ohif-viewer/platform/docs/versioned_docs/version-3.0/development/ohif-cli.md
Erik Ziegler bd1c38c00c
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>
2022-07-27 12:39:04 -04:00

8.1 KiB

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3 OHIF CLI

OHIF Command Line Interface

OHIF-v3 architecture has been re-designed to enable building applications that are easily extensible to various use cases (Modes) that behind the scene would utilize desired functionalities (Extensions) to reach the goal of the use case. Now, the question is how to create/remove/install/uninstall an extension and/or mode?

You can use the cli script that comes with the OHIF monorepo to achieve these goals.

:::note Info In the long-term, we envision our cli tool to be a separate installable package that you can invoke anywhere on your local system to achieve the same goals. In the meantime, cli will remain as part of the OHIF monorepo and needs to be invoked using the yarn command. :::

CLI Installation

You don't need to install the cli currently. You can use yarn to invoke its commands.

Commands

:::note Important All commands should run from the root of the monorepo. :::

There are various commands that can be used to interact with the OHIF-v3 CLI. If you run the following command, you will see a list of available commands.

yarn run cli --help

which will output

OHIF CLI

Options:
  -V, --version                          output the version number
  -h, --help                             display help for command

Commands:
  create-extension                       Create a new template extension
  create-mode                            Create a new template Mode
  add-extension <packageName> [version]  Adds an ohif extension
  remove-extension <packageName>         removes an ohif extension
  add-mode <packageName> [version]       Removes an ohif mode
  remove-mode <packageName>              Removes an ohif mode
  link-extension <packageDir>            Links a local OHIF extension to the Viewer to be used for development
  unlink-extension <extensionName>       Unlinks a local OHIF extension from the Viewer
  link-mode <packageDir>                 Links a local OHIF mode to the Viewer to be used for development
  unlink-mode <extensionName>            Unlinks a local OHIF mode from the Viewer
  list                                   List Added Extensions and Modes
  search [options]                       Search NPM for the list of Modes and Extensions
  help [command]                         display help for command

As seen there are commands for you such as: create-extension, create-mode, add-extension, remove-extension, add-mode, remove-mode, link-extension, unlink-extension, link-mode, unlink-mode, list, search, and help. Here we will go through each of the commands and describe them.

create-mode

If you need to create a new mode, you can use the create-mode command. This command will create a new mode template in the directory that you specify. The command will ask you couple of information/questions in order to properly create the mode metadata in the package.json file.

yarn run cli create-mode

image

Note 1: Some questions have a default answer, which is indicated inside the parenthesis. If you don't want to answer the question, just hit enter. It will use the default answer.

Note 2: As you see in the questions, you can initiate a git repository for the new mode right away by answering Y (default) to the question.

Note 3: Finally, as indicated by the green lines at the end, create-mode command only create the mode template. You will need to link the mode to the Viewer in order to use it. See the link-mode command.

If we take a look at the directory that we created, we will see the following files:

image

create-extension

Similar to the create-extension command, you can use the create-extension command to create a new extension template. This command will create a new extension template in the directory that you specify the path.

yarn run cli create-extension

Note: again similar to the create-extension command, you need to manually link the extension to the Viewer in order to use it. See the link-mode command.

link-extension command will link a local OHIF extension to the Viewer. This command will utilize yarn link to achieve so.

yarn run cli link-extension <extensionDir>

There might be situations where you want to unlink an extension from the Viewer after some developments. unlink-extension command will do so.

ohif-cli unlink-extension <extensionName>

Similar to the link-extension command, link-mode command will link a local OHIF mode to the Viewer.

yarn run cli link-mode <modeDir>

Similar to the unlink-extension command, unlink-mode command will unlink a local OHIF mode from the Viewer.

ohif-cli unlink-mode <modeName>

add-mode

OHIF is a modular viewer. This means that you can install (add) different modes to the viewer if they are published online . add-mode command will add a new mode to the viewer. It will look for the mode in the NPM registry and installs it. This command will also add the extension dependencies that the mode relies on to the Viewer (if specified in the peerDependencies section of the package.json).

:::note Important cli will validate the npm package before adding it to the Viewer. An OHIF mode should have ohif-mode as one of its keywords. :::

Note: If you don't specify the version, the latest version will be used.

yarn run cli add-mode <packageName> [version]

For instance @ohif-test/mode-clock is an example OHIF mode that we have published to NPM. This mode basically has a panel that shows the clock :)

We can add this mode to the Viewer by running the following command:

yarn run cli add-mode @ohif-test/mode-clock

After installation, the Viewer has a new mode!

image

Note: If the mode has an extension peerDependency (in this case @ohif-test/extension-clock), cli will automatically add the extension to the Viewer too.

The result

image image

add-extension

This command will add an OHIF extension to the Viewer. It will look for the extension in the NPM registry and install it.

yarn run cli add-extension <packageName> [version]

remove-mode

This command will remove the mode from the Viewer and also remove the extension dependencies that the mode relies on from the Viewer.

yarn run cli remove-mode <packageName>

remove-extension

Similar to the remove-mode command, this command will remove the extension from the Viewer.

yarn run cli remove-extension <packageName>

list

list command will list all the installed extensions and modes in the Viewer. It uses the PluginConfig.json file to list the installed extensions and modes.

yarn run cli list

an output would look like this:

image

Using search command, you can search for OHIF extensions and modes in the NPM registry. This tool can accept a --verbose flag to show more information about the results.

yarn run cli search [--verbose]

image

with the verbose flag ohif-cli search --verbose you will achieve the following output:

image

PluginConfig.json

To make all the above commands work, we have created a new file called PluginConfig.json which contains the information needed to run the commands. You don't need to (and should not) edit/update/modify this file as it is automatically generated by the CLI. You can take a look at what this file contains by going to platform/viewer/PluginConfig.json in your project's root directory. In short, this file tracks and stores all the extensions/modes and the their version that are currently being used by the viewer.