README.md

NiiVue VSCode README

WebGL 2.0 medical image viewer
This extension uses NiiVue to display images selected in VSCode.

VS Code version

The VS Code extension is published on the VS Code marketplace and can be installed via the extension tab in VS Code, searching for niivue

Browser version

The web version can be installed as a local app with file associations (only supported in Chrome)

Development

Currently my time that I can spend on this project is quite limited. I'm very happy for contributions in the form of pull requests.
Otherwise, if you would like to see a certain feature implemented, please let me know so I can prioritize the development. Either create a new issue or comment/react on an existing issue.

VS Code screenshots

List of Hotkeys

• Right Mouse: Drag with the right mouse button to zoom
• Middle Mouse: Drag with the right mouse button to pan
• Mouse Scroll: Change slice in currently hovered image
• ← →: change volume in 4D image
• V: Cycle through viewmodes
• C: Cycle through clip plane orientations in 3D render
• shift: Changes mouse behaviour to 2D dragging and 3D viewplane rotation
• H: Move the cross to R
• L: Move the cross to L
• J: Move the cross to P
• K: Move the cross to A
• ctrl+U: Move the cross to S
• ctrl+D: Move the cross to I

Features

• Open local files by selecting them in the VSCode explorer
• Selecting multiple files -> right click -> NiiVue: Compare
• Open web links to files with the command "NiiVue: Open Image" (Ctr+Shift+P)
• Open local or remote files when hovering over the link in an open editor
• Add overlays
• Works in web-based VSCode

Supported Formats

NiiVue can open several formats popular with brain imaging:

• Voxel-based formats: NIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7.
• Mesh-based formats: GIfTI, ASC, BYU/GEO/G, BrainSuite DFS, ICO/TRI, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D.
• Mesh overlay formats: GIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
• Tractography formats: TCK, TRK, TRX, VTK, AFNI .niml.tract
• DICOM: DICOM and DICOM Manifests

If niivue-vscode fails to open any of these files, please create an issue.

Developing this extension in VSCode

• Fork this repository;
• Clone this repository and open in VSCode
• Run inside the niivue-vscode folder

Installing

    npm install --global yarn
    yarn install:all

It might be required to update node first before running 'yarn install'. This can be done with the following:

    npm install --global n
    n latest

Hot Reload Development in browser

    yarn start:webview

Debugging the extension in vscode

This requires a full compilation and is slow

    yarn watch:webview

• Press F5 (a new VSCode window opens: Extension Development Host)
• Test the extension in the Extension Development Host by opening an image file
• Press Ctrl+R in the Extension Development Host for reload after a code change

Playwright Tests

The playwright tests are for the niivue webview. Install the vscode extension Playwright Test for VSCode. Open the command line and execute

    yarn start:webview

Open the vscode test interface and run the tests. New tests can be added under niivue/tests

Test in the web version of vscode

    yarn esbuild
    yarn open-in-browser

Publishing

First publish to vscode marketplace, this automatically increments the version number and creates a git commit

    vsce publish patch|minor|major [--pre-release]    

Then publish to openVSX marketplace

    npx ovsx publish --pat <openVSX access key>