larvitar 1.5.13 → 2.0.0

package/.vscode/settings.json

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

package/README.md

@@ -4,13 +4,72 @@
 
 # Larvitar
 
+[![type-coverage](https://img.shields.io/badge/dynamic/json.svg?label=type-coverage&prefix=%E2%89%A5&suffix=%&query=$.typeCoverage.atLeast&uri=https%3A%2F%2Fraw.githubusercontent.com%2Fplantain-00%2Ftype-coverage%2Fmaster%2Fpackage.json)](https://github.com/dvisionlab/Larvitar)
+
 ## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 1.5.13
-### Latest Published Release: 1.5.13
+### Current version: 2.0.0
+### Latest Published Release: 2.0.0
 
 This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornerstone-js environment.
-Orthogonal multiplanar reformat is included as well as custom loader/exporter for nrrd files and [Vuex](https://vuex.vuejs.org/) custom integration.
+
+## Features:
+
+- Orthogonal multiplanar reformat with contours generations
+- Custom loader/exporter for nrrd files
+- Segmentation masks support
+- Memory management
+- Support all dicom modalities
+- 4D Cine support
+- Anonymization functionalities
+- Cine tools and ECG Parsing
+- Masks management
+
+Full documentation and examples are available at http://www.dvisionlab.com/Larvitar/.
+
+# Typescript
+
+_Types_ can be imported from `larvitar/imaging/types` or `larvitar/imaging/tools/types`.
+
+```javascript
+import { Series } from "larvitar/imaging/types";
+
+let newSerie: Series;
+```
+
+<br>
+
+# Dependencies
+
+- `cornerstone`
+- `cornerstone-tools`
+- `dicomParser`
+- `DICOMImageLoader`
+- `webImageLoader`
+- `fileImageLoader`
+- `lodash`
+- `pako`
+- `papaparse`
+
+# Installation
+
+`yarn add larvitar`
+
+# Build package
+
+`yarn build`
+
+# Coverage
+
+Use `yarn coverage` to generate type coverage report.
+
+# Development
+
+Use `yarn dev` to have `webpack` hot-reload (live recompiling the library).
+In order to test functionalities you can serve the .html file with VSCode extension [LiveServer](https://marketplace.visualstudio.com/items?itemName=ritwickdey.LiveServer) or other similar tools.
+Once you are done, upgrade the version (README and package.json) and build the library. Docs will be compiled by the Github action.
+
+### Repository structure
 
 - `index` main file
 - `dataDictionary` json file for dicom tags
@@ -25,73 +84,44 @@ Orthogonal multiplanar reformat is included as well as custom loader/exporter fo
 - `imageRendering` provides rendering functionalities
 - `imageReslice` provides reslice functionalities
 - `imageStore` provides data storage functionalities, vuex support is integrated
+- `imageTags` using to handle dicom tags and metadata
 - `imageTools` using to handle standard and custom cornerstone tools
 - `imageUtils` utility functions on pixels and metadata tags
 - `loaders/commonLoader` common functionalities for custom loaders
 - `loaders/dicomLoader` custom loader for DICOM files with support for multiplanar reformat (axial, sagittal and coronal planes)
 - `loaders/fileLoader` custom loader for png/jpg files
+- `loaders/multiFrameLoader` custom loader for multiFrame data
 - `loaders/nrrdLoader`custom loader for nrrd files with support for multiplanar reformat (axial, sagittal and coronal planes)
 - `loaders/resliceLoader` custom loader for resliced data
-- `loaders/multiFrameLoader` custom loader for multiFrame data
+- `parsers/ecg` custom parser for ecg data
 - `parsers/nrrd` custom parser for nrrd data
+- `tools/custom/4DSliceScrollTool` is a custom cornerstone tool for handling navigation of slices in a 4D DICOM series
 - `tools/custom/contourTool` is a custom cornerstone tool for 2D visualization of segmented images
 - `tools/custom/diameterTool` is a custom cornerstone tool for 2D visualization of diameter widgets
 - `tools/custom/editMaskTool` is a custom cornerstone tool for 2D visualization of segmentation masks with brush functionalities
+- `tools/custom/EllipticalRoiOverlayTool` is a custom cornerstone tool for 2D visualization of elliptical widgets
+- `tools/custom/polygonSegmentationMixin` is a custom cornerstone tool for 2D visualization of polygonal widgets
+- `tools/custom/polylineScissorTool` is a custom cornerstone tool for 2D visualization of polyline widgets
+- `tools/custom/rectangleRoiOverlayTool` is a custom cornerstone tool for 2D visualization of rectangular widgets
 - `tools/custom/seedTool` is a custom cornerstone tool for 2D interactive seeding with custom colors and labels
+- `tools/custom/setLabelMap3D`
 - `tools/custom/thresholdsBrushTool` is a custom cornerstone tool for handling thresholds in a brush tool
-- `tools/custom/Slice4DScrollMouseWheel` is a custom cornerstone tool for handling navigation of slices in a 4D DICOM series
 - `tools/default` default tools map and configuration
+- `tools/interaction` cornerstone interaction tools 
 - `tools/io` import and export functionalities for tools
 - `tools/main` tools main functionalities
 - `tools/state` tools state management
 - `tools/segmentation` segmentation masks management
-- `modules/vuex/larvitar.js` optional vuex state module
-
-<br>
-
-**Larvitar** can be used with or without `vuex` bindings:
-
-```javascript
-import { initLarvitarStore } from "larvitar";
-import store from "@/store/index";
-
-initLarvitarStore(store); // Calling this without parameters makes Larvitar use its internal store.
-```
-
-Full documentation and examples are available at http://www.dvisionlab.com/Larvitar/.
-
-<br>
+- `tools/strategies/eraseFreeHand` strategy for erasing freehand masks
+- `tools/strategies/fillFreeHand` strategy for filling freehand masks
+- `tools/strategies/index` strategies index
 
 # Contributors
 
 - Simone Manini, D/Vision Lab
 - Mattia Ronzoni, D/Vision Lab
 - Sara Zanchi, D/Vision Lab
+- Alessandro Re, D/Vision Lab
+- Laura Borghesi, D/Vision Lab
 
-![dvisionlab logo](https://www.dvisionlab.com/images/logo_dv.png)
-
-# Dependencies
-
-- `cornerstone`
-- `cornerstone-tools`
-- `dicomParser`
-- `wadoImageLoader`
-- `webImageLoader`
-- `fileImageLoader`
-- `lodash`
-- `pako`
-- `papaparse`
-
-# Installation
-
-`yarn add larvitar`
-
-# Build package
-
-`yarn build-lib`
-
-# Development
-
-Use `yarn dev-lib` to have `rollup` hot-reload (live recompiling the library).
-In order to test functionalities you can modify the library import path in an example (see the `docs/examples` folder) to use the recompiled bundle in `dist/`, then serve the .html file with VSCode extension [LiveServer](https://marketplace.visualstudio.com/items?itemName=ritwickdey.LiveServer) or other similar tools.
-Once you are done, upgrade the version, build the library and copy it to the `docs/examples` folder. This file must be included into the commit, while docs will be compiled by the Github action.
+![dvisionlab logo](https://www.dvisionlab.com/assets/images/logo-light.png)

package/bundler/webpack.common.js

@@ -0,0 +1,27 @@
+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

@@ -0,0 +1,23 @@
+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

@@ -0,0 +1,19 @@
+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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,39 @@
+export type MetaDataReadable = {
+    anonymized?: boolean;
+    larvitarSeriesInstanceUID?: string;
+    seriesUID?: string;
+    instanceUID?: 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;
+    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;
+};