08.04.2021

Category: Cornerstonetools documentation

Cornerstonetools documentation

This directory contains the source code that powers our examples. Jekyll is a Ruby Gem. To get started using Ruby and Jekyll follow the appropriate guide for your operating system. If you're feeling a bit lost, I recommend brushing up on Jekyll Basics. I'll try to include a brief overview here as it pertains to this project, but there's no better guide than Jekyll's own docs. When changes are committed, our CI Server builds a new version of the examples site and pushes the changes to the gh-pages branches examples directory.

All files in the gh-pages branch are served using GitHub Pages. Non-prefixed directories are generated in place using Front-Matter and Liquid templating. Tool examples contain a small block of information at the top of their file that looks like this:.

The layout field tells us which layout to use as a template. The other values become page variables that can be used by the template. For example, the tool-simple layout uses the title variable like so:. Wrapping a block of code using highlight blocks causes Jekyll to render it as an example with Syntax highlighting:.

We currently include bulmaa CSS framework, to add a few classes to make styling easier. Please reference their documentation if you would like to leverage styling. Skip to content. Branch: master. Create new file Find file History. Latest commit. Latest commit Oct 22, Why Jekyll? Similar tools can share templates We can leverage "data" to generate content: collections, data files, etc.

Hello World :wave:. LengthTool ; cornerstoneTools.A module is a namespaced storage object in the store that contains the following properties:. The segmentation module deals with centralisation of 3D labelmap data for each stack of cornerstone images. The data is centralized for two reasons:.

The data is stored in a top-down hierarchal fashion, with the coarsest level being study-wide. The series object under state. Each BrushStackState is currently indexed each stack by the imageId of the first image in the stack. Each Labelmap3D object can contain multiple non-overlapping segments. To use have overlapping segments in your application, use multiple Labelmap3D s. A Labelmap2D is a 2D view of one frame of the segmentation, it is the object primarily interacted with from the cornerstone canvas, and has the following properties:.

When using a tool on a cornerstone image, you can easily access the Labelmap2D of the active Labelmap3D. This provides you all the information you need. You can grab as few or as many elements of this object as you need by destructuring appropriately. Or if using a brush you can use the drawBrushPixels helper to paint an array of 2D-coordinates to the Labelmap2D.

Both getters. Additionally getters. This is not done automatically, because the end of an operationn might depend on the task. You may have a more complicated procedure whereby you perform a series of iterative growcuts with human intervention, and only want to update the labelmap occupancy at the end.

The parent application can retrieve information about the labelmaps by querying the API. A set of setters can be linked to UI components to change the active segment, set segment color, etc, refer to the API documentation for a full list of helpers.

You may wish to access one or more Labelmap3D buffers from outside cornerstoneToolsin order to either export them to persistent storage, or display them in another framwork, such as vtkjs. To retrieve the ArrayBuffer for the activeLabelmap on an elementfrom outside of cornerstoneTools :. These functions also return the colorLUT not just its indexso that you can map another renderer to the same color scheme. Note these are just helper functions, and you can indeed fetch all the Labelmap3D objects with getters.

Modules A module is a namespaced storage object in the store that contains the following properties: Property Requirement Description configuration Mandatory An object that configures the module for app-wide usage. Configuration is intended to be manipulated by methods both internal and external to cornerstoneTools. State is intended to only be manipulated by cornerstoneTools and cornerstoneTools plugins.

There is no rigorous structure state must follow, as it will be specific to what the module is trying to accomplish. Getters can be used for more complex queries of the state e. Setters can be used for more complex input e. Top level primitives should be set by state.This documentation is for a much older version of cornerstone-tools. This is one area of tool implementation that can increase the complexity of the tool logic and make it difficult to reuse.

To address this, scope management is externalized from the tool entirely. Tool implementation is therefore constrained to respond to events for a single enabled element at a time.

Whether or not the tool data that the tool is dealing with is related to a single imageId, a stack or some other scope is not its concern. It is believed that this strategy will work for the vast majority of tool needs if not all so it is used by all cornerstone tools.

There are use cases where a tool needs to be able to operate with multiple scopes. Using the examples above, there are situations where stack specific storage is desirable for a length measurement tool as well as image specific behavior for a ROI.

Cornerstone supports this through the creation of a custom ToolStateManager.

cornerstonetools documentation

In cornerstone, tool data scope is managed through what is called a ToolStateManager. Each enabled element has a ToolStateManager associated with it.

By default, enabled elements shared a global tool state manager that stores tool data with ImageId specific scope. If a different scope is desired, a developer may create a new tool state manager that complies with the expected interface of a ToolStateManager and register it with the desired enabled elements. NOTE: The scroll tool currently includes experimental support for stack specific storage of the length measurement tool. This might be removed though to keep things simple unless there is a generic tool that we want to include where stack specific storage is really important.

The following are some notes and thoughts that impacted the design described above. It is here for reference purposes only and has not been updated to what we are currently doing.

cornerstonetools documentation

NOTE: There may also be a difference between the state used during creation of a tool and persistence of that tool. For example, a stack specific tool could be created but when saved, saves it as image specific using the currently visible imageId.

One could also envision a viewer requiring that the user explicitly "save" the tool on a given slice at which time it captures the ImageId for persistence. While cornerstone should support these kind of scenarios, the tools layer does not actually do any persistence so this concern is "pushed up" to a higher layer.

cornerstonetools documentation

Additionally, tools need a way to save and restore state to support persistent storage. Likewise, it should be possible to save tool state into these formats. Skip to content. ToolDataContext Jump to bottom. Here are some examples: A length measurement tool could store state in the ImageId specific scope if the measurement only applied to a single ImageId. In this case, the length measurement would only appear when its corresponding imageId is visible.

It would not be visible if the user displayed a different ImageId in the enabled element. If two different enabled elements displayed the same ImageId, it should show up on both. This is the most commonly desired behavior and is therefore the default for cornerstone. A ROI measurement could store state in the stack specific scope if the measurement applied to an image stack.

In this case, the ROI would continue to be visible as the user changed to different ImageIds within the stack. A flag indicating whether or not the tool is active on an enabled image could store state in the enabled element specific scope.

RESTool - Stop Developing Apps for Managing RESTful APIs / Daniel Sternlicht

In this case, the tool would be able to keep track if it is enabled on an enabled element regardless of which ImageId is currently being displayed. NOTE - this is currently handled via the jquery eventData mechanism - we may need APIs for this if we decide to not use jquery for mouse event handling.Cornerstone Tools is a JavaScript library that assists in annotating, segmenting, and measuring medical images.

This library is not stand-alone. It builds on top of Cornerstone ; a standards compliant, fast, and extensible JavaScript library that displays interactive medical images. Feel free to open it in another tab and follow along as we go through some basic examples. Or, you can create an index. The Installation page provides more options for installing Cornerstone Tools. If you find the dependencies confusing, here is a high level overview of why each is included and necessary for Cornerstone Tools to function:.

If you find this overly complicated and have alternative solutions to managing and using dependencies, we are always looking for new ideas on how to simplify the process.

Introduction

Please do not hesitate to create a GitHub issue and discuss :. Now, sensible defaults are applied when you initialize Cornerstone Tools. The cornerstoneTools.

If you wish to change modules other than the globalConfiguration module, you may pass an array of named module configuration like so:. A full list of the settings and their defaults can be found here: globalConfigurationModule.

In previous versions of Cornerstone Tools, users would need to implement their own Tool manager. This version includes the concept of "adding" Tools to Enabled elements to make tracking and managing Tool state across your application easier. When a Tool is added, its default mode is Disabled. When a Tool's mode is Activeit can be used; if it has measurement data, that data can be created or interacted with. You can read more about changing a Tool's mode in the anatomy of a tool section of our docs.

In this example, we change an added Tool's mode to Active :. Now that our Tool is Activewe should be able to use our LengthTool to draw length annotations on the Enabled element.

Having trouble or just want to see a quick demo? Check out this jsfiddle! Looking for a Deploy Preview? Deploy Preview for Cornerstone Tools.

No results matching " ". Renders our image, and provides useful events and methods to make tools that respond to viewport changes possible.

Tool Types

A tiny JavaScript debugging utility modelled after Node. Works in Node.Homepage Repository JavaScript. Provides a simple, extensible framework for creating tools on top of Cornerstone. Includes common tool implementations, and leverages DICOM metadata when available for advanced functionality. Read The Docs Edit the docs. Building one or two tools on top of Cornerstone.

However, as the number of tools grow, you begin to encounter difficult problems:. It's only dependencies are libraries within the Cornerstone family. Instead of trying to "do everything" it aims to be extensible and pluggable to aid in the rapid development of new tools.

Ideally, tools created using cornerstone-tools can be easily shared, allowing for the creation of a broader ecosystem. Below is a simplified example of creating a tool by extending cornerstone-tool 's BaseTool class. This module is distributed via npm which is bundled with node and should be installed as one of your project's dependencies :. If you need to support the IE11 Browser, you will need to provide polyfills as needed. Setting up and configuring cornerstone-tools 's depency can be the biggest hurdle to getting started.

Be sure to check out our docs for assistance. The latest major version has just been published. We are still flushing out our examples. Thanks goes to these people emoji key :. This project follows the all-contributors specification. Contributions of any kind welcome! Looking to contribute? Look for the Good First Issue label. See Bugs. Please file an issue to suggest new features.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again.

If nothing happens, download the GitHub extension for Visual Studio and try again. Provides a simple, extensible framework for creating tools on top of Cornerstone. Includes common tool implementations, and leverages DICOM metadata when available for advanced functionality. Read The Docs Edit the docs. Building one or two tools on top of Cornerstone. However, as the number of tools grow, you begin to encounter difficult problems:. It's only dependencies are libraries within the Cornerstone family.

Instead of trying to "do everything" it aims to be extensible and pluggable to aid in the rapid development of new tools. Ideally, tools created using cornerstone-tools can be easily shared, allowing for the creation of a broader ecosystem. Below is a simplified example of creating a tool by extending cornerstone-tool 's BaseTool class.

This module is distributed via npm which is bundled with node and should be installed as one of your project's dependencies :. If you need to support the IE11 Browser, you will need to provide polyfills as needed. Our BrowserList target:. Setting up and configuring cornerstone-tools 's depency can be the biggest hurdle to getting started. Be sure to check out our docs for assistance. The latest major version has just been published. We are still flushing out our examples.

Thanks goes to these people emoji key :. This project follows the all-contributors specification. Contributions of any kind welcome! Looking to contribute?In order to edit and rebuild Cornerstone, you will need to install Node.

Once you have Node. If this is not performed, you may run into issues during development. Running the build will create both the minified and un-minified versions of the library, as well as their associated source maps.

There are many ways of running simple HTTP servers. This is just one method, you can also use e. When you run the tests a 'coverage' directory will be created.

Note that this directory does not exist in the main repository, since it is solely a build artifact. Note that this URL does not work immediately, since the first step in npm test is to rebuild the library. If you have made a source code change that you think should be included in the main repository, you can contribute it back to the community by creating a Pull Request. Cornerstone Tools. Please ensure that all tests pass and you have run ESLint and fixed any issues before submitting a pull request.

Cornerstone relies on a number of open source tools, components, and free services to ensure quality and stability. We want to ensure developers can work in modern JavaScript and that end users can use the tools in both current and legacy environments. Developer Guide.

Developer Guide In order to edit and rebuild Cornerstone, you will need to install Node. Running the build npm start Running the build will create both the minified and un-minified versions of the library, as well as their associated source maps.

Automatically running the build after each source change npm run watch This command can be used if you want to debug issues or add new features to the source code. Running code linting npm run eslint Or include automatic fixing with: npm run eslint-fix Or automatically fix 'test' directory with: npm run eslint-fix-test Running the commands above will check the source code for linting issues. Submitting changes through Pull Requests If you have made a source code change that you think should be included in the main repository, you can contribute it back to the community by creating a Pull Request.

Development Toolchain and Specifications Cornerstone relies on a number of open source tools, components, and free services to ensure quality and stability. General Babel for transpilation from next generation JavaScript to more widely supported previous JavaScript versions. Testing Karma is used as a test runner Mocha is used as a test framework Chai is used for test assertions Istanbul is used to report code coverage Travis CI is used to automatically run tests.

Documentation JSDoc formatting is used for documenting the source code. Rawgit is used to serve Live Examples from the repository. We should transition this to be hosted with Github Pages as well. Writing tests Here are some general notes on writing tests which may be useful: Tests must be in the 'test' directory. Please try to ensure they follow the 'src' directory layout for simplicity.

Medical Imaging, Simplified.

Do not convert 'function ' to arrow functions i. Releasing a new version Make sure you have the latest commits from master Determine the version change you need to make based on the scope of the changes since the last release. Update the changelog Make sure to thank any code contributors! Update the package and dependency versions in "package. No results matching " ".


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