@itk-wasm/dicom NPM

@itk-wasm/dicom

Read files and images related to DICOM file format.

Installation

npm install @itk-wasm/dicom

Usage

Browser interface

Import:

import {
  applyPresentationStateToImage,
  readDicomEncapsulatedPdf,
  structuredReportToHtml,
  structuredReportToText,
  readDicomTags,
  readImageDicomFileSeries,
  setPipelinesBaseUrl,
  getPipelinesBaseUrl,
} from "@itk-wasm/dicom"

applyPresentationStateToImage

Apply a presentation state to a given DICOM image and render output as bitmap, or dicom file.

async function applyPresentationStateToImage(
  imageIn: File | BinaryFile,
  presentationStateFile: File | BinaryFile,
  options: ApplyPresentationStateToImageOptions = {}
) : Promise<ApplyPresentationStateToImageResult>

Parameter	Type	Description
`imageIn`	*File	BinaryFile*	Input DICOM file
`presentationStateFile`	*File	BinaryFile*	Process using presentation state file

ApplyPresentationStateToImageOptions interface:

Property	Type	Description
`colorOutput`	boolean	output image as RGB (default: false)
`configFile`	string	filename: string. Process using settings from configuration file
`frame`	number	frame: integer. Process using image frame f (default: 1)
`noPresentationStateOutput`	boolean	Do not get presentation state information in text stream.
`noBitmapOutput`	boolean	Do not get resulting image as bitmap output stream.
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

ApplyPresentationStateToImageResult interface:

Property	Type	Description
`presentationStateOutStream`	JsonCompatible	Output overlay information
`outputImage`	Image	Output image
`webWorker`	Worker	WebWorker used for computation.

readDicomEncapsulatedPdf

Extract PDF file from DICOM encapsulated PDF.

async function readDicomEncapsulatedPdf(
  dicomFile: File | BinaryFile,
  options: ReadDicomEncapsulatedPdfOptions = {}
) : Promise<ReadDicomEncapsulatedPdfResult>

Parameter	Type	Description
`dicomFile`	*File	BinaryFile*	Input DICOM file

ReadDicomEncapsulatedPdfOptions interface:

Property	Type	Description
`readFileOnly`	boolean	read file format only
`readDataset`	boolean	read data set without file meta information
`readXferAuto`	boolean	use TS recognition (default)
`readXferDetect`	boolean	ignore TS specified in the file meta header
`readXferLittle`	boolean	read with explicit VR little endian TS
`readXferBig`	boolean	read with explicit VR big endian TS
`readXferImplicit`	boolean	read with implicit VR little endian TS
`acceptOddLength`	boolean	accept odd length attributes (default)
`assumeEvenLength`	boolean	assume real length is one byte larger
`enableCp246`	boolean	read undefined len UN as implicit VR (default)
`disableCp246`	boolean	read undefined len UN as explicit VR
`retainUn`	boolean	retain elements as UN (default)
`convertUn`	boolean	convert to real VR if known
`enableCorrection`	boolean	enable automatic data correction (default)
`disableCorrection`	boolean	disable automatic data correction
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

ReadDicomEncapsulatedPdfResult interface:

Property	Type	Description
`pdfBinaryOutput`	Uint8Array	Output pdf file
`webWorker`	Worker	WebWorker used for computation.

structuredReportToHtml

Render DICOM SR file and data set to HTML/XHTML

async function structuredReportToHtml(
  dicomFile: File | BinaryFile,
  options: StructuredReportToHtmlOptions = {}
) : Promise<StructuredReportToHtmlResult>

Parameter	Type	Description
`dicomFile`	*File	BinaryFile*	Input DICOM file

StructuredReportToHtmlOptions interface:

Property	Type	Description
`readFileOnly`	boolean	read file format only
`readDataset`	boolean	read data set without file meta information
`readXferAuto`	boolean	use TS recognition (default)
`readXferDetect`	boolean	ignore TS specified in the file meta header
`readXferLittle`	boolean	read with explicit VR little endian TS
`readXferBig`	boolean	read with explicit VR big endian TS
`readXferImplicit`	boolean	read with implicit VR little endian TS
`processingDetails`	boolean	show currently processed content item
`unknownRelationship`	boolean	accept unknown/missing relationship type
`invalidItemValue`	boolean	accept invalid content item value
(e.g. violation of VR or VM definition)
`ignoreConstraints`	boolean	ignore relationship content constraints
`ignoreItemErrors`	boolean	do not abort on content item errors, just warn
(e.g. missing value type specific attributes)
`skipInvalidItems`	boolean	skip invalid content items (incl. sub-tree)
`disableVrChecker`	boolean	disable check for VR-conformant string values
`charsetRequire`	boolean	require declaration of ext. charset (default)
`charsetAssume`	string	charset: string, assume charset c if no extended charset declared
`charsetCheckAll`	boolean	check all data elements with string values
(default: only PN, LO, LT, SH, ST, UC and UT)
`convertToUtf8`	boolean	convert all element values that are affected
by Specific Character Set (0008,0005) to UTF-8
`urlPrefix`	string	URL: string. Append specificed URL prefix to hyperlinks of referenced composite objects in the document.
`html32`	boolean	use only HTML version 3.2 compatible features
`html40`	boolean	allow all HTML version 4.01 features (default)
`xhtml11`	boolean	comply with XHTML version 1.1 specification
`addDocumentType`	boolean	add reference to SGML document type definition
`cssReference`	string	URL: string. Add reference to specified CSS to document
`cssFile`	*string	File	TextFile*	filename: string. Embed content of specified CSS into document
`expandInline`	boolean	expand short content items inline (default)
`neverExpandInline`	boolean	never expand content items inline
`alwaysExpandInline`	boolean	always expand content items inline
`renderFullData`	boolean	render full data of content items
`sectionTitleInline`	boolean	render section titles inline, not separately
`documentTypeTitle`	boolean	use document type as document title (default)
`patientInfoTitle`	boolean	use patient information as document title
`noDocumentHeader`	boolean	do not render general document information
`renderInlineCodes`	boolean	render codes in continuous text blocks
`conceptNameCodes`	boolean	render code of concept names
`numericUnitCodes`	boolean	render code of numeric measurement units
`codeValueUnit`	boolean	use code value as measurement unit (default)
`codeMeaningUnit`	boolean	use code meaning as measurement unit
`renderAllCodes`	boolean	render all codes (implies +Ci, +Cn and +Cu)
`codeDetailsTooltip`	boolean	render code details as a tooltip (implies +Cc)
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

StructuredReportToHtmlResult interface:

Property	Type	Description
`outputText`	string	Output text file
`webWorker`	Worker	WebWorker used for computation.

structuredReportToText

Read a DICOM structured report file and generate a plain text representation

async function structuredReportToText(
  dicomFile: File | BinaryFile,
  options: StructuredReportToTextOptions = {}
) : Promise<StructuredReportToTextResult>

Parameter	Type	Description
`dicomFile`	*File	BinaryFile*	Input DICOM file

StructuredReportToTextOptions interface:

Property	Type	Description
`unknownRelationship`	boolean	Accept unknown relationship type
`invalidItemValue`	boolean	Accept invalid content item value
`ignoreConstraints`	boolean	Ignore relationship constraints
`ignoreItemErrors`	boolean	Ignore content item errors
`skipInvalidItems`	boolean	Skip invalid content items
`noDocumentHeader`	boolean	Print no document header
`numberNestedItems`	boolean	Number nested items
`shortenLongValues`	boolean	Shorten long item values
`printInstanceUid`	boolean	Print SOP Instance UID
`printSopclassShort`	boolean	Print short SOP class name
`printSopclassLong`	boolean	Print SOP class name
`printSopclassUid`	boolean	Print long SOP class name
`printAllCodes`	boolean	Print all codes
`printInvalidCodes`	boolean	Print invalid codes
`printTemplateId`	boolean	Print template identification
`indicateEnhanced`	boolean	Indicate enhanced encoding mode
`printColor`	boolean	Use ANSI escape codes
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

StructuredReportToTextResult interface:

Property	Type	Description
`outputText`	string	Output text file
`webWorker`	Worker	WebWorker used for computation.

readDicomTags

Read the tags from a DICOM file

async function readDicomTags(
  dicomFile: File | BinaryFile,
  options: ReadDicomTagsOptions = {}
) : Promise<ReadDicomTagsResult>

Parameter	Type	Description
`dicomFile`	*File	BinaryFile*	Input DICOM file.

ReadDicomTagsOptions interface:

Property	Type	Description
`tagsToRead`	JsonCompatible	A JSON object with a "tags" array of the tags to read. If not provided, all tags are read. Example tag: "0008	103e".
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

ReadDicomTagsResult interface:

Property	Type	Description
`tags`	JsonCompatible	Output tags in the file. JSON object an array of tag, value arrays. Values are encoded as UTF-8 strings.
`webWorker`	Worker	WebWorker used for computation.

readImageDicomFileSeries

Read a DICOM image series and return the associated image volume

async function readImageDicomFileSeries(
  options: ReadImageDicomFileSeriesOptions = { inputImages: [] as BinaryFile[] | File[] | string[], }
) : Promise<ReadImageDicomFileSeriesResult>

Parameter	Type	Description

ReadImageDicomFileSeriesOptions interface:

Property	Type	Description
`inputImages`	*string[]	File[]	BinaryFile[]*	File names in the series
`singleSortedSeries`	boolean	The input files are a single sorted series
`webWorker`	null or Worker or boolean	WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker.
`noCopy`	boolean	When SharedArrayBuffer's are not available, do not copy inputs.

ReadImageDicomFileSeriesResult interface:

Property	Type	Description
`outputImage`	Image	Output image volume
`sortedFilenames`	JsonCompatible	Output sorted filenames
`webWorker`	Worker	WebWorker used for computation.

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

Node interface

Import:

import {
  applyPresentationStateToImageNode,
  readDicomEncapsulatedPdfNode,
  structuredReportToHtmlNode,
  structuredReportToTextNode,
  readDicomTagsNode,
  readImageDicomFileSeriesNode,
} from "@itk-wasm/dicom"

applyPresentationStateToImageNode

Apply a presentation state to a given DICOM image and render output as bitmap, or dicom file.

async function applyPresentationStateToImageNode(
  imageIn: string,
  presentationStateFile: string,
  options: ApplyPresentationStateToImageNodeOptions = {}
) : Promise<ApplyPresentationStateToImageNodeResult>

Parameter	Type	Description
`imageIn`	string	Input DICOM file
`presentationStateFile`	string	Process using presentation state file

ApplyPresentationStateToImageNodeOptions interface:

Property	Type	Description
`colorOutput`	boolean	output image as RGB (default: false)
`configFile`	string	filename: string. Process using settings from configuration file
`frame`	number	frame: integer. Process using image frame f (default: 1)
`noPresentationStateOutput`	boolean	Do not get presentation state information in text stream.
`noBitmapOutput`	boolean	Do not get resulting image as bitmap output stream.

ApplyPresentationStateToImageNodeResult interface:

Property	Type	Description
`presentationStateOutStream`	JsonCompatible	Output overlay information
`outputImage`	Image	Output image

readDicomEncapsulatedPdfNode

Extract PDF file from DICOM encapsulated PDF.

async function readDicomEncapsulatedPdfNode(
  dicomFile: string,
  options: ReadDicomEncapsulatedPdfNodeOptions = {}
) : Promise<ReadDicomEncapsulatedPdfNodeResult>

Parameter	Type	Description
`dicomFile`	string	Input DICOM file

ReadDicomEncapsulatedPdfNodeOptions interface:

Property	Type	Description
`readFileOnly`	boolean	read file format only
`readDataset`	boolean	read data set without file meta information
`readXferAuto`	boolean	use TS recognition (default)
`readXferDetect`	boolean	ignore TS specified in the file meta header
`readXferLittle`	boolean	read with explicit VR little endian TS
`readXferBig`	boolean	read with explicit VR big endian TS
`readXferImplicit`	boolean	read with implicit VR little endian TS
`acceptOddLength`	boolean	accept odd length attributes (default)
`assumeEvenLength`	boolean	assume real length is one byte larger
`enableCp246`	boolean	read undefined len UN as implicit VR (default)
`disableCp246`	boolean	read undefined len UN as explicit VR
`retainUn`	boolean	retain elements as UN (default)
`convertUn`	boolean	convert to real VR if known
`enableCorrection`	boolean	enable automatic data correction (default)
`disableCorrection`	boolean	disable automatic data correction

ReadDicomEncapsulatedPdfNodeResult interface:

Property	Type	Description
`pdfBinaryOutput`	Uint8Array	Output pdf file

structuredReportToHtmlNode

Render DICOM SR file and data set to HTML/XHTML

async function structuredReportToHtmlNode(
  dicomFile: string,
  options: StructuredReportToHtmlNodeOptions = {}
) : Promise<StructuredReportToHtmlNodeResult>

Parameter	Type	Description
`dicomFile`	string	Input DICOM file

StructuredReportToHtmlNodeOptions interface:

Property	Type	Description
`readFileOnly`	boolean	read file format only
`readDataset`	boolean	read data set without file meta information
`readXferAuto`	boolean	use TS recognition (default)
`readXferDetect`	boolean	ignore TS specified in the file meta header
`readXferLittle`	boolean	read with explicit VR little endian TS
`readXferBig`	boolean	read with explicit VR big endian TS
`readXferImplicit`	boolean	read with implicit VR little endian TS
`processingDetails`	boolean	show currently processed content item
`unknownRelationship`	boolean	accept unknown/missing relationship type
`invalidItemValue`	boolean	accept invalid content item value
(e.g. violation of VR or VM definition)
`ignoreConstraints`	boolean	ignore relationship content constraints
`ignoreItemErrors`	boolean	do not abort on content item errors, just warn
(e.g. missing value type specific attributes)
`skipInvalidItems`	boolean	skip invalid content items (incl. sub-tree)
`disableVrChecker`	boolean	disable check for VR-conformant string values
`charsetRequire`	boolean	require declaration of ext. charset (default)
`charsetAssume`	string	charset: string, assume charset c if no extended charset declared
`charsetCheckAll`	boolean	check all data elements with string values
(default: only PN, LO, LT, SH, ST, UC and UT)
`convertToUtf8`	boolean	convert all element values that are affected
by Specific Character Set (0008,0005) to UTF-8
`urlPrefix`	string	URL: string. Append specificed URL prefix to hyperlinks of referenced composite objects in the document.
`html32`	boolean	use only HTML version 3.2 compatible features
`html40`	boolean	allow all HTML version 4.01 features (default)
`xhtml11`	boolean	comply with XHTML version 1.1 specification
`addDocumentType`	boolean	add reference to SGML document type definition
`cssReference`	string	URL: string. Add reference to specified CSS to document
`cssFile`	*string	File	TextFile*	filename: string. Embed content of specified CSS into document
`expandInline`	boolean	expand short content items inline (default)
`neverExpandInline`	boolean	never expand content items inline
`alwaysExpandInline`	boolean	always expand content items inline
`renderFullData`	boolean	render full data of content items
`sectionTitleInline`	boolean	render section titles inline, not separately
`documentTypeTitle`	boolean	use document type as document title (default)
`patientInfoTitle`	boolean	use patient information as document title
`noDocumentHeader`	boolean	do not render general document information
`renderInlineCodes`	boolean	render codes in continuous text blocks
`conceptNameCodes`	boolean	render code of concept names
`numericUnitCodes`	boolean	render code of numeric measurement units
`codeValueUnit`	boolean	use code value as measurement unit (default)
`codeMeaningUnit`	boolean	use code meaning as measurement unit
`renderAllCodes`	boolean	render all codes (implies +Ci, +Cn and +Cu)
`codeDetailsTooltip`	boolean	render code details as a tooltip (implies +Cc)

StructuredReportToHtmlNodeResult interface:

Property	Type	Description
`outputText`	string	Output text file

structuredReportToTextNode

Read a DICOM structured report file and generate a plain text representation

async function structuredReportToTextNode(
  dicomFile: string,
  options: StructuredReportToTextNodeOptions = {}
) : Promise<StructuredReportToTextNodeResult>

Parameter	Type	Description
`dicomFile`	string	Input DICOM file

StructuredReportToTextNodeOptions interface:

Property	Type	Description
`unknownRelationship`	boolean	Accept unknown relationship type
`invalidItemValue`	boolean	Accept invalid content item value
`ignoreConstraints`	boolean	Ignore relationship constraints
`ignoreItemErrors`	boolean	Ignore content item errors
`skipInvalidItems`	boolean	Skip invalid content items
`noDocumentHeader`	boolean	Print no document header
`numberNestedItems`	boolean	Number nested items
`shortenLongValues`	boolean	Shorten long item values
`printInstanceUid`	boolean	Print SOP Instance UID
`printSopclassShort`	boolean	Print short SOP class name
`printSopclassLong`	boolean	Print SOP class name
`printSopclassUid`	boolean	Print long SOP class name
`printAllCodes`	boolean	Print all codes
`printInvalidCodes`	boolean	Print invalid codes
`printTemplateId`	boolean	Print template identification
`indicateEnhanced`	boolean	Indicate enhanced encoding mode
`printColor`	boolean	Use ANSI escape codes

StructuredReportToTextNodeResult interface:

Property	Type	Description
`outputText`	string	Output text file

readDicomTagsNode

Read the tags from a DICOM file

async function readDicomTagsNode(
  dicomFile: string,
  options: ReadDicomTagsNodeOptions = {}
) : Promise<ReadDicomTagsNodeResult>

Parameter	Type	Description
`dicomFile`	string	Input DICOM file.

ReadDicomTagsNodeOptions interface:

Property	Type	Description
`tagsToRead`	JsonCompatible	A JSON object with a "tags" array of the tags to read. If not provided, all tags are read. Example tag: "0008	103e".

ReadDicomTagsNodeResult interface:

Property	Type	Description
`tags`	JsonCompatible	Output tags in the file. JSON object an array of tag, value arrays. Values are encoded as UTF-8 strings.

readImageDicomFileSeriesNode

Read a DICOM image series and return the associated image volume

async function readImageDicomFileSeriesNode(
  options: ReadImageDicomFileSeriesNodeOptions = { inputImages: [] as string[], }
) : Promise<ReadImageDicomFileSeriesNodeResult>