From 0cb2a69a40896127312007c0918a6dd50d53f6c8 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 09:20:23 -0400 Subject: [PATCH 1/9] Update build --- package-lock.json | 2659 ++++++++++++--------------------------------- package.json | 17 +- rollup.config.js | 37 - rollup.config.mjs | 38 + 4 files changed, 736 insertions(+), 2015 deletions(-) delete mode 100644 rollup.config.js create mode 100644 rollup.config.mjs diff --git a/package-lock.json b/package-lock.json index cbe85e01..7359eddf 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,15 +1,15 @@ { "name": "dcmjs", - "version": "0.24.0", + "version": "0.30.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "dcmjs", - "version": "0.24.0", + "version": "0.30.0", "license": "MIT", "dependencies": { - "@babel/runtime-corejs2": "^7.17.8", + "@babel/runtime-corejs3": "^7.22.5", "gl-matrix": "^3.1.0", "lodash.clonedeep": "^4.5.0", "loglevelnext": "^3.0.1", @@ -18,8 +18,13 @@ }, 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}, "w3c-hr-time": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/w3c-hr-time/-/w3c-hr-time-1.0.2.tgz", @@ -18765,23 +17503,6 @@ "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", "dev": true }, - "xtend": { - "version": "2.1.2", - "resolved": "https://registry.npmjs.org/xtend/-/xtend-2.1.2.tgz", - "integrity": "sha1-bv7MKk2tjmlixJAbM3znuoe10os=", - "dev": true, - "requires": { - "object-keys": "~0.4.0" - }, - "dependencies": { - "object-keys": { - "version": "0.4.0", - "resolved": "https://registry.npmjs.org/object-keys/-/object-keys-0.4.0.tgz", - "integrity": "sha1-KKaq50KN0sOpLz2V8hM13SBOAzY=", - "dev": true - } - } - }, "y18n": { "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", diff --git a/package.json b/package.json index 4630fe12..14b4c34d 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "dcmjs", - "version": "0.24.0", + "version": "0.30.0", "description": "Javascript implementation of DICOM manipulation", "main": "build/dcmjs.js", "module": "build/dcmjs.es.js", @@ -27,8 +27,13 @@ "homepage": "https://github.com/dcmjs-org/dcmjs#readme", "devDependencies": { "@babel/core": "^7.17.8", + "@babel/plugin-transform-runtime": "^7.22.5", "@babel/preset-env": "^7.16.11", "@babel/register": "^7.13.0", + "@rollup/plugin-babel": "^6.0.3", + "@rollup/plugin-commonjs": "^25.0.1", + "@rollup/plugin-json": "^6.0.0", + "@rollup/plugin-node-resolve": "^15.1.0", "acorn": "^7.1.0", "acorn-jsx": "^5.2.0", "eslint": "^8.17.0", @@ -38,18 +43,12 @@ "jest": "^27.5.1", "lint-staged": "^13.1.2", "prettier": "^2.6.2", - "rollup": "^1.31.1", - "rollup-plugin-babel": "^4.3.3", - "rollup-plugin-commonjs": "^9.3.4", - "rollup-plugin-json": "^3.1.0", - "rollup-plugin-node-builtins": "^2.1.2", - "rollup-plugin-node-globals": "^1.4.0", - "rollup-plugin-node-resolve": "^4.2.4", + "rollup": "^3.25.1", "unzipper": "^0.10.9", "xml2js": "^0.4.23" }, "dependencies": { - "@babel/runtime-corejs2": "^7.17.8", + "@babel/runtime-corejs3": "^7.22.5", "gl-matrix": "^3.1.0", "lodash.clonedeep": "^4.5.0", "loglevelnext": "^3.0.1", diff --git a/rollup.config.js b/rollup.config.js deleted file mode 100644 index 3e8b2606..00000000 --- a/rollup.config.js +++ /dev/null @@ -1,37 +0,0 @@ -import babel from "rollup-plugin-babel"; -import resolve from "rollup-plugin-node-resolve"; -import globals from "rollup-plugin-node-globals"; -import builtins from "rollup-plugin-node-builtins"; -import commonjs from "rollup-plugin-commonjs"; -import json from "rollup-plugin-json"; -import pkg from "./package.json"; - -export default { - input: "src/index.js", - output: [ - { - file: pkg.main, - format: "umd", - name: "dcmjs", - sourcemap: true - }, - { - file: pkg.module, - format: "es", - sourcemap: true - } - ], - plugins: [ - resolve({ - browser: true - }), - commonjs(), - globals(), - builtins(), - babel({ - runtimeHelpers: true, - exclude: "node_modules/**" - }), - json() - ] -}; diff --git a/rollup.config.mjs b/rollup.config.mjs new file mode 100644 index 00000000..5e9e54a3 --- /dev/null +++ b/rollup.config.mjs @@ -0,0 +1,38 @@ +import babel from "@rollup/plugin-babel"; +import resolve from "@rollup/plugin-node-resolve"; +// import globals from "rollup-plugin-node-globals"; +// import builtins from "rollup-plugin-node-builtins"; +import commonjs from "@rollup/plugin-commonjs"; +// import babelRuntime from "@rollup/plugin-transform-runtime" +import json from "@rollup/plugin-json"; +import pkg from "./package.json" assert { type: "json" }; + +export default { + input: "src/index.js", + output: [ + { + file: pkg.main, + format: "umd", + name: "dcmjs", + sourcemap: true + }, + { + file: pkg.module, + format: "es", + sourcemap: true + } + ], + plugins: [ + resolve({ + browser: true + }), + commonjs(), + // globals(), + //builtins(), + // babelRuntime(), + babel({ + exclude: "node_modules/**" + }), + json() + ] +}; From 742867f536043a1ec52d55ad190efe74366a9122 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 10:49:36 -0400 Subject: [PATCH 2/9] fix(build): Update to newer rollup/build versions and fix tests --- package-lock.json | 423 +----------------- package.json | 2 +- src/DicomMessage.js | 13 +- src/ValueRepresentation.js | 9 +- src/anonymizer.js | 1 - src/bitArray.js | 2 +- src/log.js | 9 +- test/anonymizer.test.js | 4 + test/data-options.test.js | 6 +- test/data.test.js | 6 +- .../integration/DicomMessage.readFile.test.js | 4 + test/testUtils.js | 32 +- 12 files changed, 74 insertions(+), 437 deletions(-) diff --git a/package-lock.json b/package-lock.json index 7359eddf..721268ae 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,6 +10,7 @@ "license": "MIT", "dependencies": { "@babel/runtime-corejs3": "^7.22.5", + "adm-zip": "^0.5.10", "gl-matrix": "^3.1.0", "lodash.clonedeep": "^4.5.0", "loglevelnext": "^3.0.1", @@ -35,7 +36,6 @@ "lint-staged": "^13.1.2", "prettier": "^2.6.2", "rollup": "^3.25.1", - "unzipper": "^0.10.9", "xml2js": "^0.4.23" } }, @@ -2988,6 +2988,14 @@ "node": ">=0.4.0" } }, + "node_modules/adm-zip": { + "version": "0.5.10", + "resolved": "https://registry.npmjs.org/adm-zip/-/adm-zip-0.5.10.tgz", + "integrity": "sha512-x0HvcHqVJNTPk/Bw8JbLWlWoo6Wwnsug0fnYYro1HBrjxZ3G7/AZk7Ahv8JwDe1uIcz8eBqvu86FuF1POiG7vQ==", + "engines": { + "node": ">=6.0" + } + }, "node_modules/agent-base": { "version": "6.0.2", "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz", @@ -3330,34 +3338,6 @@ "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", "dev": true }, - "node_modules/big-integer": { - "version": "1.6.48", - "resolved": "https://registry.npmjs.org/big-integer/-/big-integer-1.6.48.tgz", - "integrity": "sha512-j51egjPa7/i+RdiRuJbPdJ2FIUYYPhvYLjzoYbcMMm62ooO6F94fETG4MTs46zPAF9Brs04OajboA/qTGuz78w==", - "dev": true, - "engines": { - "node": ">=0.6" - } - }, - "node_modules/binary": { - "version": "0.3.0", - "resolved": "https://registry.npmjs.org/binary/-/binary-0.3.0.tgz", - "integrity": "sha1-n2BVO8XOjDOG87VTz/R0Yq3sqnk=", - "dev": true, - "dependencies": { - "buffers": "~0.1.1", - "chainsaw": "~0.1.0" - }, - "engines": { - "node": "*" - } - }, - "node_modules/bluebird": { - "version": "3.4.7", - "resolved": "https://registry.npmjs.org/bluebird/-/bluebird-3.4.7.tgz", - "integrity": "sha1-9y12C+Cbf3bQjtj66Ysomo0F+rM=", - "dev": true - }, "node_modules/brace-expansion": { "version": "1.1.11", "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", @@ -3433,24 +3413,6 @@ "integrity": "sha512-MQcXEUbCKtEo7bhqEs6560Hyd4XaovZlO/k9V3hjVUF/zwW7KBVdSK4gIt/bzwS9MbR5qob+F5jusZsb0YQK2A==", "dev": true }, - "node_modules/buffer-indexof-polyfill": { - "version": "1.0.1", - "resolved": "https://registry.npmjs.org/buffer-indexof-polyfill/-/buffer-indexof-polyfill-1.0.1.tgz", - "integrity": "sha1-qfuAbOgUXVQoUQznLyeLs2OmOL8=", - "dev": true, - "engines": { - "node": ">=0.10" - } - }, - "node_modules/buffers": { - "version": "0.1.1", - "resolved": "https://registry.npmjs.org/buffers/-/buffers-0.1.1.tgz", - "integrity": "sha1-skV5w77U1tOWru5tmorn9Ugqt7s=", - "dev": true, - "engines": { - "node": ">=0.2.0" - } - }, "node_modules/builtin-modules": { "version": "3.3.0", "resolved": "https://registry.npmjs.org/builtin-modules/-/builtin-modules-3.3.0.tgz", @@ -3547,18 +3509,6 @@ } ] }, - "node_modules/chainsaw": { - "version": "0.1.0", - "resolved": "https://registry.npmjs.org/chainsaw/-/chainsaw-0.1.0.tgz", - "integrity": "sha1-XqtQsor+WAdNDVgpE4iCi15fvJg=", - "dev": true, - "dependencies": { - "traverse": ">=0.3.0 <0.4" - }, - "engines": { - "node": "*" - } - }, "node_modules/chalk": { "version": "2.4.2", "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz", @@ -3794,12 +3744,6 @@ "url": "https://opencollective.com/core-js" } }, - "node_modules/core-util-is": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/core-util-is/-/core-util-is-1.0.2.tgz", - "integrity": "sha1-tf1UIgqivFq1eqtxQMlAdUUDwac=", - "dev": true - }, "node_modules/cosmiconfig": { "version": "5.0.7", "resolved": "https://registry.npmjs.org/cosmiconfig/-/cosmiconfig-5.0.7.tgz", @@ -4002,30 +3946,6 @@ "node": ">=8" } }, - "node_modules/duplexer2": { - "version": "0.1.4", - "resolved": "https://registry.npmjs.org/duplexer2/-/duplexer2-0.1.4.tgz", - "integrity": "sha1-ixLauHjA1p4+eJEFFmKjL8a93ME=", - "dev": true, - "dependencies": { - "readable-stream": "^2.0.2" - } - }, - "node_modules/duplexer2/node_modules/readable-stream": { - "version": "2.3.7", - "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.7.tgz", - "integrity": "sha512-Ebho8K4jIbHAxnuxi7o42OrZgF/ZTNcsZj6nRKyUmkhLFq8CHItp/fy6hQZuZmP/n3yZ9VBUbp4zz/mX8hmYPw==", - "dev": true, - "dependencies": { - "core-util-is": "~1.0.0", - "inherits": "~2.0.3", - 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}, "tslib": { "version": "2.5.0", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.5.0.tgz", @@ -17189,41 +16835,6 @@ "integrity": "sha512-rBJeI5CXAlmy1pV+617WB9J63U6XcazHHF2f2dbJix4XzpUF0RS3Zbj0FGIOCAva5P/d/GBOYaACQ1w+0azUkg==", "dev": true }, - "unzipper": { - "version": "0.10.9", - "resolved": "https://registry.npmjs.org/unzipper/-/unzipper-0.10.9.tgz", - "integrity": "sha512-P89p3Ha3riBDO11ubSpUpmsjQ0nl/pby2troZBgSUTOI02InbEDe/KDSAZM1s3T/VyMXnZZa81rZBxxW3yXfcg==", - "dev": true, - "requires": { - "big-integer": "^1.6.17", - "binary": "~0.3.0", - "bluebird": "~3.4.1", - "buffer-indexof-polyfill": "~1.0.0", - "duplexer2": "~0.1.4", - "fstream": "^1.0.12", - "graceful-fs": "^4.2.2", - "listenercount": "~1.0.1", - "readable-stream": "~2.3.6", - "setimmediate": "~1.0.4" - }, - "dependencies": { - "readable-stream": { - "version": "2.3.7", - "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.7.tgz", - "integrity": "sha512-Ebho8K4jIbHAxnuxi7o42OrZgF/ZTNcsZj6nRKyUmkhLFq8CHItp/fy6hQZuZmP/n3yZ9VBUbp4zz/mX8hmYPw==", - "dev": true, - "requires": { - "core-util-is": "~1.0.0", - "inherits": "~2.0.3", - "isarray": "~1.0.0", - "process-nextick-args": "~2.0.0", - "safe-buffer": "~5.1.1", - "string_decoder": "~1.1.1", - "util-deprecate": "~1.0.1" - } - } - } - }, "update-browserslist-db": { "version": "1.0.11", "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.11.tgz", @@ -17243,12 +16854,6 @@ "punycode": "^2.1.0" } }, - "util-deprecate": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz", - "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=", - "dev": true - }, "v8-compile-cache": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz", diff --git a/package.json b/package.json index 14b4c34d..ead00a45 100644 --- a/package.json +++ b/package.json @@ -44,11 +44,11 @@ "lint-staged": "^13.1.2", "prettier": "^2.6.2", "rollup": "^3.25.1", - "unzipper": "^0.10.9", "xml2js": "^0.4.23" }, "dependencies": { "@babel/runtime-corejs3": "^7.22.5", + "adm-zip": "^0.5.10", "gl-matrix": "^3.1.0", "lodash.clonedeep": "^4.5.0", "loglevelnext": "^3.0.1", diff --git a/src/DicomMessage.js b/src/DicomMessage.js index adfc197e..bcd02dbe 100644 --- a/src/DicomMessage.js +++ b/src/DicomMessage.js @@ -8,6 +8,7 @@ import { import { DicomDict } from "./DicomDict.js"; import { DicomMetaDictionary } from "./DicomMetaDictionary.js"; import { Tag } from "./Tag.js"; +import { log } from "./log.js"; import { ValueRepresentation } from "./ValueRepresentation.js"; const singleVRs = ["SQ", "OF", "OW", "OB", "UN", "LT"]; @@ -77,7 +78,7 @@ class DicomMessage { untilTag = null, includeUntilTagValue = false ) { - console.warn("DicomMessage.read to be deprecated after dcmjs 0.24.x"); + log.warn("DicomMessage.read to be deprecated after dcmjs 0.24.x"); return this._read(bufferStream, syntax, { ignoreErrors: ignoreErrors, untilTag: untilTag, @@ -91,9 +92,7 @@ class DicomMessage { untilTag = null, includeUntilTagValue = false ) { - console.warn( - "DicomMessage.readTag to be deprecated after dcmjs 0.24.x" - ); + log.warn("DicomMessage.readTag to be deprecated after dcmjs 0.24.x"); return this._readTag(bufferStream, syntax, { untilTag: untilTag, includeUntilTagValue: includeUntilTagValue @@ -127,7 +126,7 @@ class DicomMessage { coding = encodingMapping[coding]; bufferStream.setDecoder(new TextDecoder(coding)); } else if (ignoreErrors) { - console.warn( + log.warn( `Unsupported character set: ${coding}, using default character set` ); } else { @@ -136,7 +135,7 @@ class DicomMessage { } if (readInfo.values.length > 1) { if (ignoreErrors) { - console.warn( + log.warn( "Using multiple character sets is not supported, proceeding with just the first character set", readInfo.values ); @@ -160,7 +159,7 @@ class DicomMessage { return dict; } catch (err) { if (ignoreErrors) { - console.warn("WARN:", err); + log.warn("WARN:", err); return dict; } throw err; diff --git a/src/ValueRepresentation.js b/src/ValueRepresentation.js index 46acbd3a..c476f2da 100644 --- a/src/ValueRepresentation.js +++ b/src/ValueRepresentation.js @@ -1,4 +1,4 @@ -import log from "./log.js"; +import { validationLog, log } from "./log.js"; import { DicomMessage } from "./DicomMessage.js"; import { ReadBufferStream } from "./BufferStream.js"; import { WriteBufferStream } from "./BufferStream.js"; @@ -162,13 +162,14 @@ class ValueRepresentation { if (type == "ox") { // TODO: determine VR based on context (could be 1 byte pixel data) // https://github.com/dgobbi/vtk-dicom/issues/38 - log.error("Invalid vr type " + type + " - using OW"); + validationLog.error("Invalid vr type", type, "- using OW"); vr = VRinstances["OW"]; } else if (type == "xs") { - log.error("Invalid vr type " + type + " - using US"); + validationLog.error("Invalid vr type", type, "- using US"); vr = VRinstances["US"]; } else { - log.error("Invalid vr type " + type + " - using UN"); + console.log("validationLog", validationLog.level); + validationLog.error("Invalid vr type", type, "- using UN"); vr = VRinstances["UN"]; } } diff --git a/src/anonymizer.js b/src/anonymizer.js index b8639281..9d2d89da 100644 --- a/src/anonymizer.js +++ b/src/anonymizer.js @@ -1,4 +1,3 @@ -import log from "./log.js"; import { DicomMetaDictionary } from "./DicomMetaDictionary.js"; import { Tag } from "./Tag.js"; diff --git a/src/bitArray.js b/src/bitArray.js index e4f82c5b..9b0fe26b 100644 --- a/src/bitArray.js +++ b/src/bitArray.js @@ -28,7 +28,7 @@ function getBytesForBinaryFrame(numPixels) { function pack(pixelData) { const numPixels = pixelData.length; - log.log("numPixels: " + numPixels); + log.debug("numPixels: " + numPixels); const length = getBytesForBinaryFrame(numPixels); //log.log('getBytesForBinaryFrame: ' + length); diff --git a/src/log.js b/src/log.js index 039f1f8a..f05584c5 100644 --- a/src/log.js +++ b/src/log.js @@ -2,5 +2,12 @@ import loglevelnext from "loglevelnext"; const log = loglevelnext.create("dcmjs"); -export { log }; +/** + * A validation log shows issues with data validation, and not internal issues itself. + * This is validation.dcmjs to group the validation issues into a single validation set to allow + * turning validation on/off. + */ +const validationLog = loglevelnext.create("validation.dcmjs"); + +export { log, validationLog }; export default log; diff --git a/test/anonymizer.test.js b/test/anonymizer.test.js index 3c61bd50..23def9f0 100644 --- a/test/anonymizer.test.js +++ b/test/anonymizer.test.js @@ -1,5 +1,9 @@ import dcmjs from "../src/index.js"; import fs from "fs"; +import { validationLog } from "./../src/log.js"; + +// Ignore validation errors +validationLog.level = 5; const { DicomMessage } = dcmjs.data; const { cleanTags, getTagsNameToEmpty } = dcmjs.anonymizer; diff --git a/test/data-options.test.js b/test/data-options.test.js index 8f0288cb..fffbd3f8 100644 --- a/test/data-options.test.js +++ b/test/data-options.test.js @@ -3,16 +3,13 @@ import "regenerator-runtime/runtime.js"; import dcmjs from "../src/index.js"; import fs from "fs"; import path from "path"; -import os from "os"; import { promisify } from "util"; import fsPromises from "fs/promises"; import { getZippedTestDataset, getTestDataset } from "./testUtils.js"; const { DicomMetaDictionary, - DicomDict, DicomMessage, - ReadBufferStream } = dcmjs.data; const areEqual = (first, second) => @@ -79,7 +76,8 @@ it("noCopy multiframe DICOM which has trailing padding", async () => { }); }); -it("noCopy multiframe DICOM with large private tags before and after the image data", async () => { +/** Skipping this because the underlying data in the repository is broken */ +it.skip("noCopy multiframe DICOM with large private tags before and after the image data", async () => { const url = "https://github.com/dcmjs-org/data/releases/download/binary-parsing-stressors/large-private-tags.dcm"; const dcmPath = await getTestDataset(url, "large-private-tags.dcm") diff --git a/test/data.test.js b/test/data.test.js index 7e9cd547..36ac5cd9 100644 --- a/test/data.test.js +++ b/test/data.test.js @@ -7,6 +7,7 @@ import path from "path"; import { WriteBufferStream } from "../src/BufferStream"; import dcmjs from "../src/index.js"; import { getTestDataset, getZippedTestDataset } from "./testUtils.js"; +import { log } from "./../src/log.js"; import { promisify } from "util"; import arrayItem from "./arrayItem.json"; @@ -571,7 +572,8 @@ it("Reads a multiframe DICOM which has trailing padding", async () => { expect(dataset.PixelData[28].byteLength).toEqual(103194); }); -it("Reads a multiframe DICOM with large private tags before and after the image data", async () => { +/** Skipping this because the underlying data in the repository is broken */ +it.skip("Reads a multiframe DICOM with large private tags before and after the image data", async () => { const url = "https://github.com/dcmjs-org/data/releases/download/binary-parsing-stressors/large-private-tags.dcm"; const dcmPath = await getTestDataset(url, "large-private-tags.dcm") @@ -669,12 +671,14 @@ describe("With a SpecificCharacterSet tag", () => { }); it("Throws an exception on an unsupported character set", async () => { + log.level = 5; expect(() => readEncodedLongString("nope", [])).toThrow( new Error("Unsupported character set: nope") ); }); it("Doesn't throw an exception on an unsupported character set when ignoring errors", async () => { + log.level = 5; expect( readEncodedLongString("nope", [0x68, 0x69], { ignoreErrors: true }) ).toEqual("hi"); diff --git a/test/integration/DicomMessage.readFile.test.js b/test/integration/DicomMessage.readFile.test.js index c71fdbb8..6b9b6076 100644 --- a/test/integration/DicomMessage.readFile.test.js +++ b/test/integration/DicomMessage.readFile.test.js @@ -1,6 +1,10 @@ import fs from 'fs'; import path from 'path'; import dcmjs from "../../src/index.js"; +import { validationLog } from "./../../src/log.js"; + +// Ignore validation errors +validationLog.level = 5; const { DicomMessage } = dcmjs.data; diff --git a/test/testUtils.js b/test/testUtils.js index 92b2b442..44fc8b55 100644 --- a/test/testUtils.js +++ b/test/testUtils.js @@ -1,13 +1,15 @@ import fs from "fs"; -import fsPromises from "fs/promises"; import os from "os"; import path from "path"; -import unzipper from "unzipper"; import followRedirects from "follow-redirects"; -import { promisify } from "util"; +import AdmZip from 'adm-zip'; +import { validationLog } from "./../src/log.js"; const { https } = followRedirects; +// Don't show validation errors, as those are normally tested +validationLog.level = 5; + function downloadToFile(url, filePath) { return new Promise((resolve, reject) => { const fileStream = fs.createWriteStream(filePath); @@ -23,11 +25,25 @@ function downloadToFile(url, filePath) { } function unzip(zipFilePath, targetPath) { - return new Promise(resolve => { - fs.createReadStream(zipFilePath).pipe( - unzipper.Extract({ path: targetPath }).on("close", resolve) - ); - }); + return new Promise( (resolve,reject) => { + try { + // reading archives + var zip = new AdmZip(zipFilePath); + var zipEntries = zip.getEntries(); // an array of ZipEntry records + // extracts everything + zip.extractAllTo(targetPath, true); + resolve(); + } catch(e) { + reject(e); + } + }); + + // This code is broken in Node 18+, creating garbage output + // return new Promise(resolve => { + // fs.createReadStream(zipFilePath).pipe( + // unzipper.Extract({ path: targetPath }).on("close", resolve) + // ); + // }); } function ensureTestDataDir() { From b8691e22c85beea738f0aefa6357bb7bdfaeac4e Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 11:00:18 -0400 Subject: [PATCH 3/9] Update node version for tests/build --- netlify.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/netlify.toml b/netlify.toml index 22e53a37..35a2b739 100644 --- a/netlify.toml +++ b/netlify.toml @@ -11,6 +11,7 @@ base = "" publish = "examples/" command = "npm run build:examples" + environment = { NODE_VERSION = "18.16.0" } # Deploy Preview context: all deploys generated from a pull/merge request will # inherit these settings. @@ -18,3 +19,4 @@ base = "" publish = "examples/" command = "npm run build:examples" + environment = { NODE_VERSION = "18.16.0" } From faafba3d3303f9ea3e3ca93265d71dd080eeaba3 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 11:03:30 -0400 Subject: [PATCH 4/9] Update node version --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5f0ae3be..3b0c91f1 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -15,7 +15,7 @@ jobs: - name: Setup Node.js uses: actions/setup-node@v1 with: - node-version: 16 + node-version: 18 - name: Install packages uses: bahmutov/npm-install@v1 From f55ea9805b81c47e7579a7bc710316a3e5ee7871 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 13:19:21 -0400 Subject: [PATCH 5/9] Re-enable the large private, seems delete/load fixes it --- test/data-options.test.js | 3 +-- test/data.test.js | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/test/data-options.test.js b/test/data-options.test.js index fffbd3f8..80b621df 100644 --- a/test/data-options.test.js +++ b/test/data-options.test.js @@ -76,8 +76,7 @@ it("noCopy multiframe DICOM which has trailing padding", async () => { }); }); -/** Skipping this because the underlying data in the repository is broken */ -it.skip("noCopy multiframe DICOM with large private tags before and after the image data", async () => { +it("noCopy multiframe DICOM with large private tags before and after the image data", async () => { const url = "https://github.com/dcmjs-org/data/releases/download/binary-parsing-stressors/large-private-tags.dcm"; const dcmPath = await getTestDataset(url, "large-private-tags.dcm") diff --git a/test/data.test.js b/test/data.test.js index 36ac5cd9..a9e44259 100644 --- a/test/data.test.js +++ b/test/data.test.js @@ -572,8 +572,7 @@ it("Reads a multiframe DICOM which has trailing padding", async () => { expect(dataset.PixelData[28].byteLength).toEqual(103194); }); -/** Skipping this because the underlying data in the repository is broken */ -it.skip("Reads a multiframe DICOM with large private tags before and after the image data", async () => { +it("Reads a multiframe DICOM with large private tags before and after the image data", async () => { const url = "https://github.com/dcmjs-org/data/releases/download/binary-parsing-stressors/large-private-tags.dcm"; const dcmPath = await getTestDataset(url, "large-private-tags.dcm") From 80cf023ac85927f1e512eb0aea1fd7ce1eef819e Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 14:04:16 -0400 Subject: [PATCH 6/9] fix(units): Store different types of units --- src/utilities/TID300/Circle.js | 20 +++------- src/utilities/TID300/Length.js | 17 ++++---- src/utilities/TID300/index.js | 4 +- src/utilities/TID300/unit2CodingValue.js | 51 ++++++++++++++++++++++++ 4 files changed, 69 insertions(+), 23 deletions(-) create mode 100644 src/utilities/TID300/unit2CodingValue.js diff --git a/src/utilities/TID300/Circle.js b/src/utilities/TID300/Circle.js index 710e05c2..bb9abb50 100644 --- a/src/utilities/TID300/Circle.js +++ b/src/utilities/TID300/Circle.js @@ -1,5 +1,5 @@ -import { DicomMetaDictionary } from "../../DicomMetaDictionary.js"; import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; /** * Expand an array of points stored as objects into @@ -26,7 +26,9 @@ export default class Circle extends TID300Measurement { ReferencedSOPSequence, use3DSpatialCoordinates = false, perimeter, - area + area, + areaUnit = "mm2", + unit = "mm" } = this.props; // Combine all lengths to save the perimeter @@ -47,12 +49,7 @@ export default class Circle extends TID300Measurement { CodeMeaning: "Perimeter" // TODO: Look this up from a Code Meaning dictionary }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: perimeter }, ContentSequence: { @@ -79,12 +76,7 @@ export default class Circle extends TID300Measurement { CodeMeaning: "Area" // TODO: Look this up from a Code Meaning dictionary }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm2", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "SquareMilliMeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(areaUnit), NumericValue: area }, ContentSequence: { diff --git a/src/utilities/TID300/Length.js b/src/utilities/TID300/Length.js index bc418f4d..09883c84 100644 --- a/src/utilities/TID300/Length.js +++ b/src/utilities/TID300/Length.js @@ -1,9 +1,15 @@ -import { DicomMetaDictionary } from "../../DicomMetaDictionary.js"; import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; export default class Length extends TID300Measurement { contentItem() { - const { point1, point2, distance, ReferencedSOPSequence } = this.props; + const { + point1, + point2, + unit = "mm", + distance, + ReferencedSOPSequence + } = this.props; return this.getMeasurement([ { @@ -15,12 +21,7 @@ export default class Length extends TID300Measurement { CodeMeaning: "Length" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: distance }, ContentSequence: { diff --git a/src/utilities/TID300/index.js b/src/utilities/TID300/index.js index 314e1117..6f31188c 100644 --- a/src/utilities/TID300/index.js +++ b/src/utilities/TID300/index.js @@ -7,6 +7,7 @@ import Polyline from "./Polyline.js"; import Polygon from "./Polygon.js"; import Ellipse from "./Ellipse.js"; import Circle from "./Circle"; +import unit2CodingValue from "./unit2CodingValue.js"; // To be implemented: // - Cornerstone Probe @@ -73,7 +74,8 @@ const TID300 = { Polyline, Polygon, Ellipse, - Circle + Circle, + unit2CodingValue }; export { TID300Measurement, Length }; diff --git a/src/utilities/TID300/unit2CodingValue.js b/src/utilities/TID300/unit2CodingValue.js new file mode 100644 index 00000000..11126e44 --- /dev/null +++ b/src/utilities/TID300/unit2CodingValue.js @@ -0,0 +1,51 @@ +import log from "../../log.js"; + +const MM_UNIT = { + CodeValue: "mm", + CodingSchemeDesignator: "UCUM", + CodingSchemeVersion: "1.4", + CodeMeaning: "millimeter" +}; + +const MM2_UNIT = { + CodeValue: "mm2", + CodingSchemeDesignator: "UCUM", + CodingSchemeVersion: "1.4", + CodeMeaning: "SquareMilliMeter" +}; + +const NO_UNIT = { + CodeValue: "1", + CodingSchemeDesignator: "UCUM", + CodingSchemeVersion: "1.4", + CodeMeaning: "px" +}; + +const PX2_UNIT = PX_UNIT; + +const measurementMap = { + px: NO_UNIT, + mm: MM_UNIT, + mm2: MM2_UNIT, + "mm\xB2": MM2_UNIT +}; + +/** Converts the given unit into the + * specified coding values. + * Has .measurementMap on the function specifying global units for measurements. + */ +const unit2CodingValue = units => { + if (!units) return NO_UNIT; + const space = units.indexOf(" "); + const baseUnit = space === -1 ? units : units.substring(0, space); + const codingUnit = measurementMap[units] || measurementMap[baseUnit]; + if (!codingUnit) { + log.error("Unspecified units", units, type); + return MM_UNIT; + } + return codingUnit; +}; + +unit2CodingValue.measurementMap = measurementMap; + +export default unit2CodingValue; From 7e687cd28cc300ba885ddc2b65427e927aca0594 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 14:16:49 -0400 Subject: [PATCH 7/9] Fix the unit conversion code --- src/utilities/TID300/unit2CodingValue.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/utilities/TID300/unit2CodingValue.js b/src/utilities/TID300/unit2CodingValue.js index 11126e44..54de41ce 100644 --- a/src/utilities/TID300/unit2CodingValue.js +++ b/src/utilities/TID300/unit2CodingValue.js @@ -21,13 +21,14 @@ const NO_UNIT = { CodeMeaning: "px" }; -const PX2_UNIT = PX_UNIT; +const NO2_UNIT = NO_UNIT; const measurementMap = { px: NO_UNIT, mm: MM_UNIT, mm2: MM2_UNIT, - "mm\xB2": MM2_UNIT + "mm\xB2": MM2_UNIT, + "px\xB2": NO2_UNIT }; /** Converts the given unit into the @@ -40,7 +41,7 @@ const unit2CodingValue = units => { const baseUnit = space === -1 ? units : units.substring(0, space); const codingUnit = measurementMap[units] || measurementMap[baseUnit]; if (!codingUnit) { - log.error("Unspecified units", units, type); + log.error("Unspecified units", units); return MM_UNIT; } return codingUnit; From f060d806961dd9dad7eb5b9e9ae27411b9ed5acd Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 14:53:30 -0400 Subject: [PATCH 8/9] feat: Add calibration ruler object --- package.json | 2 +- src/ValueRepresentation.js | 1 - src/adapters/Cornerstone/CircleRoi.js | 14 ++--- src/utilities/TID300/Calibration.js | 41 +++++++++++++++ src/utilities/TID300/index.js | 6 ++- test/sr-tid.test.js | 74 +++++++++++++++++++++++++++ test/sr.test.js | 1 - 7 files changed, 125 insertions(+), 14 deletions(-) create mode 100644 src/utilities/TID300/Calibration.js create mode 100644 test/sr-tid.test.js delete mode 100644 test/sr.test.js diff --git a/package.json b/package.json index ead00a45..169d02c8 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "example": "examples" }, "scripts": { - "test": "jest --testTimeout 60000", + "test": "jest --testTimeout 60000 .", "build": "rollup -c", "build:examples": "npm run build && npx cpx 'build/**/*.{js,map}' examples/js", "start": "rollup -c -w", diff --git a/src/ValueRepresentation.js b/src/ValueRepresentation.js index c476f2da..93047d7a 100644 --- a/src/ValueRepresentation.js +++ b/src/ValueRepresentation.js @@ -168,7 +168,6 @@ class ValueRepresentation { validationLog.error("Invalid vr type", type, "- using US"); vr = VRinstances["US"]; } else { - console.log("validationLog", validationLog.level); validationLog.error("Invalid vr type", type, "- using UN"); vr = VRinstances["UN"]; } diff --git a/src/adapters/Cornerstone/CircleRoi.js b/src/adapters/Cornerstone/CircleRoi.js index 7a1f6287..9dd24472 100644 --- a/src/adapters/Cornerstone/CircleRoi.js +++ b/src/adapters/Cornerstone/CircleRoi.js @@ -1,22 +1,16 @@ import MeasurementReport from "./MeasurementReport"; import TID300Circle from "../../utilities/TID300/Circle"; import CORNERSTONE_4_TAG from "./cornerstone4Tag"; -import { toArray } from "../helpers.js"; const CIRCLEROI = "CircleRoi"; -const FINDING = "121071"; -const FINDING_SITE = "G-C0E3"; class CircleRoi { constructor() {} /** Gets the measurement data for cornerstone, given DICOM SR measurement data. */ static getMeasurementData(MeasurementGroup) { - const { - defaultState, - NUMGroup, - SCOORDGroup - } = MeasurementReport.getSetupMeasurementData(MeasurementGroup); + const { defaultState, NUMGroup, SCOORDGroup } = + MeasurementReport.getSetupMeasurementData(MeasurementGroup); const { GraphicData } = SCOORDGroup; @@ -71,7 +65,7 @@ class CircleRoi { static getTID300RepresentationArguments(tool) { const { cachedStats = {}, handles, finding, findingSites } = tool; const { start: center, end } = handles; - const { area, radius } = cachedStats; + const { area, areaUnit = "mm2", unit = "mm", radius } = cachedStats; const perimeter = 2 * Math.PI * radius; const points = []; @@ -83,7 +77,9 @@ class CircleRoi { return { area, + areaUnit, perimeter, + unit, radius, points, trackingIdentifierTextValue, diff --git a/src/utilities/TID300/Calibration.js b/src/utilities/TID300/Calibration.js new file mode 100644 index 00000000..8c5cb30e --- /dev/null +++ b/src/utilities/TID300/Calibration.js @@ -0,0 +1,41 @@ +import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; + +export default class Calibration extends TID300Measurement { + contentItem() { + const { + point1, + point2, + unit = "mm", + distance, + ReferencedSOPSequence + } = this.props; + + return this.getMeasurement([ + { + RelationshipType: "CONTAINS", + ValueType: "NUM", + ConceptNameCodeSequence: { + CodeValue: "102304005", + CodingSchemeDesignator: "SCT", + CodeMeaning: "Calibration Ruler" + }, + MeasuredValueSequence: { + MeasurementUnitsCodeSequence: unit2CodingValue(unit), + NumericValue: distance + }, + ContentSequence: { + RelationshipType: "INFERRED FROM", + ValueType: "SCOORD", + GraphicType: "POLYLINE", + GraphicData: [point1.x, point1.y, point2.x, point2.y], + ContentSequence: { + RelationshipType: "SELECTED FROM", + ValueType: "IMAGE", + ReferencedSOPSequence + } + } + } + ]); + } +} diff --git a/src/utilities/TID300/index.js b/src/utilities/TID300/index.js index 6f31188c..26907ae6 100644 --- a/src/utilities/TID300/index.js +++ b/src/utilities/TID300/index.js @@ -5,9 +5,10 @@ import CobbAngle from "./CobbAngle"; import Bidirectional from "./Bidirectional.js"; import Polyline from "./Polyline.js"; import Polygon from "./Polygon.js"; -import Ellipse from "./Ellipse.js"; +import Ellipse from "./Ellipse"; import Circle from "./Circle"; -import unit2CodingValue from "./unit2CodingValue.js"; +import Calibration from "./Calibration"; +import unit2CodingValue from "./unit2CodingValue"; // To be implemented: // - Cornerstone Probe @@ -75,6 +76,7 @@ const TID300 = { Polygon, Ellipse, Circle, + Calibration, unit2CodingValue }; diff --git a/test/sr-tid.test.js b/test/sr-tid.test.js new file mode 100644 index 00000000..86c8b22c --- /dev/null +++ b/test/sr-tid.test.js @@ -0,0 +1,74 @@ +import { utilities } from "../src"; + +const { Length, Circle, Calibration } = utilities.TID300; + +describe("DICOM SR TID 300/1500 tests", () => { + describe("TID300 Creation", () => { + it("Length Create", () => { + const length = new Length({ + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + unit: 'mm', + distance: 3.14, + }); + const value = length.contentItem(); + expect(value.length).toBe(3); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(3.14); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm'); + }); + + it("Circle Create", () => { + const r = 10; + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + unit: 'mm', + areaUnits: 'mm\xB2', + perimeter: 2*3.141592*r, + area: 3.141592*r*r, + }; + const circle = new Circle(props); + const value = circle.contentItem(); + expect(value.length).toBe(4); + const measured = value[3].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.area); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm2'); + }); + + + it('Calibration Create', () => { + const calibration = new Calibration({ + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + unit: 'mm', + distance: 3.14, + }); + const value = calibration.contentItem(); + expect(value.length).toBe(3); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(3.14); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm'); + }); + }); + + describe("Use Units", () => { + it("Length Units", () => { + const length = new Length({ + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + unit: 'px', + distance: 3.14, + }); + const value = length.contentItem(); + expect(value.length).toBe(3); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(3.14); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('1'); + }); + }); +}); + diff --git a/test/sr.test.js b/test/sr.test.js deleted file mode 100644 index cc877c3f..00000000 --- a/test/sr.test.js +++ /dev/null @@ -1 +0,0 @@ -it("No tests yet", () => {}); From fd48bbc9531e469d11f8d98bb72210bbb7fc89f3 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 19 Jun 2023 15:18:44 -0400 Subject: [PATCH 9/9] fix: Add units for remainder of TID300 types --- src/utilities/TID300/Bidirectional.js | 16 +-- src/utilities/TID300/Ellipse.js | 10 +- src/utilities/TID300/Polygon.js | 22 ++-- src/utilities/TID300/Polyline.js | 22 ++-- test/sr-tid.test.js | 152 +++++++++++++++++++++++++- 5 files changed, 172 insertions(+), 50 deletions(-) diff --git a/src/utilities/TID300/Bidirectional.js b/src/utilities/TID300/Bidirectional.js index bd7dd476..fba5548c 100644 --- a/src/utilities/TID300/Bidirectional.js +++ b/src/utilities/TID300/Bidirectional.js @@ -1,5 +1,6 @@ import { DicomMetaDictionary } from "../../DicomMetaDictionary.js"; import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; export default class Bidirectional extends TID300Measurement { contentItem() { @@ -8,6 +9,7 @@ export default class Bidirectional extends TID300Measurement { shortAxis, longAxisLength, shortAxisLength, + unit, ReferencedSOPSequence } = this.props; @@ -21,12 +23,7 @@ export default class Bidirectional extends TID300Measurement { CodeMeaning: "Long Axis" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: longAxisLength }, ContentSequence: { @@ -55,12 +52,7 @@ export default class Bidirectional extends TID300Measurement { CodeMeaning: "Short Axis" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: shortAxisLength }, ContentSequence: { diff --git a/src/utilities/TID300/Ellipse.js b/src/utilities/TID300/Ellipse.js index a2e6c2b1..2db4a04e 100644 --- a/src/utilities/TID300/Ellipse.js +++ b/src/utilities/TID300/Ellipse.js @@ -1,4 +1,5 @@ import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; /** * Expand an array of points stored as objects into @@ -20,7 +21,7 @@ function expandPoints(points) { export default class Ellipse extends TID300Measurement { contentItem() { - const { points, ReferencedSOPSequence, area } = this.props; + const { points, ReferencedSOPSequence, area, areaUnit } = this.props; const GraphicData = expandPoints(points); @@ -34,12 +35,7 @@ export default class Ellipse extends TID300Measurement { CodeMeaning: "AREA" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm2", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "squaremillimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(areaUnit), NumericValue: area }, ContentSequence: { diff --git a/src/utilities/TID300/Polygon.js b/src/utilities/TID300/Polygon.js index 9a31447d..0719a927 100644 --- a/src/utilities/TID300/Polygon.js +++ b/src/utilities/TID300/Polygon.js @@ -1,5 +1,6 @@ import { DicomMetaDictionary } from "../../DicomMetaDictionary.js"; import TID300Measurement from "./TID300Measurement.js"; +import unit2CodingValue from "./unit2CodingValue.js"; /** * Expand an array of points stored as objects into @@ -26,11 +27,14 @@ export default class Polygon extends TID300Measurement { contentItem() { const { points, + perimeter, + unit = "mm", + area, + areaUnit, ReferencedSOPSequence, use3DSpatialCoordinates = false } = this.props; - const perimeter = {}; const GraphicData = expandPoints(points); return this.getMeasurement([ @@ -43,12 +47,7 @@ export default class Polygon extends TID300Measurement { CodeMeaning: "Perimeter" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: perimeter }, ContentSequence: { @@ -74,13 +73,8 @@ export default class Polygon extends TID300Measurement { CodeMeaning: "Area" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm2", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "SquareMilliMeter" - }, - NumericValue: perimeter + MeasurementUnitsCodeSequence: unit2CodingValue(areaUnit), + NumericValue: area }, ContentSequence: { RelationshipType: "INFERRED FROM", diff --git a/src/utilities/TID300/Polyline.js b/src/utilities/TID300/Polyline.js index a8caca91..023ce2d2 100644 --- a/src/utilities/TID300/Polyline.js +++ b/src/utilities/TID300/Polyline.js @@ -1,5 +1,5 @@ -import { DicomMetaDictionary } from "../../DicomMetaDictionary.js"; -import TID300Measurement from "./TID300Measurement.js"; +import TID300Measurement from "./TID300Measurement"; +import unit2CodingValue from "./unit2CodingValue"; /** * Expand an array of points stored as objects into @@ -27,9 +27,11 @@ export default class Polyline extends TID300Measurement { const { points, area, + areaUnit = "mm2", ReferencedSOPSequence, use3DSpatialCoordinates = false, - perimeter + perimeter, + unit = "mm" } = this.props; const GraphicData = expandPoints(points); @@ -45,12 +47,7 @@ export default class Polyline extends TID300Measurement { CodeMeaning: "Perimeter" }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "millimeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(unit), NumericValue: perimeter }, ContentSequence: { @@ -77,12 +74,7 @@ export default class Polyline extends TID300Measurement { CodeMeaning: "Area" // TODO: Look this up from a Code Meaning dictionary }, MeasuredValueSequence: { - MeasurementUnitsCodeSequence: { - CodeValue: "mm2", - CodingSchemeDesignator: "UCUM", - CodingSchemeVersion: "1.4", - CodeMeaning: "SquareMilliMeter" - }, + MeasurementUnitsCodeSequence: unit2CodingValue(areaUnit), NumericValue: area }, ContentSequence: { diff --git a/test/sr-tid.test.js b/test/sr-tid.test.js index 86c8b22c..f661e2bf 100644 --- a/test/sr-tid.test.js +++ b/test/sr-tid.test.js @@ -1,9 +1,84 @@ import { utilities } from "../src"; -const { Length, Circle, Calibration } = utilities.TID300; +const { Length, Circle, Polygon, Polyline, Ellipse, Bidirectional, Calibration } = utilities.TID300; describe("DICOM SR TID 300/1500 tests", () => { describe("TID300 Creation", () => { + it("Polygon Create", () => { + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + unit: 'mm', + areaUnit: 'mm2', + area: 3.14, + perimeter: 25, + }; + const polyline = new Polygon(props); + const value = polyline.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.perimeter); + expect(value[3].MeasuredValueSequence.NumericValue).toBe(props.area); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm'); + }); + + it("Polyline Create", () => { + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + unit: 'mm', + areaUnit: 'mm2', + area: 3.14, + perimeter: 25, + }; + const polyline = new Polyline(props); + const value = polyline.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.perimeter); + expect(value[3].MeasuredValueSequence.NumericValue).toBe(props.area); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm'); + }); + + it("Ellipse Create", () => { + const r = 10; + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + areaUnit: 'mm\xB2', + area: 3.141592*r*r, + }; + const circle = new Ellipse(props); + const value = circle.contentItem(); + expect(value.length).toBe(3); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.area); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm2'); + }); + + it("Bidirectional Create", () => { + const bidir = new Bidirectional({ + longAxis: { + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + }, + shortAxis: { + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + }, + unit: 'mm', + longAxisLength: 3.14, + shortAxisLenght: 1.5, + }); + const value = bidir.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(3.14); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('mm'); + }); + + it("Length Create", () => { const length = new Length({ point1: {x: 3, y: 5}, @@ -24,7 +99,7 @@ describe("DICOM SR TID 300/1500 tests", () => { const props = { points: [{x: 3, y: 5}, {x: 6, y: 1}], unit: 'mm', - areaUnits: 'mm\xB2', + areaUnit: 'mm\xB2', perimeter: 2*3.141592*r, area: 3.141592*r*r, }; @@ -69,6 +144,79 @@ describe("DICOM SR TID 300/1500 tests", () => { const units = measured.MeasurementUnitsCodeSequence; expect(units.CodeValue).toBe('1'); }); + + it("Polygon Units", () => { + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + unit: 'px', + areaUnit: 'px\xB2', + area: 3.14, + perimeter: 25, + }; + const polyline = new Polygon(props); + const value = polyline.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.perimeter); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('1'); + }); + + it("Polyline Units", () => { + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + unit: 'px', + areaUnit: 'px\xB2', + area: 3.14, + perimeter: 25, + }; + const polyline = new Polyline(props); + const value = polyline.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.perimeter); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('1'); + }); + + it("Ellipse Unit", () => { + const r = 10; + const props = { + points: [{x: 3, y: 5}, {x: 6, y: 1}], + areaUnit: 'px\xB2', + area: 3.141592*r*r, + }; + const circle = new Ellipse(props); + const value = circle.contentItem(); + expect(value.length).toBe(3); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(props.area); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('1'); + }); + + it("Bidirectional Create", () => { + const bidir = new Bidirectional({ + longAxis: { + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + }, + shortAxis: { + point1: {x: 3, y: 5}, + point2: {x: 6, y: 1}, + }, + unit: 'px', + longAxisLength: 3.14, + shortAxisLenght: 1.5, + }); + const value = bidir.contentItem(); + expect(value.length).toBe(4); + const measured = value[2].MeasuredValueSequence; + expect(measured.NumericValue).toBe(3.14); + const units = measured.MeasurementUnitsCodeSequence; + expect(units.CodeValue).toBe('1'); + }); + }); });