larvitar 1.5.13 → 2.0.0

package/imaging/types.d.ts

@@ -0,0 +1,197 @@
+import { vec2 } from "cornerstone-core";
+import { DataSet } from "dicom-parser";
+import { DEFAULT_VIEWPORT } from "./imageStore";
+import { NrrdSeries } from "./loaders/nrrdLoader";
+import { MetaDataTypes } from "./MetaDataTypes";
+import { MetaDataReadable } from "./MetaDataReadable";
+
+// TODO-ts: differentiate each single metadata @szanchi
+/*export type MetadataValue =
+  | string
+  | number
+  | string[]
+  | number[]
+  | boolean
+  | null
+  | Array
+  | undefined; // null or undefined is only for nrrd*/
+
+export type MetaData = MetaDataTypes & MetaDataReadable;
+export interface Image extends cornerstone.Image {
+  render?: Function;
+  decodeTimeInMS?: number;
+  loadTimeInMS?: number;
+  webWorkerTimeInMS?: number;
+  metadata: MetaData;
+  data?: DataSet;
+  floatPixelData?: Float32Array;
+}
+
+export type Instance = {
+  metadata: MetaData;
+  pixelData?: TypedArray | null;
+  dataSet?: DataSet | null;
+  file?: File | null;
+  instanceId?: string;
+  frame?: number;
+};
+
+export type ReslicedInstance = {
+  metadata: MetaData;
+  instanceId?: string;
+  permuteTable?: [number, number, number];
+};
+
+export type StagedProtocol = {
+  numberOfStages: number; // Number of stages
+  numberOfViews: number; // Number of views in stage
+  stageName?: string; // Name of the stage
+  stageNumber?: number; // Number of the stage
+  viewName?: string; // Name of the view
+  viewNumber?: number; // Number of the view
+};
+
+export type Series = {
+  imageIds: string[];
+  instances: { [key: string]: Instance };
+  seriesDescription?: string;
+  anonymized?: boolean;
+  bytes: number;
+  seriesUID: string;
+  currentImageIdIndex: number;
+  numberOfImages?: number;
+  isMultiframe: boolean;
+  color?: boolean;
+  dataSet: DataSet | null;
+  metadata?: MetaData;
+  frameDelay?: number;
+  frameTime?: number;
+  rWaveTimeVector?: number[];
+  instanceUIDs: { [key: string]: string };
+  is4D: boolean;
+  isPDF: boolean;
+  stagedProtocol?: StagedProtocol;
+  modality: string;
+  numberOfFrames: number;
+  numberOfSlices: number;
+  numberOfTemporalPositions: number;
+  studyUID: string;
+  larvitarSeriesInstanceUID: string;
+  elements?: { [key: string]: any } | null;
+  layer: Layer;
+  orientation?: "axial" | "coronal" | "sagittal"; // this is needed for legacy reslice
+};
+
+export interface Layer extends cornerstone.EnabledElementLayer {
+  id: string;
+}
+
+export interface Viewport extends cornerstone.Viewport {
+  newImageIdIndex: number;
+  displayedArea: {
+    brhc: {
+      x: number;
+      y: number;
+    };
+  };
+}
+
+export type Contours = {
+  [key: string]: {
+    [key: string]: Array<{
+      x?: number;
+      y?: number;
+      lines: vec2[][];
+    }>;
+  };
+};
+
+export type Header = {
+  volume: Volume;
+  [imageId: string]: Instance.metadata;
+};
+
+export type Volume = {
+  imageIds: string[];
+  seriesId: string;
+  rows: number;
+  cols: number;
+  slope: number;
+  repr: string;
+  intercept: number;
+  imagePosition: [number, number];
+  numberOfSlices: number;
+  imageOrientation: [number, number, number];
+  pixelSpacing: [number, number];
+  sliceThickness: number;
+  phase?: string;
+  study_description?: string;
+  series_description?: string;
+  acquisition_date?: string;
+};
+
+export type LarvitarManager = {
+  [key: string]: NrrdSeries | Series;
+} | null;
+
+export type ImageFrame = {
+  pixelData?: Uint8ClampedArray | Uint16Array | Int16Array | Uint8Array;
+  bitsAllocated: number;
+  rows: number;
+  columns: number;
+  photometricInterpretation: string;
+  samplesPerPixel: number;
+  smallestPixelValue: number;
+  largestPixelValue: number;
+  imageData?: ImageData;
+  pixelRepresentation: number;
+};
+
+export type ImageTracker = {
+  [key: string]: string;
+} | null;
+
+// the result of readFile
+export type ImageObject = {
+  file: File;
+  instanceUID: string;
+  metadata: MetaData;
+  dataSet: DataSet;
+};
+
+export type CachingResponse = {
+  seriesId: string;
+  loading: number;
+  series: Partial<Series>;
+};
+
+export interface CustomDataSet extends DataSet {
+  repr?: string;
+}
+
+type Orientation = "axial" | "coronal" | "sagittal";
+
+type TypedArray =
+  | Float64Array
+  | Uint8Array
+  | Int8Array
+  | Uint16Array
+  | Int16Array
+  | Int32Array
+  | Uint32Array
+  | Float32Array;
+
+type StoreViewport = typeof DEFAULT_VIEWPORT;
+
+type StoreViewportOptions = {
+  numberOfSlices?: number;
+  sliceNumber?: number;
+  wc?: number;
+  ww?: number;
+  defaultWC?: number;
+  defaultWW?: number;
+  scale?: number;
+  colormap?: string;
+  tr_x?: number;
+  tr_y?: number;
+};

package/{index.js → index.ts}

@@ -1,24 +1,39 @@
 import pkg from "./package.json";
-const VERSION = pkg.version;
-console.log(`LARVITAR v${VERSION}`);
+const VERSION: string = pkg.version;
+console.groupCollapsed(
+  `%cLARVITAR %cv${VERSION}`,
+  "color: #404888; background: #209A71; font-weight: 900;",
+  "color: #BED730; background: #209A71; font-weight: 900;"
+);
 
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
+import { parseDicom } from "dicom-parser";
+
 import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 const segModule = cornerstoneTools.getModule("segmentation");
 
-import larvitarModule from "./modules/vuex/larvitar";
-
 import {
+  checkAndClearMemory,
   checkMemoryAllocation,
   getUsedMemory,
   getAvailableMemory
 } from "./imaging/monitors/memory";
 
-import { initLarvitarStore, larvitar_store } from "./imaging/imageStore";
+import {
+  getPerformanceMonitor,
+  activatePerformanceMonitor,
+  deactivatePerformanceMonitor
+} from "./imaging/monitors/performance";
+
+import store from "./imaging/imageStore";
+console.log(store);
+console.groupEnd();
 
 import { parseContours } from "./imaging/imageContours";
 
+import { parseECG } from "./imaging/parsers/ecg";
+
 import {
   getImagePresets,
   setImagePreset,
@@ -31,7 +46,6 @@ import {
   getMaxPixelValue,
   getPixelRepresentation,
   getTypedArrayFromDataType,
-  getPixelTypedArray,
   getSortedStack,
   randomId,
   getMeanValue,
@@ -133,8 +147,10 @@ import {
 
 import {
   DEFAULT_TOOLS,
+  dvTools,
   getDefaultToolsByType,
-  setDefaultToolsProps
+  setDefaultToolsProps,
+  registerExternalTool
 } from "./imaging/tools/default";
 
 import {
@@ -164,7 +180,8 @@ import {
   resetLarvitarManager,
   removeSeriesFromLarvitarManager,
   getSeriesDataFromLarvitarManager,
-  getImageFrame
+  getImageFrame,
+  getSopInstanceUIDFromLarvitarManager
 } from "./imaging/loaders/commonLoader";
 
 import {
@@ -176,7 +193,11 @@ import {
   getNrrdSerieDimensions
 } from "./imaging/loaders/nrrdLoader";
 
-import { getDicomImageId, cacheImages } from "./imaging/loaders/dicomLoader";
+import {
+  getDicomImageId,
+  cacheImage,
+  cacheImages
+} from "./imaging/loaders/dicomLoader";
 
 import { loadReslicedImage } from "./imaging/loaders/resliceLoader";
 
@@ -216,17 +237,22 @@ export {
   // global cornerstone variables
   cornerstone,
   cornerstoneTools,
+  parseDicom,
   segModule,
   cornerstoneDICOMImageLoader,
-  // vuex module
-  larvitarModule,
   // memory module
+  checkAndClearMemory,
   checkMemoryAllocation,
   getUsedMemory,
   getAvailableMemory,
+  // performance module
+  getPerformanceMonitor,
+  activatePerformanceMonitor,
+  deactivatePerformanceMonitor,
   // larvitarStore
-  initLarvitarStore,
-  larvitar_store,
+  store,
+  // parsers
+  parseECG,
   // imagePresets
   getImagePresets,
   setImagePreset,
@@ -237,7 +263,6 @@ export {
   getMaxPixelValue,
   getPixelRepresentation,
   getTypedArrayFromDataType,
-  getPixelTypedArray,
   getSortedStack,
   randomId,
   getMeanValue,
@@ -310,6 +335,7 @@ export {
   removeSeriesFromLarvitarManager,
   getSeriesDataFromLarvitarManager,
   getImageFrame,
+  getSopInstanceUIDFromLarvitarManager,
   // loaders/nrrdLoader
   buildNrrdImage,
   getNrrdImageId,
@@ -321,6 +347,7 @@ export {
   loadReslicedImage,
   // loaders/dicomLoader
   getDicomImageId,
+  cacheImage,
   cacheImages,
   // loaders/multiframeLoader
   loadMultiFrameImage,
@@ -364,8 +391,10 @@ export {
   exportAnnotations,
   // tools/default
   DEFAULT_TOOLS,
+  dvTools,
   getDefaultToolsByType,
   setDefaultToolsProps,
+  registerExternalTool,
   // tools/io
   saveAnnotations,
   loadAnnotations,

package/jsdoc.json

@@ -3,7 +3,7 @@
     "allowUnknownTags": true
   },
   "source": {
-    "include": ["imaging/", "./README.md"]
+    "include": ["dist/", "./README.md"]
   },
   "plugins": ["plugins/markdown"],
   "opts": {

package/package.json

@@ -6,22 +6,26 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.5.13",
-  "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
+  "version": "2.0.0",
+  "description": "typescript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
     "type": "git"
   },
+  "main": "index.ts",
   "scripts": {
+    "coverage": "typescript-coverage-report",
     "generate-docs": "node_modules/.bin/jsdoc -c jsdoc.json",
-    "build-lib": "rollup -c",
-    "dev-lib": "rollup -c -w"
+    "build": "webpack --config ./bundler/webpack.prod.js && cp ./dist/larvitar.js ./docs/examples/larvitar.js",
+    "dev": "webpack --progress --config ./bundler/webpack.dev.js && cp ./dist/larvitar.js ./docs/examples/larvitar.js",
+    "dev-wip": "webpack serve --config ./bundler/webpack.dev-wip.js"
   },
   "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)",
-    "Ale Re <ale.re@dvisionlab.com> (https://www.dvisionlab.com)"
+    "Ale Re <ale.re@dvisionlab.com> (https://www.dvisionlab.com)",
+    "Laura Borghesi Re <laura.borghesi@dvisionlab.com> (https://www.dvisionlab.com)"
   ],
   "license": "MIT",
   "dependencies": {
@@ -36,6 +40,7 @@
     "dicom-parser": "^1.8.13",
     "docdash": "^1.2.0",
     "hammerjs": "^2.0.8",
+    "jpeg-lossless-decoder-js": "^2.0.7",
     "keycode-js": "^3.1.0",
     "lodash": "^4.17.15",
     "pako": "^1.0.10",
@@ -43,15 +48,28 @@
     "uuid": "^8.3.2"
   },
   "devDependencies": {
-    "@rollup/plugin-json": "^4.1.0",
-    "@rollup/plugin-node-resolve": "^11.2.0",
+    "@babel/core": "^7.21.8",
+    "@types/cornerstone-core": "^2.3.0",
+    "@types/crypto-js": "^4.1.1",
+    "@types/hammerjs": "^2.0.41",
+    "@types/lodash": "^4.14.192",
+    "@types/papaparse": "^5.3.7",
+    "@types/uuid": "^9.0.1",
+    "babel-loader": "^9.1.2",
+    "clean-webpack-plugin": "^4.0.0",
+    "copy-webpack-plugin": "^11.0.0",
     "fs": "^0.0.1-security",
+    "html-loader": "^4.2.0",
+    "html-webpack-plugin": "^5.5.0",
+    "ip": "^1.1.8",
     "jsdoc": "^3.6.4",
-    "rollup": "^2.39.0",
-    "rollup-plugin-node-resolve": "^5.2.0"
-  },
-  "common": "dist/larvitar.cjs.js",
-  "module": "dist/larvitar.js",
-  "browser": "dist/larvitar.js",
-  "type": "module"
+    "portfinder-sync": "^0.0.2",
+    "ts-loader": "^9.4.2",
+    "typescript": "^5.0.2",
+    "typescript-coverage-report": "^0.7.0",
+    "webpack": "^5.76.3",
+    "webpack-bundle-analyzer": "^4.8.0",
+    "webpack-cli": "^5.0.1",
+    "webpack-dev-server": "^4.13.1"
+  }
 }

package/tsconfig.json

@@ -0,0 +1,102 @@
+{
+  "compilerOptions": {
+    /* Visit https://aka.ms/tsconfig.json to read more about this file */
+
+    /* Projects */
+    // "incremental": true,                              /* Enable incremental compilation */
+    // "composite": true,                                /* Enable constraints that allow a TypeScript project to be used with project references. */
+    // "tsBuildInfoFile": "./",                          /* Specify the folder for .tsbuildinfo incremental compilation files. */
+    // "disableSourceOfProjectReferenceRedirect": true,  /* Disable preferring source files instead of declaration files when referencing composite projects */
+    // "disableSolutionSearching": true,                 /* Opt a project out of multi-project reference checking when editing. */
+    // "disableReferencedProjectLoad": true,             /* Reduce the number of projects loaded automatically by TypeScript. */
+
+    /* Language and Environment */
+    "target": "es2016" /* Set the JavaScript language version for emitted JavaScript and include compatible library declarations. */,
+    // "lib": [],                                        /* Specify a set of bundled library declaration files that describe the target runtime environment. */
+    // "jsx": "preserve",                                /* Specify what JSX code is generated. */
+    // "experimentalDecorators": true,                   /* Enable experimental support for TC39 stage 2 draft decorators. */
+    // "emitDecoratorMetadata": true,                    /* Emit design-type metadata for decorated declarations in source files. */
+    // "jsxFactory": "",                                 /* Specify the JSX factory function used when targeting React JSX emit, e.g. 'React.createElement' or 'h' */
+    // "jsxFragmentFactory": "",                         /* Specify the JSX Fragment reference used for fragments when targeting React JSX emit e.g. 'React.Fragment' or 'Fragment'. */
+    // "jsxImportSource": "",                            /* Specify module specifier used to import the JSX factory functions when using `jsx: react-jsx*`.` */
+    // "reactNamespace": "",                             /* Specify the object invoked for `createElement`. This only applies when targeting `react` JSX emit. */
+    // "noLib": true,                                    /* Disable including any library files, including the default lib.d.ts. */
+    // "useDefineForClassFields": true,                  /* Emit ECMAScript-standard-compliant class fields. */
+
+    /* Modules */
+    "module": "commonjs" /* Specify what module code is generated. */,
+    // "rootDir": "./",                                  /* Specify the root folder within your source files. */
+    // "moduleResolution": "node",                       /* Specify how TypeScript looks up a file from a given module specifier. */
+    // "baseUrl": "./",                                  /* Specify the base directory to resolve non-relative module names. */
+    // "paths": {},                                      /* Specify a set of entries that re-map imports to additional lookup locations. */
+    // "rootDirs": [],                                   /* Allow multiple folders to be treated as one when resolving modules. */
+    // "typeRoots": [],                                  /* Specify multiple folders that act like `./node_modules/@types`. */
+    // "types": [],                                      /* Specify type package names to be included without being referenced in a source file. */
+    "allowUmdGlobalAccess": true /* Allow accessing UMD globals from modules. */,
+    "resolveJsonModule": true /* Enable importing .json files */,
+    // "noResolve": true,                                /* Disallow `import`s, `require`s or `<reference>`s from expanding the number of files TypeScript should add to a project. */
+
+    /* JavaScript Support */
+    "allowJs": true /* Allow JavaScript files to be a part of your program. Use the `checkJS` option to get errors from these files. */,
+    // "checkJs": true,                                  /* Enable error reporting in type-checked JavaScript files. */
+    // "maxNodeModuleJsDepth": 1,                        /* Specify the maximum folder depth used for checking JavaScript files from `node_modules`. Only applicable with `allowJs`. */
+
+    /* Emit */
+    "declaration": true /* Generate .d.ts files from TypeScript and JavaScript files in your project. */,
+    // "declarationMap": true,                           /* Create sourcemaps for d.ts files. */
+    // "emitDeclarationOnly": true,                      /* Only output d.ts files and not JavaScript files. */
+    // "sourceMap": true,                                /* Create source map files for emitted JavaScript files. */
+    // "outFile": "larvitar.ts" /* Specify a file that bundles all outputs into one JavaScript file. If `declaration` is true, also designates a file that bundles all .d.ts output. */,
+    "outDir": "./dist" /* Specify an output folder for all emitted files. */,
+    // "removeComments": true,                           /* Disable emitting comments. */
+    // "noEmit": true,                                   /* Disable emitting files from a compilation. */
+    // "importHelpers": true,                            /* Allow importing helper functions from tslib once per project, instead of including them per-file. */
+    // "importsNotUsedAsValues": "remove",               /* Specify emit/checking behavior for imports that are only used for types */
+    // "downlevelIteration": true,                       /* Emit more compliant, but verbose and less performant JavaScript for iteration. */
+    // "sourceRoot": "",                                 /* Specify the root path for debuggers to find the reference source code. */
+    // "mapRoot": "",                                    /* Specify the location where debugger should locate map files instead of generated locations. */
+    // "inlineSourceMap": true,                          /* Include sourcemap files inside the emitted JavaScript. */
+    // "inlineSources": true,                            /* Include source code in the sourcemaps inside the emitted JavaScript. */
+    // "emitBOM": true,                                  /* Emit a UTF-8 Byte Order Mark (BOM) in the beginning of output files. */
+    // "newLine": "crlf",                                /* Set the newline character for emitting files. */
+    // "stripInternal": true,                            /* Disable emitting declarations that have `@internal` in their JSDoc comments. */
+    // "noEmitHelpers": true,                            /* Disable generating custom helper functions like `__extends` in compiled output. */
+    // "noEmitOnError": true,                            /* Disable emitting files if any type checking errors are reported. */
+    // "preserveConstEnums": true,                       /* Disable erasing `const enum` declarations in generated code. */
+    // "declarationDir": "./",                           /* Specify the output directory for generated declaration files. */
+    // "preserveValueImports": true,                     /* Preserve unused imported values in the JavaScript output that would otherwise be removed. */
+
+    /* Interop Constraints */
+    // "isolatedModules": true,                          /* Ensure that each file can be safely transpiled without relying on other imports. */
+    // "allowSyntheticDefaultImports": true,             /* Allow 'import x from y' when a module doesn't have a default export. */
+    "esModuleInterop": true /* Emit additional JavaScript to ease support for importing CommonJS modules. This enables `allowSyntheticDefaultImports` for type compatibility. */,
+    // "preserveSymlinks": true,                         /* Disable resolving symlinks to their realpath. This correlates to the same flag in node. */
+    "forceConsistentCasingInFileNames": true /* Ensure that casing is correct in imports. */,
+
+    /* Type Checking */
+    "strict": true /* Enable all strict type-checking options. */,
+    // "noImplicitAny": false /* Enable error reporting for expressions and declarations with an implied `any` type.. */,
+    // "strictNullChecks": true,                         /* When type checking, take into account `null` and `undefined`. */
+    // "strictFunctionTypes": true,                      /* When assigning functions, check to ensure parameters and the return values are subtype-compatible. */
+    // "strictBindCallApply": true,                      /* Check that the arguments for `bind`, `call`, and `apply` methods match the original function. */
+    // "strictPropertyInitialization": true,             /* Check for class properties that are declared but not set in the constructor. */
+    // "noImplicitThis": true,                           /* Enable error reporting when `this` is given the type `any`. */
+    // "useUnknownInCatchVariables": true,               /* Type catch clause variables as 'unknown' instead of 'any'. */
+    // "alwaysStrict": true,                             /* Ensure 'use strict' is always emitted. */
+    // "noUnusedLocals": true,                           /* Enable error reporting when a local variables aren't read. */
+    // "noUnusedParameters": true,                       /* Raise an error when a function parameter isn't read */
+    // "exactOptionalPropertyTypes": true,               /* Interpret optional property types as written, rather than adding 'undefined'. */
+    // "noImplicitReturns": true,                        /* Enable error reporting for codepaths that do not explicitly return in a function. */
+    // "noFallthroughCasesInSwitch": true,               /* Enable error reporting for fallthrough cases in switch statements. */
+    // "noUncheckedIndexedAccess": true,                 /* Include 'undefined' in index signature results */
+    // "noImplicitOverride": true,                       /* Ensure overriding members in derived classes are marked with an override modifier. */
+    // "noPropertyAccessFromIndexSignature": true,       /* Enforces using indexed accessors for keys declared using an indexed type */
+    // "allowUnusedLabels": true,                        /* Disable error reporting for unused labels. */
+    // "allowUnreachableCode": true,                     /* Disable error reporting for unreachable code. */
+
+    /* Completeness */
+    // "skipDefaultLibCheck": true,                      /* Skip type checking .d.ts files that are included with TypeScript. */
+    "skipLibCheck": true /* Skip type checking all .d.ts files. */
+  },
+  "include": ["./imaging/", "./decs.d.ts"]
+}