From cd4a7e11506cd31ef0ac56067f3603076490a65e 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 | 723 +++++++++++++++++++++++++---- 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, 704 insertions(+), 85 deletions(-) create mode 100644 web_src/js/features/cornerstone.js diff --git a/package-lock.json b/package-lock.json index 76beea934e33a..3024cca0e2769 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": "2.3.0", @@ -22,7 +23,11 @@ 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+ } }, "node_modules/neo-async": { "version": "2.6.2", @@ -7789,6 +8335,14 @@ "node": ">= 0.4.0" } }, + "node_modules/nifti-reader-js": { + "version": "0.5.4", + "resolved": "https://registry.npmjs.org/nifti-reader-js/-/nifti-reader-js-0.5.4.tgz", + "integrity": "sha512-KnZMEw9Wd39x1eTTZQaF5Zjh7LbUeWcxfEj0v5VS/yTkV2y/YHrAnC6VJyf2FjrmsUOElDVjIoHGLMCkcnpiNg==", + "dependencies": { + "pako": "*" + } + }, "node_modules/nimma": { "version": "0.2.2", "resolved": "https://registry.npmjs.org/nimma/-/nimma-0.2.2.tgz", @@ -7996,7 +8550,6 @@ "version": "0.9.1", "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.1.tgz", "integrity": "sha512-74RlY5FCnhq4jRxVUPKDaRwrVNXMqsGsiW6AJw4XK8hmtm10wC0ypZBLw5IIp85NZMr91+qd1RvvENwg7jjRFw==", - "dev": true, "dependencies": { "deep-is": "^0.1.3", "fast-levenshtein": "^2.0.6", @@ -8013,7 +8566,6 @@ "version": "3.1.0", "resolved": "https://registry.npmjs.org/p-limit/-/p-limit-3.1.0.tgz", "integrity": "sha512-TYOanM3wGwNGsZN2cVTYPArw454xnXj5qmWF1bEoAc4+cU/ol7GVh7odevjp1FNHduHc3KZMcFduxU5Xc6uJRQ==", - "dev": true, "dependencies": { "yocto-queue": "^0.1.0" }, @@ -8028,7 +8580,6 @@ "version": "5.0.0", "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-5.0.0.tgz", "integrity": "sha512-LaNjtRWUBY++zB5nE/NwcaoMylSPk+S+ZHNB1TzdbMJMny6dynpAGt7X/tl/QYq3TIeE6nxHppbo2LGymrG5Pw==", - "dev": true, "dependencies": { "p-limit": "^3.0.2" }, @@ -8104,11 +8655,15 @@ "node": ">= 8" } }, + "node_modules/pako": { + "version": "1.0.11", + "resolved": "https://registry.npmjs.org/pako/-/pako-1.0.11.tgz", + "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==" + }, "node_modules/parent-module": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz", "integrity": "sha512-GQ2EWRpQV8/o+Aw8YqtfZZPfNRWZYkbidE9k5rpl/hC3vtHHBfGm2Ifi6qWV+coDGkrUKZAxE3Lot5kcsRlh+g==", - "dev": true, "dependencies": { "callsites": "^3.0.0" }, @@ -8520,7 +9075,6 @@ "version": "1.2.1", "resolved": "https://registry.npmjs.org/prelude-ls/-/prelude-ls-1.2.1.tgz", "integrity": "sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g==", - "dev": true, "engines": { "node": ">= 0.8.0" } @@ -9003,7 +9557,6 @@ "version": "4.0.0", "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-4.0.0.tgz", "integrity": "sha512-pb/MYmXstAkysRFx8piNI1tGFNQIFA3vkE3Gq4EuA1dF6gHp/+vgZqsCGJapvy8N3Q+4o7FwvquPJcnZ7RYy4g==", - "dev": true, "engines": { "node": ">=4" } @@ -9029,7 +9582,6 @@ "version": "3.0.2", "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-3.0.2.tgz", "integrity": "sha512-JZkJMZkAGFFPP2YqXZXPbMlMBgsxzE8ILs4lMIX/2o0L9UBw9O/Y3o6wFw/i9YLapcUJWwqbi3kdxIPdC62TIA==", - "dev": true, "dependencies": { "glob": "^7.1.3" }, @@ -9690,7 +10242,6 @@ "version": "3.1.1", "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz", "integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig==", - "dev": true, "engines": { "node": ">=8" }, @@ -10038,8 +10589,7 @@ "node_modules/text-table": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/text-table/-/text-table-0.2.0.tgz", - "integrity": "sha512-N+8UisAXDGk8PFXP4HAzVR9nbfmVJ3zYLAWiTIoqC5v5isinhr+r5uaO8+7r3BMfuNIufIsA7RdpVgacC2cSpw==", - "dev": true + "integrity": "sha512-N+8UisAXDGk8PFXP4HAzVR9nbfmVJ3zYLAWiTIoqC5v5isinhr+r5uaO8+7r3BMfuNIufIsA7RdpVgacC2cSpw==" }, "node_modules/throttle-debounce": { "version": "5.0.0", @@ -10090,6 +10640,14 @@ "@popperjs/core": "^2.9.0" } }, + "node_modules/to-fast-properties": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/to-fast-properties/-/to-fast-properties-2.0.0.tgz", + "integrity": "sha512-/OaKK0xYrs3DmxRYqL/yDc+FxFUVYhDlXMhRmv3z915w2HF1tnN1omB354j8VUGO/hbRzyD6Y3sA7v7GS/ceog==", + "engines": { + "node": ">=4" + } + }, "node_modules/to-regex-range": { "version": "5.0.1", "resolved": "https://registry.npmjs.org/to-regex-range/-/to-regex-range-5.0.1.tgz", @@ -10202,7 +10760,6 @@ "version": "0.4.0", "resolved": "https://registry.npmjs.org/type-check/-/type-check-0.4.0.tgz", "integrity": "sha512-XleUoc9uwGXqjWwXaUTZAmzMcFZ5858QA2vvx1Ur5xIcixXIP+8LnFDgRplU30us6teqdlskFfu+ae4K79Ooew==", - "dev": true, "dependencies": { "prelude-ls": "^1.2.1" }, @@ -10223,7 +10780,6 @@ "version": "0.20.2", "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.20.2.tgz", "integrity": "sha512-Ne+eE4r0/iWnpAxD852z3A+N0Bt5RN//NjJwRd2VFHEmrywxf5vsZlh4R6lixl6B+wz/8d+maTSAkN1FIkI3LQ==", - "dev": true, "engines": { "node": ">=10" }, @@ -11060,7 +11616,6 @@ "version": "1.2.3", "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz", "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==", - "dev": true, "engines": { "node": ">=0.10.0" } @@ -11231,8 +11786,7 @@ "node_modules/yallist": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", - "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", - "dev": true + "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==" }, "node_modules/yargs": { "version": "17.3.1", @@ -11274,7 +11828,6 @@ "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, "engines": { "node": ">=10" }, diff --git a/package.json b/package.json index 41d834771aaff..240478c122e2d 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 1d54f25884e39..f279555a8f837 100644 --- a/routers/web/repo/view.go +++ b/routers/web/repo/view.go @@ -553,6 +553,10 @@ 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 389aa2f4f2013..938a417c9eb7e 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();