feat: cornerstone3D stack and volume viewports (#2787)
* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
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---
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sidebar_position: 3
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sidebar_label: OHIF CLI
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---
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# OHIF Command Line Interface
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OHIF-v3 architecture has been re-designed to enable building applications that
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are easily extensible to various use cases (Modes) that behind the scene would
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utilize desired functionalities (Extensions) to reach the goal of the use case.
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Now, the question is _how to create/remove/install/uninstall an extension and/or
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mode?_
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You can use the `cli` script that comes with the OHIF monorepo to achieve these
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goals.
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:::note Info
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In the long-term, we envision our `cli` tool to be a separate installable
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package that you can invoke anywhere on your local system to achieve the same
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goals. In the meantime, `cli` will remain as part of the OHIF monorepo and needs
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to be invoked using the `yarn` command.
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:::
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## CLI Installation
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You don't need to install the `cli` currently. You can use `yarn` to invoke its
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commands.
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## Commands
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:::note Important
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All commands should run from the root of the monorepo.
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:::
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There are various commands that can be used to interact with the OHIF-v3 CLI. If
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you run the following command, you will see a list of available commands.
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```
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yarn run cli --help
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```
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which will output
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```
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OHIF CLI
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Options:
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-V, --version output the version number
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-h, --help display help for command
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Commands:
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create-extension Create a new template extension
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create-mode Create a new template Mode
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add-extension <packageName> [version] Adds an ohif extension
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remove-extension <packageName> removes an ohif extension
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add-mode <packageName> [version] Removes an ohif mode
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remove-mode <packageName> Removes an ohif mode
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link-extension <packageDir> Links a local OHIF extension to the Viewer to be used for development
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unlink-extension <extensionName> Unlinks a local OHIF extension from the Viewer
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link-mode <packageDir> Links a local OHIF mode to the Viewer to be used for development
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unlink-mode <extensionName> Unlinks a local OHIF mode from the Viewer
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list List Added Extensions and Modes
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search [options] Search NPM for the list of Modes and Extensions
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help [command] display help for command
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```
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As seen there are commands for you such as: `create-extension`, `create-mode`,
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`add-extension`, `remove-extension`, `add-mode`, `remove-mode`,
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`link-extension`, `unlink-extension`, `link-mode`, `unlink-mode`, `list`,
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`search`, and `help`. Here we will go through each of the commands and describe
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them.
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### create-mode
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If you need to create a new mode, you can use the `create-mode` command. This
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command will create a new mode template in the directory that you specify.
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The command will ask you couple of information/questions in order
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to properly create the mode metadata in the `package.json` file.
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```bash
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yarn run cli create-mode
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```
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<div style={{textAlign: 'center',}}>
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</div>
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Note 1: Some questions have a default answer, which is indicated inside the
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parenthesis. If you don't want to answer the question, just hit enter. It will
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use the default answer.
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Note 2: As you see in the questions, you can initiate a git repository for the
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new mode right away by answering `Y` (default) to the question.
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Note 3: Finally, as indicated by the green lines at the end, `create-mode` command only
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create the mode template. You will need to link the mode to the Viewer in order
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to use it. See the [`link-mode`](#link-mode) command.
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If we take a look at the directory that we created, we will see the following
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files:
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<div style={{maxWidth:"500px"}}>
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</div>
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### create-extension
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Similar to the `create-extension` command, you can use the `create-extension`
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command to create a new extension template. This command will create a new
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extension template in the directory that you specify the path.
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```bash
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yarn run cli create-extension
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```
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Note: again similar to the `create-extension` command, you need to manually link
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the extension to the Viewer in order to use it. See the
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[`link-mode`](#link-mode) command.
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### link-extension
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`link-extension` command will link a local OHIF extension to the Viewer. This
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command will utilize `yarn link` to achieve so.
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```bash
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yarn run cli link-extension <extensionDir>
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```
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### unlink-extension
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There might be situations where you want to unlink an extension from the Viewer
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after some developments. `unlink-extension` command will do so.
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```bash
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ohif-cli unlink-extension <extensionName>
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```
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### link-mode
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Similar to the `link-extension` command, `link-mode` command will link a local
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OHIF mode to the Viewer.
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```bash
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yarn run cli link-mode <modeDir>
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```
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### unlink-mode
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Similar to the `unlink-extension` command, `unlink-mode` command will unlink a
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local OHIF mode from the Viewer.
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```bash
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ohif-cli unlink-mode <modeName>
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```
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### add-mode
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OHIF is a modular viewer. This means that you can install (add) different modes
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to the viewer if they are published online . `add-mode` command will add a new mode to
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the viewer. It will look for the mode in the NPM registry and installs it. This
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command will also add the extension dependencies that the mode relies on to the
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Viewer (if specified in the peerDependencies section of the package.json).
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:::note Important
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`cli` will validate the npm package before adding it to the Viewer. An OHIF mode
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should have `ohif-mode` as one of its keywords.
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:::
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Note: If you don't specify the version, the latest version will be used.
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```bash
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yarn run cli add-mode <packageName> [version]
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```
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For instance `@ohif-test/mode-clock` is an example OHIF mode that we have
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published to NPM. This mode basically has a panel that shows the clock :)
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We can add this mode to the Viewer by running the following command:
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```bash
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yarn run cli add-mode @ohif-test/mode-clock
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```
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After installation, the Viewer has a new mode!
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Note: If the mode has an extension peerDependency (in this case @ohif-test/extension-clock),
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`cli` will automatically add the extension to the Viewer too.
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The result
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### add-extension
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This command will add an OHIF extension to the Viewer. It will look for the
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extension in the NPM registry and install it.
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```bash
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yarn run cli add-extension <packageName> [version]
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```
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### remove-mode
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This command will remove the mode from the Viewer and also remove the extension
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dependencies that the mode relies on from the Viewer.
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```bash
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yarn run cli remove-mode <packageName>
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```
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### remove-extension
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Similar to the `remove-mode` command, this command will remove the extension
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from the Viewer.
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```bash
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yarn run cli remove-extension <packageName>
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```
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### list
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`list` command will list all the installed extensions and modes in
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the Viewer. It uses the `PluginConfig.json` file to list the installed
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extensions and modes.
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```bash
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yarn run cli list
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```
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an output would look like this:
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<div style={{maxWidth:"500px"}}>
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</div>
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### search
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Using `search` command, you can search for OHIF extensions and modes
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in the NPM registry. This tool can accept a `--verbose` flag to show more
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information about the results.
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```bash
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yarn run cli search [--verbose]
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```
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<div style={{maxWidth:"600px"}}>
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</div>
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with the verbose flag `ohif-cli search --verbose` you will achieve the following
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output:
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<div style={{maxWidth:"600px"}}>
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</div>
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## PluginConfig.json
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To make all the above commands work, we have created a new file called `PluginConfig.json` which contains the
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information needed to run the commands. You **don't need to (and should not)**
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edit/update/modify this file as it is automatically generated by the CLI. You
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can take a look at what this file contains by going to
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`platform/viewer/PluginConfig.json` in your project's root directory. In short,
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this file tracks and stores all the extensions/modes and the their version that
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are currently being used by the viewer.
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Reference in new issue
Block a user