from "./imaging/image_store";
+import { initLarvitarStore, larvitar_store } from "./imaging/imageStore";
 
-import { parseContours } from "./imaging/image_contours";
+import { parseContours } from "./imaging/imageContours";
 
 import {
   getImagePresets,
   setImagePreset,
   setImageCustomPreset
-} from "./imaging/image_presets";
+} from "./imaging/imagePresets";
 
 import {
   getNormalOrientation,
@@ -37,7 +38,7 @@ import {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices
-} from "./imaging/image_utils";
+} from "./imaging/imageUtils";
 
 import {
   buildHeader,
@@ -45,16 +46,16 @@ import {
   buildData,
   buildDataAsync,
   importNRRDImage
-} from "./imaging/image_io";
+} from "./imaging/imageIo";
 
-import { anonymize, encrypt } from "./imaging/image_anonymization";
+import { anonymize, encrypt } from "./imaging/imageAnonymization";
 
 import {
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer
-} from "./imaging/image_layers";
+} from "./imaging/imageLayers";
 
 import {
   initializeImageLoader,
@@ -64,14 +65,14 @@ import {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack
-} from "./imaging/image_loading";
+} from "./imaging/imageLoading";
 
 import {
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing
-} from "./imaging/image_parsing";
+} from "./imaging/imageParsing";
 
 import {
   clearImageCache,
@@ -91,9 +92,9 @@ import {
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight
-} from "./imaging/image_rendering";
+} from "./imaging/imageRendering";
 
-import { resliceSeries } from "./imaging/image_reslice";
+import { resliceSeries } from "./imaging/imageReslice";
 
 import {
   addDiameterTool,
@@ -111,7 +112,7 @@ import {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig
-} from "./imaging/image_tools";
+} from "./imaging/imageTools";
 
 import {
   csToolsCreateStack,
@@ -126,13 +127,13 @@ import {
   setToolEnabled,
   setToolPassive,
   exportAnnotations
-} from "./imaging/tools/tools.main";
+} from "./imaging/tools/main";
 
 import {
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps
-} from "./imaging/tools/tools.default";
+} from "./imaging/tools/default";
 
 import {
   initSegmentationModule,
@@ -142,7 +143,7 @@ import {
   undoLastStroke,
   redoLastStroke,
   setBrushProps
-} from "./imaging/tools/tools.segmentation";
+} from "./imaging/tools/segmentation";
 
 import {
   updateLarvitarManager,
@@ -189,20 +190,21 @@ import {
   addColorMap,
   fillPixelData,
   HSVToRGB
-} from "./imaging/image_colormaps";
+} from "./imaging/imageColormaps";
 
-import { saveAnnotations, loadAnnotations } from "./imaging/tools/tools.io";
+import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
 
 import {
   addMouseKeyHandlers,
   toggleMouseToolsListeners
-} from "./imaging/tools/tools.interaction";
+} from "./imaging/tools/interaction";
 
 export {
   VERSION,
   // global cornerstone variables
   cornerstone,
   cornerstoneTools,
+  segModule,
   cornerstoneWADOImageLoader,
   // vuex module
   larvitarModule,
@@ -210,14 +212,14 @@ export {
   checkMemoryAllocation,
   getUsedMemory,
   getAvailableMemory,
-  // larvitar store
+  // larvitarStore
   initLarvitarStore,
   larvitar_store,
-  // image_presets
+  // imagePresets
   getImagePresets,
   setImagePreset,
   setImageCustomPreset,
-  // image_utils
+  // imageUtils
   getNormalOrientation,
   getMinPixelValue,
   getMaxPixelValue,
@@ -230,21 +232,21 @@ export {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices,
-  // image_io
+  // imageIo
   buildHeader,
   getCachedPixelData,
   buildData,
   buildDataAsync,
   importNRRDImage,
-  // image_anonymization
+  // imageAnonymization
   anonymize,
   encrypt,
-  // image_layers
+  // imageLayers
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer,
-  // image_loading
+  // imageLoading
   initializeImageLoader,
   initializeWebImageLoader,
   initializeFileImageLoader,
@@ -252,12 +254,12 @@ export {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack,
-  // image_parsing
+  // imageParsing
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing,
-  // image_rendering
+  // imageRendering
   clearImageCache,
   loadAndCacheImages,
   renderFileImage,
@@ -276,15 +278,15 @@ export {
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight,
-  // image_reslice
+  // imageReslice
   resliceSeries,
-  // image_colormaps
+  // imageColormaps
   getColormapsList,
   applyColorMap,
   addColorMap,
   fillPixelData,
   HSVToRGB,
-  // image_contours
+  // imageContours
   parseContours,
   // loaders/commonLoader
   updateLarvitarManager,
@@ -307,7 +309,7 @@ export {
   // loaders/dicomLoader
   getDicomImageId,
   cacheImages,
-  // loaders/multiFrameLoader
+  // loaders/multiframeLoader
   loadMultiFrameImage,
   buildMultiFrameImage,
   getMultiFrameImageId,
@@ -318,7 +320,7 @@ export {
   resetFileManager,
   populateFileManager,
   getFileImageId,
-  // image_tools
+  // imageTools
   addDiameterTool,
   addContoursTool,
   addMaskEditingTool,
@@ -334,7 +336,7 @@ export {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig,
-  // tools.main
+  // tools/main
   csToolsCreateStack,
   csToolsUpdateImageIds,
   csToolsUpdateImageIndex,
@@ -347,16 +349,16 @@ export {
   setToolEnabled,
   setToolPassive,
   exportAnnotations,
-  // tools.default
+  // tools/default
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps,
-  // tools.io
+  // tools/io
   saveAnnotations,
   loadAnnotations,
-  // tools.interaction
+  // tools/interaction
   addMouseKeyHandlers,
-  // tools.segmentation
+  // tools/segmentation
   initSegmentationModule,
   addSegmentationMask,
   setActiveLabelmap,

package/modules/vuex/larvitar.js

@@ -1,4 +1,4 @@
-// Larvitare storage
+// Larvitar Vuex storage
 
 import Vue from "vue";
 
@@ -99,6 +99,7 @@ export default {
     },
     removeSeriesIds: ({ state }, seriesId) =>
       Vue.delete(state.series, seriesId),
+    resetSeriesIds: ({ state }) => Vue.set(state.series, {}),
     setErrorLog: () => {}, // TODO LT pass elementId
 
     // Series fields setters

package/package.json

@@ -1,11 +1,13 @@
 {
   "name": "larvitar",
   "keywords": [
-    "dicom",
-    "imaging"
+    "DICOM",
+    "imaging",
+    "medical",
+    "cornerstone"
   ],
-  "version": "0.20.0",
-  "description": "javascript library for loading, rendering and interact with DICOM images",
+  "version": "1.2.2",
+  "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
     "type": "git"
@@ -18,15 +20,16 @@
   "author": "Simone Manini <simone.manini@dvisionlab.com> (https://www.dvisionlab.com)",
   "contributors": [
     "Mattia Ronzoni <mattia.ronzoni@dvisionlab.com> (https://www.dvisionlab.com)",
-    "Sara Zanchi <sara.zanchi@dvisionlab.com> (https://www.dvisionlab.com)"
+    "Sara Zanchi <sara.zanchi@dvisionlab.com> (https://www.dvisionlab.com)",
+    "Ale Re <ale.re@dvisionlab.com> (https://www.dvisionlab.com)"
   ],
   "license": "MIT",
   "dependencies": {
     "@rollup/plugin-commonjs": "^17.1.0",
-    "cornerstone-core": "^2.6.0",
+    "cornerstone-core": "^2.6.1",
     "cornerstone-file-image-loader": "^0.3.0",
-    "cornerstone-tools": "^5.3.0",
-    "cornerstone-wado-image-loader": "^3.3.2",
+    "cornerstone-tools": "^6.0.6",
+    "cornerstone-wado-image-loader": "^4.0.1",
     "cornerstone-web-image-loader": "^2.1.1",
     "crypto-js": "^4.1.1",
     "dicom-character-set": "^1.0.3",

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);
-};