From 22a1d69e00f21bd629cdcfefd4bc0adb8345fe71 Mon Sep 17 00:00:00 2001 From: Nick Guenther Date: Sun, 27 Nov 2022 03:54:24 -0500 Subject: [PATCH] cornerstone: display NIfTI and dicom image previews --- package-lock.json | 4568 +++++++++++++++------------- package.json | 5 + routers/web/repo/view.go | 4 + templates/repo/view_file.tmpl | 4 + web_src/js/features/cornerstone.js | 51 + web_src/js/index.js | 2 + 6 files changed, 2564 insertions(+), 2070 deletions(-) create mode 100644 web_src/js/features/cornerstone.js diff --git a/package-lock.json b/package-lock.json index a10225b3360c1..447c2d368e5b4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -12,6 +12,7 @@ "@citation-js/plugin-csl": "0.6.8", "@citation-js/plugin-software-formats": "0.6.1", "@claviska/jquery-minicolors": "2.3.6", + "@cornerstonejs/nifti-image-loader": "^1.0.7", "@github/markdown-toolbar-element": "2.1.1", "@github/relative-time-element": "4.3.0", "@github/text-expander-element": "2.5.0", @@ -22,7 +23,11 @@ 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"resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz", - "integrity": "sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ==", + "license": "MIT", "dependencies": { "ansi-styles": "^6.1.0", "string-width": "^5.0.1", @@ -11105,9 +11551,8 @@ "node_modules/wrap-ansi-cjs": { "name": "wrap-ansi", "version": "7.0.0", - "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", - "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==", "dev": true, + "license": "MIT", "dependencies": { "ansi-styles": "^4.0.0", "string-width": "^4.1.0", @@ -11122,8 +11567,7 @@ }, "node_modules/wrap-ansi/node_modules/ansi-regex": { "version": "6.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz", - "integrity": "sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA==", + "license": "MIT", "engines": { "node": ">=12" }, @@ -11133,8 +11577,7 @@ }, "node_modules/wrap-ansi/node_modules/ansi-styles": { "version": "6.2.1", - "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.1.tgz", - "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug==", + "license": "MIT", "engines": { "node": ">=12" }, @@ -11144,13 +11587,11 @@ }, "node_modules/wrap-ansi/node_modules/emoji-regex": { "version": "9.2.2", - "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz", - "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==" + "license": "MIT" }, "node_modules/wrap-ansi/node_modules/string-width": { "version": "5.1.2", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-5.1.2.tgz", - "integrity": "sha512-HnLOCR3vjcY8beoNLtcjZ5/nxn2afmME6lhrDrebokqMap+XbeW8n9TXpPDOqdGK5qcI3oT0GKTW6wC7EMiVqA==", + "license": "MIT", "dependencies": { "eastasianwidth": "^0.2.0", "emoji-regex": "^9.2.2", @@ -11165,8 +11606,7 @@ }, "node_modules/wrap-ansi/node_modules/strip-ansi": { "version": "7.1.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", - "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==", + "license": "MIT", "dependencies": { "ansi-regex": "^6.0.1" }, @@ -11179,14 +11619,12 @@ }, "node_modules/wrappy": { "version": "1.0.2", - "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==" + "license": "ISC" }, "node_modules/write-file-atomic": { "version": "5.0.1", - "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-5.0.1.tgz", - "integrity": "sha512-+QU2zd6OTD8XWIJCbffaiQeH9U73qIqafo1x6V1snCWYGJf6cVE0cDR4D8xRzcEnfI21IFrUPzPGtcPf8AC+Rw==", "dev": true, + "license": "ISC", "dependencies": { "imurmurhash": "^0.1.4", "signal-exit": "^4.0.1" @@ -11197,9 +11635,8 @@ }, "node_modules/ws": { "version": "8.13.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz", - "integrity": "sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA==", "dev": true, + "license": "MIT", "engines": { "node": ">=10.0.0" }, @@ -11218,18 +11655,16 @@ }, "node_modules/xml-name-validator": { "version": "4.0.0", - "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz", - "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==", "dev": true, + "license": "Apache-2.0", "engines": { "node": ">=12" } }, "node_modules/xmlchars": { "version": "2.2.0", - "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", - "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", - "dev": true + "dev": true, + "license": "MIT" }, "node_modules/xregexp": { "version": "2.0.0", @@ -11242,24 +11677,20 @@ }, "node_modules/y18n": { "version": "5.0.8", - "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", - "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", "dev": true, + "license": "ISC", "engines": { "node": ">=10" } }, "node_modules/yallist": { - "version": "3.1.1", - "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", - "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", - "dev": true + "version": "4.0.0", + "license": "ISC" }, "node_modules/yargs": { "version": "17.3.1", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.3.1.tgz", - "integrity": "sha512-WUANQeVgjLbNsEmGk20f+nlHgOqzRFpiGWVaBrYGYIGANIIu3lWjoyi0fNlFmJkvfhCZ6BXINe7/W2O2bV4iaA==", "dev": true, + "license": "MIT", "dependencies": { "cliui": "^7.0.2", "escalade": "^3.1.1", @@ -11284,18 +11715,15 @@ }, "node_modules/yargs/node_modules/yargs-parser": { "version": "21.1.1", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", - "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", "dev": true, + "license": "ISC", "engines": { "node": ">=12" } }, "node_modules/yocto-queue": { "version": "0.1.0", - "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", - "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true, + "license": "MIT", "engines": { "node": ">=10" }, diff --git a/package.json b/package.json index fe3f0691a991a..f21814e287e5a 100644 --- a/package.json +++ b/package.json @@ -7,6 +7,11 @@ "node": ">= 16.0.0" }, "dependencies": { + "cornerstone-core": "^2.6.1", + "cornerstone-tools": "^6.0.8", + "@cornerstonejs/nifti-image-loader": "^1.0.7", + "cornerstone-wado-image-loader": "^4.3.0", + "dicom-parser": "^1.8.19", "@citation-js/core": "0.6.8", "@citation-js/plugin-bibtex": "0.6.8", "@citation-js/plugin-csl": "0.6.8", diff --git a/routers/web/repo/view.go b/routers/web/repo/view.go index f041c569138f4..4b5bcfbb6628a 100644 --- a/routers/web/repo/view.go +++ b/routers/web/repo/view.go @@ -590,6 +590,10 @@ func renderFile(ctx *context.Context, entry *git.TreeEntry, treeLink, rawLink st case fInfo.st.IsImage() && (setting.UI.SVG.Enabled || !fInfo.st.IsSvgImage()): ctx.Data["IsImageFile"] = true ctx.Data["CanCopyContent"] = true + case strings.HasSuffix(strings.ToLower(blob.Name()), ".nii") || strings.HasSuffix(strings.ToLower(blob.Name()), ".nii.gz"): + ctx.Data["IsNIfTI"] = true + case strings.HasSuffix(strings.ToLower(blob.Name()), ".dcm") || strings.HasSuffix(strings.ToLower(blob.Name()), ".dicom"): + ctx.Data["IsDICOM"] = true default: if fInfo.fileSize >= setting.UI.MaxDisplayFileSize { ctx.Data["IsFileTooLarge"] = true diff --git a/templates/repo/view_file.tmpl b/templates/repo/view_file.tmpl index 96339c9699de7..ecb289ff8bb7f 100644 --- a/templates/repo/view_file.tmpl +++ b/templates/repo/view_file.tmpl @@ -86,6 +86,10 @@ {{else if .IsPDFFile}}
+ {{else if .IsNIfTI}} +
+ {{else if .IsDICOM}} +
{{else}} {{.locale.Tr "repo.file_view_raw"}} {{end}} diff --git a/web_src/js/features/cornerstone.js b/web_src/js/features/cornerstone.js new file mode 100644 index 0000000000000..6f622cde75ff4 --- /dev/null +++ b/web_src/js/features/cornerstone.js @@ -0,0 +1,51 @@ +// CornerstoneJS is a renderer and UI toolkit meant for +// medical image formats: .nii, .dcm, and some others. +// +// To use: create an element like +// +// *
+// +// and file.nii.gz will load when the page loads. +// +// Swap out 'nifti' for 'wadouri:' if using a DICOM file. +// +// +// **NOTE**: this is written using the _legacy_ cornerstone library, +// cornerstone-core, and is *not* compatible with the rewrite +// @cornerstonejs/core because @cornerstonejs/nifti-image-loader +// isn't: https://github.com/cornerstonejs/cornerstone-nifti-image-loader/issues/48#issuecomment-1271794397 +// and rendering NIfTIs is the main reason this is here at all. +// + +export async function initCornerstone() { + if (!document.querySelector('.cornerstone-viewport')) return; + + const cornerstone = await import(/* webpackChunkName: "cornerstone-core" */ 'cornerstone-core'); + const dicomParser = await import(/* webpackChunkName: "dicom-parser" */ 'dicom-parser'); + const cornerstoneWADOImageLoader = await import(/* webpackChunkName: "cornerstone-wado-image-loader" */ 'cornerstone-wado-image-loader'); + const cornerstoneNIFTIImageLoader = await import(/* webpackChunkName: "@cornerstonejs/nifti-image-loader" */ '@cornerstonejs/nifti-image-loader'); + + // why are these necessary? too much abstraction, that's why. + cornerstoneWADOImageLoader.external.dicomParser = dicomParser; + cornerstoneWADOImageLoader.external.cornerstone = cornerstone; + cornerstoneNIFTIImageLoader.external.cornerstone = cornerstone; + + for (const canvas of document.querySelectorAll('.cornerstone-viewport')) { + if (canvas.dataset.src === undefined) { + continue; + } + cornerstone.enable(canvas); + + console.info('Loading', canvas.dataset.src, 'into CornerstoneJS'); + cornerstone.loadAndCacheImage(canvas.dataset.src) + .then((image) => { + console.debug(image); + + const viewport = cornerstone.getDefaultViewportForImage(canvas, image); + cornerstone.displayImage(canvas, image, viewport); + }) + .catch((err) => { + console.error(err); + }); + } +} diff --git a/web_src/js/index.js b/web_src/js/index.js index 0c786f96fbef2..50c69f27200a7 100644 --- a/web_src/js/index.js +++ b/web_src/js/index.js @@ -75,6 +75,7 @@ import {initRepoBranchButton} from './features/repo-branch.js'; import {initCommonOrganization} from './features/common-organization.js'; import {initRepoWikiForm} from './features/repo-wiki.js'; import {initRepoCommentForm, initRepository} from './features/repo-legacy.js'; +import {initCornerstone} from './features/cornerstone.js'; import {initCopyContent} from './features/copycontent.js'; import {initCaptcha} from './features/captcha.js'; import {initRepositoryActionView} from './components/RepoActionView.vue'; @@ -170,6 +171,7 @@ onDomReady(() => { initCommitStatuses(); initCaptcha(); + initCornerstone(); initUserAuthLinkAccountView(); initUserAuthOauth2();