dicom

README

dicom

High Performance Golang DICOM Medical Image Parser

This is a (hard-ish) fork of work I did at gradienthealth which built on top of go-dicom--a golang DICOM image parsing library and command line tool. We have been working on this package with the goal of building a full-featured and high-performance dicom parser in Golang with new features and improvements. I will continue to add some (potentially API breaking) improvements on my repository fork here.

So far, improvements that have made on top of go-dicom include:

• parsing and extracting multi-frame DICOM imagery (both encapsulated and native pixel data)
• exposing a Parser golang interface to make mock-based testing easier for clients
• Channel-based streaming of Frames to a client as they are parsed out of the dicom
• Parsing performance improvements
• General refactors to the go-dicom code (though there's more work to be done here) for maintainability an readability.

Usage

To use this in your golang project, simply import our pacakge github.com/suyashkumar/dicom and then you can use our Parser for your parsing needs:

p, err := dicom.NewParserFromFile("myfile.dcm", nil)
opts := dicom.ParseOptions{DropPixelData: true}

element := p.ParseNext(opts) // parse and return the next dicom element
// or
dataset, err := p.Parse(opts) // parse whole dicom

More details about the package can be found in the godoc

CLI Tool

A CLI tool that uses this package to parse imagery and metadata out of DICOMs is provided in the dicomutil package.

Usage

dicomutil --extract-images myfile.dcm

Note: for some dicoms (with native pixel data) no automatic intensity scaling is applied yet (this is coming). You can apply this in your image viewer if needed.

Docker build

To build the tool for all platforms (Mac, Windows, Linux) from source using docker, execute the following in the cloned repo:

docker build . -t godicom
docker run -it -v $PWD/build:/go/src/github.com/suyashkumar/dicom/build godicom make release

You can then use the binaries that will show up in the build folder in your current working directory

Build manually

To build manually, ensure you have make, golang, and dep installed on your machine. Clone (or go get) this repo into your gopath then:

make

Acknowledgements

• Original go-dicom
• Grailbio go-dicom -- commits from their fork were applied to ours
• GradientHealth for supporting work I did on this while there gradienthealth/dicom
• Innolitics DICOM browser
• DICOM Specification
• Icons made by Freepik from www.flaticon.com is licensed by CC 3.0 BY

Documentation

Index

• type DirectoryRecord
  • func ParseDICOMDIR(in io.Reader) (recs []DirectoryRecord, err error)
• type ParseOptions
• type Parser
  • func NewParser(in io.Reader, bytesToRead int64, frameChannel chan *frame.Frame) (Parser, error)
  • func NewParserFromBytes(data []byte, frameChannel chan *frame.Frame) (Parser, error)
  • func NewParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) (Parser, error)
  • func NewParserFromFile(path string, frameChannel chan *frame.Frame) (Parser, error)
  • func NewUninitializedParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) Parser

Types

type DirectoryRecord

type DirectoryRecord struct {
	Path string
}

DirectoryRecord contains info about one DICOM file mentioned in DICOMDIR.

func ParseDICOMDIR

func ParseDICOMDIR(in io.Reader) (recs []DirectoryRecord, err error)

ParseDICOMDIR parses contents of a "DICOMDIR" stored in "in".

http://dicom.nema.org/medical/Dicom/2016b/output/chtml/part03/sect_F.2.2.2.html

type ParseOptions

type ParseOptions struct {
	// DropPixelData will cause the parser to skip the PixelData element
	// (bulk images) in ReadDataSet.
	DropPixelData bool

	// ReturnTags is a whitelist of tags to return.
	ReturnTags []dicomtag.Tag

	// StopAtag defines a tag at which when read (or a tag with a greater
	// value than it is read), the program will stop parsing the dicom file.
	StopAtTag *dicomtag.Tag
}

ParseOptions defines how DataSets and Elements are parsed.

type Parser

type Parser interface {
	// Parse DICOM data
	Parse(options ParseOptions) (*element.DataSet, error)
	// ParseNext reads and parses the next element
	ParseNext(options ParseOptions) *element.Element
	// DecoderError fetches an error (if exists) from the dicomio.Decoder
	DecoderError() error // This should go away as we continue refactors
	// Finish should be called after manually parsing elements using ParseNext (instead of Parse)
	Finish() error // This should maybe go away as we continue refactors
}

Parser represents an entity that can read and parse DICOMs

func NewParser

func NewParser(in io.Reader, bytesToRead int64, frameChannel chan *frame.Frame) (Parser, error)

NewParser initializes and returns a new Parser

func NewParserFromBytes

func NewParserFromBytes(data []byte, frameChannel chan *frame.Frame) (Parser, error)

NewParserFromBytes initializes and returns a new Parser from []byte

func NewParserFromDecoder

func NewParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) (Parser, error)

NewParserFromDecoder returns parser from a decoder TODO: remove or cleanup, currently needed for testing

func NewParserFromFile

func NewParserFromFile(path string, frameChannel chan *frame.Frame) (Parser, error)

NewParserFromFile initializes and returns a new dicom Parser from a file path

func NewUninitializedParserFromDecoder

func NewUninitializedParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) Parser

NewUninitializedParserFromDecoder returns parser from a decoder TODO: remove or cleanup, currently needed for testing