@itk-wasm/elastix

A toolbox for rigid and nonrigid registration of images.

👨‍💻 Live API Demo ✨

🕮 Documentation 📚

Installation

npm install @itk-wasm/elastix

Usage

Browser interface

Import:

import {
  defaultParameterMap,
  elastix,
  readParameterFiles,
  writeParameterFiles,
  setPipelinesBaseUrl,
  getPipelinesBaseUrl,
  setPipelineWorkerUrl,
  getPipelineWorkerUrl,
} from "@itk-wasm/elastix"

defaultParameterMap

Returns the default elastix parameter map for a given transform type.

async function defaultParameterMap(
  webWorker: null | Worker,
  transformName: string,
  options: DefaultParameterMapOptions = {}
) : Promise<DefaultParameterMapResult>

| Parameter | Type | Description | | :-------------: | :------: | :----------------------------------------------------------------------------- | | transformName | string | Transform name. One of: translation, rigid, affine, bspline, spline, groupwise |

DefaultParameterMapOptions interface:

| Property | Type | Description | | :-------------------: | :------: | :----------------------------------------------------------- | | numberOfResolutions | number | Number of multiscale registration resolutions. | | finalGridSpacing | number | Final grid spacing in physical units for bspline transforms. |

DefaultParameterMapResult interface:

| Property | Type | Description | | :------------: | :--------------: | :----------------------------------- | | webWorker | Worker | WebWorker used for computation | | parameterMap | JsonCompatible | Elastix parameter map representation |

elastix

Rigid and non-rigid registration of images.

async function elastix(
  webWorker: null | Worker,
  parameterObject: JsonCompatible,
  transform: string,
  options: ElastixOptions = {}
) : Promise<ElastixResult>

| Parameter | Type | Description | | :---------------: | :--------------: | :-------------------------------------- | | parameterObject | JsonCompatible | Elastix parameter object representation | | transform | string | Fixed-to-moving transform file |

ElastixOptions interface:

| Property | Type | Description | | :-------------------------------: | :--------------------------: | :------------------------------------------------------------------------------------------------------------------ | | fixed | Image | Fixed image | | moving | Image | Moving image | | initialTransform | string | File | BinaryFile | Initial transform to apply before registration | | initialTransformParameterObject | JsonCompatible | Initial elastix transform parameter object to apply before registration. Only provide this or an initial transform. |

ElastixResult interface:

| Property | Type | Description | | :------------------------: | :--------------: | :---------------------------------------------------------- | | webWorker | Worker | WebWorker used for computation | | result | Image | Resampled moving image | | transform | BinaryFile | Fixed-to-moving transform file | | transformParameterObject | JsonCompatible | Elastix optimized transform parameter object representation |

readParameterFiles

Read elastix parameter text files into a parameter object.

async function readParameterFiles(
  webWorker: null | Worker,
  options: ReadParameterFilesOptions = { parameterFiles: [] as TextFile[] | File[] | string[], }
) : Promise<ReadParameterFilesResult>

| Parameter | Type | Description | | :-------: | :--: | :---------- |

ReadParameterFilesOptions interface:

| Property | Type | Description | | :--------------: | :------------------------------: | :---------------------- | | parameterFiles | string[] | File[] | TextFile[] | Elastix parameter files |

ReadParameterFilesResult interface:

| Property | Type | Description | | :---------------: | :--------------: | :-------------------------------------- | | webWorker | Worker | WebWorker used for computation | | parameterObject | JsonCompatible | Elastix parameter object representation |

writeParameterFiles

Write an elastix parameter text file from a parameter object.

async function writeParameterFiles(
  webWorker: null | Worker,
  parameterObject: JsonCompatible,
  parameterFiles: string[]

) : Promise<WriteParameterFilesResult>

| Parameter | Type | Description | | :---------------: | :--------------: | :---------------------------------------------------------------------------------------------------------- | | parameterObject | JsonCompatible | Elastix parameter object representation. | | parameterFiles | string[] | Elastix parameter files, must have the same length as the number of parameter maps in the parameter object. |

WriteParameterFilesResult interface:

| Property | Type | Description | | :--------------: | :----------: | :---------------------------------------------------------------------------------------------------------- | | webWorker | Worker | WebWorker used for computation | | parameterFiles | TextFile[] | Elastix parameter files, must have the same length as the number of parameter maps in the parameter object. |

setPipelinesBaseUrl

Set base URL for WebAssembly assets when vendored.

function setPipelinesBaseUrl(
  baseUrl: string | URL
) : void

getPipelinesBaseUrl

Get base URL for WebAssembly assets when vendored.

function getPipelinesBaseUrl() : string | URL

setPipelineWorkerUrl

Set base URL for the itk-wasm pipeline worker script when vendored.

function setPipelineWorkerUrl(
  baseUrl: string | URL
) : void

getPipelineWorkerUrl

Get base URL for the itk-wasm pipeline worker script when vendored.

function getPipelineWorkerUrl() : string | URL

Node interface

Import:

import {
  defaultParameterMapNode,
  elastixNode,
  readParameterFilesNode,
  writeParameterFilesNode,
  setPipelinesBaseUrl,
  getPipelinesBaseUrl,
  setPipelineWorkerUrl,
  getPipelineWorkerUrl,
} from "@itk-wasm/elastix"

defaultParameterMapNode

Returns the default elastix parameter map for a given transform type.

async function defaultParameterMapNode(
  transformName: string,
  options: DefaultParameterMapOptions = {}
) : Promise<DefaultParameterMapNodeResult>

| Parameter | Type | Description | | :-------------: | :------: | :----------------------------------------------------------------------------- | | transformName | string | Transform name. One of: translation, rigid, affine, bspline, spline, groupwise |

DefaultParameterMapNodeOptions interface:

| Property | Type | Description | | :-------------------: | :------: | :----------------------------------------------------------- | | numberOfResolutions | number | Number of multiscale registration resolutions. | | finalGridSpacing | number | Final grid spacing in physical units for bspline transforms. |

DefaultParameterMapNodeResult interface:

| Property | Type | Description | | :------------: | :--------------: | :----------------------------------- | | parameterMap | JsonCompatible | Elastix parameter map representation |

elastixNode

Rigid and non-rigid registration of images.

async function elastixNode(
  parameterObject: JsonCompatible,
  transform: string,
  options: ElastixOptions = {}
) : Promise<ElastixNodeResult>

| Parameter | Type | Description | | :---------------: | :--------------: | :-------------------------------------- | | parameterObject | JsonCompatible | Elastix parameter object representation | | transform | string | Fixed-to-moving transform file |

ElastixNodeOptions interface:

| Property | Type | Description | | :-------------------------------: | :--------------------------: | :------------------------------------------------------------------------------------------------------------------ | | fixed | Image | Fixed image | | moving | Image | Moving image | | initialTransform | string | File | BinaryFile | Initial transform to apply before registration | | initialTransformParameterObject | JsonCompatible | Initial elastix transform parameter object to apply before registration. Only provide this or an initial transform. |

ElastixNodeResult interface:

| Property | Type | Description | | :------------------------: | :--------------: | :---------------------------------------------------------- | | result | Image | Resampled moving image | | transform | BinaryFile | Fixed-to-moving transform file | | transformParameterObject | JsonCompatible | Elastix optimized transform parameter object representation |

readParameterFilesNode

Read elastix parameter text files into a parameter object.

async function readParameterFilesNode(
  options: ReadParameterFilesOptions = { parameterFiles: [] as string[], }
) : Promise<ReadParameterFilesNodeResult>

| Parameter | Type | Description | | :-------: | :--: | :---------- |

ReadParameterFilesNodeOptions interface:

| Property | Type | Description | | :--------------: | :------------------------------: | :---------------------- | | parameterFiles | string[] | File[] | TextFile[] | Elastix parameter files |

ReadParameterFilesNodeResult interface:

| Property | Type | Description | | :---------------: | :--------------: | :-------------------------------------- | | parameterObject | JsonCompatible | Elastix parameter object representation |

writeParameterFilesNode

Write an elastix parameter text file from a parameter object.

async function writeParameterFilesNode(
  parameterObject: JsonCompatible,
  parameterFiles: string[]

) : Promise<WriteParameterFilesNodeResult>

| Parameter | Type | Description | | :---------------: | :--------------: | :---------------------------------------------------------------------------------------------------------- | | parameterObject | JsonCompatible | Elastix parameter object representation. | | parameterFiles | string[] | Elastix parameter files, must have the same length as the number of parameter maps in the parameter object. |

WriteParameterFilesNodeResult interface:

| Property | Type | Description | | :--------------: | :----------: | :---------------------------------------------------------------------------------------------------------- | | parameterFiles | TextFile[] | Elastix parameter files, must have the same length as the number of parameter maps in the parameter object. |