larvitar 2.0.5 → 2.0.7

package/imaging/tools/types.d.ts

@@ -58,7 +58,7 @@ export type ToolMouseKeys = {
   };
 };
 
-type HanldePosition = {
+type HandlePosition = {
   active: boolean;
   allowedOutsideImage?: boolean;
   drawnIndependently?: boolean;
@@ -94,9 +94,9 @@ type BaseToolStateData = {
 
 type AngleStateData = BaseToolStateData & {
   handles: {
-    end: HanldePosition;
-    middle: HanldePosition;
-    start: HanldePosition;
+    end: HandlePosition;
+    middle: HandlePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   rAngle: number;
@@ -104,8 +104,8 @@ type AngleStateData = BaseToolStateData & {
 
 type ArrowAnnotateStateData = BaseToolStateData & {
   handles: {
-    end: HanldePosition;
-    start: HanldePosition;
+    end: HandlePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   text: string;
@@ -113,10 +113,10 @@ type ArrowAnnotateStateData = BaseToolStateData & {
 
 type BidirectionalStateData = BaseToolStateData & {
   handles: {
-    end: HanldePosition;
-    perpendicularEnd: HanldePosition;
-    perpendicularStart: HanldePosition;
-    start: HanldePosition;
+    end: HandlePosition;
+    perpendicularEnd: HandlePosition;
+    perpendicularStart: HandlePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   isCreating: boolean;
@@ -138,20 +138,20 @@ type EllipticalRoiStateData = BaseToolStateData & {
     variance: number;
   };
   handles: {
-    end: HanldePosition;
+    end: HandlePosition;
     initialRotation: number;
-    start: HanldePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   unit: string;
 };
 
-type FreehandRoiStateData = ToolStateData & {
+type FreehandRoiStateData = BaseToolStateData & {
   area: number;
   canComplete: boolean;
   handles: {
-    points: FreehandHandleData[];
-    textBox: any;
+    points: number[];
+    textBox: HandleTextBox;
     invalidHandlePlacement: boolean;
   };
   highlight: boolean;
@@ -163,8 +163,8 @@ type FreehandRoiStateData = ToolStateData & {
 
 type LengthStateData = BaseToolStateData & {
   handles: {
-    end: HanldePosition;
-    start: HanldePosition;
+    end: HandlePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   length: number;
@@ -186,9 +186,9 @@ type RectangleRoiStateData = BaseToolStateData & {
     variance: number;
   };
   handles: {
-    end: HanldePosition;
+    end: HandlePosition;
     initialRotation: number;
-    start: HanldePosition;
+    start: HandlePosition;
     textBox: HandleTextBox;
   };
   unit: string;

package/imaging/types.d.ts

@@ -1,7 +1,5 @@
 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";
 
@@ -16,6 +14,68 @@ import { MetaDataReadable } from "./MetaDataReadable";
   | Array
   | undefined; // null or undefined is only for nrrd*/
 
+export type DEFAULT_VIEWPORT = {
+  loading: number;
+  ready: boolean;
+  minSliceId: number;
+  maxSliceId: number;
+  sliceId: number;
+  pendingSliceId?: number;
+  minTimeId: number;
+  maxTimeId: number;
+  timeId: number;
+  timestamp: number;
+  timestamps: number[];
+  timeIds: number[];
+  rows: number;
+  cols: number;
+  spacing_x: number;
+  spacing_y: number;
+  thickness: number;
+  minPixelValue: number;
+  maxPixelValue: number;
+  isColor: boolean;
+  isMultiframe: boolean;
+  isTimeserie: boolean;
+  isPDF: boolean;
+  imageIndex?: number;
+  imageId?: string;
+  numberOfSlices?: number;
+  numberOfTemporalPositions?: number;
+  timeIndex?: number;
+  viewport: {
+    scale: number;
+    rotation: number;
+    translation: {
+      x: number;
+      y: number;
+    };
+    voi: {
+      windowCenter: number;
+      windowWidth: number;
+    };
+    // redundant fields ?
+    rows: number;
+    cols: number;
+    spacing_x: number;
+    spacing_y: number;
+    thickness: number;
+  };
+  default: {
+    scale: number;
+    rotation: number;
+    translation: {
+      x: number;
+      y: number;
+    };
+    voi: {
+      windowCenter: number;
+      windowWidth: number;
+      invert: boolean;
+    };
+  };
+};
+
 export type MetaData = MetaDataTypes & MetaDataReadable;
 export interface Image extends cornerstone.Image {
   render?: Function;
@@ -198,3 +258,51 @@ type StoreViewportOptions = {
   tr_x?: number;
   tr_y?: number;
 };
+
+export type NrrdInputVolume = {
+  header: {
+    sizes: number[];
+    "space directions": number[][]; // a property with a space in the name ?? Seriously ??
+    "space origin": [number, number];
+    kinds: string[];
+    type: string;
+  };
+  data: Uint16Array; // TODO-ts: other typed arrays ?
+};
+
+export type NrrdSeries = {
+  currentImageIdIndex: number;
+  imageIds: string[];
+  instances: { [key: string]: Instance };
+  instanceUIDs: { [key: string]: string };
+  numberOfImages: number;
+  seriesDescription: string;
+  seriesUID: string;
+  customLoader: string;
+  nrrdHeader: NrrdHeader;
+  bytes: number;
+  dataSet?: DataSet;
+  metadata?: MetaData;
+  ecgData?: number[];
+};
+
+export type NrrdHeader = {
+  volume: Volume;
+  intercept: number;
+  slope: number;
+  repr: string;
+  phase: string;
+  study_description: string;
+  series_description: string;
+  acquisition_date: string;
+  [imageId: string]: string | number | Volume | NrrdInstance; // TODO-ts: fix this: we need just NrrdInstance
+};
+
+export type NrrdInstance = {
+  instanceUID: string;
+  seriesDescription: string;
+  seriesModality: string;
+  patientName: string;
+  bitsAllocated: number;
+  pixelRepresentation: string;
+};

package/package.json

@@ -6,13 +6,18 @@
     "medical",
     "cornerstone"
   ],
-  "version": "2.0.5",
+  "version": "2.0.7",
   "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",
+  "main": "dist/larvitar.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist",
+    "imaging/**/*.d.ts"
+  ],
   "scripts": {
     "coverage": "typescript-coverage-report",
     "generate-docs": "node_modules/.bin/jsdoc -c jsdoc.json",

package/.github/workflows/build-docs.yml

@@ -1,59 +0,0 @@
-name: CI-docs
-
-on:
-  pull_request:
-    types:
-      - opened
-      - reopened
-      - synchronize
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-      # CLone repo at current branch
-      - name: Clone repo
-        uses: actions/checkout@v2
-        with:
-          persist-credentials: false
-          ref: ${{ github.head_ref }}
-          token: ${{ secrets.GIT_TOKEN }}
-
-      # Setup node environment
-      - name: Setup Node.js environment
-        uses: actions/setup-node@v2
-        with:
-          node-version: "14"
-
-      # Install node modules
-      - name: Install node modules
-        run: |
-          yarn install
-
-      # Clone template
-      - name: Clone docdash template
-        uses: actions/checkout@v2
-        with:
-          repository: clenemt/docdash
-          path: ./template/docdash/
-
-      # Install docdash node modules
-      - name: Install node modules
-        working-directory: ./template/docdash/
-        run: |
-          yarn install
-
-      # Generate docs
-      - name: Generate docs
-        run: |
-          yarn generate-docs
-
-      # Commit docs on current branch (update pull request)
-      - name: Commit docs
-        uses: actions-js/push@master
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          message: "Update docs"
-          branch: ${{ github.head_ref }}
-          empty: true

package/.github/workflows/codeql-analysis.yml

@@ -1,71 +0,0 @@
-# For most projects, this workflow file will not need changing; you simply need
-# to commit it to your repository.
-#
-# You may wish to alter this file to override the set of languages analyzed,
-# or to provide custom queries or build logic.
-#
-# ******** NOTE ********
-# We have attempted to detect the languages in your repository. Please check
-# the `language` matrix defined below to confirm you have the correct set of
-# supported CodeQL languages.
-#
-name: "CodeQL"
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [ master ]
-  schedule:
-    - cron: '22 19 * * 0'
-
-jobs:
-  analyze:
-    name: Analyze
-    runs-on: ubuntu-latest
-    permissions:
-      actions: read
-      contents: read
-      security-events: write
-
-    strategy:
-      fail-fast: false
-      matrix:
-        language: [ 'javascript' ]
-        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
-        # Learn more:
-        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
-
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
-
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
-
-    #- run: |
-    #   make bootstrap
-    #   make release
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1

package/.github/workflows/deploy.yml

@@ -1,37 +0,0 @@
-# This is a basic workflow to help you get started with Actions
-
-name: CI-Release
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on:
-  release:
-    types: [published]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-
-      # Setup node environment
-      - name: Setup Node.js environment
-        uses: actions/setup-node@v1.4.4
-
-      # Clean examples and docs file
-      - name: Clean examples and docs file
-        run: |
-          cd ${{ github.workspace }}
-          rm -rf docs
-
-      # Publish to npm
-      - name: Publish to npm
-        run: |
-          echo "//registry.npmjs.org/:_authToken=${{ secrets.NPM_TOKEN }}" > ~/.npmrc
-          npm publish

package/.vscode/settings.json

@@ -1,4 +0,0 @@
-{
-"prettier.arrowParens": "avoid",
-"prettier.trailingComma": "none"
-}

package/CODE_OF_CONDUCT.md

@@ -1,76 +0,0 @@
-# Contributor Covenant Code of Conduct
-
-## Our Pledge
-
-In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to making participation in our project and
-our community a harassment-free experience for everyone, regardless of age, body
-size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
-appearance, race, religion, or sexual identity and orientation.
-
-## Our Standards
-
-Examples of behavior that contributes to creating a positive environment
-include:
-
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
-
-Examples of unacceptable behavior by participants include:
-
-* The use of sexualized language or imagery and unwelcome sexual attention or
- advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
- address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
- professional setting
-
-## Our Responsibilities
-
-Project maintainers are responsible for clarifying the standards of acceptable
-behavior and are expected to take appropriate and fair corrective action in
-response to any instances of unacceptable behavior.
-
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
-
-## Scope
-
-This Code of Conduct applies both within project spaces and in public spaces
-when an individual is representing the project or its community. Examples of
-representing a project or community include using an official project e-mail
-address, posting via an official social media account, or acting as an appointed
-representative at an online or offline event. Representation of a project may be
-further defined and clarified by project maintainers.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at info@dvisionlab.com. All
-complaints will be reviewed and investigated and will result in a response that
-is deemed necessary and appropriate to the circumstances. The project team is
-obligated to maintain confidentiality with regard to the reporter of an incident.
-Further details of specific enforcement policies may be posted separately.
-
-Project maintainers who do not follow or enforce the Code of Conduct in good
-faith may face temporary or permanent repercussions as determined by other
-members of the project's leadership.
-
-## Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
-
-[homepage]: https://www.contributor-covenant.org
-
-For answers to common questions about this code of conduct, see
-https://www.contributor-covenant.org/faq

package/MIGRATION.md

@@ -1,25 +0,0 @@
-# Introduction
-
-This guide is primarily for user with prior Larvitar v0.x experience who want to learn about the new features and changes in Larvitar v1.x. While it looks like a lot has changed, a lot of what you know and love about Larvitar is still the same; but we wanted to be as thorough as possibile and provide detailed explanations or examples for every documented change.
-
-# Notable new features
-
-We chose to migrate all functions using callback to promise. Promises are JavaScript objects that represent an eventual completion or failure of an asynchronous operation. A promise is a returned object where you attach callbacks, instead of passing callbacks into a function. the place where you attach the callback after a successful completion of a task is called, .then(). inside this you pass a callback through.
-
-# Breaking changes
-
-- imageIo module:
-  -  *getCachedPixelData* now returns a promise which will resolve to a pixel data array or fail if an error occurs
-- imageParsing module
-  - *readFiles* now returns a promise which will resolve to an image object list or fail if an error occurs
-  - *readFile* now returns a promise which will resolve to an image object or fail if an error occurs
-  - *dumpDataset* has been renamed to parseDataset [internal API]
-  - *dumpFiles* has been renamed to parseFiles [internal API]
-  - *dumpFile* has been renamed to parseFile [internal API]
--  imageRendering module
-   -  *renderImage* now returns a promise which will resolve when image is displayed
--  imageReslice module
-   -  *resliceImage* now returns a promise which will resolve when reslice data is available
--  tools/segmentation module
-   -  *addSegmentationMask* now returns a promise which will resolve when segmentation mask is added
-   -  *getActivelabelmapBuffer* now needs elementId (or its DOM HTMLElement) as param and returns the buffer parent object"

package/bundler/webpack.common.js

@@ -1,27 +0,0 @@
-module.exports = {
-  devtool: "source-map", // or inline-source-map ?
-  module: {
-    rules: [
-      // HTML
-      {
-        test: /\.(html)$/,
-        use: ["html-loader"]
-      },
-      // JS
-      {
-        test: /\.js$/,
-        exclude: /node_modules/,
-        use: ["babel-loader"]
-      },
-      // typescript support
-      {
-        test: /\.tsx?$/,
-        use: "ts-loader",
-        exclude: /node_modules/
-      }
-    ]
-  },
-  resolve: {
-    extensions: [".tsx", ".ts", ".js", ".d.ts"]
-  }
-};

package/bundler/webpack.dev.js

@@ -1,23 +0,0 @@
-const path = require("path");
-const { merge } = require("webpack-merge");
-const commonConfiguration = require("./webpack.common.js");
-const { CleanWebpackPlugin } = require("clean-webpack-plugin");
-
-module.exports = merge(commonConfiguration, {
-  entry: path.resolve(__dirname, "../index.ts"),
-  output: {
-    path: path.resolve(__dirname, "../dist"),
-    filename: "larvitar.js",
-    library: "larvitar",
-    libraryTarget: "umd"
-  },
-  mode: "development",
-  plugins: [new CleanWebpackPlugin()],
-  watch: true,
-  watchOptions: {
-    ignored: /node_modules/
-  },
-  optimization: {
-    minimize: false
-  }
-});

package/bundler/webpack.prod.js

@@ -1,19 +0,0 @@
-const path = require("path");
-const { merge } = require("webpack-merge");
-const commonConfiguration = require("./webpack.common.js");
-const { CleanWebpackPlugin } = require("clean-webpack-plugin");
-
-module.exports = merge(commonConfiguration, {
-  entry: path.resolve(__dirname, "../index.ts"),
-  output: {
-    path: path.resolve(__dirname, "../dist"),
-    filename: "larvitar.js",
-    library: "larvitar",
-    libraryTarget: "umd"
-  },
-  mode: "production",
-  plugins: [new CleanWebpackPlugin()],
-  optimization: {
-    minimize: false
-  }
-});

package/decs.d.ts

@@ -1,12 +0,0 @@
-declare module "cornerstone-math";
-declare module "cornerstone-tools";
-declare module "cornerstone-wado-image-loader";
-declare module "cornerstone-web-image-loader";
-declare module "cornerstone-file-image-loader";
-declare module "dicom-character-set";
-
-declare global {
-  interface Document {
-    documentMode?: any;
-  }
-}

package/dist/imaging/MetaDataReadable.d.ts

@@ -1,41 +0,0 @@
-export type MetaDataReadable = {
-    anonymized?: boolean;
-    larvitarSeriesInstanceUID?: string;
-    seriesUID?: string;
-    instanceUID?: string;
-    sopClassUID?: string;
-    studyUID?: string;
-    accessionNumber?: string;
-    studyDescription?: string;
-    patientName?: string;
-    patientBirthdate?: string;
-    seriesDescription?: string;
-    seriesDate?: string;
-    seriesModality?: string;
-    intercept?: number | number[];
-    slope?: number | number[];
-    pixelSpacing?: [number, number];
-    sliceThickness?: number | number[];
-    imageOrientation?: [number, number, number, number, number, number];
-    imagePosition?: [number, number] | [number, number, number] | number[];
-    rows?: number;
-    cols?: number;
-    numberOfSlices?: number;
-    numberOfFrames?: number;
-    frameTime?: number;
-    frameDelay?: number;
-    rWaveTimeVector?: number[];
-    isMultiframe?: boolean;
-    waveform?: boolean;
-    temporalPositionIdentifier?: number;
-    numberOfTemporalPositions?: number;
-    contentTime?: number;
-    is4D?: boolean;
-    windowCenter?: number | number[];
-    windowWidth?: number | number[];
-    minPixelValue?: number;
-    maxPixelValue?: number;
-    length?: number;
-    repr?: string | null;
-    mimeType?: string;
-};